CMSEE Publications
2024
- Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses.
Sjodin AR, Willig MR, Rodríguez-Durán A, Anthony SJ
Ecology and evolution (2024) 14(6):e11501 PMC4863610 10.1007/s00284-021-02607-5 - Clinical presentation of early syphilis and genomic sequences of Treponema pallidum strains in patient specimens and isolates obtained by rabbit inoculation.
Yang L, Zhang X, Chen W, Seña AC, Zheng H, Jiang Y, Zhao P, Chen R, Wang L, Ke W, Salazar JC, Parr JB, Tucker JD, Hawley KL, Caimano MJ, Hennelly CM, Aghakanian F, Bettin EB, Zhang F, Chen JS, Moody MA, Radolf JD, Yang B
The Journal of infectious diseases (2024) : 10.1093/infdis/jiae322 - Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef.
Lin S, Li L, Zhou Z, Yuan H, Saad OS, Tang J, Cai W, Yu K, Lin S
Microbiology spectrum (2024) :e0051424 10.1128/spectrum.00514-24 - Phosphorus limitation intensifies heat-stress effects on the potential mutualistic capacity in the coral-derived Symbiodinium.
Li J, Li W, Huang Y, Bu H, Zhang K, Lin S
The Science of the total environment (2024) :173912 10.1016/j.scitotenv.2024.173912 - Speciation.
Peichel CL, Bolnick DI, Brännström Å, Dieckmann U, Safran RJ
Cold Spring Harbor perspectives in biology (2024) : 10.1101/cshperspect.a041735 - Predictable and Divergent Change in the Multivariate Matrix during Parallel Adaptation.
De Lisle SP, Bolnick DI, Stuart YE
The American naturalist (2024) 204(1):15-29 10.1086/730261 - Salinity decline promotes growth and harmful blooms of a toxic alga by diverting carbon flow.
Shi X, Zou Y, Zhang Y, Ding G, Xiao Y, Lin S, Chen J
Global change biology (2024) 30(6):e17348 10.1111/gcb.17348 - Effects of astaxanthin on gut microbiota of polo ponies during deconditioning and reconditioning periods.
Kawaida MY, Maas KR, Moore TE, Reiter AS, Tillquist NM, Reed SA
Physiological reports (2024) 12(11):e16051 PMC9687066 10.1039/c9fo02555c - A meta-analysis on global change drivers and the risk of infectious disease.
Mahon MB, Sack A, Aleuy OA, Barbera C, Brown E, Buelow H, Civitello DJ, Cohen JM, de Wit LA, Forstchen M, Halliday FW, Heffernan P, Knutie SA, Korotasz A, Larson JG, Rumschlag SL, Selland E, Shepack A, Vincent N, Rohr JR
Nature (2024) 629(8013):830-836 10.1038/nature25753 - Bacterial metallothionein, PmtA, a novel stress protein found on the bacterial surface of and involved in management of oxidative stress and phagocytosis.
Maltz-Matyschsyk M, Melchiorre CK, Knecht DA, Lynes MA
mSphere (2024) 9(5):e0021024 10.1128/msphere.00210-24 - Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases.
Yuan H, Li L, Wang Y, Lin S
Harmful algae (2024) 134:102626 10.1016/j.hal.2024.102626 - Editorial: Molecular Biology of Archaea - 2022.
van Wolferen M, Ithurbide S, Santiago-Martínez MG, Charles-Orszag A
Frontiers in microbiology (2024) 15:1393932 PMC7613921 10.1038/s41564-022-01215-8 - Shining light on dinoflagellate photosystem I.
Lin S, Wu S, He J, Wang X, Grossman AR
Nature communications (2024) 15(1):3337 PMC10781511 10.1093/gbe/evad237 - WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.
Coulter AM, Cortés V, Theodore CJ, Cianciolo RE, Korstanje R, Campellone KG
Molecular biology of the cell (2024) 35(6):ar80 10.1091/mbc.E24-01-0025 - A spectral framework to map QTLs affecting joint differential networks of gene co-expression.
Hu J, Weber JN, Fuess LE, Steinel NC, Bolnick DI, Wang M
bioRxiv : the preprint server for biology (2024) : PMC5655846 10.1101/2024.03.29.587398 - Microbiome-derived acidity protects against microbial invasion in Drosophila.
Barron AJ, Agrawal S, Lesperance DNA, Doucette J, Calle S, Broderick NA
Cell reports (2024) 43(4):114087 PMC6102978 10.1128/AEM.00662-18 - Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity.
Theodore CJ, Wagner LH, Campellone KG
bioRxiv : the preprint server for biology (2024) : PMC10881176 10.1101/2024.03.12.584718 - In ovo probiotic supplementation supports hatchability and improves hatchling quality in broilers.
Gao M, Ren Y, Lu S, Reddyvari R, Venkitanarayanan K, Amalaradjou MA
Poultry science (2024) 103(6):103624 PMC7772711 10.1016/j.psj.2024.103624 - Multi-Omics Analysis of Gut Microbiota and Host Transcriptomics Reveal Dysregulated Immune Response and Metabolism in Young Adults with Irritable Bowel Syndrome.
Chen J, Zhao T, Li H, Xu W, Maas K, Singh V, Chen MH, Dorsey SG, Starkweather AR, Cong XS
International journal of molecular sciences (2024) 25(6): PMC3928520 10.1111/j.2517-6161.1995.tb02031.x - Dinoflagellate Proton-Pump Rhodopsin Genes in Long Island Sound: Diversity and Spatiotemporal Distribution.
Zhang H, Nulick KJ, Burris Z, Pierce M, Ma M, Lin S
Microorganisms (2024) 12(3): PMC10439184 10.3389/fmars.2019.00219 - Enhanced transport of bacteria along root systems by protists can impact plant health.
Micciulla JL, Shor LM, Gage DJ
Applied and environmental microbiology (2024) 90(4):e0201123 PMC4579469 10.1111/j.1574-6968.1986.tb01733.x - Prior exposure to pathogens augments host heterogeneity in susceptibility and has key epidemiological consequences.
Hawley DM, Pérez-Umphrey AM, Adelman JS, Fleming-Davies AE, Garrett-Larsen J, Geary SJ, Childs LM, Langwig KE
bioRxiv : the preprint server for biology (2024) : PMC10942282 10.1101/2024.03.05.583455 - Extracellular metallothionein as a therapeutic target in the early progression of type 1 diabetes.
Melchiorre CK, Lynes MD, Bhandari S, Su SC, Potts CM, Thees AV, Norris CE, Liaw L, Tseng YH, Lynes MA
Cell stress & chaperones (2024) 29(2):312-325 PMC3615023 10.1371/JOURNAL.PONE.0060229 - Population dynamics and bidirectional transfer of Listeria monocytogenes and Shiga toxin-producing Escherichia coli during cheese production in wooden vats.
Sun L, D'Amico DJ
Food microbiology (2024) 120:104483 10.1016/j.fm.2024.104483 - Insulin resistance before type 2 diabetes onset is associated with increased risk of albuminuria after diabetes onset: A prospective cohort study.
Willig MR, Stinson EJ, Looker HC, Piaggi P, Mitchell CM, Hanson RL, Nelson RG, Krakoff J, Chang DC
Diabetes, obesity & metabolism (2024) 26(5):1888-1896 PMC8998569 10.3390/ijms23073651 - The Role of Exercise in Statin-Associated Muscle Symptoms Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.
Mangone LA, Kwon OS, Johnson BT, Wu Y, Pescatello LS
Mayo Clinic proceedings. Innovations, quality & outcomes (2024) 8(2):131-142 PMC6465106 10.1093/eurjpc/zwad229 - Massively parallel mutant selection identifies genetic determinants of colonization of .
Miles J, Lozano GL, Rajendhran J, Stabb EV, Handelsman J, Broderick NA
mSystems (2024) 9(3):e0131723 PMC4640184 10.1016/j.celrep.2015.07.042 - WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.
Coulter AM, Cortés V, Theodore CJ, Cianciolo RE, Korstanje R, Campellone KG
bioRxiv : the preprint server for biology (2024) : PMC2763628 10.1101/2024.01.22.576497 - community transcriptomics illuminates CO-fixation potentials and supporting roles of phagotrophy and proton pump in plankton in a subtropical marginal sea.
Li H, Chen J, Yu L, Fan G, Li T, Li L, Yuan H, Wang J, Wang C, Li D, Lin S
Microbiology spectrum (2024) 12(3):e0217723 PMC5600148 10.1038/ismej.2007.70 - Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods.
Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV
Applied and environmental microbiology (2024) 90(3):e0099023 PMC6386654 10.1073/pnas.1817322116 - Rhinoplasty Preferences: Can the Public Detect Prior Surgery on Social Media?
Valentine L, Weidman AA, Stearns SA, Dennis D, Alvarez AH, Foppiani J, Lin SJ
Aesthetic plastic surgery (2024) : 10.1007/s11606-017-4246-0 - Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees.
Wu Y, Zhang L
Journal of computational biology : a journal of computational molecular cell biology (2024) 31(4):345-359 10.1089/cmb.2023.0309 - Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies.
Knutie SA, Webster CN, Vaziri GJ, Albert L, Harvey JA, LaRue M, Verrett TB, Soldo A, Koop JAH, Chaves JA, Wegrzyn JL
Global change biology (2024) 30(1):e17145 10.1111/gcb.17145 - SAND: Automated Time-Domain Modeling of NMR Spectra Applied to Metabolite Quantification.
Wu Y, Sanati O, Uchimiya M, Krishnamurthy K, Wedell J, Hoch JC, Edison AS, Delaglio F
Analytical chemistry (2024) 96(5):1843-1851 PMC3163565 10.1186/1471-2105-12-323 - Effects and mechanisms of glyphosate as phosphorus nutrient on element stoichiometry and metabolism in the diatom .
Wang C, Li J, Li S, Lin S
Applied and environmental microbiology (2024) 90(2):e0213123 PMC6852614 10.1038/30455 - Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects.
Li J, Wu S, Zhang K, Sun X, Lin W, Wang C, Lin S
Microorganisms (2024) 12(1): PMC10440436 10.3389/fmicb.2023.1205765 - Effects of spore purity on the wet heat resistance of Clostridium perfringens, Bacillus cereus and Bacillus subtilis spores.
Juneja VK, Osoria M, Altuntas EG, Taneja NK, Thakur S, Kumar GD, Setlow P
Food research international (Ottawa, Ont.) (2024) 177:113904 10.1016/j.foodres.2023.113904 - Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Cells and Spores.
Huang Y, Swarge BN, Roseboom W, Bleeker JD, Brul S, Setlow P, Kramer G
Journal of proteome research (2024) 23(2):596-608 PMC5122711 10.1128/microbiolspec.TBS-0019-2013 - Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes.
Rogers TF, Yalçın G, Briseno J, Vijayan N, Nyholm SV, Simakov O
Scientific data (2024) 11(1):40 PMC6857279 10.1016/S0022-2836(05)80360-2 - A general approach for inferring the ancestry of recent ancestors of an admixed individual.
Zhang Y, Zhang H, Wu Y
Proceedings of the National Academy of Sciences of the United States of America (2024) 121(2):e2316242120 PMC8551421 10.1073/pnas.2316242120 - Glyphosate (Roundup) as phosphorus nutrient enhances carbon and nitrogen accumulation and up-regulates phosphorus metabolisms in the haptophyte Isochrysis galbana.
Wang C, Zhang H, Wang J, Sprecher B, Lin S
The Science of the total environment (2024) 913:169715 10.1016/j.scitotenv.2023.169715 2023
- Novel plastid genome characteristics in Fugacium kawagutii and the trend of accelerated evolution of plastid proteins in dinoflagellates.
He J, Huang Y, Li L, Lin S, Ma M, Wang Y, Lin S
Genome biology and evolution (2023) : 10.1093/gbe/evad237 - In Memoriam: Wayne Lowell Nicholson, March 26, 1958-June 8, 2023.
Foster JS, Henkin TM, Romeo T, Schuerger AC, Setlow P, Ferl RJ, Rice KC, Triplett EW, Fajardo-Cavazos P
Astrobiology (2023) 24(3):227-229 10.1089/ast.2023.0100 - Evaluation of Exercise Mobile Applications for Adults with Cardiovascular Disease Risk Factors.
Chen S, Wu Y, Bushey EL, Pescatello LS
Journal of cardiovascular development and disease (2023) 10(12): PMC7930885 10.1016/j.mayocpiqo.2020.08.005 - Multifactorial resistance of spores to low-pressure plasma sterilization.
Muratov E, Rosenbaum FP, Fuchs FM, Ulrich NJ, Awakowicz P, Setlow P, Moeller R
Applied and environmental microbiology (2023) 90(1):e0132923 PMC219731 10.1016/j.mimet.2017.01.002 - sp. nov., sp. nov., sp. nov. and sp. nov., isolated from in, and around, a rainbow trout farm.
Testerman T, Varga J, Schiffer MM, Donohue H, Vieira Da Silva C, Graf J
International journal of systematic and evolutionary microbiology (2023) 73(12): 10.1099/ijsem.0.006201 - Metabolic and transcriptional activities underlie stationary-phase sensitivity to Levofloxacin.
Hare PJ, Gonzalez JR, Quelle RM, Wu YI, Mok WWK
Microbiology spectrum (2023) 12(1):e0356723 PMC208147 10.1128/jb.173.15.4700-4706.1991 - Editorial: Improving antimicrobial peptides translational potential through peptidomimetics.
Angeles-Boza AM, Santos NC, Cardoso MH
Frontiers in microbiology (2023) 14:1304997 PMC4702905 10.1093/nar/gkv1278 - Neighboring inteins interfere with one another's homing capacity.
Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U
PNAS nexus (2023) 2(11):pgad354 PMC419797 10.1101/GR.849004 - Alkaline Phosphatase PhoD Mutation Induces Fatty Acid and Long-Chain Polyunsaturated Fatty Acid (LC-PUFA)-Bound Phospholipid Production in the Model Diatom .
Zhang K, Li J, Cheng J, Lin S
Marine drugs (2023) 21(11): PMC3218662 10.1093/bioinformatics/btp612 - Protocol for an agent-based model of recombination in bacteria playing a public goods game.
Lee IPA, Eldakar OT, Gogarten JP, Andam CP
STAR protocols (2023) 4(4):102733 PMC10405257 10.1016/j.xpro.2023.102733 - CD8+ T Cell-Dependent Antitumor Activity In Vivo of a Mass Spectrometry-Identified Neoepitope despite Undetectable CD8+ Immunogenicity In Vitro.
Gillig MA, Brennick CA, George MM, Balsbaugh JL, Shcheglova TV, Mandoiu II, Rosales T, Baker BM, Srivastava PK, Karandikar SH
Journal of immunology (Baltimore, Md. : 1950) (2023) 211(12):1783-1791 PMC8210748 10.4049/jimmunol.2300356 - Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery.
Iglesias SM, Lokareddy RK, Yang R, Li F, Yeggoni DP, David Hou CF, Leroux MN, Cortines JR, Leavitt JC, Bird M, Casjens SR, White S, Teschke CM, Cingolani G
Journal of molecular biology (2023) 435(24):168365 PMC2896178 10.1016/j.jmb.2023.168365 - Locomotor effects of a fibrosis-based immune response in stickleback fish.
Matthews DG, Maciejewski MF, Wong GA, Lauder GV, Bolnick DI
The Journal of experimental biology (2023) 226(23): 10.1242/jeb.246684 - A multi-study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation.
Griffin TW, Darsan MA, Collins HI, Holohan BA, Pierce ML, Ward JE
Environmental microbiology (2023) 25(12):3435-3449 10.1111/1462-2920.16537 - 1,2-Azolylamidino ruthenium(II) complexes with DMSO ligands: electro- and photocatalysts for CO reduction.
Jennings M, Cuéllar E, Rojo A, Ferrero S, García-Herbosa G, Nganga J, Angeles-Boza AM, Martín-Alvarez JM, Miguel D, Villafañe F
Dalton transactions (Cambridge, England : 2003) (2023) 52(45):16974-16983 10.1039/d3dt01122d - HMGB2 is a potential diagnostic marker and therapeutic target for liver fibrosis and cirrhosis.
Huang Y, Liangpunsakul S, Rudraiah S, Ma J, Keshipeddy SK, Wright D, Costa A, Burgess D, Zhang Y, Huda N, Wang L, Yang Z
Hepatology communications (2023) 7(11): PMC3335123 10.1097/HC9.0000000000000299 - Cultivating Food Safety Together: Insights About the Future of Produce Safety in the U.S. Controlled Environment Agriculture Sector.
Hamilton AN, Gibson KE, Amalaradjou MA, Callahan CW, Millner PD, Ilic S, Lewis Ivey ML, Shaw AM
Journal of food protection (2023) 86(12):100190 10.1016/j.jfp.2023.100190 - Early syphilis in Guangzhou, China: presentation, molecular detection of , and genomic sequences in clinical specimens and isolates obtained by rabbit infectivity testing.
Yang L, Zhang X, Chen W, Seña AC, Zheng H, Jiang Y, Zhao P, Chen R, Wang L, Ke W, Salazar JC, Parr JB, Tucker JD, Hawley KL, Caimano MJ, Hennelly CM, Aghakanian F, Zhang F, Chen JS, Moody MA, Radolf JD, Yang B
medRxiv : the preprint server for health sciences (2023) : PMC10614984 10.1101/2023.10.17.23297169 - Archaeal Tubulin-like Proteins Modify Cell Shape in during Early Biofilm Development.
Cooper A, Makkay AM, Papke RT
Genes (2023) 14(10): PMC8406309 10.1016/j.cub.2012.05.056 - Active viral infection during blooms of a dinoflagellate indicates dinoflagellate-viral co-adaptation.
Wang J, Li L, Lin S
Applied and environmental microbiology (2023) 89(11):e0115623 PMC7931819 10.18637/jss.v025.i03 - Deconstructing interactions in the microbiota: A theoretical examination.
Yitbarek S, Guittar J, Knutie SA, Ogbunugafor CB
iScience (2023) 26(10):107875 PMC10067270 10.1016/j.physrep.2020.05.004 - Contemporary changes in phenotypic variation, and the potential consequences for eco-evolutionary dynamics.
Sanderson S, Bolnick DI, Kinnison MT, O'Dea RE, Gorné LD, Hendry AP, Gotanda KM
Ecology letters (2023) 26 Suppl 1:S127-S139 10.1111/ele.14186 - Species-dependent effects of seawater acidification on alkaline phosphatase activity in dinoflagellates.
Guo C, Li L, Lin S, Lin X
Journal of phycology (2023) 59(6):1347-1352 10.1111/jpy.13398 - Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings.
Solomon G, Love AC, Vaziri GJ, Harvey J, Verrett T, Chernicky K, Simons S, Albert L, Chaves JA, Knutie SA
Molecular ecology (2023) 32(22):6059-6069 10.1111/mec.17164 - Enhanced circularly polarized luminescence dissymmetry of [Ru(bpy)] complexes in a 3D chiral framework: a study of transparent thin films.
Zhang S, Schnable D, Elgin J, Ung G, Wu Y
Chemical communications (Cambridge, England) (2023) 59(86):12867-12870 10.1039/d3cc04083f - Research Note: In ovo and in-feed probiotic supplementation improves layer embryo and pullet growth.
Muyyarikkandy MS, Mathew E, Kuttappan D, Amalaradjou MA
Poultry science (2023) 102(12):103092 PMC6543855 10.1016/j.psj.2023.103092 - Phosphorus nutrition strategies in a Symbiodiniacean species: Implications in coral-alga symbiosis facing increasing phosphorus deficiency in future warmer oceans.
Li J, Zhang K, Li L, Wang Y, Lin S
Global change biology (2023) 29(23):6558-6571 10.1111/gcb.16945 - Deciphering the ecoevolutionary recipe of milk microbiomes.
Hird SM
Trends in ecology & evolution (2023) 38(11):1019-1021 10.1016/j.tree.2023.09.004 - Two-sided effects of the organic phosphorus phytate on a globally important marine coccolithophorid phytoplankton.
Li J, Zhang K, Li L, Wang Y, Wang C, Lin S
Microbiology spectrum (2023) 11(5):e0125523 PMC3218662 10.1186/gb-2010-11-10-r106 - Artificial intelligence for natural product drug discovery.
Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH
Nature reviews. Drug discovery (2023) 22(11):895-916 10.1186/s13321-022-00672-x - Use of Epivolve phage display to generate a monoclonal antibody with opsonic activity directed against a subdominant epitope on extracellular loop 4 of BamA (TP0326).
Ferguson MR, Delgado KN, McBride S, Orbe IC, La Vake CJ, Caimano MJ, Mendez Q, Moraes TF, Schryvers AB, Moody MA, Radolf JD, Weiner MP, Hawley KL
Frontiers in immunology (2023) 14:1222267 PMC7709521 10.1128/MMBR.00078-20 - Nylon microfibers develop a distinct plastisphere but have no apparent effects on the gut microbiome or gut tissue status in the blue mussel, Mytilus edulis.
Collins HI, Griffin TW, Holohan BA, Ward JE
Environmental microbiology (2023) 25(12):2792-2806 10.1111/1462-2920.16496 - Role of diatom-derived oxylipins in organic phosphorus recycling during coastal diatom blooms in the northern South China Sea.
Wu Z, Li QP, Rivkin RB, Lin S
The Science of the total environment (2023) 903:166518 10.1016/j.scitotenv.2023.166518 - 3D-printed epidermal sweat microfluidic systems with integrated microcuvettes for precise spectroscopic and fluorometric biochemical assays.
Yang DS, Wu Y, Kanatzidis EE, Avila R, Zhou M, Bai Y, Chen S, Sekine Y, Kim J, Deng Y, Guo H, Zhang Y, Ghaffari R, Huang Y, Rogers JA
Materials horizons (2023) 10(11):4992-5003 10.1039/d3mh00876b - Thermomechanical Properties of Neutron Irradiated AlHf-Al Thermal Neutron Absorber Materials.
Guillen DP, Toloczko MB, Prabhakaran R, Zhu Y, Lu Y, Wu Y
Materials (Basel, Switzerland) (2023) 16(16): PMC10456384 10.1016/0022-3115(93)90129-M - Resistance waxes for mutualists protected by wasp secretions.
Klassen JL
Proceedings of the National Academy of Sciences of the United States of America (2023) 120(36):e2311815120 PMC8983117 10.1073/pnas.2311815120 - Editorial: Advancing social equity through microbiology.
Oliveira LMA, Kozik A, Milligan-McClellan K, Hagan AK
Frontiers in cellular and infection microbiology (2023) 13:1260284 PMC7117800 10.1007/s10620-020-06112-w - A comparative study reveals the relative importance of prokaryotic and eukaryotic proton pump rhodopsins in a subtropical marginal sea.
Ma M, Li H, Wang C, Li T, Wang J, Yuan H, Yu L, Wang J, Li L, Lin S
ISME communications (2023) 3(1):79 PMC3090418 10.1038/s43705-023-00292-y - The impact of environmental conditions and milk type on microbial communities of wooden vats and cheeses produced therein.
Sun L, D'Amico DJ
Food microbiology (2023) 115:104319 10.1016/j.fm.2023.104319 - Editorial: Microbial associates of blood-sucking arthropods and other animals: relevance to their physiology, ecology and evolution.
Fukatsu T, Gottlieb Y, Duron O, Graf J
Frontiers in microbiology (2023) 14:1256275 PMC5007164 10.1016/j.pt.2017.04.008 - Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria.
Lee IPA, Eldakar OT, Gogarten JP, Andam CP
iScience (2023) 26(8):107344 PMC3240628 10.1038/s41579-021-00650-4 - Clinical and genomic diversity of A global, multi-center study of early syphilis to inform vaccine research.
Seña AC, Matoga MM, Yang L, Lopez-Medina E, Aghakanian F, Chen JS, Bettin EB, Caimano MJ, Chen W, Garcia-Luna JA, Hennelly CM, Jiang Y, Juliano JJ, Pospíšilová P, Ramirez L, Šmajs D, Tucker JD, Cely FV, Zheng H, Hoffman IF, Yang B, Moody MA, Hawley KL, Salazar JC, Radolf JD, Parr JB
medRxiv : the preprint server for health sciences (2023) : PMC10402240 10.1101/2023.07.19.23291250 - Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum.
Glass SE, McCourt RM, Gottschalk SD, Lewis LA, Karol KG
Journal of phycology (2023) 59(6):1133-1146 10.1111/jpy.13359 - Reproductive phenologies of phyllostomid bat populations and ensembles from lowland Amazonia.
Willig MR, Presley SJ
Journal of mammalogy (2023) 104(4):752-769 PMC6394116 10.1093/jmammal/gyad032 - Effect of plant-derived antimicrobials, eugenol, carvacrol, and β-resorcylic acid against Salmonella on organic chicken wings and carcasses.
Nair DVT, Manjankattil S, Peichel C, Martin W, Donoghue AM, Venkitanarayanan K, Kollanoor Johny A
Poultry science (2023) 102(10):102886 PMC8394320 10.1016/j.psj.2023.102886 - In vivo structure probing of RNA in : novel insights into the ribosome structure of .
Williams AM, Jolley EA, Santiago-Martínez MG, Chan CX, Gutell RR, Ferry JG, Bevilacqua PC
RNA (New York, N.Y.) (2023) 29(10):1610-1620 PMC9231505 10.1016/j.tibs.2019.01.012 - Mixoplankton and mixotrophy: future research priorities.
Millette NC, Gast RJ, Luo JY, Moeller HV, Stamieszkin K, Andersen KH, Brownlee EF, Cohen NR, Duhamel S, Dutkiewicz S, Glibert PM, Johnson MD, Leles SG, Maloney AE, Mcmanus GB, Poulton N, Princiotta SD, Sanders RW, Wilken S
Journal of plankton research (2023) 45(4):576-596 PMC2722351 10.1038/nature07236 - Conformational exchange at a CH zinc-binding site facilitates redox sensing by the PML protein.
Bregnard TA, Fairchild D, Erlandsen H, Semenova IV, Szczepaniak R, Ahmed A, Weller SK, Korzhnev DM, Bezsonova I
Structure (London, England : 1993) (2023) 31(9):1086-1099.e6 PMC3855844 10.1038/nmeth.2019 - The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location.
Dagilis AJ, Matute DR
PLoS biology (2023) 21(7):e3002185 PMC3469467 10.1016/j.mbs.2016.04.010 - CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.
Weiner S, Bansal MS
Bioinformatics (Oxford, England) (2023) 39(7): PMC3966983 10.1093/bioinformatics/btad434 - Locomotor effects of a fibrosis-based immune response in stickleback fish.
Matthews DG, Maciejewski MF, Wong GA, Lauder GV, Bolnick DI
bioRxiv : the preprint server for biology (2023) : PMC1200442 10.1101/2023.06.24.546342 - Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid.
Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O
iScience (2023) 26(7):107091 PMC6324079 10.1002/wdev.265 - Opening a can of worms: a test of the co-infection facilitation hypothesis.
Rodgers ML, Bolnick DI
Oecologia (2023) 204(2):317-325 PMC9869647 10.1126/science.abo3411 - Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology.
Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB
Integrative and comparative biology (2023) 63(6):1226-1239 PMC9699675 10.1101/pdb.ip77 - Elemental content of a host-parasite relationship in the threespine stickleback.
Grunberg RL, Braat M, Bolnick DI
Oecologia (2023) 204(2):427-437 10.1073/pnas.1620095114 - Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans.
Feregrino-Mondragón RD, Santiago-Martínez MG, Silva-Flores M, Encalada R, Reyes-Prieto A, Rodríguez-Zavala JS, Peña-Ocaña BA, Moreno-Sánchez R, Saavedra E, Jasso-Chávez R
Archives of biochemistry and biophysics (2023) 743:109667 10.1016/j.abb.2023.109667 - The relationship between microplastics in eastern oysters (Crassostrea virginica) and surrounding environmental compartments in Long Island Sound.
Mladinich K, Holohan BA, Shumway SE, Ward JE
Marine environmental research (2023) 189:106040 10.1016/j.marenvres.2023.106040 - ants promote fungus garden hygiene using -derived metabolite cues.
Kyle KE, Puckett SP, Caraballo-Rodríguez AM, Rivera-Chávez J, Samples RM, Earp CE, Raja HA, Pearce CJ, Ernst M, van der Hooft JJJ, Adams ME, Oberlies NH, Dorrestein PC, Klassen JL, Balunas MJ
Proceedings of the National Academy of Sciences of the United States of America (2023) 120(25):e2219373120 PMC10288546 10.7910/DVN/MAYHMQ - Opening a can of worms: a test of the coinfection facilitation hypothesis.
Rodgers ML, Bolnick DI
bioRxiv : the preprint server for biology (2023) : PMC10245757 10.1101/2023.05.18.541347 - Local adaptation and host specificity to copepod intermediate hosts by the tapeworm .
Shim KC, Peterson CR, Bolnick DI
Ecology and evolution (2023) 13(6):e10155 PMC5488926 10.1126/science.abo3411 - Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Informatics Tool for Metabolomics and Data Visualization of Molecules from Complex Biological Samples.
Samples RM, Puckett SP, Balunas MJ
Analytical chemistry (2023) 95(23):8770-8779 10.1021/acs.analchem.2c04632 - Neutrophil extracellular traps and extracellular histones potentiate IL-17 inflammation in periodontitis.
Kim TS, Silva LM, Theofilou VI, Greenwell-Wild T, Li L, Williams DW, Ikeuchi T, Brenchley L, , Bugge TH, Diaz PI, Kaplan MJ, Carmona-Rivera C, Moutsopoulos NM
The Journal of experimental medicine (2023) 220(9): PMC5701758 10.1016/j.chom.2017.06.014 - Understanding the evolution of immune genes in jawed vertebrates.
Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H
Journal of evolutionary biology (2023) 36(6):847-873 PMC7936018 10.1093/gbe/evab023 - Green land: Multiple perspectives on green algal evolution and the earliest land plants.
McCourt RM, Lewis LA, Strother PK, Delwiche CF, Wickett NJ, de Vries J, Bowman JL
American journal of botany (2023) 110(5):e16175 10.1002/ajb2.16175 - In ovo probiotic supplementation promotes muscle growth and development in broiler embryos.
Muyyarikkandy MS, Schlesinger M, Ren Y, Gao M, Liefeld A, Reed S, Amalaradjou MA
Poultry science (2023) 102(7):102744 PMC7936221 10.1016/j.psj.2023.102744 - A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.
Zhang L, Abhari N, Colijn C, Wu Y
Genome research (2023) 33(7):1053-1060 PMC6915859 10.1186/s12859-019-3209-3 - Cell-surface anchoring of Listeria adhesion protein on L. monocytogenes is fastened by internalin B for pathogenesis.
Liu D, Bai X, Helmick HDB, Samaddar M, Amalaradjou MAR, Li X, Tenguria S, Gallina NLF, Xu L, Drolia R, Aryal UK, Moreira GMSG, Hust M, Seleem MN, Kokini JL, Ostafe R, Cox A, Bhunia AK
Cell reports (2023) 42(5):112515 10.1016/j.celrep.2023.112515 - Phosphate limitation and ocean acidification co-shape phytoplankton physiology and community structure.
Lin S
Nature communications (2023) 14(1):2699 PMC5997998 10.1016/j.ecss.2016.11.016 - Building consensus around the assessment and interpretation of Symbiodiniaceae diversity.
Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, Del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE
PeerJ (2023) 11:e15023 PMC5309854 10.1038/ncomms14213 - Randomized Trial to Test a Chemo-Mechanical Antiplaque Regimen as Adjunct to Periodontal Therapy.
Li L, Hayashi-Okada Y, Falkner KL, Cervi S, Andrusz S, Shimizu Y, Zambon JJ, Kirkwood KL, Schifferle RE, Diaz PI
JDR clinical and translational research (2023) :23800844231167065 10.1177/23800844231167065 - Are Purple Finches () the Next Host for a Mycoplasmal Conjunctivitis Epidemic?
Reinoso-Pérez MT, Dhondt KV, Levitskiy AA, Dupont G, Tulman ER, Geary SJ, Dhondt AA
Avian diseases (2023) 67(1):42-48 10.1637/aviandiseases-D-22-00047 - Identification and characterization of new proteins crucial for bacterial spore resistance and germination.
Yu B, Kanaan J, Shames H, Wicander J, Aryal M, Li Y, Korza G, Brul S, Kramer G, Li YQ, Nichols FC, Hao B, Setlow P
Frontiers in microbiology (2023) 14:1161604 PMC2837993 10.1021/acs.jproteome.5b00976 - YtpP and Thioredoxin A Are New Players in the Coenzyme-A-Mediated Defense Mechanism against Cellular Stress.
Tossounian MA, Baczynska M, Dalton W, Peak-Chew SY, Undzenas K, Korza G, Filonenko V, Skehel M, Setlow P, Gout I
Antioxidants (Basel, Switzerland) (2023) 12(4): PMC4416841 10.1146/annurev.micro.55.1.333 - NMR detection and conformational dependence of two, three, and four-bond isotope shifts due to deuteration of backbone amides.
Alexandrescu AT, Dregni AJ, Teschke CM
Journal of biomolecular NMR (2023) 77(3):93-109 PMC2631424 10.1007/s10858-013-9733-y - Editorial: Syphilis infection: clinical, epidemiology, basic science, and behavioral research.
Zhou P, Ye M, Tucker JD, Zhang L, Radolf JD
Frontiers in immunology (2023) 14:1182069 PMC10117985 10.3389/fimmu.2023.1182069 - Molecular Ecological Analyses Illuminate Distinct Factors Regulating Formation and Demise of a Harmful Dinoflagellate Bloom.
Yu L, Li T, Li H, Ma M, Li L, Lin S
Microbiology spectrum (2023) 11(3):e0515722 PMC7334889 10.1038/nmeth.3176 - Development of a biomarker signature using grating-coupled fluorescence plasmonic microarray for diagnosis of MIS-C.
Maltz-Matyschsyk M, Melchiorre CK, Herbst KW, Hogan AH, Dibble K, O'Sullivan B, Graf J, Jadhav A, Lawrence DA, Lee WT, Carson KJ, Radolf JD, Salazar JC, Lynes MA,
Frontiers in bioengineering and biotechnology (2023) 11:1066391 PMC6349798 10.1007/s00467-018-4087-z - Single-Cell RNA Sequencing Reveals Microevolution of the Stickleback Immune System.
Fuess LE, Bolnick DI
Genome biology and evolution (2023) 15(4): PMC5241818 10.1093/gbe/evad053 - Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds.
Herder EA, Skeen HR, Lutz HL, Hird SM
Microbiology spectrum (2023) 11(3):e0374922 PMC6313546 10.1016/j.syapm.2017.09.005 - Methods for Culturing Anaerobic Microorganisms.
Santiago-Martínez MG, Ferry JG
Methods in molecular biology (Clifton, N.J.) (2023) 2648:231-238 10.1038/s41396-021-01025-6 - Elevated nest temperature has opposing effects on host species infested with parasitic nest flies.
Albert L, Rumschlag S, Parker A, Vaziri G, Knutie SA
Oecologia (2023) 201(4):877-886 10.1111/j.1467-9868.2010.00749.x - GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction.
Al Seesi S, Al-Okaily A, Shcheglova TV, Sherafat E, Alqahtani FH, Hagymasi AT, Kaur A, Srivastava PK, Măndoiu II
Journal of computational biology : a journal of computational molecular cell biology (2023) 30(4):538-551 10.1089/cmb.2022.0491 - The Impact of Early Life Experiences and Gut Microbiota on Neurobehavioral Development in Preterm Infants: A Longitudinal Cohort Study.
Chen J, Li H, Zhao T, Chen K, Chen MH, Sun Z, Xu W, Maas K, Lester BM, Cong XS
Microorganisms (2023) 11(3): PMC8855098 10.1016/j.chom.2022.04.005 - Stimulating Transcription in Antibiotic-Tolerant Escherichia coli Sensitizes It to Fluoroquinolone and Nonfluoroquinolone Topoisomerase Inhibitors.
LaGree TJ, Byrd BA, Quelle RM, Schofield SL, Mok WWK
Antimicrobial agents and chemotherapy (2023) 67(4):e0163922 PMC2746677 10.1016/j.ymeth.2009.02.010 - Phytoplankton and Microzooplankton Community Structure and Assembly Mechanisms in Northwestern Pacific Ocean Estuaries with Environmental Heterogeneity and Geographic Segregation.
Sun Y, Li H, Wang X, Jin Y, Nagai S, Lin S
Microbiology spectrum (2023) 11(2):e0492622 PMC3965112 10.1111/ecog.00986 - Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate .
Zhang K, Shen Z, Yang W, Guo J, Yan Z, Li J, Lin J, Cao X, Tang J, Liu Z, Zhou Z, Lin S
Frontiers in microbiology (2023) 13:1116975 PMC8233357 10.1016/j.ecoenv.2019.109953 - New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed.
Setlow P, Christie G
Microbiology and molecular biology reviews : MMBR (2023) 87(2):e0008022 PMC4715516 10.1111/jam.14573 - F-actin-rich territories coordinate apoptosome assembly and caspase activation during DNA damage-induced intrinsic apoptosis.
King VL, Campellone KG
Molecular biology of the cell (2023) 34(5):ar41 PMC2763628 10.1091/mbc.E22-04-0119 - Branching out in different directions: Emerging cellular functions for the Arp2/3 complex and WASP-family actin nucleation factors.
Campellone KG, Lebek NM, King VL
European journal of cell biology (2023) 102(2):151301 PMC3290644 10.1091/mbc.E11-12-0992 - The Synergy between Zinc and Antimicrobial Peptides: An Insight into Unique Bioinorganic Interactions.
Donaghy C, Javellana JG, Hong YJ, Djoko K, Angeles-Boza AM
Molecules (Basel, Switzerland) (2023) 28(5): PMC8267837 10.3390/ijms22136971 - Soil Protists Can Actively Redistribute Beneficial Bacteria along Medicago truncatula Roots.
Hawxhurst CJ, Micciulla JL, Bridges CM, Shor M, Gage DJ, Shor LM
Applied and environmental microbiology (2023) 89(3):e0181922 PMC10057870 10.1094/PBIOMES-05-20-0040-TA - The Mixoplankton Database - diversity of photo-phago-trophic plankton in form, function and distribution across the global ocean.
Mitra A, Caron DA, Faure E, Flynn KJ, Gonçalves Leles S, Hansen PJ, McManus GB, Not F, do Rosario Gomes H, Santoferrara L, Stoecker DK, Tillmann U
The Journal of eukaryotic microbiology (2023) :e12972 10.1111/jeu.12972 - Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
Bansal MS, Măndoiu II, Moussa M, Patterson M, Rajasekaran S, Skums P, Zelikovsky A
Journal of computational biology : a journal of computational molecular cell biology (2023) 30(4):363-365 10.1089/cmb.2023.29085.msb - The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.
Gosselin SP, Arsenault DR, Jennings CA, Gogarten JP
Genes (2023) 14(2): PMC1079044 10.1073/pnas.33.9.253 - Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide.
Korza G, DePratti S, Fairchild D, Wicander J, Kanaan J, Shames H, Nichols FC, Cowan A, Brul S, Setlow P
Journal of applied microbiology (2023) 134(3): PMC2897682 10.1021/acs.jproteome.5b00976 - The dominance of coinfecting parasites' indirect effects on host traits.
Bolnick DI, Arruda S, Polania C, Simonse L, Padhiar A, Roth A, Rodgers ML
bioRxiv : the preprint server for biology (2023) : PMC8308605 10.1101/2022.05.15.491937 - High Heterotrophic Plasticity of Massive Coral Contributes to Its Tolerance to Bioaccumulated Microplastics.
Zhou Z, Tang J, Cao X, Wu C, Cai W, Lin S
Environmental science & technology (2023) 57(8):3391-3401 10.1021/acs.est.2c08188 - Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover.
Grond K, Louyakis AS, Hird SM
mSystems (2023) 8(2):e0112822 PMC4302049 10.1186/s13059-014-0550-8 - Periodontal disease is associated with increased gut colonization of pathogenic Haemophilus parainfluenzae in patients with Crohn's disease.
Sohn J, Li L, Zhang L, Genco RJ, Falkner KL, Tettelin H, Rowsam AM, Smiraglia DJ, Novak JM, Diaz PI, Sun Y, Kirkwood KL
Cell reports (2023) 42(2):112120 PMC3412702 10.1186/1471-2105-13-134 - Highly Miniaturized, Low-Power CMOS ASIC Chip for Long-Term Continuous Glucose Monitoring.
Gudlavalleti RH, Xi X, Legassey A, Chan PY, Li J, Burgess D, Giardina C, Papadimitrakopoulos F, Jain F
Journal of diabetes science and technology (2023) :19322968231153419 10.1177/19322968231153419 - DaTeR: error-correcting phylogenetic chronograms using relative time constraints.
Mondal A, Rangel LT, Payette JG, Fournier GP, Bansal MS
Bioinformatics (Oxford, England) (2023) 39(2): PMC7056644 10.1093/bioinformatics/btad084 - A Single-Administration Microneedle Skin Patch for Multi-Burst Release of Vaccine against SARS-CoV-2.
Tran KTM, Gavitt TD, Le TT, Graichen A, Lin F, Liu Y, Tulman ER, Szczepanek SM, Nguyen TD
Advanced materials technologies (2023) :2200905 PMC7349596 10.1002/admt.202200905 - The impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants: A longitudinal cohort study.
Chen J, Li H, Zhao T, Chen K, Chen MH, Sun Z, Xu W, Maas K, Lester B, Cong X
medRxiv : the preprint server for health sciences (2023) : PMC9509490 10.1038/s41390-022-02021-y - Microbiome derived acidity protects against microbial invasion in .
Barron AJ, Lesperance DNA, Doucette J, Calle S, Broderick NA
bioRxiv : the preprint server for biology (2023) : PMC6102978 10.1038/nrmicro3074 - Detecting genomic deletions from high-throughput sequence data with unsupervised learning.
Li X, Wu Y
BMC bioinformatics (2023) 23(Suppl 8):568 PMC3106182 10.1093/bioinformatics/btr174 - Genomic instability caused by Arp2/3 complex inactivation results in micronucleus biogenesis and cellular senescence.
Haarer EL, Theodore CJ, Guo S, Frier RB, Campellone KG
PLoS genetics (2023) 19(1):e1010045 PMC3855844 10.1038/nmeth.2019 - Role of Spore Core Water Content and pH in the Accumulation and Utilization of Spores' Large 3-Phosphoglyceric Acid Depot, and the Crucial Role of This Depot in Generating ATP Early during Spore Germination.
Korza G, Goulet M, DeMarco A, Wicander J, Setlow P
Microorganisms (2023) 11(1): PMC7051807 10.1126/sciadv.abd6385 - "Failure To Launch": Development of a Reproductive Organ Linked to Symbiotic Bacteria.
McAnulty SJ, Kerwin AH, Koch E, Nuttall B, Suria AM, Collins AJ, Schleicher TR, Rader BA, Nyholm SV
mBio (2023) 14(1):e0213122 PMC3156573 10.1038/nmeth.f.303 - BosR and PlzA reciprocally regulate RpoS function to sustain Borrelia burgdorferi in ticks and mammals.
Grassmann AA, Tokarz R, Golino C, McLain MA, Groshong AM, Radolf JD, Caimano MJ
The Journal of clinical investigation (2023) 133(5): PMC4302049 10.1186/s13059-014-0550-8 - A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.
Podgorski JM, Freeman K, Gosselin S, Huet A, Conway JF, Bird M, Grecco J, Patel S, Jacobs-Sera D, Hatfull G, Gogarten JP, Ravantti J, White SJ
Structure (London, England : 1993) (2023) 31(3):282-294.e5 PMC4044616 10.1128/JVI.01629-15 - High-throughput sequencing reveals omnivorous and preferential diets of the rotifer .
Liang D, Luo H, Huang C, Ye Z, Sun S, Dong J, Liang M, Lin S, Yang Y
Frontiers in microbiology (2023) 13:1048619 PMC4517865 10.1371/journal.pone.0133060 - Exercise for counteracting weight recurrence after bariatric surgery: a systematic review and meta-analysis of randomized controlled trials.
Bond DS, Manuel KM, Wu Y, Livingston J, Papasavas PK, Baillot A, Pescatello LS
Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery (2023) 19(6):641-650 PMC8725202 10.1016/j.soard.2022.12.029 - Incorporation of 53BP1 into phase-separated bodies in cancer cells during aberrant mitosis.
Bleiler M, Cyr A, Wright DL, Giardina C
Journal of cell science (2023) 136(1): PMC3664841 10.1126/science.1231573 - Sex-specific gut microbiome profiles among preterm infants during the neonatal intensive care hospitalization.
Chen J, Li H, Maas K, Starkweather A, Chen M, Cong X
Interdisciplinary nursing research (2023) 1(1):6-13 PMC5296308 10.1097/NR9.0000000000000004 - Trends of fecal calprotectin levels and associations with early life experience in preterm infants.
Xu W, Zhang Y, Zhao W, Chen J, Maas K, Hussain N, Henderson WA, Cong X
Interdisciplinary nursing research (2023) 1(1):36-42 PMC6377820 10.1097/NR9.0000000000000006 2022
- Generation of Multiple Arbovirus-like Particles Using a Rapid Recombinant Vaccinia Virus Expression Platform.
Wang Y, Griffiths A, Brackney DE, Verardi PH
Pathogens (Basel, Switzerland) (2022) 11(12): PMC4337530 10.1128/JVI.03432-14 - Photoresponsive polymeric microneedles: An innovative way to monitor and treat diseases.
Singh P, Youden B, Carrier A, Oakes K, Servos M, Jiang R, Lin S, Nguyen TD, Zhang X
Journal of controlled release : official journal of the Controlled Release Society (2022) 353:1050-1067 10.1016/j.jconrel.2022.12.036 - Draft Genome Sequence of Plesiomonas shigelloides MD22D9, Isolated from the Digestive Tract of Macrobdella decora.
Casale A, Maldonado CA, Taropawala O, O'Sullivan B, Graf J
Microbiology resource announcements (2022) 12(1):e0093922 PMC5001611 10.1093/nar/gkw569 - High-resolution cryo-EM structure of the virus Sf6 genome delivery tail machine.
Li F, Hou CD, Yang R, Whitehead R, Teschke CM, Cingolani G
Science advances (2022) 8(49):eadc9641 PMC441615 10.1126/sciadv.adc9641 - Isolation, identification and toxicity of three strains of Heterocapsa (Dinophyceae) in a harmful event in Fujian, China.
Wu X, Liu Y, Weng Y, Li L, Lin S
Harmful algae (2022) 120:102355 10.1016/j.hal.2022.102355 - Anti-infective properties of the protective culture Hafnia alvei B16 in food and intestinal models against multi-drug resistant Salmonella.
Aljasir SF, D'Amico DJ
Food microbiology (2022) 110:104159 10.1016/j.fm.2022.104159 - Nondestructive and multiplex differentiation of pathogenic microorganisms from spoilage microflora on seafood using paper chromogenic array and neural network.
Yang M, Luo Y, Sharma A, Jia Z, Wang S, Wang D, Lin S, Perreault W, Purohit S, Gu T, Dillow H, Liu X, Yu H, Zhang B
Food research international (Ottawa, Ont.) (2022) 162(Pt B):112052 10.1016/j.foodres.2022.112052 - Species divergence under competition and shared predation.
Roesti M, Groh JS, Blain SA, Huss M, Rassias P, Bolnick DI, Stuart YE, Peichel CL, Schluter D
Ecology letters (2022) 26(1):111-123 10.1111/ele.14138 - Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids.
Haji D, Vailionis J, Stukel M, Gordon E, Lemmon EM, Lemmon AR, Simon C
Scientific reports (2022) 12(1):20559 PMC4151186 10.5344/ajev.2007.58.2.211 - Sample size re-estimation in Phase 2 dose-finding: Conditional power versus Bayesian predictive power.
Liu Q, Hu G, Ye B, Wang S, Wu Y
Pharmaceutical statistics (2022) 22(2):349-364 10.1002/pst.2275 - An ancient enzyme finds a new home: Prevalence and neofunctionalization of trypsin in marine phytoplankton.
You Y, Sun X, Lin S
Journal of phycology (2022) 59(1):152-166 10.1111/jpy.13300 - Time-Resolved Proteomics of Germinating Spores of .
Gao X, Swarge BN, Roseboom W, Setlow P, Brul S, Kramer G
International journal of molecular sciences (2022) 23(21): PMC4402510 10.1093/nar/gkv007 - Discovery of 3'--β-Glucosyltubercidin and the Nucleoside Specific Glycosyltransferase AvpGT through Genome Mining.
Pasternak ARO, Balunas MJ, Zechel DL
ACS chemical biology (2022) 17(12):3507-3514 10.1021/acschembio.2c00707 - Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales, Dinophyceae).
Gómez F, Gourvil P, Li T, Huang Y, Zhang H, Courcot L, Artigas LF, Soler Onís E, Gutiérrez-Rodríguez A, Lin S
Journal of phycology (2022) 59(1):70-86 10.1111/jpy.13298 - Determining the Properties that Govern Selective Ingestion and Egestion of Microplastics by the Blue Mussel () and Eastern Oyster ().
Mladinich K, Holohan BA, Shumway SE, Brown K, Ward JE
Environmental science & technology (2022) 56(22):15770-15779 10.1021/acs.est.2c06402 - B cells oppose Mycoplasma pneumoniae vaccine enhanced disease and limit bacterial colonization of the lungs.
Gavitt TD, Mara AB, Goodridge ML, Ozyck RG, Reinhardt E, Miller JM, Hunte M, Tulman ER, Frasca S, Silbart LK, Geary SJ, Szczepanek SM
NPJ vaccines (2022) 7(1):130 PMC98411 10.1016/S0021-9258(19)69848-0 - Characterization of microbial community assembly on new wooden vats for use in cheese production.
Sun L, D'Amico DJ
Food microbiology (2022) 109:104154 10.1016/j.fm.2022.104154 - CHANGES IN TISSUE TROPISM OF MYCOPLASMA GALLISEPTICUM FOLLOWING HOST JUMP.
Reinoso-Pérez MT, Levitskiy AA, Dhondt KV, Cole N, Tulman E, Geary SJ, Dhondt AA
Journal of wildlife diseases (2022) 58(4):716-724 10.7589/JWD-D-21-00187 - Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return.
Horne WH, Volpe RP, Korza G, DePratti S, Conze IH, Shuryak I, Grebenc T, Matrosova VY, Gaidamakova EK, Tkavc R, Sharma A, Gostinčar C, Gunde-Cimerman N, Hoffman BM, Setlow P, Daly MJ
Astrobiology (2022) 22(11):1337-1350 PMC110589 10.1007/s11214-020-00722-6 - Cardiometabolic Biomarkers and Habitual Caffeine Consumption Associate with the Adverse Ambulatory Blood Pressure Response to Strenuous Physical Exertion among Firefighters.
Berkowsky RS, Zaleski AL, Taylor BA, Chen MH, Gans KM, Wu Y, Parducci PM, Zhang Y, Fernandez AB, Pescatello LS
Nutrients (2022) 14(19): PMC4656907 10.3945/jn.115.219634 - Gut microbiome insights from 16S rRNA analysis of 17-year periodical cicadas (Hemiptera: Magicicada spp.) Broods II, VI, and X.
Brumfield KD, Raupp MJ, Haji D, Simon C, Graf J, Cooley JR, Janton ST, Meister RC, Huq A, Colwell RR, Hasan NA
Scientific reports (2022) 12(1):16967 PMC4021573 10.2307/1942268 - High-throughput nanopore sequencing of tandem repeat genes and reveals clade-specific patterns and recapitulates global whole genome phylogeny.
Lieberman NAP, Armstrong TD, Chung B, Pfalmer D, Hennelly CM, Haynes A, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Conte ID, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitja O, Rompalo A, Mulcahy F, Hook EW, Hoffman IF, Matoga MM, Zheng H, Yang B, Lopez-Medina E, Ramirez LG, Radolf JD, Hawley KL, Salazar JC, Lukehart SA, Seña AC, Parr JB, Giacani L, Greninger AL
Frontiers in microbiology (2022) 13:1007056 PMC3630124 10.1371/journal.pntd.0002172 - Active meiosis during dinoflagellate blooms: A 'sex for proliferation' hypothesis.
Lin S, Yu L, Wu X, Li M, Zhang Y, Luo H, Li H, Li T, Li L
Harmful algae (2022) 118:102307 10.1016/j.hal.2022.102307 - The functional oral microbiome: Biofilm environment, polymicrobial interactions, and community dynamics.
Kreth J, Koo H, Diaz PI
Molecular oral microbiology (2022) 37(5):165-166 10.1111/omi.12390 - Genomic versus Plasmid-Borne Expression of Germinant Receptor Proteins in Bacillus cereus Strain 14579.
Wang Y, Setlow P, Brul S
Microorganisms (2022) 10(9): PMC3685010 10.1111/j.1574-6968.2001.tb10930.x - Changes in the Spore Proteome of in Response to Introduction of Plasmids.
Gao X, Swarge BN, Roseboom W, Wang Y, Dekker HL, Setlow P, Brul S, Kramer G
Microorganisms (2022) 10(9): PMC2661013 10.1111/j.1365-2672.2008.04048.x - Transcriptomic and metabolic signatures of diatom plasticity to light fluctuations.
Zhou L, Gao S, Yang W, Wu S, Huan L, Xie X, Wang X, Lin S, Wang G
Plant physiology (2022) 190(4):2295-2314 PMC8015109 10.1093/plphys/kiac455 - Wireless multi-lateral optofluidic microsystems for real-time programmable optogenetics and photopharmacology.
Wu Y, Wu M, Vázquez-Guardado A, Kim J, Zhang X, Avila R, Kim JT, Deng Y, Yu Y, Melzer S, Bai Y, Yoon H, Meng L, Zhang Y, Guo H, Hong L, Kanatzidis EE, Haney CR, Waters EA, Banks AR, Hu Z, Lie F, Chamorro LP, Sabatini BL, Huang Y, Kozorovitskiy Y, Rogers JA
Nature communications (2022) 13(1):5571 PMC8211450 10.7554/eLife.64041 - virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
Zaman S, Sledzieski S, Berger B, Wu YC, Bansal MS
Journal of computational biology : a journal of computational molecular cell biology (2022) 30(1):3-20 PMC7095418 10.1089/cmb.2021.0507 - Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media.
Balseiro-Romero M, Prieto-Fernández Á, Shor LM, Ghoshal S, Baveye PC, Ortega-Calvo JJ
Environmental science & technology (2022) 56(19):13975-13984 PMC2483759 10.1021/es5056484 - Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.
Bansal MS
Methods in molecular biology (Clifton, N.J.) (2022) 2569:233-252 10.1109/TCBB.2018.2846253 - Evolutionary gain and loss of a pathological immune response to parasitism.
Weber JN, Steinel NC, Peng F, Shim KC, Lohman BK, Fuess LE, Subramanian S, Lisle SP, Bolnick DI
Science (New York, N.Y.) (2022) 377(6611):1206-1211 PMC7901769 10.1126/sciadv.abg5285 - Preservation of exopolymeric substances in estuarine sediments.
Duteil T, Bourillot R, Braissant O, Grégoire B, Leloup M, Portier E, Brigaud B, Féniès H, Svahn I, Henry A, Yokoyama Y, Visscher PT
Frontiers in microbiology (2022) 13:921154 PMC91491 10.5194/bg-7-483-2010 - A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility.
Testerman T, Beka L, Reichley SR, King S, Welch TJ, Wiens GD, Graf J
FEMS microbiology ecology (2022) 98(10): 10.1093/femsec/fiac101 - Exercise to Treat Hypertension: Late Breaking News on Exercise Prescriptions That FITT.
Alves AJ, Wu Y, Lopes S, Ribeiro F, Pescatello LS
Current sports medicine reports (2022) 21(8):280-288 10.1249/JSR.0000000000000983 - Joint inference of ancestry and genotypes of parents from children.
Zhang Y, Wu Y
iScience (2022) 25(8):104768 PMC4750478 10.1016/j.isci.2022.104768 - A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples.
Chen W, Luo H, Zeng L, Pan Y, Parr JB, Jiang Y, Cunningham CH, Hawley KL, Radolf JD, Ke W, Ou J, Yang J, Yang B, Zheng H
Nature communications (2022) 13(1):4671 PMC6956564 10.1038/s41596-019-0210-2 - Long-term spatiotemporal variation in density of a tropical folivore: responses to a complex disturbance regime.
Willig MR, Presley SJ
Oecologia (2022) 199(4):979-994 10.1016/j.biocon.2020.108891 - Causes of infant deaths and patterns of associated factors in Eastern Ethiopia: Results of verbal autopsy (InterVA-4) study.
Mebrahtom S, Worku A, Gage DJ
PloS one (2022) 17(8):e0270245 PMC2779934 10.4269/ajtmh.2008.78.106 - Computational approach to modeling microbiome landscapes associated with chronic human disease progression.
Li L, Sohn J, Genco RJ, Wactawski-Wende J, Goodison S, Diaz PI, Sun Y
PLoS computational biology (2022) 18(8):e1010373 PMC4893271 10.1046/j.1461-0248.2001.00230.x - Vaccination with Mycoplasma pneumoniae membrane lipoproteins induces IL-17A driven neutrophilia that mediates Vaccine-Enhanced Disease.
Mara AB, Gavitt TD, Tulman ER, Miller JM, He W, Reinhardt EM, Ozyck RG, Goodridge ML, Silbart LK, Szczepanek SM, Geary SJ
NPJ vaccines (2022) 7(1):86 PMC6202950 10.3389/fimmu.2018.02405 - Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22.
Woodbury BM, Motwani T, Leroux MN, Barnes LF, Lyktey NA, Banerjee S, Dedeo CL, Jarrold MF, Teschke CM
Viruses (2022) 14(7): PMC4424107 10.1111/j.1365-2958.2006.05203.x - Viral Nucleases from Herpesviruses and Coronavirus in Recombination and Proofreading: Potential Targets for Antiviral Drug Discovery.
Wright LR, Wright DL, Weller SK
Viruses (2022) 14(7): PMC8640510 10.1038/s41418-021-00900-1 - Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes.
Green EA, Klassen JL
mSphere (2022) 7(4):e0098921 PMC3998144 10.1093/bioinformatics/btu033 - A surprise landing on the of macrocyclic dibridgehead diorganoarsines: syntheses, structures, and reactivities.
Zarcone SR, Verardi PJ, Bhuvanesh N, Gladysz JA
Chemical communications (Cambridge, England) (2022) 58(62):8694-8697 10.1039/d2cc03235j - Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton.
You Y, Sun X, Ma M, He J, Li L, Porto FW, Lin S
Nature communications (2022) 13(1):4022 PMC8788711 10.1128/AEM.02097-21 - Synthesis and Characterization of Preacinetobactin and 5-Phenyl Preacinetobactin.
Bray JM, Pierce S, Angeles-Boza AM, Peczuh MW
Molecules (Basel, Switzerland) (2022) 27(12): PMC1362951 10.1016/S1044-0305(99)00068-9 - Transcriptomic Responses of Upon Treatments of -Cinnamaldehyde, Carvacrol, and Eugenol.
Ranjitkar S, Duan JE, Srirattana K, Alqahtani F, Tulman ER, Mandoiu I, Venkitanarayanan K, Tian X
Frontiers in microbiology (2022) 13:888433 PMC6977290 10.1186/s12864-020-6460-0 - Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera).
Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C
Systematic biology (2022) 71(6):1504-1523 10.1093/sysbio/syac043 - Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon.
Robison T, Nelson JM, Hauser DA, Lewis LA, Li FW
American journal of botany (2022) 109(6):939-951 10.1002/ajb2.16015 - The B-box1 domain of PML mediates SUMO E2-E3 complex formation through an atypical interaction with UBC9.
Bregnard T, Ahmed A, Semenova IV, Weller SK, Bezsonova I
Biophysical chemistry (2022) 287:106827 PMC4393527 10.1093/bioinformatics/btu830 - Editorial: Physiological Regulation and Homeostasis Among Coral Holobiont Partners.
Lin S, Yu K, Zhou Z
Frontiers in physiology (2022) 13:921401 PMC8551165 10.1111/jpy.13156 - Genetic differentiation and phylogeography of rotifer and populations between Southeastern China and eastern North America: High intercontinental differences.
Liang D, McManus GB, Wang Q, Sun X, Liu Z, Lin S, Yang Y
Ecology and evolution (2022) 12(5):e8912 PMC3810850 10.1007/s10750-017-3407-9 - Metallated Anticancer Peptides: An Expanded Mechanism that Encompasses Physical and Chemical Bilayer Disruption.
Mihailescu E, Comert F, Heinrich F, Chowdhury A, Schoeneck M, Darling C, Anderson K, Libardo MD, Angeles-Boza A, Silin V, Cotten M
FASEB journal : official publication of the Federation of American Societies for Experimental Biology (2022) 36 Suppl 1: 10.1096/fasebj.2022.36.S1.R4666 - Guanine Nucleotide-Dependent Conformational Selection Regulates Distinct Alternate Ribosome Bound States of the Translation Factor BipA.
Montovano G, Buckley TS, Sharawy M, May ER, Anand GS, Robinson VL
FASEB journal : official publication of the Federation of American Societies for Experimental Biology (2022) 36 Suppl 1: 10.1096/fasebj.2022.36.S1.0R518 - Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.
Krucinska J, Lombardo MN, Erlandsen H, Estrada A, Si D, Viswanathan K, Wright DL
Communications biology (2022) 5(1):459 PMC3069751 10.1107/S0907444911001314 - Visualization of SpoVAEa Protein Dynamics in Dormant Spores of and Dynamic Changes in Their Germinosomes and SpoVAEa during Germination.
Wang Y, Vischer NOE, Wekking D, Boggian A, Setlow P, Brul S
Microbiology spectrum (2022) 10(3):e0066622 PMC8617281 10.1038/s41467-021-27235-2 - Relationship between the subgingival microbiome and menopausal hormone therapy use: The Buffalo OsteoPerio study.
Soliman AI, LaMonte MJ, Hovey KM, McSkimming DI, Andrews CA, Diaz PI, Buck MJ, Sun Y, Millen AE, Wactawski-Wende J
Journal of periodontology (2022) 93(11):1635-1648 PMC5074386 10.1128/mBio.00166-16 - From island biogeography to landscape and metacommunity ecology: A macroecological perspective of bat communities.
Presley SJ, Willig MR
Annals of the New York Academy of Sciences (2022) 1514(1):43-61 10.1111/nyas.14785 - Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states.
Whitehead RD, Teschke CM, Alexandrescu AT
Protein science : a publication of the Protein Society (2022) 31(5):e4321 PMC3052747 10.1002/pro.4321 - Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19.
Bivins A, Kaya D, Ahmed W, Brown J, Butler C, Greaves J, Leal R, Maas K, Rao G, Sherchan S, Sills D, Sinclair R, Wheeler RT, Mansfeldt C
The Science of the total environment (2022) 835:155347 PMC8751019 10.1021/acs.est.1c04623 - Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization.
Schmidbaur H, Kawaguchi A, Clarence T, Fu X, Hoang OP, Zimmermann B, Ritschard EA, Weissenbacher A, Foster JS, Nyholm SV, Bates PA, Albertin CB, Tanaka E, Simakov O
Nature communications (2022) 13(1):2172 PMC5360930 10.1002/bies.201100001 - Functional differentiation and complementation of alkaline phosphatases and choreography of DOP scavenging in a marine diatom.
Zhang K, Li J, Wang J, Lin X, Li L, You Y, Wu X, Zhou Z, Lin S
Molecular ecology (2022) 31(12):3389-3399 10.1111/mec.16475 - Implantable Aptamer-Graphene Microtransistors for Real-Time Monitoring of Neurochemical Release in Vivo.
Wu G, Zhang N, Matarasso A, Heck I, Li H, Lu W, Phaup JG, Schneider MJ, Wu Y, Weng Z, Sun H, Gao Z, Zhang X, Sandberg SG, Parvin D, Seaholm E, Islam SK, Wang X, Phillips PEM, Castro DC, Ding S, Li DP, Bruchas MR, Zhang Y
Nano letters (2022) 22(9):3668-3677 PMC5262197 10.1101/2020.05.25.115675 - Physiological and metabolic effects of glyphosate as the sole P source on a cosmopolitan phytoplankter and biogeochemical implications.
Wang C, Sun X, Wang J, Tang JM, Gu Y, Lin S
The Science of the total environment (2022) 832:155094 10.1016/j.scitotenv.2022.155094 - Effects of intramuscularly injected plant-derived antimicrobials in the mouse model.
Johnson EJ, Duan JE, Srirattana K, Venkitanarayanan K, Tulman ER, Tian XC
Scientific reports (2022) 12(1):5937 PMC6811576 10.1093/jac/33.3.387 - Thirteen new species of Chilecicada Sanborn, 2014 (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae) expand the highly endemic cicada fauna of Chile.
Sanborn AF, Cole JA, Stukel M, Ukasik P, Veloso C, Gonzalez VA, Karkar JB, Simon C
Zootaxa (2022) 5078(1):170 10.11646/zootaxa.5078.1.1 - Survivability of spores in fermented pork summer sausage during refrigerated storage.
Flock G, Yin HB, Chen CH, Pellissery AJ, Venkitanarayanan K
Veterinary world (2022) 15(1):162-167 PMC2293200 10.14202/vetworld.2022.162-167 - Evaluating the Methodological Quality of Postexercise Hypotension Aerobic Exercise Interventions.
Day C, Wu Y, Pescatello LS
Frontiers in physiology (2022) 13:851950 PMC5064144 10.1097/HJH.0000000000002115 - Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth.
Testerman T, Li Z, Galuppo B, Graf J, Santoro N
Hepatology communications (2022) 6(8):1962-1974 PMC8714082 10.1101/2021.01.20.427420 - Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment.
Hare PJ, Englander HE, Mok WWK
Journal of applied microbiology (2022) 132(6):4020-4032 PMC7293176 10.1101/2021.10.24.465352 - Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine.
Koopman N, Remijas L, Seppen J, Setlow P, Brul S
International journal of molecular sciences (2022) 23(6): PMC8342367 10.1007/s11274-021-03108-0 - Organization and dynamics of the SpoVAEa protein and its surrounding inner membrane lipids, upon germination of Bacillus subtilis spores.
Wen J, Vischer NOE, de Vos AL, Manders EMM, Setlow P, Brul S
Scientific reports (2022) 12(1):4944 PMC6002552 10.1038/nprot.2006.4 - Clostridioides difficile Infection Dysregulates Brain Dopamine Metabolism.
Vinithakumari AA, Padhi P, Hernandez B, Lin SJ, Dunkerson-Kurzhumov A, Showman L, Breitzman M, Stokes C, Sulaiman Y, Tangudu C, Kuttappan DA, Muyyarikkandy MS, Willette AA, Phillips GJ, Anantharam V, Perera A, Sponseller BA, Kanthasamy A, Mooyottu S
Microbiology spectrum (2022) 10(2):e0007322 PMC4995106 10.1007/s11064-018-2653-1 - Publisher Correction: A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner.
Nyholm SV, McFall-Ngai MJ
Nature reviews. Microbiology (2022) 20(5):315 10.1038/s41579-022-00723-y - Complex community-wide consequences of consumer sexual dimorphism.
De Lisle SP, Schrieber SJ, Bolnick DI
The Journal of animal ecology (2022) 91(5):958-969 PMC5949143 10.1007/s00285-017-1187-5 - Interactive effects of acidification and copper exposure on the reproduction and metabolism of coral endosymbiont Cladocopium goreaui.
Tang J, Cai W, Yan Z, Zhang K, Zhou Z, Zhao J, Lin S
Marine pollution bulletin (2022) 177:113508 10.1016/j.marpolbul.2022.113508 - Wireless, battery-free push-pull microsystem for membrane-free neurochemical sampling in freely moving animals.
Wu G, Heck I, Zhang N, Phaup G, Zhang X, Wu Y, Stalla DE, Weng Z, Sun H, Li H, Zhang Z, Ding S, Li DP, Zhang Y
Science advances (2022) 8(8):eabn2277 PMC4354627 10.1126/sciadv.abn2277 - Comparison of knowledge and awareness of infection control practices among nurses in India: A cross-sectional survey.
Sodhi K, Arya M, Chanchalani G, Sinha V, Dominic Savio R, Ak AK, Ahmed A, Jagiasi B, Agarwal D, Jagathkar G, Khasne R, Sahasrabudhe SS, Jha SK, Sahoo TK, Mittal V, Hr H, Bansal S, Agarwal C, Kumar M
American journal of infection control (2022) : 10.1016/j.ajic.2022.02.014 - The risk of water, sanitation and hygiene on diarrhea-related infant mortality in eastern Ethiopia: a population-based nested case-control.
Mebrahtom S, Worku A, Gage DJ
BMC public health (2022) 22(1):343 PMC6743165 10.1186/s12889-019-7273-4 - Exploring synergy and its role in antimicrobial peptide biology.
Howell M, Wenc AK, Donaghy CM, Wasche DV, Abissi I, Naing MD, Pierce S, Angeles-Boza AM
Methods in enzymology (2022) 663:99-130 10.1016/bs.mie.2021.09.017 - Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.
Wang S, Reeve SM, Holt GT, Ojewole AA, Frenkel MS, Gainza P, Keshipeddy S, Fowler VG, Wright DL, Donald BR
PLoS computational biology (2022) 18(2):e1009855 PMC2144501 10.1002/prot.22383 - Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts.
Stephens ME, Benjamino J, Graf J, Gage DJ
mSphere (2022) 7(1):e0002122 PMC3424584 10.1093/nar/gks596 - Aspergillus nidulans Septa Are Indispensable for Surviving Cell Wall Stress.
Spence RN, Huso W, Edwards H, Doan A, Reese S, Harris SD, Srivastava R, Marten MR
Microbiology spectrum (2022) 10(1):e0206321 PMC4643482 10.1016/j.fgb.2019.01.003 - Alterations of host-gut microbiome interactions in multiple sclerosis.
Cantoni C, Lin Q, Dorsett Y, Ghezzi L, Liu Z, Pan Y, Chen K, Han Y, Li Z, Xiao H, Gormley M, Liu Y, Bokoliya S, Panier H, Suther C, Evans E, Deng L, Locca A, Mikesell R, Obert K, Newland P, Wu Y, Salter A, Cross AH, Tarr PI, Lovett-Racke A, Piccio L, Zhou Y
EBioMedicine (2022) 76:103798 PMC6342642 10.1016/j.ebiom.2021.103798 - Two-Metal Ion-Dependent Enzymes as Potential Antiviral Targets in Human Herpesviruses.
DiScipio KA, Weerasooriya S, Szczepaniak R, Hazeen A, Wright LR, Wright DL, Weller SK
mBio (2022) 13(1):e0322621 PMC2447070 10.1128/JVI.00455-08 - Bacterial Indole as a Multifunctional Regulator of Klebsiella oxytoca Complex Enterotoxicity.
Ledala N, Malik M, Rezaul K, Paveglio S, Provatas A, Kiel A, Caimano M, Zhou Y, Lindgren J, Krasulova K, Illes P, Dvořák Z, Kortagere S, Kienesberger S, Cosic A, Pöltl L, Zechner EL, Ghosh S, Mani S, Radolf JD, Matson AP
mBio (2022) 13(1):e0375221 PMC7136958 10.1038/nature07935 - Heat Activation and Inactivation of Bacterial Spores: Is There an Overlap?
Wen J, Smelt JPPM, Vischer NOE, de Vos AL, Setlow P, Brul S
Applied and environmental microbiology (2022) 88(5):e0232421 PMC3607599 10.1371/journal.pone.0058972 - Interacting phenotypes and the coevolutionary process: Interspecific indirect genetic effects alter coevolutionary dynamics.
De Lisle SP, Bolnick DI, Brodie ED, Moore AJ, McGlothlin JW
Evolution; international journal of organic evolution (2022) 76(3):429-444 PMC153611 10.1101/503904 - Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells.
Harvey HJ, Chubynsky MV, Sprittles JE, Shor LM, Mooney SJ, Wildman RD, Avery SV
Computational and structural biotechnology journal (2022) 20:128-138 PMC5673896 10.1016/j.csbj.2021.11.039 2021
- 18S rRNA gene amplicon sequencing combined with culture-based surveys of maize rhizosphere protists reveal dominant, plant-enriched and culturable community members.
Taerum SJ, Micciulla J, Corso G, Steven B, Gage DJ, Triplett LR
Environmental microbiology reports (2021) 14(1):110-118 10.1111/1758-2229.13038 - Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea.
Yuan H, Li T, Li H, Wang C, Li L, Lin X, Lin S
Microorganisms (2021) 9(12): PMC8223512 10.3389/fmolb.2021.685757 - Playing by their own rules: the vertebrate archaeome.
Hird SM
Trends in microbiology (2021) 30(2):102-103 10.1016/j.tim.2021.12.002 - Multivariate log-contrast regression with sub-compositional predictors: Testing the association between preterm infants' gut microbiome and neurobehavioral outcomes.
Liu X, Cong X, Li G, Maas K, Chen K
Statistics in medicine (2021) 41(3):580-594 10.1002/sim.9273 - Isolation from a fish kill and transcriptomic characterization of Gyrodinium jinhaense off Long Island Sound.
Sprecher BN, Zhang H, Park G, Lin S
Harmful algae (2021) 110:102136 10.1016/j.hal.2021.102136 - The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwin's finches in Galápagos.
Romine MG, Knutie SA, Crow CM, Vaziri GJ, Chaves JA, Koop JAH, Lamichhaney S
G3 (Bethesda, Md.) (2021) 12(2): PMC5411770 10.1371/journal.pone.0019706 - PmtA Regulates Pyocyanin Expression and Biofilm Formation in .
Thees AV, Pietrosimone KM, Melchiorre CK, Marden JN, Graf J, Lynes MA, Maltz-Matyschsyk M
Frontiers in microbiology (2021) 12:789765 PMC8636135 10.3389/fmicb.2021.789765 - A distinct complex of PRP19-related and trypanosomatid-specific proteins is required for pre-mRNA splicing in trypanosomes.
Srivastava A, Ambrósio DL, Tasak M, Gosavi U, Günzl A
Nucleic acids research (2021) 49(22):12929-12942 PMC5343452 10.1093/nar/gkab1152 - Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters.
Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK
Microorganisms (2021) 9(11): PMC8620850 10.3390/microorganisms9112277 - Chronic cannabis smoking-enriched oral pathobiont drives behavioral changes, macrophage infiltration, and increases β-amyloid protein production in the brain.
Luo Z, Fitting S, Robinson C, Benitez A, Li M, Wu Y, Fu X, Amato D, Ning W, Funderburg N, Wang X, Zhou Z, Yu X, Wagner A, Cong X, Xu W, Maas K, Wolf BJ, Huang L, Yu J, Scott A, Mcrae-Clark A, Hamlett ED, Jiang W
EBioMedicine (2021) 74:103701 PMC5791180 10.2174/1570162X16666180703151208 - Bacterial cooperation through horizontal gene transfer.
