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2014 Publications

  1. Bae J, Ricciardi CJ, Esposito D, Komarnytsky S, Hu P, Curry BJ, Brown PL, Gao ZG, Biggerstaff JP, Chen JG, Zhao L. 2014. Activation of pattern recognition receptors in brown adipocytes induces inflammation and suppresses uncoupling protein 1 expression and mitochondrial respiration. American Journal of Physiology-Cell Physiology 306:C918-C930.
  2. Balazs A, Krifaton C, Risa A, Cserhati M, Kukolya J, Toth A, Hahn J, Szoboszlay S, Eldridge M, Wang J, Kriszt B. 2014. Biodegradation of 5 alpha-dihydrotestosterone to non-androgenic products. International Biodeterioration & Biodegradation 93:162-167.
  3. Boyle D, Fox JE, Akerman JM, Sloman KA, Henry TB, Handy RD. 2014. Minimal effects of waterborne exposure to single-walled carbon nanotubes on behaviour and physiology of juvenile rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology 146:154-164.
  4. Campbell AG, Schwientek P, Vishnivetskaya T, Woyke T, Levy S, Beall CJ, Griffen A, Leys E, Podar M. 2014. Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environmental Microbiology 16:2635-2643. doi:10.1111/1462-2920.12461.
  5. Capiro NL, Wang YG, Hatt JK, Lebron CA, Pennell KD, Loffler FE. 2014. Distribution of organohalide-respiring bacteria between solid and aqueous phases. Environmental Science & Technology 48:10878-10887.
  6. Chauhan A, Layton AC, Vishnivetskaya TA, Williams D, Pfiffner SM, Rekepalli B, Stackhouse B, Lau MCY, Phelps TJ, Mykytczuk N, Ronholm J, Whyte L, Onstott TC, Sayler GS. 2014. Metagenomes from thawing low-soil-organic-carbon mineral cryosols and permafrost of the Canadian high Arctic. Genome Announcements 2:doi 10.1128/genomeA.01217-14.
  7. Chauhan A, Smartt A, Wang J, Utturkar S, Frank A, Bi M, Liu J, Williams D, Xu T, Eldridge M, Arreaza A, Rogers A, Gonzalez HC, Layton AC, Baxter HL, Mazarei M, DeBruyn JM, Stewart CN, Jr., Brown SD, Hauser LJ, Sayler GS. 2014. Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass. Genome Announcements 2:doi 10.1128/genomeA.00777-14.
  8. Close D, Xu T, Ripp S, Sayler G. 2014. Real-time bioluminescent tracking of cellular population dynamics, p. 107-116. In Badr CE (ed.), Methods in Molecular Biology, Bioluminescent Imaging, vol. 1098. Humana Press, New York, NY.
  9. Connolly MH, Dutkosky RM, Heah TP, Sayler GS, Henry TB. 2014. Temporal dynamics of oocyte growth and vitellogenin gene expression in zebrafish (Danio rerio). Zebrafish 11:107-114.
  10. Cretnik S, Bernstein A, Shouakar-Stash O, Loffler F, Elsner M. 2014. Chlorine isotope effects from isotope ratio mass spectrometry suggest intramolecular C-Cl bond competition in trichloroethene (TCE) reductive dehalogenation. Molecules 19:6450-6473.
  11. Harris J, Eldridge M, Sayler G, Layton A, Baudry J. 2014. A computational approach predicting CYP450 metabolism and estrogenic activity of an endocrine disrupting compound (PCB-30). Environmental Toxicology & Chemistry 33:1615-1623.
  12. Harris AP, Techtmann SM, Stelling SC, Utturkar SM, Alshibli NK, Brown SD, Hazen TC. 2014. Draft genome sequence of Pseudoalteromonas sp. strain ND6B, an oil-degrading isolate from eastern Mediterranean sea water collected at a depth of 1,210 meters. Genome Announcements 2:e01212-14.
  13. Huang E-C, Zhao Y, Chen G, Baek S, McEntee M, Minkin S, Biggerstaff J, Whelan J. 2014. Zyflamend, a polyherbal mixture, down regulates class I and class II histone deacetylases and increases p21 levels in castrate-resistant prostate cancer cells. BMC Complementary and Alternative Medicine 14:68.