Lee IPA, Eldakar OT, Gogarten JP, Andam CP
Trends in ecology & evolution (2021) 37(3):223-232 10.1016/j.tree.2021.11.006 - Effect of actinorhizal root exudates on the proteomes of Frankia soli NRRL B-16219, a strain colonizing the root tissues of its actinorhizal host via intercellular pathway.
Gueddou A, Sarker I, Sen A, Ghodhbane-Gtari F, Benson DR, Armengaud J, Gtari M
Research in microbiology (2021) 173(1-2):103900 10.1016/j.resmic.2021.103900 - Detecting Flavobacterial Fish Pathogens in the Environment via High-Throughput Community Analysis.
Testerman T, Beka L, McClure EA, Reichley SR, King S, Welch TJ, Graf J
Applied and environmental microbiology (2021) 88(2):e0209221 10.1128/AEM.02092-21 - Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020).
Jha SK, MĂndoiu I, Rajasekaran S, Skums P, Zelikovsky A
Journal of computational biology : a journal of computational molecular cell biology (2021) 28(11):1033-1034 10.1089/cmb.2021.29048.skj - Differential adhesion regulates neurite placement via a retrograde zippering mechanism.
Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler WA, Shroff H, Colón-Ramos DA
eLife (2021) 10: PMC8843091 10.7554/eLife.71171 - The Association of Socioeconomic Factors With Outcomes for Coronary Artery Bypass Surgery.
Hannan EL, Wu Y, Cozzens K, Friedrich M, Chikwe J, Adams DH, Sundt TM, Girardi L, Smith CR, Lahey SJ, Gold JP, Wechsler A
The Annals of thoracic surgery (2021) 114(4):1318-1325 10.1016/j.athoracsur.2021.10.006 - Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape.
Kunkel G, Madani M, White SJ, Verardi PH, Tarakanova A
Biophysical journal (2021) 120(24):5592-5618 PMC5199616 10.1101/2020.04.07.023903 - Phytate as a Phosphorus Nutrient with Impacts on Iron Stress-Related Gene Expression for Phytoplankton: Insights from the Diatom .
Li J, Zhang K, Lin X, Li L, Lin S
Applied and environmental microbiology (2021) 88(2):e0209721 10.1128/AEM.02097-21 - Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope.
Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK
Nature communications (2021) 12(1):6423 PMC8571378 10.1038/s41467-021-26646-5 - Resistance properties and the role of the inner membrane and coat of Bacillus subtilis spores with extreme wet heat resistance.
Kanaan J, Murray J, Higgins R, Nana M, DeMarco AM, Korza G, Setlow P
Journal of applied microbiology (2021) 132(3):2157-2166 10.1111/jam.15345 - An insight into molecular taxonomy of bufonids, microhylids, and dicroglossid frogs: First genetic records from Pakistan.
Akram A, Rais M, Lopez-Hervas K, Tarvin RD, Saeed M, Bolnick DI, Cannatella DC
Ecology and evolution (2021) 11(20):14175-14216 PMC8525160 10.1002/ece3.8134 - Dynamics of Germinosome Formation and FRET-Based Analysis of Interactions between GerD and Germinant Receptor Subunits in Spores.
Wang Y, Breedijk RMP, Hink MA, Bults L, Vischer NOE, Setlow P, Brul S
International journal of molecular sciences (2021) 22(20): PMC8539644 10.3390/ijms222011230 - The Epithelial-Stromal Microenvironment in Early Colonic Neoplasia.
Ideta T, Li B, Flynn C, Igarashi Y, Lowman G, Looney T, Devers TJ, Birk J, Forouhar F, Giardina C, Rosenberg DW
Molecular cancer research : MCR (2021) 20(1):56-61 PMC6826139 10.1016/j.cell.2008.03.039 - Identification of Apocarotenoids as Chemical Markers of In Vitro Anti-Inflammatory Activity for Spirulina Supplements.
Tan KC, Pham TX, Lee Y, Lee JY, Balunas MJ
Journal of agricultural and food chemistry (2021) 69(43):12674-12685 10.1021/acs.jafc.1c03015 - Advances in the Evolution and Ecology of 13- and 17-Year Periodical Cicadas.
Simon C, Cooley JR, Karban R, Sota T
Annual review of entomology (2021) 67:457-482 10.1146/annurev-ento-072121-061108 - Probiotic potential of commercial dairy-associated protective cultures: In vitro and in vivo protection against Listeria monocytogenes infection.
Aljasir SF, D'Amico DJ
Food research international (Ottawa, Ont.) (2021) 149:110699 10.1016/j.foodres.2021.110699 - Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts.
Ingala MR, Albert L, Addesso A, Watkins MJ, Knutie SA
Animal microbiome (2021) 3(1):67 PMC8487522 10.1186/s42523-021-00130-3 - Between-population differences in constitutive and infection-induced gene expression in threespine stickleback.
Fuess LE, Weber JN, den Haan S, Steinel NC, Shim KC, Bolnick DI
Molecular ecology (2021) 30(24):6791-6805 PMC6345051 10.1186/s13567-019-0622-6 - Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese.
Sun L, D'Amico DJ
mSystems (2021) 6(5):e0083021 PMC8547439 10.1128/mSystems.00830-21 - Sick of eating: Eco-evo-immuno dynamics of predators and their trophically acquired parasites.
Fleischer SR, Bolnick DI, Schreiber SJ
Evolution; international journal of organic evolution (2021) 75(11):2842-2856 PMC8985590 10.1111/evo.14353 - Distribution Patterns of Ciliate Diversity in the South China Sea.
Liu W, McManus GB, Lin X, Huang H, Zhang W, Tan Y
Frontiers in microbiology (2021) 12:689688 PMC8446678 10.3389/fmicb.2021.689688 - Applied ecoimmunology: using immunological tools to improve conservation efforts in a changing world.
Ohmer MEB, Costantini D, Czirják GÁ, Downs CJ, Ferguson LV, Flies A, Franklin CE, Kayigwe AN, Knutie S, Richards-Zawacki CL, Cramp RL
Conservation physiology (2021) 9(1):coab074 PMC8422949 10.1093/conphys/coab074 - Survival on Peaches and Nectarines under Conditions Simulating Commercial Stone-Fruit Packinghouse Operations.
Kuttappan D, Muyyarikkandy MS, Mathew E, Amalaradjou MA
International journal of environmental research and public health (2021) 18(17): PMC8431221 10.3390/ijerph18179174 - High Resolution Analysis of Proteome Dynamics during Sporulation.
Tu Z, Dekker HL, Roseboom W, Swarge BN, Setlow P, Brul S, Kramer G
International journal of molecular sciences (2021) 22(17): PMC8431406 10.3390/ijms22179345 - Fatty acid metabolism and colon cancer protection by dietary methyl donor restriction.
Aladelokun O, Hanley M, Mu J, Giardina JC, Rosenberg DW, Giardina C
Metabolomics : Official journal of the Metabolomic Society (2021) 17(9):80 PMC8416812 10.1007/s11306-021-01831-1 - A gatekeeper protein contributes to T3SS2 function via interaction with an ATPase in Vibrio parahaemolyticus.
Lin IT, Tulman ER, Geary SJ, Zhou X
Microbiological research (2021) 252:126857 10.1016/j.micres.2021.126857 - Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis.
Chen J, Li H, Hird SM, Chen MH, Xu W, Maas K, Cong X
Frontiers in cellular and infection microbiology (2021) 11:671074 PMC8387566 10.3389/fcimb.2021.671074 - Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins.
Leavitt JC, Gilcrease EB, Woodbury BM, Teschke CM, Casjens SR
Viruses (2021) 13(8): PMC8402733 10.3390/v13081504 - Oral Enrichment of Streptococcus and its Role in Systemic Inflammation Related to Monocyte Activation in Humans with Cocaine Use Disorder.
Fu X, Cheng D, Luo Z, Wagner A, Fitting S, Cong X, Xu W, Maas K, Wan Z, Zhu J, Zhou Z, Stoops WW, McRae-Clark A, Jiang W
Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology (2021) 17(1-2):305-317 PMC5030690 10.1007/s11481-021-10007-6 - Protective Effect of Baicalin against Infection in Mice.
Pellissery AJ, Vinayamohan PG, Kuttappan DA, Mishra N, Fragomeni BO, Maas K, Mooyottu S, Venkitanarayanan K
Antibiotics (Basel, Switzerland) (2021) 10(8): PMC8388895 10.3390/antibiotics10080926 - Copy number variation of a fatty acid desaturase gene associated with ecological divergence in freshwater stickleback populations.
Ishikawa A, Stuart YE, Bolnick DI, Kitano J
Biology letters (2021) 17(8):20210204 PMC8385377 10.1098/rsbl.2021.0204 - Oxidative damage increases with degree of simulated bacterial infection, but not ectoparasitism, in tree swallow nestlings.
Butler MW, Stierhoff EN, Carpenetti JM, Bertone MA, Addesso AM, Knutie SA
The Journal of experimental biology (2021) 224(18): 10.1242/jeb.243116 - Excitotoxic stimulation activates distinct pathogenic and protective expression signatures in the hippocampus.
Caba E, Sherman MD, Farizatto KLG, Alcira B, Wang HW, Giardina C, Shin DG, Sandefur CI, Bahr BA
Journal of cellular and molecular medicine (2021) 25(18):9011-9027 PMC8435451 10.1111/jcmm.16864 - Nanoemulsified Carvacrol as a Novel Washing Treatment Reduces Escherichia coli O157:H7 on Spinach and Lettuce.
Chen CH, Yin HB, Teng ZI, Byun S, Guan Y, Luo Y, Upadhyay A, Patel J
Journal of food protection (2021) 84(12):2163-2173 10.4315/JFP-21-151 - Avian gut microbiomes taking flight.
Bodawatta KH, Hird SM, Grond K, Poulsen M, Jønsson KA
Trends in microbiology (2021) 30(3):268-280 10.1016/j.tim.2021.07.003 - An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.
Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP
Genome biology and evolution (2021) 13(9): PMC8483891 10.1093/gbe/evab187 - Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions.
Lin S, Song B, Morse D
Journal of phycology (2021) 57(6):1674-1678 10.1111/jpy.13206 - Multi-Omics Analysis on Neurodevelopment in Preterm Neonates: A Protocol Paper.
Casavant SG, Chen J, Xu W, Lainwala S, Matson A, Chen MH, Starkweather A, Maas K, Cong XS
Nursing research (2021) 70(6):462-468 PMC8563389 10.1097/NNR.0000000000000548 - Cytotoxic effects on cancerous and non-cancerous cells of trans-cinnamaldehyde, carvacrol, and eugenol.
Ranjitkar S, Zhang D, Sun F, Salman S, He W, Venkitanarayanan K, Tulman ER, Tian X
Scientific reports (2021) 11(1):16281 PMC8358038 10.1038/s41598-021-95394-9 - Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder.
Shamilov R, Robinson VL, Aneskievich BJ
International journal of molecular sciences (2021) 22(15): PMC8348711 10.3390/ijms22157912 - Macroevolutionary foundations of a recently evolved innate immune defense.
Vrtílek M, Bolnick DI
Evolution; international journal of organic evolution (2021) 75(10):2600-2612 PMC8488947 10.1111/evo.14316 - Chemical Gradients of Plant Substrates in an Fungus Garden.
Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC
mSystems (2021) 6(4):e0060121 PMC8409729 10.1128/mSystems.00601-21 - Effects of Host Species Identity and Diet on the Biodiversity of the Microbiota in Puerto Rican Bats.
Presley SJ, Graf J, Hassan AF, Sjodin AR, Willig MR
Current microbiology (2021) 78(9):3526-3540 10.1371/journal.pone.0001425 - New model integrates innate responses, PML-NB formation, epigenetic control and reactivation from latency.
Weller SK, Deluca NA
EMBO reports (2021) 22(9):e53496 PMC8419697 10.15252/embr.202153496 - Draft Genome Sequence of Aeromonas popoffii ID682, Isolated from a Natural Water Source in Idaho.
Testerman T, Reichley SR, King S, Graf J
Microbiology resource announcements (2021) 10(29):e0044521 PMC8297452 10.1128/MRA.00445-21 - Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support.
Gosselin S, Fullmer MS, Feng Y, Gogarten JP
Systematic biology (2021) 71(2):396-409 PMC2667022 10.1002/9781118960608.obm00010.pub2 - Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data.
Rondel FM, Hosseini R, Sahoo B, Knyazev S, Mandric I, Stewart F, Măndoiu II, Pasaniuc B, Porozov Y, Zelikovsky A
Journal of computational biology : a journal of computational molecular cell biology (2021) 28(8):842-855 PMC8575064 10.1089/cmb.2021.0053 - Draft Genome Sequence of Janthinobacterium lividum ID1246, Isolated from a Rainbow Trout Hatchery Biofilm.
Testerman T, Reichley SR, King S, Graf J
Microbiology resource announcements (2021) 10(28):e0044421 PMC8280877 10.1128/MRA.00444-21 - PlzA is a bifunctional c-di-GMP biosensor that promotes tick and mammalian host-adaptation of Borrelia burgdorferi.
Groshong AM, Grassmann AA, Luthra A, McLain MA, Provatas AA, Radolf JD, Caimano MJ
PLoS pathogens (2021) 17(7):e1009725 PMC8323883 10.1371/journal.ppat.1009725 - In Silico Evolution of High-Performing Metal Organic Frameworks for Methane Adsorption.
Beauregard N, Pardakhti M, Srivastava R
Journal of chemical information and modeling (2021) 61(7):3232-3239 10.1021/acs.jcim.0c01479 - Editorial Expression of Concern.
Bolnick DI, Fox JW, Débarre F, Dietrich EI, Phelps SM, Jordan A, Torminalis S
The American naturalist (2021) 198(2):313-316 10.1086/714867 - TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread.
Dhar S, Zhang C, Mandoiu II, Bansal MS
IEEE/ACM transactions on computational biology and bioinformatics (2021) 19(1):230-242 PMC5850600 10.1109/TCBB.2021.3096455 - The Evolutionary Origins of Extreme Halophilic Archaeal Lineages.
Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP
Genome biology and evolution (2021) 13(8): PMC8350355 10.1093/gbe/evab166 - Use of anthropogenic-related nest material and nest parasite prevalence have increased over the past two centuries in Australian birds.
Potvin DA, Opitz F, Townsend KA, Knutie SA
Oecologia (2021) 196(4):1207-1217 10.3161/000164509X482768 - Epigenetic effects of parasites and pesticides on captive and wild nestling birds.
McNew SM, Boquete MT, Espinoza-Ulloa S, Andres JA, Wagemaker NCAM, Knutie SA, Richards CL, Clayton DH
Ecology and evolution (2021) 11(12):7713-7729 PMC8216931 10.1002/ece3.7606 - Do the combined blood pressure effects of exercise and antihypertensive medications add up to the sum of their parts? A systematic meta-review.
Pescatello LS, Wu Y, Gao S, Livingston J, Sheppard BB, Chen MH
BMJ open sport & exercise medicine (2021) 7(1):e000895 PMC7818845 10.1136/bmjsem-2020-000895 - The impact of body fat on thermoregulation during exercise in the heat: A systematic review and meta-analysis.
Morrissey MC, Wu Y, Zuk EF, Livingston J, Casa DJ, Pescatello LS
Journal of science and medicine in sport (2021) 24(8):843-850 10.1016/j.jsams.2021.06.004 - A canonical metacommunity structure over 3 decades: ecologically consistent but spatially dynamic patterns in a hurricane-prone montane forest.
Willig MR, Presley SJ, Cullerton EI
Oecologia (2021) 196(3):919-933 10.1111/j.1420-9101.2011.02297.x - SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum.
Zhang K, Zhou Z, Li J, Wang J, Yu L, Lin S
Communications biology (2021) 4(1):797 PMC8233357 10.1038/s42003-021-02284-x - Stepping forward in antibody-drug conjugate development.
Jin Y, Schladetsch MA, Huang X, Balunas MJ, Wiemer AJ
Pharmacology & therapeutics (2021) 229:107917 PMC6864847 10.1016/j.pharmthera.2021.107917 - A GATA3 Targeting Nucleic Acid Nanocapsule for Gene Regulation in Asthma.
Gavitt TD, Hartmann AK, Sawant SS, Mara AB, Szczepanek SM, Rouge JL
ACS nano (2021) 15(7):11192-11201 PMC9200080 10.1021/acsnano.0c07781 - Editorial Expression of Concern.
Bolnick DI
The American naturalist (2021) 198(1):177 10.1086/714375 - Copper-binding anticancer peptides from the piscidin family: an expanded mechanism that encompasses physical and chemical bilayer disruption.
Comert F, Heinrich F, Chowdhury A, Schoeneck M, Darling C, Anderson KW, Libardo MDJ, Angeles-Boza AM, Silin V, Cotten ML, Mihailescu M
Scientific reports (2021) 11(1):12620 PMC8208971 10.1038/s41598-021-91670-w - Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, .
Kerwin AH, McAnulty SJ, Nyholm SV
The Biological bulletin (2021) 240(3):205-218 10.1086/713965 - SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis.
Moussa M, Măndoiu II
Journal of computational biology : a journal of computational molecular cell biology (2021) 28(8):820-841 10.1089/cmb.2021.0051 - Antimicrobial Susceptibility Testing of Antimicrobial Peptides Requires New and Standardized Testing Structures.
Meurer M, O'Neil DA, Lovie E, Simpson L, Torres MDT, de la Fuente-Nunez C, Angeles-Boza AM, Kleinsorgen C, Mercer DK, von Köckritz-Blickwede M
ACS infectious diseases (2021) 7(8):2205-2208 PMC8764967 10.1021/acsinfecdis.1c00210 - Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit.
Hall MD, Anderson JM, Anderson A, Baker D, Bradner J, Brimacombe KR, Campbell EA, Corbett KS, Carter K, Cherry S, Chiang L, Cihlar T, de Wit E, Denison M, Disney M, Fletcher CV, Ford-Scheimer SL, Götte M, Grossman AC, Hayden FG, Hazuda DJ, Lanteri CA, Marston H, Mesecar AD, Moore S, Nwankwo JO, O'Rear J, Painter G, Singh Saikatendu K, Schiffer CA, Sheahan TP, Shi PY, Smyth HD, Sofia MJ, Weetall M, Weller SK, Whitley R, Fauci AS, Austin CP, Collins FS, Conley AJ, Davis MI
The Journal of infectious diseases (2021) 224(Supplement):S1-S21 PMC8280938 10.1093/infdis/jiab305 - The AcrAB-TolC Efflux Pump Impacts Persistence and Resistance Development in Stationary-Phase Escherichia coli following Delafloxacin Treatment.
Byrd BA, Zenick B, Rocha-Granados MC, Englander HE, Hare PJ, LaGree TJ, DeMarco AM, Mok WWK
Antimicrobial agents and chemotherapy (2021) 65(8):e0028121 PMC8284433 10.1128/AAC.00281-21 - A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner.
Nyholm SV, McFall-Ngai MJ
Nature reviews. Microbiology (2021) 19(10):666-679 PMC8440403 10.1038/s41579-021-00557-0 - Properties of spores of Bacillus subtilis with or without a transposon that decreases spore germination and increases spore wet heat resistance.
Luo Y, Korza G, DeMarco AM, Kuipers OP, Li YQ, Setlow P
Journal of applied microbiology (2021) : 10.1111/jam.15163 - Urban living influences the nesting success of Darwin's finches in the Galápagos Islands.
Harvey JA, Chernicky K, Simons SR, Verrett TB, Chaves JA, Knutie SA
Ecology and evolution (2021) 11(10):5038-5048 PMC8131787 10.1002/ece3.7360 - Transcriptomic and isotopic data reveal central role of ammonium in facilitating the growth of the mixotrophic dinoflagellate, Dinophysis acuminata.
Hattenrath-Lehmann TK, Nanjappa D, Zhang H, Yu L, Goleski JA, Lin S, Gobler CJ
Harmful algae (2021) 104:102031 10.1016/j.hal.2021.102031 - Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation.
Benjamin SJ, Hawley KL, Vera-Licona P, La Vake CJ, Cervantes JL, Ruan Y, Radolf JD, Salazar JC
BMC immunology (2021) 22(1):32 PMC8127205 10.1186/s12865-021-00418-8 - Dodecylamine rapidly kills of spores of multiple Firmicute species: properties of the killed spores and the mechanism of the killing.
DeMarco AM, Korza G, Rocha Granados M, Mok WWK, Setlow P
Journal of applied microbiology (2021) : 10.1111/jam.15137 - Male and female reproductive fitness costs of an immune response in natural populations.
De Lisle SP, Bolnick DI
Evolution; international journal of organic evolution (2021) 75(10):2509-2523 PMC8488946 10.1111/evo.14266 - A comparison of two Tai Chi interventions tailored for different health outcomes.
Wu Y, Senk C, Coll P, Glenney S, Zaborowski K, Fortinsky R, Taylor B, Park C, Benson K, McGowan M, DiBiasi S, Chen MH, Pescatello L
Complementary therapies in medicine (2021) 59:102731 10.1016/j.ctim.2021.102731 - Structural modeling of the OMPeome: a roadmap for deconvolution of syphilis pathogenesis and development of a syphilis vaccine.
Hawley KL, Montezuma-Rusca JM, Delgado KN, Singh N, Uversky VN, Caimano MJ, Radolf JD, Luthra A
Journal of bacteriology (2021) : 10.1128/JB.00082-21 - Levels and Characteristics of mRNAs in Spores of Firmicute Species.
Byrd B, Camilleri E, Korza G, Craft DL, Green J, Rocha Granados M, Mok WWK, Caimano MJ, Setlow P
Journal of bacteriology (2021) 203(14):e0001721 PMC8315741 10.1128/JB.00017-21 - β-Oxochlorin cobalt(II) complexes catalyze the electrochemical reduction of CO.
Nganga J, Chaudhri N, Brückner C, Angeles-Boza AM
Chemical communications (Cambridge, England) (2021) 57(36):4396-4399 10.1039/d1cc00573a - Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback.
Fuess LE, den Haan S, Ling F, Weber JN, Steinel NC, Bolnick DI
mBio (2021) 12(3): PMC8262870 10.1128/mBio.00145-21 - Red Fluorescence of European Hedgehog (Erinaceus europaeus) Spines Results from Free-Base Porphyrins of Potential Microbial Origin.
Hamchand R, Lafountain AM, Büchel R, Maas KR, Hird SM, Warren M, Frank HA, Brückner C
Journal of chemical ecology (2021) 47(6):588-596 10.1128/mBio.01286-14 - Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae.
Li X, Hou Z, Xu C, Shi X, Yang L, Lewis LA, Zhong B
Genome biology and evolution (2021) 13(7): PMC8271138 10.1093/gbe/evab101 - Supporting Biomedical Research Training for Historically Underrepresented Undergraduates Using Interprofessional, Nonformal Education Structures.
Marriott LK, Link AR, Anitori R, Blackwell E, Blas A, Brock J, Burke T, Burrows JA, Cabrera AP, Helsham D, Liban LB, Mackiewicz MR, Maruyama M, Milligan-Myhre KCA, Pangelinan PJC, Hattori-Uchima M, Reed R, Simon BE, Solomon B, Trinidad AMO, Wyatt LR, Covarrubia AD, Zell A, Keller TE, Morris C, Crespo CJ
The journal of scholarship of teaching and learning : JoSoTL (2021) 21(1):241-286 PMC5008902 10.1187/cbe.16-03-0138 - Predicting the Structure and Dynamics of Membrane Protein GerAB from .
Blinker S, Vreede J, Setlow P, Brul S
International journal of molecular sciences (2021) 22(7): PMC8038838 10.3390/ijms22073793 - Sodium butyrate modulates chicken macrophage proteins essential for Salmonella Enteritidis invasion.
Gupta A, Bansal M, Liyanage R, Upadhyay A, Rath N, Donoghue A, Sun X
PloS one (2021) 16(4):e0250296 PMC8081216 10.1371/journal.pone.0250296 - Nothing in Evolution Makes Sense Except in the Light of Biology.
Reiskind MOB, Moody ML, Bolnick DI, Hanifin CT, Farrior CE
Bioscience (2021) 71(4):370-382 PMC8038875 10.1093/biosci/biaa170 - The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis.
King VL, Leclair NK, Coulter AM, Campellone KG
PLoS genetics (2021) 17(4):e1009512 PMC8084344 10.1371/journal.pgen.1009512 - Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus.
Hua Z, Ouellette M, Makkay AM, Papke RT, Zhaxybayeva O
The ISME journal (2021) 15(10):2853-2864 PMC8443641 10.1038/s41396-021-00960-8 - Nondestructive multiplex detection of foodborne pathogens with background microflora and symbiosis using a paper chromogenic array and advanced neural network.
Jia Z, Luo Y, Wang D, Dinh QN, Lin S, Sharma A, Block EM, Yang M, Gu T, Pearlstein AJ, Yu H, Zhang B
Biosensors & bioelectronics (2021) 183:113209 10.1016/j.bios.2021.113209 - Molecular Physiological Characterization of a High Heat Resistant Spore Forming Food Isolate.
Tu Z, Setlow P, Brul S, Kramer G
Microorganisms (2021) 9(3): PMC8005191 10.3390/microorganisms9030667 - Unraveling the implications of multiple histidine residues in the potent antimicrobial peptide Gaduscidin-1.
Portelinha J, Heilemann K, Jin J, Angeles-Boza AM
Journal of inorganic biochemistry (2021) 219:111391 10.1016/j.jinorgbio.2021.111391 - Draft Genome Sequences of sp. Strains GY75 and GY617, Isolated from the Hindgut of Reticulitermes flavipes.
Bridges CM, Gage DJ
Microbiology resource announcements (2021) 10(12): PMC7996457 10.1128/MRA.00079-21 - Professor A. Douglas Kinghorn. A Lifetime Career Dedicated to Outstanding Service to Natural Product Sciences.
Balunas MJ, Cragg GM, Gibbons S, Mata R
Journal of natural products (2021) 84(3):549-552 10.1021/acs.jnatprod.0c01371 - Single dose of a replication-defective vaccinia virus expressing Zika virus-like particles is protective in mice.
Jasperse B, O'Connell CM, Wang Y, Verardi PH
Scientific reports (2021) 11(1):6492 PMC7985303 10.1038/s41598-021-85951-7 - Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale.
Oita S, Ibáñez A, Lutzoni F, Miadlikowska J, Geml J, Lewis LA, Hom EFY, Carbone I, U'Ren JM, Arnold AE
Communications biology (2021) 4(1):313 PMC7943826 10.1038/s42003-021-01826-7 - Epigenetic effects of silver nanoparticles and ionic silver in Tetrahymena thermophila.
Pan Y, Lin S, Zhang W
The Science of the total environment (2021) 768:144659 10.1016/j.scitotenv.2020.144659 - Metallothioneins alter macrophage phenotype and represent novel therapeutic targets for acetaminophen-induced liver injury.
Devisscher L, Van Campenhout S, Lefere S, Raevens S, Tilleman L, Van Nieuwerburgh F, Van Eeckhoutte HP, Hoorens A, Lynes MA, Geerts A, Laukens D, Van Vlierberghe H
Journal of leukocyte biology (2021) 111(1):123-133 10.1002/JLB.3A0820-527R - Development of a Novel Clinical Decision Support System for Exercise Prescription Among Patients With Multiple Cardiovascular Disease Risk Factors.
Pescatello LS, Wu Y, Panza GA, Zaleski A, Guidry M
Mayo Clinic proceedings. Innovations, quality & outcomes (2021) 5(1):193-203 PMC7930885 10.1016/j.mayocpiqo.2020.08.005 - TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
Sledzieski S, Zhang C, Mandoiu I, Bansal MS
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2021) 26:119-130 - Microbial signatures of health, gingivitis, and periodontitis.
Abusleme L, Hoare A, Hong BY, Diaz PI
Periodontology 2000 (2021) 86(1):57-78 10.1111/prd.12362 - : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech.
McClure EA, Nelson MC, Lin A, Graf J
Applied and environmental microbiology (2021) 87(10): PMC8117757 10.1128/AEM.02082-20 - Nitrogen availability improves the physiological resilience of coral endosymbiont Cladocopium goreaui to high temperature.
Zhou Z, Zhang K, Wang L, Su Y, Wang J, Song T, Yang X, Tang J, Lin S
Journal of phycology (2021) 57(4):1187-1198 10.1111/jpy.13156 - Evolution and roles of cytokinin genes in angiosperms 1: Do ancient IPTs play housekeeping while non-ancient IPTs play regulatory roles?
Wang X, Lin S, Liu D, Gan L, McAvoy R, Ding J, Li Y
Horticulture research (2021) 7(1):28 10.1371/journal.pone.0070603 - Ferroptosis and its potential as a therapeutic target.
Yuan H, Pratte J, Giardina C
Biochemical pharmacology (2021) 186:114486 10.1016/j.bcp.2021.114486 - Structural and developmental principles of neuropil assembly in C. elegans.
Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA
Nature (2021) 591(7848):99-104 PMC8385650 10.1038/s41586-020-03169-5 - Methane Generation from CO with a Molecular Rhenium Catalyst.
Nganga JK, Wolf LM, Mullick K, Reinheimer E, Saucedo C, Wilson ME, Grice KA, Ertem MZ, Angeles-Boza AM
Inorganic chemistry (2021) 60(6):3572-3584 10.1021/acs.inorgchem.0c02579 - North American Fireflies Host Low Bacterial Diversity.
Green EA, Smedley SR, Klassen JL
Microbial ecology (2021) 82(3):793-804 10.7717/peerj.1190 - Roles of Alkaline Phosphatase PhoA in Algal Metabolic Regulation under Phosphorus-replete Conditions.
Zhang K, Li J, Zhou Z, Huang R, Lin S
Journal of phycology (2021) 57(3):703-707 10.1111/jpy.13151 - High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon.
Graf J, Ledala N, Caimano MJ, Jackson E, Gratalo D, Fasulo D, Driscoll MD, Coleman S, Matson AP
mBio (2021) 12(1): PMC8545133 10.1128/mBio.03656-20 - Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery.
Hurley A, Chevrette MG, Acharya DD, Lozano GL, Garavito M, Heinritz J, Balderrama L, Beebe M, DenHartog ML, Corinaldi K, Engels R, Gutierrez A, Jona O, Putnam JHI, Rhodes B, Tsang T, Hernandez S, Bascom-Slack C, Blum JE, Price PA, Davis D, Klein J, Pultorak J, Sullivan NL, Mouncey NJ, Dorrestein PC, Miller S, Broderick NA, Handelsman J
mBio (2021) 12(1): PMC8545114 10.1128/mBio.03432-20 - Identification of Native Cross-Links in Spore Coat Proteins.
Ursem R, Swarge B, Abhyankar WR, Buncherd H, de Koning LJ, Setlow P, Brul S, Kramer G
Journal of proteome research (2021) 20(3):1809-1816 PMC7944565 10.1021/acs.jproteome.1c00025 - Adaptation reduces competitive dominance and alters community assembly.
Nadeau CP, Farkas TE, Makkay AM, Papke RT, Urban MC
Proceedings. Biological sciences (2021) 288(1945):20203133 PMC7935105 10.1098/rspb.2020.3133 - Antimicrobial effects of a bioactive glycolipid on spore-forming spoilage bacteria in milk.
Sun L, Atkinson K, Zhu M, D'Amico DJ
Journal of dairy science (2021) 104(4):4002-4011 10.3168/jds.2020-19769 - Lipid moieties of Mycoplasma pneumoniae lipoproteins are the causative factor of vaccine-enhanced disease.
Mara AB, Gavitt TD, Tulman ER, Geary SJ, Szczepanek SM
NPJ vaccines (2021) 5(1):31 10.1093/nar/gky1106 - What evolutionary processes maintain MHC IIꞵ diversity within and among populations of stickleback?
Peng F, Ballare KM, Hollis Woodard S, den Haan S, Bolnick DI
Molecular ecology (2021) 30(7):1659-1671 PMC8049082 10.1111/mec.15840 - Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2.
Boshans LL, Soh H, Wood WM, Nolan TM, Mandoiu II, Yanagawa Y, Tzingounis AV, Nishiyama A
Scientific reports (2021) 11(1):3552 PMC7878775 10.1038/s41598-021-82931-9 - Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019).
Mandoiu I, Murali TM, Narasimhan G, Rajasekaran S, Skums P, Zelikovsky A
Journal of computational biology : a journal of computational molecular cell biology (2021) 28(2):115-116 10.1089/cmb.2021.29034.im - Bidirectional relationships between weight stigma and pediatric obesity: A systematic review and meta-analysis.
Ma L, Chu M, Li Y, Wu Y, Yan AF, Johnson B, Wang Y
Obesity reviews : an official journal of the International Association for the Study of Obesity (2021) 22(6):e13178 10.1111/obr.13178 - Draft Genome Sequences of sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite.
Bridges CM, Nelson MC, Graf J, Gage DJ
Microbiology resource announcements (2021) 10(4): PMC7844080 10.1128/MRA.01427-20 - Terrestrial Green Algae Show Higher Tolerance to Dehydration than Do Their Aquatic Sister-Species.
Terlova EF, Holzinger A, Lewis LA
Microbial ecology (2021) 82(3):770-782 PMC7612456 10.1007/s00248-020-01679-3 - Optogenetics in Enables Spatial Control of Exopolysaccharide Production and Biofilm Structure.
Pirhanov A, Bridges CM, Goodwin RA, Guo YS, Furrer J, Shor LM, Gage DJ, Cho YK
ACS synthetic biology (2021) 10(2):345-356 10.1021/acssynbio.0c00498 - Complete mitochondrial genome of the water vole, (Cricetidae, Rodentia).
Alqahtani F, Duckett D, Pirro S, Mandoiu II
Mitochondrial DNA. Part B, Resources (2021) 5(3):2498-2499 PMC7782294 10.1080/23802359.2020.1780640 - Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components.
Barandouzi ZA, Lee J, Maas K, Starkweather AR, Cong XS
Journal of personalized medicine (2021) 11(1): PMC7827153 10.3390/jpm11010035 - Arthropods are not declining but are responsive to disturbance in the Luquillo Experimental Forest, Puerto Rico.
Schowalter TD, Pandey M, Presley SJ, Willig MR, Zimmerman JK
Proceedings of the National Academy of Sciences of the United States of America (2021) 118(2): PMC7812834 10.1073/pnas.2002556117 - The Antimicrobial Peptide Gad-1 Clears Pseudomonas aeruginosa Biofilms under Cystic Fibrosis Conditions.
Portelinha J, Angeles-Boza AM
Chembiochem : a European journal of chemical biology (2021) 22(9):1646-1655 10.1002/cbic.202000816 - Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism.
Goldstein SL, Klassen JL
Frontiers in microbiology (2021) 11:621041 PMC7793712 10.3389/fmicb.2020.621041 - Host-specific functional compartmentalization within the oligopeptide transporter during the Borrelia burgdorferi enzootic cycle.
Groshong AM, McLain MA, Radolf JD
PLoS pathogens (2021) 17(1):e1009180 PMC7822543 10.1371/journal.ppat.1009180 - Application of bioactive glycolipids to control Listeria monocytogenes biofilms and as post-lethality contaminants in milk and cheese.
Sun L, Forauer EC, Brown SRB, D'Amico DJ
Food microbiology (2021) 95:103683 10.1016/j.fm.2020.103683 2020
- Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy.
Sherafat E, Force J, Măndoiu II
BMC bioinformatics (2020) 21(Suppl 18):498 PMC7772914 10.1186/s12859-020-03813-x - A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen.
Hoare A, Wang H, Meethil A, Abusleme L, Hong BY, Moutsopoulos NM, Marsh PD, Hajishengallis G, Diaz PI
The ISME journal (2020) 15(5):1490-1504 PMC8115154 10.1038/s41396-020-00865-y - (1,2-Azole)bis(bipyridyl)ruthenium(II) Complexes: Electrochemistry, Luminescent Properties, And Electro- And Photocatalysts for CO Reduction.
Cuéllar E, Pastor L, García-Herbosa G, Nganga J, Angeles-Boza AM, Diez-Varga A, Torroba T, Martín-Alvarez JM, Miguel D, Villafañe F
Inorganic chemistry (2020) 60(2):692-704 10.1021/acs.inorgchem.0c02716 - Characterization of Heterogeneity and Dynamics of Lysis of Single Cells upon Prophage Induction During Spore Germination, Outgrowth, and Vegetative Growth Using Raman Tweezers and Live-Cell Phase-Contrast Microscopy.
Wu MY, Li WW, Christie G, Setlow P, Li YQ
Analytical chemistry (2020) 93(3):1443-1450 10.1021/acs.analchem.0c03341 - Integrated RNA-seq and Proteomic Studies Reveal Resource Reallocation towards Energy Metabolism and Defense in in Response to CO Increase.
Zhang M, Zhen Y, Mi T, Lin S
Applied and environmental microbiology (2020) : PMC8090871 10.1128/AEM.02614-20 - : Immune subversion activities and role in periodontal dysbiosis.
Hajishengallis G, Diaz PI
Current oral health reports (2020) 7(1):12-21 PMC7747940 10.1007/s40496-020-00249-3 - microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing.
Gil JC, Helal ZH, Risatti G, Hird SM
PeerJ (2020) 8:e10424 PMC7718787 10.7717/peerj.10424 - Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.
Makkay AM, Louyakis AS, Ram-Mohan N, Gophna U, Gogarten JP, Papke RT
Scientific reports (2020) 10(1):22297 PMC7749143 10.1038/s41598-020-79296-w - Biomimetic Boroxine-Based Multifunctional Thermosets via One-Pot Synthesis.
Yang X, Guo M, Wu Y, Xue S, Li Z, Zhou H, Smith AT, Sun L
ACS applied materials & interfaces (2020) 12(50):56445-56453 10.1021/acsami.0c16736 - An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection.
Brennick CA, George MM, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Schietinger A, Mandoiu II, Srivastava PK
The Journal of clinical investigation (2020) 131(3): PMC7843235 10.1172/JCI142823 - Receptor-targeted engineered probiotics mitigate lethal Listeria infection.
Drolia R, Amalaradjou MAR, Ryan V, Tenguria S, Liu D, Bai X, Xu L, Singh AK, Cox AD, Bernal-Crespo V, Schaber JA, Applegate BM, Vemulapalli R, Bhunia AK
Nature communications (2020) 11(1):6344 PMC7732855 10.1038/s41467-020-20200-5 - Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses.
Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White RA, Burns BP, Coolen MJL
Frontiers in microbiology (2020) 11:560336 PMC7702295 10.3389/fmicb.2020.560336 - Adding the third dimension to studies of parallel evolution of morphology and function: An exploration based on parapatric lake-stream stickleback.
Haines GE, Stuart YE, Hanson D, Tasneem T, Bolnick DI, Larsson HCE, Hendry AP
Ecology and evolution (2020) 10(23):13297-13311 PMC7713967 10.1002/ece3.6929 - Lyme Disease in Humans.
Radolf JD, Strle K, Lemieux JE, Strle F
Current issues in molecular biology (2020) 42:333-384 PMC7946767 10.21775/cimb.042.333 - Development and application of aerobic, chemically defined media for Dysgonomonas.
Bridges CM, Gage DJ
Anaerobe (2020) 67:102302 10.1016/j.anaerobe.2020.102302 - Transdermal microneedles for the programmable burst release of multiple vaccine payloads.
Tran KTM, Gavitt TD, Farrell NJ, Curry EJ, Mara AB, Patel A, Brown L, Kilpatrick S, Piotrowska R, Mishra N, Szczepanek SM, Nguyen TD
Nature biomedical engineering (2020) 5(9):998-1007 10.1128/cdli.4.4.415-422.1997 - Subgingival fungi, Archaea, and viruses under the omics loupe.
Diaz PI
Periodontology 2000 (2020) 85(1):82-89 10.1111/prd.12352 - The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback.
Härer A, Bolnick DI, Rennison DJ
Molecular ecology (2020) 30(2):451-463 10.1111/mec.15746 - Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748, Isolated from a Dragonfly.
Green EA, Klassen JL
Microbiology resource announcements (2020) 9(47): PMC7679083 10.1128/MRA.00422-20 - Trends and Transitions in 150 Years of .
Smocovitis VB, Bolnick DI, Moore CM, Morse PL
The American naturalist (2020) 196(6):663-678 10.1086/711418 - Analysis of disulphide bond linkage between CoA and protein cysteine thiols during sporulation and in spores of Bacillus species.
Zhyvoloup A, Yu BYK, Baković J, Davis-Lunn M, Tossounian MA, Thomas N, Tsuchiya Y, Peak-Chew SY, Wigneshweraraj S, Filonenko V, Skehel M, Setlow P, Gout I
FEMS microbiology letters (2020) 367(23): PMC8127865 10.1093/femsle/fnaa174 - Transcriptome profiling reveals versatile dissolved organic nitrogen utilization, mixotrophy, and N conservation in the dinoflagellate Prorocentrum shikokuense under N deficiency.
Li H, Li L, Yu L, Yang X, Shi X, Wang J, Li J, Lin S
The Science of the total environment (2020) 763:143013 10.1016/j.scitotenv.2020.143013 - Abundant synthesis of long-chain polyunsaturated fatty acids in Eutreptiella sp. (Euglenozoa) revealed by chromatographic and transcriptomic analyses.
Kuo RC, Zhang H, Stuart JD, Provatas AA, Hannick L, Lin S
Journal of phycology (2020) 57(2):577-591 10.1111/jpy.13105 - Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.
Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL
Nature microbiology (2020) 6(1):136 PMC7752755 10.1038/s41564-020-00827-2 - Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease.
Bao K, Li X, Poveda L, Qi W, Selevsek N, Gumus P, Emingil G, Grossmann J, Diaz PI, Hajishengallis G, Bostanci N, Belibasakis GN
Frontiers in cellular and infection microbiology (2020) 10:588155 PMC7566166 10.3389/fcimb.2020.588155 - The influence of host tissue on M. gallisepticum vlhA gene expression.
Pflaum K, Tulman ER, Canter J, Dhondt KV, Reinoso-Perez MT, Dhondt AA, Geary SJ
Veterinary microbiology (2020) 251:108891 10.1016/j.vetmic.2020.108891 - Cycloheximide-Producing Associated With and Fungus-Farming Ambrosia Beetles.
Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen JL, Carlson CM, Clardy J, Currie CR
Frontiers in microbiology (2020) 11:562140 PMC7546818 10.3389/fmicb.2020.562140 - Novel guanidine compounds inhibit platelet-derived growth factor receptor alpha transcription and oligodendrocyte precursor cell proliferation.
Medved J, Wood WM, van Heyst MD, Sherafat A, Song JY, Sakya S, Wright DL, Nishiyama A
Glia (2020) 69(3):792-811 PMC7856068 10.1002/glia.23930 - Outcomes From Re-Treatment and Cerebrospinal Fluid Analyses in Patients With Syphilis Who Had Serological Nonresponse or Lack of Seroreversion After Initial Therapy.
Zhang X, Shahum A, Yang LG, Xue Y, Wang L, Yang B, Zheng H, Chen JS, Radolf JD, Seña AC
Sexually transmitted diseases (2020) 48(6):443-450 PMC8058108 10.1097/OLQ.0000000000001321 - Depression prevalence based on the Edinburgh Postnatal Depression Scale compared to Structured Clinical Interview for DSM DIsorders classification: Systematic review and individual participant data meta-analysis.
Lyubenova A, Neupane D, Levis B, Wu Y, Sun Y, He C, Krishnan A, Bhandari PM, Negeri Z, Imran M, Rice DB, Azar M, Chiovitti MJ, Saadat N, Riehm KE, Boruff JT, Ioannidis JPA, Cuijpers P, Gilbody S, Kloda LA, Patten SB, Shrier I, Ziegelstein RC, Comeau L, Mitchell ND, Tonelli M, Vigod SN, Aceti F, Barnes J, Bavle AD, Beck CT, Bindt C, Boyce PM, Bunevicius A, Chaudron LH, Favez N, Figueiredo B, Garcia-Esteve L, Giardinelli L, Helle N, Howard LM, Kohlhoff J, Kusminskas L, Kozinszky Z, Lelli L, Leonardou AA, Meuti V, Radoš SN, García PN, Pawlby SJ, Quispel C, Robertson-Blackmore E, Rochat TJ, Sharp DJ, Siu BWM, Stein A, Stewart RC, Tadinac M, Tandon SD, Tendais I, Töreki A, Torres-Giménez A, Tran TD, Trevillion K, Turner K, Vega-Dienstmaier JM, Benedetti A, Thombs BD
International journal of methods in psychiatric research (2020) 30(1):e1860 PMC7992289 10.1002/mpr.1860 - Differential enrichment and physiological impacts of ingested microplastics in scleractinian corals in situ.
Tang J, Wu Z, Wan L, Cai W, Chen S, Wang X, Luo J, Zhou Z, Zhao J, Lin S
Journal of hazardous materials (2020) 404(Pt B):124205 10.1016/j.jhazmat.2020.124205 - Gut Bacteria Mediate Nutrient Availability in Diets.
Lesperance DNA, Broderick NA
Applied and environmental microbiology (2020) 87(1): PMC7755257 10.1128/AEM.01401-20 - Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana.
Graf J, Nelson MC, Colston SM
Microbiology resource announcements (2020) 9(42): PMC7561689 10.1128/MRA.00922-20 - Sodium Butyrate Reduces Enteritidis Infection of Chicken Enterocytes and Expression of Inflammatory Host Genes .
Gupta A, Bansal M, Wagle B, Sun X, Rath N, Donoghue A, Upadhyay A
Frontiers in microbiology (2020) 11:553670 PMC7524895 10.3389/fmicb.2020.553670 - Use of bacteria community analysis to distinguish groundwater recharge sources to shallow wells.
Higgins MA, Robbins GA, Maas KR, Binkhorst GK
Journal of environmental quality (2020) 49(6):1530-1540 10.1002/jeq2.20150 - Hybrid Coronary Revascularization Versus Conventional Coronary Artery Bypass Surgery: Utilization and Comparative Outcomes.
Hannan EL, Wu Y, Cozzens K, Sundt TM, Girardi L, Chikwe J, Wechsler A, Smith CR, Gold JP, Lahey SJ, Jordan D
Circulation. Cardiovascular interventions (2020) 13(10):e009386 10.1161/CIRCINTERVENTIONS.120.009386 - Peptide-Ruthenium Conjugate as an Efficient Photosensitizer for the Inactivation of Multidrug-Resistant Bacteria.
Pierce S, Jennings MP, Juliano SA, Angeles-Boza AM
Inorganic chemistry (2020) 59(20):14866-14870 10.1021/acs.inorgchem.0c02491 - The Cu(II) Reductase RclA Protects against the Combination of Hypochlorous Acid and Intracellular Copper.
Derke RM, Barron AJ, Billiot CE, Chaple IF, Lapi SE, Broderick NA, Gray MJ
mBio (2020) 11(5): PMC7527725 10.1128/mBio.01905-20 - Broadening Participation in Scientific Conferences during the Era of Social Distancing.
Fulcher MR, Bolton ML, Millican MD, Michalska-Smith MJ, Dundore-Arias JP, Handelsman J, Klassen JL, Milligan-Myhre KC, Shade A, Wolfe BE, Kinkel LL
Trends in microbiology (2020) 28(12):949-952 PMC7507981 10.1016/j.tim.2020.08.004 - Early life disruption of the microbiota affects organ development and cytokine gene expression in threespine stickleback.
Kirschman LJ, Khadjinova A, Ireland K, Milligan-Myhre KC
Integrative and comparative biology (2020) 63(1):250-62 PMC3162596 10.1093/icb/icaa136 - The interactive effects of titanium dioxide nanoparticles and light on heterotrophic bacteria and microalgae associated with marine aggregates in nearshore waters.
Haynes VN, Ward JE
Marine environmental research (2020) 161:105146 10.1016/j.marenvres.2020.105146 - Microbial dark matter filling the niche in hypersaline microbial mats.
Wong HL, MacLeod FI, White RA, Visscher PT, Burns BP
Microbiome (2020) 8(1):135 PMC7495880 10.1186/s40168-020-00910-0 - Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis.
Luthra A, Montezuma-Rusca JM, La Vake CJ, LeDoyt M, Delgado KN, Davenport TC, Fiel-Gan M, Caimano MJ, Radolf JD, Hawley KL
PLoS pathogens (2020) 16(9):e1008871 PMC7521688 10.1371/journal.ppat.1008871 - Enhancing iCVD Modification of Electrospun Membranes for Membrane Distillation Using a 3D Printed Scaffold.
Beauregard N, Al-Furaiji M, Dias G, Worthington M, Suresh A, Srivastava R, Burkey DD, McCutcheon JR
Polymers (2020) 12(9): PMC7570062 10.3390/polym12092074 - Critically Appraising the Significance of the Oral Mycobiome.
Diaz PI, Dongari-Bagtzoglou A
Journal of dental research (2020) 100(2):133-140 PMC8173349 10.1177/0022034520956975 - Methylation Pattern and Expression Dynamics of Methylase and Photosystem Genes Under varying light Intensities in Fugacium kawagutii (Symbiodiniaceae).
Yang F, Li L, Lin S
Journal of phycology (2020) 56(6):1738-1747 10.1111/jpy.13070 - Sympathetic nervous tone limits the development of myeloid-derived suppressor cells.
Nevin JT, Moussa M, Corwin WL, Mandoiu II, Srivastava PK
Science immunology (2020) 5(51): 10.1126/sciimmunol.aay9368 - An Evolving View of Phylogenetic Support.
Simon C
Systematic biology (2020) 71(4):921-928 10.1093/sysbio/syaa068 - Sub-lethal effects of permethrin exposure on a passerine: implications for managing ectoparasites in wild bird nests.
Bulgarella M, Knutie SA, Voss MA, Cunninghame F, Florence-Bennett BJ, Robson G, Keyzers RA, Taylor LM, Lester PJ, Heimpel GE, Causton CE
Conservation physiology (2020) 8(1):coaa076 PMC7416766 10.1093/conphys/coaa076 - Physiological and transcriptomic responses to N-deficiency and ammonium: Nitrate shift in Fugacium kawagutii (Symbiodiniaceae).
Li T, Chen X, Lin S
The Science of the total environment (2020) 753:141906 10.1016/j.scitotenv.2020.141906 - Scale-dependent effects of host patch traits on species composition in a stickleback parasite metacommunity.
Bolnick DI, Resetarits EJ, Ballare K, Stuart YE, Stutz WE
Ecology (2020) 101(12):e03181 PMC7757261 10.1002/ecy.3181 - Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion.
Smith SA, Maurer-Alcalá XX, Yan Y, Katz LA, Santoferrara LF, McManus GB
Genome biology and evolution (2020) 12(9):1616-1622 PMC7523726 10.1093/gbe/evaa185 - HPV-EM: an accurate HPV detection and genotyping EM algorithm.
Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J
Scientific reports (2020) 10(1):14340 PMC7459114 10.3892/ol.2017.7327 - Ten simple rules to increase computational skills among biologists with Code Clubs.
Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough JMA, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD
PLoS computational biology (2020) 16(8):e1008119 PMC7451508 10.1371/journal.pcbi.1008119 - The social network: Impact of host and microbial interactions on bacterial antibiotic tolerance and persistence.
Rocha-Granados MC, Zenick B, Englander HE, Mok WWK
Cellular signalling (2020) 75:109750 10.1016/j.cellsig.2020.109750 - Analysis of 5'-NAD capping of mRNAs in dormant spores of Bacillus subtilis.
Craft DL, Korza G, Zhang Y, Frindert J, Jäschke A, Caimano MJ, Setlow P
FEMS microbiology letters (2020) 367(17): 10.1093/femsle/fnaa143 - Correction to "A Potent Host Defense Peptide Triggers DNA Damage and Is Active against Multidrug-Resistant Gram-Negative Pathogens".
Juliano SA, Serafim LF, Duay SS, Chavez MH, Sharma G, Rooney M, Comert F, Pierce S, Radulescu A, Cotten ML, Mihailescu M, May ER, Greenwood AI, Prabhakar R, Angeles-Boza AM
ACS infectious diseases (2020) 6(9):2542 10.1021/acsinfecdis.0c00549 - Inferring the ancestry of parents and grandparents from genetic data.
Pei J, Zhang Y, Nielsen R, Wu Y
PLoS computational biology (2020) 16(8):e1008065 PMC7449501 10.1371/journal.pcbi.1008065 - In the beginning: egg-microbe interactions and consequences for animal hosts.
Nyholm SV
Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2020) 375(1808):20190593 PMC7435154 10.1098/rstb.2019.0593 - Investigating Synthesis of the MalS Malic Enzyme during Bacillus subtilis Spore Germination and Outgrowth and the Influence of Spore Maturation and Sporulation Conditions.
Swarge B, Nafid C, Vischer N, Kramer G, Setlow P, Brul S
mSphere (2020) 5(4): PMC7407067 10.1128/mSphere.00464-20 - Antimicrobial Susceptibility Testing of Antimicrobial Peptides to Better Predict Efficacy.
Mercer DK, Torres MDT, Duay SS, Lovie E, Simpson L, von Köckritz-Blickwede M, de la Fuente-Nunez C, O'Neil DA, Angeles-Boza AM
Frontiers in cellular and infection microbiology (2020) 10:326 PMC7358464 10.3389/fcimb.2020.00326 - Bacillus spore germination: Knowns, unknowns and what we need to learn.
Christie G, Setlow P
Cellular signalling (2020) 74:109729 10.1016/j.cellsig.2020.109729 - Analysis of Treponema pallidum Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres.
Chen W, Šmajs D, Hu Y, Ke W, Pospíšilová P, Hawley KL, Caimano MJ, Radolf JD, Sena A, Tucker JD, Yang B, Juliano JJ, Zheng H, Parr JB
The Journal of infectious diseases (2020) 223(5):848-853 PMC8171795 10.1093/infdis/jiaa449 - Visualization of Germination Proteins in Putative Germinosomes.
Wang Y, de Boer R, Vischer N, van Haastrecht P, Setlow P, Brul S
International journal of molecular sciences (2020) 21(15): PMC7432890 10.3390/ijms21155198 - Immune-challenged vampire bats produce fewer contact calls.
Stockmaier S, Bolnick DI, Page RA, Josic D, Carter GG
Biology letters (2020) 16(7):20200272 PMC7423039 10.1098/rsbl.2020.0272 - Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats.
White RA, Visscher PT, Burns BP
Trends in microbiology (2020) 29(3):204-213 10.1016/j.tim.2020.06.004 - Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach.
Wu Y
Bioinformatics (Oxford, England) (2020) 36(Suppl_1):i326-i334 PMC7355278 10.1093/bioinformatics/btaa465 - Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community.
Griffin TW, Baer JG, Ward JE
Microbial ecology (2020) 81(1):180-192 10.3354/meps038201 - Applications of Bacillus subtilis Spores in Biotechnology and Advanced Materials.
Zhang X, Al-Dossary A, Hussain M, Setlow P, Li J
Applied and environmental microbiology (2020) 86(17): PMC7440806 10.1128/AEM.01096-20 - SAGER: a database of Symbiodiniaceae and Algal Genomic Resource.
Yu L, Li T, Li L, Lin X, Li H, Liu C, Guo C, Lin S
Database : the journal of biological databases and curation (2020) 2020: PMC7334889 10.1093/database/baaa051 - Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D'.
Suria AM, Tan KC, Kerwin AH, Gitzel L, Abini-Agbomson L, Bertenshaw JM, Sewell J, Nyholm SV, Balunas MJ
mSphere (2020) 5(4): PMC7333567 10.1128/mSphere.00166-20 - Rapid image deconvolution and multiview fusion for optical microscopy.
Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, Shroff H
Nature biotechnology (2020) 38(11):1337-1346 PMC7642198 10.1038/s41587-020-0560-x - Effect of Gut Microbiota and PNPLA3 rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth.
Monga Kravetz A, Testerman T, Galuppo B, Graf J, Pierpont B, Siebel S, Feinn R, Santoro N
The Journal of clinical endocrinology and metabolism (2020) 105(10): PMC7458486 10.1210/clinem/dgaa382 - The effect of protective cultures on Staphylococcus aureus growth and enterotoxin production.
Aljasir SF, D'Amico DJ
Food microbiology (2020) 91:103541 10.1016/j.fm.2020.103541 - Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae.
Saad OS, Lin X, Ng TY, Li L, Ang P, Lin S
Frontiers in microbiology (2020) 11:847 PMC7264167 10.3389/fmicb.2020.00847 - Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.
McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD,
Cell reports. Medicine (2020) 1(1): PMC7289043 10.1016/j.xcrm.2020.100004 - A multivariate view of parallel evolution.
De Lisle SP, Bolnick DI
Evolution; international journal of organic evolution (2020) 74(7):1466-1481 10.1111/evo.14035 - Roadmap for naming uncultivated Archaea and Bacteria.
Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL
Nature microbiology (2020) 5(8):987-994 PMC7381421 10.1073/pnas.1720115115 - More than just nestlings: incidence of subcutaneous Philornis (Diptera: Muscidae) nest flies in adult birds.
Quiroga MA, Hayes TI, Hayes CD, Garrod H, Soares L, Knutie SA, Latta SC, Anderson DL
Parasitology research (2020) 119(7):2337-2342 10.1007/s00436-020-06696-2 - Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding.
Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB
The Journal of eukaryotic microbiology (2020) 67(5):612-622 10.1111/jeu.12813 - Glycerol Utilization By Phytoplankton.
Wang C, Baseler S, Lin S
Journal of phycology (2020) 56(5):1157-1167 10.1111/jpy.13031 - Rising to the challenge: designing, implementing and reporting exercise oncology trials in understudied populations.
Lahart IM, Weller SK, Kirkham AA
British journal of cancer (2020) 123(2):173-175 PMC7374541 10.1016/j.tics.2019.07.009 - A Chemical Counterpunch: Chromobacterium violaceum ATCC 31532 Produces Violacein in Response to Translation-Inhibiting Antibiotics.
Lozano GL, Guan C, Cao Y, Borlee BR, Broderick NA, Stabb EV, Handelsman J
mBio (2020) 11(3): PMC7240160 10.1128/mBio.00948-20 - Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in .
Chelius C, Huso W, Reese S, Doan A, Lincoln S, Lawson K, Tran B, Purohit R, Glaros T, Srivastava R, Harris SD, Marten MR
Molecular & cellular proteomics : MCP (2020) 19(8):1310-1329 PMC8014999 10.1074/mcp.RA119.001769 - Type I Interferons Ameliorate Zinc Intoxication of Candida glabrata by Macrophages and Promote Fungal Immune Evasion.
Riedelberger M, Penninger P, Tscherner M, Hadriga B, Brunnhofer C, Jenull S, Stoiber A, Bourgeois C, Petryshyn A, Glaser W, Limbeck A, Lynes MA, Schabbauer G, Weiss G, Kuchler K
iScience (2020) 23(5):101121 PMC7232100 10.1016/j.isci.2020.101121 - High throughput sequencing of 18S rRNA and its gene to characterize a Prorocentrum shikokuense (Dinophyceae) bloom.
Zhang Y, Lin X, Li T, Li H, Lin L, Luo H, Li L, Ji N, Lin S
Harmful algae (2020) 94:101809 10.1016/j.hal.2020.101809 - Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host.
Stephens ME, Gage DJ
PloS one (2020) 15(5):e0233065 PMC7228121 10.1371/journal.pone.0233065 - Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families.
Wade T, Rangel LT, Kundu S, Fournier GP, Bansal MS
PloS one (2020) 15(5):e0232950 PMC7228096 10.1371/journal.pone.0232950 - The role of the microbiota in periodontal disease.
Curtis MA, Diaz PI, Van Dyke TE
Periodontology 2000 (2020) 83(1):14-25 10.1111/prd.12296 - Tai Ji Quan as antihypertensive lifestyle therapy: A systematic review and meta-analysis.
Wu Y, Johnson BT, Chen S, Chen Y, Livingston J, Pescatello LS
Journal of sport and health science (2020) 10(2):211-221 PMC7987647 10.1016/j.jshs.2020.03.007 - Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice.
Lee J, d'Aigle J, Atadja L, Quaicoe V, Honarpisheh P, Ganesh BP, Hassan A, Graf J, Petrosino J, Putluri N, Zhu L, Durgan DJ, Bryan RM, McCullough LD, Venna VR
Circulation research (2020) 127(4):453-465 PMC7415518 10.1161/CIRCRESAHA.119.316448 - Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum.
Pyatibratov MG, Syutkin AS, Quax TEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV
MicrobiologyOpen (2020) 9(7):e1047 PMC7349177 10.1002/mbo3.1047 - Microbiomes as modulators of Drosophila melanogaster homeostasis and disease.
Lesperance DN, Broderick NA
Current opinion in insect science (2020) 39:84-90 PMC7302976 10.1016/j.cois.2020.03.003 - Adding SNX to the mix: SNX9 drives filopodia biogenesis.
Lebek NM, Campellone KG
The Journal of cell biology (2020) 219(4): PMC7147100 10.1083/jcb.202002086 - Bridging the Gap: Plant-Endophyte Interactions as a Roadmap to Understanding Small-Molecule Communication in Marine Microbiomes.
Samples RM, Balunas MJ
Chembiochem : a European journal of chemical biology (2020) 21(19):2708-2721 10.1002/cbic.202000064 - Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species.
Li G, Yin B, Li J, Wang J, Wei W, Bolnick DI, Wan X, Zhu B, Zhang Z
The ISME journal (2020) 14(7):1795-1808 PMC7305154 10.1038/s41396-020-0646-y - Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.
Bansal MS
Algorithms for molecular biology : AMB (2020) 15:6 PMC7155338 10.1186/s13015-020-00166-1 - The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes.
Hong BY, Hoare A, Cardenas A, Dupuy AK, Choquette L, Salner AL, Schauer PK, Hegde U, Peterson DE, Dongari-Bagtzoglou A, Strausbaugh LD, Diaz PI
Journal of dental research (2020) 99(6):730-738 PMC7243416 10.1177/0022034520915879 - Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology.
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Nature methods (2020) 17(5):551 PMC7200595 10.1038/s41592-020-0828-6 - Lipid moieties of lipoproteins are the causative factor of vaccine-enhanced disease.
Mara AB, Gavitt TD, Tulman ER, Geary SJ, Szczepanek SM
NPJ vaccines (2020) 5(1):31 PMC7142147 10.1038/s41541-020-0181-x - The Clinical Utility of Neuromotor Exercise as Antihypertensive Lifestyle Therapy.
Wu Y, Pescatello LS
Current sports medicine reports (2020) 19(4):133-136 10.1249/JSR.0000000000000700 - Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin.
Van de Perre F, Willig MR, Presley SJ, Mukinzi IJ, Gambalemoke MS, Leirs H, Verheyen E
Royal Society open science (2020) 7(3):191582 PMC7137932 10.1098/rsos.191582 - The effect of hyperbaric oxygen on mitochondrial and glycolytic energy metabolism: the caloristasis concept.
Tezgin D, Giardina C, Perdrizet GA, Hightower LE
Cell stress & chaperones (2020) 25(4):667-677 PMC7332662 10.1007/s12192-020-01100-5 - A Potent Host Defense Peptide Triggers DNA Damage and Is Active against Multidrug-Resistant Gram-Negative Pathogens.
Juliano SA, Serafim LF, Duay SS, Heredia Chavez M, Sharma G, Rooney M, Comert F, Pierce S, Radulescu A, Cotten ML, Mihailescu M, May ER, Greenwood AI, Prabhakar R, Angeles-Boza AM
ACS infectious diseases (2020) 6(5):1250-1263 PMC7772950 10.1021/acsinfecdis.0c00051 - Genetic tool development in marine protists: emerging model organisms for experimental cell biology.
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Nature methods (2020) 17(5):481-494 PMC7200600 10.1038/s41592-020-0796-x - Replication-inducible vaccinia virus vectors with enhanced safety in vivo.
O'Connell CM, Jasperse B, Hagen CJ, Titong A, Verardi PH
PloS one (2020) 15(4):e0230711 PMC7117657 10.1371/journal.pone.0230711 - antivirulence activity of baicalin against .
Pellissery AJ, Vinayamohan PG, Venkitanarayanan K
Journal of medical microbiology (2020) 69(4):631-639 10.1099/jmm.0.001179 - Spatial heterogeneity of the shorebird gastrointestinal microbiome.
Grond K, Guilani H, Hird SM
Royal Society open science (2020) 7(1):191609 PMC7029916 10.1098/rsos.191609 - Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas.
Talagrand-Reboul E, Colston SM, Graf J, Lamy B, Jumas-Bilak E
Genome biology and evolution (2020) 12(5):535-552 PMC7250499 10.1093/gbe/evaa055 - WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility.
Kabrawala S, Zimmer MD, Campellone KG
PLoS genetics (2020) 16(3):e1008694 PMC7112243 10.1371/journal.pgen.1008694 - Context Is Key: Comparative Biology Illuminates the Vertebrate Microbiome.
Hird SM
mBio (2020) 11(2): PMC7064755 10.1128/mBio.00153-20 - Targeting the pregnane X receptor using microbial metabolite mimicry.
Dvořák Z, Kopp F, Costello CM, Kemp JS, Li H, Vrzalová A, Štěpánková M, Bartoňková I, Jiskrová E, Poulíková K, Vyhlídalová B, Nordstroem LU, Karunaratne CV, Ranhotra HS, Mun KS, Naren AP, Murray IA, Perdew GH, Brtko J, Toporova L, Schön A, Wallace BD, Walton WG, Redinbo MR, Sun K, Beck A, Kortagere S, Neary MC, Chandran A, Vishveshwara S, Cavalluzzi MM, Lentini G, Cui JY, Gu H, March JC, Chatterjee S, Matson A, Wright D, Flannigan KL, Hirota SA, Sartor RB, Mani S
EMBO molecular medicine (2020) 12(4):e11621 PMC7136958 10.15252/emmm.201911621 - Evolution and roles of cytokinin genes in angiosperms 1: Do ancient play housekeeping while non-ancient play regulatory roles?
Wang X, Lin S, Liu D, Gan L, McAvoy R, Ding J, Li Y
Horticulture research (2020) 7:28 PMC7049300 10.1038/s41438-019-0211-x - InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining.
Wu Z, Wu Y, Gao J
BMC genomics (2020) 21(Suppl 1):173 PMC7057458 10.1186/s12864-020-6585-1 - Detecting circular RNA from high-throughput sequence data with de Bruijn graph.
Li X, Wu Y
BMC genomics (2020) 21(Suppl 1):749 PMC7057571 10.1186/s12864-019-6154-7 - Broad Protection of Pigs against Heterologous PRRSV Strains by a GP5-Mosaic DNA Vaccine Prime/GP5-Mosaic rVaccinia (VACV) Vaccine Boost.
Cui J, O'Connell CM, Hagen C, Sawicki K, Smyth JA, Verardi PH, Kruiningen HJV, Garmendia AE
Vaccines (2020) 8(1): PMC7157218 10.3390/vaccines8010106 - Bridging the gap between theory and practice in elucidating modular gene regulatory sequence organisation within genomes.
Seto K, Mok W, Stone J
Genome (2020) 63(6):281-289 10.1139/gen-2019-0150 - Identification and expression analysis of meiosis-related genes in the harmful alga Heterosigma akashiwo (Raphidophyceae).
Ji N, Huang J, Zhang Z, Zhou L, Shen X, Lin S
Harmful algae (2020) 92:101736 10.1016/j.hal.2019.101736 - Utilization of various forms of nitrogen and expression regulation of transporters in the harmful alga Heterosigma akashiwo (Raphidophyceae).
Ji N, Zhang Z, Huang J, Zhou L, Deng S, Shen X, Lin S
Harmful algae (2020) 92:101770 10.1016/j.hal.2020.101770 - Sickness effects on social interactions depend on the type of behaviour and relationship.
Stockmaier S, Bolnick DI, Page RA, Carter GG
The Journal of animal ecology (2020) 89(6):1387-1394 10.1111/1365-2656.13193 - Characterizing ciguatoxin (CTX)- and Non-CTX-producing strains of Gambierdiscus balechii using comparative transcriptomics.
Wu Z, Luo H, Yu L, Lee WH, Li L, Mak YL, Lin S, Lam PKS
The Science of the total environment (2020) 717:137184 10.1016/j.scitotenv.2020.137184 - Transcriptomic and physiological responses of Skeletonema costatum to ATP utilization.
Zhang X, Lin S, Liu D
Environmental microbiology (2020) 22(5):1861-1869 10.1111/1462-2920.14944 - Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies.
Yang M, Zhu G, Korza G, Sun X, Setlow P, Li J
Applied and environmental microbiology (2020) 86(8): PMC7117931 10.1128/AEM.02938-19 - Draft Genome Sequences of Campylobacter jejuni Strains Isolated from Poultry.
Wagle BR, Marasini D, Upadhyaya I, Shrestha S, Arsi K, Donoghue AM, Carbonero F, Donoghue DJ, Maas K, Upadhyay A
Microbiology resource announcements (2020) 9(7): PMC7019061 10.1128/MRA.01272-19 - Microhabitat contributes to microgeographic divergence in threespine stickleback.
Maciejewski MF, Jiang C, Stuart YE, Bolnick DI
Evolution; international journal of organic evolution (2020) 74(4):749-763 10.1111/evo.13942 - Compatibility of Commercially Produced Protective Cultures with Common Cheesemaking Cultures and Their Antagonistic Effect on Foodborne Pathogens.
Gensler CA, Brown SRB, Aljasir SF, D'Amico DJ
Journal of food protection (2020) 83(6):1010-1019 10.4315/JFP-19-614 - Role of glucosyltransferase R in biofilm interactions between Streptococcus oralis and Candida albicans.
Souza JGS, Bertolini M, Thompson A, Mansfield JM, Grassmann AA, Maas K, Caimano MJ, Barao VAR, Vickerman MM, Dongari-Bagtzoglou A
The ISME journal (2020) 14(5):1207-1222 PMC7174356 10.1038/s41396-020-0608-4 - Eleven grand challenges in single-cell data science.
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A
Genome biology (2020) 21(1):31 PMC7007675 10.1186/s13059-020-1926-6 - DNA Damage Kills Bacterial Spores and Cells Exposed to 222-Nanometer UV Radiation.
Taylor W, Camilleri E, Craft DL, Korza G, Granados MR, Peterson J, Szczpaniak R, Weller SK, Moeller R, Douki T, Mok WWK, Setlow P
Applied and environmental microbiology (2020) 86(8): PMC7117916 10.1128/AEM.03039-19 - The gut microbiota response to helminth infection depends on host sex and genotype.
Ling F, Steinel N, Weber J, Ma L, Smith C, Correa D, Zhu B, Bolnick D, Wang G
The ISME journal (2020) 14(5):1141-1153 PMC7174316 10.1038/s41396-020-0589-3 - Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study.
Cao L, Lee SG, Melough MM, Sakaki JR, Maas KR, Koo SI, Chun OK
Nutrients (2020) 12(2): PMC7070352 10.3390/nu12020290 - RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metals.
Li T, Lin X, Yu L, Lin S, Rodriguez IB, Ho TY
The Science of the total environment (2020) 705:135767 10.1016/j.scitotenv.2019.135767 - Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Specimens Collected in Palau.
Maloney KN, Botts RT, Davis TS, Okada BK, Maloney EM, Leber CA, Alvarado O, Brayton C, Caraballo-Rodríguez AM, Chari JV, Chicoine B, Crompton JC, Davis SR, Gromek SM, Kurnianda V, Quach K, Samples RM, Shieh V, Sultana CM, Tanaka J, Dorrestein PC, Balunas MJ, McFadden CS
Journal of natural products (2020) 83(3):693-705 10.1021/acs.jnatprod.9b01128 - Nuclear Gene Transformation in the Dinoflagellate .
Sprecher BN, Zhang H, Lin S
Microorganisms (2020) 8(1): PMC7022241 10.3390/microorganisms8010126 - A meta-analysis reveals temperature, dose, life stage, and taxonomy influence host susceptibility to a fungal parasite.
Sauer EL, Cohen JM, Lajeunesse MJ, McMahon TA, Civitello DJ, Knutie SA, Nguyen K, Roznik EA, Sears BF, Bessler S, Delius BK, Halstead N, Ortega N, Venesky MD, Young S, Rohr JR
Ecology (2020) 101(4):e02979 10.1002/ecy.2979 - A draft genome sequence of the elusive giant squid, Architeuthis dux.
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP
GigaScience (2020) 9(1): PMC6962438 10.1093/gigascience/giz152 - Disruption of CXCR6 Ameliorates Kidney Inflammation and Fibrosis in Deoxycorticosterone Acetate/Salt Hypertension.
Wu Y, An C, Jin X, Hu Z, Wang Y
Scientific reports (2020) 10(1):133 PMC6954216 10.1038/s41598-019-56933-7 - Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback.
Bolnick DI, Ballare KM
Ecology letters (2020) 23(3):495-505 PMC7325224 10.1111/ele.13448 - Mass spectrometry searches using MASST.
Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC
Nature biotechnology (2020) 38(1):23-26 PMC7236533 10.1007/s11306-007-0082-2 2019
- Host tolerance and resistance to parasitic nest flies differs between two wild bird species.
Grab KM, Hiller BJ, Hurlbert JH, Ingram ME, Parker AB, Pokutnaya DY, Knutie SA
Ecology and evolution (2019) 9(21):12144-12155 PMC6854101 10.1002/ece3.5682 - DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network.
Cai L, Wu Y, Gao J
BMC bioinformatics (2019) 20(1):665 PMC6909530 10.1186/s12859-019-3299-y - Gut Microbiomes of the Eastern Oyster () and the Blue Mussel (): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities.
Pierce ML, Ward JE
mSphere (2019) 4(6): PMC6908423 10.1128/mSphere.00730-19 - The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery.
van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FPJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee JH, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O'Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG
ACS central science (2019) 5(11):1824-1833 PMC6891855 10.1021/acscentsci.9b00806 - Microplastic exposure represses the growth of endosymbiotic dinoflagellate Cladocopium goreaui in culture through affecting its apoptosis and metabolism.
Su Y, Zhang K, Zhou Z, Wang J, Yang X, Tang J, Li H, Lin S
Chemosphere (2019) 244:125485 10.1016/j.chemosphere.2019.125485 - Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.
Yang Y, Ashworth AJ, Willett C, Cook K, Upadhyay A, Owens PR, Ricke SC, DeBruyn JM, Moore PA
Frontiers in microbiology (2019) 10:2639 PMC6872647 10.3389/fmicb.2019.02639 - Temporally varying disruptive selection in the medium ground finch ().
Beausoleil MO, Frishkoff LO, M'Gonigle LK, Raeymaekers JAM, Knutie SA, De León LF, Huber SK, Chaves JA, Clayton DH, Koop JAH, Podos J, Sharpe DMT, Hendry AP, Barrett RDH
Proceedings. Biological sciences (2019) 286(1916):20192290 PMC6939253 10.1098/rspb.2019.2290 - Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens.
Boyce GR, Gluck-Thaler E, Slot JC, Stajich JE, Davis WJ, James TY, Cooley JR, Panaccione DG, Eilenberg J, De Fine Licht HH, Macias AM, Berger MC, Wickert KL, Stauder CM, Spahr EJ, Maust MD, Metheny AM, Simon C, Kritsky G, Hodge KT, Humber RA, Gullion T, Short DPG, Kijimoto T, Mozgai D, Arguedas N, Kasson MT
Fungal ecology (2019) 41:147-164 PMC6876628 10.1016/j.funeco.2019.06.002 - The Herpes Simplex Virus 1 Immediate Early Protein ICP22 Is a Functional Mimic of a Cellular J Protein.
Adlakha M, Livingston CM, Bezsonova I, Weller SK
Journal of virology (2019) 94(4): PMC6997750 10.1128/JVI.01564-19 - Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.
Krucinska J, Lombardo MN, Erlandsen H, Hazeen A, Duay SS, Pattis JG, Robinson VL, May ER, Wright DL
Scientific reports (2019) 9(1):17106 PMC6863902 10.1038/s41598-019-53301-3 - No evidence for phylosymbiosis in western chipmunk species.
Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM
FEMS microbiology ecology (2019) 96(1): 10.1093/femsec/fiz182 - Inactivation of Escherichia coli O157:H7 in apple cider by resveratrol and naringenin.
Surendran Nair M, Ma F, Lau P, Upadhyaya I, Venkitanarayanan K
Food microbiology (2019) 86:103327 10.1016/j.fm.2019.103327 - Shielding the Next Generation: Symbiotic Bacteria from a Reproductive Organ Protect Bobtail Squid Eggs from Fungal Fouling.
Kerwin AH, Gromek SM, Suria AM, Samples RM, Deoss DJ, O'Donnell K, Frasca S, Sutton DA, Wiederhold NP, Balunas MJ, Nyholm SV
mBio (2019) 10(5): PMC6819662 10.1128/mBio.02376-19 - Editorial: Characterizing Modern Microbialites and the Geobiological Processes Underlying Their Formation.
Foster JS, Reid RP, Visscher PT, Dupraz C
Frontiers in microbiology (2019) 10:2299 PMC6794560 10.3389/fmicb.2019.02299 - Illuminating the dark depths inside coral.
Liu C, Cheng SH, Lin S
Cellular microbiology (2019) 22(1):e13122 10.1111/cmi.13122 - Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.
Diaz PI, Valm AM
Journal of dental research (2019) 99(1):18-25 PMC6927214 10.1177/0022034519880157 - Transcriptional and Pathological Host Responses to Coinfection with Virulent or Attenuated Mycoplasma gallisepticum and Low-Pathogenic Avian Influenza A Virus in Chickens.
Canter JA, Tulman ER, Beaudet J, Lee DH, May M, Szczepanek SM, Geary SJ
Infection and immunity (2019) 88(1): PMC6921668 10.1128/IAI.00607-19 - NMR Mapping of Disordered Segments from a Viral Scaffolding Protein Enclosed in a 23 MDa Procapsid.
Whitehead RD, Teschke CM, Alexandrescu AT
Biophysical journal (2019) 117(8):1387-1392 PMC6817520 10.1016/j.bpj.2019.08.038 - Biased movement drives local cryptic coloration on distinct urban pavements.
Edelaar P, Baños-Villalba A, Quevedo DP, Escudero G, Bolnick DI, Jordán-Andrade A
Proceedings. Biological sciences (2019) 286(1912):20191343 PMC6790761 10.1098/rspb.2019.1343 - Characterization and Expression Analysis of Genes in Suggest Different Divergences of Tandem Duplicates.
Wang X, Lin S, Liu D, Wang Q, McAvoy R, Ding J, Li Y
Frontiers in genetics (2019) 10:805 PMC6752658 10.3389/fgene.2019.00805 - Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment.
Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA
eLife (2019) 8: PMC6773444 10.7554/eLife.47606 - Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin Resistant .
Reeve SM, Si D, Krucinska J, Yan Y, Viswanathan K, Wang S, Holt GT, Frenkel MS, Ojewole AA, Estrada A, Agabiti SS, Alverson JB, Gibson ND, Priestley ND, Wiemer AJ, Donald BR, Wright DL
ACS infectious diseases (2019) 5(11):1896-1906 PMC7025792 10.1021/acsinfecdis.9b00222 - Comparison of major depression diagnostic classification probability using the SCID, CIDI, and MINI diagnostic interviews among women in pregnancy or postpartum: An individual participant data meta-analysis.
Levis B, McMillan D, Sun Y, He C, Rice DB, Krishnan A, Wu Y, Azar M, Sanchez TA, Chiovitti MJ, Bhandari PM, Neupane D, Saadat N, Riehm KE, Imran M, Boruff JT, Cuijpers P, Gilbody S, Ioannidis JPA, Kloda LA, Patten SB, Shrier I, Ziegelstein RC, Comeau L, Mitchell ND, Tonelli M, Vigod SN, Aceti F, Alvarado R, Alvarado-Esquivel C, Bakare MO, Barnes J, Beck CT, Bindt C, Boyce PM, Bunevicius A, Couto TCE, Chaudron LH, Correa H, de Figueiredo FP, Eapen V, Fernandes M, Figueiredo B, Fisher JRW, Garcia-Esteve L, Giardinelli L, Helle N, Howard LM, Khalifa DS, Kohlhoff J, Kusminskas L, Kozinszky Z, Lelli L, Leonardou AA, Lewis BA, Maes M, Meuti V, Nakić Radoš S, Navarro García P, Nishi D, Okitundu Luwa E-Andjafono D, Robertson-Blackmore E, Rochat TJ, Rowe HJ, Siu BWM, Skalkidou A, Stein A, Stewart RC, Su KP, Sundström-Poromaa I, Tadinac M, Tandon SD, Tendais I, Thiagayson P, Töreki A, Torres-Giménez A, Tran TD, Trevillion K, Turner K, Vega-Dienstmaier JM, Wynter K, Yonkers KA, Benedetti A, Thombs BD
International journal of methods in psychiatric research (2019) 28(4):e1803 PMC7027670 10.1002/mpr.1803 - mSphere of Influence: an Inupiat Journey in Science.
Milligan-Myhre KCA
mSphere (2019) 4(5): PMC6751493 10.1128/mSphere.00595-19 - Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom.
Yu L, Zhang Y, Li M, Wang C, Lin X, Li L, Shi X, Guo C, Lin S
The Science of the total environment (2019) 699:134323 10.1016/j.scitotenv.2019.134323 - The RpoS Gatekeeper in : An Invariant Regulatory Scheme That Promotes Spirochete Persistence in Reservoir Hosts and Niche Diversity.
Caimano MJ, Groshong AM, Belperron A, Mao J, Hawley KL, Luthra A, Graham DE, Earnhart CG, Marconi RT, Bockenstedt LK, Blevins JS, Radolf JD
Frontiers in microbiology (2019) 10:1923 PMC6719511 10.3389/fmicb.2019.01923 - Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach.
Wu Y
Bioinformatics (Oxford, England) (2019) 36(3):742-750 10.1093/bioinformatics/btz676 - Understanding Maladaptation by Uniting Ecological and Evolutionary Perspectives.
Brady SP, Bolnick DI, Barrett RDH, Chapman L, Crispo E, Derry AM, Eckert CG, Fraser DJ, Fussmann GF, Gonzalez A, Guichard F, Lamy T, Lane J, McAdam AG, Newman AEM, Paccard A, Robertson B, Rolshausen G, Schulte PM, Simons AM, Vellend M, Hendry A
The American naturalist (2019) 194(4):495-515 10.1086/705020 - -Cinnamaldehyde, Eugenol and Carvacrol Reduce Biofilms and Modulate Expression of Select Genes and Proteins.
Wagle BR, Upadhyay A, Upadhyaya I, Shrestha S, Arsi K, Liyanage R, Venkitanarayanan K, Donoghue DJ, Donoghue AM
Frontiers in microbiology (2019) 10:1837 PMC6698798 10.3389/fmicb.2019.01837 - Antimicrobial and Antibiofilm Activities of Helical Antimicrobial Peptide Sequences Incorporating Metal-Binding Motifs.
Agbale CM, Sarfo JK, Galyuon IK, Juliano SA, Silva GGO, Buccini DF, Cardoso MH, Torres MDT, Angeles-Boza AM, de la Fuente-Nunez C, Franco OL
Biochemistry (2019) 58(36):3802-3812 10.1021/acs.biochem.9b00440 - Efomycins K and L From a Termite-Associated sp. M56 and Their Putative Biosynthetic Origin.
Klassen JL, Lee SR, Poulsen M, Beemelmanns C, Kim KH
Frontiers in microbiology (2019) 10:1739 PMC6691879 10.3389/fmicb.2019.01739 - Trends in Solid Adsorbent Materials Development for CO Capture.
Pardakhti M, Jafari T, Tobin Z, Dutta B, Moharreri E, Shemshaki NS, Suib S, Srivastava R
ACS applied materials & interfaces (2019) 11(38):34533-34559 10.1021/acsami.9b08487 - Causes of maladaptation.
Brady SP, Bolnick DI, Angert AL, Gonzalez A, Barrett RDH, Crispo E, Derry AM, Eckert CG, Fraser DJ, Fussmann GF, Guichard F, Lamy T, McAdam AG, Newman AEM, Paccard A, Rolshausen G, Simons AM, Hendry AP
Evolutionary applications (2019) 12(7):1229-1242 PMC6691215 10.1111/eva.12844 - Energy-Geometry Dependency of Molecular Structures: A Multistep Machine Learning Approach.
Moharreri E, Pardakhti M, Srivastava R, Suib SL
ACS combinatorial science (2019) 21(9):614-621 10.1021/acscombsci.9b00028 - Mechanisms of enhanced bacterial endospore inactivation during sterilization by ohmic heating.
Schottroff F, Pyatkovskyy T, Reineke K, Setlow P, Sastry SK, Jaeger H
Bioelectrochemistry (Amsterdam, Netherlands) (2019) 130:107338 10.1016/j.bioelechem.2019.107338 - Non-Conventional Metal Ion Cofactor Requirement of Dinoflagellate Alkaline Phosphatase and Translational Regulation by Phosphorus Limitation.
Lin X, Guo C, Li L, Li T, Lin S
Microorganisms (2019) 7(8): PMC6723241 10.3390/microorganisms7080232 - Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses.
Dedeo CL, Cingolani G, Teschke CM
Annual review of virology (2019) 6(1):141-160 PMC6947915 10.1146/annurev-virology-092818-015819 - Correction: Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons.
Grond K, Perreau JM, Loo WT, Spring AJ, Cavanaugh CM, Hird SM
PloS one (2019) 14(7):e0220347 PMC6650065 10.1371/journal.pone.0220347 - Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis.
Lynch JB, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG
Journal of bacteriology (2019) 201(20): PMC6755730 10.1128/JB.00319-19 - Selective Ingestion and Egestion of Plastic Particles by the Blue Mussel () and Eastern Oyster (): Implications for Using Bivalves as Bioindicators of Microplastic Pollution.
Ward JE, Zhao S, Holohan BA, Mladinich KM, Griffin TW, Wozniak J, Shumway SE
Environmental science & technology (2019) 53(15):8776-8784 10.1021/acs.est.9b02073 - Accumulation and Release of Rare Earth Ions by Spores of Species and the Location of These Ions in Spores.
Dong W, Li S, Camilleri E, Korza G, Yankova M, King SM, Setlow P
Applied and environmental microbiology (2019) 85(17): PMC6696969 10.1128/AEM.00956-19 - Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection.
Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK
JCI insight (2019) 5: PMC6675551 10.1172/jci.insight.129152 - Microbiomes, Community Ecology, and the Comparative Method.
Hird SM
mSystems (2019) 4(3): PMC6533377 10.1128/mSystems.00112-19 - Flourishing deep-sea AAP bacteria detected by flow cytometric sorting and molecular analysis.
Qiu D, Huang L, Liu X, Lin S
PLoS ONE (2019) 14(6):e0218753 10.1371/journal.pone.0218753 - Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons.
Grond K, Perreau JM, Loo WT, Spring AJ, Cavanaugh CM, Hird SM
PloS one (2019) 14(6):e0217804 PMC6578490 10.1371/journal.pone.0217804 - Structure guided in-vitro to in-vivo pharmacokinetic optimization of propargyl-linked antifolates.
Lombardo MN, G-Dayanandan N, Keshipeddy S, Zhou W, Si D, Reeve SM, Alverson J, Barney P, Walker L, Hoody J, Priestley N, Obach RS, Wright DL
Drug Metab. Dispos. (2019) : 10.1124/dmd.119.086504 - Integrated Analysis of Clinical and Microbiome Risk Factors Associated with the Development of Oral Candidiasis during Cancer Chemotherapy.
Diaz PI, Hong BY, Dupuy AK, Choquette L, Thompson A, Salner AL, Schauer PK, Hegde U, Burleson JA, Strausbaugh LD, Peterson DE, Dongari-Bagtzoglou A
Journal of fungi (Basel, Switzerland) (2019) 5(2): PMC6617088 10.3390/jof5020049 - Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis.
Rader B, McAnulty SJ, Nyholm SV
MicrobiologyOpen (2019) 8(10):e858 PMC6813443 10.1002/mbo3.858 - Methylome Dynamics of Bovine Gametes and Early Embryos.
Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC
Frontiers in genetics (2019) 10:512 PMC6546829 10.3389/fgene.2019.00512 - Phylogenetic supertree and functional trait database for all extant parrots.
Burgio KR, Davis KE, Dreiss LM, Cisneros LM, Klingbeil BT, Presley SJ, Willig MR
Data in brief (2019) 24:103882 PMC6520560 10.1016/j.dib.2019.103882 - Keeping it fresh.
Klassen JL
eLife (2019) 8: PMC6561751 10.7554/eLife.48268 - Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein.
Asija K, Teschke CM
Virology (2019) 534:45-53 PMC6614003 10.1016/j.virol.2019.05.021 - In vitro efficacy of sodium selenite in reducing toxin production, spore outgrowth and antibiotic resistance in hypervirulent Clostridium difficile.
Pellissery AJ, Vinayamohan PG, Yin HB, Mooyottu S, Venkitanarayanan K
Journal of medical microbiology (2019) 68(7):1118-1128 10.1099/jmm.0.001008 - Classification of Tea Aromas Using Multi-Nanoparticle Based Chemiresistor Arrays.
Gao T, Wang Y, Zhang C, Pittman ZA, Oliveira AM, Fu K, Zhao J, Srivastava R, Willis BG
Sensors (Basel, Switzerland) (2019) 19(11): PMC6603602 10.3390/s19112547 - GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads.
Chu C, Li X, Wu Y
BMC genomics (2019) 20(Suppl 5):426 PMC6551238 10.1186/s12864-019-5703-4 - Identification and characterization of putative Aeromonas spp. T3SS effectors.
Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP
PloS one (2019) 14(6):e0214035 PMC6548356 10.1371/journal.pone.0214035 - Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback.
Rennison DJ, Stuart YE, Bolnick DI, Peichel CL
Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2019) 374(1777):20180241 PMC6560272 10.1098/rstb.2018.0241 - Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae.
Fučíková K, Lewis PO, Neupane S, Karol KG, Lewis LA
PeerJ (2019) 7:e6899 PMC6525593 10.7717/peerj.6899 - Populations are not declining and food webs are not collapsing at the Luquillo Experimental Forest.
Willig MR, Woolbright L, Presley SJ, Schowalter TD, Waide RB, Heartsill Scalley T, Zimmerman JK, González G, Lugo AE
Proceedings of the National Academy of Sciences of the United States of America (2019) 116(25):12143-12144 PMC6589750 10.1073/pnas.1820456116 - Checkerboard metacommunity structure: an incoherent concept.
Presley SJ, Mello JHF, Willig MR
Oecologia (2019) 190(2):323-331 10.1007/s00442-019-04420-1 - Flagellar regulation mediated by the Rcs pathway is required for virulence in the fish pathogen Yersinia ruckeri.
Jozwick AKS, LaPatra SE, Graf J, Welch TJ
Fish & shellfish immunology (2019) 91:306-314 10.1016/j.fsi.2019.05.036 - Structural and functional analyses of the N-terminal domain of the A subunit of a spore germinant receptor.
Li Y, Jin K, Perez-Valdespino A, Federkiewicz K, Davis A, Maciejewski MW, Setlow P, Hao B
Proceedings of the National Academy of Sciences of the United States of America (2019) 116(23):11470-11479 PMC6561283 10.1073/pnas.1903675116 - The VP1 G-H loop hypervariable epitope contributes to protective immunity against Foot and Mouth Disease Virus in swine.
Fernandez-Sainz I, Gavitt TD, Koster M, Ramirez-Medina E, Rodriguez YY, Wu P, Silbart LK, de Los Santos T, Szczepanek SM
Vaccine (2019) 37(26):3435-3442 10.1016/j.vaccine.2019.05.019 - A Hydrophobic Network: Intersubunit and Intercapsomer Interactions Stabilizing the Bacteriophage P22 Capsid.
Asija K, Teschke CM
Journal of virology (2019) 93(14): PMC6600197 10.1128/JVI.00727-19 - Properties of Aged Spores of .
Camilleri E, Korza G, Green J, Yuan J, Li YQ, Caimano MJ, Setlow P
J. Bacteriol. (2019) : 10.1128/JB.00231-19 - Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments.
Grattepanche JD, Juarez DL, Wood CC, McManus GB, Katz LA
PloS one (2019) 14(5):e0215872 PMC6502329 10.1371/journal.pone.0215872 - Fecal Microbiomes in Premature Infants With and Without Parenteral Nutrition-Associated Cholestasis.
Mokha JS, Davidovics ZH, Maas K, Caimano MJ, Matson A
Journal of pediatric gastroenterology and nutrition (2019) 69(2):224-230 10.1097/MPG.0000000000002352 - The evolution of hybrid fitness during speciation.
Dagilis AJ, Kirkpatrick M, Bolnick DI
PLoS genetics (2019) 15(5):e1008125 PMC6502311 10.1371/journal.pgen.1008125 - Thioredoxin-1 confines T cell alloresponse and pathogenicity in graft-versus-host disease.
Sofi MH, Wu Y, Schutt SD, Dai M, Daenthanasanmak A, Heinrichs Voss J, Nguyen H, Bastian D, Iamsawat S, Selvam SP, Liu C, Maulik N, Ogretmen B, Jin J, Mehrotra S, Yu XZ
The Journal of clinical investigation (2019) 129(7):2760-2774 PMC6597211 10.1172/JCI122899 - Comprehensive Analysis of Aspergillus nidulans PKA Phosphorylome Identifies a Novel Mode of CreA Regulation.
Ribeiro LFC, Chelius C, Boppidi KR, Naik NS, Hossain S, Ramsey JJJ, Kumar J, Ribeiro LF, Ostermeier M, Tran B, Ah Goo Y, de Assis LJ, Ulas M, Bayram O, Goldman GH, Lincoln S, Srivastava R, Harris SD, Marten MR
mBio (2019) 10(2): PMC6495382 10.1128/mBio.02825-18 - Visualization of Germinosomes and the Inner Membrane in Bacillus subtilis Spores.
Wen J, Pasman R, Manders EMM, Setlow P, Brul S
Journal of visualized experiments : JoVE (2019) (146): 10.3791/59388 - Mechanism of inactivation of Bacillus subtilis spores by high pressure CO at high temperature.
Rao L, Zhao L, Wang Y, Chen F, Hu X, Setlow P, Liao X
Food microbiology (2019) 82:36-45 10.1016/j.fm.2019.01.014 - Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.
Hong BY, Sobue T, Choquette L, Dupuy AK, Thompson A, Burleson JA, Salner AL, Schauer PK, Joshi P, Fox E, Shin DG, Weinstock GM, Strausbaugh LD, Dongari-Bagtzoglou A, Peterson DE, Diaz PI
Microbiome (2019) 7(1):66 PMC6482518 10.1186/s40168-019-0679-5 - Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands.
Knutie SA, Chaves JA, Gotanda KM
Molecular ecology (2019) 28(9):2441-2450 10.1111/mec.15088 - Candida albicans induces mucosal bacterial dysbiosis that promotes invasive infection.
Bertolini M, Ranjan A, Thompson A, Diaz PI, Sobue T, Maas K, Dongari-Bagtzoglou A
PLoS pathogens (2019) 15(4):e1007717 PMC6497318 10.1371/journal.ppat.1007717 - Altered Immune Landscape and Disrupted Coral- Symbiosis in the Scleractinian Coral by Challenge.
Zhou Z, Zhao S, Tang J, Liu Z, Wu Y, Wang Y, Lin S
Front Physiol (2019) 10:366 (PMC6454040) 10.3389/fphys.2019.00366 - House Dust Mite-Induced Allergic Lung Inflammation Is Not Exacerbated in Sickle Cell Disease Mice.
Jiang C, Gavitt TD, Szczepanek SM
International archives of allergy and immunology (2019) 179(3):192-200 10.1159/000499043 - Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in .
Lin S, Yu L, Zhang H
Microorganisms (2019) 7(4): (PMC6517890) 10.3390/microorganisms7040096 - Edible Coatings Fortified With Carvacrol Reduce on Chicken Wingettes and Modulate Expression of Select Virulence Genes.
Shrestha S, Wagle BR, Upadhyay A, Arsi K, Upadhyaya I, Donoghue DJ, Donoghue AM
Frontiers in microbiology (2019) 10:583 PMC6448016 10.3389/fmicb.2019.00583 - Sediment organic carbon and temperature effects on methylmercury concentration: A mesocosm experiment.
Buckman KL, Seelen EA, Mason RP, Balcom P, Taylor VF, Ward JE, Chen CY
The Science of the total environment (2019) 666:1316-1326 PMC6461384 10.1016/j.scitotenv.2019.02.302 - Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom.
Zhang Y, Lin X, Shi X, Lin L, Luo H, Li L, Lin S
Front Microbiol (2019) 10:590 (PMC6439486) 10.3389/fmicb.2019.00590 - Annual environmental variation influences host tolerance to parasites.
McNew SM, Knutie SA, Goodman GB, Theodosopoulos A, Saulsberry A, Yépez R J, Bush SE, Clayton DH
Proceedings. Biological sciences (2019) 286(1897):20190049 PMC6408884 10.1098/rspb.2019.0049 - The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy.
Newcomer RL, Schrad JR, Gilcrease EB, Casjens SR, Feig M, Teschke CM, Alexandrescu AT, Parent KN
eLife (2019) 8: PMC6449081 10.7554/eLife.45345 - CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors.
Sedlacek AL, Younker TP, Zhou YJ, Borghesi L, Shcheglova T, Mandoiu II, Binder RJ
JCI insight (2019) 4(7): PMC6483634 10.1172/jci.insight.127239 - Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21.
Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP
Microbiology resource announcements (2019) 8(12): PMC6430316 10.1128/MRA.00096-19 - Analysis of the antiparasitic and anticancer activity of the coconut palm (Cocos nucifera L. ARECACEAE) from the natural reserve of Punta Patiño, Darién.
Tayler NM, Boya CA, Herrera L, Moy J, Ng M, Pineda L, Almanza A, Rosero S, Coronado LM, Correa R, Santamaría R, Caballero Z, Durant-Archibold AA, Tidgewell KJ, Balunas MJ, Gerwick WH, Spadafora A, Gutiérrez M, Spadafora C
PloS one (2019) 14(4):e0214193 PMC6445518 10.1371/journal.pone.0214193 - Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents.
Hajian B, Scocchera E, Shoen C, Krucinska J, Viswanathan K, G-Dayanandan N, Erlandsen H, Estrada A, Mikušová K, Korduláková J, Cynamon M, Wright D
Cell chemical biology (2019) 26(6):781-791.e6 PMC6588435 10.1016/j.chembiol.2019.02.013 - Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A.
Duay SS, Sharma G, Prabhakar R, Angeles-Boza AM, May ER
The journal of physical chemistry. B (2019) 123(15):3163-3176 PMC6545919 10.1021/acs.jpcb.8b11496 - Inhibition of PGE/EP4 receptor signaling enhances oxaliplatin efficacy in resistant colon cancer cells through modulation of oxidative stress.
Huang H, Aladelokun O, Ideta T, Giardina C, Ellis LM, Rosenberg DW
Scientific reports (2019) 9(1):4954 PMC6427013 10.1038/s41598-019-40848-4 - The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.
Fullmer MS, Ouellette M, Louyakis AS, Papke RT, Gogarten JP
Genes (2019) 10(3): PMC6471742 10.3390/genes10030233 - Isolation of novel quorum-sensing active bacteria from microbial mats in Shark Bay Australia.
Charlesworth JC, Watters C, Wong HL, Visscher PT, Burns BP
FEMS microbiology ecology (2019) 95(4): 10.1093/femsec/fiz035 - Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System.
Lozano GL, Park HB, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman J
Applied and environmental microbiology (2019) 85(10): PMC6498172 10.1128/AEM.03058-18 - Spore Resistance to Simulated Mars Surface Conditions.
Cortesão M, Fuchs FM, Commichau FM, Eichenberger P, Schuerger AC, Nicholson WL, Setlow P, Moeller R
Frontiers in microbiology (2019) 10:333 PMC6399134 10.3389/fmicb.2019.00333 - Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic.
Barrett TC, Mok WWK, Murawski AM, Brynildsen MP
Nature communications (2019) 10(1):1177 PMC6414640 10.1038/s41467-019-09058-4 - The amazing HK97 fold: versatile results of modest differences.
Duda RL, Teschke CM
Current opinion in virology (2019) 36:9-16 PMC6626583 10.1016/j.coviro.2019.02.001 - Appreciating the Multiple Processes Increasing Individual or Population Fitness.
Edelaar P, Bolnick DI
Trends in ecology & evolution (2019) 34(5):435-446 10.1016/j.tree.2019.02.001 - Mitochondrial Genomics Reveals Shared Phylogeographic Patterns and Demographic History among Three Periodical Cicada Species Groups.
Du Z, Hasegawa H, Cooley JR, Simon C, Yoshimura J, Cai W, Sota T, Li H
Molecular biology and evolution (2019) 36(6):1187-1200 PMC6526903 10.1093/molbev/msz051 - Guild-level responses of bats to habitat conversion in a lowland Amazonian rainforest: species composition and biodiversity.
Willig MR, Presley SJ, Plante JL, Bloch CP, Solari S, Pacheco V, Weaver SC
Journal of mammalogy (2019) 100(1):223-238 PMC6394116 10.1093/jmammal/gyz023 - Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior.
Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J
MBio (2019) 10(2): (PMC6401489) 10.1128/mBio.02846-18 - Efficacy of plant-derived antimicrobials for controlling Salmonella Schwarzengrund on dry pet food.
Chen CH, Yin HB, Upadhayay A, Brown S, Venkitanarayanan K
International journal of food microbiology (2019) 296:1-7 10.1016/j.ijfoodmicro.2019.02.007 - Impacts of thermal mismatches on chytrid fungus Batrachochytrium dendrobatidis prevalence are moderated by life stage, body size, elevation and latitude.
Cohen JM, McMahon TA, Ramsay C, Roznik EA, Sauer EL, Bessler S, Civitello DJ, Delius BK, Halstead N, Knutie SA, Nguyen KH, Ortega N, Sears B, Venesky MD, Young S, Rohr JR
Ecology letters (2019) 22(5):817-825 10.1111/ele.13239 - Synthetic Polymers To Promote Cooperative Cu Activity for O Activation: Poly vs Mono.
Thanneeru S, Milazzo N, Lopes A, Wei Z, Angeles-Boza AM, He J
Journal of the American Chemical Society (2019) 141(10):4252-4256 10.1021/jacs.9b01093 - Conservation and Divergence of the I-Domain Inserted into the Ubiquitous HK97 Coat Protein Fold in P22-Like Bacteriophages.
Tripler TN, Kaplan AR, Alexandrescu AT, Teschke CM
Journal of virology (2019) 93(9): PMC6475800 10.1128/JVI.00007-19 - Architect of Virus Assembly: the Portal Protein Nucleates Procapsid Assembly in Bacteriophage P22.
Motwani T, Teschke CM
Journal of virology (2019) 93(9): PMC6475791 10.1128/JVI.00187-19 - Correction: A PRRSV GP5-Mosaic vaccine: Protection of pigs from challenge and ex vivo detection of IFNγ responses against several genotype 2 strains.
Cui J, O'Connell CM, Costa A, Pan Y, Smyth JA, Verardi PH, Burgess DJ, Van Kruiningen HJ, Garmendia AE
PloS one (2019) 14(2):e0213091 PMC6386357 10.1371/journal.pone.0213091 - Yoga as Antihypertensive Lifestyle Therapy: A Systematic Review and Meta-analysis.
Wu Y, Johnson BT, Acabchuk RL, Chen S, Lewis HK, Livingston J, Park CL, Pescatello LS
Mayo Clinic proceedings (2019) 94(3):432-446 10.1016/j.mayocp.2018.09.023 - Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria.
Bik HM, Alexiev A, Aulakh SK, Bharadwaj L, Flanagan J, Haggerty JM, Hird SM, Jospin G, Lang JM, Sauder LA, Neufeld JD, Shaver A, Sethi A, Eisen JA, Coil DA
mSphere (2019) 4(1): (PMC6382968) 10.1128/mSphere.00043-19 - Locality Sensitive Imputation for Single Cell RNA-Seq Data.
Moussa M, Măndoiu II
Journal of computational biology : a journal of computational molecular cell biology (2019) 26(8):822-835 PMC6703247 10.1089/cmb.2018.0236 - Analysis of the mRNAs in Spores of Bacillus subtilis.
Korza G, Camilleri E, Green J, Robinson J, Nagler K, Moeller R, Caimano MJ, Setlow P
J. Bacteriol. (2019) 201(9): (PMC6456856) 10.1128/JB.00007-19 - Evaluation of DESS as a storage medium for microbial community analysis.
Lee KM, Adams M, Klassen JL
PeerJ (2019) 7:e6414 PMC6368006 10.7717/peerj.6414 - Assessing Combinability of Phylogenomic Data Using Bayes Factors.
Neupane S, Fučíková K, Lewis LA, Kuo L, Chen MH, Lewis PO
Systematic biology (2019) 68(5):744-754 10.1093/sysbio/syz007 - YwqL (EndoV), ExoA and PolA act in a novel alternative excision pathway to repair deaminated DNA bases in Bacillus subtilis.
Patlán AG, Ayala-García VM, Valenzuela-García LI, Meneses-Plascencia J, Vargas-Arias PL, Barraza-Salas M, Setlow P, Brieba LG, Pedraza-Reyes M
PloS one (2019) 14(2):e0211653 PMC6364969 10.1371/journal.pone.0211653 - SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.
Kundu S, Bansal MS
Bioinformatics (Oxford, England) (2019) 35(18):3496-3498 10.1093/bioinformatics/btz081 - Structural and Functional Studies of Bacterial Enolase, a Potential Target against Gram-Negative Pathogens.
Krucinska J, Falcone E, Erlandsen H, Hazeen A, Lombardo MN, Estrada A, Robinson VL, Anderson AC, Wright DL
Biochemistry (2019) 58(9):1188-1197 PMC6511404 10.1021/acs.biochem.8b01298 - The antimicrobial potential of Streptomyces from insect microbiomes.
Chevrette MG, Carlson CM, Ortega HE, Thomas C, Ananiev GE, Barns KJ, Book AJ, Cagnazzo J, Carlos C, Flanigan W, Grubbs KJ, Horn HA, Hoffmann FM, Klassen JL, Knack JJ, Lewin GR, McDonald BR, Muller L, Melo WGP, Pinto-Tomás AA, Schmitz A, Wendt-Pienkowski E, Wildman S, Zhao M, Zhang F, Bugni TS, Andes DR, Pupo MT, Currie CR
Nature communications (2019) 10(1):516 PMC6355912 10.1038/s41467-019-08438-0 - Evaluation of INSeq To Identify Genes Essential for PGPR2 Corn Root Colonization.
Sivakumar R, Ranjani J, Vishnu US, Jayashree S, Lozano GL, Miles J, Broderick NA, Guan C, Gunasekaran P, Handelsman J, Rajendhran J
G3 (Bethesda, Md.) (2019) 9(3):651-661 PMC6404608 10.1534/g3.118.200928 - A PRRSV GP5-Mosaic vaccine: Protection of pigs from challenge and ex vivo detection of IFNγ responses against several genotype 2 strains.
Cui J, O'Connell CM, Costa A, Pan Y, Smyth JA, Verardi PH, Burgess DJ, Van Kruiningen HJ, Garmendia AE
PloS one (2019) 14(1):e0208801 PMC6354972 10.1371/journal.pone.0208801 - Gender inequalities among authors who contributed equally.
Broderick NA, Casadevall A
eLife (2019) 8: PMC6353592 10.7554/eLife.36399 - Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress.
Chelius CL, Ribeiro LFC, Huso W, Kumar J, Lincoln S, Tran B, Goo YA, Srivastava R, Harris SD, Marten MR
Fungal genetics and biology : FG & B (2019) 125:1-12 10.1016/j.fgb.2019.01.003 - Initial evidence of functional siRNA machinery in dinoflagellates.
Zhang C, Lin S
Harmful Algae (2019) 81:53-58 10.1016/j.hal.2018.11.014 - Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.
Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV
Proceedings of the National Academy of Sciences of the United States of America (2019) 116(8):3030-3035 PMC6386654 10.1073/pnas.1817322116 - Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.
Goldstein S, Beka L, Graf J, Klassen JL
BMC genomics (2019) 20(1):23 PMC6325685 10.1186/s12864-018-5381-7 - Tropolone-induced effects on the unfolded protein response pathway and apoptosis in multiple myeloma cells are dependent on iron.
Haney SL, Varney ML, Safranek HR, Chhonker YS, G-Dayanandan N, Talmon G, Murry DJ, Wiemer AJ, Wright DL, Holstein SA
Leukemia research (2019) 77:17-27 PMC6456044 10.1016/j.leukres.2018.12.007 - Post-Glycosylation Diversification (PGD): An Approach for Assembling Collections of Glycosylated Small Molecules.
Cannone Z, Shaqra AM, Lorenc C, Henowitz L, Keshipeddy S, Robinson VL, Zweifach A, Wright D, Peczuh MW
ACS combinatorial science (2019) 21(3):192-197 10.1021/acscombsci.8b00139 - Snake Fungal Disease in Colubridae Snakes in Connecticut, USA in 2015 and 2017.
Licitra D, Quinn DP, Reeder JE, Gavitt T, Dickson J, Hess B, Mangold BJ, Tuttle AD, Rosas-Rosas A, Frasca S, Szczepanek SM
Journal of wildlife diseases (2019) 55(3):658-662 10.7589/2018-04-100 - Herpes simplex virus 1 ICP8 mutant lacking annealing activity is deficient for viral DNA replication.
Weerasooriya S, DiScipio KA, Darwish AS, Bai P, Weller SK
Proceedings of the National Academy of Sciences of the United States of America (2019) 116(3):1033-1042 PMC6338833 10.1073/pnas.1817642116 2018
- One Hundred Mitochondrial Genomes of Cicadas.
Łukasik P, Chong RA, Nazario K, Matsuura Y, Bublitz AC, Campbell MA, Meyer MC, Van Leuven JT, Pessacq P, Veloso C, Simon C, McCutcheon JP
The Journal of heredity (2018) 110(2):247-256 PMC6784412 10.1093/jhered/esy068 - Contemporaneous radiations of fungi and plants linked to symbiosis.
Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S
Nat Commun (2018) 9(1):5451 (PMC6303338) 10.1038/s41467-018-07849-9 - Reports from a Healthy Community: The 7th Conference on Beneficial Microbes.
Mandel MJ, Broderick NA, Martens EC, Guillemin K
Appl. Environ. Microbiol. (2018) : (PMC6498156) 10.1128/AEM.02562-18 - Immunologic Pathways in Protective versus Maladaptive Host Responses to Attenuated and Pathogenic Strains of Mycoplasma gallisepticum.
Beaudet J, Tulman ER, Pflaum K, Canter JA, Silbart LK, Geary SJ
Infection and immunity (2018) 87(3): PMC6386537 10.1128/IAI.00613-18 - Enteropathogenic E. coli relies on collaboration between the formin mDia1 and the Arp2/3 complex for actin pedestal biogenesis and maintenance.
Velle KB, Campellone KG
PLoS Pathog. (2018) 14(12):e1007485 (PMC6310289) 10.1371/journal.ppat.1007485 - High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.
Kopac S, Beatty H, Gialopsos P, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Ng V, Ivanova N, Kyrpides N, Woyke T, Klassen JL
Microbiol Resour Announc (2018) 7(2): (PMC6211366) 10.1128/MRA.00871-18 - Single-cell analysis reveals individual spore responses to simulated space vacuum.
He L, Wang S, Cortesão M, Wu M, Moeller R, Setlow P, Li YQ
NPJ Microgravity (2018) 4:26 (PMC6279783) 10.1038/s41526-018-0059-7 - The Costs of Living Together: Immune Responses to the Microbiota and Chronic Gut Inflammation.
Kirschman LJ, Milligan-Myhre KC
Applied and environmental microbiology (2018) 85(10): PMC3667473 10.1111/1365-2656.12973 - Isolation of an algicidal bacterium and its effects against the harmful-algal- bloom dinoflagellate Prorocentrum donghaiense (Dinophyceae).
Shi X, Liu L, Li Y, Xiao Y, Ding G, Lin S, Chen J
Harmful Algae (2018) 80:72-79 10.1016/j.hal.2018.09.003 - Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.
Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G, Nielsen R
Mol. Biol. Evol. (2018) 35(12):2913-2927 (PMC6278860) 10.1093/molbev/msy185 - Experimental studies addressing the longevity of Bacillus subtilis spores - The first data from a 500-year experiment.
Ulrich N, Nagler K, Laue M, Cockell CS, Setlow P, Moeller R
PLoS ONE (2018) 13(12):e0208425 (PMC6279046) 10.1371/journal.pone.0208425 - Dosage Compensation and Gene Expression of the X Chromosome in Sheep.
Duan JE, Flock K, Jue N, Zhang M, Jones A, Seesi SA, Mandoiu I, Pillai S, Hoffman M, O'Neill R, Zinn S, Govoni K, Reed S, Jiang H, Jiang ZC, Tian XC
G3 (Bethesda) (2018) 9(1):305-314 (PMC6325915) 10.1534/g3.118.200815 - Viral Proteins U41 and U70 of Human Herpesvirus 6A Are Dispensable for Telomere Integration.
Wight DJ, Wallaschek N, Sanyal A, Weller SK, Flamand L, Kaufer BB
Viruses (2018) 10(11): (PMC6267051) 10.3390/v10110656 - Genome size-dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism.
Hou Y, Ji N, Zhang H, Shi X, Han H, Lin S
J. Phycol. (2018) 55(1):37-46 10.1111/jpy.12815 - "Her Joyous Enthusiasm for Her Life-Work …": Early Women Authors in The American Naturalist.
Bronstein JL, Bolnick DI
Am. Nat. (2018) 192(6):655-663 10.1086/700119 - Changes in Endosymbiont Complexity Drive Host-Level Compensatory Adaptations in Cicadas.
Campbell MA, Łukasik P, Meyer MC, Buckner M, Simon C, Veloso C, Michalik A, McCutcheon JP
MBio (2018) 9(6): (PMC6234865) 10.1128/mBio.02104-18 - Direct oxygen isotope effect identifies the rate-determining step of electrocatalytic OER at an oxidic surface.
Haschke S, Mader M, Schlicht S, Roberts AM, Angeles-Boza AM, Barth JAC, Bachmann J
Nat Commun (2018) 9(1):4565 (PMC6212532) 10.1038/s41467-018-07031-1 - Might hyperbaric oxygen therapy (HBOT) reduce renal injury in diabetic people with diabetes mellitus? From preclinical models to human metabolomics.
Harrison LE, Giardina C, Hightower LE, Anderson C, Perdrizet GA
Cell Stress Chaperones (2018) 23(6):1143-1152 (PMC6237687) 10.1007/s12192-018-0944-8 - CircMarker: a fast and accurate algorithm for circular RNA detection.
Li X, Chu C, Pei J, Măndoiu I, Wu Y
BMC Genomics (2018) 19(Suppl 6):572 (PMC6101086) 10.1186/s12864-018-4926-0 - Single cell RNA-seq data clustering using TF-IDF based methods.
Moussa M, Măndoiu II
BMC Genomics (2018) 19(Suppl 6):569 (PMC6101073) 10.1186/s12864-018-4922-4 - On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.
Kundu S, Bansal MS
BMC Bioinformatics (2018) 19(Suppl 9):290 (PMC6101088) 10.1186/s12859-018-2269-0 - An improved approach for reconstructing consensus repeats from short sequence reads.
Chu C, Pei J, Wu Y
BMC Genomics (2018) 19(Suppl 6):566 (PMC6101065) 10.1186/s12864-018-4920-6 - The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.
Hird SM, Ganz H, Eisen JA, Boyce WM
mSphere (2018) 3(5): (PMC6200988) 10.1128/mSphere.00382-18 - A dysbiotic microbiome triggers T17 cells to mediate oral mucosal immunopathology in mice and humans.
Dutzan N, Kajikawa T, Abusleme L, Greenwell-Wild T, Zuazo CE, Ikeuchi T, Brenchley L, Abe T, Hurabielle C, Martin D, Morell RJ, Freeman AF, Lazarevic V, Trinchieri G, Diaz PI, Holland SM, Belkaid Y, Hajishengallis G, Moutsopoulos NM
Sci Transl Med (2018) 10(463): (PMC6330016) 10.1126/scitranslmed.aat0797 - Antibiotic-Resistant in the Food Supply and the Potential Role of Antibiotic Alternatives for Control.
V T Nair D, Venkitanarayanan K, Kollanoor Johny A
Foods (2018) 7(10): (PMC6210005) 10.3390/foods7100167 - A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and subfamily classification.
Marshall DC, Moulds M, Hill KBR, Price BW, Wade EJ, Owen CL, Goemans G, Marathe K, Sarkar V, Cooley JR, Sanborn AF, Kunte K, Villet MH, Simon C
Zootaxa (2018) 4424(1):1-64 10.11646/zootaxa.4424.1.1 - Identification and Expression Analysis of an Atypical Alkaline Phosphatase in .
Li T, Guo C, Zhang Y, Wang C, Lin X, Lin S
Front Microbiol (2018) 9:2156 (PMC6156274) 10.3389/fmicb.2018.02156 - Triplicate parallel life cycle divergence despite gene flow in periodical cicadas.
Fujisawa T, Koyama T, Kakishima S, Cooley JR, Simon C, Yoshimura J, Sota T
Commun Biol (2018) 1:26 (PMC6123741) 10.1038/s42003-018-0025-7 - Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006.
Corral P, de la Haba RR, Infante-Domínguez C, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A
Int. J. Syst. Evol. Microbiol. (2018) 68(11):3657-3665 10.1099/ijsem.0.003005 - Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis.
Abusleme L, Diaz PI, Freeman AF, Greenwell-Wild T, Brenchley L, Desai JV, Ng WI, Holland SM, Lionakis MS, Segre JA, Kong HH, Moutsopoulos NM
JCI Insight (2018) 3(17): (PMC6171814) 10.1172/jci.insight.122061 - Variable Lipoprotein Hemagglutinin A Gene () Expression in Variant Mycoplasma gallisepticum Strains .
Pflaum K, Tulman ER, Beaudet J, Canter J, Geary SJ
Infect. Immun. (2018) 86(11): (PMC6204691) 10.1128/IAI.00524-18 - Acute microplastic exposure raises stress response and suppresses detoxification and immune capacities in the scleractinian coral Pocillopora damicornis.
Tang J, Ni X, Zhou Z, Wang L, Lin S
Environ. Pollut. (2018) 243(Pt A):66-74 10.1016/j.envpol.2018.08.045 - Role of glutamine synthetase in angiogenesis beyond glutamine synthesis.
Eelen G, Dubois C, Cantelmo AR, Goveia J, Brüning U, DeRan M, Jarugumilli G, van Rijssel J, Saladino G, Comitani F, Zecchin A, Rocha S, Chen R, Huang H, Vandekeere S, Kalucka J, Lange C, Morales-Rodriguez F, Cruys B, Treps L, Ramer L, Vinckier S, Brepoels K, Wyns S, Souffreau J, Schoonjans L, Lamers WH, Wu Y, Haustraete J, Hofkens J, Liekens S, Cubbon R, Ghesquière B, Dewerchin M, Gervasio FL, Li X, van Buul JD, Wu X, Carmeliet P
Nature (2018) 561(7721):63-69 10.1038/s41586-018-0466-7 - Field-Based Evidence for Microplastic in Marine Aggregates and Mussels: Implications for Trophic Transfer.
Zhao S, Ward JE, Danley M, Mincer TJ
Environ. Sci. Technol. (2018) 52(19):11038-11048 10.1021/acs.est.8b03467 - Distinct systemic microbiome and microbial translocation are associated with plasma level of anti-CD4 autoantibody in HIV infection.
Xu W, Luo Z, Alekseyenko AV, Martin L, Wan Z, Ling B, Qin Z, Heath SL, Maas K, Cong X, Jiang W
Sci Rep (2018) 8(1):12863 (PMC6110826) 10.1038/s41598-018-31116-y - BioTIME: A database of biodiversity time series for the Anthropocene.
Dornelas M, Antão LH, Moyes F, Bates AE, Magurran AE, Adam D, Akhmetzhanova AA, Appeltans W, Arcos JM, Arnold H, Ayyappan N, Badihi G, Baird AH, Barbosa M, Barreto TE, Bässler C, Bellgrove A, Belmaker J, Benedetti-Cecchi L, Bett BJ, Bjorkman AD, Błażewicz M, Blowes SA, Bloch CP, Bonebrake TC, Boyd S, Bradford M, Brooks AJ, Brown JH, Bruelheide H, Budy P, Carvalho F, Castañeda-Moya E, Chen CA, Chamblee JF, Chase TJ, Siegwart Collier L, Collinge SK, Condit R, Cooper EJ, Cornelissen JHC, Cotano U, Kyle Crow S, Damasceno G, Davies CH, Davis RA, Day FP, Degraer S, Doherty TS, Dunn TE, Durigan G, Duffy JE, Edelist D, Edgar GJ, Elahi R, Elmendorf SC, Enemar A, Ernest SKM, Escribano R, Estiarte M, Evans BS, Fan TY, Turini Farah F, Loureiro Fernandes L, Farneda FZ, Fidelis A, Fitt R, Fosaa AM, Daher Correa Franco GA, Frank GE, Fraser WR, García H, Cazzolla Gatti R, Givan O, Gorgone-Barbosa E, Gould WA, Gries C, Grossman GD, Gutierréz JR, Hale S, Harmon ME, Harte J, Haskins G, Henshaw DL, Hermanutz L, Hidalgo P, Higuchi P, Hoey A, Van Hoey G, Hofgaard A, Holeck K, Hollister RD, Holmes R, Hoogenboom M, Hsieh CH, Hubbell SP, Huettmann F, Huffard CL, Hurlbert AH, Macedo Ivanauskas N, Janík D, Jandt U, Jażdżewska A, Johannessen T, Johnstone J, Jones J, Jones FAM, Kang J, Kartawijaya T, Keeley EC, Kelt DA, Kinnear R, Klanderud K, Knutsen H, Koenig CC, Kortz AR, Král K, Kuhnz LA, Kuo CY, Kushner DJ, Laguionie-Marchais C, Lancaster LT, Min Lee C, Lefcheck JS, Lévesque E, Lightfoot D, Lloret F, Lloyd JD, López-Baucells A, Louzao M, Madin JS, Magnússon B, Malamud S, Matthews I, McFarland KP, McGill B, McKnight D, McLarney WO, Meador J, Meserve PL, Metcalfe DJ, Meyer CFJ, Michelsen A, Milchakova N, Moens T, Moland E, Moore J, Mathias Moreira C, Müller J, Murphy G, Myers-Smith IH, Myster RW, Naumov A, Neat F, Nelson JA, Paul Nelson M, Newton SF, Norden N, Oliver JC, Olsen EM, Onipchenko VG, Pabis K, Pabst RJ, Paquette A, Pardede S, Paterson DM, Pélissier R, Peñuelas J, Pérez-Matus A, Pizarro O, Pomati F, Post E, Prins HHT, Priscu JC, Provoost P, Prudic KL, Pulliainen E, Ramesh BR, Mendivil Ramos O, Rassweiler A, Rebelo JE, Reed DC, Reich PB, Remillard SM, Richardson AJ, Richardson JP, van Rijn I, Rocha R, Rivera-Monroy VH, Rixen C, Robinson KP, Ribeiro Rodrigues R, de Cerqueira Rossa-Feres D, Rudstam L, Ruhl H, Ruz CS, Sampaio EM, Rybicki N, Rypel A, Sal S, Salgado B, Santos FAM, Savassi-Coutinho AP, Scanga S, Schmidt J, Schooley R, Setiawan F, Shao KT, Shaver GR, Sherman S, Sherry TW, Siciński J, Sievers C, da Silva AC, Rodrigues da Silva F, Silveira FL, Slingsby J, Smart T, Snell SJ, Soudzilovskaia NA, Souza GBG, Maluf Souza F, Castro Souza V, Stallings CD, Stanforth R, Stanley EH, Mauro Sterza J, Stevens M, Stuart-Smith R, Rondon Suarez Y, Supp S, Yoshio Tamashiro J, Tarigan S, Thiede GP, Thorn S, Tolvanen A, Teresa Zugliani Toniato M, Totland Ø, Twilley RR, Vaitkus G, Valdivia N, Vallejo MI, Valone TJ, Van Colen C, Vanaverbeke J, Venturoli F, Verheye HM, Vianna M, Vieira RP, Vrška T, Quang Vu C, Van Vu L, Waide RB, Waldock C, Watts D, Webb S, Wesołowski T, White EP, Widdicombe CE, Wilgers D, Williams R, Williams SB, Williamson M, Willig MR, Willis TJ, Wipf S, Woods KD, Woehler EJ, Zawada K, Zettler ML, Hickler T
Glob. Ecol. Biogeogr. (2018) 27(7):760-786 (PMC6099392) 10.1111/geb.12729 - Phagosomal Copper-Promoted Oxidative Attack on Intracellular Mycobacterium tuberculosis.
Libardo MDJ, de la Fuente-Nuñez C, Anand K, Krishnamoorthy G, Kaiser P, Pringle SC, Dietz C, Pierce S, Smith MB, Barczak A, Kaufmann SHE, Singh A, Angeles-Boza AM
ACS Infect Dis (2018) 4(11):1623-1634 10.1021/acsinfecdis.8b00171 - NMR assignments for monomeric phage L decoration protein.
Newcomer RL, Belato HB, Teschke CM, Alexandrescu AT
Biomol NMR Assign (2018) 12(2):339-343 (PMC6374774) 10.1007/s12104-018-9836-1 - Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads.
Talagrand-Reboul E, Latif-Eugenín F, Beaz-Hidalgo R, Colston S, Figueras MJ, Graf J, Jumas-Bilak E, Lamy B
PLoS ONE (2018) 13(8):e0201428 (PMC6093642) 10.1371/journal.pone.0201428 - Observations on research with spores of Bacillales and Clostridiales species.
Setlow P
Journal of applied microbiology (2018) 126(2):348-358 PMC6329651 10.1111/jam.14067 - The periodical cicada four-year acceleration hypothesis revisited and the polyphyletic nature of Brood V, including an updated crowd-source enhanced map (Hemiptera: Cicadidae: ).
Cooley JR, Arguedas N, Bonaros E, Bunker G, Chiswell SM, DeGiovine A, Edwards M, Hassanieh D, Haji D, Knox J, Kritsky G, Mills C, Mozgai D, Troutman R, Zyla J, Hasegawa H, Sota T, Yoshimura J, Simon C
PeerJ (2018) 6:e5282 (PMC6074776) 10.7717/peerj.5282 - Opsin expression predicts male nuptial color in threespine stickleback.
Brock CD, Rennison D, Veen T, Bolnick DI
Ecol Evol (2018) 8(14):7094-7102 (PMC6065272) 10.1002/ece3.4231 - Intracellular membranes of bacterial endospores are reservoirs for spore core membrane expansion during spore germination.
Laue M, Han HM, Dittmann C, Setlow P
Sci Rep (2018) 8(1):11388 (PMC6065386) 10.1038/s41598-018-29879-5 - Altered secretion patterns and cell wall organization caused by loss of PodB function in the filamentous fungus Aspergillus nidulans.
Boppidi KR, Ribeiro LFC, Iambamrung S, Nelson SM, Wang Y, Momany M, Richardson EA, Lincoln S, Srivastava R, Harris SD, Marten MR
Sci Rep (2018) 8(1):11433 (PMC6065416) 10.1038/s41598-018-29615-z - Comparative toxicity of Corexit 9500, oil, and a Corexit/oil mixture on the eastern oyster, Crassostrea virginica (Gmelin).
Jasperse L, Levin M, Tsantiris K, Smolowitz R, Perkins C, Ward JE, De Guise S
Aquat. Toxicol. (2018) 203:10-18 10.1016/j.aquatox.2018.07.015 - Role of DNA Repair and Protective Components in Bacillus subtilis Spore Resistance to Inactivation by 400-nm-Wavelength Blue Light.
Djouiai B, Thwaite JE, Laws TR, Commichau FM, Setlow B, Setlow P, Moeller R
Appl. Environ. Microbiol. (2018) 84(19): (PMC6147000) 10.1128/AEM.01604-18 - Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses.
Duan JE, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian XC
Epigenetics (2018) 13(8):793-807 (PMC6224220) 10.1080/15592294.2018.1503489 - Defining microbiome function.
Klassen JL
Nat Microbiol (2018) 3(8):864-869 10.1038/s41564-018-0189-4 - Microbiome Analyses for Toxicological Studies.
Benjamino J, Beka L, Graf J
Curr Protoc Toxicol (2018) :e53 10.1002/cptx.53 - Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients.
Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J
MBio (2018) 9(4): (PMC6058295) 10.1128/mBio.01328-18 - CD11c MHCII GM-CSF-bone marrow-derived dendritic cells act as antigen donor cells and as antigen presenting cells in neoepitope-elicited tumor immunity against a mouse fibrosarcoma.
Ebrahimi-Nik H, Corwin WL, Shcheglova T, Das Mohapatra A, Mandoiu II, Srivastava PK
Cancer Immunol. Immunother. (2018) 67(9):1449-1459 (PMC6132860) 10.1007/s00262-018-2202-4 - Metallothionein: A Novel Therapeutic Target for Treatment of Inflammatory Bowel Disease.
Dostie KE, Thees AV, Lynes MA
Curr. Pharm. Des. (2018) 24(27):3155-3161 10.2174/1381612824666180717110236 - An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.
Li L, Bansal MS
IEEE/ACM transactions on computational biology and bioinformatics (2018) 16(1):63-76 10.1109/TCBB.2018.2846253 - Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes.
Wong HL, White RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP
ISME J (2018) 12(11):2619-2639 (PMC6194083) 10.1038/s41396-018-0208-8 - Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma.
Adami AJ, Bracken SJ, Guernsey LA, Rafti E, Maas KR, Graf J, Matson AP, Thrall RS, Schramm CM
Pediatr. Res. (2018) 84(3):426-434 (PMC6258300) 10.1038/s41390-018-0031-y - Effect of modified atmosphere packaging on the growth of spoilage microorganisms and Listeria monocytogenes on fresh cheese.
Brown SRB, Forauer EC, D'Amico DJ
J. Dairy Sci. (2018) 101(9):7768-7779 10.3168/jds.2017-14217 - Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire.
Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S
ISME J (2018) 12(10):2559-2574 (PMC6154966) 10.1038/s41396-018-0166-1 - Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis.
Lindberg TP, Caimano MJ, Hagadorn JI, Bennett EM, Maas K, Brownell EA, Matson AP
The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians (2018) 33(3):349-358 10.1080/14767058.2018.1490719 - Morphology and molecular phylogeny of epizoic araphid diatoms on marine zooplankton, including Pseudofalcula hyalina gen. & comb. nov. (Fragilariophyceae, Bacillariophyta).
Gómez F, Wang L, Lin S
J. Phycol. (2018) 54(4):557-570 10.1111/jpy.12760 - Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of subsp. , the Syphilis Spirochete.
Kumar S, Caimano MJ, Anand A, Dey A, Hawley KL, LeDoyt ME, La Vake CJ, Cruz AR, Ramirez LG, Paštěková L, Bezsonova I, Šmajs D, Salazar JC, Radolf JD
MBio (2018) 9(3): (PMC6016234) 10.1128/mBio.01006-18 - Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.
Méheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E
Genome Biol. (2018) 19(1):75 (PMC5992828) 10.1186/s13059-018-1454-9 - Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes.
Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S
ISME J (2018) 12(9):2198-2210 (PMC6092436) 10.1038/s41396-018-0153-6 - The C-terminus of the oncoprotein TGAT is necessary for plasma membrane association and efficient RhoA-mediated signaling.
van Unen J, Botman D, Yin T, Wu YI, Hink MA, Gadella TWJ, Postma M, Goedhart J
BMC Cell Biol. (2018) 19(1):6 (PMC5992656) 10.1186/s12860-018-0155-2 - -Cinnamaldehyde and Eugenol Increase Sensitivity to Beta-Lactam Antibiotics.
Karumathil DP, Nair MS, Gaffney J, Kollanoor-Johny A, Venkitanarayanan K
Front Microbiol (2018) 9:1011 (PMC5974060) 10.3389/fmicb.2018.01011 - Geographical variation in colour of female threespine stickleback ().
French CM, Ingram T, Bolnick DI
PeerJ (2018) 6:e4807 (PMC5960269) 10.7717/peerj.4807 - Circadian and irradiance effects on expression of antenna protein genes and pigment contents in dinoflagellate Prorocentrum donghaiense (Dinophycae).
Shi X, Li L, Lin S
Harmful Algae (2018) 75:27-34 10.1016/j.hal.2018.04.002 - Lessons from bacteriophages part 2: A saga of scientific breakthroughs and prospects for their use in human health.
Asija K, Teschke CM
PLoS Pathog. (2018) 14(5):e1006970 (PMC5957327) 10.1371/journal.ppat.1006970 - Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution.
Asija K, Teschke CM
PLoS Pathog. (2018) 14(5):e1006971 (PMC5957328) 10.1371/journal.ppat.1006971 - Spindle Assembly Disruption and Cancer Cell Apoptosis with a CLTC-Binding Compound.
Bond MJ, Bleiler M, Harrison LE, Scocchera EW, Nakanishi M, G-Dayanan N, Keshipeddy S, Rosenberg DW, Wright DL, Giardina C
Mol. Cancer Res. (2018) 16(9):1361-1372 (PMC6125173) 10.1158/1541-7786.MCR-18-0178 - RecPhyloXML: a format for reconciled gene trees.
Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V
Bioinformatics (2018) 34(21):3646-3652 (PMC6198865) 10.1093/bioinformatics/bty389 - Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration.
Benjamino J, Lincoln S, Srivastava R, Graf J
Microbiome (2018) 6(1):86 (PMC5944116) 10.1186/s40168-018-0469-5 - Inhibition and Inactivation of Escherichia coli O157:H7 Biofilms by Selenium.
Nair MS, Upadhyay A, Fancher S, Upadhyaya I, Dey S, Kollanoor-Johny A, Zhao J, Venkitanarayanan K
J. Food Prot. (2018) 81(6):926-933 10.4315/0362-028X.JFP-17-427 - Age-related changes in the gut microbiota influence systemic inflammation and stroke outcome.
Spychala MS, Venna VR, Jandzinski M, Doran SJ, Durgan DJ, Ganesh BP, Ajami NJ, Putluri N, Graf J, Bryan RM, McCullough LD
Ann. Neurol. (2018) 84(1):23-36 (PMC6119509) 10.1002/ana.25250 - Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life.
McManus HA, Fučíková K, Lewis PO, Lewis LA, Karol KG
Am. J. Bot. (2018) 105(3):315-329 10.1002/ajb2.1066 - Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Li H, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R
Nat Commun (2018) 9(1):1811 (PMC5931568) 10.1038/s41467-018-04260-2 - RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.
Bansal MS, Kellis M, Kordi M, Kundu S
Bioinformatics (2018) 34(18):3214-3216 (PMC6137995) 10.1093/bioinformatics/bty314 - Influenza Vaccination Protects Against Pandemic H1N1 Infection in Sickle Cell Disease Mice.
Roberts S, Metzger DW, Szczepanek SM
Viral Immunol. (2018) 31(6):470-471 10.1089/vim.2018.0024 - Systematic analysis of complex genetic interactions.
Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL
Science (2018) 360(6386): (PMC6215713) 10.1126/science.aao1729 - Electrocardiographic effects of hawthorn (Crataegus oxyacantha) in healthy volunteers: A randomized controlled trial.
Trexler SE, Nguyen E, Gromek SM, Balunas MJ, Baker WL
Phytother Res (2018) 32(8):1642-1646 10.1002/ptr.6094 - Reconciling biodiversity and carbon stock conservation in an Afrotropical forest landscape.
Van de Perre F, Willig MR, Presley SJ, Bapeamoni Andemwana F, Beeckman H, Boeckx P, Cooleman S, de Haan M, De Kesel A, Dessein S, Grootaert P, Huygens D, Janssens SB, Kearsley E, Kabeya PM, Leponce M, Van den Broeck D, Verbeeck H, Würsten B, Leirs H, Verheyen E
Sci Adv (2018) 4(3):eaar6603 (PMC5903881) 10.1126/sciadv.aar6603 - Propagating annotations of molecular networks using in silico fragmentation.
da Silva RR, Wang M, Nothias LF, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, Dorrestein PC
PLoS Comput. Biol. (2018) 14(4):e1006089 (PMC5927460) 10.1371/journal.pcbi.1006089 - CLADES: A classification-based machine learning method for species delimitation from population genetic data.
Pei J, Chu C, Li X, Lu B, Wu Y
Mol Ecol Resour (2018) : 10.1111/1755-0998.12887 - Genotypic and Lipid Analyses of Strains From the Archaeal Genus Reveal Insights Into Their Taxonomy, Divergence, and Population Structure.
de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT
Front Microbiol (2018) 9:512 (PMC5890160) 10.3389/fmicb.2018.00512 - Morphology and Molecular Phylogeny of Peritrich Ciliate Epibionts on Pelagic Diatoms: Vorticella oceanica and Pseudovorticella coscinodisci sp. nov. (Ciliophora, Peritrichia).
Gómez F, Wang L, Lin S
Protist (2018) 169(2):268-279 10.1016/j.protis.2018.03.003 - Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474, Isolated from a Cavern Brook in the Moravia Region of the Czech Republic.
Colston SM, Navarro A, Martinez-Murcia AJ, Graf J
Genome Announc (2018) 6(15): (PMC5897817) 10.1128/genomeA.00227-18 - Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905, Isolated from a Hot Spring in Vila-Real, Portugal.
Colston SM, Navarro A, Martinez-Murcia AJ, Graf J
Genome Announc (2018) 6(15): (PMC5897795) 10.1128/genomeA.00226-18 - Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Li H, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R
Nat Commun (2018) 9(1):1341 (PMC5890265) 10.1038/s41467-018-03724-9 - Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of from Oahu, Hawaii.
Kerwin AH, Nyholm SV
mSphere (2018) 3(2): (PMC5874440) 10.1128/mSphere.00531-17 - Formation of stromatolite lamina at the interface of oxygenic-anoxygenic photosynthesis.
Pace A, Bourillot R, Bouton A, Vennin E, Braissant O, Dupraz C, Duteil T, Bundeleva I, Patrier P, Galaup S, Yokoyama Y, Franceschi M, Virgone A, Visscher PT
Geobiology (2018) 16(4):378-398 10.1111/gbi.12281 - Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.
Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U
Genes (Basel) (2018) 9(3): (PMC5867893) 10.3390/genes9030172 - Transcriptional coupling (Mfd) and DNA damage scanning (DisA) coordinate excision repair events for efficient Bacillus subtilis spore outgrowth.
Valenzuela-García LI, Ayala-García VM, Regalado-García AG, Setlow P, Pedraza-Reyes M
Microbiologyopen (2018) 7(5):e00593 (PMC6182552) 10.1002/mbo3.593 - Actin dynamics and function.
Gupton SL, Campellone KG
Mol. Biol. Cell (2018) 29(6):696-697 (PMC6003229) 10.1091/mbc.E18-01-0010 - Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass.
Smith DL, Kerns JP, Walker NR, Payne AF, Horvath B, Inguagiato JC, Kaminski JE, Tomaso-Peterson M, Koch PL
PLoS ONE (2018) 13(3):e0194216 (PMC5844563) 10.1371/journal.pone.0194216 - Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.
Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT
Genes (Basel) (2018) 9(3): (PMC5867850) 10.3390/genes9030129 - Acute exposure to TiO nanoparticles produces minimal apparent effects on oyster, Crassostrea virginica (Gmelin), hemocytes.
Doyle JJ, Ward JE, Wikfors GH
Mar. Pollut. Bull. (2018) 127:512-523 10.1016/j.marpolbul.2017.12.039 - Combination of multilocus sequence typing and pulsed-field gel electrophoresis reveals an association of molecular clonality with the emergence of extensive-drug resistance (XDR) in Salmonella.
Cao Y, Shen Y, Cheng L, Zhang X, Wang C, Wang Y, Zhou X, Chao G, Wu Y
Microbiol. Res. (2018) 207:170-176 10.1016/j.micres.2017.12.001 - Draft Genome Sequence of DUP 13076, Which Exhibits Potent Antipathogenic Effects against Serovars Enteritidis, Typhimurium, and Heidelberg.
Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA
Genome Announc (2018) 6(7): (PMC5814482) 10.1128/genomeA.00065-18 - Draft Genome Sequence of NRRL B-442, a Potential Probiotic Strain.
Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA
Genome Announc (2018) 6(7): (PMC5814505) 10.1128/genomeA.00046-18 - Deposition of Bacteria and Bacterial Spores by Bathroom Hot-Air Hand Dryers.
Huesca-Espitia LDC, Aslanzadeh J, Feinn R, Joseph G, Murray TS, Setlow P
Appl. Environ. Microbiol. (2018) 84(8): (PMC5881072) 10.1128/AEM.00044-18 - Effects of lowering water activity by various humectants on germination of spores of Bacillus species with different germinants.
Rao L, Feeherry FE, Ghosh S, Liao X, Lin X, Zhang P, Li Y, Doona CJ, Setlow P
Food Microbiol. (2018) 72:112-127 10.1016/j.fm.2017.11.012 - Role of membrane-tension gated Ca flux in cell mechanosensation.
He L, Tao J, Maity D, Si F, Wu Y, Wu T, Prasath V, Wirtz D, Sun SX
J. Cell. Sci. (2018) 131(4): (PMC5868948) 10.1242/jcs.208470 - Metatranscriptome analysis reveals environmental and diel regulation of a Heterosigma akashiwo (raphidophyceae) bloom.
Ji N, Lin L, Li L, Yu L, Zhang Y, Luo H, Li M, Shi X, Wang DZ, Lin S
Environ. Microbiol. (2018) 20(3):1078-1094 10.1111/1462-2920.14045 - Oral Microbiome Characterization in Murine Models.
Abusleme L, Hong BY, Hoare A, Konkel JE, Diaz PI, Moutsopoulos NM
Bio Protoc (2018) 7(24): (PMC5760993) - Germination, Outgrowth, and Vegetative-Growth Kinetics of Dry-Heat-Treated Individual Spores of Bacillus Species.
He L, Chen Z, Wang S, Wu M, Setlow P, Li YQ
Appl. Environ. Microbiol. (2018) 84(7): (PMC5861817) 10.1128/AEM.02618-17 - Chemotherapy-induced oral mucositis and associated infections in a novel organotypic model.
Sobue T, Bertolini M, Thompson A, Peterson DE, Diaz PI, Dongari-Bagtzoglou A
Mol Oral Microbiol (2018) 33(3):212-223 (PMC5945319) 10.1111/omi.12214 - Glyphosate Shapes a Dinoflagellate-Associated Bacterial Community While Supporting Algal Growth as Sole Phosphorus Source.
Wang C, Lin X, Li L, Lin L, Lin S
Front Microbiol (2018) 8:2530 (PMC5742145) 10.3389/fmicb.2017.02530 2017
- Psychological well-being, dental esthetics, and psychosocial impacts in adolescent orthodontic patients: A prospective longitudinal study.
Deng X, Wang YJ, Deng F, Liu PL, Wu Y
Am J Orthod Dentofacial Orthop (2017) 153(1):87-96.e2 10.1016/j.ajodo.2017.05.028 - Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.
Łukasik P, Nazario K, Van Leuven JT, Campbell MA, Meyer M, Michalik A, Pessacq P, Simon C, Veloso C, McCutcheon JP
Proc. Natl. Acad. Sci. U.S.A. (2017) 115(2):E226-E235 (PMC5777040) 10.1073/pnas.1712321115 - Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis.
Van Dyke TE, Diaz PI, Moutsopoulos N, Alekseyenko AV, Ioannidou E
JDR Clin Trans Res (2017) 3(1):6-9 (PMC5734462) 10.1177/2380084417728488 - Control of Listeria monocytogenes in whole milk using antimicrobials applied individually and in combination.
Kozak SM, Brown SRB, Bobak Y, D'Amico DJ
J. Dairy Sci. (2017) 101(3):1889-1900 10.3168/jds.2017-13648 - Acidification of Model Cheese Brines To Control Listeria monocytogenes.
Brown SRB, Millán-Borrero NC, Carbonella JC, Micheletti AJP, D'Amico DJ
J. Food Prot. (2017) 81(1):79-83 10.4315/0362-028X.JFP-17-325 - Peptide Uptake Is Essential for Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter.
Groshong AM, Dey A, Bezsonova I, Caimano MJ, Radolf JD
MBio (2017) 8(6): (PMC5736914) - Analysis of killing of growing cells and dormant and germinated spores of Bacillus species by black silicon nanopillars.
Ghosh S, Niu S, Yankova M, Mecklenburg M, King SM, Ravichandran J, Kalia RK, Nakano A, Vashishta P, Setlow P
Sci Rep (2017) 7(1):17768 (PMC5736721) - Efficacy of Antimicrobials Applied Individually and in Combination for Controlling Listeria monocytogenes as Surface Contaminants on Queso Fresco.
Kozak SM, Bobak Y, D'Amico DJ
J. Food Prot. (2017) 81(1):46-53 10.4315/0362-028X.JFP-17-279 - Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England.
Tucker SJ, McManus GB, Katz LA, Grattepanche JD
Front Microbiol (2017) 8:2178 (PMC5715329) - Letter from the Editor.
Bolnick DI
Am. Nat. (2017) 191(1):iii-v 10.1086/694918 - High-mobility-group protein 2 regulated by microRNA-127 and small heterodimer partner modulates pluripotency of mouse embryonic stem cells and liver tumor initiating cells.
Zhao Y, Yang Z, Wu J, Wu R, Keshipeddy SK, Wright D, Wang L
Hepatol Commun (2017) 1(8):816-830 (PMC5678910) 10.1002/hep4.1086 - Optogenetic activation of EphB2 receptor in dendrites induced actin polymerization by activating Arg kinase.
Locke C, Machida K, Wu Y, Yu J
Biol Open (2017) 6(12):1820-1830 (PMC5769660) 10.1242/bio.029900 - Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile.
Farias ME, Rasuk MC, Gallagher KL, Contreras M, Kurth D, Fernandez AB, Poiré D, Novoa F, Visscher PT
PLoS ONE (2017) 12(11):e0186867 (PMC5687714) - Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas.
Campbell MA, Łukasik P, Simon C, McCutcheon JP
Curr. Biol. (2017) 27(22):3568-3575.e3 10.1016/j.cub.2017.10.008 - A look into centrosome abnormalities in colon cancer cells, how they arise and how they might be targeted therapeutically.
Harrison LE, Bleiler M, Giardina C
Biochem. Pharmacol. (2017) 147:1-8 (PMC5733729) 10.1016/j.bcp.2017.11.003 - Dartintinnus alderae n. g., n. sp., a Brackish Water Tintinnid (Ciliophora, Spirotrichea) with Dual-ended Lorica Collapsibility.
Smith SA, Song W, Gavrilova NA, Kurilov AV, Liu W, McManus GB, Santoferrara LF
J. Eukaryot. Microbiol. (2017) 65(3):400-411 10.1111/jeu.12485 - Analysis of the Germination of Individual Spores with and without Germinant Receptors and Cortex-Lytic Enzymes.
Wang S, Brunt J, Peck MW, Setlow P, Li YQ
Front Microbiol (2017) 8:2047 (PMC5661016) - Utilization of urea and expression profiles of related genes in the dinoflagellate Prorocentrum donghaiense.
Jing X, Lin S, Zhang H, Koerting C, Yu Z
PLoS ONE (2017) 12(11):e0187837 (PMC5678928) 10.1371/journal.pone.0187837 - Novel tropolones induce the unfolded protein response pathway and apoptosis in multiple myeloma cells.
Haney SL, Allen C, Varney ML, Dykstra KM, Falcone ER, Colligan SH, Hu Q, Aldridge AM, Wright DL, Wiemer AJ, Holstein SA
Oncotarget (2017) 8(44):76085-76098 (PMC5652688) 10.18632/oncotarget.18543 - Creation of forest edges has a global impact on forest vertebrates.
Pfeifer M, Lefebvre V, Peres CA, Banks-Leite C, Wearn OR, Marsh CJ, Butchart SHM, Arroyo-Rodríguez V, Barlow J, Cerezo A, Cisneros L, D'Cruze N, Faria D, Hadley A, Harris SM, Klingbeil BT, Kormann U, Lens L, Medina-Rangel GF, Morante-Filho JC, Olivier P, Peters SL, Pidgeon A, Ribeiro DB, Scherber C, Schneider-Maunoury L, Struebig M, Urbina-Cardona N, Watling JI, Willig MR, Wood EM, Ewers RM
Nature (2017) 551(7679):187-191 (PMC5681864) - USP7-Specific Inhibitors Target and Modify the Enzyme's Active Site via Distinct Chemical Mechanisms.
Pozhidaeva A, Valles G, Wang F, Wu J, Sterner DE, Nguyen P, Weinstock J, Kumar KGS, Kanyo J, Wright D, Bezsonova I
Cell Chem Biol (2017) 24(12):1501-1512.e5 10.1016/j.chembiol.2017.09.004 - IFNγ Enhances CD64-Potentiated Phagocytosis of Opsonized with Human Syphilitic Serum by Human Macrophages.
Hawley KL, Cruz AR, Benjamin SJ, La Vake CJ, Cervantes JL, LeDoyt M, Ramirez LG, Mandich D, Fiel-Gan M, Caimano MJ, Radolf JD, Salazar JC
Front Immunol (2017) 8:1227 (PMC5633599) - HOUSE FINCH ( HAEMORHOUS MEXICANUS)-ASSOCIATED MYCOPLASMA GALLISEPTICUM IDENTIFIED IN LESSER GOLDFINCH ( SPINUS PSALTRIA) AND WESTERN SCRUB JAY ( APHELOCOMA CALIFORNICA) USING STRAIN-SPECIFIC QUANTITATIVE PCR.
Allen CR, Mara A, Tulman ER, Ley DH, Geary SJ
J. Wildl. Dis. (2017) 54(1):180-185 10.7589/2017-04-079 - The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola.
Puthenveetil R, Kumar S, Caimano MJ, Dey A, Anand A, Vinogradova O, Radolf JD
Sci Rep (2017) 7(1):13260 (PMC5643300) - A 3D-printed microbial cell culture platform with PEGDA hydrogel barriers for differential substrate delivery.
Kadilak AL, Rehaag JC, Harrington CA, Shor LM
Biomicrofluidics (2017) 11(5):54109 (PMC5624803) - Syphilis.
Peeling RW, Mabey D, Kamb ML, Chen XS, Radolf JD, Benzaken AS
Nat Rev Dis Primers (2017) 3:17073 (PMC5809176) - Gene Expression Response of Serotype Enteritidis Phage Type 8 to Subinhibitory Concentrations of the Plant-Derived Compounds -Cinnamaldehyde and Eugenol.
Kollanoor Johny A, Frye JG, Donoghue A, Donoghue DJ, Porwollik S, McClelland M, Venkitanarayanan K
Front Microbiol (2017) 8:1828 (PMC5623010) - Synthesis of Mesoporous CoS and NiCoS with Superior Supercapacitive Performance Using a Facile Solid-Phase Sulfurization.
Jin L, Liu B, Wu Y, Thanneeru S, He J
ACS Appl Mater Interfaces (2017) 9(42):36837-36848 10.1021/acsami.7b11453 - Neurodevelopmental disease-associated de novo mutations and rare sequence variants affect TRIO GDP/GTP exchange factor activity.
Katrancha SM, Wu Y, Zhu M, Eipper BA, Koleske AJ, Mains RE
Hum. Mol. Genet. (2017) 26(23):4728-4740 (PMC5886096) 10.1093/hmg/ddx355 - Formation of Holmium Oxide in Pores of Mesoporous Carbon Nanoparticles as Substrates for Neutron-Activatable Radiotherapeutics.
Kim J, Luo ZX, Wu Y, Lu X, Jay M
Carbon N Y (2017) 117:92-99 (PMC5619678) 10.1016/j.carbon.2017.02.085 - The Exonuclease Activity of Herpes Simplex Virus 1 UL12 Is Required for Production of Viral DNA That Can Be Packaged To Produce Infectious Virus.
Grady LM, Szczepaniak R, Murelli RP, Masaoka T, Le Grice SFJ, Wright DL, Weller SK
J. Virol. (2017) 91(23): (PMC5686714) 10.1128/JVI.01380-17 - The balance between Gα-Cdc42/Rac and Gα/-RhoA pathways determines endothelial barrier regulation by sphingosine-1-phosphate.
Reinhard NR, Mastop M, Yin T, Wu Y, Bosma EK, Gadella TWJ, Goedhart J, Hordijk PL
Mol. Biol. Cell (2017) 28(23):3371-3382 (PMC5687037) 10.1091/mbc.E17-03-0136 - Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System.
Lohman BK, Steinel NC, Weber JN, Bolnick DI
Front Immunol (2017) 8:1071 (PMC5600903) - Phytochemicals reduce aflatoxin-induced toxicity in chicken embryos.
Yin HB, Chen CH, Darre MJ, Donoghue AM, Donoghue DJ, Venkitanarayanan K
Poult. Sci. (2017) 96(10):3725-3732 - Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution.
Song B, Morse D, Song Y, Fu Y, Lin X, Wang W, Cheng S, Chen W, Liu X, Lin S
Genome Biol Evol (2017) 9(8):2037-2047 (PMC5585692) 10.1093/gbe/evx144 - Nuclease activity gives an edge to host-defense peptide piscidin 3 over piscidin 1, rendering it more effective against persisters and biofilms.
Libardo MDJ, Bahar AA, Ma B, Fu R, McCormick LE, Zhao J, McCallum SA, Nussinov R, Ren D, Angeles-Boza AM, Cotten ML
FEBS J. (2017) 284(21):3662-3683 (PMC6361529) - The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation.
Zhang W, Pan Y, Yang J, Chen H, Holohan B, Vaudrey J, Lin S, McManus GB
Environ. Microbiol. (2017) 20(2):462-476 10.1111/1462-2920.13916 - Cardiolipin mediates membrane and channel interactions of the mitochondrial TIM23 protein import complex receptor Tim50.
Malhotra K, Modak A, Nangia S, Daman TH, Gunsel U, Robinson VL, Mokranjac D, May ER, Alder NN
Sci Adv (2017) 3(9):e1700532 (PMC5580885) 10.1126/sciadv.1700532 - Many-to-one form-to-function mapping weakens parallel morphological evolution.
Thompson CJ, Ahmed NI, Veen T, Peichel CL, Hendry AP, Bolnick DI, Stuart YE
Evolution (2017) 71(11):2738-2749 - Hold the salt: Freshwater origin of primary plastids.
Lewis LA
Proc. Natl. Acad. Sci. U.S.A. (2017) 114(37):9759-9760 (PMC5604047) - The components of biodiversity, with a particular focus on phylogenetic information.
Scheiner SM, Kosman E, Presley SJ, Willig MR
Ecol Evol (2017) 7(16):6444-6454 (PMC5574767) - Transcriptomic and physiological analyses of the dinoflagellate Karenia mikimotoi reveal non-alkaline phosphatase-based molecular machinery of ATP utilisation.
Luo H, Lin X, Li L, Lin L, Zhang C, Lin S
Environ. Microbiol. (2017) 19(11):4506-4518 10.1111/1462-2920.13899 - The Treponema pallidum Outer Membrane.
Radolf JD, Kumar S
Curr. Top. Microbiol. Immunol. (2017) 415:1-38 (PMC5924592) 10.1007/82_2017_44 - Levels of L-malate and other low molecular weight metabolites in spores of Bacillus species and Clostridium difficile.
Korza G, Abini-Agbomson S, Setlow B, Shen A, Setlow P
PLoS ONE (2017) 12(8):e0182656 (PMC5574573) - Angiosarcoma Developing in an Arteriovenous Fistula after Kidney Transplantation.
Costa BNL, Rivera CF, Rodríguez MC, Romero TH, Muñiz AL, Hermida TF, Lista FS, Díaz PI, Hernández ÁA
Case Rep Transplant (2017) 2017:2426859 (PMC5563407) - Ecological Therapeutic Opportunities for Oral Diseases.
Hoare A, Marsh PD, Diaz PI
Microbiol Spectr (2017) 5(4): (PMC5573124) - Two Distinct Mechanisms Govern RpoS-Mediated Repression of Tick-Phase Genes during Mammalian Host Adaptation by , the Lyme Disease Spirochete.
Grove AP, Liveris D, Iyer R, Petzke M, Rudman J, Caimano MJ, Radolf JD, Schwartz I
MBio (2017) 8(4): (PMC5565969) - The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.
Banker SE, Wade EJ, Simon C
Mol. Phylogenet. Evol. (2017) 116:172-181 10.1016/j.ympev.2017.08.009 - Contrasting effects of environment and genetics generate a continuum of parallel evolution.
Stuart YE, Veen T, Weber JN, Hanson D, Ravinet M, Lohman BK, Thompson CJ, Tasneem T, Doggett A, Izen R, Ahmed N, Barrett RDH, Hendry AP, Peichel CL, Bolnick DI
Nat Ecol Evol (2017) 1(6):158 - Ullmann Reaction Catalyzed by Heterogeneous Mesoporous Copper/Manganese Oxide: A Kinetic and Mechanistic Analysis.
Mullick K, Biswas S, Kim C, Ramprasad R, Angeles-Boza AM, Suib SL
Inorg Chem (2017) 56(17):10290-10297 - Upregulation and Identification of Antibiotic Activity of a Marine-Derived Streptomyces sp. via Co-Cultures with Human Pathogens.
Sung AA, Gromek SM, Balunas MJ
Mar Drugs (2017) 15(8): (PMC5577605) - Machine Learning Using Combined Structural and Chemical Descriptors for Prediction of Methane Adsorption Performance of Metal Organic Frameworks (MOFs).
Pardakhti M, Moharreri E, Wanik D, Suib SL, Srivastava R
ACS Comb Sci (2017) 19(10):640-645 - Carvacrol reduces Clostridium difficile sporulation and spore outgrowth in vitro.
Mooyottu S, Flock G, Venkitanarayanan K
J. Med. Microbiol. (2017) 66(8):1229-1234 - A viral scaffolding protein triggers portal ring oligomerization and incorporation during procapsid assembly.
Motwani T, Lokareddy RK, Dunbar CA, Cortines JR, Jarrold MF, Cingolani G, Teschke CM
Sci Adv (2017) 3(7):e1700423 (PMC5529062) - Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance.
Leles SG, Mitra A, Flynn KJ, Stoecker DK, Hansen PJ, Calbet A, McManus GB, Sanders RW, Caron DA, Not F, Hallegraeff GM, Pitta P, Raven JA, Johnson MD, Glibert PM, Våge S
Proc. Biol. Sci. (2017) 284(1860): (PMC5563798) - Melanomacrophage Centers As a Histological Indicator of Immune Function in Fish and Other Poikilotherms.
Steinel NC, Bolnick DI
Front Immunol (2017) 8:827 (PMC5512340) - Extracellular motility and cell-to-cell transmission of enterohemorrhagic E. coli is driven by EspFU-mediated actin assembly.
Velle KB, Campellone KG
PLoS Pathog. (2017) 13(8):e1006501 (PMC5557606) 10.1371/journal.ppat.1006501 - Molecular mechanism of glucose-6-phosphate utilization in the dinoflagellate Karenia mikimotoi.
Zhang C, Luo H, Huang L, Lin S
Harmful Algae (2017) 67:74-84 10.1016/j.hal.2017.06.006 - Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions.
Dheilly NM, Bolnick D, Bordenstein S, Brindley PJ, Figuères C, Holmes EC, Martínez Martínez J, Phillips AJ, Poulin R, Rosario K
mSystems (2017) 2(4): (PMC5516220) - The UL8 subunit of the helicase-primase complex of herpes simplex virus promotes DNA annealing and has a high affinity for replication forks.
Bermek O, Weller SK, Griffith JD
J. Biol. Chem. (2017) 292(38):15611-15621 (PMC5612096) 10.1074/jbc.M117.799064 - Transcriptional Profiling of the Chicken Tracheal Response to Virulent Mycoplasma gallisepticum Strain R.
Beaudet J, Tulman ER, Pflaum K, Liao X, Kutish GF, Szczepanek SM, Silbart LK, Geary SJ
Infect. Immun. (2017) 85(10): (PMC5607433) 10.1128/IAI.00343-17 - Gene expression stasis and plasticity following migration into a foreign environment.
Lohman BK, Stutz WE, Bolnick DI
Mol. Ecol. (2017) 26(18):4657-4670 - The contribution of marine aggregate-associated bacteria to the accumulation of pathogenic bacteria in oysters: an agent-based model.
Kramer AM, Ward JE, Dobbs FC, Pierce ML, Drake JM
Ecol Evol (2017) 6(20):7397-7408 (PMC5513250) 10.1002/ece3.2467 - An Amish founder mutation disrupts a PI(3)P-WHAMM-Arp2/3 complex-driven autophagosomal remodeling pathway.
Mathiowetz AJ, Baple E, Russo AJ, Coulter AM, Carrano E, Brown JD, Jinks RN, Crosby AH, Campellone KG
Mol. Biol. Cell (2017) 28(19):2492-2507 (PMC5597322) 10.1091/mbc.E17-01-0022 - Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites.
Kolev NG, Günzl A, Tschudi C
Mol. Biochem. Parasitol. (2017) 216:52-55 (PMC5582990) - Insights into the red algae and eukaryotic evolution from the genome of (Bangiophyceae, Rhodophyta).
Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE
Proc. Natl. Acad. Sci. U.S.A. (2017) 114(31):E6361-E6370 (PMC5547612) 10.1073/pnas.1703088114 - Germination of Spores of the Orders Bacillales and Clostridiales.
Setlow P, Wang S, Li YQ
Annu. Rev. Microbiol. (2017) 71:459-477 - Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus .
López-Hermoso C, de la Haba RR, Sánchez-Porro C, Papke RT, Ventosa A
Front Microbiol (2017) 8:1107 (PMC5479898) - Synergistic Antimicrobial Combinations Inhibit and Inactivate Listeria monocytogenes in Neutral and Acidic Broth Systems.
Kozak SM, Margison KM, D'amico DJ
J. Food Prot. (2017) 80(8):1266-1272 10.4315/0362-028X.JFP-17-035 - β-Resorcylic Acid, a Phytophenolic Compound, Reduces Campylobacter jejuni in Postharvest Poultry.
Wagle BR, Arsi K, Upadhyay A, Shrestha S, Venkitanarayanan K, Donoghue AM, Donoghue DJ
J. Food Prot. (2017) 80(8):1243-1251 - A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the Locus.
Roman TS, Cannon ME, Vadlamudi S, Buchkovich ML, Wolford BN, Welch RP, Morken MA, Kwon GJ, Varshney A, Kursawe R, Wu Y, Jackson AU, Erdos MR, Kuusisto J, Laakso M, Scott LJ, Boehnke M, Collins FS, Parker SCJ, Stitzel ML, Mohlke KL
Diabetes (2017) 66(9):2521-2530 (PMC5860374) 10.2337/db17-0464 - Cell Cycle-Dependent Expression Dynamics of G1/S Specific Cyclin, Cellulose Synthase and Cellulase in the Dinoflagellate .
Shi X, Ma M, Lin S
Front Microbiol (2017) 8:1118 (PMC5476699) 10.3389/fmicb.2017.01118 - A route-based pathway analysis framework integrating mutation information and gene expression data.
Zhao Y, Hoang TH, Joshi P, Hong SH, Giardina C, Shin DG
Methods (2017) 124:3-12 - Optogenetic activation of Plexin-B1 reveals contact repulsion between osteoclasts and osteoblasts.
Deb Roy A, Yin T, Choudhary S, Rodionov V, Pilbeam CC, Wu YI
Nat Commun (2017) 8:15831 (PMC5482063) 10.1038/ncomms15831 - Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
Kordi M, Bansal MS
IEEE/ACM transactions on computational biology and bioinformatics (2017) 16(4):1077-1090 10.1109/TCBB.2017.2710342 - Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire.
Gerasimov E, Zelikovsky A, Măndoiu I, Ionov Y
BMC Bioinformatics (2017) 18(Suppl 8):244 (PMC5471937) - Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data.
Mandric I, Temate-Tiagueu Y, Shcheglova T, Al Seesi S, Zelikovsky A, Mandoiu II
Bioinformatics (2017) 33(20):3302-3304 - Phenotypic plasticity drives a depth gradient in male conspicuousness in threespine stickleback, Gasterosteus aculeatus.
Brock CD, Cummings ME, Bolnick DI
Evolution (2017) 71(8):2022-2036 - Recent evolution of extreme cestode growth suppression by a vertebrate host.
Weber JN, Steinel NC, Shim KC, Bolnick DI
Proc. Natl. Acad. Sci. U.S.A. (2017) 114(25):6575-6580 (PMC5488926) - Integrating dimensions of biodiversity in choreotrichs and oligotrichs of marine plankton.
Santoferrara LF, McManus GB
Eur. J. Protistol. (2017) 61(Pt B):323-330 - Effect of Dietary Minerals on Virulence Attributes of .
Bhattaram V, Upadhyay A, Yin HB, Mooyottu S, Venkitanarayanan K
Front Microbiol (2017) 8:911 (PMC5437166) - Correction for Kirkham et al., "Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A".
Kirkham JK, Park SH, Nguyen TN, Lee JH, Günzl A
Mol. Cell. Biol. (2017) 37(12): (PMC5452717) - Plasticity contributes to a fine-scale depth gradient in sticklebacks' visual system.
Veen T, Brock C, Rennison D, Bolnick D
Mol. Ecol. (2017) 26(16):4339-4350 - Frequency dependence limits divergent evolution by favouring rare immigrants over residents.
Bolnick DI, Stutz WE
Nature (2017) 546(7657):285-288 - Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate.
Shi X, Lin X, Li L, Li M, Palenik B, Lin S
ISME J (2017) 11(10):2209-2218 (PMC5607363) 10.1038/ismej.2017.81 - Peritoneal B-1b and B-2 B-cells confer long-term protection from pneumococcal serotype 3 infection after vaccination with Prevnar-13 and are defective in sickle cell disease mice.
Cotte C, Szczepanek SM
Vaccine (2017) 35(28):3520-3522 10.1016/j.vaccine.2017.05.039 - A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses.
Louyakis AS, Mobberley JM, Vitek BE, Visscher PT, Hagan PD, Reid RP, Kozdon R, Orland IJ, Valley JW, Planavsky NJ, Casaburi G, Foster JS
Astrobiology (2017) 17(5):413-430 (PMC5767104) - Brain morphology of the threespine stickleback () varies inconsistently with respect to habitat complexity: A test of the Clever Foraging Hypothesis.
Ahmed NI, Thompson C, Bolnick DI, Stuart YE
Ecol Evol (2017) 7(10):3372-3380 (PMC5433989) - Evolutionary Biology Needs Wild Microbiomes.
Hird SM
Front Microbiol (2017) 8:725 (PMC5404107) 10.3389/fmicb.2017.00725 - Trans-Cinnamaldehyde, Carvacrol, and Eugenol Reduce Colonization Factors and Expression of Virulence Genes .
Upadhyay A, Arsi K, Wagle BR, Upadhyaya I, Shrestha S, Donoghue AM, Donoghue DJ
Front Microbiol (2017) 8:713 (PMC5403884) 10.3389/fmicb.2017.00713 - Protective Effect of Carvacrol against Gut Dysbiosis and Associated Disease in a Mouse Model.
Mooyottu S, Flock G, Upadhyay A, Upadhyaya I, Maas K, Venkitanarayanan K
Front Microbiol (2017) 8:625 (PMC5399026) - How Does Membrane Oxidation Affect Cell Delivery and Cell Killing?
Libardo MDJ, Wang TY, Pellois JP, Angeles-Boza AM
Trends Biotechnol. (2017) 35(8):686-690 (PMC5522782) - Isolation, Biosynthesis and Chemical Modifications of Rubterolones A-F: Rare Tropolone Alkaloids from Actinomadura sp. 5-2.
Guo H, Benndorf R, Leichnitz D, Klassen JL, Vollmers J, Görls H, Steinacker M, Weigel C, Dahse HM, Kaster AK, de Beer ZW, Poulsen M, Beemelmanns C
Chemistry (2017) 23(39):9338-9345 - Characterization of trimethoprim resistant dihydrofolate reductase mutants by mass spectrometry and inhibition by propargyl-linked antifolates.
Cammarata M, Thyer R, Lombardo M, Anderson A, Wright D, Ellington A, Brodbelt JS
Chem Sci (2017) 8(5):4062-4072 (PMC6020862) 10.1039/c6sc05235e - Teleosts as Model Organisms To Understand Host-Microbe Interactions.
Lescak EA, Milligan-Myhre KC
Journal of bacteriology (2017) 199(15): PMC2829049 10.1371/journal.pgen.1000862 - Natural selection on MHC IIβ in parapatric lake and stream stickleback: Balancing, divergent, both or neither?
Stutz WE, Bolnick DI
Mol. Ecol. (2017) 26(18):4772-4786 - Application of β-Resorcylic Acid as Potential Antimicrobial Feed Additive to Reduce Colonization in Broiler Chickens.
Wagle BR, Upadhyay A, Arsi K, Shrestha S, Venkitanarayanan K, Donoghue AM, Donoghue DJ
Front Microbiol (2017) 8:599 (PMC5382206) - Draft Genome Sequence of the Fish Pathogen Strain CSF-298-10.
Evenhuis JP, LaPatra SE, Graf J
Genome Announc (2017) 5(15): (PMC5391422) - Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes.
Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP
Sci Rep (2017) 7:46160 (PMC5387419) - Attenuated Phenotype of a Recent House Finch-Associated Mycoplasma gallisepticum Isolate in Domestic Poultry.
Pflaum K, Tulman ER, Beaudet J, Liao X, Dhondt KV, Dhondt AA, Hawley DM, Ley DH, Kerr KM, Geary SJ
Infect. Immun. (2017) 85(6): (PMC5442625) 10.1128/IAI.00185-17 - Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut.
Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA
Genome biology and evolution (2017) 9(3):504-520 PMC2844994 10.1093/gbe/evx014 - Enhancement of Non-photochemical Quenching as an Adaptive Strategy under Phosphorus Deprivation in the Dinoflagellate .
Cui Y, Zhang H, Lin S
Front Microbiol (2017) 8:404 (PMC5350143) 10.3389/fmicb.2017.00404 - Phosphorylated cortactin recruits Vav2 guanine nucleotide exchange factor to activate Rac3 and promote invadopodial function in invasive breast cancer cells.
Rosenberg BJ, Gil-Henn H, Mader CC, Halo T, Yin T, Condeelis J, Machida K, Wu YI, Koleske AJ
Mol. Biol. Cell (2017) 28(10):1347-1360 (PMC5426849) 10.1091/mbc.E16-12-0885 - Membrane Oxidation in Cell Delivery and Cell Killing Applications.
Wang TY, Libardo MDJ, Angeles-Boza AM, Pellois JP
ACS Chem. Biol. (2017) 12(5):1170-1182 (PMC5905413) - Clines Arc through Multivariate Morphospace.
Lohman BK, Berner D, Bolnick DI
Am. Nat. (2017) 189(4):354-367 - Tumor Control Index as a new tool to assess tumor growth in experimental animals.
Corwin WL, Ebrahimi-Nik H, Floyd SM, Tavousi P, Mandoiu II, Srivastava PK
J. Immunol. Methods (2017) 445:71-76 - Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides.
Wyche TP, Ruzzini AC, Beemelmanns C, Kim KH, Klassen JL, Cao S, Poulsen M, Bugni TS, Currie CR, Clardy J
Org. Lett. (2017) 19(7):1772-1775 (PMC6013059) - Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme-The spore photoproduct lyase.
Yang L, Jian Y, Setlow P, Li L
DNA Repair (Amst.) (2017) 53:31-42 (PMC5654379) - Pharmaceutical analysis of a novel propargyl-linked antifolate antibiotic in the mouse.
Hoody J, Alverson JB, Keshipeddy S, Barney PA, Walker L, Anderson AC, Wright DL, Priestley ND
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. (2017) 1051:54-59 (PMC5635995) 10.1016/j.jchromb.2017.02.026 - Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses.
Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM
mSystems (2017) 2(1): (PMC5347185) 10.1128/mSystems.00188-16 - Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea).
Santoferrara LF, Alder VV, McManus GB
Mol. Phylogenet. Evol. (2017) 112:12-22 - Oxidized Derivatives of Linoleic Acid in Pediatric Metabolic Syndrome: Is Their Pathogenic Role Modulated by the Genetic Background and the Gut Microbiota?
Tricò D, Di Sessa A, Caprio S, Chalasani N, Liu W, Liang T, Graf J, Herzog RI, Johnson CD, Umano GR, Feldstein AE, Santoro N
Antioxidants & redox signaling (2017) 30(2):241-250 PMC6277079 10.1089/ars.2017.7049 - Electrochemical Reduction of CO Catalyzed by Re(pyridine-oxazoline)(CO)Cl Complexes.
Nganga JK, Samanamu CR, Tanski JM, Pacheco C, Saucedo C, Batista VS, Grice KA, Ertem MZ, Angeles-Boza AM
Inorg Chem (2017) 56(6):3214-3226 - Influence of Feeding Type on Gut Microbiome Development in Hospitalized Preterm Infants.
Cong X, Judge M, Xu W, Diallo A, Janton S, Brownell EA, Maas K, Graf J
Nurs Res (2017) 66(2):123-133 (PMC5334772) - Exploration of the Innate Immune System of Styela clava: Zn Binding Enhances the Antimicrobial Activity of the Tunicate Peptide Clavanin A.
Juliano SA, Pierce S, deMayo JA, Balunas MJ, Angeles-Boza AM
Biochemistry (2017) 56(10):1403-1414 - Efficacy of Plant-Derived Antimicrobials in Controlling Enterohemorrhagic Escherichia coli Virulence In Vitro.
Baskaran SA, Kollanoor-Johny A, Nair MS, Venkitanarayanan K
J. Food Prot. (2017) 79(11):1965-1970 - Photocatalytic effects of titanium dioxide nanoparticles on aquatic organisms-Current knowledge and suggestions for future research.
Haynes VN, Ward JE, Russell BJ, Agrios AG
Aquat. Toxicol. (2017) 185:138-148 10.1016/j.aquatox.2017.02.012 - Macrotermycins A-D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39.
Beemelmanns C, Ramadhar TR, Kim KH, Klassen JL, Cao S, Wyche TP, Hou Y, Poulsen M, Bugni TS, Currie CR, Clardy J
Org. Lett. (2017) 19(5):1000-1003 (PMC6006516) - The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae).
Gómez F, Qiu D, Lin S
J. Eukaryot. Microbiol. (2017) 64(5):668-677 10.1111/jeu.12403 - Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis.
Surendran Nair M, Amalaradjou MA, Venkitanarayanan K
Adv. Appl. Microbiol. (2017) 98:1-29 - STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies.
Pei J, Wu Y
Bioinformatics (2017) 33(12):1789-1797 10.1093/bioinformatics/btx079 - Heterogeneous mesoporous manganese oxide catalyst for aerobic and additive-free oxidative aromatization of N-heterocycles.
Mullick K, Biswas S, Angeles-Boza AM, Suib SL
Chem. Commun. (Camb.) (2017) 53(14):2256-2259 - Reply to Johnson et al.: Functionally active cryptophyte cell membrane and cytoplasm indicate intact symbionts within .
Qiu D, Lin L, Lin S
Proc. Natl. Acad. Sci. U.S.A. (2017) 114(7):E1043-E1044 (PMC5321010) 10.1073/pnas.1620409114 - Detection and Manipulation of the Stress Response Protein Metallothionein.
Bhandari S, Melchiorre C, Dostie K, Laukens D, Devisscher L, Louwrier A, Thees A, Lynes MA
Curr Protoc Toxicol (2017) 71:17.19.1-17.19.28 - Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.
Lokareddy RK, Sankhala RS, Roy A, Afonine PV, Motwani T, Teschke CM, Parent KN, Cingolani G
Nat Commun (2017) 8:14310 (PMC5290284) - How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas.
Owen CL, Marshall DC, Hill KBR, Simon C
Syst. Biol. (2017) 66(4):569-589 10.1093/sysbio/syw078 - The Role of Hemocytes in the Hawaiian Bobtail Squid, : A Model Organism for Studying Beneficial Host-Microbe Interactions.
McAnulty SJ, Nyholm SV
Front Microbiol (2017) 7:2013 (PMC5216023) 10.3389/fmicb.2016.02013 - A Clostridium difficile-Specific, Gel-Forming Protein Required for Optimal Spore Germination.
Donnelly ML, Li W, Li YQ, Hinkel L, Setlow P, Shen A
MBio (2017) 8(1): (PMC5241399) - On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier.
Dutzan N, Abusleme L, Bridgeman H, Greenwell-Wild T, Zangerle-Murray T, Fife ME, Bouladoux N, Linley H, Brenchley L, Wemyss K, Calderon G, Hong BY, Break TJ, Bowdish DME, Lionakis MS, Jones SA, Trinchieri G, Diaz PI, Belkaid Y, Konkel JE, Moutsopoulos NM
Immunity (2017) 46(1):133-147 (PMC5263257) - Symbiont-induced odorant binding proteins mediate insect host hematopoiesis.
Benoit JB, Vigneron A, Broderick NA, Wu Y, Sun JS, Carlson JR, Aksoy S, Weiss BL
Elife (2017) 6: (PMC5231409) 10.7554/eLife.19535 - The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project.
Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, Phillips HR, Alhusseini TI, Bedford FE, Bennett DJ, Booth H, Burton VJ, Chng CW, Choimes A, Correia DL, Day J, Echeverría-Londoño S, Emerson SR, Gao D, Garon M, Harrison ML, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, Pask-Hale GD, Pynegar EL, Robinson AN, Sanchez-Ortiz K, Senior RA, Simmons BI, White HJ, Zhang H, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Albertos B, Alcala EL, Del Mar Alguacil M, Alignier A, Ancrenaz M, Andersen AN, Arbeláez-Cortés E, Armbrecht I, Arroyo-Rodríguez V, Aumann T, Axmacher JC, Azhar B, Azpiroz AB, Baeten L, Bakayoko A, Báldi A, Banks JE, Baral SK, Barlow J, Barratt BI, Barrico L, Bartolommei P, Barton DM, Basset Y, Batáry P, Bates AJ, Baur B, Bayne EM, Beja P, Benedick S, Berg Å, Bernard H, Berry NJ, Bhatt D, Bicknell JE, Bihn JH, Blake RJ, Bobo KS, Bóçon R, Boekhout T, Böhning-Gaese K, Bonham KJ, Borges PA, Borges SH, Boutin C, Bouyer J, Bragagnolo C, Brandt JS, Brearley FQ, Brito I, Bros V, Brunet J, Buczkowski G, Buddle CM, Bugter R, Buscardo E, Buse J, Cabra-García J, Cáceres NC, Cagle NL, Calviño-Cancela M, Cameron SA, Cancello EM, Caparrós R, Cardoso P, Carpenter D, Carrijo TF, Carvalho AL, Cassano CR, Castro H, Castro-Luna AA, Rolando CB, Cerezo A, Chapman KA, Chauvat M, Christensen M, Clarke FM, Cleary DF, Colombo G, Connop SP, Craig MD, Cruz-López L, Cunningham SA, D'Aniello B, D'Cruze N, da Silva PG, Dallimer M, Danquah E, Darvill B, Dauber J, Davis AL, Dawson J, de Sassi C, de Thoisy B, Deheuvels O, Dejean A, Devineau JL, Diekötter T, Dolia JV, Domínguez E, Dominguez-Haydar Y, Dorn S, Draper I, Dreber N, Dumont B, Dures SG, Dynesius M, Edenius L, Eggleton P, Eigenbrod F, Elek Z, Entling MH, Esler KJ, de Lima RF, Faruk A, Farwig N, Fayle TM, Felicioli A, Felton AM, Fensham RJ, Fernandez IC, Ferreira CC, Ficetola GF, Fiera C, Filgueiras BK, Fırıncıoğlu HK, Flaspohler D, Floren A, Fonte SJ, Fournier A, Fowler RE, Franzén M, Fraser LH, Fredriksson GM, Freire GB, Frizzo TL, Fukuda D, Furlani D, Gaigher R, Ganzhorn JU, García KP, Garcia-R JC, Garden JG, Garilleti R, Ge BM, Gendreau-Berthiaume B, Gerard PJ, Gheler-Costa C, Gilbert B, Giordani P, Giordano S, Golodets C, Gomes LG, Gould RK, Goulson D, Gove AD, Granjon L, Grass I, Gray CL, Grogan J, Gu W, Guardiola M, Gunawardene NR, Gutierrez AG, Gutiérrez-Lamus DL, Haarmeyer DH, Hanley ME, Hanson T, Hashim NR, Hassan SN, Hatfield RG, Hawes JE, Hayward MW, Hébert C, Helden AJ, Henden JA, Henschel P, Hernández L, Herrera JP, Herrmann F, Herzog F, Higuera-Diaz D, Hilje B, Höfer H, Hoffmann A, Horgan FG, Hornung E, Horváth R, Hylander K, Isaacs-Cubides P, Ishida H, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Hernández FJ, Johnson MF, Jolli V, Jonsell M, Juliani SN, Jung TS, Kapoor V, Kappes H, Kati V, Katovai E, Kellner K, Kessler M, Kirby KR, Kittle AM, Knight ME, Knop E, Kohler F, Koivula M, Kolb A, Kone M, Kőrösi Á, Krauss J, Kumar A, Kumar R, Kurz DJ, Kutt AS, Lachat T, Lantschner V, Lara F, Lasky JR, Latta SC, Laurance WF, Lavelle P, Le Féon V, LeBuhn G, Légaré JP, Lehouck V, Lencinas MV, Lentini PE, Letcher SG, Li Q, Litchwark SA, Littlewood NA, Liu Y, Lo-Man-Hung N, López-Quintero CA, Louhaichi M, Lövei GL, Lucas-Borja ME, Luja VH, Luskin MS, MacSwiney G MC, Maeto K, Magura T, Mallari NA, Malone LA, Malonza PK, Malumbres-Olarte J, Mandujano S, Måren IE, Marin-Spiotta E, Marsh CJ, Marshall EJ, Martínez E, Martínez Pastur G, Moreno Mateos D, Mayfield MM, Mazimpaka V, McCarthy JL, McCarthy KP, McFrederick QS, McNamara S, Medina NG, Medina R, Mena JL, Mico E, Mikusinski G, Milder JC, Miller JR, Miranda-Esquivel DR, Moir ML, Morales CL, Muchane MN, Muchane M, Mudri-Stojnic S, Munira AN, Muoñz-Alonso A, Munyekenye BF, Naidoo R, Naithani A, Nakagawa M, Nakamura A, Nakashima Y, Naoe S, Nates-Parra G, Navarrete Gutierrez DA, Navarro-Iriarte L, Ndang'ang'a PK, Neuschulz EL, Ngai JT, Nicolas V, Nilsson SG, Noreika N, Norfolk O, Noriega JA, Norton DA, Nöske NM, Nowakowski AJ, Numa C, O'Dea N, O'Farrell PJ, Oduro W, Oertli S, Ofori-Boateng C, Oke CO, Oostra V, Osgathorpe LM, Otavo SE, Page NV, Paritsis J, Parra-H A, Parry L, Pe'er G, Pearman PB, Pelegrin N, Pélissier R, Peres CA, Peri PL, Persson AS, Petanidou T, Peters MK, Pethiyagoda RS, Phalan B, Philips TK, Pillsbury FC, Pincheira-Ulbrich J, Pineda E, Pino J, Pizarro-Araya J, Plumptre AJ, Poggio SL, Politi N, Pons P, Poveda K, Power EF, Presley SJ, Proença V, Quaranta M, Quintero C, Rader R, Ramesh BR, Ramirez-Pinilla MP, Ranganathan J, Rasmussen C, Redpath-Downing NA, Reid JL, Reis YT, Rey Benayas JM, Rey-Velasco JC, Reynolds C, Ribeiro DB, Richards MH, Richardson BA, Richardson MJ, Ríos RM, Robinson R, Robles CA, Römbke J, Romero-Duque LP, Rös M, Rosselli L, Rossiter SJ, Roth DS, Roulston TH, Rousseau L, Rubio AV, Ruel JC, Sadler JP, Sáfián S, Saldaña-Vázquez RA, Sam K, Samnegård U, Santana J, Santos X, Savage J, Schellhorn NA, Schilthuizen M, Schmiedel U, Schmitt CB, Schon NL, Schüepp C, Schumann K, Schweiger O, Scott DM, Scott KA, Sedlock JL, Seefeldt SS, Shahabuddin G, Shannon G, Sheil D, Sheldon FH, Shochat E, Siebert SJ, Silva FA, Simonetti JA, Slade EM, Smith J, Smith-Pardo AH, Sodhi NS, Somarriba EJ, Sosa RA, Soto Quiroga G, St-Laurent MH, Starzomski BM, Stefanescu C, Steffan-Dewenter I, Stouffer PC, Stout JC, Strauch AM, Struebig MJ, Su Z, Suarez-Rubio M, Sugiura S, Summerville KS, Sung YH, Sutrisno H, Svenning JC, Teder T, Threlfall CG, Tiitsaar A, Todd JH, Tonietto RK, Torre I, Tóthmérész B, Tscharntke T, Turner EC, Tylianakis JM, Uehara-Prado M, Urbina-Cardona N, Vallan D, Vanbergen AJ, Vasconcelos HL, Vassilev K, Verboven HA, Verdasca MJ, Verdú JR, Vergara CH, Vergara PM, Verhulst J, Virgilio M, Vu LV, Waite EM, Walker TR, Wang HF, Wang Y, Watling JI, Weller B, Wells K, Westphal C, Wiafe ED, Williams CD, Willig MR, Woinarski JC, Wolf JH, Wolters V, Woodcock BA, Wu J, Wunderle JM, Yamaura Y, Yoshikura S, Yu DW, Zaitsev AS, Zeidler J, Zou F, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JP, Purvis A
Ecol Evol (2017) 7(1):145-188 (PMC5215197) - An improved protocol for harvesting Bacillus subtilis colony biofilms.
Fuchs FM, Driks A, Setlow P, Moeller R
J. Microbiol. Methods (2017) 134:7-13 - The terrestrial green macroalga Prasiola calophylla (Trebouxiophyceae, Chlorophyta): ecophysiological performance under water-limiting conditions.
Holzinger A, Herburger K, Blaas K, Lewis LA, Karsten U
Protoplasma (2017) 254(4):1755-1767 (PMC5474099) - The Genetic Diversity of and Associated Cryptophytes.
Johnson MD, Beaudoin DJ, Laza-Martinez A, Dyhrman ST, Fensin E, Lin S, Merculief A, Nagai S, Pompeu M, Setälä O, Stoecker DK
Front Microbiol (2017) 7:2017 (PMC5168500) 10.3389/fmicb.2016.02017 - Metabolite exchange between microbiome members produces compounds that influence behavior.
Fischer CN, Trautman EP, Crawford JM, Stabb EV, Handelsman J, Broderick NA
Elife (2017) 6: (PMC5222558) 10.7554/eLife.18855 - Oral supplementation of trans-cinnamaldehyde reduces uropathogenic Escherichia coli colonization in a mouse model.
Narayanan A, Muyyarikkandy MS, Mooyottu S, Venkitanarayanan K, Amalaradjou MA
Lett. Appl. Microbiol. (2017) 64(3):192-197 - Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs.
Kerwin AH, Nyholm SV
Environ. Microbiol. (2017) 19(4):1463-1475 10.1111/1462-2920.13665 - On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
Kordi M, Bansal MS
IEEE/ACM Trans Comput Biol Bioinform (2017) 14(3):587-599 - Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea.
Prunetti L, Graf M, Blaby IK, Peil L, Makkay AM, Starosta AL, Papke RT, Oshima T, Wilson DN, de Crécy-Lagard V
Archaea (2017) 2016:7316725 (PMC5178350) - Post-Hurricane Successional Dynamics in Abundance and Diversity of Canopy Arthropods in a Tropical Rainforest.
Schowalter TD, Willig MR, Presley SJ
Environ. Entomol. (2017) 46(1):11-20 2016
- Resist Globally, Infect Locally: A Transcontinental Test of Adaptation by Stickleback and Their Tapeworm Parasite.
Weber JN, Kalbe M, Shim KC, Erin NI, Steinel NC, Ma L, Bolnick DI
Am. Nat. (2016) 189(1):43-57 - Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis.
Schincaglia GP, Hong BY, Rosania A, Barasz J, Thompson A, Sobue T, Panagakos F, Burleson JA, Dongari-Bagtzoglou A, Diaz PI
J. Dent. Res. (2016) 96(1):47-55 - The flagellar master operon flhDC is a pleiotropic regulator involved in motility and virulence of the fish pathogen Yersinia ruckeri.
Jozwick AK, Graf J, Welch TJ
J. Appl. Microbiol. (2016) 122(3):578-588 - Behavioural hypervolumes of spider communities predict community performance and disbandment.
Pruitt JN, Bolnick DI, Sih A, DiRienzo N, Pinter-Wollman N
Proc. Biol. Sci. (2016) 283(1844): (PMC5204141) - Direct Substitution of Arylalkynyl Carbinols Provides Access to Diverse Terminal Acetylene Building Blocks.
G-Dayanandan N, Scocchera EW, Keshipeddy S, Jones HF, Anderson AC, Wright DL
Org. Lett. (2016) 19(1):142-145 (PMC5253071) 10.1021/acs.orglett.6b03438 - MRSA Isolates from United States Hospitals Carry dfrG and dfrK Resistance Genes and Succumb to Propargyl-Linked Antifolates.
Reeve SM, Scocchera EW, G-Dayanadan N, Keshipeddy S, Krucinska J, Hajian B, Ferreira J, Nailor M, Aeschlimann J, Wright DL, Anderson AC
Cell Chem Biol (2016) 23(12):1458-1467 (PMC5228619) 10.1016/j.chembiol.2016.11.007 - Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf.
Grattepanche JD, McManus GB, Katz LA
PLoS ONE (2016) 11(12):e0167659 (PMC5147948) - Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record.
Sforna MC, Daye M, Philippot P, Somogyi A, van Zuilen MA, Medjoubi K, Gérard E, Jamme F, Dupraz C, Braissant O, Glunk C, Visscher PT
Geobiology (2016) 15(2):259-279 - Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction.
Dick AA, Harlow TJ, Gogarten JP
Mol. Phylogenet. Evol. (2016) 107:338-344 - Is LUCA a thermophilic progenote?
Gogarten JP, Deamer D
Nat Microbiol (2016) 1:16229 - Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative.
Hertach T, Puissant S, Gogala M, Trilar T, Hagmann R, Baur H, Kunz G, Wade EJ, Loader SP, Simon C, Nagel P
PLoS ONE (2016) 11(11):e0165562 (PMC5112989) 10.1371/journal.pone.0165562 - Kinetics of recruitment and allosteric activation of ARHGEF25 isoforms by the heterotrimeric G-protein Gαq.
van Unen J, Yin T, Wu YI, Mastop M, Gadella TW, Goedhart J
Sci Rep (2016) 6:36825 (PMC5105084) 10.1038/srep36825 - Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.
Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TC, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR
mSystems (2016) 1(2): (PMC5069740) - Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche.
Kopac SM, Klassen JL
Front Microbiol (2016) 7:1647 (PMC5073103) - Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth.
Goffredo M, Mass K, Parks EJ, Wagner DA, McClure EA, Graf J, Savoye M, Pierpont B, Cline G, Santoro N
J. Clin. Endocrinol. Metab. (2016) 101(11):4367-4376 (PMC5095239) - Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback.
Weber JN, Bradburd GS, Stuart YE, Stutz WE, Bolnick DI
Evolution (2016) 71(2):342-356 - NMR assignments for the insertion domain of bacteriophage Sf6 coat protein.
Tripler TN, Teschke CM, Alexandrescu AT
Biomol NMR Assign (2016) 11(1):35-38 (PMC5344723) - Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen.
Radolf JD, Deka RK, Anand A, Šmajs D, Norgard MV, Yang XF
Nat. Rev. Microbiol. (2016) 14(12):744-759 (PMC5106329) - Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential.
Marden JN, McClure EA, Beka L, Graf J
Front Microbiol (2016) 7:1569 (PMC5061737) - Mining the oral mycobiome: Methods, components, and meaning.
Diaz PI, Hong BY, Dupuy AK, Strausbaugh LD
Virulence (2016) 8(3):313-323 (PMC5411240) - Cryptophyte farming by symbiotic ciliate host detected in situ.
Qiu D, Huang L, Lin S
Proc. Natl. Acad. Sci. U.S.A. (2016) 113(43):12208-12213 (PMC5087057) 10.1073/pnas.1612483113 - Genomic divergence and lack of introgressive hybridization between two 13-year periodical cicadas support life cycle switching in the face of climate change.
Koyama T, Ito H, Fujisawa T, Ikeda H, Kakishima S, Cooley JR, Simon C, Yoshimura J, Sota T
Mol. Ecol. (2016) 25(21):5543-5556 10.1111/mec.13858 - Does Sequence Conservation Provide Evidence for Biological Function?
Omer S, Harlow TJ, Gogarten JP
Trends Microbiol. (2016) 25(1):11-18 - Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.
Cisneros LM, Fagan ME, Willig MR
PeerJ (2016) 4:e2551 (PMC5068362) - Evaluating Exercise Prescription and Instructional Methods Used in Tai Chi Studies Aimed at Improving Balance in Older Adults: A Systematic Review.
Wu Y, MacDonald HV, Pescatello LS
J Am Geriatr Soc (2016) 64(10):2074-2080 10.1111/jgs.14242 - Novel α-substituted tropolones promote potent and selective caspase-dependent leukemia cell apoptosis.
Li J, Falcone ER, Holstein SA, Anderson AC, Wright DL, Wiemer AJ
Pharmacol. Res. (2016) 113(Pt A):438-448 (PMC5107114) 10.1016/j.phrs.2016.09.020 - Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a Tunicate Collected in Long Island Sound.
deMayo JA, Maas KR, Klassen JL, Balunas MJ
Genome Announc (2016) 4(5): (PMC5064096) - More wrinkles to Bt susceptibility.
Broderick NA
Virulence (2016) 7(8):853-855 (PMC5160410) 10.1080/21505594.2016.1244596 - Direct Tracking of Particles and Quantification of Margination in Blood Flow.
Carboni EJ, Bognet BH, Bouchillon GM, Kadilak AL, Shor LM, Ward MD, Ma AWK
Biophys. J. (2016) 111(7):1487-1495 (PMC5052466) - Aag Hypoxanthine-DNA Glycosylase Is Synthesized in the Forespore Compartment and Involved in Counteracting the Genotoxic and Mutagenic Effects of Hypoxanthine and Alkylated Bases in DNA during Bacillus subtilis Sporulation.
Ayala-García VM, Valenzuela-García LI, Setlow P, Pedraza-Reyes M
J. Bacteriol. (2016) 198(24):3345-3354 (PMC5116938) - Characterization of germinants and their receptors for spores of non-food-borne Clostridium perfringens strain F4969.
Banawas S, Paredes-Sabja D, Setlow P, Sarker MR
Microbiology (Reading, Engl.) (2016) 162(11):1972-1983 - Developmental change in translation initiation alters the localization of a common microbial protein necessary for Toxoplasma chronic infection.
Milligan-Myhre K, Wilson SK, Knoll LJ
Molecular microbiology (2016) 102(6):1086-1098 PMC3255658 10.1111/mmi.13538 - Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.
Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV, Balunas MJ
Front Microbiol (2016) 7:1342 (PMC5014874) - The cicadas (Hemiptera: Cicadidae) of India, Bangladesh, Bhutan, Myanmar, Nepal and Sri Lanka: an annotated provisional catalogue, regional checklist and bibliography.
Price BW, Allan EL, Marathe K, Sarkar V, Simon C, Kunte K
Biodivers Data J (2016) (4):e8051 (PMC5018104) 10.3897/BDJ.4.e8051 - Distension of the toga of Thermotoga maritima involves continued growth of the outer envelope as cells enter the stationary phase.
Ranjit C, Noll KM
FEMS Microbiol. Lett. (2016) 363(19): - Changes in Bacillus Spore Small Molecules, rRNA, Germination, and Outgrowth after Extended Sublethal Exposure to Various Temperatures: Evidence that Protein Synthesis Is Not Essential for Spore Germination.
Korza G, Setlow B, Rao L, Li Q, Setlow P
J. Bacteriol. (2016) 198(24):3254-3264 (PMC5116929) - Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.
Gromek SM, Sung AA, Klassen JL, Balunas MJ
Genome Announc (2016) 4(5): (PMC5026429) - Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates.
Lombardo MN, G-Dayanandan N, Wright DL, Anderson AC
ACS Infect Dis (2016) 2(2):149-56 (PMC5108240) 10.1021/acsinfecdis.5b00129 - Central Role of the Copper-Binding Motif in the Complex Mechanism of Action of Ixosin: Enhancing Oxidative Damage and Promoting Synergy with Ixosin B.
Libardo MD, Gorbatyuk VY, Angeles-Boza AM
ACS Infect Dis (2016) 2(1):71-81 - Efficacy of Trans-cinnamaldehyde and Eugenol in Reducing Acinetobacter baumannii Adhesion to and Invasion of Human Keratinocytes and Controlling Wound Infection In Vitro.
Karumathil DP, Surendran-Nair M, Venkitanarayanan K
Phytother Res (2016) 30(12):2053-2059 - Synthesis and biological evaluation of santacruzamate A analogues for anti-proliferative and immunomodulatory activity.
Gromek SM, deMayo JA, Maxwell AT, West AM, Pavlik CM, Zhao Z, Li J, Wiemer AJ, Zweifach A, Balunas MJ
Bioorg. Med. Chem. (2016) 24(21):5183-5196 (PMC5065774) - Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile.
Fernandez AB, Rasuk MC, Visscher PT, Contreras M, Novoa F, Poire DG, Patterson MM, Ventosa A, Farias ME
Front Microbiol (2016) 7:1284 (PMC4992683) - -NOD Mice Having a Lyn Tyrosine Kinase Mutation Exhibit Abnormal Neutrophil Chemotaxis.
Wu Y, Hannigan M, Zhan L, Madri JA, Huang CK
J. Cell. Physiol. (2016) 232(7):1689-1695 10.1002/jcp.25583 - Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development.
Karunakaran DK, Al Seesi S, Banday AR, Baumgartner M, Olthof A, Lemoine C, Măndoiu II, Kanadia RN
BMC Genomics (2016) 17 Suppl 5:495 (PMC5009874) - Inferring metabolic pathway activity levels from RNA-Seq data.
Temate-Tiagueu Y, Seesi SA, Mathew M, Mandric I, Rodriguez A, Bean K, Cheng Q, Glebova O, Măndoiu I, Lopanik NB, Zelikovsky A
BMC Genomics (2016) 17 Suppl 5:542 (PMC5009525) - Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis.
Hajian B, Scocchera E, Keshipeddy S, G-Dayanandan N, Shoen C, Krucinska J, Reeve S, Cynamon M, Anderson AC, Wright DL
PLoS ONE (2016) 11(8):e0161740 (PMC5006990) 10.1371/journal.pone.0161740 - Progress, pitfalls and parallel universes: a history of insect phylogenetics.
Kjer KM, Simon C, Yavorskaya M, Beutel RG
J R Soc Interface (2016) 13(121): (PMC5014063) 10.1098/rsif.2016.0363 - Dietary Methyl Donor Depletion Suppresses Intestinal Adenoma Development.
Hanley MP, Kadaveru K, Perret C, Giardina C, Rosenberg DW
Cancer Prev Res (Phila) (2016) 9(10):812-820 (PMC5053888) - Microbial and diagenetic steps leading to the mineralisation of Great Salt Lake microbialites.
Pace A, Bourillot R, Bouton A, Vennin E, Galaup S, Bundeleva I, Patrier P, Dupraz C, Thomazo C, Sansjofre P, Yokoyama Y, Franceschi M, Anguy Y, Pigot L, Virgone A, Visscher PT
Sci Rep (2016) 6:31495 (PMC4985759) - Subgingival Microbiome Shifts and Community Dynamics in Periodontal Diseases.
Diaz PI, Hoare A, Hong BY
J Calif Dent Assoc (2016) 44(7):421-35 - An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates.
Lou DI, Kim ET, Meyerson NR, Pancholi NJ, Mohni KN, Enard D, Petrov DA, Weller SK, Weitzman MD, Sawyer SL
Cell Host Microbe (2016) 20(2):178-88 (PMC4982468) 10.1016/j.chom.2016.07.003 - Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusions.
Bolnick DI, Hendrix K, Jordan LA, Veen T, Brock CD
Biol. Lett. (2016) 12(8): (PMC5014039) - Localization of the Houdinisome (Ejection Proteins) inside the Bacteriophage P22 Virion by Bubblegram Imaging.
Wu W, Leavitt JC, Cheng N, Gilcrease EB, Motwani T, Teschke CM, Casjens SR, Steven AC
MBio (2016) 7(4): (PMC4992974) - Measurement of the accurate mass of a 50 MDa infectious virus.
Keifer DZ, Motwani T, Teschke CM, Jarrold MF
Rapid Commun. Mass Spectrom. (2016) 30(17):1957-62 (PMC5137368) - Prevalence of Multidrug-Resistant Bacteria on Fresh Vegetables Collected from Farmers' Markets in Connecticut.
Karumathil DP, Yin HB, Kollanoor-Johny A, Venkitanarayanan K
J. Food Prot. (2016) 79(8):1446-51 - Draft Genome Sequence of Lactococcus garvieae Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States.
Nelson MC, Varney JS, Welch TJ, Graf J
Genome Announc (2016) 4(4): (PMC4974324) - Coming of Age: Considerations in the Prescription of Exercise for Older Adults.
Zaleski AL, Taylor BA, Panza GA, Wu Y, Pescatello LS, Thompson PD, Fernandez AB
Methodist Debakey Cardiovasc J (2016) 12(2):98-104 (PMC4969034) 10.14797/mdcj-12-2-98 - Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates.
Graf J
Annu. Rev. Microbiol. (2016) 70:375-93 - Alternate promoter usage generates two subpopulations of the neuronal RhoGEF Kalirin-7.
Miller MB, Yan Y, Wu Y, Hao B, Mains RE, Eipper BA
J. Neurochem. (2016) 140(6):889-902 (PMC5274606) 10.1111/jnc.13749 - Impact of a homing intein on recombination frequency and organismal fitness.
Naor A, Altman-Price N, Soucy SM, Green AG, Mitiagin Y, Turgeman-Grott I, Davidovich N, Gogarten JP, Gophna U
Proc. Natl. Acad. Sci. U.S.A. (2016) 113(32):E4654-61 (PMC4987785) - Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories.
Boucher N, Noll KM
Extremophiles (2016) 20(5):771-83 - Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel.
Ram-Mohan N, Oren A, Papke RT
Extremophiles (2016) 20(5):747-57 - Charged Nonclassical Antifolates with Activity Against Gram-Positive and Gram-Negative Pathogens.
Scocchera E, Reeve SM, Keshipeddy S, Lombardo MN, Hajian B, Sochia AE, Alverson JB, Priestley ND, Anderson AC, Wright DL
ACS Med Chem Lett (2016) 7(7):692-6 (PMC4948012) 10.1021/acsmedchemlett.6b00120 - Use of Raman Spectroscopy and Phase-Contrast Microscopy To Characterize Cold Atmospheric Plasma Inactivation of Individual Bacterial Spores.
Wang S, Doona CJ, Setlow P, Li YQ
Appl. Environ. Microbiol. (2016) 82(19):5775-84 (PMC5038032) - Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes.
Kenedy MR, Scott EJ, Shrestha B, Anand A, Iqbal H, Radolf JD, Dyer DW, Akins DR
BMC Microbiol. (2016) 16(1):141 (PMC4939628) - Biomonitoring in the Era of the Exposome.
Dennis KK, Marder E, Balshaw DM, Cui Y, Lynes MA, Patti GJ, Rappaport SM, Shaughnessy DT, Vrijheid M, Barr DB
Environ. Health Perspect. (2016) 125(4):502-510 (PMC5381997) - Unexpected biodiversity of ciliates in marine samples from below the photic zone.
Grattepanche JD, Santoferrara LF, McManus GB, Katz LA
Mol. Ecol. (2016) 25(16):3987-4000 - Inactivation of Acinetobacter baumannii Biofilms on Polystyrene, Stainless Steel, and Urinary Catheters by Octenidine Dihydrochloride.
Narayanan A, Nair MS, Karumathil DP, Baskaran SA, Venkitanarayanan K, Amalaradjou MA
Front Microbiol (2016) 7:847 (PMC4899441) - Distinct Transcriptional Changes and Epithelial-Stromal Interactions Are Altered in Early-Stage Colon Cancer Development.
Mo A, Jackson S, Varma K, Carpino A, Giardina C, Devers TJ, Rosenberg DW
Mol. Cancer Res. (2016) 14(9):795-804 (PMC5025366) - Antibacterial Antifolates: From Development through Resistance to the Next Generation.
Estrada A, Wright DL, Anderson AC
Cold Spring Harb Perspect Med (2016) 6(8): (PMC4968165) 10.1101/cshperspect.a028324 - Effects of High-Pressure Treatment on Spores of Clostridium Species.
Doona CJ, Feeherry FE, Setlow B, Wang S, Li W, Nichols FC, Talukdar PK, Sarker MR, Li YQ, Shen A, Setlow P
Appl. Environ. Microbiol. (2016) 82(17):5287-97 (PMC4988188) - Phosphorus Deficiency Inhibits Cell Division But Not Growth in the Dinoflagellate Amphidinium carterae.
Li M, Shi X, Guo C, Lin S
Front Microbiol (2016) 7:826 (PMC4887478) 10.3389/fmicb.2016.00826 - An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.
Wu Y
Bioinformatics (2016) 32(12):i225-i233 (PMC4908345) 10.1093/bioinformatics/btw261 - Charged Propargyl-Linked Antifolates Reveal Mechanisms of Antifolate Resistance and Inhibit Trimethoprim-Resistant MRSA Strains Possessing Clinically Relevant Mutations.
Reeve SM, Scocchera E, Ferreira JJ, G-Dayanandan N, Keshipeddy S, Wright DL, Anderson AC
J. Med. Chem. (2016) 59(13):6493-500 (PMC5257293) 10.1021/acs.jmedchem.6b00688 - Morphological and molecular characterization of Ptychodiscus noctiluca revealed the polyphyletic nature of the order Ptychodiscales (Dinophyceae).
Gómez F, Qiu D, Dodge JD, Lopes RM, Lin S
J. Phycol. (2016) 52(5):793-805 10.1111/jpy.12438 - House Finch (Haemorhous mexicanus) Conjunctivitis, and Mycoplasma spp. Isolated from North American Wild Birds, 1994-2015.
Ley DH, Hawley DM, Geary SJ, Dhondt AA
J. Wildl. Dis. (2016) 52(3):669-73 (PMC4961609) 10.7589/2015-09-244 - Inactivation of Salmonella enteritidis on shell eggs by coating with phytochemicals.
Upadhyaya I, Yin HB, Surendran Nair M, Chen CH, Lang R, Darre MJ, Venkitanarayanan K
Poult. Sci. (2016) 95(9):2106-11 - Metallothionein regulates intracellular zinc signaling during CD4(+) T cell activation.
Rice JM, Zweifach A, Lynes MA
BMC Immunol. (2016) 17(1):13 (PMC4890327) - Inactivation of Listeria monocytogenes, Salmonella spp. and Escherichia coli O157:H7 on cantaloupes by octenidine dihydrochloride.
Upadhyay A, Chen CH, Yin H, Upadhyaya I, Fancher S, Liu Y, Nair MS, Jankelunas L, Patel JR, Venkitanarayanan K
Food Microbiol. (2016) 58:121-7 - Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza.
Watanabe S, Fučíková K, Lewis LA, Lewis PO
Am. J. Bot. (2016) 103(5):865-75 - Selenium reduces enterohemorrhagic Escherichia coli O157:H7 verotoxin production and globotriaosylceramide receptor expression on host cells.
Surendran-Nair M, Kollanoor-Johny A, Ananda-Baskaran S, Norris C, Lee JY, Venkitanarayanan K
Future Microbiol (2016) 11:745-56 - Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila-microbe interactions.
Broderick NA
Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016) 371(1695): (PMC4874392) 10.1098/rstb.2015.0295 - Estimating Bayesian Phylogenetic Information Content.
Lewis PO, Chen MH, Kuo L, Lewis LA, Fučíková K, Neupane S, Wang YB, Shi D
Syst. Biol. (2016) 65(6):1009-1023 (PMC5066063) - Spatiotemporal analysis of RhoA/B/C activation in primary human endothelial cells.
Reinhard NR, van Helden SF, Anthony EC, Yin T, Wu YI, Goedhart J, Gadella TW, Hordijk PL
Sci Rep (2016) 6:25502 (PMC4857094) 10.1038/srep25502 - Ischemic stroke induces gut permeability and enhances bacterial translocation leading to sepsis in aged mice.
Crapser J, Ritzel R, Verma R, Venna VR, Liu F, Chauhan A, Koellhoffer E, Patel A, Ricker A, Maas K, Graf J, McCullough LD
Aging (Albany NY) (2016) 8(5):1049-63 (PMC4931853) - Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender.
Cong X, Xu W, Janton S, Henderson WA, Matson A, McGrath JM, Maas K, Graf J
PLoS ONE (2016) 11(4):e0152751 (PMC4844123) - Efficient Activation of Apoptotic Signaling during Mitotic Arrest with AK301.
Chopra A, Bond MJ, Bleiler M, Yeagley M, Wright D, Giardina C
PLoS ONE (2016) 11(4):e0153818 (PMC4838221) - In vivo efficacy of trans-cinnamaldehyde, carvacrol, and thymol in attenuating Listeria monocytogenes infection in a Galleria mellonella model.
Upadhyay A, Venkitanarayanan K
J Nat Med (2016) 70(3):667-72 - Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta).
Fučíková K, Lewis LA, Lewis PO
Data Brief (2016) 7:558-70 (PMC4802548) - Development of an Enhanced Phenotypic Screen of Cytotoxic T-Lymphocyte Lytic Granule Exocytosis Suitable for Use with Synthetic Compound and Natural Product Collections.
Zhao Z, deMayo JA, West AM, Balunas MJ, Zweifach A
J Biomol Screen (2016) 21(6):556-66 - Evaluation of TagSeq, a reliable low-cost alternative for RNAseq.
Lohman BK, Weber JN, Bolnick DI
Mol Ecol Resour (2016) 16(6):1315-1321 - Phylogenetic Analyses of Three Genes of Pedinomonas noctilucae, the Green Endosymbiont of the Marine Dinoflagellate Noctiluca scintillans, Reveal its Affiliation to the Order Marsupiomonadales (Chlorophyta, Pedinophyceae) under the Reinstated Name Protoeuglena noctilucae.
Wang L, Lin X, Goes JI, Lin S
Protist (2016) 167(2):205-16 10.1016/j.protis.2016.02.005 - Acquiring Structural Information on Virus Particles with Charge Detection Mass Spectrometry.
Keifer DZ, Motwani T, Teschke CM, Jarrold MF
J. Am. Soc. Mass Spectrom. (2016) 27(6):1028-36 (PMC5095694) - Contextual Role of a Salt Bridge in the Phage P22 Coat Protein I-Domain.
Harprecht C, Okifo O, Robbins KJ, Motwani T, Alexandrescu AT, Teschke CM
J. Biol. Chem. (2016) 291(21):11359-72 (PMC4900280) - Eugenol in combination with lactic acid bacteria attenuates Listeria monocytogenes virulence in vitro and in invertebrate model Galleria mellonella.
Upadhyay A, Upadhyaya I, Mooyottu S, Venkitanarayanan K
J. Med. Microbiol. (2016) 65(6):443-55 - Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov.
Sciuto K, Lewis LA, Verleyen E, Moro I, La Rocca N
J. Phycol. (2016) 51(6):1172-88 - Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton.
Lin S, Litaker RW, Sunda WG
J. Phycol. (2016) 52(1):10-36 10.1111/jpy.12365 - Differential Growth Responses of Marine Phytoplankton to Herbicide Glyphosate.
Wang C, Lin X, Li L, Lin S
PLoS ONE (2016) 11(3):e0151633 (PMC4795549) 10.1371/journal.pone.0151633 - REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.
Chu C, Nielsen R, Wu Y
PLoS ONE (2016) 11(3):e0150719 (PMC4792456) 10.1371/journal.pone.0150719 - Cyclin-Dependent Kinase CRK9, Required for Spliced Leader trans Splicing of Pre-mRNA in Trypanosomes, Functions in a Complex with a New L-Type Cyclin and a Kinetoplastid-Specific Protein.
Badjatia N, Park SH, Ambrósio DL, Kirkham JK, Günzl A
PLoS Pathog. (2016) 12(3):e1005498 (PMC4783070) - Clinical Effects of Lactobacillus rhamnosus in Non-Surgical Treatment of Chronic Periodontitis: A Randomized Placebo-Controlled Trial With 1-Year Follow-Up.
Morales A, Carvajal P, Silva N, Hernandez M, Godoy C, Rodriguez G, Cabello R, Garcia-Sesnich J, Hoare A, Diaz PI, Gamonal J
J. Periodontol. (2016) 87(8):944-52 - The RecA-Dependent SOS Response Is Active and Required for Processing of DNA Damage during Bacillus subtilis Sporulation.
Ramírez-Guadiana FH, Barajas-Ornelas Rdel C, Corona-Bautista SU, Setlow P, Pedraza-Reyes M
PLoS ONE (2016) 11(3):e0150348 (PMC4773242) - Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes.
Benjamino J, Graf J
Front Microbiol (2016) 7:171 (PMC4756164) - Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening.
Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A
J Biomol Screen (2016) 21(6):535-47 - Poor Long-Term Efficacy of Prevnar-13 in Sickle Cell Disease Mice Is Associated with an Inability to Sustain Pneumococcal-Specific Antibody Titers.
Szczepanek SM, Roberts S, Rogers K, Cotte C, Adami AJ, Bracken SJ, Salmon S, Secor ER, Thrall RS, Andemariam B, Metzger DW
PLoS ONE (2016) 11(2):e0149261 (PMC4766082) 10.1371/journal.pone.0149261 - Antimicrobial eugenol nanoemulsion prepared by gum arabic and lecithin and evaluation of drying technologies.
Hu Q, Gerhard H, Upadhyaya I, Venkitanarayanan K, Luo Y
Int. J. Biol. Macromol. (2016) 87:130-40 - Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution.
Fučíková K, Lewis PO, Lewis LA
Mol. Phylogenet. Evol. (2016) 98:176-83 - Effects of Trace Metal Concentrations on the Growth of the Coral Endosymbiont Symbiodinium kawagutii.
Rodriguez IB, Lin S, Ho J, Ho TY
Front Microbiol (2016) 7:82 (PMC4744903) 10.3389/fmicb.2016.00082 - Draft Genome Sequence of Shewanella sp. Strain P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia echinata.
Rischer M, Klassen JL, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2016) 4(1): (PMC4759057) - A Cumulative Spore Killing Approach: Synergistic Sporicidal Activity of Dilute Peracetic Acid and Ethanol at Low pH Against Clostridium difficile and Bacillus subtilis Spores.
Nerandzic MM, Sankar C T, Setlow P, Donskey CJ
Open Forum Infect Dis (2016) 3(1):ofv206 (PMC4751341) - Current therapeutic role and medicinal potential of Scutellaria barbata in Traditional Chinese Medicine and Western research.
Tao G, Balunas MJ
J Ethnopharmacol (2016) 182:170-80 - Potentiating the Heat Inactivation of Escherichia coli O157:H7 in Ground Beef Patties by Natural Antimicrobials.
Surendran Nair M, Lau P, Belskie K, Fancher S, Chen CH, Karumathil DP, Yin HB, Liu Y, Ma F, Upadhyaya I, Upadhyay A, Mancini R, Venkitanarayanan K
Front Microbiol (2016) 7:15 (PMC4735374) - Uptake and levels of the antibiotic berberine in individual dormant and germinating Clostridium difficile and Bacillus cereus spores as measured by laser tweezers Raman spectroscopy.
Wang S, Setlow B, Setlow P, Li YQ
J. Antimicrob. Chemother. (2016) 71(6):1540-6 - Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA
Nat Commun (2016) 7:10507 (PMC4748124) - Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?
Santoferrara LF, Grattepanche JD, Katz LA, McManus GB
ISME J (2016) 10(7):1779-90 (PMC4918432) - Correction: Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics.
Hong BY, Furtado Araujo MV, Strausbaugh LD, Terzi E, Ioannidou E, Diaz PI
PLoS ONE (2016) 11(2):e0148893 (PMC4740418) - Rab1 recruits WHAMM during membrane remodeling but limits actin nucleation.
Russo AJ, Mathiowetz AJ, Hong S, Welch MD, Campellone KG
Mol. Biol. Cell (2016) 27(6):967-78 (PMC4791140) 10.1091/mbc.E15-07-0508 - F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling.
Heemskerk N, Schimmel L, Oort C, van Rijssel J, Yin T, Ma B, van Unen J, Pitter B, Huveneers S, Goedhart J, Wu Y, Montanez E, Woodfin A, van Buul JD
Nat Commun (2016) 7:10493 (PMC4737874) 10.1038/ncomms10493 - Improvement of Biological Indicators by Uniformly Distributing Bacillus subtilis Spores in Monolayers To Evaluate Enhanced Spore Decontamination Technologies.
Raguse M, Fiebrandt M, Stapelmann K, Madela K, Laue M, Lackmann JW, Thwaite JE, Setlow P, Awakowicz P, Moeller R
Appl. Environ. Microbiol. (2016) 82(7):2031-2038 (PMC4807530) - Medusamide A, a Panamanian Cyanobacterial Depsipeptide with Multiple β-Amino Acids.
Fenner AM, Engene N, Spadafora C, Gerwick WH, Balunas MJ
Org. Lett. (2016) 18(3):352-5 - Standardized Assessment of Biodiversity Trends in Tropical Forest Protected Areas: The End Is Not in Sight.
Beaudrot L, Ahumada JA, O'Brien T, Alvarez-Loayza P, Boekee K, Campos-Arceiz A, Eichberg D, Espinosa S, Fegraus E, Fletcher C, Gajapersad K, Hallam C, Hurtado J, Jansen PA, Kumar A, Larney E, Lima MG, Mahony C, Martin EH, McWilliam A, Mugerwa B, Ndoundou-Hockemba M, Razafimahaimodison JC, Romero-Saltos H, Rovero F, Salvador J, Santos F, Sheil D, Spironello WR, Willig MR, Winarni NL, Zvoleff A, Andelman SJ
PLoS Biol. (2016) 14(1):e1002357 (PMC4718630) - Rapid Remodeling of Invadosomes by Gi-coupled Receptors: DISSECTING THE ROLE OF Rho GTPases.
Kedziora KM, Leyton-Puig D, Argenzio E, Boumeester AJ, van Butselaar B, Yin T, Wu YI, van Leeuwen FN, Innocenti M, Jalink K, Moolenaar WH
J. Biol. Chem. (2016) 291(9):4323-33 (PMC4813461) 10.1074/jbc.M115.695940 - Comparative Gut Microbiota of 59 Neotropical Bird Species.
Hird SM, Sánchez C, Carstens BC, Brumfield RT
Front Microbiol (2016) 6:1403 (PMC4685052) 10.3389/fmicb.2015.01403 2015
- Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.
Newcomer RL, Fraser LCR, Teschke CM, Alexandrescu AT
Biophys. J. (2015) 109(12):2666-2677 (PMC4699920) - Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings.
Ott BM, Beka L, Graf J, Rio RV
Genome Announc (2015) 3(6): (PMC4683228) - Draft Genome Sequences of Six Pseudoalteromonas Strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, Which Induce Larval Settlement and Metamorphosis in Hydractinia echinata.
Klassen JL, Wolf T, Rischer M, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2015) 3(6): (PMC4683232) - Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations.
Milligan-Myhre K, Small CM, Mittge EK, Agarwal M, Currey M, Cresko WA, Guillemin K
Disease models & mechanisms (2015) 9(2):187-98 PMC3017379 10.3354/ame028141 - ICP8 Filament Formation Is Essential for Replication Compartment Formation during Herpes Simplex Virus Infection.
Darwish AS, Grady LM, Bai P, Weller SK
J. Virol. (2015) 90(5):2561-70 (PMC4810729) 10.1128/JVI.02854-15 - Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.
Klassen JL, Rischer M, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2015) 3(6): (PMC4675935) - An examination of the factors influencing mercury and methylmercury particulate distributions, methylation and demethylation rates in laboratory-generated marine snow.
Ortiz VL, Mason RP, Ward JE
Mar Chem (2015) 177(Pt 5):753-762 (PMC4669965) 10.1016/j.marchem.2015.07.006 - Uptake of and Resistance to the Antibiotic Berberine by Individual Dormant, Germinating and Outgrowing Bacillus Spores as Monitored by Laser Tweezers Raman Spectroscopy.
Wang S, Yu J, Suvira M, Setlow P, Li YQ
PLoS ONE (2015) 10(12):e0144183 (PMC4670213) - Untwisting the Caenorhabditis elegans embryo.
Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H
Elife (2015) 4: (PMC4764590) 10.7554/eLife.10070 - Space station image captures a red tide ciliate bloom at high spectral and spatial resolution.
Dierssen H, McManus GB, Chlus A, Qiu D, Gao BC, Lin S
Proc. Natl. Acad. Sci. U.S.A. (2015) 112(48):14783-7 (PMC4672822) - Spliced leader RNA trans-splicing discovered in copepods.
Yang F, Xu D, Zhuang Y, Yi X, Huang Y, Chen H, Lin S, Campbell DA, Sturm NR, Liu G, Zhang H
Sci Rep (2015) 5:17411 (PMC4664967) 10.1038/srep17411 - Integration of linear and dendritic actin nucleation in Nck-induced actin comets.
Borinskaya S, Velle KB, Campellone KG, Talman A, Alvarez D, Agaisse H, Wu YI, Loew LM, Mayer BJ
Mol. Biol. Cell (2015) 27(2):247-59 (PMC4713129) 10.1091/mbc.E14-11-1555 - Memory of Germinant Stimuli in Bacterial Spores.
Wang S, Faeder JR, Setlow P, Li YQ
MBio (2015) 6(6):e01859-15 (PMC4669388) - The challenge of resistance in antimicrobial drug development.
Anderson AC, Wright DL
Future Microbiol (2015) 10(11):1709-10 (PMC4733617) 10.2217/fmb.15.75 - Exposure to pairs of Aeromonas strains enhances virulence in the Caenorhabditis elegans infection model.
Mosser T, Talagrand-Reboul E, Colston SM, Graf J, Figueras MJ, Jumas-Bilak E, Lamy B
Front Microbiol (2015) 6:1218 (PMC4631986) - Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover.
Li YF, Shi J, Nelson MC, Chen PH, Graf J, Li Y, Yu Z
Bioresour. Technol. (2015) 200:744-52 - Complementary Effects of Host Defense Peptides Piscidin 1 and Piscidin 3 on DNA and Lipid Membranes: Biophysical Insights into Contrasting Biological Activities.
Hayden RM, Goldberg GK, Ferguson BM, Schoeneck MW, Libardo MD, Mayeux SE, Shrestha A, Bogardus KA, Hammer J, Pryshchep S, Lehman HK, McCormick ML, Blazyk J, Angeles-Boza AM, Fu R, Cotten ML
J Phys Chem B (2015) 119(49):15235-46 - Global Changes in Mycoplasma gallisepticum Phase-Variable Lipoprotein Gene vlhA Expression during In Vivo Infection of the Natural Chicken Host.
Pflaum K, Tulman ER, Beaudet J, Liao X, Geary SJ
Infect. Immun. (2015) 84(1):351-5 (PMC4693984) 10.1128/IAI.01092-15 - The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.
Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D
Science (2015) 350(6261):691-4 10.1126/science.aad0408 - Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions.
Murfin KE, Whooley AC, Klassen JL, Goodrich-Blair H
BMC Genomics (2015) 16:889 (PMC4630870) - A systematic review of syphilis serological treatment outcomes in HIV-infected and HIV-uninfected persons: rethinking the significance of serological non-responsiveness and the serofast state after therapy.
Seña AC, Zhang XH, Li T, Zheng HP, Yang B, Yang LG, Salazar JC, Cohen MS, Moody MA, Radolf JD, Tucker JD
BMC Infect. Dis. (2015) 15:479 (PMC4625448) - Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats.
Wong HL, Smith DL, Visscher PT, Burns BP
Sci Rep (2015) 5:15607 (PMC4620479) - Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).
Marshall DC, Hill KB, Moulds M, Vanderpool D, Cooley JR, Mohagan AB, Simon C
Syst. Biol. (2015) 65(1):16-34 10.1093/sysbio/syv069 - Water and Small-Molecule Permeation of Dormant Bacillus subtilis Spores.
Knudsen SM, Cermak N, Delgado FF, Setlow B, Setlow P, Manalis SR
J. Bacteriol. (2015) 198(1):168-77 (PMC4686191) - Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A.
Kirkham JK, Park SH, Nguyen TN, Lee JH, Günzl A
Mol. Cell. Biol. (2015) 36(1):95-107 (PMC4702606) - Plasma membrane restricted RhoGEF activity is sufficient for RhoA-mediated actin polymerization.
van Unen J, Reinhard NR, Yin T, Wu YI, Postma M, Gadella TW, Goedhart J
Sci Rep (2015) 5:14693 (PMC4592971) 10.1038/srep14693 - Treponema pallidum in Gel Microdroplets: A Method for Topological Analysis of BamA (TP0326) and Localization of Rare Outer Membrane Proteins.
Luthra A, Anand A, Radolf JD
Methods Mol. Biol. (2015) 1329:67-75 - Widespread positive but weak assortative mating by diet within stickleback populations.
Ingram T, Jiang Y, Rangel R, Bolnick DI
Ecol Evol (2015) 5(16):3352-63 (PMC4569031) - Rapidly diverging evolution of an atypical alkaline phosphatase (PhoA(aty)) in marine phytoplankton: insights from dinoflagellate alkaline phosphatases.
Lin X, Wang L, Shi X, Lin S
Front Microbiol (2015) 6:868 (PMC4548154) 10.3389/fmicb.2015.00868 - Labelling and optical erasure of synaptic memory traces in the motor cortex.
Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H
Nature (2015) 525(7569):333-8 (PMC4634641) 10.1038/nature15257 - Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding.
Bauer WJ, Luthra A, Zhu G, Radolf JD, Malkowski MG, Caimano MJ
J. Struct. Biol. (2015) 192(1):48-58 (PMC4605270) - Fighting Ebola with novel spore decontamination technologies for the military.
Doona CJ, Feeherry FE, Kustin K, Olinger GG, Setlow P, Malkin AJ, Leighton T
Front Microbiol (2015) 6:663 (PMC4533522) - Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia.
Campbell MA, Van Leuven JT, Meister RC, Carey KM, Simon C, McCutcheon JP
Proc. Natl. Acad. Sci. U.S.A. (2015) 112(33):10192-9 (PMC4547289) 10.1073/pnas.1421386112 - Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract.
Maltz M, LeVarge BL, Graf J
Front Microbiol (2015) 6:763 (PMC4516982) - The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis.
Fullmer MS, Soucy SM, Gogarten JP
Front Microbiol (2015) 6:728 (PMC4523029) - Minimum Information about a Biosynthetic Gene cluster.
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO
Nat. Chem. Biol. (2015) 11(9):625-31 (PMC5714517) - A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly.
D'Lima NG, Teschke CM
J. Virol. (2015) 89(20):10569-79 (PMC4580156) - Metallothionein differentially affects the host response to Listeria infection both with and without an additional stress from cold-restraint.
Emeny RT, Kasten-Jolly J, Mondal T, Lynes MA, Lawrence DA
Cell Stress Chaperones (2015) 20(6):1013-22 (PMC4595426) - Photochemistry and Photobiology of the Spore Photoproduct: A 50-Year Journey.
Setlow P, Li L
Photochem. Photobiol. (2015) 91(6):1263-90 (PMC4631623) - An examination of the ingestion, bioaccumulation, and depuration of titanium dioxide nanoparticles by the blue mussel (Mytilus edulis) and the eastern oyster (Crassostrea virginica).
Doyle JJ, Ward JE, Mason R
Mar. Environ. Res. (2015) 110:45-52 10.1016/j.marenvres.2015.07.020 - Molecular phylogenetics, diversification, and systematics of Tibicen Latreille 1825 and allied cicadas of the tribe Cryptotympanini, with three new genera and emphasis on species from the USA and Canada(Hemiptera: Auchenorrhyncha: Cicadidae).
Hill KB, Marshall DC, Moulds MS, Simon C
Zootaxa (2015) 3985(2):219-51 10.11646/zootaxa.3985.2.3 - Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System.
Cong X, Henderson WA, Graf J, McGrath JM
Adv Neonatal Care (2015) 15(5):314-23; quiz E1-2 (PMC4583334) - Structural Characterization of Interaction between Human Ubiquitin-specific Protease 7 and Immediate-Early Protein ICP0 of Herpes Simplex Virus-1.
Pozhidaeva AK, Mohni KN, Dhe-Paganon S, Arrowsmith CH, Weller SK, Korzhnev DM, Bezsonova I
J. Biol. Chem. (2015) 290(38):22907-18 (PMC4645603) 10.1074/jbc.M115.664805 - Inhibiting Microbial Toxins Using Plant-Derived Compounds and Plant Extracts.
Upadhyay A, Mooyottu S, Yin H, Nair MS, Bhattaram V, Venkitanarayanan K
Medicines (Basel) (2015) 2(3):186-211 (PMC5456214) - Bastimolide A, a Potent Antimalarial Polyhydroxy Macrolide from the Marine Cyanobacterium Okeania hirsuta.
Shao CL, Linington RG, Balunas MJ, Centeno A, Boudreau P, Zhang C, Engene N, Spadafora C, Mutka TS, Kyle DE, Gerwick L, Wang CY, Gerwick WH
J. Org. Chem. (2015) 80(16):7849-55 - Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback.
Jiang Y, Torrance L, Peichel CL, Bolnick DI
Evolution (2015) 69(9):2517-24 - Controlling Aspergillus flavus and Aspergillus parasiticus growth and aflatoxin production in poultry feed using carvacrol and trans-cinnamaldehyde.
Yin HB, Chen CH, Kollanoor-Johny A, Darre MJ, Venkitanarayanan K
Poult. Sci. (2015) 94(9):2183-90 - An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.
Yuan J, Li M, Lin S
PLoS ONE (2015) 10(7):e0133060 (PMC4517865) 10.1371/journal.pone.0133060 - Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling.
Mobberley JM, Khodadad CL, Visscher PT, Reid RP, Hagan P, Foster JS
Sci Rep (2015) 5:12601 (PMC4515876) - HSV-I and the cellular DNA damage response.
Smith S, Weller SK
Future Virol (2015) 10(4):383-397 (PMC4508672) 10.2217/fvl.15.18 - Involvement of Coat Proteins in Bacillus subtilis Spore Germination in High-Salinity Environments.
Nagler K, Setlow P, Reineke K, Driks A, Moeller R
Appl. Environ. Microbiol. (2015) 81(19):6725-35 (PMC4561714) - Horizontal gene transfer: building the web of life.
Soucy SM, Huang J, Gogarten JP
Nat. Rev. Genet. (2015) 16(8):472-82 - Unlocking the Sporicidal Potential of Ethanol: Induced Sporicidal Activity of Ethanol against Clostridium difficile and Bacillus Spores under Altered Physical and Chemical Conditions.
Nerandzic MM, Sunkesula VC, C TS, Setlow P, Donskey CJ
PLoS ONE (2015) 10(7):e0132805 (PMC4503543) - Reducing Colonization and Eggborne Transmission of Salmonella Enteritidis in Layer Chickens by In-Feed Supplementation of Caprylic Acid.
Upadhyaya I, Upadhyay A, Yin HB, Nair MS, Bhattaram VK, Karumathil D, Kollanoor-Johny A, Khan MI, Darre MJ, Curtis PA, Venkitanarayanan K
Foodborne Pathog. Dis. (2015) 12(7):591-7 - Screening for Suitable Reference Genes for Quantitative Real-Time PCR in Heterosigma akashiwo (Raphidophyceae).
Ji N, Li L, Lin L, Lin S
PLoS ONE (2015) 10(7):e0132183 (PMC4489630) 10.1371/journal.pone.0132183 - Among-lake reciprocal transplants induce convergent expression of immune genes in threespine stickleback.
Stutz WE, Schmerer M, Coates JL, Bolnick DI
Mol. Ecol. (2015) 24(18):4629-46 - A local VE-cadherin and Trio-based signaling complex stabilizes endothelial junctions through Rac1.
Timmerman I, Heemskerk N, Kroon J, Schaefer A, van Rijssel J, Hoogenboezem M, van Unen J, Goedhart J, Gadella TW, Yin T, Wu Y, Huveneers S, van Buul JD
J. Cell. Sci. (2015) 128(16):3041-54 10.1242/jcs.168674 - Spore Resistance Properties.
Setlow P
Microbiol Spectr (2015) 2(5): - A method to investigate protein association with intact sealed mycobacterial membrane vesicles.
D'Lima NG, Teschke CM
Anal. Biochem. (2015) 485:109-11 - Nonracemic Antifolates Stereoselectively Recruit Alternate Cofactors and Overcome Resistance in S. aureus.
Keshipeddy S, Reeve SM, Anderson AC, Wright DL
J. Am. Chem. Soc. (2015) 137(28):8983-90 (PMC4733634) 10.1021/jacs.5b01442 - Effect of organic loading on the microbiota in a temperature-phased anaerobic digestion (TPAD) system co-digesting dairy manure and waste whey.
Li YF, Abraham C, Nelson MC, Chen PH, Graf J, Yu Z
Appl. Microbiol. Biotechnol. (2015) 99(20):8777-92 - Rhodopsin gene expression regulated by the light dark cycle, light spectrum and light intensity in the dinoflagellate Prorocentrum.
Shi X, Li L, Guo C, Lin X, Li M, Lin S
Front Microbiol (2015) 6:555 (PMC4451421) 10.3389/fmicb.2015.00555 - Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73.
Jinks RN, Puffenberger EG, Baple E, Harding B, Crino P, Fogo AB, Wenger O, Xin B, Koehler AE, McGlincy MH, Provencher MM, Smith JD, Tran L, Al Turki S, Chioza BA, Cross H, Harlalka GV, Hurles ME, Maroofian R, Heaps AD, Morton MC, Stempak L, Hildebrandt F, Sadowski CE, Zaritsky J, Campellone K, Morton DH, Wang H, Crosby A, Strauss KA
Brain (2015) 138(Pt 8):2173-90 (PMC4511861) 10.1093/brain/awv153 - End stage renal disease as a modifier of the periodontal microbiome.
Araújo MV, Hong BY, Fava PL, Khan S, Burleson JA, Fares G, Samson W, Strausbaugh LD, Diaz PI, Ioannidou E
BMC Nephrol (2015) 16:80 (PMC4460699) - Microbial diversity of hypersaline environments: a metagenomic approach.
Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT
Curr. Opin. Microbiol. (2015) 25:80-7 - WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.
Santella A, Catena R, Kovacevic I, Shah P, Yu Z, Marquina-Solis J, Kumar A, Wu Y, Schaff J, Colón-Ramos D, Shroff H, Mohler WA, Bao Z
BMC Bioinformatics (2015) 16:189 (PMC4459063) 10.1186/s12859-015-0627-8 - Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts.
Murfin KE, Lee MM, Klassen JL, McDonald BR, Larget B, Forst S, Stock SP, Currie CR, Goodrich-Blair H
MBio (2015) 6(3):e00076 (PMC4462624) - Bird biodiversity assessments in temperate forest: the value of point count versus acoustic monitoring protocols.
Klingbeil BT, Willig MR
PeerJ (2015) 3:e973 (PMC4451018) - Self-sustained reduction of multiple metals in a microbial fuel cell-microbial electrolysis cell hybrid system.
Li Y, Wu Y, Liu B, Luan H, Vadas T, Guo W, Ding J, Li B
Bioresour. Technol. (2015) 192:238-46 10.1016/j.biortech.2015.05.030 - Population-Specific Covariation between Immune Function and Color of Nesting Male Threespine Stickleback.
Bolnick DI, Shim KC, Schmerer M, Brock CD
PLoS ONE (2015) 10(6):e0126000 (PMC4454680) - Efficacy of fumigation with Trans-cinnamaldehyde and eugenol in reducing Salmonella enterica serovar Enteritidis on embryonated egg shells.
Upadhyaya I, Yin HB, Nair MS, Chen CH, Upadhyay A, Darre MJ, Venkitanarayanan K
Poult. Sci. (2015) 94(7):1685-90 - Location and stoichiometry of the protease CspB and the cortex-lytic enzyme SleC in Clostridium perfringens spores.
Banawas S, Korza G, Paredes-Sabja D, Li Y, Hao B, Setlow P, Sarker MR
Food Microbiol. (2015) 50:83-7 - Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions.
Chimileski S, Papke RT
Front Microbiol (2015) 6:362 (PMC4419858) - Horizontal gene transfer, dispersal and haloarchaeal speciation.
Papke RT, Corral P, Ram-Mohan N, de la Haba RR, Sánchez-Porro C, Makkay A, Ventosa A
Life (Basel) (2015) 5(2):1405-26 (PMC4500145) - Cyclic di-GMP modulates gene expression in Lyme disease spirochetes at the tick-mammal interface to promote spirochete survival during the blood meal and tick-to-mammal transmission.
Caimano MJ, Dunham-Ems S, Allard AM, Cassera MB, Kenedy M, Radolf JD
Infect. Immun. (2015) 83(8):3043-60 (PMC4496621) - Microbiome profiles in periodontitis in relation to host and disease characteristics.
Hong BY, Furtado Araujo MV, Strausbaugh LD, Terzi E, Ioannidou E, Diaz PI
PLoS ONE (2015) 10(5):e0127077 (PMC4436126) - Female stickleback prefer shallow males: Sexual selection on nest microhabitat.
Bolnick DI, Shim KC, Brock CD
Evolution (2015) 69(6):1643-1653 - Preface to the proceedings of Halophiles 2013.
Papke RT
Front Microbiol (2015) 6:341 (PMC4406061) - Characterization of the Dynamic Germination of Individual Clostridium difficile Spores Using Raman Spectroscopy and Differential Interference Contrast Microscopy.
Wang S, Shen A, Setlow P, Li YQ
J. Bacteriol. (2015) 197(14):2361-73 (PMC4524193) - Long-Term Exposure to House Dust Mite Leads to the Suppression of Allergic Airway Disease Despite Persistent Lung Inflammation.
Bracken SJ, Adami AJ, Szczepanek SM, Ehsan M, Natarajan P, Guernsey LA, Shahriari N, Rafti E, Matson AP, Schramm CM, Thrall RS
Int. Arch. Allergy Immunol. (2015) 166(4):243-58 (PMC4485530) 10.1159/000381058 - Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota.
Smith CC, Snowberg LK, Gregory Caporaso J, Knight R, Bolnick DI
ISME J (2015) 9(11):2515-26 (PMC4611514) - Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.
Ouellette M, Jackson L, Chimileski S, Papke RT
Front Microbiol (2015) 6:251 (PMC4389544) - Hybrid peptide ATCUN-sh-Buforin: Influence of the ATCUN charge and stereochemistry on antimicrobial activity.
Libardo MD, Paul TJ, Prabhakar R, Angeles-Boza AM
Biochimie (2015) 113:143-55 - Ancient horizontal gene transfer and the last common ancestors.
Fournier GP, Andam CP, Gogarten JP
BMC Evol. Biol. (2015) 15:70 (PMC4427996) - Regulation of VDR Expression in Apc-Mutant Mice, Human Colon Cancers and Adenomas.
Giardina C, Nakanishi M, Khan A, Kuratnik A, Xu W, Brenner B, Rosenberg DW
Cancer Prev Res (Phila) (2015) 8(5):387-99 (PMC4417398) - Measuring propargyl-linked drug populations inside bacterial cells, and their interaction with a dihydrofolate reductase target, by Raman microscopy.
Heidari-Torkabadi H, Che T, Lombardo MN, Wright DL, Anderson AC, Carey PR
Biochemistry (2015) 54(17):2719-26 10.1021/acs.biochem.5b00202 - Nature's favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold.
Suhanovsky MM, Teschke CM
Virology (2015) 479-480:487-97 (PMC4424165) - Interplay between chemotaxis and contact inhibition of locomotion determines exploratory cell migration.
Lin B, Yin T, Wu YI, Inoue T, Levchenko A
Nat Commun (2015) 6:6619 (PMC4391292) 10.1038/ncomms7619 - Modulation of pumping rate by two species of marine bivalve molluscs in response to neurotransmitters: Comparison of in vitro and in vivo results.
Frank DM, Deaton L, Shumway SE, Holohan BA, Ward JE
Comp. Biochem. Physiol., Part A Mol. Integr. Physiol. (2015) 185:150-8 10.1016/j.cbpa.2015.03.015 - Isolation and characterization of microsatellite markers useful for exploring introgression among species in the diverse New Zealand cicada genus Kikihia.
Wade EJ, Simon C
J. Insect Sci. (2015) 15: (PMC4535467) 10.1093/jisesa/iev016 - Fukuyoa paulensis gen. et sp. nov., a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae).
Gómez F, Qiu D, Lopes RM, Lin S
PLoS ONE (2015) 10(4):e0119676 (PMC4382304) 10.1371/journal.pone.0119676 - A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326.
Luthra A, Anand A, Hawley KL, LeDoyt M, La Vake CJ, Caimano MJ, Cruz AR, Salazar JC, Radolf JD
J. Bacteriol. (2015) 197(11):1906-20 (PMC4420902) - Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN.
Anand A, LeDoyt M, Karanian C, Luthra A, Koszelak-Rosenblum M, Malkowski MG, Puthenveetil R, Vinogradova O, Radolf JD
J. Biol. Chem. (2015) 290(19):12313-31 (PMC4424362) - The GerW protein is not involved in the germination of spores of Bacillus species.
Cruz-Mora J, Pérez-Valdespino A, Gupta S, Withange N, Kuwana R, Takamatsu H, Christie G, Setlow P
PLoS ONE (2015) 10(3):e0119125 (PMC4366231) - Evolution of the indoor biome.
Martin LJ, Adams RI, Bateman A, Bik HM, Hawks J, Hird SM, Hughes D, Kembel SW, Kinney K, Kolokotronis SO, Levy G, McClain C, Meadow JF, Medina RF, Mhuireach G, Moreau CS, Munshi-South J, Nichols LM, Palmer C, Popova L, Schal C, Täubel M, Trautwein M, Ugalde JA, Dunn RR
Trends Ecol. Evol. (Amst.) (2015) 30(4):223-32 10.1016/j.tree.2015.02.001 - Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.
Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV
Front Microbiol (2015) 6:123 (PMC4337385) - Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts.
Beinart RA, Nyholm SV, Dubilier N, Girguis PR
Environ Microbiol Rep (2015) 6(6):656-64 - Anticarcinogenic properties of medium chain fatty acids on human colorectal, skin and breast cancer cells in vitro.
Narayanan A, Baskaran SA, Amalaradjou MA, Venkitanarayanan K
Int J Mol Sci (2015) 16(3):5014-27 (PMC4394462) - Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake.
Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A
Int. J. Syst. Evol. Microbiol. (2015) 65(Pt 6):1770-8 - This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.
Mandoiu I, Pop M, Rajasekaran S, Spouge JL
Int J Bioinform Res Appl (2015) 10(4-5):341-4 - In-feed supplementation of trans-cinnamaldehyde reduces layer-chicken egg-borne transmission of Salmonella enterica serovar enteritidis.
Upadhyaya I, Upadhyay A, Kollanoor-Johny A, Mooyottu S, Baskaran SA, Yin HB, Schreiber DT, Khan MI, Darre MJ, Curtis PA, Venkitanarayanan K
Appl. Environ. Microbiol. (2015) 81(9):2985-94 (PMC4393446) - NMR assignments for the insertion domain of bacteriophage CUS-3 coat protein.
Tripler TN, Maciejewski MW, Teschke CM, Alexandrescu AT
Biomol NMR Assign (2015) 9(2):333-6 (PMC4544682) - Integrative analysis of 111 reference human epigenomes.
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning A, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes MJ, Bates D, Bell RJ, Bennett DA, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso MJ, Charnecki T, Chen H, Chen Z, Cheng JB, Cho S, Chu A, Chung WY, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass IA, Gnirke A, Gormley M, Gu H, Gu J, Hafler DA, Hangauer MJ, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson AR, Jia H, Jiang P, Johnson AK, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee AY, Lee K, Li J, Li N, Li Y, Ligon KL, Lin S, Lin Y, Liu J, Liu Y, Luckey CJ, Ma YP, Maire C, Marson A, Mattick JS, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukamel E, Nagarajan RP, Neri F, Nery J, Nguyen T, O'Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson NE, Raghuraman S, Raney BJ, Raubitschek A, Reynolds AP, Richards H, Riehle K, Rinaudo P, Robinson JF, Rockweiler NB, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian SL, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won KJ, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen CA, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M
Nature (2015) 518(7539):317-30 (PMC4530010) - The effects of heat activation on Bacillus spore germination, with nutrients or under high pressure, with or without various germination proteins.
Luu S, Cruz-Mora J, Setlow B, Feeherry FE, Doona CJ, Setlow P
Appl. Environ. Microbiol. (2015) 81(8):2927-38 (PMC4375313) - HSV cheats the executioner.
Mossman KL, Weller SK
Cell Host Microbe (2015) 17(2):148-51 10.1016/j.chom.2015.01.013 - Competitive (13)C and (18)O kinetic isotope effects on CO2 reduction catalyzed by Re(bpy)(CO)3Cl.
Schneider TW, Angeles-Boza AM
Dalton Trans (2015) 44(19):8784-7 - Metabolic pathway predictions for metabolomics: a molecular structure matching approach.
Hamdalla MA, Rajasekaran S, Grant DF, Măndoiu II
J Chem Inf Model (2015) 55(3):709-18 - Complete Genome Sequence of the Novel Leech Symbiont Mucinivorans hirudinis M3T.
Nelson MC, Bomar L, Graf J
Genome Announc (2015) 3(1): (PMC4319616) - Covarying variances: more morphologically variable populations also exhibit more diet variation.
Snowberg LK, Hendrix KM, Bolnick DI
Oecologia (2015) 178(1):89-101 - Hyperbaric oxygen therapy (HBOT) suppresses biomarkers of cell stress and kidney injury in diabetic mice.
Verma R, Chopra A, Giardina C, Sabbisetti V, Smyth JA, Hightower LE, Perdrizet GA
Cell Stress Chaperones (2015) 20(3):495-505 (PMC4406928) - Complete Genome Sequence of Yersinia ruckeri Strain CSF007-82, Etiologic Agent of Red Mouth Disease in Salmonid Fish.
Nelson MC, LaPatra SE, Welch TJ, Graf J
Genome Announc (2015) 3(1): (PMC4319512) - Slow leakage of Ca-dipicolinic acid from individual bacillus spores during initiation of spore germination.
Wang S, Setlow P, Li YQ
J. Bacteriol. (2015) 197(6):1095-103 (PMC4336336) - Mycoplasma gallisepticum in vivo induced antigens expressed during infection in chickens.
Ron M, Gorelick-Ashkenazi A, Levisohn S, Nir-Paz R, Geary SJ, Tulman E, Lysnyansky I, Yogev D
Vet. Microbiol. (2015) 175(2-4):265-74 10.1016/j.vetmic.2014.12.007 - Discrimination of closely related species in tintinnid ciliates: new insights on crypticity and polymorphism in the genus Helicostomella.
Santoferrara LF, Tian M, Alder VA, McManus GB
Protist (2015) 166(1):78-92 - Protist-facilitated particle transport using emulated soil micromodels.
Rubinstein RL, Kadilak AL, Cousens VC, Gage DJ, Shor LM
Environ. Sci. Technol. (2015) 49(3):1384-91 - Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana.
Nelson MC, Bomar L, Maltz M, Graf J
Int. J. Syst. Evol. Microbiol. (2015) 65(Pt 3):990-5 (PMC4811647) - Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling.
Das S, Yin T, Yang Q, Zhang J, Wu YI, Yu J
Proc. Natl. Acad. Sci. U.S.A. (2015) 112(3):E267-76 (PMC4311845) 10.1073/pnas.1409667112 - The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts.
Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, Phillips HR, Senior RA, Bennett DJ, Booth H, Choimes A, Correia DL, Day J, Echeverría-Londoño S, Garon M, Harrison ML, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, White HJ, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Ancrenaz M, Arbeláez-Cortés E, Armbrecht I, Azhar B, Azpiroz AB, Baeten L, Báldi A, Banks JE, Barlow J, Batáry P, Bates AJ, Bayne EM, Beja P, Berg Å, Berry NJ, Bicknell JE, Bihn JH, Böhning-Gaese K, Boekhout T, Boutin C, Bouyer J, Brearley FQ, Brito I, Brunet J, Buczkowski G, Buscardo E, Cabra-García J, Calviño-Cancela M, Cameron SA, Cancello EM, Carrijo TF, Carvalho AL, Castro H, Castro-Luna AA, Cerda R, Cerezo A, Chauvat M, Clarke FM, Cleary DF, Connop SP, D'Aniello B, da Silva PG, Darvill B, Dauber J, Dejean A, Diekötter T, Dominguez-Haydar Y, Dormann CF, Dumont B, Dures SG, Dynesius M, Edenius L, Elek Z, Entling MH, Farwig N, Fayle TM, Felicioli A, Felton AM, Ficetola GF, Filgueiras BK, Fonte SJ, Fraser LH, Fukuda D, Furlani D, Ganzhorn JU, Garden JG, Gheler-Costa C, Giordani P, Giordano S, Gottschalk MS, Goulson D, Gove AD, Grogan J, Hanley ME, Hanson T, Hashim NR, Hawes JE, Hébert C, Helden AJ, Henden JA, Hernández L, Herzog F, Higuera-Diaz D, Hilje B, Horgan FG, Horváth R, Hylander K, Isaacs-Cubides P, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Jonsell M, Jung TS, Kapoor V, Kati V, Katovai E, Kessler M, Knop E, Kolb A, Kőrösi Á, Lachat T, Lantschner V, Le Féon V, LeBuhn G, Légaré JP, Letcher SG, Littlewood NA, López-Quintero CA, Louhaichi M, Lövei GL, Lucas-Borja ME, Luja VH, Maeto K, Magura T, Mallari NA, Marin-Spiotta E, Marshall EJ, Martínez E, Mayfield MM, Mikusinski G, Milder JC, Miller JR, Morales CL, Muchane MN, Muchane M, Naidoo R, Nakamura A, Naoe S, Nates-Parra G, Navarrete Gutierrez DA, Neuschulz EL, Noreika N, Norfolk O, Noriega JA, Nöske NM, O'Dea N, Oduro W, Ofori-Boateng C, Oke CO, Osgathorpe LM, Paritsis J, Parra-H A, Pelegrin N, Peres CA, Persson AS, Petanidou T, Phalan B, Philips TK, Poveda K, Power EF, Presley SJ, Proença V, Quaranta M, Quintero C, Redpath-Downing NA, Reid JL, Reis YT, Ribeiro DB, Richardson BA, Richardson MJ, Robles CA, Römbke J, Romero-Duque LP, Rosselli L, Rossiter SJ, Roulston TH, Rousseau L, Sadler JP, Sáfián S, Saldaña-Vázquez RA, Samnegård U, Schüepp C, Schweiger O, Sedlock JL, Shahabuddin G, Sheil D, Silva FA, Slade EM, Smith-Pardo AH, Sodhi NS, Somarriba EJ, Sosa RA, Stout JC, Struebig MJ, Sung YH, Threlfall CG, Tonietto R, Tóthmérész B, Tscharntke T, Turner EC, Tylianakis JM, Vanbergen AJ, Vassilev K, Verboven HA, Vergara CH, Vergara PM, Verhulst J, Walker TR, Wang Y, Watling JI, Wells K, Williams CD, Willig MR, Woinarski JC, Wolf JH, Woodcock BA, Yu DW, Zaitsev AS, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JP, Purvis A
Ecol Evol (2015) 4(24):4701-35 (PMC4278822) 2014
- Analysis of metabolism in dormant spores of Bacillus species by 31P nuclear magnetic resonance analysis of low-molecular-weight compounds.
Ghosh S, Korza G, Maciejewski M, Setlow P
J. Bacteriol. (2014) 197(5):992-1001 (PMC4325094) - The spliceosomal PRP19 complex of trypanosomes.
Ambrósio DL, Badjatia N, Günzl A
Mol. Microbiol. (2014) 95(5):885-901 (PMC4374492) - Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina.
Guo Z, Zhang H, Lin S
PLoS ONE (2014) 9(12):e114941 (PMC4266641) 10.1371/journal.pone.0114941 - Intraspecific competition reduces niche width in experimental populations.
Parent CE, Agashe D, Bolnick DI
Ecol Evol (2014) 4(20):3978-90 (PMC4242580) - Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons.
Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DK, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN
Dev Neurobiol (2014) 75(9):895-907 - Natural products as exquisitely potent cytotoxic payloads for antibody- drug conjugates.
Gromek SM, Balunas MJ
Curr Top Med Chem (2014) 14(24):2822-34 - Copper-binding tripeptide motif increases potency of the antimicrobial peptide Anoplin via Reactive Oxygen Species generation.
Libardo MD, Nagella S, Lugo A, Pierce S, Angeles-Boza AM
Biochem. Biophys. Res. Commun. (2014) 456(1):446-51 - Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons.
Banday AR, Baumgartner M, Al Seesi S, Karunakaran DK, Venkatesh A, Congdon S, Lemoine C, Kilcollins AM, Mandoiu I, Punzo C, Kanadia RN
Cell Cycle (2014) 13(16):2526-41 (PMC4614993) - Improved gene tree error correction in the presence of horizontal gene transfer.
Bansal MS, Wu YC, Alm EJ, Kellis M
Bioinformatics (2014) 31(8):1211-8 (PMC4393519) - Batch, design optimization, and DNA sequencing study for continuous 1,3-propanediol production from waste glycerol by a soil-based inoculum.
Kanjilal B, Noshadi I, Bautista EJ, Srivastava R, Parnas RS
Appl. Microbiol. Biotechnol. (2014) 99(5):2105-17 - Characterization of a multidrug resistant C. difficile meat isolate.
Mooyottu S, Flock G, Kollanoor-Johny A, Upadhyaya I, Jayarao B, Venkitanarayanan K
Int. J. Food Microbiol. (2014) 192:111-6 - Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments.
Bernhard JM, Kormas K, Pachiadaki MG, Rocke E, Beaudoin DJ, Morrison C, Visscher PT, Cobban A, Starczak VR, Edgcomb VP
Front Microbiol (2014) 5:605 (PMC4233946) - Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates.
Al Seesi S, Tiagueu YT, Zelikovsky A, Măndoiu II
BMC Genomics (2014) 15 Suppl 8:S2 (PMC4248812) - Feature selection and classifier performance on diverse bio- logical datasets.
Hemphill E, Lindsay J, Lee C, Măndoiu II, Nelson CE
BMC Bioinformatics (2014) 15 Suppl 1:S4 (PMC4248652) - Antibiofilm Effect of Octenidine Hydrochloride on Staphylococcus aureus, MRSA and VRSA.
Amalaradjou MA, Venkitanarayanan K
Pathogens (2014) 3(2):404-16 (PMC4243453) - Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host adaptation.
Iyer R, Caimano MJ, Luthra A, Axline D, Corona A, Iacobas DA, Radolf JD, Schwartz I
Mol. Microbiol. (2014) 95(3):509-38 (PMC4429771) - GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.
Chu C, Zhang J, Wu Y
PLoS ONE (2014) 9(11):e113324 (PMC4244156) 10.1371/journal.pone.0113324 - A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B
Nature (2014) 515(7527):355-64 (PMC4266106) - Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.
Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J
MBio (2014) 5(6):e02136 (PMC4251997) - Viruses of haloarchaea.
Luk AW, Williams TJ, Erdmann S, Papke RT, Cavicchioli R
Life (Basel) (2014) 4(4):681-715 (PMC4284463) - Optogenetics: optical control of a photoactivatable Rac in living cells.
Yin T, Wu YI
Methods Mol. Biol. (2014) 1251:277-89 10.1007/978-1-4939-2080-8_15 - Enterococcus faecalis 6-phosphogluconolactonase is required for both commensal and pathogenic interactions with Manduca sexta.
Holt JF, Kiedrowski MR, Frank KL, Du J, Guan C, Broderick NA, Dunny GM, Handelsman J
Infect. Immun. (2014) 83(1):396-404 (PMC4288895) 10.1128/IAI.02442-14 - Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.
Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y
Bioinformatics (2014) 31(5):682-90 - Analysis of the dynamics of a Bacillus subtilis spore germination protein complex during spore germination and outgrowth.
Troiano AJ, Zhang J, Cowan AE, Yu J, Setlow P
J. Bacteriol. (2014) 197(2):252-61 (PMC4272593) - A coalescent-based method for population tree inference with haplotypes.
Wu Y
Bioinformatics (2014) 31(5):691-8 (PMC4341064) 10.1093/bioinformatics/btu710 - The putative herpes simplex virus 1 chaperone protein UL32 modulates disulfide bond formation during infection.
Albright BS, Kosinski A, Szczepaniak R, Cook EA, Stow ND, Conway JF, Weller SK
J. Virol. (2014) 89(1):443-53 (PMC4301124) 10.1128/JVI.01913-14 - Demystifying the RAD fad.
Puritz JB, Matz MV, Toonen RJ, Weber JN, Bolnick DI, Bird CE
Mol. Ecol. (2014) 23(24):5937-42 - Combating pathogenic microorganisms using plant-derived antimicrobials: a minireview of the mechanistic basis.
Upadhyay A, Upadhyaya I, Kollanoor-Johny A, Venkitanarayanan K
Biomed Res Int (2014) 2014:761741 (PMC4178913) - Crystal structures of Klebsiella pneumoniae dihydrofolate reductase bound to propargyl-linked antifolates reveal features for potency and selectivity.
Lamb KM, Lombardo MN, Alverson J, Priestley ND, Wright DL, Anderson AC
Antimicrob. Agents Chemother. (2014) 58(12):7484-91 (PMC4249513) 10.1128/AAC.03555-14 - Season-specific and guild-specific effects of anthropogenic landscape modification on metacommunity structure of tropical bats.
Cisneros LM, Fagan ME, Willig MR
J Anim Ecol (2014) 84(2):373-85 - Microbial secondary metabolites and their impacts on insect symbioses.
Klassen JL
Curr Opin Insect Sci (2014) 4:15-22 - Characterization of Clostridium difficile isolates from human fecal samples and retail meat from Pennsylvania.
Varshney JB, Very KJ, Williams JL, Hegarty JP, Stewart DB, Lumadue J, Venkitanarayanan K, Jayarao BM
Foodborne Pathog. Dis. (2014) 11(10):822-9 - Tending a complex microbiota requires major immune complexity.
Stagaman K, Guillemin K, Milligan-Myhre K
Molecular ecology (2014) 23(19):4679-81 PMC3081661 10.1111/mec.12895 - Mono-allelic VSG expression by RNA polymerase I in Trypanosoma brucei: expression site control from both ends?
Günzl A, Kirkham JK, Nguyen TN, Badjatia N, Park SH
Gene (2014) 556(1):68-73 (PMC4272636) - Architecture and assembly of the Bacillus subtilis spore coat.
Plomp M, Carroll AM, Setlow P, Malkin AJ
PLoS ONE (2014) 9(9):e108560 (PMC4178626) - ILP-based maximum likelihood genome scaffolding.
Lindsay J, Salooti H, Măndoiu I, Zelikovsky A
BMC Bioinformatics (2014) 15 Suppl 9:S9 (PMC4168704) - Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity.
Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK
J. Exp. Med. (2014) 211(11):2231-48 (PMC4203949) - Therapeutic targeting of the inflammome.
Wright KT, Giardina C, Vella AT
Biochem. Pharmacol. (2014) 92(2):184-91 (PMC4722871) - Phosphorylation of the TATA-binding protein activates the spliced leader silencing pathway in Trypanosoma brucei.
Hope R, Ben-Mayor E, Friedman N, Voloshin K, Biswas D, Matas D, Drori Y, Günzl A, Michaeli S
Sci Signal (2014) 7(341):ra85 - Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one.
Van Leuven JT, Meister RC, Simon C, McCutcheon JP
Cell (2014) 158(6):1270-1280 10.1016/j.cell.2014.07.047 - Mistaking geography for biology: inferring processes from species distributions.
Warren DL, Cardillo M, Rosauer DF, Bolnick DI
Trends Ecol. Evol. (Amst.) (2014) 29(10):572-80 - Hydrogen peroxide production from glycerol metabolism is dispensable for virulence of Mycoplasma gallisepticum in the tracheas of chickens.
Szczepanek SM, Boccaccio M, Pflaum K, Liao X, Geary SJ
Infect. Immun. (2014) 82(12):4915-20 (PMC4249280) 10.1128/IAI.02208-14 - Evaluation of an integrated framework for biodiversity with a new metric for functional dispersion.
Presley SJ, Scheiner SM, Willig MR
PLoS ONE (2014) 9(8):e105818 (PMC4141827) - Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer.
Chimileski S, Franklin MJ, Papke RT
BMC Biol. (2014) 12:65 (PMC4180959) - Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench.
Diaz PI, Strausbaugh LD, Dongari-Bagtzoglou A
Front Cell Infect Microbiol (2014) 4:101 (PMC4114182) - Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta).
Fučíková K, Lewis PO, González-Halphen D, Lewis LA
Genome Biol Evol (2014) 6(8):2170-80 (PMC4159012) - The phylogenetic utility of acetyltransferase (ARD1) and glutaminyl tRNA synthetase (QtRNA) for reconstructing Cenozoic relationships as exemplified by the large Australian cicada Pauropsalta generic complex.
Owen CL, Marshall DC, Hill KB, Simon C
Mol. Phylogenet. Evol. (2014) 83:258-77 10.1016/j.ympev.2014.07.008 - Efficacy of plant-derived compounds combined with hydrogen peroxide as antimicrobial wash and coating treatment for reducing Listeria monocytogenes on cantaloupes.
Upadhyay A, Upadhyaya I, Mooyottu S, Kollanoor-Johny A, Venkitanarayanan K
Food Microbiol. (2014) 44:47-53 - Individual diet has sex-dependent effects on vertebrate gut microbiota.
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R
Nat Commun (2014) 5:4500 (PMC4279269) - Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.
Hu S, Guo Z, Li T, Carpenter EJ, Liu S, Lin S
PLoS ONE (2014) 9(7):e103528 (PMC4110036) 10.1371/journal.pone.0103528 - Plant-derived antimicrobials reduce E. coli O157:H7 virulence factors critical for colonization in cattle gastrointestinal tract in vitro.
Ananda Baskaran S, Venkitanarayanan K
Biomed Res Int (2014) 2014:212395 (PMC4090510) - Phosphorylation of Dok1 by Abl family kinases inhibits CrkI transforming activity.
Ng KY, Yin T, Machida K, Wu YI, Mayer BJ
Oncogene (2014) 34(20):2650-9 (PMC4302068) 10.1038/onc.2014.210 - Colonization state influences the hemocyte proteome in a beneficial squid-Vibrio symbiosis.
Schleicher TR, VerBerkmoes NC, Shah M, Nyholm SV
Mol. Cell Proteomics (2014) 13(10):2673-86 (PMC4188995) 10.1074/mcp.M113.037259 - Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology.
Stutz WE, Bolnick DI
PLoS ONE (2014) 9(7):e100587 (PMC4103772) - Inteins as indicators of gene flow in the halobacteria.
Soucy SM, Fullmer MS, Papke RT, Gogarten JP
Front Microbiol (2014) 5:299 (PMC4071816) - Recombination promoted by DNA viruses: phage λ to herpes simplex virus.
Weller SK, Sawitzke JA
Annu. Rev. Microbiol. (2014) 68:237-58 (PMC4303060) 10.1146/annurev-micro-091313-103424 - The Portable Chemical Sterilizer (PCS), D-FENS, and D-FEND ALL: novel chlorine dioxide decontamination technologies for the military.
Doona CJ, Feeherry FE, Setlow P, Malkin AJ, Leighton TJ
J Vis Exp (2014) (88):e4354 (PMC4208883) - Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S
Genome Res. (2014) 24(7):1209-23 (PMC4079975) 10.1101/gr.159384.113 - De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton.
Santoferrara LF, Guida S, Zhang H, McManus GB
PLoS ONE (2014) 9(7):e101418 (PMC4077812) - Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.
Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE
Mol. Ecol. (2014) 23(19):4831-45 - BIOFRAG - a new database for analyzing BIOdiversity responses to forest FRAGmentation.
Pfeifer M, Lefebvre V, Gardner TA, Arroyo-Rodriguez V, Baeten L, Banks-Leite C, Barlow J, Betts MG, Brunet J, Cerezo A, Cisneros LM, Collard S, D'Cruze N, da Silva Motta C, Duguay S, Eggermont H, Eigenbrod F, Hadley AS, Hanson TR, Hawes JE, Heartsill Scalley T, Klingbeil BT, Kolb A, Kormann U, Kumar S, Lachat T, Lakeman Fraser P, Lantschner V, Laurance WF, Leal IR, Lens L, Marsh CJ, Medina-Rangel GF, Melles S, Mezger D, Oldekop JA, Overal WL, Owen C, Peres CA, Phalan B, Pidgeon AM, Pilia O, Possingham HP, Possingham ML, Raheem DC, Ribeiro DB, Ribeiro Neto JD, Douglas Robinson W, Robinson R, Rytwinski T, Scherber C, Slade EM, Somarriba E, Stouffer PC, Struebig MJ, Tylianakis JM, Tscharntke T, Tyre AJ, Urbina Cardona JN, Vasconcelos HL, Wearn O, Wells K, Willig MR, Wood E, Young RP, Bradley AV, Ewers RM
Ecol Evol (2014) 4(9):1524-37 (PMC4063456) - Structure of the herpes simplex virus 1 genome: manipulation of nicks and gaps can abrogate infectivity and alter the cellular DNA damage response.
Smith S, Reuven N, Mohni KN, Schumacher AJ, Weller SK
J. Virol. (2014) 88(17):10146-56 (PMC4136335) 10.1128/JVI.01723-14 - The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.
Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ
PLoS Biol. (2014) 12(6):e1001889 (PMC4068987) 10.1371/journal.pbio.1001889 - Pareto-optimal phylogenetic tree reconciliation.
Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M
Bioinformatics (2014) 30(12):i87-95 (PMC4058917) - Applications of biosynthesized metallic nanoparticles - a review.
Schröfel A, Kratošová G, Šafařík I, Šafaříková M, Raška I, Shor LM
Acta Biomater (2014) 10(10):4023-42 - Tropolones as lead-like natural products: the development of potent and selective histone deacetylase inhibitors.
Ononye SN, VanHeyst MD, Oblak EZ, Zhou W, Ammar M, Anderson AC, Wright DL
ACS Med Chem Lett (2014) 4(8):757-61 (PMC4027479) 10.1021/ml400158k - AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.
Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y
PLoS ONE (2014) 9(6):e98844 (PMC4044049) - Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome.
Mungpakdee S, Shinzato C, Takeuchi T, Kawashima T, Koyanagi R, Hisata K, Tanaka M, Goto H, Fujie M, Lin S, Satoh N, Shoguchi E
Genome Biol Evol (2014) 6(6):1408-22 (PMC4079212) 10.1093/gbe/evu109 - Metagenomic analysis of the medicinal leech gut microbiota.
Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J
Front Microbiol (2014) 5:151 (PMC4029005) - Comparing the behavior of multidrug-resistant and pansusceptible Salmonella during the production and aging of a Gouda cheese manufactured from raw milk.
D'Amico DJ, Druart MJ, Donnelly CW
J. Food Prot. (2014) 77(6):903-13 10.4315/0362-028X.JFP-13-515 - Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach.
Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A
Front Microbiol (2014) 5:196 (PMC4021199) - Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R
Ecol. Lett. (2014) 17(8):979-87 (PMC4084827) - Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.
Rizzo AA, Suhanovsky MM, Baker ML, Fraser LC, Jones LM, Rempel DL, Gross ML, Chiu W, Alexandrescu AT, Teschke CM
Structure (2014) 22(6):830-41 (PMC4068711) - Sub-inhibitory concentrations of trans-cinnamaldehyde attenuate virulence in Cronobacter sakazakii in vitro.
Amalaradjou MA, Kim KS, Venkitanarayanan K
Int J Mol Sci (2014) 15(5):8639-55 (PMC4057751) - High-precision fitting measurements of the kinetics of size changes during germination of individual Bacillus spores.
Liang J, Zhang P, Setlow P, Li YQ
Appl. Environ. Microbiol. (2014) 80(15):4606-15 (PMC4148796) - Contrasting patterns of phenotype-dependent parasitism within and among populations of threespine stickleback.
Stutz WE, Lau OL, Bolnick DI
Am. Nat. (2014) 183(6):810-25 - Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria.
Grattepanche JD, Santoferrara LF, McManus GB, Katz LA
Trends Microbiol. (2014) 22(8):432-7 - Improved bioactivity of antimicrobial peptides by addition of amino-terminal copper and nickel (ATCUN) binding motifs.
Libardo MD, Cervantes JL, Salazar JC, Angeles-Boza AM
ChemMedChem (2014) 9(8):1892-901 (PMC4440792) - Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.
Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT
Front Microbiol (2014) 5:143 (PMC3988388) - Population and genomic analysis of the genus Halorubrum.
Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT
Front Microbiol (2014) 5:140 (PMC3990103) - Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing.
Abusleme L, Hong BY, Dupuy AK, Strausbaugh LD, Diaz PI
J Oral Microbiol (2014) 6: (PMC4000428) - Monitoring of commitment, blocking, and continuation of nutrient germination of individual Bacillus subtilis spores.
Zhang P, Liang J, Yi X, Setlow P, Li YQ
J. Bacteriol. (2014) 196(13):2443-54 (PMC4054174) - DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.
Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J
PLoS ONE (2014) 9(4):e94819 (PMC3986227) - A new strategy of RNA interference that targets heterologous sequences reveals CITFA1 as an essential component of class I transcription factor A in Trypanosoma brucei.
Park SH, Nguyen BN, Kirkham JK, Nguyen TN, Günzl A
Eukaryotic Cell (2014) 13(6):785-95 (PMC4054280) - Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.
Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J
PLoS ONE (2014) 9(4):e94249 (PMC3983156) - Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater).
Hird SM, Carstens BC, Cardiff SW, Dittmann DL, Brumfield RT
PeerJ (2014) 2:e321 (PMC3970801) 10.7717/peerj.321 - Lacustrine Nostoc (Nostocales) and associated microbiome generate a new type of modern clotted microbialite.
Graham LE, Knack JJ, Piotrowski MJ, Wilcox LW, Cook ME, Wellman CH, Taylor W, Lewis LA, Arancibia-Avila P
J. Phycol. (2014) 50(2):280-91 - Function of the SpoVAEa and SpoVAF proteins of Bacillus subtilis spores.
Perez-Valdespino A, Li Y, Setlow B, Ghosh S, Pan D, Korza G, Feeherry FE, Doona CJ, Li YQ, Hao B, Setlow P
J. Bacteriol. (2014) 196(11):2077-88 (PMC4010985) - HSV-1 protein expression using recombinant baculoviruses.
Grady LM, Bai P, Weller SK
Methods Mol. Biol. (2014) 1144:293-304 (PMC4427568) 10.1007/978-1-4939-0428-0_20 - Antifolate agents: a patent review (2010 - 2013).
Anderson AC, Wright DL
Expert Opin Ther Pat (2014) 24(6):687-97 10.1517/13543776.2014.898062 - Biochemical characterization of a nitrogen-type phosphotransferase system reveals that enzyme EI(Ntr) integrates carbon and nitrogen signaling in Sinorhizobium meliloti.
Goodwin RA, Gage DJ
J. Bacteriol. (2014) 196(10):1901-7 (PMC4011000) - Carvacrol and trans-cinnamaldehyde reduce Clostridium difficile toxin production and cytotoxicity in vitro.
Mooyottu S, Kollanoor-Johny A, Flock G, Bouillaut L, Upadhyay A, Sonenshein AL, Venkitanarayanan K
Int J Mol Sci (2014) 15(3):4415-30 (PMC3975404) - Studies on the antiproliferative effects of tropolone derivatives in Jurkat T-lymphocyte cells.
Ononye SN, Vanheyst MD, Giardina C, Wright DL, Anderson AC
Bioorg. Med. Chem. (2014) 22(7):2188-93 (PMC4011186) - Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.
Dupuy AK, David MS, Li L, Heider TN, Peterson JD, Montano EA, Dongari-Bagtzoglou A, Diaz PI, Strausbaugh LD
PLoS ONE (2014) 9(3):e90899 (PMC3948697) - Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein.
Cortines JR, Motwani T, Vyas AA, Teschke CM
J. Virol. (2014) 88(10):5287-97 (PMC4019102) - Extracellular DNA metabolism in Haloferax volcanii.
Chimileski S, Dolas K, Naor A, Gophna U, Papke RT
Front Microbiol (2014) 5:57 (PMC3929857) - Metallothionein and stress combine to affect multiple organ systems.
Lynes MA, Hidalgo J, Manso Y, Devisscher L, Laukens D, Lawrence DA
Cell Stress Chaperones (2014) 19(5):605-11 (PMC4147071) - Cyclopropene cycloadditions with annulated furans: total synthesis of (+)- and (-)-frondosin B and (+)-frondosin A.
Oblak EZ, VanHeyst MD, Li J, Wiemer AJ, Wright DL
J. Am. Chem. Soc. (2014) 136(11):4309-15 10.1021/ja413106t - Characterization of the digestive tract microbiota of Hirudo orientalis (medicinal leech) and antibiotic resistance profile.
Whitaker IS, Maltz M, Siddall ME, Graf J
Plast. Reconstr. Surg. (2014) 133(3):408e-418e - Propargyl-linked antifolates are dual inhibitors of Candida albicans and Candida glabrata.
G-Dayanandan N, Paulsen JL, Viswanathan K, Keshipeddy S, Lombardo MN, Zhou W, Lamb KM, Sochia AE, Alverson JB, Priestley ND, Wright DL, Anderson AC
J. Med. Chem. (2014) 57(6):2643-56 (PMC3983340) 10.1021/jm401916j - Guest editors' introduction to the special section on bioinformatics research and applications.
Mandoiu II, Wang J, Zelikovsky A
IEEE/ACM Trans Comput Biol Bioinform (2014) 10(6):1345-6 - Analysis of the loss in heat and acid resistance during germination of spores of Bacillus species.
Luu S, Setlow P
J. Bacteriol. (2014) 196(9):1733-40 (PMC3993331) - Microgeographic adaptation and the spatial scale of evolution.
Richardson JL, Urban MC, Bolnick DI, Skelly DK
Trends Ecol. Evol. (Amst.) (2014) 29(3):165-76 - Structural and functional analysis of the GerD spore germination protein of Bacillus species.
Li Y, Jin K, Ghosh S, Devarakonda P, Carlson K, Davis A, Stewart KA, Cammett E, Pelczar Rossi P, Setlow B, Lu M, Setlow P, Hao B
J. Mol. Biol. (2014) 426(9):1995-2008 (PMC4038265) - Xenodiagnosis for posttreatment Lyme disease syndrome: resolving the conundrum or adding to it?
Bockenstedt LK, Radolf JD
Clin. Infect. Dis. (2014) 58(7):946-8 (PMC3952604) - Effect of chlorine exposure on the survival and antibiotic gene expression of multidrug resistant Acinetobacter baumannii in water.
Karumathil DP, Yin HB, Kollanoor-Johny A, Venkitanarayanan K
Int J Environ Res Public Health (2014) 11(2):1844-54 (PMC3945572) - In vitro assays of chemotaxis as a window into mechanisms of toxicant-induced immunomodulation.
Pietrosimone KM, Bhandari S, Lemieux MG, Knecht DA, Lynes MA
Curr Protoc Toxicol (2014) 58:Unit 18.17. - Sensitivity enhancement of a grating-based surface plasmon-coupled emission (SPCE) bionsor chip using gold thickness.
Yuk JS, Guignon EF, Lynes MA
Chem Phys Lett (2014) 591:5-9 (PMC3909983) - Evaluation of the Borrelia burgdorferi BBA64 protein as a protective immunogen in mice.
Brandt KS, Patton TG, Allard AS, Caimano MJ, Radolf JD, Gilmore RD
Clin. Vaccine Immunol. (2014) 21(4):526-33 (PMC3993113) - Germination of spores of Bacillus species: what we know and do not know.
Setlow P
J. Bacteriol. (2014) 196(7):1297-305 (PMC3993344) - Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta).
Fučíková K, Lewis PO, Lewis LA
J. Phycol. (2014) 50(1):14-25 - Microbiological Quality and Safety Issues in Cheesemaking.
D'Amico DJ
Microbiol Spectr (2014) 2(1):CM-0011-2012 10.1128/microbiolspec.CM-0011-2012 - Role of metallothioneins as danger signals in the pathogenesis of colitis.
Devisscher L, Hindryckx P, Lynes MA, Waeytens A, Cuvelier C, De Vos F, Vanhove C, Vos MD, Laukens D
J. Pathol. (2014) 233(1):89-100 - Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods.
Santoferrara LF, Grattepanche JD, Katz LA, McManus GB
Environ. Microbiol. (2014) 16(9):2752-63 - Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile.
Farías ME, Contreras M, Rasuk MC, Kurth D, Flores MR, Poiré DG, Novoa F, Visscher PT
Extremophiles (2014) 18(2):311-29 - Multiple dimensions of bat biodiversity along an extensive tropical elevational gradient.
Cisneros LM, Burgio KR, Dreiss LM, Klingbeil BT, Patterson BD, Presley SJ, Willig MR
J Anim Ecol (2014) 83(5):1124-36 - Changing microspatial patterns of sulfate-reducing microorganisms (SRM) during cycling of marine stromatolite mats.
Petrisor AI, Szyjka S, Kawaguchi T, Visscher PT, Norman RS, Decho AW
Int J Mol Sci (2014) 15(1):850-77 (PMC3907843) - Antibiotic-dependent expression of early transcription factor subunits leads to stringent control of vaccinia virus replication.
Hagen CJ, Titong A, Sarnoski EA, Verardi PH
Virus Res. (2014) 181:43-52 - Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.
Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM
PLoS ONE (2014) 8(12):e84300 (PMC3877268) - Bromelain Inhibits Allergic Sensitization and Murine Asthma via Modulation of Dendritic Cells.
Secor ER, Szczepanek SM, Castater CA, Adami AJ, Matson AP, Rafti ET, Guernsey L, Natarajan P, McNamara JT, Schramm CM, Thrall RS, Silbart LK
Evid Based Complement Alternat Med (2014) 2013:702196 (PMC3870104) 10.1155/2013/702196 - Dihydroxyacetone metabolism in Haloferax volcanii.
Ouellette M, Makkay AM, Papke RT
Front Microbiol (2014) 4:376 (PMC3863723) - DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species.
Wang L, Zhuang Y, Zhang H, Lin X, Lin S
Harmful Algae (2014) 31:100-113 10.1016/j.hal.2013.10.013 2013
- NMR structure of the HWE kinase associated response regulator Sma0114 in its activated state.
Sheftic SR, White E, Gage DJ, Alexandrescu AT
Biochemistry (2013) 53(2):311-22 - HrpA, an RNA helicase involved in RNA processing, is required for mouse infectivity and tick transmission of the Lyme disease spirochete.
Salman-Dilgimen A, Hardy PO, Radolf JD, Caimano MJ, Chaconas G
PLoS Pathog. (2013) 9(12):e1003841 (PMC3868530) - Coibacins A and B: total synthesis and stereochemical revision.
Carneiro VM, Avila CM, Balunas MJ, Gerwick WH, Pilli RA
J. Org. Chem. (2013) 79(2):630-42 (PMC3962765) - The magnitude of local adaptation under genotype-dependent dispersal.
Bolnick DI, Otto SP
Ecol Evol (2013) 3(14):4722-35 (PMC3867907) - Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression sites in Trypanosoma brucei.
Nguyen TN, Müller LS, Park SH, Siegel TN, Günzl A
Nucleic Acids Res. (2013) 42(5):3164-76 (PMC3950698) - Algorithms for genome-scale phylogenetics using gene tree parsimony.
Bansal MS, Eulenstein O
IEEE/ACM Trans Comput Biol Bioinform (2013) 10(4):939-56 - False positives in Biolog EcoPlates™ and MT2 MicroPlates™ caused by calcium.
Pierce ML, Ward JE, Dobbs FC
J. Microbiol. Methods (2013) 97:20-4 10.1016/j.mimet.2013.12.002 - Structural modeling and physicochemical characterization provide evidence that P66 forms a β-barrel in the Borrelia burgdorferi outer membrane.
Kenedy MR, Luthra A, Anand A, Dunn JP, Radolf JD, Akins DR
J. Bacteriol. (2013) 196(4):859-72 (PMC3911182) - High salinity alters the germination behavior of Bacillus subtilis spores with nutrient and nonnutrient germinants.
Nagler K, Setlow P, Li YQ, Moeller R
Appl. Environ. Microbiol. (2013) 80(4):1314-21 (PMC3911066) - Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools.
Huang Y, Khan MI, Khan M, Măndoiu I, Măndoiu II
PLoS ONE (2013) 8(11):e81842 (PMC3843705) - Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.
Wu YC, Rasmussen MD, Bansal MS, Kellis M
Genome Res. (2013) 24(3):475-86 (PMC3941112) - Evolutionary inferences from the analysis of exchangeability.
Hendry AP, Kaeuffer R, Crispo E, Peichel CL, Bolnick DI
Evolution (2013) 67(12):3429-41 (PMC3852416) - Viscous dynamics of Lyme disease and syphilis spirochetes reveal flagellar torque and drag.
Harman M, Vig DK, Radolf JD, Wolgemuth CW
Biophys. J. (2013) 105(10):2273-80 (PMC3838743) - Interaction of apurinic/apyrimidinic endonucleases Nfo and ExoA with the DNA integrity scanning protein DisA in the processing of oxidative DNA damage during Bacillus subtilis spore outgrowth.
Campos SS, Ibarra-Rodriguez JR, Barajas-Ornelas RC, Ramírez-Guadiana FH, Obregón-Herrera A, Setlow P, Pedraza-Reyes M
J. Bacteriol. (2013) 196(3):568-78 (PMC3911150) - Rapid inactivation of Salmonella Enteritidis on shell eggs by plant-derived antimicrobials.
Upadhyaya I, Upadhyay A, Kollanoor-Johny A, Baskaran SA, Mooyottu S, Darre MJ, Venkitanarayanan K
Poult. Sci. (2013) 92(12):3228-35 - Mobility of core water in Bacillus subtilis spores by 2H NMR.
Kaieda S, Setlow B, Setlow P, Halle B
Biophys. J. (2013) 105(9):2016-23 (PMC3824542) - IL-18 expression results in a recombinant vaccinia virus that is highly attenuated and immunogenic.
Verardi PH, Legrand FA, Chan KS, Peng Y, Jones LA, Yilma TD
J. Interferon Cytokine Res. (2013) 34(3):169-78 (PMC3942681) - Santacruzamate A, a potent and selective histone deacetylase inhibitor from the Panamanian marine cyanobacterium cf. Symploca sp.
Pavlik CM, Wong CY, Ononye S, Lopez DD, Engene N, McPhail KL, Gerwick WH, Balunas MJ
J. Nat. Prod. (2013) 76(11):2026-33 (PMC3879121) - Monitoring rates and heterogeneity of high-pressure germination of bacillus spores by phase-contrast microscopy of individual spores.
Kong L, Doona CJ, Setlow P, Li YQ
Appl. Environ. Microbiol. (2013) 80(1):345-53 (PMC3911021) - Use of a recombinant vaccinia virus expressing interferon gamma for post-exposure protection against vaccinia and ectromelia viruses.
Holechek SA, Denzler KL, Heck MC, Schriewer J, Buller RM, Legrand FA, Verardi PH, Jones LA, Yilma T, Jacobs BL
PLoS ONE (2013) 8(10):e77879 (PMC3798613) - Biology of the Marine Heterotrophic Dinoflagellate : Current Status and Future Directions.
Guo Z, Zhang H, Liu S, Lin S
Microorganisms (2013) 1(1):33-57 (PMC5029500) 10.3390/microorganisms1010033 - Trypanosoma brucei harbours a divergent XPB helicase paralogue that is specialized in nucleotide excision repair and conserved among kinetoplastid organisms.
Badjatia N, Nguyen TN, Lee JH, Günzl A
Mol. Microbiol. (2013) 90(6):1293-308 (PMC3864625) - Resistance of Bacillus subtilis spore DNA to lethal ionizing radiation damage relies primarily on spore core components and DNA repair, with minor effects of oxygen radical detoxification.
Moeller R, Raguse M, Reitz G, Okayasu R, Li Z, Klein S, Setlow P, Nicholson WL
Appl. Environ. Microbiol. (2013) 80(1):104-9 (PMC3911009) - Stromatolitic knobs in Storr's Lake (San Salvador, Bahamas): a model system for formation and alteration of laminae.
Dupraz C, Fowler A, Tobias C, Visscher PT
Geobiology (2013) 11(6):527-48 - Development of intestinal organoids as tissue surrogates: cell composition and the epigenetic control of differentiation.
Cao L, Kuratnik A, Xu W, Gibson JD, Kolling F, Falcone ER, Ammar M, Van Heyst MD, Wright DL, Nelson CE, Giardina C
Mol. Carcinog. (2013) 54(3):189-202 - Herpes simplex virus type 1 single strand DNA binding protein and helicase/primase complex disable cellular ATR signaling.
Mohni KN, Smith S, Dee AR, Schumacher AJ, Weller SK
PLoS Pathog. (2013) 9(10):e1003652 (PMC3789782) 10.1371/journal.ppat.1003652 - An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees.
Wu Y
J. Comput. Biol. (2013) 20(10):792-804 (PMC3791036) 10.1089/cmb.2013.0072 - Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract.
Bomar L, Stephens WZ, Nelson MC, Velle K, Guillemin K, Graf J
Genome Announc (2013) 1(5): (PMC3790095) - Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response.
Xu H, Sobue T, Thompson A, Xie Z, Poon K, Ricker A, Cervantes J, Diaz PI, Dongari-Bagtzoglou A
Cell. Microbiol. (2013) 16(2):214-31 (PMC3956708) - Kinetics of germination of individual spores of Geobacillus stearothermophilus as measured by raman spectroscopy and differential interference contrast microscopy.
Zhou T, Dong Z, Setlow P, Li YQ
PLoS ONE (2013) 8(9):e74987 (PMC3772816) - Elucidating features that drive the design of selective antifolates using crystal structures of human dihydrofolate reductase.
Lamb KM, G-Dayanandan N, Wright DL, Anderson AC
Biochemistry (2013) 52(41):7318-26 (PMC3855305) 10.1021/bi400852h - Distribution and evolution of the mobile vma-1b intein.
Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP
Mol. Biol. Evol. (2013) 30(12):2676-87 - Stereodivergent resolution of oxabicyclic ketones: preparation of key intermediates for platensimycin and other natural products.
VanHeyst MD, Oblak EZ, Wright DL
J. Org. Chem. (2013) 78(20):10555-9 10.1021/jo4017502 - Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.
Bansal MS, Alm EJ, Kellis M
J. Comput. Biol. (2013) 20(10):738-54 (PMC3791060) - Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum.
Bautista EJ, Zinski J, Szczepanek SM, Johnson EL, Tulman ER, Ching WM, Geary SJ, Srivastava R
PLoS Comput. Biol. (2013) 9(9):e1003208 (PMC3764002) - Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere.
Herron PM, Gage DJ, Arango Pinedo C, Haider ZK, Cardon ZG
Front Plant Sci (2013) 4:323 (PMC3759012) - Efficacy of plant-derived antimicrobials as antimicrobial wash treatments for reducing enterohemorrhagic Escherichia coli O157:H7 on apples.
Baskaran SA, Upadhyay A, Kollanoor-Johny A, Upadhyaya I, Mooyottu S, Roshni Amalaradjou MA, Schreiber D, Venkitanarayanan K
J. Food Sci. (2013) 78(9):M1399-404 - Updating categorical soil maps using limited survey data by Bayesian Markov chain cosimulation.
Li W, Zhang C, Dey DK, Willig MR
ScientificWorldJournal (2013) 2013:587284 (PMC3762187) - Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12.
Butzin NC, Secinaro MA, Swithers KS, Gogarten JP, Noll KM
Appl. Environ. Microbiol. (2013) 79(22):7006-12 (PMC3811540) - The Clostridium perfringens germinant receptor protein GerKC is located in the spore inner membrane and is crucial for spore germination.
Banawas S, Paredes-Sabja D, Korza G, Li Y, Hao B, Setlow P, Sarker MR
J. Bacteriol. (2013) 195(22):5084-91 (PMC3811594) - In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics.
Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF
J Chem Inf Model (2013) 53(9):2483-92 (PMC3819714) - Signal recognition particle RNA in dinoflagellates and the Perkinsid Perkinsus marinus.
Zhang H, Campbell DA, Sturm NR, Rosenblad MA, Dungan CF, Lin S
Protist (2013) 164(5):748-61 10.1016/j.protis.2013.07.004 - Safety mechanism assisted by the repressor of tetracycline (SMART) vaccinia virus vectors for vaccines and therapeutics.
Grigg P, Titong A, Jones LA, Yilma TD, Verardi PH
Proc. Natl. Acad. Sci. U.S.A. (2013) 110(38):15407-12 (PMC3780884) - Poor fit to the multispecies coalescent is widely detectable in empirical data.
Reid NM, Hird SM, Brown JM, Pelletier TA, McVay JD, Satler JD, Carstens BC
Syst. Biol. (2013) 63(3):322-33 10.1093/sysbio/syt057 - Reconstruction of ancestral 16S rRNA reveals mutation bias in the evolution of optimal growth temperature in the Thermotogae phylum.
Green AG, Swithers KS, Gogarten JF, Gogarten JP
Mol. Biol. Evol. (2013) 30(11):2463-74 - MyD88 deficiency markedly worsens tissue inflammation and bacterial clearance in mice infected with Treponema pallidum, the agent of syphilis.
Silver AC, Dunne DW, Zeiss CJ, Bockenstedt LK, Radolf JD, Salazar JC, Fikrig E
PLoS ONE (2013) 8(8):e71388 (PMC3734110) - The DNA helicase-primase complex as a target for herpes viral infection.
Weller SK, Kuchta RD
Expert Opin. Ther. Targets (2013) 17(10):1119-32 (PMC4098783) 10.1517/14728222.2013.827663 - A conserved ClpP-like protease involved in spore outgrowth in Bacillus subtilis.
Traag BA, Pugliese A, Setlow B, Setlow P, Losick R
Mol. Microbiol. (2013) 90(1):160-6 (PMC3808192) - Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.
Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A
BMC Bioinformatics (2013) 14 Suppl 9:S2 (PMC3698000) - Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia.
Edgcomb VP, Bernhard JM, Summons RE, Orsi W, Beaudoin D, Visscher PT
ISME J (2013) 8(2):418-29 (PMC3906805) - Human TLR8 is activated upon recognition of Borrelia burgdorferi RNA in the phagosome of human monocytes.
Cervantes JL, La Vake CJ, Weinerman B, Luu S, O'Connell C, Verardi PH, Salazar JC
J. Leukoc. Biol. (2013) 94(6):1231-41 (PMC3828603) - Observation of the dynamic germination of single bacterial spores using rapid Raman imaging.
Kong L, Setlow P, Li YQ
J Biomed Opt (2013) 19(1):11003 - Asymmetric selection and the evolution of extraordinary defences.
Urban MC, Bürger R, Bolnick DI
Nat Commun (2013) 4:2085 (PMC3710097) - Direct analysis of water content and movement in single dormant bacterial spores using confocal Raman microspectroscopy and Raman imaging.
Kong L, Setlow P, Li YQ
Anal. Chem. (2013) 85(15):7094-101 - Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.
Papke RT, de la Haba RR, Infante-Domínguez C, Pérez D, Sánchez-Porro C, Lapierre P, Ventosa A
Genome Announc (2013) 1(4): (PMC3695434) - Proof that dinoflagellate spliced leader (DinoSL) is a useful hook for fishing dinoflagellate transcripts from mixed microbial samples: Symbiodinium kawagutii as a case study.
Zhang H, Zhuang Y, Gill J, Lin S
Protist (2013) 164(4):510-27 10.1016/j.protis.2013.04.002 - Antibiofilm effect of plant derived antimicrobials on Listeria monocytogenes.
Upadhyay A, Upadhyaya I, Kollanoor-Johny A, Venkitanarayanan K
Food Microbiol. (2013) 36(1):79-89 - Numbers of individual nutrient germinant receptors and other germination proteins in spores of Bacillus subtilis.
Stewart KA, Setlow P
J. Bacteriol. (2013) 195(16):3575-82 (PMC3754565) - Transgenic sickle cell disease mice have high mortality and dysregulated immune responses after vaccination.
Szczepanek SM, Secor ER, Bracken SJ, Guernsey L, Rafti E, Matson A, Thrall RS, Andemariam B
Pediatr. Res. (2013) 74(2):141-7 (PMC4487511) 10.1038/pr.2013.85 - Polyadenylation of 18S rRNA in algae(1).
Zhuang Y, Zhang H, Lin S
J. Phycol. (2013) 49(3):570-9 10.1111/jpy.12068 - Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas.
Bernhard JM, Edgcomb VP, Visscher PT, McIntyre-Wressnig A, Summons RE, Bouxsein ML, Louis L, Jeglinski M
Proc. Natl. Acad. Sci. U.S.A. (2013) 110(24):9830-4 (PMC3683713) - The effects of model choice and mitigating bias on the ribosomal tree of life.
Lasek-Nesselquist E, Gogarten JP
Mol. Phylogenet. Evol. (2013) 69(1):17-38 - Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.
de la Haba RR, Sánchez-Porro C, León MJ, Papke RT, Ventosa A
Genome Announc (2013) 1(3): (PMC3662824) - Effect of plant derived antimicrobials on Salmonella enteritidis adhesion to and invasion of primary chicken oviduct epithelial cells in vitro and virulence gene expression.
Upadhyaya I, Upadhyay A, Kollanoor-Johny A, Darre MJ, Venkitanarayanan K
Int J Mol Sci (2013) 14(5):10608-25 (PMC3676857) - Dynamic dosing assay relating real-time respiration responses of Staphylococcus aureus biofilms to changing microchemical conditions.
Deng J, Dhummakupt A, Samson PC, Wikswo JP, Shor LM
Anal. Chem. (2013) 85(11):5411-9 - A novel RNA polymerase-binding protein controlling genes involved in spore germination in Bacillus subtilis.
Traag BA, Ramirez-Peralta A, Wang Erickson AF, Setlow P, Losick R
Mol. Microbiol. (2013) 89(1):113-22 (PMC3694343) - Assortative mating in animals.
Jiang Y, Bolnick DI, Kirkpatrick M
Am. Nat. (2013) 181(6):E125-38 - MalF is essential for persistence of Mycoplasma gallisepticum in vivo.
Tseng CW, Kanci A, Citti C, Rosengarten R, Chiu CJ, Chen ZH, Geary SJ, Browning GF, Markham PF
Microbiology (Reading, Engl.) (2013) 159(Pt 7):1459-70 10.1099/mic.0.067553-0 - Intestinal organoids as tissue surrogates for toxicological and pharmacological studies.
Kuratnik A, Giardina C
Biochem. Pharmacol. (2013) 85(12):1721-6 - Identification of new proteins that modulate the germination of spores of bacillus species.
Ramirez-Peralta A, Gupta S, Butzin XY, Setlow B, Korza G, Leyva-Vazquez MA, Christie G, Setlow P
J. Bacteriol. (2013) 195(13):3009-21 (PMC3697528) - Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.
Diaz PI, Hong BY, Frias-Lopez J, Dupuy AK, Angeloni M, Abusleme L, Terzi E, Ioannidou E, Strausbaugh LD, Dongari-Bagtzoglou A
Clin. Vaccine Immunol. (2013) 20(6):920-30 (PMC3675961) - Transcriptomic study reveals widespread spliced leader trans-splicing, short 5'-UTRs and potential complex carbon fixation mechanisms in the euglenoid Alga Eutreptiella sp.
Kuo RC, Zhang H, Zhuang Y, Hannick L, Lin S
PLoS ONE (2013) 8(4):e60826 (PMC3621762) 10.1371/journal.pone.0060826 - Unambiguous identification of the second 2+ state in 12C and the structure of the Hoyle state.
Zimmerman WR, Ahmed MW, Bromberger B, Stave SC, Breskin A, Dangendorf V, Delbar T, Gai M, Henshaw SS, Mueller JM, Sun C, Tittelmeier K, Weller HR, Wu YK
Phys. Rev. Lett. (2013) 110(15):152502 10.1103/PhysRevLett.110.152502 - Inactivation of Listeria monocytogenes on frankfurters by plant-derived antimicrobials alone or in combination with hydrogen peroxide.
Upadhyay A, Upadhyaya I, Kollanoor-Johny A, Ananda Baskaran S, Mooyottu S, Karumathil D, Venkitanarayanan K
Int. J. Food Microbiol. (2013) 163(2-3):114-8 - Activity and regulation of various forms of CwlJ, SleB, and YpeB proteins in degrading cortex peptidoglycan of spores of Bacillus species in vitro and during spore germination.
Li Y, Butzin XY, Davis A, Setlow B, Korza G, Üstok FI, Christie G, Setlow P, Hao B
J. Bacteriol. (2013) 195(11):2530-40 (PMC3676066) - Cloning and characterization of a hybridoma secreting a 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-specific monoclonal antibody and recombinant F(ab).
Wanczyk H, Barker T, Rood D, Zapata DI, Howell AR, Richardson SK, Zinckgraf J, Marusov GP, Lynes MA, Silbart LK
Toxins (Basel) (2013) 5(3):568-89 (PMC3705279) - Highly sensitive grating coupler-based surface plasmon-coupled emission (SPCE) biosensor for immunoassay.
Yuk JS, Guignon EF, Lynes MA
Analyst (2013) 138(9):2576-82 - Independent divergence of 13- and 17-y life cycles among three periodical cicada lineages.
Sota T, Yamamoto S, Cooley JR, Hill KB, Simon C, Yoshimura J
Proc. Natl. Acad. Sci. U.S.A. (2013) 110(17):6919-24 (PMC3637745) 10.1073/pnas.1220060110 - ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis.
Klassen JL, Currie CR
PLoS ONE (2013) 8(3):e58387 (PMC3590147) - Trypanosome cdc2-related kinase 9 controls spliced leader RNA cap4 methylation and phosphorylation of RNA polymerase II subunit RPB1.
Badjatia N, Ambrósio DL, Lee JH, Günzl A
Mol. Cell. Biol. (2013) 33(10):1965-75 (PMC3647971) - The major outer sheath protein (Msp) of Treponema denticola has a bipartite domain architecture and exists as periplasmic and outer membrane-spanning conformers.
Anand A, Luthra A, Edmond ME, Ledoyt M, Caimano MJ, Radolf JD
J. Bacteriol. (2013) 195(9):2060-71 (PMC3624580) - Cephalopod genomics: A plan of strategies and organization.
Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, da Fonseca RR, Di Cristo C, Dilkes BP, Edsinger-Gonzales E, Freeman RM, Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A, Pungor JR, Rosenthal JJ, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW
Stand Genomic Sci (2013) 7(1):175-88 (PMC3570802) 10.4056/sigs.3136559 - Novel inositol catabolic pathway in Thermotoga maritima.
Rodionova IA, Leyn SA, Burkart MD, Boucher N, Noll KM, Osterman AL, Rodionov DA
Environ. Microbiol. (2013) 15(8):2254-66 - Inactivation of Escherichia coli O157:H7 on cattle hides by caprylic acid and β-resorcylic acid.
Baskaran SA, Bhattaram V, Upadhyaya I, Upadhyay A, Kollanoor-Johny A, Schreiber D, Venkitanarayanan K
J. Food Prot. (2013) 76(2):318-22 - The tandem ring opening/ring closing metathesis route to oxaspirocycles: an approach to phelligridin G.
Cooper HD, Wright DL
Molecules (2013) 18(2):2438-48 (PMC6269797) 10.3390/molecules18022438 - Guiding lights: recent developments in optogenetic control of biochemical signals.
Yin T, Wu YI
Pflugers Arch. (2013) 465(3):397-408 10.1007/s00424-013-1244-x - Expression level of Bacillus subtilis germinant receptors determines the average rate but not the heterogeneity of spore germination.
Zhang JQ, Griffiths KK, Cowan A, Setlow P, Yu J
J. Bacteriol. (2013) 195(8):1735-40 (PMC3624553) - Quantitation of nucleosome acetylation and other histone posttranslational modifications using microscale NU-ELISA.
Dai B, Giardina C, Rasmussen TP
Methods Mol. Biol. (2013) 981:167-76 - Identification of novel compounds that enhance colon cancer cell sensitivity to inflammatory apoptotic ligands.
Chopra AS, Kuratnik A, Scocchera EW, Wright DL, Giardina C
Cancer Biol. Ther. (2013) 14(5):436-49 (PMC3672188) - Structural analysis of the active sites of dihydrofolate reductase from two species of Candida uncovers ligand-induced conformational changes shared among species.
Paulsen JL, Viswanathan K, Wright DL, Anderson AC
Bioorg. Med. Chem. Lett. (2013) 23(5):1279-84 (PMC3579541) 10.1016/j.bmcl.2013.01.008 - Cell sorting analysis of geographically separated hypersaline environments.
Zhaxybayeva O, Stepanauskas R, Mohan NR, Papke RT
Extremophiles (2013) 17(2):265-75 - BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.
Hamdalla MA, Mandoiu II, Hill DW, Rajasekaran S, Grant DF
J Chem Inf Model (2013) 53(3):601-12 (PMC3866231) - Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R
Bioinformatics (2013) 29(5):571-9 - Topology and accessibility of germination proteins in the Bacillus subtilis spore inner membrane.
Korza G, Setlow P
J. Bacteriol. (2013) 195(7):1484-91 (PMC3624538) - Pulling the trigger on lyme arthritis.
Radolf JD
J. Infect. Dis. (2013) 207(6):877-9 (PMC3571446) - The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation.
Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, Gamonal J, Diaz PI
ISME J (2013) 7(5):1016-25 (PMC3635234) - Use of plant-derived antimicrobials for improving the safety of poultry products.
Venkitanarayanan K, Kollanoor-Johny A, Darre MJ, Donoghue AM, Donoghue DJ
Poult. Sci. (2013) 92(2):493-501 - Quorum sensing in extreme environments.
Montgomery K, Charlesworth JC, LeBard R, Visscher PT, Burns BP
Life (Basel) (2013) 3(1):131-48 (PMC4187201) - Early host-pathogen interactions in marine bivalves: evidence that the alveolate parasite Perkinsus marinus infects through the oyster mantle during rejection of pseudofeces.
Allam B, Carden WE, Ward JE, Ralph G, Winnicki S, Pales Espinosa E
J. Invertebr. Pathol. (2013) 113(1):26-34 10.1016/j.jip.2012.12.011 2012
- Experimental and computational evidence of metal-O2 activation and rate-limiting proton-coupled electron transfer in a copper amine oxidase.
Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP
J Phys Chem B (2012) 117(1):218-29 - Pre-Posting and OLEB.
Schwartz AW, Cleaves HJ, Gogarten JP
Orig Life Evol Biosph (2012) 42(6):517 - Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.
Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A
In Silico Biol. (Gedrukt) (2012) 11(5-6):251-61 - Reconstructing viral quasispecies from NGS amplicon reads.
Mancuso N, Tork B, Skums P, Ganova-Raeva L, Măndoiu I, Zelikovsky A
In Silico Biol. (Gedrukt) (2012) 11(5-6):237-49 - Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes.
Tippery NP, Fučíková K, Lewis PO, Lewis LA
J. Phycol. (2012) 48(6):1482-93 - Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism.
Chan CX, Blouin NA, Zhuang Y, Zäuner S, Prochnik SE, Lindquist E, Lin S, Benning C, Lohr M, Yarish C, Gantt E, Grossman AR, Lu S, Müller K, W Stiller J, Brawley SH, Bhattacharya D
J. Phycol. (2012) 48(6):1328-42 10.1111/j.1529-8817.2012.01229.x - Quantifying homologous replacement of loci between haloarchaeal species.
Williams D, Gogarten JP, Papke RT
Genome Biol Evol (2012) 4(12):1223-44 (PMC3542582) - Volatility in mRNA secondary structure as a design principle for antisense.
Johnson E, Srivastava R
Nucleic Acids Res. (2012) 41(3):e43 (PMC3562002) - Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses.
Nyholm SV, Graf J
Nat. Rev. Microbiol. (2012) 10(12):815-27 (PMC3870473) - Nonpeptidic lysosomal modulators derived from z-phe-ala-diazomethylketone for treating protein accumulation diseases.
Viswanathan K, Hoover DJ, Hwang J, Wisniewski ML, Ikonne US, Bahr BA, Wright DL
ACS Med Chem Lett (2012) 3(11):920-4 (PMC4025860) 10.1021/ml300197h - Ectobiotic and endobiotic bacteria associated with Eutreptiella sp. isolated from Long Island Sound.
Kuo RC, Lin S
Protist (2012) 164(1):60-74 10.1016/j.protis.2012.08.004 - Characterization of a novel class I transcription factor A (CITFA) subunit that is indispensable for transcription by the multifunctional RNA polymerase I of Trypanosoma brucei.
Nguyen TN, Nguyen BN, Lee JH, Panigrahi AK, Günzl A
Eukaryotic Cell (2012) 11(12):1573-81 (PMC3536272) - Efficient herpes simplex virus 1 replication requires cellular ATR pathway proteins.
Mohni KN, Dee AR, Smith S, Schumacher AJ, Weller SK
J. Virol. (2012) 87(1):531-42 (PMC3536419) 10.1128/JVI.02504-12 - LC-MS/MS Identification of a Bromelain Peptide Biomarker from Ananas comosus Merr.
Secor ER, Szczepanek SM, Singh A, Guernsey L, Natarajan P, Rezaul K, Han DK, Thrall RS, Silbart LK
Evid Based Complement Alternat Med (2012) 2012:548486 (PMC3467939) 10.1155/2012/548486 - lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.
Hird SM
PLoS ONE (2012) 7(10):e46847 (PMC3468592) 10.1371/journal.pone.0046847 - Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3.
Lucas S, Han J, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Detter JC, Han C, Tapia R, Land M, Hauser L, Kyrpides NC, Ivanova N, Pagani I, Vannier P, Oger P, Bartlett DH, Noll KM, Woyke T, Jebbar M
J. Bacteriol. (2012) 194(21):5974-5 (PMC3486111) - Viridin analogs derived from steroidal building blocks.
Viswanathan K, Ononye SN, Cooper HD, Kyle Hadden M, Anderson AC, Wright DL
Bioorg. Med. Chem. Lett. (2012) 22(22):6919-22 10.1016/j.bmcl.2012.09.015 - The furan route to tropolones: probing the antiproliferative effects of β-thujaplicin analogs.
Oblak EZ, Bolstad ES, Ononye SN, Priestley ND, Hadden MK, Wright DL
Org. Biomol. Chem. (2012) 10(43):8597-604 10.1039/c2ob26553b - Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling.
Shen QT, Hsiue PP, Sindelar CV, Welch MD, Campellone KG, Wang HW
J. Cell Biol. (2012) 199(1):111-24 (PMC3461504) 10.1083/jcb.201204010 - Splenic morphological changes are accompanied by altered baseline immunity in a mouse model of sickle-cell disease.
Szczepanek SM, McNamara JT, Secor ER, Natarajan P, Guernsey LA, Miller LA, Ballesteros E, Jellison E, Thrall RS, Andemariam B
Am. J. Pathol. (2012) 181(5):1725-34 (PMC3483810) 10.1016/j.ajpath.2012.07.034 - NMR assignments for the telokin-like domain of bacteriophage P22 coat protein.
Rizzo AA, Fraser LC, Sheftic SR, Suhanovsky MM, Teschke CM, Alexandrescu AT
Biomol NMR Assign (2012) 7(2):257-60 (PMC3537855) - Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq.
Bomar L, Graf J
Biol. Bull. (2012) 223(1):155-66 (PMC3732745) - Host/microbe interactions revealed through "omics" in the symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri.
Rader BA, Nyholm SV
Biol. Bull. (2012) 223(1):103-11 10.1086/BBLv223n1p103 - Chloroplast symbiosis in a marine ciliate: ecophysiology and the risks and rewards of hosting foreign organelles.
McManus GB, Schoener DM, Haberlandt K
Front Microbiol (2012) 3:321 (PMC3432870) - Limited, episodic diversification and contrasting phylogeography in a New Zealand cicada radiation.
Marshall DC, Hill KB, Marske KA, Chambers C, Buckley TR, Simon C
BMC Evol. Biol. (2012) 12:177 (PMC3537654) 10.1186/1471-2148-12-177 - Alternative excision repair of ultraviolet B- and C-induced DNA damage in dormant and developing spores of Bacillus subtilis.
Ramírez-Guadiana FH, Barraza-Salas M, Ramírez-Ramírez N, Ortiz-Cortés M, Setlow P, Pedraza-Reyes M
J. Bacteriol. (2012) 194(22):6096-104 (PMC3486385) - Herpes simplex viruses: mechanisms of DNA replication.
Weller SK, Coen DM
Cold Spring Harb Perspect Biol (2012) 4(9):a013011 (PMC3428768) 10.1101/cshperspect.a013011 - TreeFix: statistically informed gene tree error correction using species trees.
Wu YC, Rasmussen MD, Bansal MS, Kellis M
Syst. Biol. (2012) 62(1):110-20 (PMC3526801) - Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria.
Gallagher KL, Kading TJ, Braissant O, Dupraz C, Visscher PT
Geobiology (2012) 10(6):518-30 - The HSV-1 exonuclease, UL12, stimulates recombination by a single strand annealing mechanism.
Schumacher AJ, Mohni KN, Kan Y, Hendrickson EA, Stark JM, Weller SK
PLoS Pathog. (2012) 8(8):e1002862 (PMC3415443) 10.1371/journal.ppat.1002862 - The impact of HGT on phylogenomic reconstruction methods.
Lapierre P, Lasek-Nesselquist E, Gogarten JP
Brief. Bioinformatics (2012) 15(1):79-90 - Studies of the di-iron(VI) Intermediate in ferrate-dependent oxygen evolution from water.
Sarma R, Angeles-Boza AM, Brinkley DW, Roth JP
J. Am. Chem. Soc. (2012) 134(37):15371-86 - Analysis of the effects of a gerP mutation on the germination of spores of Bacillus subtilis.
Butzin XY, Troiano AJ, Coleman WH, Griffiths KK, Doona CJ, Feeherry FE, Wang G, Li YQ, Setlow P
J. Bacteriol. (2012) 194(21):5749-58 (PMC3486119) - An evolutionary ecology of individual differences.
Dall SR, Bell AM, Bolnick DI, Ratnieks FL
Ecol. Lett. (2012) 15(10):1189-98 (PMC3962499) - Mining the salivary proteome with grating-coupled surface plasmon resonance imaging and surface plasmon coupled emission microarrays.
Molony RD, Rice JM, Yuk JS, Shetty V, Dey D, Lawrence DA, Lynes MA
Curr Protoc Toxicol (2012) Chapter 18:Unit 18.16.1-19 (PMC3461276) - Themes and variations of viral small terminase proteins.
Teschke CM
Structure (2012) 20(8):1291-2 (PMC3419939) - Nuclear magnetic resonance structure and dynamics of the response regulator Sma0114 from Sinorhizobium meliloti.
Sheftic SR, Garcia PP, White E, Robinson VL, Gage DJ, Alexandrescu AT
Biochemistry (2012) 51(35):6932-41 (PMC4346371) - Non-random gene flow: an underappreciated force in evolution and ecology.
Edelaar P, Bolnick DI
Trends Ecol. Evol. (Amst.) (2012) 27(12):659-65 - Unraveling the role of the C-terminal helix turn helix of the coat-binding domain of bacteriophage P22 scaffolding protein.
Padilla-Meier GP, Gilcrease EB, Weigele PR, Cortines JR, Siegel M, Leavitt JC, Teschke CM, Casjens SR
J. Biol. Chem. (2012) 287(40):33766-80 (PMC3460473) - Effect of inorganic and organic ligands on the bioavailability of methylmercury as determined by using a mer-lux bioreporter.
Ndu U, Mason RP, Zhang H, Lin S, Visscher PT
Appl. Environ. Microbiol. (2012) 78(20):7276-82 (PMC3457092) - Hyperbaric oxygen preconditioning protects skin from UV-A damage.
Fuller AM, Giardina C, Hightower LE, Perdrizet GA, Tierney CA
Cell Stress Chaperones (2012) 18(1):97-107 (PMC3508122) - MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1).
Stiller JW, Perry J, Rymarquis LA, Accerbi M, Green PJ, Prochnik S, Lindquist E, Chan CX, Yarish C, Lin S, Zhuang Y, Blouin NA, Brawley SH
J. Phycol. (2012) 48(4):883-96 10.1111/j.1529-8817.2012.01138.x - The role of reticulate evolution in creating innovation and complexity.
Swithers KS, Soucy SM, Gogarten JP
Int J Evol Biol (2012) 2012:418964 (PMC3403396) - Immune evasion and recognition of the syphilis spirochete in blood and skin of secondary syphilis patients: two immunologically distinct compartments.
Cruz AR, Ramirez LG, Zuluaga AV, Pillay A, Abreu C, Valencia CA, La Vake C, Cervantes JL, Dunham-Ems S, Cartun R, Mavilio D, Radolf JD, Salazar JC
PLoS Negl Trop Dis (2012) 6(7):e1717 (PMC3398964) - Acetylenic linkers in lead compounds: a study of the stability of the propargyl-linked antifolates.
Zhou W, Viswanathan K, Hill D, Anderson AC, Wright DL
Drug Metab. Dispos. (2012) 40(10):2002-8 (PMC3463820) 10.1124/dmd.112.046870 - Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.
Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM, Butzin NC
Genome Biol Evol (2012) 4(8):730-9 (PMC3509894) - Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.
Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbø CL
Genome Biol Evol (2012) 4(8):700-8 (PMC3516359) - Coibacins A-D, antileishmanial marine cyanobacterial polyketides with intriguing biosynthetic origins.
Balunas MJ, Grosso MF, Villa FA, Engene N, McPhail KL, Tidgewell K, Pineda LM, Gerwick L, Spadafora C, Kyle DE, Gerwick WH
Org. Lett. (2012) 14(15):3878-81 (PMC3449157) - Guest editors' introduction.
Chen J, Măndoiu I, Sunderraman R, Wang J, Zelikovsky A
BMC Bioinformatics (2012) 13 Suppl 1:S1 (PMC3382435) - A vaccinia virus renaissance: new vaccine and immunotherapeutic uses after smallpox eradication.
Verardi PH, Titong A, Hagen CJ
Hum Vaccin Immunother (2012) 8(7):961-70 (PMC3495727) - Strain-specific colonization patterns and serum modulation of multi-species oral biofilm development.
Biyikoğlu B, Ricker A, Diaz PI
Anaerobe (2012) 18(4):459-70 (PMC3410037) - Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs.
Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM
PLoS ONE (2012) 7(6):e40236 (PMC3387000) - Analysis of the Raman spectra of Ca(2+)-dipicolinic acid alone and in the bacterial spore core in both aqueous and dehydrated environments.
Kong L, Setlow P, Li YQ
Analyst (2012) 137(16):3683-9 - Low species barriers in halophilic archaea and the formation of recombinant hybrids.
Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U
Curr. Biol. (2012) 22(15):1444-8 - Crystal structure of the catalytic domain of the Bacillus cereus SleB protein, important in cortex peptidoglycan degradation during spore germination.
Li Y, Jin K, Setlow B, Setlow P, Hao B
J. Bacteriol. (2012) 194(17):4537-45 (PMC3415495) - Area under the curve as a tool to measure kinetics of tumor growth in experimental animals.
Duan F, Simeone S, Wu R, Grady J, Mandoiu I, Srivastava PK
J. Immunol. Methods (2012) 382(1-2):224-8 - Caprylic acid reduces Salmonella Enteritidis populations in various segments of digestive tract and internal organs of 3- and 6-week-old broiler chickens, therapeutically.
Kollanoor-Johny A, Mattson T, Baskaran SA, Amalaradjou MA, Hoagland TA, Darre MJ, Khan MI, Schreiber DT, Donoghue AM, Donoghue DJ, Venkitanarayanan K
Poult. Sci. (2012) 91(7):1686-94 - Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae.
Nyholm SV, Song P, Dang J, Bunce C, Girguis PR
PLoS ONE (2012) 7(6):e38267 (PMC3372519) 10.1371/journal.pone.0038267 - Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.
Andam CP, Harlow TJ, Papke RT, Gogarten JP
BMC Evol. Biol. (2012) 12:85 (PMC3436685) - Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.
Bansal MS, Alm EJ, Kellis M
Bioinformatics (2012) 28(12):i283-91 (PMC3371857) - Quartet decomposition server: a platform for analyzing phylogenetic trees.
Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y
BMC Bioinformatics (2012) 13:123 (PMC3447714) - Chloroplast gene arrangement variation within a closely related group of green algae (Trebouxiophyceae, Chlorophyta).
Letsch MR, Lewis LA
Mol. Phylogenet. Evol. (2012) 64(3):524-32 - Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early stage of squid colonization.
Fidopiastis PM, Rader BA, Gerling DG, Gutierrez NA, Watkins KH, Frey MW, Nyholm SV, Whistler CA
J. Bacteriol. (2012) 194(15):3995-4002 (PMC3416539) 10.1128/JB.00108-12 - Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small- and large-subunit rRNA genes.
Santoferrara LF, McManus GB, Alder VA
J. Eukaryot. Microbiol. (2012) 59(4):423-6 - Extensive variation in surface lipoprotein gene content and genomic changes associated with virulence during evolution of a novel North American house finch epizootic strain of Mycoplasma gallisepticum.
Tulman ER, Liao X, Szczepanek SM, Ley DH, Kutish GF, Geary SJ
Microbiology (Reading, Engl.) (2012) 158(Pt 8):2073-88 10.1099/mic.0.058560-0 - Plant-derived antimicrobials reduce Listeria monocytogenes virulence factors in vitro, and down-regulate expression of virulence genes.
Upadhyay A, Johny AK, Amalaradjou MA, Ananda Baskaran S, Kim KS, Venkitanarayanan K
Int. J. Food Microbiol. (2012) 157(1):88-94 - Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin.
Carr G, Poulsen M, Klassen JL, Hou Y, Wyche TP, Bugni TS, Currie CR, Clardy J
Org. Lett. (2012) 14(11):2822-5 (PMC3365539) - Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics.
Collins AJ, Schleicher TR, Rader BA, Nyholm SV
Front Immunol (2012) 3:91 (PMC3349304) 10.3389/fimmu.2012.00091 - Bacterial symbioses of the medicinal leech Hirudo verbana.
Nelson MC, Graf J
Gut Microbes (2012) 3(4):322-31 (PMC3463490) - Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata.
Zellmer AJ, Hanes MM, Hird SM, Carstens BC
Syst. Biol. (2012) 61(5):763-77 10.1093/sysbio/sys048 - An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
Zhang J, Wang J, Wu Y
BMC Bioinformatics (2012) 13 Suppl 6:S6 (PMC3358659) 10.1186/1471-2105-13-S6-S6 - Membrane-deforming proteins play distinct roles in actin pedestal biogenesis by enterohemorrhagic Escherichia coli.
Campellone KG, Siripala AD, Leong JM, Welch MD
J. Biol. Chem. (2012) 287(24):20613-24 (PMC3370245) 10.1074/jbc.M112.363473 - Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.
Duitama J, Srivastava PK, Măndoiu II
BMC Genomics (2012) 13 Suppl 2:S6 (PMC3394419) - Microbial strain prioritization using metabolomics tools for the discovery of natural products.
Hou Y, Braun DR, Michel CR, Klassen JL, Adnani N, Wyche TP, Bugni TS
Anal. Chem. (2012) 84(10):4277-83 (PMC3352271) - Using high throughput sequencing to explore the biodiversity in oral bacterial communities.
Diaz PI, Dupuy AK, Abusleme L, Reese B, Obergfell C, Choquette L, Dongari-Bagtzoglou A, Peterson DE, Terzi E, Strausbaugh LD
Mol Oral Microbiol (2012) 27(3):182-201 (PMC3789374) - Effects of the SpoVT regulatory protein on the germination and germination protein levels of spores of Bacillus subtilis.
Ramirez-Peralta A, Stewart KA, Thomas SK, Setlow B, Chen Z, Li YQ, Setlow P
J. Bacteriol. (2012) 194(13):3417-25 (PMC3434735) - Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes.
Collins AJ, LaBarre BA, Won BS, Shah MV, Heng S, Choudhury MH, Haydar SA, Santiago J, Nyholm SV
Appl. Environ. Microbiol. (2012) 78(12):4200-8 (PMC3370523) 10.1128/AEM.07437-11 - Analysis of immunoarrays using a gold grating-based dual mode surface plasmon-coupled emission (SPCE) sensor chip.
Yuk JS, Gibson GN, Rice JM, Guignon EF, Lynes MA
Analyst (2012) 137(11):2574-81 - Ecology. How bacterial lineages emerge.
Papke RT, Gogarten JP
Science (2012) 336(6077):45-6 - Measurement of cellular chemotaxis with ECIS/Taxis.
Pietrosimone KM, Yin X, Knecht DA, Lynes MA
J Vis Exp (2012) (62): (PMC3460541) - Germination protein levels and rates of germination of spores of Bacillus subtilis with overexpressed or deleted genes encoding germination proteins.
Stewart KA, Yi X, Ghosh S, Setlow P
J. Bacteriol. (2012) 194(12):3156-64 (PMC3370836) - Prospective screening of novel antibacterial inhibitors of dihydrofolate reductase for mutational resistance.
Frey KM, Viswanathan K, Wright DL, Anderson AC
Antimicrob. Agents Chemother. (2012) 56(7):3556-62 (PMC3393473) 10.1128/AAC.06263-11 - Oxygen kinetic isotope effects upon catalytic water oxidation by a monomeric ruthenium complex.
Angeles-Boza AM, Roth JP
Inorg Chem (2012) 51(8):4722-9 - Efficacy of octenidine hydrochloride for reducing Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes on cattle hides.
Baskaran SA, Upadhyay A, Upadhyaya I, Bhattaram V, Venkitanarayanan K
Appl. Environ. Microbiol. (2012) 78(12):4538-41 (PMC3370563) - Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales.
Nesbø CL, Bradnan DM, Adebusuyi A, Dlutek M, Petrus AK, Foght J, Doolittle WF, Noll KM
Extremophiles (2012) 16(3):387-93 - TprC/D (Tp0117/131), a trimeric, pore-forming rare outer membrane protein of Treponema pallidum, has a bipartite domain structure.
Anand A, Luthra A, Dunham-Ems S, Caimano MJ, Karanian C, LeDoyt M, Cruz AR, Salazar JC, Radolf JD
J. Bacteriol. (2012) 194(9):2321-33 (PMC3347077) - Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.
Wu Y
Evolution (2012) 66(3):763-775 10.1111/j.1558-5646.2011.01476.x - Borrelia burgdorferi requires the alternative sigma factor RpoS for dissemination within the vector during tick-to-mammal transmission.
Dunham-Ems SM, Caimano MJ, Eggers CH, Radolf JD
PLoS Pathog. (2012) 8(2):e1002532 (PMC3280991) - New abundant microbial groups in aquatic hypersaline environments.
Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F
Sci Rep (2012) 1:135 (PMC3216616) - Levels of germination proteins in dormant and superdormant spores of Bacillus subtilis.
Ghosh S, Scotland M, Setlow P
J. Bacteriol. (2012) 194(9):2221-7 (PMC3347068) - Toward new therapeutics for skin and soft tissue infections: propargyl-linked antifolates are potent inhibitors of MRSA and Streptococcus pyogenes.
Viswanathan K, Frey KM, Scocchera EW, Martin BD, Swain Iii PW, Alverson JB, Priestley ND, Anderson AC, Wright DL
PLoS ONE (2012) 7(2):e29434 (PMC3274548) 10.1371/journal.pone.0029434 - Reduction of Salmonella enterica serovar enteritidis colonization in 20-day-old broiler chickens by the plant-derived compounds trans-cinnamaldehyde and eugenol.
Kollanoor-Johny A, Mattson T, Baskaran SA, Amalaradjou MA, Babapoor S, March B, Valipe S, Darre M, Hoagland T, Schreiber D, Khan MI, Donoghue A, Donoghue D, Venkitanarayanan K
Appl. Environ. Microbiol. (2012) 78(8):2981-7 (PMC3318785) - Role of a SpoVA protein in dipicolinic acid uptake into developing spores of Bacillus subtilis.
Li Y, Davis A, Korza G, Zhang P, Li YQ, Setlow B, Setlow P, Hao B
J. Bacteriol. (2012) 194(8):1875-84 (PMC3318455) - Effects of sporulation conditions on the germination and germination protein levels of Bacillus subtilis spores.
Ramirez-Peralta A, Zhang P, Li YQ, Setlow P
Appl. Environ. Microbiol. (2012) 78(8):2689-97 (PMC3318806) - Xenoepitope substitution avoids deceptive imprinting and broadens the immune response to foot-and-mouth disease virus.
Szczepanek SM, Barrette RW, Rood D, Alejo D, Silbart LK
Clin. Vaccine Immunol. (2012) 19(4):461-7 (PMC3318270) 10.1128/CVI.00035-12 - The heterogeneous motility of the Lyme disease spirochete in gelatin mimics dissemination through tissue.
Harman MW, Dunham-Ems SM, Caimano MJ, Belperron AA, Bockenstedt LK, Fu HC, Radolf JD, Wolgemuth CW
Proc. Natl. Acad. Sci. U.S.A. (2012) 109(8):3059-64 (PMC3286914) - Bacterial Toxin Fusion Proteins Elicit Mucosal Immunity against a Foot-and-Mouth Disease Virus Antigen When Administered Intranasally to Guinea Pigs.
Challa S, Szczepanek SM, Rood D, Barrette RW, Silbart LK
Adv Virol (2012) 2011:713769 (PMC3265312) 10.1155/2011/713769 - Acute sensitization of colon cancer cells to inflammatory cytokines by prophase arrest.
Kuratnik A, Senapati VE, Verma R, Mellone BG, Vella AT, Giardina C
Biochem. Pharmacol. (2012) 83(9):1217-28 (PMC3299870) - The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics.
Hamdalla M, Grant D, Mandoiu I, Hill D, Rajasekaran S, Ammar R
IEEE Int Conf Comput Adv Bio Med Sci (2012) 2012: (PMC4593623) - Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback.
Kaeuffer R, Peichel CL, Bolnick DI, Hendry AP
Evolution (2012) 66(2):402-18 (PMC4499166) - Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea).
Santoferrara LF, McManus GB, Alder VA
Protist (2012) 164(1):24-36 - Vaccination of BALB/c mice with an avirulent Mycoplasma pneumoniae P30 mutant results in disease exacerbation upon challenge with a virulent strain.
Szczepanek SM, Majumder S, Sheppard ES, Liao X, Rood D, Tulman ER, Wyand S, Krause DC, Silbart LK, Geary SJ
Infect. Immun. (2012) 80(3):1007-14 (PMC3294651) 10.1128/IAI.06078-11 - Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
Klassen JL, Currie CR
BMC Genomics (2012) 13:14 (PMC3322347) - CD14 cooperates with complement receptor 3 to mediate MyD88-independent phagocytosis of Borrelia burgdorferi.
Hawley KL, Olson CM, Iglesias-Pedraz JM, Navasa N, Cervantes JL, Caimano MJ, Izadi H, Ingalls RR, Pal U, Salazar JC, Radolf JD, Anguita J
Proc. Natl. Acad. Sci. U.S.A. (2012) 109(4):1228-32 (PMC3268315) - Of ticks, mice and men: understanding the dual-host lifestyle of Lyme disease spirochaetes.
Radolf JD, Caimano MJ, Stevenson B, Hu LT
Nat. Rev. Microbiol. (2012) 10(2):87-99 (PMC3313462) 2011
- Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life.
Fournier GP, Andam CP, Alm EJ, Gogarten JP
Orig Life Evol Biosph (2011) 41(6):621-32 - Effects of sialidase knockout and complementation on virulence of Mycoplasma gallisepticum.
May M, Szczepanek SM, Frasca S, Gates AE, Demcovitz DL, Moneypenny CG, Brown DR, Geary SJ
Vet. Microbiol. (2011) 157(1-2):91-5 10.1016/j.vetmic.2011.12.004 - Applications of next-generation sequencing to phylogeography and phylogenetics.
McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT
Mol. Phylogenet. Evol. (2011) 66(2):526-38 10.1016/j.ympev.2011.12.007 - Dynamics of the assembly of a complex macromolecular structure--the coat of spores of the bacterium Bacillus subtilis.
Setlow P
Mol. Microbiol. (2011) 83(2):241-4 - Multifocus confocal Raman microspectroscopy for rapid single-particle analysis.
Kong L, Zhang P, Setlow P, Li YQ
J Biomed Opt (2011) 16(12):120503 - Vitamin D resistance and colon cancer prevention.
Giardina C, Madigan JP, Tierney CA, Brenner BM, Rosenberg DW
Carcinogenesis (2011) 33(3):475-82 (PMC3384070) - Green tea extract suppresses NFκB activation and inflammatory responses in diet-induced obese rats with nonalcoholic steatohepatitis.
Park HJ, Lee JY, Chung MY, Park YK, Bower AM, Koo SI, Giardina C, Bruno RS
J. Nutr. (2011) 142(1):57-63 - Microbial diversity and interactions in subgingival biofilm communities.
Diaz PI
Front Oral Biol (2011) 15:17-40 - Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb.
Klassen JL, Adams SM, Bramhacharya S, Giles SS, Goodwin LA, Woyke T, Currie CR
J. Bacteriol. (2011) 193(24):6999-7000 (PMC3232846) - Effects of cortex peptidoglycan structure and cortex hydrolysis on the kinetics of Ca(2+)-dipicolinic acid release during Bacillus subtilis spore germination.
Zhang P, Thomas S, Li YQ, Setlow P
J. Bacteriol. (2011) 194(3):646-52 (PMC3264087) - Antigen-specific T cell phenotyping microarrays using grating coupled surface plasmon resonance imaging and surface plasmon coupled emission.
Rice JM, Stern LJ, Guignon EF, Lawrence DA, Lynes MA
Biosens Bioelectron (2011) 31(1):264-9 (PMC3249003) - Synergistic interaction between Candida albicans and commensal oral streptococci in a novel in vitro mucosal model.
Diaz PI, Xie Z, Sobue T, Thompson A, Biyikoglu B, Ricker A, Ikonomou L, Dongari-Bagtzoglou A
Infect. Immun. (2011) 80(2):620-32 (PMC3264323) - Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences.
McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT
Mol. Phylogenet. Evol. (2011) 62(1):397-406 10.1016/j.ympev.2011.10.012 - Home and away- the evolutionary dynamics of homing endonucleases.
Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L
BMC Evol. Biol. (2011) 11:324 (PMC3229294) - Invasion of protein coding genes by green algal ribosomal group I introns.
McManus HA, Lewis LA, Fučíková K, Haugen P
Mol. Phylogenet. Evol. (2011) 62(1):109-16 - Roles of endonuclease V, uracil-DNA glycosylase, and mismatch repair in Bacillus subtilis DNA base-deamination-induced mutagenesis.
López-Olmos K, Hernández MP, Contreras-Garduño JA, Robleto EA, Setlow P, Yasbin RE, Pedraza-Reyes M
J. Bacteriol. (2011) 194(2):243-52 (PMC3256648) - A microarray biosensor for multiplexed detection of microbes using grating-coupled surface plasmon resonance imaging.
Marusov G, Sweatt A, Pietrosimone K, Benson D, Geary SJ, Silbart LK, Challa S, Lagoy J, Lawrence DA, Lynes MA
Environ. Sci. Technol. (2011) 46(1):348-59 (PMC3312245) - Inferring viral quasispecies spectra from 454 pyrosequencing reads.
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A
BMC Bioinformatics (2011) 12 Suppl 6:S1 (PMC3194189) - Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri.
Schleicher TR, Nyholm SV
PLoS ONE (2011) 6(10):e25649 (PMC3187790) 10.1371/journal.pone.0025649 - SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.
Zhang J, Wu Y
Bioinformatics (2011) 27(23):3228-34 10.1093/bioinformatics/btr563 - Decoding bacteriophage P22 assembly: identification of two charged residues in scaffolding protein responsible for coat protein interaction.
Cortines JR, Weigele PR, Gilcrease EB, Casjens SR, Teschke CM
Virology (2011) 421(1):1-11 (PMC3208733) - Development of an efficient in vitro transcription system for bloodstream form Trypanosoma brucei reveals life cycle-independent functionality of class I transcription factor A.
Park SH, Nguyen TN, Günzl A
Mol. Biochem. Parasitol. (2011) 181(1):29-36 (PMC3215803) - The transition from closed to open conformation of Treponema pallidum outer membrane-associated lipoprotein TP0453 involves membrane sensing and integration by two amphipathic helices.
Luthra A, Zhu G, Desrosiers DC, Eggers CH, Mulay V, Anand A, McArthur FA, Romano FB, Caimano MJ, Heuck AP, Malkowski MG, Radolf JD
J. Biol. Chem. (2011) 286(48):41656-68 (PMC3308875) - DNA mismatch repair proteins are required for efficient herpes simplex virus 1 replication.
Mohni KN, Mastrocola AS, Bai P, Weller SK, Heinen CD
J. Virol. (2011) 85(23):12241-53 (PMC3209375) 10.1128/JVI.05487-11 - Alkaline Phosphatase Gene Sequence And Transcriptional Regulation By Phosphate Limitation In Amphidinium Carterae (Dinophyceae)(1).
Lin X, Zhang H, Huang B, Lin S
J. Phycol. (2011) 47(5):1110-20 10.1111/j.1529-8817.2011.01038.x - Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores.
Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Saunders E, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Lykidis A, Land ML, Brettin T, Stetter KO, Nelson KE, Gogarten JP, Noll KM
J. Bacteriol. (2011) 193(20):5869-70 (PMC3187219) - Biased gene transfer and its implications for the concept of lineage.
Andam CP, Gogarten JP
Biol. Direct (2011) 6:47 (PMC3191353) - Study of host-microbe interactions in zebrafish.
Milligan-Myhre K, Charette JR, Phennicie RT, Stephens WZ, Rawls JF, Guillemin K, Kim CH
Methods in cell biology (2011) 105:87-116 PMC2293046 10.1016/B978-0-12-381320-6.00004-7 - Ecology. Biodiversity and productivity.
Willig MR
Science (2011) 333(6050):1709-10 - A rooted net of life.
Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP
Biol. Direct (2011) 6:45 (PMC3189188) - The coenzyme A disulphide reductase of Borrelia burgdorferi is important for rapid growth throughout the enzootic cycle and essential for infection of the mammalian host.
Eggers CH, Caimano MJ, Malizia RA, Kariu T, Cusack B, Desrosiers DC, Hazlett KR, Claiborne A, Pal U, Radolf JD
Mol. Microbiol. (2011) 82(3):679-97 (PMC3226778) - Serodiagnosis of syphilis in the recombinant era: reversal of fortune.
Hoover KW, Radolf JD
J. Infect. Dis. (2011) 204(9):1295-6 (PMC3182307) - Use of inactivated Escherichia coli enterotoxins to enhance respiratory mucosal adjuvanticity during vaccination in swine.
Barrette RW, Szczepanek SM, Rood D, Challa S, Avery N, Vajdy M, Kramer E, Rodriguez L, Silbart LK
Clin. Vaccine Immunol. (2011) 18(11):1996-8 (PMC3209021) 10.1128/CVI.05273-11 - Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea.
Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM
J. Bacteriol. (2011) 193(19):5566-7 (PMC3187421) - Meningitis caused by Mycoplasma mycoides subspecies capri in a goat.
Schumacher VL, Hinckley L, Liao X, Tulman E, Geary SJ, Smyth JA
J. Vet. Diagn. Invest. (2011) 23(3):565-9 10.1177/1040638711403413 - The community effects of phenotypic and genetic variation within a predator population.
Schreiber SJ, Bürger R, Bolnick DI
Ecology (2011) 92(8):1582-93 - Detecting highways of horizontal gene transfer.
Bansal MS, Banay G, Gogarten JP, Shamir R
J. Comput. Biol. (2011) 18(9):1087-114 - Effects of founding genetic variation on adaptation to a novel resource.
Agashe D, Falk JJ, Bolnick DI
Evolution (2011) 65(9):2481-91 - Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.
Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P
PLoS ONE (2011) 6(8):e23774 (PMC3158100) - Recombinant Rift Valley fever vaccines induce protective levels of antibody in baboons and resistance to lethal challenge in mice.
Papin JF, Verardi PH, Jones LA, Monge-Navarro F, Brault AC, Holbrook MR, Worthy MN, Freiberg AN, Yilma TD
Proc. Natl. Acad. Sci. U.S.A. (2011) 108(36):14926-31 (PMC3169153) - Transcriptomes of Frankia sp. strain CcI3 in growth transitions.
Bickhart DM, Benson DR
BMC Microbiol. (2011) 11:192 (PMC3188489) - The biology of Frankia sp. strains in the post-genome era.
Benson DR, Brooks JM, Huang Y, Bickhart DM, Mastronunzio JE
Mol. Plant Microbe Interact. (2011) 24(11):1310-6 - Shifting paradigm on Bacillus thuringiensis toxin and a natural model for Enterococcus faecalis septicemia.
Graf J
MBio (2011) 2(4): (PMC3157895) - Maturation of released spores is necessary for acquisition of full spore heat resistance during Bacillus subtilis sporulation.
Sanchez-Salas JL, Setlow B, Zhang P, Li YQ, Setlow P
Appl. Environ. Microbiol. (2011) 77(19):6746-54 (PMC3187105) - Characterization of Staphylococcus aureus strains isolated from raw milk utilized in small-scale artisan cheese production.
D'amico DJ, Donnelly CW
J. Food Prot. (2011) 74(8):1353-8 10.4315/0362-028X.JFP-10-533 - Transcription by the multifunctional RNA polymerase I in Trypanosoma brucei functions independently of RPB7.
Park SH, Nguyen TN, Kirkham JK, Lee JH, Günzl A
Mol. Biochem. Parasitol. (2011) 180(1):35-42 (PMC3171583) - Experimental and computational investigations of oxygen reactivity in a heme and tyrosyl radical-containing fatty acid α-(di)oxygenase.
Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP
Biochemistry (2011) 50(34):7375-89 - The ecological causes of individual specialisation.
Araújo MS, Bolnick DI, Layman CA
Ecol. Lett. (2011) 14(9):948-58 - Bacteriophage P22 capsid size determination: roles for the coat protein telokin-like domain and the scaffolding protein amino-terminus.
Suhanovsky MM, Teschke CM
Virology (2011) 417(2):418-29 (PMC3163742) - Growth and development of Frankia spp. strain CcI3 at the single-hypha level in liquid culture.
Huang Y, Benson DR
Arch. Microbiol. (2011) 194(1):21-8 - Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry.
Boucher N, Noll KM
Appl. Environ. Microbiol. (2011) 77(18):6395-9 (PMC3187129) - Borrelia burgdorferi requires glycerol for maximum fitness during the tick phase of the enzootic cycle.
Pappas CJ, Iyer R, Petzke MM, Caimano MJ, Radolf JD, Schwartz I
PLoS Pathog. (2011) 7(7):e1002102 (PMC3131272) - Examination of a virulence mutant uncovers the ribosome biogenesis regulatory protein of Toxoplasma gondii.
Milligan-Myhre KC, Rooney PJ, Knoll LJ
The Journal of parasitology (2011) 97(6):1173-7 PMC2000323 10.1645/GE-2741.1 - Synergism between different germinant receptors in the germination of Bacillus subtilis spores.
Yi X, Liu J, Faeder JR, Setlow P
J. Bacteriol. (2011) 193(18):4664-71 (PMC3165675) - Germination proteins in the inner membrane of dormant Bacillus subtilis spores colocalize in a discrete cluster.
Griffiths KK, Zhang J, Cowan AE, Yu J, Setlow P
Mol. Microbiol. (2011) 81(4):1061-77 - Disulfide bond formation contributes to herpes simplex virus capsid stability and retention of pentons.
Szczepaniak R, Nellissery J, Jadwin JA, Makhov AM, Kosinski A, Conway JF, Weller SK
J. Virol. (2011) 85(17):8625-34 (PMC3165804) 10.1128/JVI.00214-11 - Proteomic analysis of the mode of antibacterial action of trans-cinnamaldehyde against Cronobacter sakazakii 415.
Amalaradjou MA, Venkitanarayanan K
Foodborne Pathog. Dis. (2011) 8(10):1095-102 - Structure-based functional studies of the effects of amino acid substitutions in GerBC, the C subunit of the Bacillus subtilis GerB spore germinant receptor.
Li Y, Catta P, Stewart KA, Dufner M, Setlow P, Hao B
J. Bacteriol. (2011) 193(16):4143-52 (PMC3147670) - Efficient inhibition of germination of coat-deficient bacterial spores by multivalent metal cations, including terbium (Tb³+).
Yi X, Bond C, Sarker MR, Setlow P
Appl. Environ. Microbiol. (2011) 77(15):5536-9 (PMC3147435) - Does intraspecific size variation in a predator affect its diet diversity and top-down control of prey?
Ingram T, Stutz WE, Bolnick DI
PLoS ONE (2011) 6(6):e20782 (PMC3110768) - PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'.
Hird SM, Brumfield RT, Carstens BC
Mol Ecol Resour (2011) 11(4):743-8 10.1111/j.1755-0998.2011.03005.x - Biased gene transfer in microbial evolution.
Andam CP, Gogarten JP
Nat. Rev. Microbiol. (2011) 9(7):543-55 - Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus Perkinsus as a unique group of alveolates.
Zhang H, Campbell DA, Sturm NR, Dungan CF, Lin S
PLoS ONE (2011) 6(5):e19933 (PMC3101222) 10.1371/journal.pone.0019933 - Quantitative analysis of spatial-temporal correlations during germination of spores of Bacillus Species.
Zhang J, Garner W, Setlow P, Yu J
J. Bacteriol. (2011) 193(15):3765-72 (PMC3147528) - Antifolate agents: a patent review (2006 - 2010).
Wright DL, Anderson AC
Expert Opin Ther Pat (2011) 21(9):1293-308 (PMC3156879) 10.1517/13543776.2011.587804 - Conformational changes in bacteriophage P22 scaffolding protein induced by interaction with coat protein.
Padilla-Meier GP, Teschke CM
J. Mol. Biol. (2011) 410(2):226-40 (PMC3125579) - The hybrid histidine kinase Hk1 is part of a two-component system that is essential for survival of Borrelia burgdorferi in feeding Ixodes scapularis ticks.
Caimano MJ, Kenedy MR, Kairu T, Desrosiers DC, Harman M, Dunham-Ems S, Akins DR, Pal U, Radolf JD
Infect. Immun. (2011) 79(8):3117-30 (PMC3147546) - Monitoring the wet-heat inactivation dynamics of single spores of Bacillus species by using Raman tweezers, differential interference contrast microscopy, and nucleic acid dye fluorescence microscopy.
Zhang P, Kong L, Wang G, Setlow P, Li YQ
Appl. Environ. Microbiol. (2011) 77(14):4754-69 (PMC3147409) - Disulfide bond formation in the herpes simplex virus 1 UL6 protein is required for portal ring formation and genome encapsidation.
Albright BS, Nellissery J, Szczepaniak R, Weller SK
J. Virol. (2011) 85(17):8616-24 (PMC3165836) 10.1128/JVI.00123-11 - Pharmacological inhibition of Mdm2 triggers growth arrest and promotes DNA breakage in mouse colon tumors and human colon cancer cells.
Rigatti MJ, Verma R, Belinsky GS, Rosenberg DW, Giardina C
Mol. Carcinog. (2011) 51(5):363-78 (PMC3162984) - Inferring ethnicity from mitochondrial DNA sequence.
Lee C, Măndoiu II, Nelson CE
BMC Proc (2011) 5 Suppl 2:S11 (PMC3090759) - Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.
Collins AJ, Nyholm SV
J. Bacteriol. (2011) 193(13):3397-8 (PMC3133266) 10.1128/JB.05139-11 - Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers.
Kong L, Zhang P, Wang G, Yu J, Setlow P, Li YQ
Nat Protoc (2011) 6(5):625-39 - Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.
Andam CP, Fournier GP, Gogarten JP
FEMS Microbiol. Rev. (2011) 35(5):756-67 - Genomic understanding of dinoflagellates.
Lin S
Res. Microbiol. (2011) 162(6):551-69 10.1016/j.resmic.2011.04.006 - Estimation of alternative splicing isoform frequencies from RNA-Seq data.
Nicolae M, Mangul S, Măndoiu II, Zelikovsky A
Algorithms Mol Biol (2011) 6(1):9 (PMC3107792) - TP0326, a Treponema pallidum β-barrel assembly machinery A (BamA) orthologue and rare outer membrane protein.
Desrosiers DC, Anand A, Luthra A, Dunham-Ems SM, LeDoyt M, Cummings MA, Eshghi A, Cameron CE, Cruz AR, Salazar JC, Caimano MJ, Radolf JD
Mol. Microbiol. (2011) 80(6):1496-515 (PMC3115443) - Multilocus sequence analysis of the family Halomonadaceae.
de la Haba RR, Márquez MC, Papke RT, Ventosa A
Int. J. Syst. Evol. Microbiol. (2011) 62(Pt 3):520-38 - Hybridization, mitochondrial DNA phylogeography, and prediction of the early stages of reproductive isolation: lessons from New Zealand cicadas (genus Kikihia).
Marshall DC, Hill KB, Cooley JR, Simon C
Syst. Biol. (2011) 60(4):482-502 10.1093/sysbio/syr017 - Directed culturing of microorganisms using metatranscriptomics.
Bomar L, Maltz M, Colston S, Graf J
MBio (2011) 2(2):e00012-11 (PMC3069634) - Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete.
Grubbs KJ, Biedermann PH, Suen G, Adams SM, Moeller JA, Klassen JL, Goodwin LA, Woyke T, Munk AC, Bruce D, Detter C, Tapia R, Han CS, Currie CR
J. Bacteriol. (2011) 193(11):2890-1 (PMC3133108) - Tandem metathesis reactions of oxabicyclo[2.2.1]heptenes: studies on the spirocyclic core of cyclopamine.
Oblak EZ, G-Dayanandan N, Wright DL
Org. Lett. (2011) 13(9):2433-5 10.1021/ol200706f - Highly substituted oxabicyclic derivatives from furan: synthesis of (±)-platensimycin.
Oblak EZ, Wright DL
Org. Lett. (2011) 13(9):2263-5 10.1021/ol2005775 - Role of the Nfo and ExoA apurinic/apyrimidinic endonucleases in radiation resistance and radiation-induced mutagenesis of Bacillus subtilis spores.
Moeller R, Setlow P, Pedraza-Reyes M, Okayasu R, Reitz G, Nicholson WL
J. Bacteriol. (2011) 193(11):2875-9 (PMC3133121) - Kinetics of germination of wet-heat-treated individual spores of Bacillus species, monitored by Raman spectroscopy and differential interference contrast microscopy.
Wang G, Zhang P, Setlow P, Li YQ
Appl. Environ. Microbiol. (2011) 77(10):3368-79 (PMC3126438) - Germination of individual Bacillus subtilis spores with alterations in the GerD and SpoVA proteins, which are important in spore germination.
Wang G, Yi X, Li YQ, Setlow P
J. Bacteriol. (2011) 193(9):2301-11 (PMC3133087) - Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.
Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II
BMC Bioinformatics (2011) 12 Suppl 1:S53 (PMC3044311) - Why intraspecific trait variation matters in community ecology.
Bolnick DI, Amarasekare P, Araújo MS, Bürger R, Levine JM, Novak M, Rudolf VH, Schreiber SJ, Urban MC, Vasseur DA
Trends Ecol. Evol. (Amst.) (2011) 26(4):183-92 (PMC3088364) - Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data.
Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J
PLoS ONE (2011) 6(2):e16751 (PMC3040217) - In vitro antimicrobial properties of caprylic acid, monocaprylin, and sodium caprylate against Dermatophilus congolensis.
Valipe SR, Nadeau JA, Annamali T, Venkitanarayanan K, Hoagland T
Am. J. Vet. Res. (2011) 72(3):331-5 - Trans-cinnamaldehyde decreases attachment and invasion of uropathogenic Escherichia coli in urinary tract epithelial cells by modulating virulence gene expression.
Amalaradjou MA, Narayanan A, Venkitanarayanan K
J. Urol. (2011) 185(4):1526-31 - Effect of trans-cinnamaldehyde on inhibition and inactivation of Cronobacter sakazakii biofilm on abiotic surfaces.
Amalaradjou MA, Venkitanarayanan K
J. Food Prot. (2011) 74(2):200-8 - Phagosomal signaling by Borrelia burgdorferi in human monocytes involves Toll-like receptor (TLR) 2 and TLR8 cooperativity and TLR8-mediated induction of IFN-beta.
Cervantes JL, Dunham-Ems SM, La Vake CJ, Petzke MM, Sahay B, Sellati TJ, Radolf JD, Salazar JC
Proc. Natl. Acad. Sci. U.S.A. (2011) 108(9):3683-8 (PMC3048123) - Extremely variable conservation of γ-type small, acid-soluble proteins from spores of some species in the bacterial order Bacillales.
Vyas J, Cox J, Setlow B, Coleman WH, Setlow P
J. Bacteriol. (2011) 193(8):1884-92 (PMC3133055) - Study of in situ 1-butanol pervaporation from A-B-E fermentation using a PDMS composite membrane: validity of solution-diffusion model for pervaporative A-B-E fermentation.
Li SY, Srivastava R, Parnas RS
Biotechnol. Prog. (2011) 27(1):111-20 - A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.
Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A
Int. J. Syst. Evol. Microbiol. (2011) 61(Pt 12):2984-95 - In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.
Naor A, Lazary R, Barzel A, Papke RT, Gophna U
PLoS ONE (2011) 6(1):e15833 (PMC3024317) - MOLECULAR PHYLOGENETIC RELATIONSHIPS IN THE FRESHWATER FAMILY HYDRODICTYACEAE (SPHAEROPLEALES, CHLOROPHYCEAE), WITH AN EMPHASIS ON PEDIASTRUM DUPLEX(1).
McManus HA, Lewis LA
J. Phycol. (2011) 47(1):152-63 - DISTINGUISHING MULTIPLE LINEAGES OF PEDIASTRUM DUPLEX WITH MORPHOMETRICS AND A PROPOSAL FOR LACUNASTRUM GEN. NOV(1).
McManus HA, Lewis LA, Schultz ET
J. Phycol. (2011) 47(1):123-30 - Ancient origins determine global biogeography of hot and cold desert cyanobacteria.
Bahl J, Lau MC, Smith GJ, Vijaykrishna D, Cary SC, Lacap DC, Lee CK, Papke RT, Warren-Rhodes KA, Wong FK, McKay CP, Pointing SB
Nat Commun (2011) 2:163 (PMC3105302) - Water administration of the medium-chain fatty acid caprylic acid produced variable efficacy against enteric Campylobacter colonization in broilers.
Metcalf JH, Donoghue AM, Venkitanarayanan K, Reyes-Herrera I, Aguiar VF, Blore PJ, Donoghue DJ
Poult. Sci. (2011) 90(2):494-7 - Performance of batch, fed-batch, and continuous A-B-E fermentation with pH-control.
Li SY, Srivastava R, Suib SL, Li Y, Parnas RS
Bioresour. Technol. (2011) 102(5):4241-50 - Behavior of Escherichia coli O157:H7 during the manufacture and aging of Gouda and stirred-curd Cheddar cheeses manufactured from raw milk.
D'Amico DJ, Druart MJ, Donnelly CW
J. Food Prot. (2011) 73(12):2217-24 2010
- Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.
Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ
Syst. Biol. (2010) 60(2):117-25 (PMC3038350) - BB0844, an RpoS-regulated protein, is dispensable for Borrelia burgdorferi infectivity and maintenance in the mouse-tick infectious cycle.
Banik S, Terekhova D, Iyer R, Pappas CJ, Caimano MJ, Radolf JD, Schwartz I
Infect. Immun. (2010) 79(3):1208-17 (PMC3067486) - Catalytic mechanism of a heme and tyrosyl radical-containing fatty acid α-(di)oxygenase.
Mukherjee A, Angeles-Boza AM, Huff GS, Roth JP
J. Am. Chem. Soc. (2010) 133(2):227-38 - Inactivation of Salmonella spp. on tomatoes by plant molecules.
Mattson TE, Johny AK, Amalaradjou MA, More K, Schreiber DT, Patel J, Venkitanarayanan K
Int. J. Food Microbiol. (2010) 144(3):464-8 - Herpes simplex virus reorganizes the cellular DNA repair and protein quality control machinery.
Weller SK
PLoS Pathog. (2010) 6(11):e1001105 (PMC2991270) 10.1371/journal.ppat.1001105 - Haplotype inference from short sequence reads using a population genealogical history model.
Zhang J, Wu Y
Pac Symp Biocomput (2010) :288-99 - Effect of trans-cinnamaldehyde on reducing resistance to environmental stresses in Cronobacter sakazakii.
Amalaradjou MA, Venkitanarayanan K
Foodborne Pathog. Dis. (2010) 8(3):403-9 - Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved.
Paredes-Sabja D, Setlow P, Sarker MR
Trends Microbiol. (2010) 19(2):85-94 - Anti-inflammatory effects of freeze-dried black raspberry powder in ulcerative colitis.
Montrose DC, Horelik NA, Madigan JP, Stoner GD, Wang LS, Bruno RS, Park HJ, Giardina C, Rosenberg DW
Carcinogenesis (2010) 32(3):343-50 (PMC3047236) - The type II secretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii.
Maltz M, Graf J
Appl. Environ. Microbiol. (2010) 77(2):597-603 (PMC3020562) - Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus.
Klassen JL, Foght JM
Extremophiles (2010) 15(1):45-57 - iGTP: a software package for large-scale gene tree parsimony analysis.
Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O
BMC Bioinformatics (2010) 11:574 (PMC3002902) - New methods for inference of local tree topologies with recombinant SNP sequences in populations.
Wu Y
IEEE/ACM Trans Comput Biol Bioinform (2010) 8(1):182-93 10.1109/TCBB.2009.27 - Herpes simplex virus type 1 helicase-primase: DNA binding and consequent protein oligomerization and primase activation.
Chen Y, Bai P, Mackay S, Korza G, Carson JH, Kuchta RD, Weller SK
J. Virol. (2010) 85(2):968-78 (PMC3019990) 10.1128/JVI.01690-10 - Bacterial communities in the 'petola' microbial mat from the Sečovlje salterns (Slovenia).
Tkavc R, Gostinčar C, Turk M, Visscher PT, Oren A, Gunde-Cimerman N
FEMS Microbiol. Ecol. (2010) 75(1):48-62 - Guest Editors' introduction to the special section on bioinformatics research and applications.
Mandoiu I, Narasimhan G, Pan Y, Zhang Y
IEEE/ACM Trans Comput Biol Bioinform (2010) 7(4):577-8 - Effects of Mn and Fe levels on Bacillus subtilis spore resistance and effects of Mn2+, other divalent cations, orthophosphate, and dipicolinic acid on protein resistance to ionizing radiation.
Granger AC, Gaidamakova EK, Matrosova VY, Daly MJ, Setlow P
Appl. Environ. Microbiol. (2010) 77(1):32-40 (PMC3019732) - Combination of Raman tweezers and quantitative differential interference contrast microscopy for measurement of dynamics and heterogeneity during the germination of individual bacterial spores.
Zhang P, Kong L, Wang G, Setlow P, Li YQ
J Biomed Opt (2010) 15(5):56010 - Generation of endosomolytic reagents by branching of cell-penetrating peptides: tools for the delivery of bioactive compounds to live cells in cis or trans.
Angeles-Boza AM, Erazo-Oliveras A, Lee YJ, Pellois JP
Bioconjug. Chem. (2010) 21(12):2164-7 (PMC3074029) - Evolution of the Archaea: emerging views on origins and phylogeny.
Fournier GP, Dick AA, Williams D, Gogarten JP
Res. Microbiol. (2010) 162(1):92-8 - Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates.
Lin S, Zhang H, Zhuang Y, Tran B, Gill J
Proc. Natl. Acad. Sci. U.S.A. (2010) 107(46):20033-8 (PMC2993343) 10.1073/pnas.1007246107 - Exact computation of coalescent likelihood for panmictic and subdivided populations under the infinite sites model.
Wu Y
IEEE/ACM Trans Comput Biol Bioinform (2010) 7(4):611-8 10.1109/TCBB.2010.2 - Antibacterial autophagy occurs at PI(3)P-enriched domains of the endoplasmic reticulum and requires Rab1 GTPase.
Huang J, Birmingham CL, Shahnazari S, Shiu J, Zheng YT, Smith AC, Campellone KG, Heo WD, Gruenheid S, Meyer T, Welch MD, Ktistakis NT, Kim PK, Klionsky DJ, Brumell JH
Autophagy (2010) 7(1):17-26 (PMC3039730) 10.4161/auto.7.1.13840 - Multiple-trap laser tweezers Raman spectroscopy for simultaneous monitoring of the biological dynamics of multiple individual cells.
Zhang P, Kong L, Setlow P, Li YQ
Opt Lett (2010) 35(20):3321-3 - Physical interaction between the herpes simplex virus type 1 exonuclease, UL12, and the DNA double-strand break-sensing MRN complex.
Balasubramanian N, Bai P, Buchek G, Korza G, Weller SK
J. Virol. (2010) 84(24):12504-14 (PMC3004347) 10.1128/JVI.01506-10 - Intestinal lineage commitment of embryonic stem cells.
Cao L, Gibson JD, Miyamoto S, Sail V, Verma R, Rosenberg DW, Nelson CE, Giardina C
Differentiation (2010) 81(1):1-10 - NMR assignments for the Sinorhizobium meliloti response regulator Sma0114.
Sheftic SR, Garcia PP, Robinson VL, Gage DJ, Alexandrescu AT
Biomol NMR Assign (2010) 5(1):55-8 (PMC4343204) - WASH, WHAMM and JMY: regulation of Arp2/3 complex and beyond.
Rottner K, Hänisch J, Campellone KG
Trends Cell Biol. (2010) 20(11):650-61 10.1016/j.tcb.2010.08.014 - A TFIIH-associated mediator head is a basal factor of small nuclear spliced leader RNA gene transcription in early-diverged trypanosomes.
Lee JH, Cai G, Panigrahi AK, Dunham-Ems S, Nguyen TN, Radolf JD, Asturias FJ, Günzl A
Mol. Cell. Biol. (2010) 30(23):5502-13 (PMC2976424) - Surface immunolabeling and consensus computational framework to identify candidate rare outer membrane proteins of Treponema pallidum.
Cox DL, Luthra A, Dunham-Ems S, Desrosiers DC, Salazar JC, Caimano MJ, Radolf JD
Infect. Immun. (2010) 78(12):5178-94 (PMC2981305) - Monitoring the kinetics of uptake of a nucleic acid dye during the germination of single spores of Bacillus species.
Kong L, Zhang P, Yu J, Setlow P, Li YQ
Anal. Chem. (2010) 82(20):8717-24 - Role of acetyl-phosphate in activation of the Rrp2-RpoN-RpoS pathway in Borrelia burgdorferi.
Xu H, Caimano MJ, Lin T, He M, Radolf JD, Norris SJ, Gherardini F, Gheradini F, Wolfe AJ, Yang XF
PLoS Pathog. (2010) 6(9):e1001104 (PMC2940757) - ATR and ATRIP are recruited to herpes simplex virus type 1 replication compartments even though ATR signaling is disabled.
Mohni KN, Livingston CM, Cortez D, Weller SK
J. Virol. (2010) 84(23):12152-64 (PMC2976399) 10.1128/JVI.01643-10 - Znu is the predominant zinc importer in Yersinia pestis during in vitro growth but is not essential for virulence.
Desrosiers DC, Bearden SW, Mier I, Abney J, Paulley JT, Fetherston JD, Salazar JC, Radolf JD, Perry RD
Infect. Immun. (2010) 78(12):5163-77 (PMC2981304) - Characterization of a two-component regulatory system that regulates succinate-mediated catabolite repression in Sinorhizobium meliloti.
Garcia PP, Bringhurst RM, Arango Pinedo C, Gage DJ
J. Bacteriol. (2010) 192(21):5725-35 (PMC2953702) - In vivo effects of brown tide on the feeding function of the gill of the northern quahog Mercenaria mercenaria (Bivalvia: Veneridae).
Robbins HM, Bricelj VM, Ward JE
Biol. Bull. (2010) 219(1):61-71 10.1086/BBLv219n1p61 - Role of epicellular molecules in the selection of particles by the blue mussel, Mytilus edulis.
Espinosa EP, Hassan D, Ward JE, Shumway SE, Allam B
Biol. Bull. (2010) 219(1):50-60 10.1086/BBLv219n1p50 - Enterohemorrhagic E. coli requires N-WASP for efficient type III translocation but not for EspFU-mediated actin pedestal formation.
Vingadassalom D, Campellone KG, Brady MJ, Skehan B, Battle SE, Robbins D, Kapoor A, Hecht G, Snapper SB, Leong JM
PLoS Pathog. (2010) 6(8):e1001056 (PMC2924363) 10.1371/journal.ppat.1001056 - Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis.
Marvasi M, Visscher PT, Casillas Martinez L
FEMS Microbiol. Lett. (2010) 313(1):1-9 - A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.
Bansal MS, Shamir R
IEEE/ACM Trans Comput Biol Bioinform (2010) 8(3):848-50 - Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling.
Hird S, Kubatko L, Carstens B
Mol. Phylogenet. Evol. (2010) 57(2):888-98 10.1016/j.ympev.2010.08.006 - Long-term dynamics of tropical walking sticks in response to multiple large-scale and intense disturbances.
Willig MR, Presley SJ, Bloch CP
Oecologia (2010) 165(2):357-68 - Determinants of bacteriophage P22 polyhead formation: the role of coat protein flexibility in conformational switching.
Suhanovsky MM, Parent KN, Dunn SE, Baker TS, Teschke CM
Mol. Microbiol. (2010) 77(6):1568-82 (PMC2945288) - Crystal structure of the GerBC component of a Bacillus subtilis spore germinant receptor.
Li Y, Setlow B, Setlow P, Hao B
J. Mol. Biol. (2010) 402(1):8-16 (PMC3607951) - Introns, alternative splicing, spliced leader trans-splicing and differential expression of pcna and cyclin in Perkinsus marinus.
Zhang H, Dungan CF, Lin S
Protist (2010) 162(1):154-67 10.1016/j.protis.2010.03.003 - Natural compounds with aromatase inhibitory activity: an update.
Balunas MJ, Kinghorn AD
Planta Med. (2010) 76(11):1087-93 (PMC2965731) - Enhancing the thermal destruction of Escherichia coli O157:H7 in ground beef patties by trans-cinnamaldehyde.
Amalaradjou MA, Baskaran SA, Ramanathan R, Johny AK, Charles AS, Valipe SR, Mattson T, Schreiber D, Juneja VK, Mancini R, Venkitanarayanan K
Food Microbiol. (2010) 27(6):841-4 - Effect of subinhibitory concentrations of plant-derived molecules in increasing the sensitivity of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 to antibiotics.
Johny AK, Hoagland T, Venkitanarayanan K
Foodborne Pathog. Dis. (2010) 7(10):1165-70 - Introgression at differentially aged hybrid zones in red-tailed chipmunks.
Hird S, Reid N, Demboski J, Sullivan J
Genetica (2010) 138(8):869-83 10.1007/s10709-010-9470-z - The pre-mRNA splicing machinery of trypanosomes: complex or simplified?
Günzl A
Eukaryotic Cell (2010) 9(8):1159-70 (PMC2918933) - Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.
Klassen JL
PLoS ONE (2010) 5(6):e11257 (PMC2889829) - Identification of rep-associated factors in herpes simplex virus type 1-induced adeno-associated virus type 2 replication compartments.
Nicolas A, Alazard-Dany N, Biollay C, Arata L, Jolinon N, Kuhn L, Ferro M, Weller SK, Epstein AL, Salvetti A, Greco A
J. Virol. (2010) 84(17):8871-87 (PMC2919046) 10.1128/JVI.00725-10 - Genetic identities of Cryptic species in the Strombidium stylifer/apolatum/oculatum cluster, including a description of Strombidium rassoulzadegani n. sp.
McManus GB, Xu D, Costas BA, Katz LA
J. Eukaryot. Microbiol. (2010) 57(4):369-78 - Hyperbaric oxygen treatment induces antioxidant gene expression.
Godman CA, Joshi R, Giardina C, Perdrizet G, Hightower LE
Ann. N. Y. Acad. Sci. (2010) 1197:178-83 - Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees.
Wu Y
Bioinformatics (2010) 26(12):i140-8 (PMC2881383) 10.1093/bioinformatics/btq198 - Identification of lipoprotein MslA as a neoteric virulence factor of Mycoplasma gallisepticum.
Szczepanek SM, Frasca S, Schumacher VL, Liao X, Padula M, Djordjevic SP, Geary SJ
Infect. Immun. (2010) 78(8):3475-83 (PMC2916287) 10.1128/IAI.00154-10 - Secondary syphilis in cali, Colombia: new concepts in disease pathogenesis.
Cruz AR, Pillay A, Zuluaga AV, Ramirez LG, Duque JE, Aristizabal GE, Fiel-Gan MD, Jaramillo R, Trujillo R, Valencia C, Jagodzinski L, Cox DL, Radolf JD, Salazar JC
PLoS Negl Trop Dis (2010) 4(5):e690 (PMC2872645) - Photophysical properties, DNA photocleavage, and photocytotoxicity of a series of dppn dirhodium(II,II) complexes.
Joyce LE, Aguirre JD, Angeles-Boza AM, Chouai A, Fu PK, Dunbar KR, Turro C
Inorg Chem (2010) 49(12):5371-6 - Biased gene transfer mimics patterns created through shared ancestry.
Andam CP, Williams D, Gogarten JP
Proc. Natl. Acad. Sci. U.S.A. (2010) 107(23):10679-84 (PMC2890805) - Biogeochemical cycling and microbial diversity in the thrombolitic microbialites of Highborne Cay, Bahamas.
Myshrall KL, Mobberley JM, Green SJ, Visscher PT, Havemann SA, Reid RP, Foster JS
Geobiology (2010) 8(4):337-54 - Antibiofilm effect of trans-cinnamaldehyde on uropathogenic Escherichia coli.
Amalaradjou MA, Narayanan A, Baskaran SA, Venkitanarayanan K
J. Urol. (2010) 184(1):358-63 - Cytoskeleton-modulating effectors of enteropathogenic and enterohaemorrhagic Escherichia coli: Tir, EspFU and actin pedestal assembly.
Campellone KG
FEBS J. (2010) 277(11):2390-402 10.1111/j.1742-4658.2010.07653.x - Factors affecting variability in time between addition of nutrient germinants and rapid dipicolinic acid release during germination of spores of Bacillus species.
Zhang P, Garner W, Yi X, Yu J, Li YQ, Setlow P
J. Bacteriol. (2010) 192(14):3608-19 (PMC2897343) - Intraspecific genetic variation and competition interact to influence niche expansion.
Agashe D, Bolnick DI
Proc. Biol. Sci. (2010) 277(1696):2915-24 (PMC2982016) - Specialization of trophic position and habitat use by sticklebacks in an adaptive radiation.
Matthews B, Marchinko KB, Bolnick DI, Mazumder A
Ecology (2010) 91(4):1025-34 - Inactivation of Escherichia coli O157:H7 in apple juice and apple cider by trans-cinnamaldehyde.
Baskaran SA, Amalaradjou MA, Hoagland T, Venkitanarayanan K
Int. J. Food Microbiol. (2010) 141(1-2):126-9 - Diversity of oligotrichia and choreotrichia ciliates in coastal marine sediments and in overlying plankton.
Doherty M, Tamura M, Vriezen JA, McManus GB, Katz LA
Appl. Environ. Microbiol. (2010) 76(12):3924-35 (PMC2893510) - Studies of the commitment step in the germination of spores of bacillus species.
Yi X, Setlow P
J. Bacteriol. (2010) 192(13):3424-33 (PMC2897682) - Using comparative genome analysis to identify problems in annotated microbial genomes.
Poptsova MS, Gogarten JP
Microbiology (Reading, Engl.) (2010) 156(Pt 7):1909-17 - Identification of 'Candidatus Piscichlamydia salmonis' in Arctic charr Salvelinus alpinus during a survey of charr production facilities in North America.
Draghi A, Bebak J, Daniels S, Tulman ER, Geary SJ, West AB, Popov VL, Frasca S
Dis. Aquat. Org. (2010) 89(1):39-49 10.3354/dao02171 - Development of safe and efficacious viral vaccines for animals.
Yilma T, Verardi P, Jones L
Crit. Rev. Immunol. (2010) 30(3):223-37 - Characterization of bacterial spore germination using integrated phase contrast microscopy, Raman spectroscopy, and optical tweezers.
Kong L, Zhang P, Setlow P, Li YQ
Anal. Chem. (2010) 82(9):3840-7 - Broad specificity AhpC-like peroxiredoxin and its thioredoxin reductant in the sparse antioxidant defense system of Treponema pallidum.
Parsonage D, Desrosiers DC, Hazlett KR, Sun Y, Nelson KJ, Cox DL, Radolf JD, Poole LB
Proc. Natl. Acad. Sci. U.S.A. (2010) 107(14):6240-5 (PMC2851974) - 'Let the phage do the work': using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants.
Teschke CM, Parent KN
Virology (2010) 401(2):119-30 (PMC2862144) - A nucleator arms race: cellular control of actin assembly.
Campellone KG, Welch MD
Nat. Rev. Mol. Cell Biol. (2010) 11(4):237-51 (PMC2929822) 10.1038/nrm2867 - Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene.
Hou Y, Zhang H, Miranda L, Lin S
PLoS ONE (2010) 5(3):e9545 (PMC2832698) 10.1371/journal.pone.0009545 - Filling the gaps in the genomic landscape.
Williams D, Gogarten JP, Lapierre P
Genome Biol. (2010) 11(2):103 (PMC2872866) - Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders.
Fournier GP, Neumann JE, Gogarten JP
PLoS ONE (2010) 5(3):e9437 (PMC2830423) - Identification of residues within ligand-binding domain 1 (LBD1) of the Borrelia burgdorferi OspC protein required for function in the mammalian environment.
Earnhart CG, Leblanc DV, Alix KE, Desrosiers DC, Radolf JD, Marconi RT
Mol. Microbiol. (2010) 76(2):393-408 (PMC2917209) - Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.
Bansal MS, Burleigh JG, Eulenstein O
BMC Bioinformatics (2010) 11 Suppl 1:S42 (PMC3009515) - Foraging trait (co)variances in stickleback evolve deterministically and do not predict trajectories of adaptive diversification.
Berner D, Stutz WE, Bolnick DI
Evolution (2010) 64(8):2265-77 - Rooting the ribosomal tree of life.
Fournier GP, Gogarten JP
Mol. Biol. Evol. (2010) 27(8):1792-801 - Robinson-Foulds supertrees.
Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D
Algorithms Mol Biol (2010) 5:18 (PMC2846952) - Ecological release from interspecific competition leads to decoupled changes in population and individual niche width.
Bolnick DI, Ingram T, Stutz WE, Snowberg LK, Lau OL, Paull JS
Proc. Biol. Sci. (2010) 277(1689):1789-97 (PMC2871882) - Isolation and Characterization of Aromatase Inhibitors from Brassaiopsis glomerulata (Araliaceae).
Balunas MJ, Su B, Riswan S, Fong HH, Brueggemeier RW, Pezzuto JM, Kinghorn AD
Phytochem Lett (2010) 2(1):29-33 (PMC2748821) - Obtaining hemocytes from the Hawaiian bobtail squid Euprymna scolopes and observing their adherence to symbiotic and non-symbiotic bacteria.
Collins AJ, Nyholm SV
J Vis Exp (2010) (36): (PMC2830252) 10.3791/1714 - Caprylic Acid reduces enteric campylobacter colonization in market-aged broiler chickens but does not appear to alter cecal microbial populations.
Solís de los Santos F, Hume M, Venkitanarayanan K, Donoghue AM, Hanning I, Slavik MF, Aguiar VF, Metcalf JH, Reyes-Herrera I, Blore PJ, Donoghue DJ
J. Food Prot. (2010) 73(2):251-7 - Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis.
Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ
Proc. Natl. Acad. Sci. U.S.A. (2010) 107(5):2259-64 (PMC2836665) 10.1073/pnas.0909712107 - Comparative genomic analyses of attenuated strains of Mycoplasma gallisepticum.
Szczepanek SM, Tulman ER, Gorton TS, Liao X, Lu Z, Zinski J, Aziz F, Frasca S, Kutish GF, Geary SJ
Infect. Immun. (2010) 78(4):1760-71 (PMC2849401) 10.1128/IAI.01172-09 - Ciliate diversity and distribution across an environmental and depth gradient in Long Island Sound, USA.
Doherty M, Tamura M, Costas BA, Ritchie ME, McManus GB, Katz LA
Environ. Microbiol. (2010) 12(4):886-98 - Phosphoinositides influence pathogen surfing: EPEC rights the SHIP.
Campellone KG
Cell Host Microbe (2010) 7(1):1-2 10.1016/j.chom.2009.12.006 - Characterization of wet-heat inactivation of single spores of bacillus species by dual-trap Raman spectroscopy and elastic light scattering.
Zhang P, Kong L, Setlow P, Li YQ
Appl. Environ. Microbiol. (2010) 76(6):1796-805 (PMC2837993) - The carnivorous pale pitcher plant harbors diverse, distinct, and time-dependent bacterial communities.
Koopman MM, Fuselier DM, Hird S, Carstens BC
Appl. Environ. Microbiol. (2010) 76(6):1851-60 (PMC2838028) 10.1128/AEM.02440-09 - Characterization of the invasive and inflammatory traits of oral Campylobacter rectus in a murine model of fetoplacental growth restriction and in trophoblast cultures.
Arce RM, Diaz PI, Barros SP, Galloway P, Bobetsis Y, Threadgill D, Offenbacher S
J. Reprod. Immunol. (2010) 84(2):145-53 (PMC2904603) - Selective inhibitor of proteasome's caspase-like sites sensitizes cells to specific inhibition of chymotrypsin-like sites.
Britton M, Lucas MM, Downey SL, Screen M, Pletnev AA, Verdoes M, Tokhunts RA, Amir O, Goddard AL, Pelphrey PM, Wright DL, Overkleeft HS, Kisselev AF
Chem. Biol. (2010) 16(12):1278-89 (PMC2807417) 10.1016/j.chembiol.2009.11.015 - Quorum sensing in natural environments: emerging views from microbial mats.
Decho AW, Norman RS, Visscher PT
Trends Microbiol. (2010) 18(2):73-80 - Physiological requirements for carbonate precipitation during biofilm development of Bacillus subtilis etfA mutant.
Marvasi M, Visscher PT, Perito B, Mastromei G, Casillas-Martínez L
FEMS Microbiol. Ecol. (2010) 71(3):341-50 - Superdormant spores of bacillus species germinate normally with high pressure, peptidoglycan fragments, and bryostatin.
Wei J, Shah IM, Ghosh S, Dworkin J, Hoover DG, Setlow P
J. Bacteriol. (2010) 192(5):1455-8 (PMC2820858) - Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements.
Swithers KS, Senejani AG, Fournier GP, Gogarten JP
BMC Evol. Biol. (2010) 9:303 (PMC2814812) - Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli.
Jain R, Srivastava R
BMC Syst Biol (2010) 3:121 (PMC2813233) 2009
- The role of the immune system in the initiation and persistence of the Euprymna scolopes--Vibrio fischeri symbiosis.
McFall-Ngai M, Nyholm SV, Castillo MG
Semin. Immunol. (2009) 22(1):48-53 (PMC3992935) 10.1016/j.smim.2009.11.003 - Identification of mammalian orthologs using local synteny.
Jun J, Mandoiu II, Nelson CE
BMC Genomics (2009) 10:630 (PMC2807883) - Dragonamide E, a modified linear lipopeptide from Lyngbya majuscula with antileishmanial activity.
Balunas MJ, Linington RG, Tidgewell K, Fenner AM, Ureña LD, Togna GD, Kyle DE, Gerwick WH
J. Nat. Prod. (2009) 73(1):60-6 (PMC2834186) - Herpes simplex virus type 1 immediate-early protein ICP22 is required for VICE domain formation during productive viral infection.
Bastian TW, Livingston CM, Weller SK, Rice SA
J. Virol. (2009) 84(5):2384-94 (PMC2820935) 10.1128/JVI.01686-09 - Towards the understanding of resistance mechanisms in clinically isolated trimethoprim-resistant, methicillin-resistant Staphylococcus aureus dihydrofolate reductase.
Frey KM, Lombardo MN, Wright DL, Anderson AC
J. Struct. Biol. (2009) 170(1):93-7 (PMC2841211) 10.1016/j.jsb.2009.12.011 - Anticancer activity of heteroleptic diimine complexes of dirhodium: a study of intercalating properties, hydrophobicity and in cellulo activity.
Aguirre JD, Angeles-Boza AM, Chouai A, Turro C, Pellois JP, Dunbar KR
Dalton Trans (2009) (48):10806-12 - CD14 signaling restrains chronic inflammation through induction of p38-MAPK/SOCS-dependent tolerance.
Sahay B, Patsey RL, Eggers CH, Salazar JC, Radolf JD, Sellati TJ
PLoS Pathog. (2009) 5(12):e1000687 (PMC2781632) - Detection, isolation, and incidence of Listeria spp. in small-scale artisan cheese processing facilities: a methods comparison.
D'Amico DJ, Donnelly CW
J. Food Prot. (2009) 72(12):2499-507 - Microbial species richness and metabolic activities in hypersaline microbial mats: insight into biosignature formation through lithification.
Baumgartner LK, Dupraz C, Buckley DH, Spear JR, Pace NR, Visscher PT
Astrobiology (2009) 9(9):861-74 - Hyperbaric oxygen induces a cytoprotective and angiogenic response in human microvascular endothelial cells.
Godman CA, Chheda KP, Hightower LE, Perdrizet G, Shin DG, Giardina C
Cell Stress Chaperones (2009) 15(4):431-42 (PMC3082642) - Who is the BosR around here anyway?
Samuels DS, Radolf JD
Mol. Microbiol. (2009) 74(6):1295-9 (PMC3005592) - Effects of forespore-specific overexpression of apurinic/apyrimidinic endonuclease Nfo on the DNA-damage resistance properties of Bacillus subtilis spores.
Barraza-Salas M, Ibarra-Rodríguez JR, Mellado SJ, Salas-Pacheco JM, Setlow P, Pedraza-Reyes M
FEMS Microbiol. Lett. (2009) 302(2):159-65 - Live imaging reveals a biphasic mode of dissemination of Borrelia burgdorferi within ticks.
Dunham-Ems SM, Caimano MJ, Pal U, Wolgemuth CW, Eggers CH, Balic A, Radolf JD
J. Clin. Invest. (2009) 119(12):3652-65 (PMC2786795) - Micro-scale water potential gradients visualized in soil around plant root tips using microbiosensors.
Herron PM, Gage DJ, Cardon ZG
Plant Cell Environ. (2009) 33(2):199-210 - The physical state of water in bacterial spores.
Sunde EP, Setlow P, Hederstedt L, Halle B
Proc. Natl. Acad. Sci. U.S.A. (2009) 106(46):19334-9 (PMC2780810) - Bacterial contamination of hands increases risk of cross-contamination among low-income Puerto Rican meal preparers.
Dharod JM, Paciello S, Bermúdez-Millán A, Venkitanarayanan K, Damio G, Pérez-Escamilla R
J Nutr Educ Behav (2009) 41(6):389-97 (PMC3184459) - Lectins associated with the feeding organs of the oyster Crassostrea virginica can mediate particle selection.
Espinosa EP, Perrigault M, Ward JE, Shumway SE, Allam B
Biol. Bull. (2009) 217(2):130-41 10.1086/BBLv217n2p130 - Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer.
Olendzenski L, Gogarten JP
Ann. N. Y. Acad. Sci. (2009) 1178:137-45 - Structural and genetic analysis of X-ray scattering by spores of Bacillus subtilis.
Qiu X, Setlow P
J. Bacteriol. (2009) 191(24):7620-2 (PMC2786606) - Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.
Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR
BMC Genomics (2009) 10:468 (PMC2770080) - Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis.
Klassen JL
J. Bacteriol. (2009) 191(24):7500-8 (PMC2786601) - Cryo-electron tomography elucidates the molecular architecture of Treponema pallidum, the syphilis spirochete.
Izard J, Renken C, Hsieh CE, Desrosiers DC, Dunham-Ems S, La Vake C, Gebhardt LL, Limberger RJ, Cox DL, Marko M, Radolf JD
J. Bacteriol. (2009) 191(24):7566-80 (PMC2786590) - Virus-Induced Chaperone-Enriched (VICE) domains function as nuclear protein quality control centers during HSV-1 infection.
Livingston CM, Ifrim MF, Cowan AE, Weller SK
PLoS Pathog. (2009) 5(10):e1000619 (PMC2752995) 10.1371/journal.ppat.1000619 - The birth of new genes by RNA- and DNA-mediated duplication during mammalian evolution.
Jun J, Ryvkin P, Hemphill E, Mandoiu I, Nelson C
J. Comput. Biol. (2009) 16(10):1429-44 - A novel domain in translational GTPase BipA mediates interaction with the 70S ribosome and influences GTP hydrolysis.
deLivron MA, Makanji HS, Lane MC, Robinson VL
Biochemistry (2009) 48(44):10533-41 10.1021/bi901026z - Plasmids that insert into the rhamnose utilization locus, rha: a versatile tool for genetic studies in Sinorhizobium meliloti.
Arango Pinedo C, Gage DJ
J. Mol. Microbiol. Biotechnol. (2009) 17(4):201-10 - Formation and diagenesis of modern marine calcified cyanobacteria.
Planavsky N, Reid RP, Lyons TW, Myshrall KL, Visscher PT
Geobiology (2009) 7(5):566-76 - DNA damage response to the Mdm2 inhibitor nutlin-3.
Verma R, Rigatti MJ, Belinsky GS, Godman CA, Giardina C
Biochem. Pharmacol. (2009) 79(4):565-74 (PMC2794967) - Prokaryotic evolution and the tree of life are two different things.
Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W
Biol. Direct (2009) 4:34 (PMC2761302) - ELLIPTOCHLORIS MARINA SP. NOV. (TREBOUXIOPHYCEAE, CHLOROPHYTA), SYMBIOTIC GREEN ALGA OF THE TEMPERATE PACIFIC SEA ANEMONES ANTHOPLEURA XANTHOGRAMMICA AND A. ELEGANTISSIMA (ANTHOZOA, CNIDARIA)(1).
Letsch MR, Muller-Parker G, Friedl T, Lewis LA
J. Phycol. (2009) 45(5):1127-35 - Characterization of single heat-activated Bacillus spores using laser tweezers Raman spectroscopy.
Zhang P, Setlow P, Li Y
Opt Express (2009) 17(19):16480-91 - Diminished exoproteome of Frankia spp. in culture and symbiosis.
Mastronunzio JE, Huang Y, Benson DR
Appl. Environ. Microbiol. (2009) 75(21):6721-8 (PMC2772416) - Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.
Hou Y, Lin S
PLoS ONE (2009) 4(9):e6978 (PMC2737104) 10.1371/journal.pone.0006978 - Workshop report: modeling the molecular mechanism of bacterial spore germination and elucidating reasons for germination heterogeneity.
Indest KJ, Buchholz WG, Faeder JR, Setlow P
J. Food Sci. (2009) 74(6):R73-8 - Patterns and causes of species richness: a general simulation model for macroecology.
Gotelli NJ, Anderson MJ, Arita HT, Chao A, Colwell RK, Connolly SR, Currie DJ, Dunn RR, Graves GR, Green JL, Grytnes JA, Jiang YH, Jetz W, Kathleen Lyons S, McCain CM, Magurran AE, Rahbek C, Rangel TF, Soberón J, Webb CO, Willig MR
Ecol. Lett. (2009) 12(9):873-86 - Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.
Burleigh JG, Bansal MS, Wehe A, Eulenstein O
J. Comput. Biol. (2009) 16(8):1071-83 - Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana.
Kikuchi Y, Bomar L, Graf J
Environ. Microbiol. (2009) 11(10):2758-70 - Trees in the web of life.
Swithers KS, Gogarten JP, Fournier GP
J. Biol. (2009) 8(6):54 (PMC2737374) - Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid.
Dipippo JL, Nesbø CL, Dahle H, Doolittle WF, Birkland NK, Noll KM
Int. J. Syst. Evol. Microbiol. (2009) 59(Pt 12):2991-3000 - Live cell cytotoxicity studies: documentation of the interactions of antitumor active dirhodium compounds with nuclear DNA.
Aguirre JD, Angeles-Boza AM, Chouai A, Pellois JP, Turro C, Dunbar KR
J. Am. Chem. Soc. (2009) 131(32):11353-60 - The protease CspB is essential for initiation of cortex hydrolysis and dipicolinic acid (DPA) release during germination of spores of Clostridium perfringens type A food poisoning isolates.
Paredes-Sabja D, Setlow P, Sarker MR
Microbiology (Reading, Engl.) (2009) 155(Pt 10):3464-72 - Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas.
Baumgartner LK, Spear JR, Buckley DH, Pace NR, Reid RP, Dupraz C, Visscher PT
Environ. Microbiol. (2009) 11(10):2710-9 - Superdormant spores of Bacillus species have elevated wet-heat resistance and temperature requirements for heat activation.
Ghosh S, Zhang P, Li YQ, Setlow P
J. Bacteriol. (2009) 191(18):5584-91 (PMC2737942) - Manipulations of metallothionein gene dose accelerate the response to Listeria monocytogenes.
Emeny RT, Marusov G, Lawrence DA, Pederson-Lane J, Yin X, Lynes MA
Chem. Biol. Interact. (2009) 181(2):243-53 - Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.
Fournier GP, Huang J, Gogarten JP
Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2009) 364(1527):2229-39 (PMC2873001) - Mustard gas exposure and carcinogenesis of lung.
Hosseini-khalili A, Haines DD, Modirian E, Soroush M, Khateri S, Joshi R, Zendehdel K, Ghanei M, Giardina C
Mutat. Res. (2009) 678(1):1-6 (PMC2811761) - In vitro biological activity and structural analysis of 2,4-diamino-5-(2'-arylpropargyl)pyrimidine inhibitors of Candida albicans.
Paulsen JL, Liu J, Bolstad DB, Smith AE, Priestley ND, Wright DL, Anderson AC
Bioorg. Med. Chem. (2009) 17(14):4866-72 (PMC2724765) 10.1016/j.bmc.2009.06.021 - Roles of small, acid-soluble spore proteins and core water content in survival of Bacillus subtilis spores exposed to environmental solar UV radiation.
Moeller R, Setlow P, Reitz G, Nicholson WL
Appl. Environ. Microbiol. (2009) 75(16):5202-8 (PMC2725452) - Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus).
Hird S, Sullivan J
Mol. Ecol. (2009) 18(14):3097-109 10.1111/j.1365-294X.2009.04196.x - Prevalence of genes encoding the type three secretion system and the effectors AexT and AexU in the Aeromonas veronii group.
Silver AC, Graf J
DNA Cell Biol. (2009) 28(8):383-8 - Marine aggregates facilitate ingestion of nanoparticles by suspension-feeding bivalves.
Ward JE, Kach DJ
Mar. Environ. Res. (2009) 68(3):137-42 10.1016/j.marenvres.2009.05.002 - Phenotype-dependent native habitat preference facilitates divergence between parapatric lake and stream stickleback.
Bolnick DI, Snowberg LK, Patenia C, Stutz WE, Ingram T, Lau OL
Evolution (2009) 63(8):2004-16 - Activation of human monocytes by live Borrelia burgdorferi generates TLR2-dependent and -independent responses which include induction of IFN-beta.
Salazar JC, Duhnam-Ems S, La Vake C, Cruz AR, Moore MW, Caimano MJ, Velez-Climent L, Shupe J, Krueger W, Radolf JD
PLoS Pathog. (2009) 5(5):e1000444 (PMC2679197) - Allee effect in the selection for prime-numbered cycles in periodical cicadas.
Tanaka Y, Yoshimura J, Simon C, Cooley JR, Tainaka K
Proc. Natl. Acad. Sci. U.S.A. (2009) 106(22):8975-9 (PMC2690011) 10.1073/pnas.0900215106 - Prophylactic supplementation of caprylic acid in feed reduces Salmonella enteritidis colonization in commercial broiler chicks.
Johny AK, Baskaran SA, Charles AS, Amalaradjou MA, Darre MJ, Khan MI, Hoagland TA, Schreiber DT, Donoghue AM, Donoghue DJ, Venkitanarayanan K
J. Food Prot. (2009) 72(4):722-7 - Treponema pallidum, the stealth pathogen, changes, but how?
Radolf JD, Desrosiers DC
Mol. Microbiol. (2009) 72(5):1081-6 (PMC2975512) - Glacial refugia in a maritime temperate climate: cicada (Kikihia subalpina) mtDNA phylogeography in New Zealand.
Marshall DC, Hill KB, Fontaine KM, Buckley TR, Simon C
Mol. Ecol. (2009) 18(9):1995-2009 - Spliceosomal proteomics in Trypanosoma brucei reveal new RNA splicing factors.
Luz Ambrósio D, Lee JH, Panigrahi AK, Nguyen TN, Cicarelli RM, Günzl A
Eukaryotic Cell (2009) 8(7):990-1000 (PMC2708463) - Bioactive 5,6-dihydro-alpha-pyrone derivatives from Hyptis brevipes.
Deng Y, Balunas MJ, Kim JA, Lantvit DD, Chin YW, Chai H, Sugiarso S, Kardono LB, Fong HH, Pezzuto JM, Swanson SM, de Blanco EJ, Kinghorn AD
J. Nat. Prod. (2009) 72(6):1165-9 (PMC2883770) - Outer membrane protein A (OmpA) of Cronobacter sakazakii binds fibronectin and contributes to invasion of human brain microvascular endothelial cells.
Nair MK, Venkitanarayanan K, Silbart LK, Kim KS
Foodborne Pathog. Dis. (2009) 6(4):495-501 - The gene-duplication problem: near-linear time algorithms for NNI-based local searches.
Bansal MS, Eulenstein O, Wehe A
IEEE/ACM Trans Comput Biol Bioinform (2009) 6(2):221-31 - Preventing infective complications following leech therapy: is practice keeping pace with current research?
Whitaker IS, Kamya C, Azzopardi EA, Graf J, Kon M, Lineaweaver WC
Microsurgery (2009) 29(8):619-25 - Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex.
Lee JH, Jung HS, Günzl A
Nucleic Acids Res. (2009) 37(11):3811-20 (PMC2699521) - Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements.
Zhang H, Campbell DA, Sturm NR, Lin S
Mol. Biol. Evol. (2009) 26(8):1757-71 (PMC2734150) 10.1093/molbev/msp083 - Effect of octenidine hydrochloride on planktonic cells and biofilms of Listeria monocytogenes.
Amalaradjou MA, Norris CE, Venkitanarayanan K
Appl. Environ. Microbiol. (2009) 75(12):4089-92 (PMC2698330) - Elastic and inelastic light scattering from single bacterial spores in an optical trap allows the monitoring of spore germination dynamics.
Peng L, Chen D, Setlow P, Li YQ
Anal. Chem. (2009) 81(10):4035-42 (PMC2717560) - Redox-regulated Inhibition of T7 RNA polymerase via establishment of disulfide linkages by substituted Dppz dirhodium(II,II) complexes.
Aguirre JD, Chifotides HT, Angeles-Boza AM, Chouai A, Turro C, Dunbar KR
Inorg Chem (2009) 48(10):4435-44 - GerO, a putative Na+/H+-K+ antiporter, is essential for normal germination of spores of the pathogenic bacterium Clostridium perfringens.
Paredes-Sabja D, Setlow P, Sarker MR
J. Bacteriol. (2009) 191(12):3822-31 (PMC2698388) - Role of GerKB in germination and outgrowth of Clostridium perfringens spores.
Paredes-Sabja D, Setlow P, Sarker MR
Appl. Environ. Microbiol. (2009) 75(11):3813-7 (PMC2687284) - On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM
Proc. Natl. Acad. Sci. U.S.A. (2009) 106(14):5865-70 (PMC2667022) - Antibacterial effect of plant-derived antimicrobials on major bacterial mastitis pathogens in vitro.
Ananda Baskaran S, Kazmer GW, Hinckley L, Andrew SM, Venkitanarayanan K
J. Dairy Sci. (2009) 92(4):1423-9 - The shape of the competition and carrying capacity kernels affects the likelihood of disruptive selection.
Baptestini EM, de Aguiar MA, Bolnick DI, Araújo MS
J. Theor. Biol. (2009) 259(1):5-11 - Ancient gene transfer as a tool in phylogenetic reconstruction.
Huang J, Gogarten JP
Methods Mol. Biol. (2009) 532:127-39 - Gene transfer: who benefits?
Olendzenski L, Gogarten JP
Methods Mol. Biol. (2009) 532:3-9 - Interdomain transfers of sugar transporters overcome barriers to gene expression.
Noll KM, Thirangoon K
Methods Mol. Biol. (2009) 532:309-22 - PrimerHunter: a primer design tool for PCR-based virus subtype identification.
Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II, Nelson CE
Nucleic Acids Res. (2009) 37(8):2483-92 (PMC2677861) - Local production of IFN-gamma by invariant NKT cells modulates acute Lyme carditis.
Olson CM, Bates TC, Izadi H, Radolf JD, Huber SA, Boyson JE, Anguita J
J. Immunol. (2009) 182(6):3728-34 (PMC2679988) - Levels and localization of mechanosensitive channel proteins in Bacillus subtilis.
Wahome PG, Cowan AE, Setlow B, Setlow P
Arch. Microbiol. (2009) 191(5):403-14 - Crystal structures of wild-type and mutant methicillin-resistant Staphylococcus aureus dihydrofolate reductase reveal an alternate conformation of NADPH that may be linked to trimethoprim resistance.
Frey KM, Liu J, Lombardo MN, Bolstad DB, Wright DL, Anderson AC
J. Mol. Biol. (2009) 387(5):1298-308 (PMC2723953) 10.1016/j.jmb.2009.02.045 - Resource dynamics influence the strength of non-consumptive predator effects on prey.
Preisser EL, Bolnick DI, Grabowski JH
Ecol. Lett. (2009) 12(4):315-23 - Tandem affinity purification of proteins.
Günzl A, Schimanski B
Curr Protoc Protein Sci (2009) Chapter 19:Unit 19.19 - Inhibitors of phosphoinositide-3-kinase: a structure-based approach to understanding potency and selectivity.
Sundstrom TJ, Anderson AC, Wright DL
Org. Biomol. Chem. (2009) 7(5):840-50 10.1039/b819067b - Surfactants, aromatic and isoprenoid compounds, and fatty acid biosynthesis inhibitors suppress Staphylococcus aureus production of toxic shock syndrome toxin 1.
McNamara PJ, Syverson RE, Milligan-Myhre K, Frolova O, Schroeder S, Kidder J, Hoang T, Proctor RA
Antimicrobial agents and chemotherapy (2009) 53(5):1898-906 PMC1068626 10.1128/AAC.01293-08 - Borrelia burgdorferi bba74 is expressed exclusively during tick feeding and is regulated by both arthropod- and mammalian host-specific signals.
Mulay VB, Caimano MJ, Iyer R, Dunham-Ems S, Liveris D, Petzke MM, Schwartz I, Radolf JD
J. Bacteriol. (2009) 191(8):2783-94 (PMC2668432) - SleC is essential for cortex peptidoglycan hydrolysis during germination of spores of the pathogenic bacterium Clostridium perfringens.
Paredes-Sabja D, Setlow P, Sarker MR
J. Bacteriol. (2009) 191(8):2711-20 (PMC2668406) - Autoinducers extracted from microbial mats reveal a surprising diversity of N-acylhomoserine lactones (AHLs) and abundance changes that may relate to diel pH.
Decho AW, Visscher PT, Ferry J, Kawaguchi T, He L, Przekop KM, Norman RS, Reid RP
Environ. Microbiol. (2009) 11(2):409-20 - Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes.
Nyholm SV, Stewart JJ, Ruby EG, McFall-Ngai MJ
Environ. Microbiol. (2009) 11(2):483-93 (PMC2652691) 10.1111/j.1462-2920.2008.01788.x - Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica.
Aislabie J, Jordan S, Ayton J, Klassen JL, Barker GM, Turner S
Can. J. Microbiol. (2009) 55(1):21-36 - First Report of Anthracnose Disease of Ornamental Feather Reed Grass (Calamagrostis × acutifolia 'Karl Foerster') Caused by Colletotrichum cereale.
Crouch JA, Inguagiato JC
Plant Dis. (2009) 93(2):203 - Estimating the size of the bacterial pan-genome.
Lapierre P, Gogarten JP
Trends Genet. (2009) 25(3):107-10 - Towards new antifolates targeting eukaryotic opportunistic infections.
Liu J, Bolstad DB, Bolstad ES, Wright DL, Anderson AC
Eukaryotic Cell (2009) 8(4):483-6 (PMC2669212) 10.1128/EC.00298-08 - Probing the active site of Candida glabrata dihydrofolate reductase with high resolution crystal structures and the synthesis of new inhibitors.
Liu J, Bolstad DB, Smith AE, Priestley ND, Wright DL, Anderson AC
Chem Biol Drug Des (2009) 73(1):62-74 (PMC2838185) 10.1111/j.1747-0285.2008.00745.x - Peptidoglycan monomer release and Vibrio fischeri.
Nyholm SV
J. Bacteriol. (2009) 191(7):1997-9 (PMC2655520) 10.1128/JB.01801-08 - Selection for prime-number intervals in a numerical model of periodical cicada evolution.
Yoshimura J, Hayashi T, Tanaka Y, Tainaka K, Simon C
Evolution (2009) 63(1):288-94 10.1111/j.1558-5646.2008.00545.x - Isolation and characterization of superdormant spores of Bacillus species.
Ghosh S, Setlow P
J. Bacteriol. (2009) 191(6):1787-97 (PMC2648361) - Retrieval of missing spliced leader in dinoflagellates.
Zhang H, Lin S
PLoS ONE (2009) 4(1):e4129 (PMC2606063) 10.1371/journal.pone.0004129 - Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP
Genome Biol Evol (2009) 1:325-39 (PMC2817427) 2008
- Role of proP and proU in betaine uptake by Yersinia enterocolitica under cold and osmotic stress conditions.
Annamalai T, Venkitanarayanan K
Appl. Environ. Microbiol. (2008) 75(6):1471-7 (PMC2655450) - High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding.
Lin S, Zhang H, Hou Y, Zhuang Y, Miranda L
Appl. Environ. Microbiol. (2008) 75(5):1279-90 (PMC2648164) 10.1128/AEM.01578-08 - The natural feed additive caprylic acid decreases Campylobacter jejuni colonization in market-aged broiler chickens.
Solis de los Santos F, Donoghue AM, Venkitanarayanan K, Metcalf JH, Reyes-Herrera I, Dirain ML, Aguiar VF, Blore PJ, Donoghue DJ
Poult. Sci. (2008) 88(1):61-4 - Inactivation of Enterobacter sakazakii in reconstituted infant formula by trans-cinnamaldehyde.
Amalaradjou MA, Hoagland TA, Venkitanarayanan K
Int. J. Food Microbiol. (2008) 129(2):146-9 - Ultrafast ligand exchange: detection of a pentacoordinate Ru(II) intermediate and product formation.
Liu Y, Turner DB, Singh TN, Angeles-Boza AM, Chouai A, Dunbar KR, Turro C
J. Am. Chem. Soc. (2008) 131(1):26-7 - Lower levels of gamma interferon expressed by a pseudotyped single-cycle simian immunodeficiency virus enhance immunogenicity in rats.
Peng Y, Lin FC, Verardi PH, Jones LA, Yilma TD
J. Virol. (2008) 83(4):1592-601 (PMC2643767) - NKT cells prevent chronic joint inflammation after infection with Borrelia burgdorferi.
Tupin E, Benhnia MR, Kinjo Y, Patsey R, Lena CJ, Haller MC, Caimano MJ, Imamura M, Wong CH, Crotty S, Radolf JD, Sellati TJ, Kronenberg M
Proc. Natl. Acad. Sci. U.S.A. (2008) 105(50):19863-8 (PMC2604993) - Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat.
Braissant O, Decho AW, Przekop KM, Gallagher KL, Glunk C, Dupraz C, Visscher PT
FEMS Microbiol. Ecol. (2008) 67(2):293-307 - Enhanced detection of Listeria spp. in farmstead cheese processing environments through dual primary enrichment, PCR, and molecular subtyping.
D'Amico DJ, Donnelly CW
J. Food Prot. (2008) 71(11):2239-48 - Mouse models for the study of colon carcinogenesis.
Rosenberg DW, Giardina C, Tanaka T
Carcinogenesis (2008) 30(2):183-96 (PMC2639048) - Incorporation of CD40 ligand into the envelope of pseudotyped single-cycle Simian immunodeficiency viruses enhances immunogenicity.
Lin FC, Peng Y, Jones LA, Verardi PH, Yilma TD
J. Virol. (2008) 83(3):1216-27 (PMC2620918) - A practical method for exact computation of subtree prune and regraft distance.
Wu Y
Bioinformatics (2008) 25(2):190-6 10.1093/bioinformatics/btn606 - Synthetic and crystallographic studies of a new inhibitor series targeting Bacillus anthracis dihydrofolate reductase.
Beierlein JM, Frey KM, Bolstad DB, Pelphrey PM, Joska TM, Smith AE, Priestley ND, Wright DL, Anderson AC
J. Med. Chem. (2008) 51(23):7532-40 (PMC2645930) 10.1021/jm800776a - Reduction of Escherichia coli O157:H7 in cattle drinking-water by trans-cinnamaldehyde.
Charles AS, Baskaran SA, Murcott C, Schreiber D, Hoagland T, Venkitanarayanan K
Foodborne Pathog. Dis. (2008) 5(6):763-71 - An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem.
Bansal MS, Eulenstein O
IEEE/ACM Trans Comput Biol Bioinform (2008) 5(4):514-24 - Dormant spores receive an unexpected wake-up call.
Setlow P
Cell (2008) 135(3):410-2 - Genotype error detection using Hidden Markov Models of haplotype diversity.
Kennedy J, Măndoiu I, Paşaniuc B
J. Comput. Biol. (2008) 15(9):1155-71 - Repetitive N-WASP-binding elements of the enterohemorrhagic Escherichia coli effector EspF(U) synergistically activate actin assembly.
Campellone KG, Cheng HC, Robbins D, Siripala AD, McGhie EJ, Hayward RD, Welch MD, Rosen MK, Koronakis V, Leong JM
PLoS Pathog. (2008) 4(10):e1000191 (PMC2567903) 10.1371/journal.ppat.1000191 - HPrK regulates succinate-mediated catabolite repression in the gram-negative symbiont Sinorhizobium meliloti.
Pinedo CA, Gage DJ
J. Bacteriol. (2008) 191(1):298-309 (PMC2612420) - Assortative mating by diet in a phenotypically unimodal but ecologically variable population of stickleback.
Snowberg LK, Bolnick DI
Am. Nat. (2008) 172(5):733-9 - Structure-based approach to the development of potent and selective inhibitors of dihydrofolate reductase from cryptosporidium.
Bolstad DB, Bolstad ES, Frey KM, Wright DL, Anderson AC
J. Med. Chem. (2008) 51(21):6839-52 (PMC2584871) 10.1021/jm8009124 - Revisiting the classics: considering nonconsumptive effects in textbook examples of predator-prey interactions.
Peckarsky BL, Abrams PA, Bolnick DI, Dill LM, Grabowski JH, Luttbeg B, Orrock JL, Peacor SD, Preisser EL, Schmitz OJ, Trussell GC
Ecology (2008) 89(9):2416-25 - When predators don't eat their prey: nonconsumptive predator effects on prey dynamics.
Preisser EL, Bolnick DI
Ecology (2008) 89(9):2414-5 - Structure-guided development of efficacious antifungal agents targeting Candida glabrata dihydrofolate reductase.
Liu J, Bolstad DB, Smith AE, Priestley ND, Wright DL, Anderson AC
Chem. Biol. (2008) 15(9):990-6 (PMC2610858) 10.1016/j.chembiol.2008.07.013 - The short chain fatty acid butyrate induces promoter demethylation and reactivation of RARbeta2 in colon cancer cells.
Spurling CC, Suhl JA, Boucher N, Nelson CE, Rosenberg DW, Giardina C
Nutr Cancer (2008) 60(5):692-702 - Light-dependant biostabilisation of sediments by stromatolite assemblages.
Paterson DM, Aspden RJ, Visscher PT, Consalvey M, Andres MS, Decho AW, Stolz J, Reid RP
PLoS ONE (2008) 3(9):e3176 (PMC2526175) - HDAC3 impacts multiple oncogenic pathways in colon cancer cells with effects on Wnt and vitamin D signaling.
Godman CA, Joshi R, Tierney BR, Greenspan E, Rasmussen TP, Wang HW, Shin DG, Rosenberg DW, Giardina C
Cancer Biol. Ther. (2008) 7(10):1570-80 (PMC2614677) - Interaction of enterohemorrhagic Escherichia coli (EHEC) with mammalian cells: cell adhesion, type III secretion, and actin pedestal formation.
Savage PJ, Campellone KG, Leong JM
Curr Protoc Microbiol (2008) Chapter 5:Unit 5A.1 10.1002/9780471729259.mc05a01s05 - Characterization of spores of Bacillus subtilis that lack most coat layers.
Ghosh S, Setlow B, Wahome PG, Cowan AE, Plomp M, Malkin AJ, Setlow P
J. Bacteriol. (2008) 190(20):6741-8 (PMC2566211) - Low incidence of foodborne pathogens of concern in raw milk utilized for farmstead cheese production.
D'Amico DJ, Groves E, Donnelly CW
J. Food Prot. (2008) 71(8):1580-9 - 60-day aging requirement does not ensure safety of surface-mold-ripened soft cheeses manufactured from raw or pasteurized milk when Listeria monocytogenes is introduced as a postprocessing contaminant.
D'Amico DJ, Druart MJ, Donnelly CW
J. Food Prot. (2008) 71(8):1563-71 - Network analysis reveals contrasting effects of intraspecific competition on individual vs. population diets.
Araújo MS, Guimarães PR, Svanbäck R, Pinheiro A, Guimarães P, Dos Reis SF, Bolnick DI
Ecology (2008) 89(7):1981-93 - Sampling and quantitative analysis of clean B. subtilis spores at sub-monolayer coverage by reflectance fourier transform infrared microscopy using gold-coated filter substrates.
Brooke H, Perkins DL, Setlow B, Setlow P, Bronk BV, Myrick ML
Appl Spectrosc (2008) 62(8):881-8 - Characterization of the digestive-tract microbiota of Hirudo orientalis, a european medicinal leech.
Laufer AS, Siddall ME, Graf J
Appl. Environ. Microbiol. (2008) 74(19):6151-4 (PMC2565982) - Natural products as aromatase inhibitors.
Balunas MJ, Su B, Brueggemeier RW, Kinghorn AD
Anticancer Agents Med Chem (2008) 8(6):646-82 (PMC3074486) - Protozoal digestion of coat-defective Bacillus subtilis spores produces "rinds" composed of insoluble coat protein.
Carroll AM, Plomp M, Malkin AJ, Setlow P
Appl. Environ. Microbiol. (2008) 74(19):5875-81 (PMC2565959) - Guest editors' introduction to the special section on bioinformatics research and applications.
Mandoiu II, Pan Y, Zelikovsky A
IEEE/ACM Trans Comput Biol Bioinform (2008) 5(3):321-2 - Germination of spores of Clostridium difficile strains, including isolates from a hospital outbreak of Clostridium difficile-associated disease (CDAD).
Paredes-Sabja D, Bond C, Carman RJ, Setlow P, Sarker MR
Microbiology (Reading, Engl.) (2008) 154(Pt 8):2241-50 - Association mapping of complex diseases with ancestral recombination graphs: models and efficient algorithms.
Wu Y
J. Comput. Biol. (2008) 15(7):667-84 10.1089/cmb.2007.0116 - Structural mechanism of WASP activation by the enterohaemorrhagic E. coli effector EspF(U).
Cheng HC, Skehan BM, Campellone KG, Leong JM, Rosen MK
Nature (2008) 454(7207):1009-13 (PMC2719906) 10.1038/nature07160 - Salmonella enterica serovar Typhimurium BipA exhibits two distinct ribosome binding modes.
deLivron MA, Robinson VL
J. Bacteriol. (2008) 190(17):5944-52 (PMC2519513) 10.1128/JB.00763-08 - WHAMM is an Arp2/3 complex activator that binds microtubules and functions in ER to Golgi transport.
Campellone KG, Webb NJ, Znameroski EA, Welch MD
Cell (2008) 134(1):148-61 (PMC2556884) 10.1016/j.cell.2008.05.032 - Concerted gene recruitment in early plant evolution.
Huang J, Gogarten JP
Genome Biol. (2008) 9(7):R109 (PMC2530860) - Steady Plio-Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada radiation.
Marshall DC, Slon K, Cooley JR, Hill KB, Simon C
Mol. Phylogenet. Evol. (2008) 48(3):1054-66 10.1016/j.ympev.2008.05.007 - The multiple gene duplication problem revisited.
Bansal MS, Eulenstein O
Bioinformatics (2008) 24(13):i132-8 (PMC2718628) - Hsp70B' and Hsp72 form a complex in stressed human colon cells and each contributes to cytoprotection.
Noonan E, Giardina C, Hightower L
Exp. Cell Res. (2008) 314(13):2468-76 - Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae.
Nyholm SV, Robidart J, Girguis PR
Biol. Bull. (2008) 214(3):255-65 10.2307/25470667 - Xanthones from the botanical dietary supplement mangosteen (Garcinia mangostana) with aromatase inhibitory activity.
Balunas MJ, Su B, Brueggemeier RW, Kinghorn AD
J. Nat. Prod. (2008) 71(7):1161-6 (PMC2572570) - The many faces of fear: comparing the pathways and impacts of nonconsumptive predator effects on prey populations.
Preisser EL, Bolnick DI
PLoS ONE (2008) 3(6):e2465 (PMC2409076) - Localization of the germination protein GerD to the inner membrane in Bacillus subtilis spores.
Pelczar PL, Setlow P
J. Bacteriol. (2008) 190(16):5635-41 (PMC2519376) - mRNA EDITING AND SPLICED-LEADER RNA TRANS-SPLICING GROUPS OXYRRHIS, NOCTILUCA, HETEROCAPSA, AND AMPHIDINIUM AS BASAL LINEAGES OF DINOFLAGELLATES(1).
Zhang H, Lin S
J. Phycol. (2008) 44(3):703-11 10.1111/j.1529-8817.2008.00521.x - Unsupervised learning in detection of gene transfer.
Hamel L, Nahar N, Poptsova MS, Zhaxybayeva O, Gogarten JP
J. Biomed. Biotechnol. (2008) 2008:472719 (PMC2288707) - Therapeutic supplementation of caprylic acid in feed reduces Campylobacter jejuni colonization in broiler chicks.
Solis de los Santos F, Donoghue AM, Venkitanarayanan K, Reyes-Herrera I, Metcalf JH, Dirain ML, Aguiar VF, Blore PJ, Donoghue DJ
Appl. Environ. Microbiol. (2008) 74(14):4564-6 (PMC2493180) - ATPase activity of Mycobacterium tuberculosis SecA1 and SecA2 proteins and its importance for SecA2 function in macrophages.
Hou JM, D'Lima NG, Rigel NW, Gibbons HS, McCann JR, Braunstein M, Teschke CM
J. Bacteriol. (2008) 190(14):4880-7 (PMC2447007) - Reverse evolution of armor plates in the threespine stickleback.
Kitano J, Bolnick DI, Beauchamp DA, Mazur MM, Mori S, Nakano T, Peichel CL
Curr. Biol. (2008) 18(10):769-774 - DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Wehe A, Bansal MS, Burleigh JG, Eulenstein O
Bioinformatics (2008) 24(13):1540-1 - Release of small molecules during germination of spores of Bacillus Species.
Setlow B, Wahome PG, Setlow P
J. Bacteriol. (2008) 190(13):4759-63 (PMC2446799) - Characterization of Clostridium perfringens spores that lack SpoVA proteins and dipicolinic acid.
Paredes-Sabja D, Setlow B, Setlow P, Sarker MR
J. Bacteriol. (2008) 190(13):4648-59 (PMC2446781) - Role of dipicolinic acid in the germination, stability, and viability of spores of Bacillus subtilis.
Magge A, Granger AC, Wahome PG, Setlow B, Vepachedu VR, Loshon CA, Peng L, Chen D, Li YQ, Setlow P
J. Bacteriol. (2008) 190(14):4798-807 (PMC2446992) - Highly scalable genotype phasing by entropy minimization.
Gusev A, Măndoiu II, Paşaniuc B
IEEE/ACM Trans Comput Biol Bioinform (2008) 5(2):252-61 - Predictable patterns of disruptive selection in stickleback in postglacial lakes.
Bolnick DI, Lau OL
Am. Nat. (2008) 172(1):1-11 - Roles of DacB and spm proteins in clostridium perfringens spore resistance to moist heat, chemicals, and UV radiation.
Paredes-Sabja D, Sarker N, Setlow B, Setlow P, Sarker MR
Appl. Environ. Microbiol. (2008) 74(12):3730-8 (PMC2446547) - Oligomerization of ICP4 and rearrangement of heat shock proteins may be important for herpes simplex virus type 1 prereplicative site formation.
Livingston CM, DeLuca NA, Wilkinson DE, Weller SK
J. Virol. (2008) 82(13):6324-36 (PMC2447070) 10.1128/JVI.00455-08 - The long strange trip of Borrelia burgdorferi outer-surface protein C.
Radolf JD, Caimano MJ
Mol. Microbiol. (2008) 69(1):1-4 - PhyloFinder: an intelligent search engine for phylogenetic tree databases.
Chen D, Burleigh JG, Bansal MS, Fernández-Baca D
BMC Evol. Biol. (2008) 8:90 (PMC2362120) - Comparative assessment of a metabolically attenuated Mycoplasma gallisepticum mutant as a live vaccine for the prevention of avian respiratory mycoplasmosis.
Gates AE, Frasca S, Nyaoke A, Gorton TS, Silbart LK, Geary SJ
Vaccine (2008) 26(16):2010-9 10.1016/j.vaccine.2008.02.010 - Caprylic acid supplemented in feed reduces enteric Campylobacter jejuni colonization in ten-day-old broiler chickens.
Solis de Los Santos F, Donoghue AM, Venkitanarayanan K, Dirain ML, Reyes-Herrera I, Blore PJ, Donoghue DJ
Poult. Sci. (2008) 87(4):800-4 - Ancient hybridization and mitochondrial capture between two species of chipmunks.
Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J
Mol. Ecol. (2008) 17(5):1313-27 10.1111/j.1365-294X.2007.03640.x - Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species.
Lee KS, Bumbaca D, Kosman J, Setlow P, Jedrzejas MJ
Proc. Natl. Acad. Sci. U.S.A. (2008) 105(8):2806-11 (PMC2268541) - Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production.
Pinedo CA, Bringhurst RM, Gage DJ
J. Bacteriol. (2008) 190(8):2947-56 (PMC2293241) - Differences in carotenoid composition among hymenobacter and related strains support a tree-like model of carotenoid evolution.
Klassen JL, Foght JM
Appl. Environ. Microbiol. (2008) 74(7):2016-22 (PMC2292609) - Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes.
Bolnick DI, Turelli M, López-Fernández H, Wainwright PC, Near TJ
Genetics (2008) 178(2):1037-48 (PMC2248366) - Reattachment of anterior teeth fragments: a conservative approach.
Macedo GV, Diaz PI, De O Fernandes CA, Ritter AV
J Esthet Restor Dent (2008) 20(1):5-18; discussion 19-20 - Dihydrofolate reductase inhibitors: developments in antiparasitic chemotherapy.
Bolstad DB, Bolstad ES, Wright DL, Anderson AC
Expert Opin Ther Pat (2008) 18(2):143-57 10.1517/13543776.18.2.143 - Hsp70B' regulation and function.
Noonan EJ, Place RF, Giardina C, Hightower LE
Cell Stress Chaperones (2008) 12(4):393-402 (PMC2134801) - Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts.
Mastronunzio JE, Tisa LS, Normand P, Benson DR
BMC Genomics (2008) 9:47 (PMC2266912) - Vertical distribution of methane metabolism in microbial mats of the Great Sippewissett Salt Marsh.
Buckley DH, Baumgartner LK, Visscher PT
Environ. Microbiol. (2008) 10(4):967-77 - Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.
Sharma AK, Zhaxybayeva O, Papke RT, Doolittle WF
Environ. Microbiol. (2008) 10(4):1039-56 - An improved cell recovery method for iron oxidizing bacterial (IOB) enrichments.
Yu R, Graf J, Smets BF
J. Microbiol. Methods (2008) 72(3):235-40 - Role of the Nfo and ExoA apurinic/apyrimidinic endonucleases in repair of DNA damage during outgrowth of Bacillus subtilis spores.
Ibarra JR, Orozco AD, Rojas JA, López K, Setlow P, Yasbin RE, Pedraza-Reyes M
J. Bacteriol. (2008) 190(6):2031-8 (PMC2258865) - Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales.
Noll KM, Lapierre P, Gogarten JP, Nanavati DM
BMC Evol. Biol. (2008) 8:7 (PMC2246101) - Anti-tumor necrosis factor-alpha activation of Borrelia burgdorferi spirochetes in antibiotic-treated murine Lyme borreliosis: an unproven conclusion.
Wormser GP, Barthold SW, Shapiro ED, Dattwyler RJ, Bakken JS, Steere AC, Bockenstedt LK, Radolf JD
J. Infect. Dis. (2008) 196(12):1865-6; author reply 1866-7 - Structural and functional characterization of an organic hydroperoxide resistance protein from Mycoplasma gallisepticum.
Jenkins C, Samudrala R, Geary SJ, Djordjevic SP
J. Bacteriol. (2008) 190(6):2206-16 (PMC2258871) 10.1128/JB.01685-07 - Mitochondrial cob and cox1 genes and editing of the corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of the genus Dinophysis.
Zhang H, Bhattacharya D, Maranda L, Lin S
Appl. Environ. Microbiol. (2008) 74(5):1546-54 (PMC2258633) 10.1128/AEM.02103-07 - THE EVOLUTIONARY ECOLOGY OF A SEPIOLID SQUID-VIBRIO ASSOCIATION: FROM CELL TO ENVIRONMENT.
Nyholm SV, Nishiguchi MK
Vie Milieu (2008) 58(2):175-184 (PMC2857784) 2007
- Clostridium perfringens spore germination: characterization of germinants and their receptors.
Paredes-Sabja D, Torres JA, Setlow P, Sarker MR
J. Bacteriol. (2007) 190(4):1190-201 (PMC2238220) - What causes partial F1 hybrid viability? Incomplete penetrance versus genetic variation.
López-Fernández H, Bolnick DI
PLoS ONE (2007) 2(12):e1294 (PMC2121587) - EspFU, a type III-translocated effector of actin assembly, fosters epithelial association and late-stage intestinal colonization by E. coli O157:H7.
Ritchie JM, Brady MJ, Riley KN, Ho TD, Campellone KG, Herman IM, Donohue-Rolfe A, Tzipori S, Waldor MK, Leong JM
Cell. Microbiol. (2007) 10(4):836-47 (PMC2504705) 10.1111/j.1462-5822.2007.01087.x - Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia.
Fournier GP, Gogarten JP
J. Bacteriol. (2007) 190(3):1124-7 (PMC2223567) - Roles of the major, small, acid-soluble spore proteins and spore-specific and universal DNA repair mechanisms in resistance of Bacillus subtilis spores to ionizing radiation from X rays and high-energy charged-particle bombardment.
Moeller R, Setlow P, Horneck G, Berger T, Reitz G, Rettberg P, Doherty AJ, Okayasu R, Nicholson WL
J. Bacteriol. (2007) 190(3):1134-40 (PMC2223577) - Utilizing endoscopic technology to reveal real-time proteomic alterations in response to chemoprevention.
Nakanishi M, Ménoret A, Belinsky GS, Giardina C, Godman CA, Vella AT, Rosenberg DW
Proteomics Clin Appl (2007) 1(12):1660-6 - Highly scalable algorithms for robust string barcoding.
Dasgupta B, Konwar KM, Mandoiu II, Shvartsman AA
Int J Bioinform Res Appl (2007) 1(2):145-61 - Genomic plasticity in prokaryotes: the case of the square haloarchaeon.
Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F
ISME J (2007) 1(3):235-45 - Rapid preclinical detection of sheeppox virus by a real-time PCR assay.
Balinsky CA, Delhon G, Smoliga G, Prarat M, French RA, Geary SJ, Rock DL, Rodriguez LL
J. Clin. Microbiol. (2007) 46(2):438-42 (PMC2238129) 10.1128/JCM.01953-07 - Chemokine and cytokine gene expression profiles in chickens inoculated with Mycoplasma gallisepticum strains Rlow or GT5.
Mohammed J, Frasca S, Cecchini K, Rood D, Nyaoke AC, Geary SJ, Silbart LK
Vaccine (2007) 25(51):8611-21 10.1016/j.vaccine.2007.09.057 - Multifunctional class I transcription in Trypanosoma brucei depends on a novel protein complex.
Brandenburg J, Schimanski B, Nogoceke E, Nguyen TN, Padovan JC, Chait BT, Cross GA, Günzl A
EMBO J. (2007) 26(23):4856-66 (PMC2099468) - Antimalarial activity of the anticancer and proteasome inhibitor bortezomib and its analog ZL3B.
Reynolds JM, El Bissati K, Brandenburg J, Günzl A, Mamoun CB
BMC Clin Pharmacol (2007) 7:13 (PMC2213633) - Role of bacterial OmpA and host cytoskeleton in the invasion of human intestinal epithelial cells by Enterobacter sakazakii.
Mohan Nair MK, Venkitanarayanan K
Pediatr. Res. (2007) 62(6):664-9 - Highly scalable genotype phasing by entropy minimization.
Pasaniuc B, Mandoiu I
Conf Proc IEEE Eng Med Biol Soc (2007) 1:3482-6 - Direct interaction between the N- and C-terminal portions of the herpes simplex virus type 1 origin binding protein UL9 implies the formation of a head-to-tail dimer.
Chattopadhyay S, Weller SK
J. Virol. (2007) 81(24):13659-67 (PMC2168873) 10.1128/JVI.01204-07 - Phagocytosis of Borrelia burgdorferi, the Lyme disease spirochete, potentiates innate immune activation and induces apoptosis in human monocytes.
Cruz AR, Moore MW, La Vake CJ, Eggers CH, Salazar JC, Radolf JD
Infect. Immun. (2007) 76(1):56-70 (PMC2223637) - Signature of a primitive genetic code in ancient protein lineages.
Fournier GP, Gogarten JP
J. Mol. Evol. (2007) 65(4):425-36 - Hsp70B' regulation and function.
Noonan EJ, Place RF, Giardina C, Hightower LE
Cell Stress Chaperones (2007) 12(3):219-29 (PMC1971232) - A three-gene dinoflagellate phylogeny suggests monophyly of prorocentrales and a basal position for amphidinium and heterocapsa.
Zhang H, Bhattacharya D, Lin S
J. Mol. Evol. (2007) 65(4):463-74 10.1007/s00239-007-9038-4 - How moist heat kills spores of Bacillus subtilis.
Coleman WH, Chen D, Li YQ, Cowan AE, Setlow P
J. Bacteriol. (2007) 189(23):8458-66 (PMC2168948) - HDAC3 overexpression and colon cancer cell proliferation and differentiation.
Spurling CC, Godman CA, Noonan EJ, Rasmussen TP, Rosenberg DW, Giardina C
Mol. Carcinog. (2007) 47(2):137-47 - Evidence for paternal leakage in hybrid periodical cicadas (Hemiptera: Magicicada spp.).
Fontaine KM, Cooley JR, Simon C
PLoS ONE (2007) 2(9):e892 (PMC1963320) 10.1371/journal.pone.0000892 - Comparison between self-reported and observed food handling behaviors among Latinas.
Dharod JM, Pérez-Escamilla R, Paciello S, Bermúdez-Millán A, Venkitanarayanan K, Damio G
J. Food Prot. (2007) 70(8):1927-32 - Natural selection in populations subject to a migration load.
Bolnick DI, Nosil P
Evolution (2007) 61(9):2229-43 - Effect of a small, acid-soluble spore protein from Clostridium perfringens on the resistance properties of Bacillus subtilis spores.
Leyva-Illades JF, Setlow B, Sarker MR, Setlow P
J. Bacteriol. (2007) 189(21):7927-31 (PMC2168745) - Photosynthetic recovery following desiccation of desert green algae (Chlorophyta) and their aquatic relatives.
Gray DW, Lewis LA, Cardon ZG
Plant Cell Environ. (2007) 30(10):1240-55 - Characterization of amorphous solids with weak glass transitions using high ramp rate differential scanning calorimetry.
Katayama DS, Carpenter JF, Manning MC, Randolph TW, Setlow P, Menard KP
J Pharm Sci (2007) 97(2):1013-24 - Characterization of a Neochlamydia-like bacterium associated with epitheliocystis in cultured Arctic charr Salvelinus alpinus.
Draghi A, Bebak J, Popov VL, Noble AC, Geary SJ, West AB, Byrne P, Frasca S
Dis. Aquat. Org. (2007) 76(1):27-38 10.3354/dao076027 - Searching for species in haloarchaea.
Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF
Proc. Natl. Acad. Sci. U.S.A. (2007) 104(35):14092-7 (PMC1955782) - Effect of axial coordination on the electronic structure and biological activity of dirhodium(II,II) complexes.
Aguirre JD, Lutterman DA, Angeles-Boza AM, Dunbar KR, Turro C
Inorg Chem (2007) 46(18):7494-502 - Inactivation of Listeria monocytogenes on frankfurters by monocaprylin alone or in combination with acetic acid.
Garcia M, Amalaradjou MA, Nair MK, Annamalai T, Surendranath S, Lee S, Hoagland T, Dzurec D, Faustman C, Venkitanarayanan K
J. Food Prot. (2007) 70(7):1594-9 - Sheeppox virus kelch-like gene SPPV-019 affects virus virulence.
Balinsky CA, Delhon G, Afonso CL, Risatti GR, Borca MV, French RA, Tulman ER, Geary SJ, Rock DL
J. Virol. (2007) 81(20):11392-401 (PMC2045533) 10.1128/JVI.01093-07 - Behavioural genetics: evolutionary fingerprint of the 'invisible hand'.
Bolnick DI
Curr. Biol. (2007) 17(15):R596-7 - Polyhead formation in phage P22 pinpoints a region in coat protein required for conformational switching.
Parent KN, Suhanovsky MM, Teschke CM
Mol. Microbiol. (2007) 65(5):1300-10 (PMC3215258) - Growth, osmotic downshock resistance and differentiation of Bacillus subtilis strains lacking mechanosensitive channels.
Wahome PG, Setlow P
Arch. Microbiol. (2007) 189(1):49-58 - Analysis of the RpoS regulon in Borrelia burgdorferi in response to mammalian host signals provides insight into RpoS function during the enzootic cycle.
Caimano MJ, Iyer R, Eggers CH, Gonzalez C, Morton EA, Gilbert MA, Schwartz I, Radolf JD
Mol. Microbiol. (2007) 65(5):1193-217 (PMC2967192) - Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana.
Silver AC, Rabinowitz NM, Küffer S, Graf J
J. Bacteriol. (2007) 189(19):6763-72 (PMC2045196) - Enhanced phosphorylation of transcription factor sp1 in response to herpes simplex virus type 1 infection is dependent on the ataxia telangiectasia-mutated protein.
Iwahori S, Shirata N, Kawaguchi Y, Weller SK, Sato Y, Kudoh A, Nakayama S, Isomura H, Tsurumi T
J. Virol. (2007) 81(18):9653-64 (PMC2045397) 10.1128/JVI.00568-07 - Active RNA polymerase I of Trypanosoma brucei harbors a novel subunit essential for transcription.
Nguyen TN, Schimanski B, Günzl A
Mol. Cell. Biol. (2007) 27(17):6254-63 (PMC1952147) - Does species diversity limit productivity in natural grassland communities?
Grace JB, Michael Anderson T, Smith MD, Seabloom E, Andelman SJ, Meche G, Weiher E, Allain LK, Jutila H, Sankaran M, Knops J, Ritchie M, Willig MR
Ecol. Lett. (2007) 10(8):680-9 - The general transition metal (Tro) and Zn2+ (Znu) transporters in Treponema pallidum: analysis of metal specificities and expression profiles.
Desrosiers DC, Sun YC, Zaidi AA, Eggers CH, Cox DL, Radolf JD
Mol. Microbiol. (2007) 65(1):137-52 - A putative leucine zipper within the herpes simplex virus type 1 UL6 protein is required for portal ring formation.
Nellissery JK, Szczepaniak R, Lamberti C, Weller SK
J. Virol. (2007) 81(17):8868-77 (PMC1951442) 10.1128/JVI.00739-07 - A hyperconserved protein in Prochlorococcus and marine Synechococcus.
Zhaxybayeva O, Gogarten JP, Doolittle WF
FEMS Microbiol. Lett. (2007) 274(1):30-4 - Analysis of interactions between nutrient germinant receptors and SpoVA proteins of Bacillus subtilis spores.
Vepachedu VR, Setlow P
FEMS Microbiol. Lett. (2007) 274(1):42-7 - Transcriptional responses of Mycoplasma gallisepticum strain R in association with eukaryotic cells.
Cecchini KR, Gorton TS, Geary SJ
J. Bacteriol. (2007) 189(16):5803-7 (PMC1952027) 10.1128/JB.00667-07 - Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase.
Kelly SJ, Li J, Setlow P, Jedrzejas MJ
Proteins (2007) 68(4):961-71 - Crystallization and preliminary X-ray analysis of the complex between a Bacillus subtilis alpha/beta-type small acid-soluble spore protein and DNA.
Bumbaca D, Kosman J, Setlow P, Henderson RK, Jedrzejas MJ
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. (2007) 63(Pt 6):503-6 (PMC2335083) - A mutation in the human herpes simplex virus type 1 UL52 zinc finger motif results in defective primase activity but can recruit viral polymerase and support viral replication efficiently.
Chen Y, Livingston CM, Carrington-Lawrence SD, Bai P, Weller SK
J. Virol. (2007) 81(16):8742-51 (PMC1951384) 10.1128/JVI.00174-07 - Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
Huang J, Gogarten JP
Genome Biol. (2007) 8(6):R99 (PMC2394758) - Comparative support for the niche variation hypothesis that more generalized populations also are more heterogeneous.
Bolnick DI, Svanbäck R, Araújo MS, Persson L
Proc. Natl. Acad. Sci. U.S.A. (2007) 104(24):10075-9 (PMC1891261) - Characterization of a catalase gene from Aeromonas veronii, the digestive-tract symbiont of the medicinal leech.
Rio RV, Anderegg M, Graf J
Microbiology (Reading, Engl.) (2007) 153(Pt 6):1897-906 - Single-dose prophylaxis against Lyme disease.
Wormser GP, Dattwyler RJ, Shapiro ED, Dumler JS, O'Connell S, Radolf JD, Nadelman RB
Lancet Infect Dis (2007) 7(6):371-3 - Enterohaemorrhagic and enteropathogenic Escherichia coli Tir proteins trigger a common Nck-independent actin assembly pathway.
Brady MJ, Campellone KG, Ghildiyal M, Leong JM
Cell. Microbiol. (2007) 9(9):2242-53 10.1111/j.1462-5822.2007.00954.x - Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations.
Silver AC, Kikuchi Y, Fadl AA, Sha J, Chopra AK, Graf J
Proc. Natl. Acad. Sci. U.S.A. (2007) 104(22):9481-6 (PMC1890520) - Evolution of rhodopsin ion pumps in haloarchaea.
Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT
BMC Evol. Biol. (2007) 7:79 (PMC1885257) - Stormwater runoff and export changes with development in a traditional and low impact subdivision.
Dietz ME, Clausen JC
J. Environ. Manage. (2007) 87(4):560-6 - Heavy metal ions in normal physiology, toxic stress, and cytoprotection.
Lynes MA, Kang YJ, Sensi SL, Perdrizet GA, Hightower LE
Ann. N. Y. Acad. Sci. (2007) 1113:159-72 - MAPKAPK2-mediated LSP1 phosphorylation and FMLP-induced neutrophil polarization.
Wu Y, Zhan L, Ai Y, Hannigan M, Gaestel M, Huang CK, Madri JA
Biochem. Biophys. Res. Commun. (2007) 358(1):170-5 10.1016/j.bbrc.2007.04.104 - Levels of Ca2+-dipicolinic acid in individual bacillus spores determined using microfluidic Raman tweezers.
Huang SS, Chen D, Pelczar PL, Vepachedu VR, Setlow P, Li YQ
J. Bacteriol. (2007) 189(13):4681-7 (PMC1913426) - The evolution of eukaryotes.
Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA
Science (2007) 316(5824):542-3; author reply 542-3 - The Mycoplasma gallisepticum OsmC-like protein MG1142 resides on the cell surface and binds heparin.
Jenkins C, Geary SJ, Gladd M, Djordjevic SP
Microbiology (Reading, Engl.) (2007) 153(Pt 5):1455-63 10.1099/mic.0.2006/004937-0 - GroEL/S substrate specificity based on substrate unfolding propensity.
Parent KN, Teschke CM
Cell Stress Chaperones (2007) 12(1):20-32 (PMC1852890) - Assessment of the kinetics of Treponema pallidum dissemination into blood and tissues in experimental syphilis by real-time quantitative PCR.
Salazar JC, Rathi A, Michael NL, Radolf JD, Jagodzinski LL
Infect. Immun. (2007) 75(6):2954-8 (PMC1932886) - BranchClust: a phylogenetic algorithm for selecting gene families.
Poptsova MS, Gogarten JP
BMC Bioinformatics (2007) 8:120 (PMC1853112) - High-throughput SNP genotyping by SBE/SBH.
Măndoiu II, Prăjescu C
IEEE Trans Nanobioscience (2007) 6(1):28-35 - Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
Senejani AG, Gogarten JP
Int. J. Biol. Sci. (2007) 3(4):205-11 (PMC1802021) - The power of phylogenetic approaches to detect horizontally transferred genes.
Poptsova MS, Gogarten JP
BMC Evol. Biol. (2007) 7:45 (PMC1847511) - Spliced leader RNA trans-splicing in dinoflagellates.
Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S
Proc. Natl. Acad. Sci. U.S.A. (2007) 104(11):4618-23 (PMC1838650) 10.1073/pnas.0700258104 - Using delta13C stable isotopes to quantify individual-level diet variation.
Araújo MS, Bolnick DI, Machado G, Giaretta AA, dos Reis SF
Oecologia (2007) 152(4):643-54 - Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors.
Marshall DC, Simon C, Buckley TR
Syst. Biol. (2007) 55(6):993-1003 10.1080/10635150601087641 - I will survive: DNA protection in bacterial spores.
Setlow P
Trends Microbiol. (2007) 15(4):172-80 - 'GM-gene-deletor': fused loxP-FRT recognition sequences dramatically improve the efficiency of FLP or CRE recombinase on transgene excision from pollen and seed of tobacco plants.
Luo K, Duan H, Zhao D, Zheng X, Deng W, Chen Y, Stewart CN, McAvoy R, Jiang X, Wu Y, He A, Pei Y, Li Y
Plant Biotechnol. J. (2007) 5(2):263-274 10.1111/j.1467-7652.2006.00237.x - Purification of components of the translation elongation factor complex of Plasmodium falciparum by tandem affinity purification.
Takebe S, Witola WH, Schimanski B, Günzl A, Ben Mamoun C
Eukaryotic Cell (2007) 6(4):584-91 (PMC1865644) - Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7.
Campellone KG, Roe AJ, Løbner-Olesen A, Murphy KC, Magoun L, Brady MJ, Donohue-Rolfe A, Tzipori S, Gally DL, Leong JM, Marinus MG
Mol. Microbiol. (2007) 63(5):1468-81 10.1111/j.1365-2958.2007.05602.x - Treponema pallidum elicits innate and adaptive cellular immune responses in skin and blood during secondary syphilis: a flow-cytometric analysis.
Salazar JC, Cruz AR, Pope CD, Valderrama L, Trujillo R, Saravia NG, Radolf JD
J. Infect. Dis. (2007) 195(6):879-87 (PMC2131710) - Spatial and temporal population dynamics of a naturally occurring two-species microbial community inside the digestive tract of the medicinal leech.
Kikuchi Y, Graf J
Appl. Environ. Microbiol. (2007) 73(6):1984-91 (PMC1828818) - Automated real-time measurements of leukocyte chemotaxis.
Hadjout N, Yin X, Knecht DA, Lynes MA
J. Immunol. Methods (2007) 320(1-2):70-80 (PMC1934897) - Emerging technologies: systems biology.
Srivastava R, Varner J
Biotechnol. Prog. (2007) 23(1):24-7 - Highly efficient ligands for dihydrofolate reductase from Cryptosporidium hominis and Toxoplasma gondii inspired by structural analysis.
Pelphrey PM, Popov VM, Joska TM, Beierlein JM, Bolstad ES, Fillingham YA, Wright DL, Anderson AC
J. Med. Chem. (2007) 50(5):940-50 10.1021/jm061027h - Spliced leader RNA gene transcription in Trypanosoma brucei requires transcription factor TFIIH.
Lee JH, Nguyen TN, Schimanski B, Günzl A
Eukaryotic Cell (2007) 6(4):641-9 (PMC1865645) - Antisense-RNA-mediated decreased synthesis of small, acid-soluble spore proteins leads to decreased resistance of clostridium perfringens spores to moist heat and UV radiation.
Raju D, Setlow P, Sarker MR
Appl. Environ. Microbiol. (2007) 73(7):2048-53 (PMC1855649) - Intraspecific competition drives increased resource use diversity within a natural population.
Svanbäck R, Bolnick DI
Proc. Biol. Sci. (2007) 274(1611):839-44 (PMC2093969) - Phagocytosis of Borrelia burgdorferi and Treponema pallidum potentiates innate immune activation and induces gamma interferon production.
Moore MW, Cruz AR, LaVake CJ, Marzo AL, Eggers CH, Salazar JC, Radolf JD
Infect. Immun. (2007) 75(4):2046-62 (PMC1865718) - Learning geomicrobiology as a team using microbial mats, a multidisciplinary approach.
Rios-Velazquez C, Casillas-Martinez L, Visscher PT
J Microbiol Biol Educ (2007) 8(1):28-35 (PMC3577146) 2006
- Relationships between inhibitory activity against a cancer cell line panel, profiles of plants collected, and compound classes isolated in an anticancer drug discovery project.
Balunas MJ, Jones WP, Chin YW, Mi Q, Farnsworth NR, Soejarto DD, Cordell GA, Swanson SM, Pezzuto JM, Chai HB, Kinghorn AD
Chem. Biodivers. (2006) 3(8):897-915 - Borrelia burgdorferi BBA74, a periplasmic protein associated with the outer membrane, lacks porin-like properties.
Mulay V, Caimano MJ, Liveris D, Desrosiers DC, Radolf JD, Schwartz I
J. Bacteriol. (2006) 189(5):2063-8 (PMC1855751) - Herpes simplex virus eliminates host mitochondrial DNA.
Saffran HA, Pare JM, Corcoran JA, Weller SK, Smiley JR
EMBO Rep. (2006) 8(2):188-93 (PMC1796774) 10.1038/sj.embor.7400878 - The Lyme disease agent Borrelia burgdorferi requires BB0690, a Dps homologue, to persist within ticks.
Li X, Pal U, Ramamoorthi N, Liu X, Desrosiers DC, Eggers CH, Anderson JF, Radolf JD, Fikrig E
Mol. Microbiol. (2006) 63(3):694-710 - Pseudotyped single-cycle simian immunodeficiency viruses expressing gamma interferon augment T-cell priming responses in vitro.
Peng Y, Lin FC, Verardi PH, Jones LA, McChesney MB, Yilma TD
J. Virol. (2006) 81(5):2187-95 (PMC1865962) - Dirhodium(II,II) complexes: molecular characteristics that affect in vitro activity.
Angeles-Boza AM, Chifotides HT, Aguirre JD, Chouai A, Fu PK, Dunbar KR, Turro C
J. Med. Chem. (2006) 49(23):6841-7 - Role of SpoVA proteins in release of dipicolinic acid during germination of Bacillus subtilis spores triggered by dodecylamine or lysozyme.
Vepachedu VR, Setlow P
J. Bacteriol. (2006) 189(5):1565-72 (PMC1855772) - Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR
Genome Res. (2006) 17(1):7-15 (PMC1716269) - Bayesian-based selection of metabolic objective functions.
Knorr AL, Jain R, Srivastava R
Bioinformatics (2006) 23(3):351-7 - Investigation of bacteriophage MS2 viral dynamics using model discrimination analysis and the implications for phage therapy.
Jain R, Knorr AL, Bernacki J, Srivastava R
Biotechnol. Prog. (2006) 22(6):1650-8 - Role of GerD in germination of Bacillus subtilis spores.
Pelczar PL, Igarashi T, Setlow B, Setlow P
J. Bacteriol. (2006) 189(3):1090-8 (PMC1797312) - Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.
Gogarten JP, Hilario E
BMC Evol. Biol. (2006) 6:94 (PMC1654191) - Expression of secretory phospholipase A2 in colon tumor cells potentiates tumor growth.
Belinsky GS, Rajan TV, Saria EA, Giardina C, Rosenberg DW
Mol. Carcinog. (2006) 46(2):106-16 - Systematic tuning of parameters in support vector clustering.
Yilmaz O, Achenie LE, Srivastava R
Math Biosci (2006) 205(2):252-70 - Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species.
Nukui M, Mello LV, Littlejohn JE, Setlow B, Setlow P, Kim K, Leighton T, Jedrzejas MJ
Biophys. J. (2006) 92(3):977-88 (PMC1779985) - Phage P22 procapsids equilibrate with free coat protein subunits.
Parent KN, Suhanovsky MM, Teschke CM
J. Mol. Biol. (2006) 365(2):513-22 (PMC2790821) - Cell number-dependent regulation of Hsp70B' expression: evidence of an extracellular regulator.
Noonan EJ, Place RF, Rasoulpour RJ, Giardina C, Hightower LE
J. Cell. Physiol. (2006) 210(1):201-11 - Genomics and the bacterial species problem.
Doolittle WF, Papke RT
Genome Biol. (2006) 7(9):116 (PMC1794555) - The physiological roles of extracellular metallothionein.
Lynes MA, Zaffuto K, Unfricht DW, Marusov G, Samson JS, Yin X
Exp. Biol. Med. (Maywood) (2006) 231(9):1548-54 - Inactivation of escherichia coli O157:H7 in cattle drinking water by sodium caprylate.
Amalaradjou MA, Annamalai T, Marek P, Rezamand P, Schreiber D, Hoagland T, Venkitanarayanan K
J. Food Prot. (2006) 69(9):2248-52 - Aberrant crypt foci in patients with a positive family history of sporadic colorectal cancer.
Stevens RG, Swede H, Heinen CD, Jablonski M, Grupka M, Ross B, Parente M, Tirnauer JS, Giardina C, Rajan TV, Rosenberg DW, Levine J
Cancer Lett. (2006) 248(2):262-8 - Circumvention and reactivation of the p53 oncogene checkpoint in mouse colon tumors.
Aizu W, Belinsky GS, Flynn C, Noonan EJ, Boes CC, Godman CA, Doshi B, Nambiar PR, Rosenberg DW, Giardina C
Biochem. Pharmacol. (2006) 72(8):981-91 - Localization of the transglutaminase cross-linking sites in the Bacillus subtilis spore coat protein GerQ.
Monroe A, Setlow P
J. Bacteriol. (2006) 188(21):7609-16 (PMC1636287) - Bacterial interactions and successions during plaque development.
Kolenbrander PE, Palmer RJ, Rickard AH, Jakubovics NS, Chalmers NI, Diaz PI
Periodontol. 2000 (2006) 42:47-79 - Enterohaemorrhagic Escherichia coli Tir requires a C-terminal 12-residue peptide to initiate EspF-mediated actin assembly and harbours N-terminal sequences that influence pedestal length.
Campellone KG, Brady MJ, Alamares JG, Rowe DC, Skehan BM, Tipper DJ, Leong JM
Cell. Microbiol. (2006) 8(9):1488-503 10.1111/j.1462-5822.2006.00728.x - Asymmetric male and female genetic histories among Native Americans from Eastern North America.
Bolnick DA, Bolnick DI, Smith DG
Mol. Biol. Evol. (2006) 23(11):2161-74 - Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT
Genome Res. (2006) 16(9):1099-108 (PMC1557764) - The synthesis and role of the mechanosensitive channel of large conductance in growth and differentiation of Bacillus subtilis.
Wahome PG, Setlow P
Arch. Microbiol. (2006) 186(5):377-83 - Development of a dinoflagellate-oriented PCR primer set leads to detection of picoplanktonic dinoflagellates from Long Island Sound.
Lin S, Zhang H, Hou Y, Miranda L, Bhattacharya D
Appl. Environ. Microbiol. (2006) 72(8):5626-30 (PMC1538694) 10.1128/AEM.00586-06 - fester, A candidate allorecognition receptor from a primitive chordate.
Nyholm SV, Passegue E, Ludington WB, Voskoboynik A, Mitchel K, Weissman IL, De Tomaso AW
Immunity (2006) 25(1):163-73 10.1016/j.immuni.2006.04.011 - Leeches and their microbiota: naturally simple symbiosis models.
Graf J, Kikuchi Y, Rio RV
Trends Microbiol. (2006) 14(8):365-71 - Culture-independent characterization of the digestive-tract microbiota of the medicinal leech reveals a tripartite symbiosis.
Worthen PL, Gode CJ, Graf J
Appl. Environ. Microbiol. (2006) 72(7):4775-81 (PMC1489327) - Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species.
Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT
BMC Genomics (2006) 7:171 (PMC1560387) - Drug discovery from natural sources.
Chin YW, Balunas MJ, Chai HB, Kinghorn AD
AAPS J (2006) 8(2):E239-53 (PMC3231566) - The application of cathodic reductions and anodic oxidations in the synthesis of complex molecules.
Sperry JB, Wright DL
Chem Soc Rev (2006) 35(7):605-21 10.1039/b512308a - Role of the rpoS gene in the survival of Vibrio parahaemolyticus in artificial seawater and fish homogenate.
Vasudevan P, Venkitanarayanan K
J. Food Prot. (2006) 69(6):1438-42 - Investigating the role of small, acid-soluble spore proteins (SASPs) in the resistance of Clostridium perfringens spores to heat.
Raju D, Waters M, Setlow P, Sarker MR
BMC Microbiol. (2006) 6:50 (PMC1501028) - Herpes simplex virus type I disrupts the ATR-dependent DNA-damage response during lytic infection.
Wilkinson DE, Weller SK
J. Cell. Sci. (2006) 119(Pt 13):2695-703 (PMC4427570) 10.1242/jcs.02981 - Analysis of complexes of inhibitors with Cryptosporidium hominis DHFR leads to a new trimethoprim derivative.
Popov VM, Chan DC, Fillingham YA, Atom Yee W, Wright DL, Anderson AC
Bioorg. Med. Chem. Lett. (2006) 16(16):4366-70 10.1016/j.bmcl.2006.05.047 - Purification of an eight subunit RNA polymerase I complex in Trypanosoma brucei.
Nguyen TN, Schimanski B, Zahn A, Klumpp B, Günzl A
Mol. Biochem. Parasitol. (2006) 149(1):27-37 - Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
Huang J, Gogarten JP
Trends Genet. (2006) 22(7):361-6 - The two helicases of herpes simplex virus type 1 (HSV-1).
Chattopadhyay S, Chen Y, Weller SK
Front. Biosci. (2006) 11:2213-23 - Exact and approximation algorithms for DNA tag set design.
Măndoiu II, Trincă D
J. Comput. Biol. (2006) 13(3):732-44 - Rapid succession within the Veillonella population of a developing human oral biofilm in situ.
Palmer RJ, Diaz PI, Kolenbrander PE
J. Bacteriol. (2006) 188(11):4117-24 (PMC1482915) - Transcription of the Bacillus subtilis gerK operon, which encodes a spore germinant receptor, and comparison with that of operons encoding other germinant receptors.
Igarashi T, Setlow P
J. Bacteriol. (2006) 188(11):4131-6 (PMC1482912) - Role of dipicolinic acid in resistance and stability of spores of Bacillus subtilis with or without DNA-protective alpha/beta-type small acid-soluble proteins.
Setlow B, Atluri S, Kitchel R, Koziol-Dube K, Setlow P
J. Bacteriol. (2006) 188(11):3740-7 (PMC1482921) - Quantitative analysis of multi-component spherical virus assembly: scaffolding protein contributes to the global stability of phage P22 procapsids.
Parent KN, Zlotnick A, Teschke CM
J. Mol. Biol. (2006) 359(4):1097-106 - Simultaneous collection of rapid chlorophyll fluorescence induction kinetics, fluorescence quenching parameters, and environmental data using an automated PAM-2000/CR10X data logging system.
Gray DW, Cardon ZG, Lewis LA
Photosyn. Res. (2006) 87(3):295-301 - Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).
Buckley TR, Cordeiro M, Marshall DC, Simon C
Syst. Biol. (2006) 55(3):411-25 10.1080/10635150600697283 - Metallothionein and anti-metallothionein, complementary elements of cadmium-induced renal disease.
Lynes MA, Yin X
Toxicol. Sci. (2006) 91(1):1-3 - Reconstructing asymmetrical reproductive character displacement in a periodical cicada contact zone.
Cooley JR, Marshall DC, Hill KB, Simon C
J. Evol. Biol. (2006) 19(3):855-68 10.1111/j.1420-9101.2005.01056.x - Interference by naturally occurring fatty acids in a noncellular enzyme-based aromatase bioassay.
Balunas MJ, Su B, Landini S, Brueggemeier RW, Kinghorn AD
J. Nat. Prod. (2006) 69(4):700-3 - Molecular requirements for the colonization of Hirudo medicinalis by Aeromonas veronii.
Graf J
Prog. Mol. Subcell. Biol. (2006) 41:291-303 - DNA binding activity of the herpes simplex virus type 1 origin binding protein, UL9, can be modulated by sequences in the N terminus: correlation between transdominance and DNA binding.
Chattopadhyay S, Weller SK
J. Virol. (2006) 80(9):4491-500 (PMC1471996) 10.1128/JVI.80.9.4491-4500.2006 - Cloning and sequencing of the ompA gene of Enterobacter sakazakii and development of an ompA-targeted PCR for rapid detection of Enterobacter sakazakii in infant formula.
Mohan Nair MK, Venkitanarayanan KS
Appl. Environ. Microbiol. (2006) 72(4):2539-46 (PMC1449048) - Molecular characterization of subject-specific oral microflora during initial colonization of enamel.
Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, Palmer RJ, Kolenbrander PE
Appl. Environ. Microbiol. (2006) 72(4):2837-48 (PMC1449052) - Levels of glycine betaine in growing cells and spores of Bacillus species and lack of effect of glycine betaine on dormant spore resistance.
Loshon CA, Wahome PG, Maciejewski MW, Setlow P
J. Bacteriol. (2006) 188(8):3153-8 (PMC1447009) - Isolation and characterization of proliferating cell nuclear antigen from the dinoflagellate Pfiesteria piscicida.
Zhang H, Hou Y, Lin S
J. Eukaryot. Microbiol. (2006) 53(2):142-50 10.1111/j.1550-7408.2005.00085.x - Exploiting pathogenic Escherichia coli to model transmembrane receptor signalling.
Hayward RD, Leong JM, Koronakis V, Campellone KG
Nat. Rev. Microbiol. (2006) 4(5):358-70 10.1038/nrmicro1391 - Saturation to improve pollutant retention in a rain garden.
Dietz ME, Clausen JC
Environ. Sci. Technol. (2006) 40(4):1335-40 - A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei.
Schimanski B, Brandenburg J, Nguyen TN, Caimano MJ, Günzl A
Nucleic Acids Res. (2006) 34(6):1676-84 (PMC1409817) - Sigma factor selectivity in Borrelia burgdorferi: RpoS recognition of the ospE/ospF/elp promoters is dependent on the sequence of the -10 region.
Eggers CH, Caimano MJ, Radolf JD
Mol. Microbiol. (2006) 59(6):1859-75 - Role of oxyR in the oral anaerobe Porphyromonas gingivalis.
Diaz PI, Slakeski N, Reynolds EC, Morona R, Rogers AH, Kolenbrander PE
J. Bacteriol. (2006) 188(7):2454-62 (PMC1428421) - Inactivation of microorganisms in milk and apple cider treated with ultrasound.
D'Amico DJ, Silk TM, Wu J, Guo M
J. Food Prot. (2006) 69(3):556-63 - YtkD and MutT protect vegetative cells but not spores of Bacillus subtilis from oxidative stress.
Castellanos-Juárez FX, Alvarez-Alvarez C, Yasbin RE, Setlow B, Setlow P, Pedraza-Reyes M
J. Bacteriol. (2006) 188(6):2285-9 (PMC1428130) - The forespore line of gene expression in Bacillus subtilis.
Wang ST, Setlow B, Conlon EM, Lyon JL, Imamura D, Sato T, Setlow P, Losick R, Eichenberger P
J. Mol. Biol. (2006) 358(1):16-37 - Identification of fibronectin-binding proteins in Mycoplasma gallisepticum strain R.
May M, Papazisi L, Gorton TS, Geary SJ
Infect. Immun. (2006) 74(3):1777-85 (PMC1418676) 10.1128/IAI.74.3.1777-1785.2006 - Multi-species outcomes in a common model of sympatric speciation.
Bolnick DI
J. Theor. Biol. (2006) 241(4):734-44 - Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars.
Nanavati DM, Thirangoon K, Noll KM
Appl. Environ. Microbiol. (2006) 72(2):1336-45 (PMC1392961) - Cytometry on a chip: cellular phenotypic and functional analysis using grating-coupled surface plasmon resonance.
Jin GB, Unfricht DW, Fernandez SM, Lynes MA
Biosens Bioelectron (2006) 22(2):200-6 - Stormwater runoff quality and quantity from asphalt, paver, and crushed stone driveways in Connecticut.
Gilbert JK, Clausen JC
Water Res. (2006) 40(4):826-32 - Identification of a virulence-associated determinant, dihydrolipoamide dehydrogenase (lpd), in Mycoplasma gallisepticum through in vivo screening of transposon mutants.
Hudson P, Gorton TS, Papazisi L, Cecchini K, Frasca S, Geary SJ
Infect. Immun. (2006) 74(2):931-9 (PMC1360363) 10.1128/IAI.74.2.931-939.2006 - Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species.
Lapierre P, Shial R, Gogarten JP
Syst. Appl. Microbiol. (2006) 29(1):15-23 - The cycloaddition strategy for the synthesis of natural products containing carbocyclic seven-membered rings.
Battiste MA, Pelphrey PM, Wright DL
Chemistry (2006) 12(13):3438-47 10.1002/chem.200501083 - Ancient gene duplications and the root(s) of the tree of life.
Zhaxybayeva O, Lapierre P, Gogarten JP
Protoplasma (2006) 227(1):53-64 2005
- Architecture of infection thread networks in developing root nodules induced by the symbiotic bacterium Sinorhizobium meliloti on Medicago truncatula.
Monahan-Giovanelli H, Pinedo CA, Gage DJ
Plant Physiol. (2005) 140(2):661-70 (PMC1361332) - The Bacillus subtilis spore coat provides "eat resistance" during phagocytic predation by the protozoan Tetrahymena thermophila.
Klobutcher LA, Ragkousi K, Setlow P
Proc. Natl. Acad. Sci. U.S.A. (2005) 103(1):165-70 (PMC1324984) - Electrochemical annulation of five-membered rings through dearomatization of furans and thiophenes.
Sperry JB, Ghiviriga I, Wright DL
Chem. Commun. (Camb.) (2005) (2):194-6 10.1039/b513532j - Cooperativity between different nutrient receptors in germination of spores of Bacillus subtilis and reduction of this cooperativity by alterations in the GerB receptor.
Atluri S, Ragkousi K, Cortezzo DE, Setlow P
J. Bacteriol. (2005) 188(1):28-36 (PMC1317597) - Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta).
Lewis LA, Lewis PO
Syst. Biol. (2005) 54(6):936-47 - Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat.
Decker KL, Potter CS, Bebout BM, Marais DJ, Carpenter S, Discipulo M, Hoehler TM, Miller SR, Thamdrup B, Turk KA, Visscher PT
FEMS Microbiol. Ecol. (2005) 52(3):377-95 - The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.
Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F
Proc. Natl. Acad. Sci. U.S.A. (2005) 102(50):18147-52 (PMC1312414) - Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae).
Near TJ, Bolnick DI, Wainwright PC
Evolution (2005) 59(8):1768-82 - Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae).
Bolnick DI, Near TJ
Evolution (2005) 59(8):1754-67 - Mitochondrial cytochrome b mRNA editing in dinoflagellates: possible ecological and evolutionary associations?
Zhang H, Lin S
J. Eukaryot. Microbiol. (2005) 52(6):538-45 10.1111/j.1550-7408.2005.00060.x - Furans, thiophenes and related heterocycles in drug discovery.
Sperry JB, Wright DL
Curr Opin Drug Discov Devel (2005) 8(6):723-40 - Isolation and characterization of a protochordate histocompatibility locus.
De Tomaso AW, Nyholm SV, Palmeri KJ, Ishizuka KJ, Ludington WB, Mitchel K, Weissman IL
Nature (2005) 438(7067):454-9 (PMC1401502) 10.1038/nature04150 - Expression of major cold shock proteins and genes by Yersinia enterocolitica in synthetic medium and foods.
Annamalai T, Venkitanarayanan K
J. Food Prot. (2005) 68(11):2454-8 - Diversity of bat-associated Leptospira in the Peruvian Amazon inferred by bayesian phylogenetic analysis of 16S ribosomal DNA sequences.
Matthias MA, Díaz MM, Campos KJ, Calderon M, Willig MR, Pacheco V, Gotuzzo E, Gilman RH, Vinetz JM
Am. J. Trop. Med. Hyg. (2005) 73(5):964-74 (PMC2270400) - Highly efficient tandem affinity purification of trypanosome protein complexes based on a novel epitope combination.
Schimanski B, Nguyen TN, Günzl A
Eukaryotic Cell (2005) 4(11):1942-50 (PMC1287860) - Development of a cob-18S rRNA gene real-time PCR assay for quantifying Pfiesteria shumwayae in the natural environment.
Zhang H, Lin S
Appl. Environ. Microbiol. (2005) 71(11):7053-63 (PMC1287735) 10.1128/AEM.71.11.7053-7063.2005 - Alternate sigma factor RpoS is required for the in vivo-specific repression of Borrelia burgdorferi plasmid lp54-borne ospA and lp6.6 genes.
Caimano MJ, Eggers CH, Gonzalez CA, Radolf JD
J. Bacteriol. (2005) 187(22):7845-52 (PMC1280317) - Development of real-time diagnostic assays specific for Mycoplasma mycoides subspecies mycoides Small Colony.
Gorton TS, Barnett MM, Gull T, French RA, Lu Z, Kutish GF, Adams LG, Geary SJ
Vet. Microbiol. (2005) 111(1-2):51-8 10.1016/j.vetmic.2005.09.013 - HDACs and the senescent phenotype of WI-38 cells.
Place RF, Noonan EJ, Giardina C
BMC Cell Biol. (2005) 6:37 (PMC1285358) - Role of the Nfo (YqfS) and ExoA apurinic/apyrimidinic endonucleases in protecting Bacillus subtilis spores from DNA damage.
Salas-Pacheco JM, Setlow B, Setlow P, Pedraza-Reyes M
J. Bacteriol. (2005) 187(21):7374-81 (PMC1272979) - Developing unified theories in ecology as exemplified with diversity gradients.
Scheiner SM, Willig MR
Am. Nat. (2005) 166(4):458-69 - Grating-coupled surface plasmon resonance: a cell and protein microarray platform.
Unfricht DW, Colpitts SL, Fernandez SM, Lynes MA
Proteomics (2005) 5(17):4432-42 - Photocytotoxicity of a new Rh2(II,II) complex: increase in cytotoxicity upon irradiation similar to that of PDT agent hematoporphyrin.
Angeles-Boza AM, Bradley PM, Fu PK, Shatruk M, Hilfiger MG, Dunbar KR, Turro C
Inorg Chem (2005) 44(21):7262-4 - Factors influencing germination of Bacillus subtilis spores via activation of nutrient receptors by high pressure.
Black EP, Koziol-Dube K, Guan D, Wei J, Setlow B, Cortezzo DE, Hoover DG, Setlow P
Appl. Environ. Microbiol. (2005) 71(10):5879-87 (PMC1265928) - Photocurable hard and porous biomaterials from ROMP precursors cross-linked with diyl radicals.
Enholm E, Joshi A, Wright DL
Bioorg. Med. Chem. Lett. (2005) 15(23):5262-5 10.1016/j.bmcl.2005.08.060 - Drug discovery from medicinal plants.
Balunas MJ, Kinghorn AD
Life Sci. (2005) 78(5):431-41 - Site-directed mutagenesis and structural studies suggest that the germination protease, GPR, in spores of Bacillus species is an atypical aspartic acid protease.
Carroll TM, Setlow P
J. Bacteriol. (2005) 187(20):7119-25 (PMC1251623) - Metallothionein mediates leukocyte chemotaxis.
Yin X, Knecht DA, Lynes MA
BMC Immunol. (2005) 6:21 (PMC1262721) - Antibacterial effect of caprylic acid and monocaprylin on major bacterial mastitis pathogens.
Nair MK, Joy J, Vasudevan P, Hinckley L, Hoagland TA, Venkitanarayanan KS
J. Dairy Sci. (2005) 88(10):3488-95 - Antibacterial effect of monocaprylin on Escherichia coli O157:H7 in apple juice.
Nair MK, Abouelezz H, Hoagland T, Venkitanarayanan K
J. Food Prot. (2005) 68(9):1895-9 - Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains.
Morandi A, Zhaxybayeva O, Gogarten JP, Graf J
J. Bacteriol. (2005) 187(18):6561-4 (PMC1236645) - TP0453, a concealed outer membrane protein of Treponema pallidum, enhances membrane permeability.
Hazlett KR, Cox DL, Decaffmeyer M, Bennett MP, Desrosiers DC, La Vake CJ, La Vake ME, Bourell KW, Robinson EJ, Brasseur R, Radolf JD
J. Bacteriol. (2005) 187(18):6499-508 (PMC1236642) - Archaeal diversity along a soil salinity gradient prone to disturbance.
Walsh DA, Papke RT, Doolittle WF
Environ. Microbiol. (2005) 7(10):1655-66 - Phylogeographic patterns of Hawaiian Megalagrion damselflies (Odonata: Coenagrionidae) correlate with Pleistocene island boundaries.
Jordan S, Simon C, Foote D, Englund RA
Mol. Ecol. (2005) 14(11):3457-70 10.1111/j.1365-294X.2005.02669.x - Horizontal gene transfer, genome innovation and evolution.
Gogarten JP, Townsend JP
Nat. Rev. Microbiol. (2005) 3(9):679-87 - Correlates of immune protection in chickens vaccinated with Mycoplasma gallisepticum strain GT5 following challenge with pathogenic M. gallisepticum strain R(low).
Javed MA, Frasca S, Rood D, Cecchini K, Gladd M, Geary SJ, Silbart LK
Infect. Immun. (2005) 73(9):5410-9 (PMC1231071) 10.1128/IAI.73.9.5410-5419.2005 - Beta interferon and gamma interferon synergize to block viral DNA and virion synthesis in herpes simplex virus-infected cells.
Pierce AT, DeSalvo J, Foster TP, Kosinski A, Weller SK, Halford WP
J. Gen. Virol. (2005) 86(Pt 9):2421-32 (PMC1366490) 10.1099/vir.0.80979-0 - Microbial lithification in marine stromatolites and hypersaline mats.
Dupraz C, Visscher PT
Trends Microbiol. (2005) 13(9):429-38 - Lipoprotein-dependent and -independent immune responses to spirochetal infection.
Salazar JC, Pope CD, Moore MW, Pope J, Kiely TG, Radolf JD
Clin. Diagn. Lab. Immunol. (2005) 12(8):949-58 (PMC1182186) - Localization of SpoVAD to the inner membrane of spores of Bacillus subtilis.
Vepachedu VR, Setlow P
J. Bacteriol. (2005) 187(16):5677-82 (PMC1196082) - Characterization of a multisubunit transcription factor complex essential for spliced-leader RNA gene transcription in Trypanosoma brucei.
Schimanski B, Nguyen TN, Günzl A
Mol. Cell. Biol. (2005) 25(16):7303-13 (PMC1190248) - Photosensitization of DNA by dipicolinic acid, a major component of spores of Bacillus species.
Douki T, Setlow B, Setlow P
Photochem. Photobiol. Sci. (2005) 4(8):591-7 - Herpes simplex virus type 1 DNA polymerase requires the mammalian chaperone hsp90 for proper localization to the nucleus.
Burch AD, Weller SK
J. Virol. (2005) 79(16):10740-9 (PMC1182622) 10.1128/JVI.79.16.10740-10749.2005 - The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic.
Huang J, Xu Y, Gogarten JP
Mol. Biol. Evol. (2005) 22(11):2142-6 - Electrostatic interactions govern both nucleation and elongation during phage P22 procapsid assembly.
Parent KN, Doyle SM, Anderson E, Teschke CM
Virology (2005) 340(1):33-45 - Gene expression influences on metal immunomodulation.
Lynes MA, Fontenot AP, Lawrence DA, Rosenspire AJ, Pollard KM
Toxicol. Appl. Pharmacol. (2005) 210(1-2):9-16 - Herpes simplex virus type 1 single-strand DNA binding protein ICP8 enhances the nuclease activity of the UL12 alkaline nuclease by increasing its processivity.
Reuven NB, Weller SK
J. Virol. (2005) 79(14):9356-8 (PMC1168754) 10.1128/JVI.79.14.9356-9358.2005 - Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.
Chen Y, Carrington-Lawrence SD, Bai P, Weller SK
J. Virol. (2005) 79(14):9088-96 (PMC1168741) 10.1128/JVI.79.14.9088-9096.2005 - DNA-BAR: distinguisher selection for DNA barcoding.
DasGupta B, Konwar KM, Mandoiu II, Shvartsman AA
Bioinformatics (2005) 21(16):3424-6 - Isolation and characterization of Mycoplasma sphenisci sp. nov. from the choana of an aquarium-reared jackass penguin (Spheniscus demersus).
Frasca S, Weber ES, Urquhart H, Liao X, Gladd M, Cecchini K, Hudson P, May M, Gast RJ, Gorton TS, Geary SJ
J. Clin. Microbiol. (2005) 43(6):2976-9 (PMC1151952) 10.1128/JCM.43.6.2976-2979.2005 - HDAC inhibition prevents NF-kappa B activation by suppressing proteasome activity: down-regulation of proteasome subunit expression stabilizes I kappa B alpha.
Place RF, Noonan EJ, Giardina C
Biochem. Pharmacol. (2005) 70(3):394-406 - PentaPlot: a software tool for the illustration of genome mosaicism.
Hamel L, Zhaxybayeva O, Gogarten JP
BMC Bioinformatics (2005) 6:139 (PMC1177926) - Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes.
Alfaro ME, Bolnick DI, Wainwright PC
Am. Nat. (2005) 165(6):E140-54 - Nef from pathogenic simian immunodeficiency virus is a negative factor for vaccinia virus.
Chan KS, Verardi PH, Legrand FA, Yilma TD
Proc. Natl. Acad. Sci. U.S.A. (2005) 102(24):8734-9 (PMC1142211) - The gem-dialkyl effect in electron transfer reactions: rapid synthesis of seven-membered rings through an electrochemical annulation.
Sperry JB, Wright DL
J. Am. Chem. Soc. (2005) 127(22):8034-5 10.1021/ja051826+ - Inhibition of the herpes simplex virus type 1 DNA polymerase induces hyperphosphorylation of replication protein A and its accumulation at S-phase-specific sites of DNA damage during infection.
Wilkinson DE, Weller SK
J. Virol. (2005) 79(11):7162-71 (PMC1112160) 10.1128/JVI.79.11.7162-7171.2005 - Studies on the reactivity of CDDO, a promising new chemopreventive and chemotherapeutic agent: implications for a molecular mechanism of action.
Couch RD, Browning RG, Honda T, Gribble GW, Wright DL, Sporn MB, Anderson AC
Bioorg. Med. Chem. Lett. (2005) 15(9):2215-9 10.1016/j.bmcl.2005.03.031 - Expression profile of osteoblast lineage at defined stages of differentiation.
Kalajzic I, Staal A, Yang WP, Wu Y, Johnson SE, Feyen JH, Krueger W, Maye P, Yu F, Zhao Y, Kuo L, Gupta RR, Achenie LE, Wang HW, Shin DG, Rowe DW
J. Biol. Chem. (2005) 280(26):24618-26 10.1074/jbc.M413834200 - Nck-independent actin assembly is mediated by two phosphorylated tyrosines within enteropathogenic Escherichia coli Tir.
Campellone KG, Leong JM
Mol. Microbiol. (2005) 56(2):416-32 http:/10.1111/j.1365-2958.2005.04558.x - Many-to-One Mapping of Form to Function: A General Principle in Organismal Design?
Wainwright PC, Alfaro ME, Bolnick DI, Hulsey CD
Integr. Comp. Biol. (2005) 45(2):256-62 - Cytoplasmic phospholipase A2 levels correlate with apoptosis in human colon tumorigenesis.
Dong M, Johnson M, Rezaie A, Ilsley JN, Nakanishi M, Sanders MM, Forouhar F, Levine J, Montrose DC, Giardina C, Rosenberg DW
Clin. Cancer Res. (2005) 11(6):2265-71 - Interaction between individual protein components of the GerA and GerB nutrient receptors that trigger germination of Bacillus subtilis spores.
Igarashi T, Setlow P
J. Bacteriol. (2005) 187(7):2513-8 (PMC1065238) - The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight.
Nicholson WL, Schuerger AC, Setlow P
Mutat. Res. (2005) 571(1-2):249-64 - Substrate specificities and expression patterns reflect the evolutionary divergence of maltose ABC transporters in Thermotoga maritima.
Nanavati DM, Nguyen TN, Noll KM
J. Bacteriol. (2005) 187(6):2002-9 (PMC1064059) - Solid-phase immunoassays.
Lynes MA
Curr Protoc Toxicol (2005) Chapter 18:Unit18.7 - Cyclooxygenase-2 regulation in colon cancer cells: modulation of RNA polymerase II elongation by histone deacetylase inhibitors.
Tong X, Yin L, Joshi S, Rosenberg DW, Giardina C
J. Biol. Chem. (2005) 280(16):15503-9 - Vaccinia viruses with a serpin gene deletion and expressing IFN-gamma induce potent immune responses without detectable replication in vivo.
Legrand FA, Verardi PH, Chan KS, Peng Y, Jones LA, Yilma TD
Proc. Natl. Acad. Sci. U.S.A. (2005) 102(8):2940-5 (PMC548597) - Effect of erythorbate, storage and high-oxygen packaging on premature browning in ground beef.
Suman SP, Faustman C, Lee S, Tang J, Sepe HA, Vasudevan P, Annamalai T, Manojkumar M, Marek P, Venkitanarayanan KS
Meat Sci. (2005) 69(2):363-9 - Oxabicyclo[3.2.1]octane derivatives as highly reactive dienophiles: synthesis of bicyclo[5.n.0] systems.
Pelphrey P, Jasinski J, Butcher RJ, Wright DL
Org. Lett. (2005) 7(3):423-5 10.1021/ol047725i - Signaling through CD14 attenuates the inflammatory response to Borrelia burgdorferi, the agent of Lyme disease.
Benhnia MR, Wroblewski D, Akhtar MN, Patel RA, Lavezzi W, Gangloff SC, Goyert SM, Caimano MJ, Radolf JD, Sellati TJ
J. Immunol. (2005) 174(3):1539-48 - Genome-genome interactions: bacterial communities in initial dental plaque.
Kolenbrander PE, Egland PG, Diaz PI, Palmer RJ
Trends Microbiol. (2005) 13(1):11-5 - Inactivation of Enterobacter sakazakii in reconstituted infant formula by monocaprylin.
Nair MK, Joy J, Venkitanarayanan KS
J. Food Prot. (2005) 67(12):2815-9 - Education and changes in residential nonpoint source pollution.
Dietz ME, Clausen JC, Filchak KK
Environ Manage (2005) 34(5):684-90 - Were arachnids the first to use combinatorial peptide libraries?
Sollod BL, Wilson D, Zhaxybayeva O, Gogarten JP, Drinkwater R, King GF
Peptides (2005) 26(1):131-9 2004
- Evaluation of HIV-1 kinetic models using quantitative discrimination analysis.
Knorr AL, Srivastava R
Bioinformatics (2004) 21(8):1668-77 - DNA binding and photocleavage in vitro by new dirhodium(II) dppz complexes: correlation to cytotoxicity and photocytotoxicity.
Angeles-Boza AM, Bradley PM, Fu PK, Wicke SE, Bacsa J, Dunbar KR, Turro C
Inorg Chem (2004) 43(26):8510-9 - Frequent recombination in a saltern population of Halorubrum.
Papke RT, Koenig JE, Rodríguez-Valera F, Doolittle WF
Science (2004) 306(5703):1928-9 - The p50-p50 NF-kappaB complex as a stimulus-specific repressor of gene activation.
Tong X, Yin L, Washington R, Rosenberg DW, Giardina C
Mol. Cell. Biochem. (2004) 265(1-2):171-83 - A second-site suppressor of a folding defect functions via interactions with a chaperone network to improve folding and assembly in vivo.
Parent KN, Ranaghan MJ, Teschke CM
Mol. Microbiol. (2004) 54(4):1036-50 - Effect of muscle source on premature browning in ground beef.
Suman SP, Faustman C, Lee S, Tang J, Sepe HA, Vasudevan P, Annamalai T, Manojkumar M, Marek P, Decesare M, Venkitanarayanan KS
Meat Sci. (2004) 68(3):457-61 - Altered specificity of Hint-W123Q supports a role for Hint inhibition by ASW in avian sex determination.
Parks KP, Seidle H, Wright N, Sperry JB, Bieganowski P, Howitz K, Wright DL, Brenner C
Physiol. Genomics (2004) 20(1):12-4 (PMC2556054) 10.1152/physiolgenomics.00204.2004 - RpoS is not central to the general stress response in Borrelia burgdorferi but does control expression of one or more essential virulence determinants.
Caimano MJ, Eggers CH, Hazlett KR, Radolf JD
Infect. Immun. (2004) 72(11):6433-45 (PMC523033) - Phylogenetic placement of "zoochlorellae" (Chlorophyta), algal symbiont of the temperate sea anemone Anthopleura elegantissima.
Lewis LA, Muller-Parker G
Biol. Bull. (2004) 207(2):87-92 - Analysis of promoter elements involved in the transcriptional initiation of RpoS-dependent Borrelia burgdorferi genes.
Eggers CH, Caimano MJ, Radolf JD
J. Bacteriol. (2004) 186(21):7390-402 (PMC523197) - Effects of the binding of alpha/beta-type small, acid-soluble spore proteins on the photochemistry of DNA in spores of Bacillus subtilis and in vitro.
Douki T, Setlow B, Setlow P
Photochem. Photobiol. (2004) 81(1):163-9 - Green algae and the origin of land plants.
Lewis LA, McCourt RM
Am. J. Bot. (2004) 91(10):1535-56 - Analysis of the germination of spores of Bacillus subtilis with temperature sensitive spo mutations in the spoVA operon.
Vepachedu VR, Setlow P
FEMS Microbiol. Lett. (2004) 239(1):71-7 - New chiral building blocks from tetrabromocyclopropene and furan.
Pelphrey PM, Abboud KA, Wright DL
J. Org. Chem. (2004) 69(20):6931-3 10.1021/jo048991c - Failure to detect binding of Trypanosoma brucei SNAPc to U2 and U6 snRNA gene sequences by in vitro transcription competition and pull-down assays.
Schimanski B, Ma L, Günzl A
Mol. Biochem. Parasitol. (2004) 137(2):293-6 - Experimental assessment of the roles of linear plasmids lp25 and lp28-1 of Borrelia burgdorferi throughout the infectious cycle.
Grimm D, Eggers CH, Caimano MJ, Tilly K, Stewart PE, Elias AF, Radolf JD, Rosa PA
Infect. Immun. (2004) 72(10):5938-46 (PMC517563) - Networks by design: a revolution in ecology.
Andelman SJ, Willig MR
Science (2004) 305(5690):1565-7 - Transglutaminase-mediated cross-linking of GerQ in the coats of Bacillus subtilis spores.
Ragkousi K, Setlow P
J. Bacteriol. (2004) 186(17):5567-75 (PMC516844) - SecA folding kinetics: a large dimeric protein rapidly forms multiple native states.
Doyle SM, Bilsel O, Teschke CM
J. Mol. Biol. (2004) 341(1):199-214 - Catalysis of strand exchange by the HSV-1 UL12 and ICP8 proteins: potent ICP8 recombinase activity is revealed upon resection of dsDNA substrate by nuclease.
Reuven NB, Willcox S, Griffith JD, Weller SK
J. Mol. Biol. (2004) 342(1):57-71 (PMC4412345) 10.1016/j.jmb.2004.07.012 - Azoxymethane-induced pre-adipocyte factor 1 (Pref-1) functions as a differentiation inhibitor in colonic epithelial cells.
Dong M, Guda K, Nambiar PR, Nakanishi M, Lichtler AC, Nishikawa M, Giardina C, Rosenberg DW
Carcinogenesis (2004) 25(11):2239-46 - EspFU is a translocated EHEC effector that interacts with Tir and N-WASP and promotes Nck-independent actin assembly.
Campellone KG, Robbins D, Leong JM
Dev. Cell (2004) 7(2):217-28 10.1016/j.devcel.2004.07.004 - Differential gene expression to investigate the effect of (5Z)-4-bromo- 5-(bromomethylene)-3-butyl-2(5H)-furanone on Bacillus subtilis.
Ren D, Bedzyk LA, Setlow P, England DF, Kjelleberg S, Thomas SM, Ye RW, Wood TK
Appl. Environ. Microbiol. (2004) 70(8):4941-9 (PMC492336) - Scalable heuristics for design of DNA probe arrays.
Kahng AB, Măndoiu II, Pevzner PA, Reda S, Zelikovsky AZ
J. Comput. Biol. (2004) 11(2-3):429-47 - The winnowing: establishing the squid-vibrio symbiosis.
Nyholm SV, McFall-Ngai MJ
Nat. Rev. Microbiol. (2004) 2(8):632-42 10.1038/nrmicro957 - Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat.
Nguyen TN, Ejaz AD, Brancieri MA, Mikula AM, Nelson KE, Gill SR, Noll KM
J. Bacteriol. (2004) 186(14):4824-8 (PMC438634) - Borrelia burgdorferi outer surface protein (osp) B expression independent of ospA.
Liang FT, Caimano MJ, Radolf JD, Fikrig E
Microb. Pathog. (2004) 37(1):35-40 - Nuclear sequestration of cellular chaperone and proteasomal machinery during herpes simplex virus type 1 infection.
Burch AD, Weller SK
J. Virol. (2004) 78(13):7175-85 (PMC421678) 10.1128/JVI.78.13.7175-7185.2004 - Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes.
Gage DJ
Microbiol. Mol. Biol. Rev. (2004) 68(2):280-300 (PMC419923) - Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes.
Near TJ, Bolnick DI, Wainwright PC
Mol. Phylogenet. Evol. (2004) 32(1):344-57 - Survival and growth characteristics of Escherichia coli O157:H7 in pasteurized and unpasteurized Cheddar cheese whey.
Marek P, Nair MK, Hoagland T, Venkitanarayanan K
Int. J. Food Microbiol. (2004) 94(1):1-7 - The importance of physical isolation to microbial diversification.
Papke RT, Ward DM
FEMS Microbiol. Ecol. (2004) 48(3):293-303 - Waiting for sympatric speciation.
Bolnick DI
Evolution (2004) 58(4):895-9 - Electrooxidative coupling of furans and silyl enol ethers: application to the synthesis of annulated furans.
Sperry JB, Whitehead CR, Ghiviriga I, Walczak RM, Wright DL
J. Org. Chem. (2004) 69(11):3726-34 10.1021/jo049889i - In vitro inactivation of Escherichia coli O157:H7 in bovine rumen fluid by caprylic acid.
Annamalai T, Mohan Nair MK, Marek P, Vasudevan P, Schreiber D, Knight R, Hoagland T, Venkitanarayanan K
J. Food Prot. (2004) 67(5):884-8 - Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores.
Frenkiel-Krispin D, Sack R, Englander J, Shimoni E, Eisenstein M, Bullitt E, Horowitz-Scherer R, Hayes CS, Setlow P, Minsky A, Wolf SG
J. Bacteriol. (2004) 186(11):3525-30 (PMC415783) - Lipids in the inner membrane of dormant spores of Bacillus species are largely immobile.
Cowan AE, Olivastro EM, Koppel DE, Loshon CA, Setlow B, Setlow P
Proc. Natl. Acad. Sci. U.S.A. (2004) 101(20):7733-8 (PMC419675) - Effects of a gerF (lgt) mutation on the germination of spores of Bacillus subtilis.
Igarashi T, Setlow B, Paidhungat M, Setlow P
J. Bacteriol. (2004) 186(10):2984-91 (PMC400631) - Similarity of mammalian body size across the taxonomic hierarchy and across space and time.
Smith FA, Brown JH, Haskell JP, Lyons SK, Alroy J, Charnov EL, Dayan T, Enquist BJ, Ernest SK, Hadly EA, Jones KE, Kaufman DM, Marquet PA, Maurer BA, Niklas KJ, Porter WP, Tiffney B, Willig MR
Am. Nat. (2004) 163(5):672-91 - Can intraspecific competition drive disruptive selection? An experimental test in natural populations of sticklebacks.
Bolnick DI
Evolution (2004) 58(3):608-18 - Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism.
Alfaro ME, Bolnick DI, Wainwright PC
Evolution (2004) 58(3):495-503 - A hybrid clustering approach to recognition of protein families in 114 microbial genomes.
Harlow TJ, Gogarten JP, Ragan MA
BMC Bioinformatics (2004) 5:45 (PMC420232) - Genome mosaicism and organismal lineages.
Zhaxybayeva O, Lapierre P, Gogarten JP
Trends Genet. (2004) 20(5):254-60 - Studies on NADH oxidase and alkyl hydroperoxide reductase produced by Porphyromonas gingivalis.
Diaz PI, Zilm PS, Wasinger V, Corthals GL, Rogers AH
Oral Microbiol. Immunol. (2004) 19(3):137-43 - Gene expression in Bacillus subtilis surface biofilms with and without sporulation and the importance of yveR for biofilm maintenance.
Ren D, Bedzyk LA, Setlow P, Thomas SM, Ye RW, Wood TK
Biotechnol. Bioeng. (2004) 86(3):344-64 - Recruitment of cellular recombination and repair proteins to sites of herpes simplex virus type 1 DNA replication is dependent on the composition of viral proteins within prereplicative sites and correlates with the induction of the DNA damage response.
Wilkinson DE, Weller SK
J. Virol. (2004) 78(9):4783-96 (PMC387708) 10.1128/jvi.78.9.4783-4796.2004 - The UL12.5 gene product of herpes simplex virus type 1 exhibits nuclease and strand exchange activities but does not localize to the nucleus.
Reuven NB, Antoku S, Weller SK
J. Virol. (2004) 78(9):4599-608 (PMC387724) 10.1128/jvi.78.9.4599-4608.2004 - Direct DNA photocleavage by a new intercalating dirhodium(II/II) complex: comparison to Rh2(mu-O2CCH3)4.
Bradley PM, Angeles-Boza AM, Dunbar KR, Turro C
Inorg Chem (2004) 43(8):2450-2 - A multi-component reaction (MCR) approach to the synthesis of highly diverse polymers with polypeptide-like features.
Robotham CV, Baker C, Cuevas B, Abboud K, Wright DL
Mol. Divers. (2004) 6(3-4):237-44 - Killing of Bacillus subtilis spores by a modified Fenton reagent containing CuCl2 and ascorbic acid.
Shapiro MP, Setlow B, Setlow P
Appl. Environ. Microbiol. (2004) 70(4):2535-9 (PMC383127) - Butyrate suppresses Cox-2 activation in colon cancer cells through HDAC inhibition.
Tong X, Yin L, Giardina C
Biochem. Biophys. Res. Commun. (2004) 317(2):463-71 - Silica-induced apoptosis in mouse alveolar macrophages is initiated by lysosomal enzyme activity.
Thibodeau MS, Giardina C, Knecht DA, Helble J, Hubbard AK
Toxicol. Sci. (2004) 80(1):34-48 - Cladogenesis, coalescence and the evolution of the three domains of life.
Zhaxybayeva O, Gogarten JP
Trends Genet. (2004) 20(4):182-7 - Microtiter assay for glutamine synthetase biosynthetic activity using inorganic phosphate detection.
Gawronski JD, Benson DR
Anal. Biochem. (2004) 327(1):114-8 - A requirement of MAPKAPK2 in the uropod localization of PTEN during FMLP-induced neutrophil chemotaxis.
Wu Y, Hannigan MO, Kotlyarov A, Gaestel M, Wu D, Huang CK
Biochem. Biophys. Res. Commun. (2004) 316(3):666-72 10.1016/j.bbrc.2004.02.107 - Assessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences.
Clawson ML, Bourret A, Benson DR
Mol. Phylogenet. Evol. (2004) 31(1):131-8 - Visualization of the phylogenetic content of five genomes using dekapentagonal maps.
Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP
Genome Biol. (2004) 5(3):R20 (PMC395770) - Induction of potent humoral and cell-mediated immune responses by attenuated vaccinia virus vectors with deleted serpin genes.
Legrand FA, Verardi PH, Jones LA, Chan KS, Peng Y, Yilma TD
J. Virol. (2004) 78(6):2770-9 (PMC353749) - Molecular cloning and antiserum development of cyclin box in the brown tide alga Aureococcus anophagefferens.
Lin S, Magaletti E, Carpenter EJ
Mar. Biotechnol. (2004) 2(6):577-86 10.1007/s101260000044 - The effect of oxygen on the growth and physiology of Porphyromonas gingivalis.
Diaz PI, Rogers AH
Oral Microbiol. Immunol. (2004) 19(2):88-94 - A concerted mechanism for the suppression of a folding defect through interactions with chaperones.
Doyle SM, Anderson E, Parent KN, Teschke CM
J. Biol. Chem. (2004) 279(17):17473-82 - The Trypanosoma brucei spliced leader RNA and rRNA gene promoters have interchangeable TbSNAP50-binding elements.
Schimanski B, Laufer G, Gontcharova L, Günzl A
Nucleic Acids Res. (2004) 32(2):700-9 (PMC373353) - Clustering of Nck by a 12-residue Tir phosphopeptide is sufficient to trigger localized actin assembly.
Campellone KG, Rankin S, Pawson T, Kirschner MW, Tipper DJ, Leong JM
J. Cell Biol. (2004) 164(3):407-16 (PMC2172230) 10.1083/jcb.200306032 - Bridged synthons from tetrabromocyclopropene: studies on the rearrangement of the primary Diels-Alder adduct with 2,5-dimethylfuran.
Orugunty RS, Ghiviriga I, Abboud KA, Battiste MA, Wright DL
J. Org. Chem. (2004) 69(2):570-2 10.1021/jo0352631 - Bicyclo[3.2.1]octane synthons from cyclopropenes: functionalization of cycloadducts by nucleophilic additions.
Orugunty RS, Wright DL, Battiste MA, Helmich RJ, Abboud K
J. Org. Chem. (2004) 69(2):406-16 10.1021/jo035240m - Intracellular symbionts and other bacteria associated with deer ticks (Ixodes scapularis) from Nantucket and Wellfleet, Cape Cod, Massachusetts.
Benson MJ, Gawronski JD, Eveleigh DE, Benson DR
Appl. Environ. Microbiol. (2004) 70(1):616-20 (PMC321306) 2003
- Sexual dimorphism and adaptive speciation: two sides of the same ecological coin.
Bolnick DI, Doebeli M
Evolution (2003) 57(11):2433-49 - Inexpensive vaccines and rapid diagnostic kits tailor-made for the global eradication of rinderpest, and technology transfer to Africa and Asia.
Yilma T, Aziz F, Ahmad S, Jones L, Ngotho R, Wamwayi H, Beyene B, Yesus M, Egziabher B, Diop M, Sarr J, Verardi P
Dev Biol (Basel) (2003) 114:99-111 - Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli.
Murphy KC, Campellone KG
BMC Mol. Biol. (2003) 4:11 (PMC317293) 10.1186/1471-2199-4-11 - Borrelia burgdorferi transcriptome in the central nervous system of non-human primates.
Narasimhan S, Caimano MJ, Liang FT, Santiago F, Laskowski M, Philipp MT, Pachner AR, Radolf JD, Fikrig E, Camaino MJ
Proc. Natl. Acad. Sci. U.S.A. (2003) 100(26):15953-8 (PMC307674) - The Rep protein of adeno-associated virus type 2 interacts with single-stranded DNA-binding proteins that enhance viral replication.
Stracker TH, Cassell GD, Ward P, Loo YM, van Breukelen B, Carrington-Lawrence SD, Hamatake RK, van der Vliet PC, Weller SK, Melendy T, Weitzman MD
J. Virol. (2003) 78(1):441-53 (PMC303412) 10.1128/jvi.78.1.441-453.2004 - Spore germination.
Setlow P
Curr. Opin. Microbiol. (2003) 6(6):550-6 - Leptospirosis: a zoonotic disease of global importance.
Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, Lovett MA, Levett PN, Gilman RH, Willig MR, Gotuzzo E, Vinetz JM
Lancet Infect Dis (2003) 3(12):757-71 - Identification of aryl-phospho-beta-D-glucosidases in Bacillus subtilis.
Setlow B, Cabrera-Hernandez A, Cabrera-Martinez RM, Setlow P
Arch. Microbiol. (2003) 181(1):60-7 - Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern.
Papke RT, Douady CJ, Doolittle WF, Rodríguez-Valera F
Environ. Microbiol. (2003) 5(11):1039-45 - Detection of Penicillium expansum by polymerase chain reaction.
Marek P, Annamalai T, Venkitanarayanan K
Int. J. Food Microbiol. (2003) 89(2-3):139-44 - Lateral gene transfer and the origins of prokaryotic groups.
Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbø CL, Case RJ, Doolittle WF
Annu. Rev. Genet. (2003) 37:283-328 - The role of DNA recombination in herpes simplex virus DNA replication.
Wilkinson DE, Weller SK
IUBMB Life (2003) 55(8):451-8 10.1080/15216540310001612237 - Effects of carboxy-terminal modifications and pH on binding of a Bacillus subtilis small, acid-soluble spore protein to DNA.
Kosman J, Setlow P
J. Bacteriol. (2003) 185(20):6095-103 (PMC225040) - Spliceosomal introns: new insights into their evolution.
Zhaxybayeva O, Gogarten JP
Curr. Biol. (2003) 13(19):R764-6 - Transcriptional control of a rRNA promoter of the nodulating symbiont Sinorhizobium meliloti.
Rosado M, Gage DJ
FEMS Microbiol. Lett. (2003) 226(1):15-22 - An improved probability mapping approach to assess genome mosaicism.
Zhaxybayeva O, Gogarten JP
BMC Genomics (2003) 4(1):37 (PMC222983) - Rapid unfolding of a domain populates an aggregation-prone intermediate that can be recognized by GroEL.
Doyle SM, Anderson E, Zhu D, Braswell EH, Teschke CM
J. Mol. Biol. (2003) 332(4):937-51 - Folding of phage P22 coat protein monomers: kinetic and thermodynamic properties.
Anderson E, Teschke CM
Virology (2003) 313(1):184-97 - The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low).
Papazisi L, Gorton TS, Kutish G, Markham PF, Browning GF, Nguyen DK, Swartzell S, Madan A, Mahairas G, Geary SJ
Microbiology (Reading, Engl.) (2003) 149(Pt 9):2307-16 10.1099/mic.0.26427-0 - p53 and its co-activator p300 are inversely regulated in the mouse colon in response to carcinogen.
Aizu W, Guda K, Nambiar P, Xin T, Thibodeau M, Rosenberg DW, Giardina C
Toxicol. Lett. (2003) 144(2):213-24 - Coevolution of markers of innate and adaptive immunity in skin and peripheral blood of patients with erythema migrans.
Salazar JC, Pope CD, Sellati TJ, Feder HM, Kiely TG, Dardick KR, Buckman RL, Moore MW, Caimano MJ, Pope JG, Krause PJ, Radolf JD
J. Immunol. (2003) 171(5):2660-70 - Existence of transdominant and potentiating mutants of UL9, the herpes simplex virus type 1 origin-binding protein, suggests that levels of UL9 protein may be regulated during infection.
Marintcheva B, Weller SK
J. Virol. (2003) 77(17):9639-51 (PMC187383) 10.1128/jvi.77.17.9639-9651.2003 - Point mutations in exon I of the herpes simplex virus putative terminase subunit, UL15, indicate that the most conserved residues are essential for cleavage and packaging.
Przech AJ, Yu D, Weller SK
J. Virol. (2003) 77(17):9613-21 (PMC187393) 10.1128/jvi.77.17.9613-9621.2003 - Phage evolution: new worlds of genomic diversity.
Papke RT, Doolittle WF
Curr. Biol. (2003) 13(15):R606-7 - Directional sensing requires G beta gamma-mediated PAK1 and PIX alpha-dependent activation of Cdc42.
Li Z, Hannigan M, Mo Z, Liu B, Lu W, Wu Y, Smrcka AV, Wu G, Li L, Liu M, Huang CK, Wu D
Cell (2003) 114(2):215-27 - Increasing health burden of human babesiosis in endemic sites.
Krause PJ, McKay K, Gadbaw J, Christianson D, Closter L, Lepore T, Telford SR, Sikand V, Ryan R, Persing D, Radolf JD, Spielman A
Am. J. Trop. Med. Hyg. (2003) 68(4):431-6 - Geographical isolation in hot spring cyanobacteria.
Papke RT, Ramsing NB, Bateson MM, Ward DM
Environ. Microbiol. (2003) 5(8):650-9 - Silica-induced caspase activation in mouse alveolar macrophages is dependent upon mitochondrial integrity and aspartic proteolysis.
Thibodeau M, Giardina C, Hubbard AK
Toxicol. Sci. (2003) 76(1):91-101 - Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity.
Nyholm SV, McFall-Ngai MJ
Appl. Environ. Microbiol. (2003) 69(7):3932-7 (PMC165210) 10.1128/aem.69.7.3932-3937.2003 - Shrinking the biologic world--nanobiotechnologies for toxicology.
Zieziulewicz TJ, Unfricht DW, Hadjout N, Lynes MA, Lawrence DA
Toxicol. Sci. (2003) 74(2):235-44 - Cytadherence-deficient mutants of Mycoplasma gallisepticum generated by transposon mutagenesis.
Mudahi-Orenstein S, Levisohn S, Geary SJ, Yogev D
Infect. Immun. (2003) 71(7):3812-20 (PMC162017) 10.1128/iai.71.7.3812-3820.2003 - Reducing colonization of Salmonella Enteritidis in chicken by targeting outer membrane proteins.
Khan MI, Fadl AA, Venkitanarayanan KS
J. Appl. Microbiol. (2003) 95(1):142-5 - The herpes simplex virus type 1 alkaline nuclease and single-stranded DNA binding protein mediate strand exchange in vitro.
Reuven NB, Staire AE, Myers RS, Weller SK
J. Virol. (2003) 77(13):7425-33 (PMC164775) 10.1128/jvi.77.13.7425-7433.2003 - Synthesis, structures, and conformational characteristics of calixarene monoanions and dianions.
Hanna TA, Liu L, Angeles-Boza AM, Kou X, Gutsche CD, Ejsmont K, Watson WH, Zakharov LN, Incarvito CD, Rheingold AL
J. Am. Chem. Soc. (2003) 125(20):6228-38 - Induced stabilization of IkappaBalpha can facilitate its re-synthesis and prevent sequential degradation.
Place RF, Haspeslagh D, Giardina C
J. Cell. Physiol. (2003) 195(3):470-8 - Interspecific hybridization induced amplification of Mdm2 on double minutes in a Mus hybrid.
Brown JD, Strbuncelj M, Giardina C, O'Neill RJ
Cytogenet. Genome Res. (2003) 98(2-3):184-8 - A plasmid-encoded nicotinamidase (PncA) is essential for infectivity of Borrelia burgdorferi in a mammalian host.
Purser JE, Lawrenz MB, Caimano MJ, Howell JK, Radolf JD, Norris SJ
Mol. Microbiol. (2003) 48(3):753-64 - Effects of overexpression of nutrient receptors on germination of spores of Bacillus subtilis.
Cabrera-Martinez RM, Tovar-Rojo F, Vepachedu VR, Setlow P
J. Bacteriol. (2003) 185(8):2457-64 (PMC152624) - Penton release from P22 heat-expanded capsids suggests importance of stabilizing penton-hexon interactions during capsid maturation.
Teschke CM, McGough A, Thuman-Commike PA
Biophys. J. (2003) 84(4):2585-92 (PMC1302824) - The Treponema pallidum tro operon encodes a multiple metal transporter, a zinc-dependent transcriptional repressor, and a semi-autonomously expressed phosphoglycerate mutase.
Hazlett KR, Rusnak F, Kehres DG, Bearden SW, La Vake CJ, La Vake ME, Maguire ME, Perry RD, Radolf JD
J. Biol. Chem. (2003) 278(23):20687-94 - Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures.
Visscher PT, Baumgartner LK, Buckley DH, Rogers DR, Hogan ME, Raleigh CD, Turk KA, Des Marais DJ
Environ. Microbiol. (2003) 5(4):296-308 - The ecology of individuals: incidence and implications of individual specialization.
Bolnick DI, Svanbäck R, Fordyce JA, Yang LH, Davis JM, Hulsey CD, Forister ML
Am. Nat. (2003) 161(1):1-28 - A soluble protein is immobile in dormant spores of Bacillus subtilis but is mobile in germinated spores: implications for spore dormancy.
Cowan AE, Koppel DE, Setlow B, Setlow P
Proc. Natl. Acad. Sci. U.S.A. (2003) 100(7):4209-14 (PMC404470) - Mechanisms of anemia in SHP-1 protein tyrosine phosphatase-deficient "viable motheaten" mice.
Lyons BL, Lynes MA, Burzenski L, Joliat MJ, Hadjout N, Shultz LD
Exp. Hematol. (2003) 31(3):234-43 - Identification of a new gene essential for germination of Bacillus subtilis spores with Ca2+-dipicolinate.
Ragkousi K, Eichenberger P, van Ooij C, Setlow P
J. Bacteriol. (2003) 185(7):2315-29 (PMC151495) - Behavior of enteroaggregative Escherichia coli in bottled spring and mineral water.
Vasudevan P, Annamalai T, Sartori L, Hoagland T, Venkitanarayanan K
J. Food Prot. (2003) 66(3):497-500 - Recruitment of polymerase to herpes simplex virus type 1 replication foci in cells expressing mutant primase (UL52) proteins.
Carrington-Lawrence SD, Weller SK
J. Virol. (2003) 77(7):4237-47 (PMC150627) 10.1128/jvi.77.7.4237-4247.2003 - Tails of two Tirs: actin pedestal formation by enteropathogenic E. coli and enterohemorrhagic E. coli O157:H7.
Campellone KG, Leong JM
Curr. Opin. Microbiol. (2003) 6(1):82-90 - Adaptation of the Lyme disease spirochaete to the mammalian host environment results in enhanced glycosaminoglycan and host cell binding.
Parveen N, Caimano M, Radolf JD, Leong JM
Mol. Microbiol. (2003) 47(5):1433-44 - Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.
Raymond J, Zhaxybayeva O, Gogarten JP, Blankenship RE
Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2003) 358(1429):223-30 (PMC1693105) - UV photochemistry of DNA in vitro and in Bacillus subtilis spores at earth-ambient and low atmospheric pressure: implications for spore survival on other planets or moons in the solar system.
Nicholson WL, Setlow B, Setlow P
Astrobiology (2003) 2(4):417-25 - Inhibition of transcription in vitro by anticancer active dirhodium(II) complexes.
Sorasaenee K, Fu PK, Angeles-Boza AM, Dunbar KR, Turro C
Inorg Chem (2003) 42(4):1267-71 - Inverse association between phospholipase A2 and COX-2 expression during mouse colon tumorigenesis.
Dong M, Guda K, Nambiar PR, Rezaie A, Belinsky GS, Lambeau G, Giardina C, Rosenberg DW
Carcinogenesis (2003) 24(2):307-15 - Small, acid-soluble proteins as biomarkers in mass spectrometry analysis of Bacillus spores.
Hathout Y, Setlow B, Cabrera-Martinez RM, Fenselau C, Setlow P
Appl. Environ. Microbiol. (2003) 69(2):1100-7 (PMC143666) - Molecular systematics and adaptive radiation of Hawaii's endemic Damselfly genus Megalagrion (Odonata: Coenagrionidae).
Jordan S, Simon C, Polhemus D
Syst. Biol. (2003) 52(1):89-109 10.1080/10635150390132803 - Helicase motif Ia is involved in single-strand DNA-binding and helicase activities of the herpes simplex virus type 1 origin-binding protein, UL9.
Marintcheva B, Weller SK
J. Virol. (2003) 77(4):2477-88 (PMC141079) 10.1128/jvi.77.4.2477-2488.2003 - Gene transfer: gene swapping craze reaches eukaryotes.
Gogarten JP
Curr. Biol. (2003) 13(2):R53-4 - Characterization of the stringent response and rel(Bbu) expression in Borrelia burgdorferi.
Bugrysheva J, Dobrikova EY, Sartakova ML, Caimano MJ, Daniels TJ, Radolf JD, Godfrey HP, Cabello FC
J. Bacteriol. (2003) 185(3):957-65 (PMC142832) - Mitogen-activated protein kinase in Pfiesteria piscicida and its growth rate-related expression.
Lin S, Zhang H
Appl. Environ. Microbiol. (2003) 69(1):343-9 (PMC152464) 10.1128/aem.69.1.343-349.2003 2002
- Phenotypic and genotypic characterization of bovine mastitis isolates of Staphylococcus aureus for biofilm formation.
Vasudevan P, Nair MK, Annamalai T, Venkitanarayanan KS
Vet. Microbiol. (2002) 92(1-2):179-85 - Synthesis of functionalized pyrans by domino metathesis reaction of oxabicyclo derivatives: dramatic effect of remote substituents on reactivity and selectivity.
Usher LC, Estrella-Jimenez M, Ghiviriga I, Wright DL
Angew. Chem. Int. Ed. Engl. (2002) 41(23):4560-2 10.1002/1521-3773(20021202)41:23<4560::AID-ANIE - Analysis of infection thread development using Gfp- and DsRed-expressing Sinorhizobium meliloti.
Gage DJ
J. Bacteriol. (2002) 184(24):7042-6 (PMC135452) - Whole-genome analysis of photosynthetic prokaryotes.
Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE
Science (2002) 298(5598):1616-20 - Prokaryotic evolution in light of gene transfer.
Gogarten JP, Doolittle WF, Lawrence JG
Mol. Biol. Evol. (2002) 19(12):2226-38 - GapA and CrmA coexpression is essential for Mycoplasma gallisepticum cytadherence and virulence.
Papazisi L, Frasca S, Gladd M, Liao X, Yogev D, Geary SJ
Infect. Immun. (2002) 70(12):6839-45 (PMC133084) 10.1128/iai.70.12.6839-6845.2002 - Periplasmic maltose- and glucose-binding protein activities in cell-free extracts of Thermotoga maritima.
Nanavati D, Noll KM, Romano AH
Microbiology (Reading, Engl.) (2002) 148(Pt 11):3531-7 - A modified live Mycoplasma gallisepticum vaccine to protect chickens from respiratory disease.
Papazisi L, Silbart LK, Frasca S, Rood D, Liao X, Gladd M, Javed MA, Geary SJ
Vaccine (2002) 20(31-32):3709-19 - Treatment of parking lot stormwater using a StormTreat system.
Sonstrom RS, Clausen JC, Askew DR
Environ. Sci. Technol. (2002) 36(20):4441-6 - Growing old with nuclear factor-kappaB.
Giardina C, Hubbard AK
Cell Stress Chaperones (2002) 7(2):207-12 (PMC514819) - Two-step electrochemical annulation for the assembly of polycyclic systems.
Whitehead CR, Sessions EH, Ghiviriga I, Wright DL
Org. Lett. (2002) 4(21):3763-5 - Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci.
Snoeyenbos-West OL, Salcedo T, McManus GB, Katz LA
Int. J. Syst. Evol. Microbiol. (2002) 52(Pt 5):1901-13 - The immune response to infection with Treponema pallidum, the stealth pathogen.
Salazar JC, Hazlett KR, Radolf JD
Microbes Infect. (2002) 4(11):1133-40 - Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket.
Liu H, Radhakrishnan P, Magoun L, Prabu M, Campellone KG, Savage P, He F, Schiffer CA, Leong JM
Mol. Microbiol. (2002) 45(6):1557-73 - Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ.
Nyholm SV, Deplancke B, Gaskins HR, Apicella MA, McFall-Ngai MJ
Appl. Environ. Microbiol. (2002) 68(10):5113-22 (PMC126412) 10.1128/aem.68.10.5113-5122.2002 - PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA.
Rigden DJ, Setlow P, Setlow B, Bagyan I, Stein RA, Jedrzejas MJ
Protein Sci. (2002) 11(10):2370-81 (PMC2373696) - Protection of DNA by alpha/beta-type small, acid-soluble proteins from Bacillus subtilis spores against cytosine deamination.
Sohail A, Hayes CS, Divvela P, Setlow P, Bhagwat AS
Biochemistry (2002) 41(38):11325-30 - Establishment and characterization of a new osteogenic cell line (MOS-J) from a spontaneous C57BL/6J mouse osteosarcoma.
Joliat MJ, Umeda S, Lyons BL, Lynes MA, Shultz LD
In Vivo (2002) 16(4):223-8 - Control of inducer accumulation plays a key role in succinate-mediated catabolite repression in Sinorhizobium meliloti.
Bringhurst RM, Gage DJ
J. Bacteriol. (2002) 184(19):5385-92 (PMC135350) - PCR-based identification of bacteria associated with endodontic infections.
Fouad AF, Barry J, Caimano M, Clawson M, Zhu Q, Carver R, Hazlett K, Radolf JD
J. Clin. Microbiol. (2002) 40(9):3223-31 (PMC130810) - Cellular immunity, but not gamma interferon, is essential for resolution of Babesia microti infection in BALB/c mice.
Clawson ML, Paciorkowski N, Rajan TV, La Vake C, Pope C, La Vake M, Wikel SK, Krause PJ, Radolf JD
Infect. Immun. (2002) 70(9):5304-6 (PMC128260) - Metallothionein suppresses collagen-induced arthritis via induction of TGF-beta and down-regulation of proinflammatory mediators.
Youn J, Hwang SH, Ryoo ZY, Lynes MA, Paik DJ, Chung HS, Kim HY
Clin. Exp. Immunol. (2002) 129(2):232-9 (PMC1906452) - Inteins: structure, function, and evolution.
Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E
Annu. Rev. Microbiol. (2002) 56:263-87 - The product of the UL12.5 gene of herpes simplex virus type 1 is not essential for lytic viral growth and is not specifically associated with capsids.
Martinez R, Goldstein JN, Weller SK
Virology (2002) 298(2):248-57 - Role of the alternating reading frame (P19)-p53 pathway in an in vivo murine colon tumor model.
Nambiar PR, Giardina C, Guda K, Aizu W, Raja R, Rosenberg DW
Cancer Res. (2002) 62(13):3667-74 - Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates.
Lin S, Zhang H, Spencer DF, Norman JE, Gray MW
J. Mol. Biol. (2002) 320(4):727-39 - Contribution of neelaredoxin to oxygen tolerance by Treponema pallidum.
Hazlett KR, Cox DL, Sikkink RA, Auch'ere F, Rusnak F, Radolf JD
Meth. Enzymol. (2002) 353:140-56 - Base-change mutations induced by various treatments of Bacillus subtilis spores with and without DNA protective small, acid-soluble spore proteins.
del Carmen Huesca Espitia L, Caley C, Bagyan I, Setlow P
Mutat. Res. (2002) 503(1-2):77-84 - Silver-promoted reactions of bicyclo[3.2.1]octadiene derivatives.
Orugunty RS, Wright DL, Battiste MA, Abboud KA
Org. Lett. (2002) 4(12):1997-2000 - Mechanisms of induction of germination of Bacillus subtilis spores by high pressure.
Paidhungat M, Setlow B, Daniels WB, Hoover D, Papafragkou E, Setlow P
Appl. Environ. Microbiol. (2002) 68(6):3172-5 (PMC123951) - Multi site polyadenylation and transcriptional response to stress of a vacuolar type H+-ATPase subunit A gene in Arabidopsis thaliana.
Magnotta SM, Gogarten JP
BMC Plant Biol. (2002) 2:3 (PMC103671) - Identification of loci critical for replication and compatibility of a Borrelia burgdorferi cp32 plasmid and use of a cp32-based shuttle vector for the expression of fluorescent reporters in the lyme disease spirochaete.
Eggers CH, Caimano MJ, Clawson ML, Miller WG, Samuels DS, Radolf JD
Mol. Microbiol. (2002) 43(2):281-95 - Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera.
Buckley TR, Arensburger P, Simon C, Chambers GK
Syst. Biol. (2002) 51(1):4-18 10.1080/106351502753475844 - Disease-specific diagnosis of coinfecting tickborne zoonoses: babesiosis, human granulocytic ehrlichiosis, and Lyme disease.
Krause PJ, McKay K, Thompson CA, Sikand VK, Lentz R, Lepore T, Closter L, Christianson D, Telford SR, Persing D, Radolf JD, Spielman A
Clin. Infect. Dis. (2002) 34(9):1184-91 - Using functional morphology to examine the ecology and evolution of specialization.
Ferry-Graham LA, Bolnick DI, Wainwright PC
Integr. Comp. Biol. (2002) 42(2):265-77 - Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.
Zhaxybayeva O, Gogarten JP
BMC Genomics (2002) 3:4 (PMC100357) - A tyrosine-phosphorylated 12-amino-acid sequence of enteropathogenic Escherichia coli Tir binds the host adaptor protein Nck and is required for Nck localization to actin pedestals.
Campellone KG, Giese A, Tipper DJ, Leong JM
Mol. Microbiol. (2002) 43(5):1227-41 - The crystal structure of Zn(II)-free Treponema pallidum TroA, a periplasmic metal-binding protein, reveals a closed conformation.
Lee YH, Dorwart MR, Hazlett KR, Deka RK, Norgard MV, Radolf JD, Hasemann CA
J. Bacteriol. (2002) 184(8):2300-4 (PMC134957) - Absence of CD5 dramatically reduces progression of pulmonary inflammatory lesions in SHP-1 protein-tyrosine phosphatase-deficient 'viable motheaten' mice.
Joliat MJ, Lang PA, Lyons BL, Burzenski L, Lynes MA, Yi T, Sundberg JP, Shultz LD
J. Autoimmun. (2002) 18(2):105-17 - Clonal polymorphism of Borrelia burgdorferi strain B31 MI: implications for mutagenesis in an infectious strain background.
Elias AF, Stewart PE, Grimm D, Caimano MJ, Eggers CH, Tilly K, Bono JL, Akins DR, Radolf JD, Schwan TG, Rosa P
Infect. Immun. (2002) 70(4):2139-50 (PMC127854) - Identification of Salmonella enteritidis outer membrane proteins expressed during attachment to human intestinal epithelial cells.
Fadl AA, Venkitanarayanan KS, Khan MI
J. Appl. Microbiol. (2002) 92(1):180-6 - Fusobacterium nucleatum supports the growth of Porphyromonas gingivalis in oxygenated and carbon-dioxide-depleted environments.
Diaz PI, Zilm PS, Rogers AH
Microbiology (Reading, Engl.) (2002) 148(Pt 2):467-72 - Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity.
Rigden DJ, Mello LV, Setlow P, Jedrzejas MJ
J. Mol. Biol. (2002) 315(5):1129-43 - Detection and quantification of Pfiesteria piscicida by using the mitochondrial cytochrome b gene.
Zhang H, Lin S
Appl. Environ. Microbiol. (2002) 68(2):989-94 (PMC126730) 10.1128/aem.68.2.989-994.2002 - Consumer acceptance of raw apples treated with an antibacterial solution designed for home use.
McWatters KH, Doyle MP, Walker SL, Rimal AP, Venkitanarayanan K
J. Food Prot. (2002) 65(1):106-10 - Inactivation of Escherichia coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes on apples, oranges, and tomatoes by lactic acid with hydrogen peroxide.
Venkitanarayanan KS, Lin CM, Bailey H, Doyle MP
J. Food Prot. (2002) 65(1):100-5 - Localization of the cortex lytic enzyme CwlJ in spores of Bacillus subtilis.
Bagyan I, Setlow P
J. Bacteriol. (2002) 184(4):1219-24 (PMC134822) - Killing of spores of Bacillus subtilis by peroxynitrite appears to be caused by membrane damage.
Genest PC, Setlow B, Melly E, Setlow P
Microbiology (Reading, Engl.) (2002) 148(Pt 1):307-14 - Inactivation of Escherichia coli O157: H7 and Listeria monocytogenes by PR-26, a synthetic antibacterial peptide.
Annamalai T, Venkitanarayanan KS, Hoagland TA, Khan MI
J. Food Prot. (2002) 64(12):1929-34 2001
- Long-term sterilizing immunity to rinderpest in cattle vaccinated with a recombinant vaccinia virus expressing high levels of the fusion and hemagglutinin glycoproteins.
Verardi PH, Aziz FH, Ahmad S, Jones LA, Beyene B, Ngotho RN, Wamwayi HM, Yesus MG, Egziabher BG, Yilma TD
J. Virol. (2001) 76(2):484-91 (PMC136817) - The products of the spoVA operon are involved in dipicolinic acid uptake into developing spores of Bacillus subtilis.
Tovar-Rojo F, Chander M, Setlow B, Setlow P
J. Bacteriol. (2001) 184(2):584-7 (PMC139579) - Automated real-time measurement of chemotactic cell motility.
Hadjout N, Laevsky G, Knecht DA, Lynes MA
BioTechniques (2001) 31(5):1130-8 - The intein of the Thermoplasma A-ATPase A subunit: structure, evolution and expression in E. coli.
Senejani AG, Hilario E, Gogarten JP
BMC Biochem. (2001) 2:13 (PMC60005) - Effects of hemizygous CD45 expression in the autoimmune Fasl(gld/gld) syndrome.
Brooks WP, Lynes MA
Cell. Immunol. (2001) 212(1):24-34 - Transgenics in crops.
Li Y, Wu YH, McAvoy R, Duan H, Li Y
Biotechnol Annu Rev (2001) 7:239-60 - A tale of two HSV-1 helicases: roles of phage and animal virus helicases in DNA replication and recombination.
Marintcheva B, Weller SK
Prog. Nucleic Acid Res. Mol. Biol. (2001) 70:77-118 - The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid.
Newcomb WW, Juhas RM, Thomsen DR, Homa FL, Burch AD, Weller SK, Brown JC
J. Virol. (2001) 75(22):10923-32 (PMC114672) 10.1128/JVI.75.22.10923-10932.2001 - Butyrate suppression of colonocyte NF-kappa B activation and cellular proteasome activity.
Yin L, Laevsky G, Giardina C
J. Biol. Chem. (2001) 276(48):44641-6 - Cellular and molecular mechanisms regulating silica-induced adhesion molecule expression in mice.
Hubbard AK, Thibodeau M, Giardina C
J. Environ. Pathol. Toxicol. Oncol. (2001) 20 Suppl 1:45-51 - Aberrant transforming growth factor-beta signaling in azoxymethane-induced mouse colon tumors.
Guda K, Giardina C, Nambiar P, Cui H, Rosenberg DW
Mol. Carcinog. (2001) 31(4):204-13 - In vivo manipulation of endogenous metallothionein with a monoclonal antibody enhances a T-dependent humoral immune response.
Canpolat E, Lynes MA
Toxicol. Sci. (2001) 62(1):61-70 - Feeding activity, absorption efficiency and suspension feeding processes in the ascidian, Halocynthia pyriformis (Stolidobranchia: Ascidiacea): responses to variations in diet quantity and quality.
Armsworthy SL, MacDonald BA, Ward JE
J. Exp. Mar. Biol. Ecol. (2001) 260(1):41-69 - Cytokine-induced stabilization of newly synthesized I(kappa)B-alpha.
Place RF, Haspeslagh D, Hubbard AK, Giardina C
Biochem. Biophys. Res. Commun. (2001) 283(4):813-20 - Alleviation of a defect in protein folding by increasing the rate of subunit assembly.
Aramli LA, Teschke CM
J. Biol. Chem. (2001) 276(27):25372-7 - Liposome-mediated DNA uptake and transient expression in Thermotoga.
Yu JS, Vargas M, Mityas C, Noll KM
Extremophiles (2001) 5(1):53-60 - The UL5 and UL52 subunits of the herpes simplex virus type 1 helicase-primase subcomplex exhibit a complex interdependence for DNA binding.
Biswas N, Weller SK
J. Biol. Chem. (2001) 276(20):17610-9 10.1074/jbc.M010107200 - Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor.
Bringhurst RM, Cardon ZG, Gage DJ
Proc. Natl. Acad. Sci. U.S.A. (2001) 98(8):4540-5 (PMC31870) - Phosphoglycerate kinase-triose-phosphate isomerase complex from Thermotoga neapolitana.
Yu JS, Noll KM
Meth. Enzymol. (2001) 331:78-89 - Differential gene expression in Thermotoga neapolitana in response to growth substrate.
Nguyen TN, Borges KM, Romano AH, Noll KM
FEMS Microbiol. Lett. (2001) 195(1):79-83 - DMSP-consuming bacteria associated with the calanoid copepod Acartia tonsa (Dana).
Tang KW, Visscher PT, Dam HG
J. Exp. Mar. Biol. Ecol. (2001) 256(2):185-198 - Interactions of herpes simplex virus type 1 with ND10 and recruitment of PML to replication compartments.
Burkham J, Coen DM, Hwang CB, Weller SK
J. Virol. (2001) 75(5):2353-67 (PMC114819) 10.1128/JVI.75.5.2353-2367.2001 - Herpes simplex virus DNA cleavage and packaging proteins associate with the procapsid prior to its maturation.
Sheaffer AK, Newcomb WW, Gao M, Yu D, Weller SK, Brown JC, Tenney DJ
J. Virol. (2001) 75(2):687-98 (PMC113965) 10.1128/JVI.75.2.687-698.2001 2000
- Vaccinia virus vectors with an inactivated gamma interferon receptor homolog gene (B8R) are attenuated In vivo without a concomitant reduction in immunogenicity.
Verardi PH, Jones LA, Aziz FH, Ahmad S, Yilma TD
J. Virol. (2000) 75(1):11-8 (PMC113892) - Analysis of cytadherence-deficient, GapA-negative Mycoplasma gallisepticum strain R.
Papazisi L, Troy KE, Gorton TS, Liao X, Geary SJ
Infect. Immun. (2000) 68(12):6643-9 (PMC97761) 10.1128/iai.68.12.6643-6649.2000 - Residues within the conserved helicase motifs of UL9, the origin-binding protein of herpes simplex virus-1, are essential for helicase activity but not for dimerization or origin binding activity.
Marintcheva B, Weller SK
J. Biol. Chem. (2000) 276(9):6605-15 10.1074/jbc.M007743200 - Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment.
Nyholm SV, Stabb EV, Ruby EG, McFall-Ngai MJ
Proc. Natl. Acad. Sci. U.S.A. (2000) 97(18):10231-5 (PMC27829) 10.1073/pnas.97.18.10231 - Evidence for controlled incorporation of herpes simplex virus type 1 UL26 protease into capsids.
Sheaffer AK, Newcomb WW, Brown JC, Gao M, Weller SK, Tenney DJ
J. Virol. (2000) 74(15):6838-48 (PMC112201) 10.1128/jvi.74.15.6838-6848.2000 - PCR-mediated gene replacement in Escherichia coli.
Murphy KC, Campellone KG, Poteete AR
Gene (2000) 246(1-2):321-30 - Isolation of herpes simplex virus procapsids from cells infected with a protease-deficient mutant virus.
Newcomb WW, Trus BL, Cheng N, Steven AC, Sheaffer AK, Tenney DJ, Weller SK, Brown JC
J. Virol. (2000) 74(4):1663-73 (PMC111641) 10.1128/jvi.74.4.1663-1673.2000 1999
- CONVERGENT EVOLUTION OF COURTSHIP SONGS AMONG CRYPTIC SPECIES OF THE CARNEA GROUP OF GREEN LACEWINGS (NEUROPTERA: CHRYSOPIDAE: CHRYSOPERLA).
Henry CS, Wells MLM, Simon CM
Evolution (1999) 53(4):1165-1179 10.1111/j.1558-5646.1999.tb04530.x - A mutation in the C-terminal putative Zn2+ finger motif of UL52 severely affects the biochemical activities of the HSV-1 helicase-primase subcomplex.
Biswas N, Weller SK
J. Biol. Chem. (1999) 274(12):8068-76 10.1074/jbc.274.12.8068 - Substrate specificity and stereoselectivity of rat brain microsomal anandamide amidohydrolase.
Lang W, Qin C, Lin S, Khanolkar AD, Goutopoulos A, Fan P, Abouzid K, Meng Z, Biegel D, Makriyannis A
J. Med. Chem. (1999) 42(5):896-902 10.1021/jm980461j - Structure-activity relationships of pyrazole derivatives as cannabinoid receptor antagonists.
Lan R, Liu Q, Fan P, Lin S, Fernando SR, McCallion D, Pertwee R, Makriyannis A
J. Med. Chem. (1999) 42(4):769-76 10.1021/jm980363y 0
(0) :