  14. Hurt RA, Robeson MS, Shakya M, Moberly JG, Vishnivetskaya T, Gu BH, Elias DA. 2014. Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments. PLoS ONE 9:e102826.
  15. Ichihashia O, Vishnivetskaya T, Borole AP. 2014. High performance bioanode development for fermentable substrates via controlled electroactive biofilm growth. ChemElectroChem 1:1940-1947.
  16. Im J, Prevatte CW, Lee HG, Campagna SR, Loeffler FE. 2014. 4-Methylphenol produced in freshwater sediment microcosms is not a bisphenol A metabolite. Chemosphere 117:521-526.
  17. Im J, Walshe-Langford GE, Moon J-W, Loeffler FE. 2014. Environmental fate of the next generation refrigerant 2,3,3,3-tetrafluoropropene (HFO-1234yf). Environmental Science & Technology 48:13181-13187.
  18. Jang M-H, Kim W-K, Lee S-K, Henry TB, Park J-W. 2014. Uptake, tissue distribution, and depuration of total silver in Common Carp (Cyprinus carpio) after aqueous exposure to silver nanoparticles. Environmental Science & Technology 48:11568-11574.
  19. Justicia-Leon SD, Higgins S, Mack EE, Griffiths DR, Tang SQ, Edwards EA, Loffler FE. 2014. Bioaugmentation with distinct Dehalobacter strains achieves chloroform detoxification in microcosms. Environmental Science & Technology 48:1851-1858.
  20. Kelemen RK, He GF, Woo HL, Lane T, Rempe C, Wang J, Cockburn IA, Amino R, Ganusov VV, Berry MW. 2014. Classification of T cell movement tracks allows for prediction of cell function. International Journal of Computational Biology and Drug Design 7:113-129.
  21. Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A. 2014. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio 5:doi 10.1128/mBio.01041-14.
  22. Lambert D, Clark C, Busko N, Walker FR, Layton A, Hawkins S. 2014. A study of cattle producer preferences for best management practices in an East Tennessee watershed. Journal of Soil and Water Conservation 69:41-53.
  23. Lamendella R, Strutt S, Borglin S, Chakraborty R, Tas N, Mason OU, Hultman J, Prestat E, Hazen TC, Jansson JK. 2014. Assessments of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Frontiers in Microbiology 5:doi 10.3389/fmicb.2014.00130.
  24. Lancaster WA, Menon AL, Scott I, Poole FL, Vaccaro BJ, Thorgersen MP, Geller J, Hazen TC, Hurt RA, Jr., Brown SD, Elias DA, Adams MWW. 2014. Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization. Metallomics 6:1004-1013.
  25. Layton AC, Chauhan A, Williams DE, Mailloux B, Knappett PSK, Ferguson AS, McKay LD, Alam MJ, Matin Ahmed K, van Geen A, Sayler GS. 2014. Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from Bangladesh. Genome Announcements 2:doi 10.1128/genomeA.01170-14.
  26. Lee S, Geller JT, Torok T, Wu CH, Singer M, Reid FC, Tarjan DR, Hazen TC, Arkin AP, Hillson NJ. 2014. Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. PLoS ONE 9:doi 10.1371/journal.pone.0105689.
  27. Linville JL, Rodriguez M, Brown SD, Mielenz JR, Cox CD. 2014. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain. BMC Microbiology 14:doi 10.1186/s12866-014-0215-5.
  28. Martinez RJ, Wu CH, Beazley MJ, Andersen GL, Conrad ME, Hazen TC, Taillefert M, Sobecky PA. 2014. Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments. PLoS ONE 9. doi: 10.1371/journal.pone.0100383.
  29. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Balum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. 2014. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME Journal 8:1464-1475.
  30. McNeil PL, Boyle D, Henry TB, Handy RD, Sloman KA. 2014. Effects of metal nanoparticles on the lateral line system and behaviour in early life stages of zebrafish (Danio rerio). Aquatic Toxicology 152:318-323.
  31. Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y, Saito Y, Tame A, Uematsu K, Loeffler FE, Takai K, Imachi H. 2014. Sphaerochaeta multiformis sp nov.; an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. International Journal of Systematic and Evolutionary Microbiology 64:4147-4154.
  32. Padilla-Crespo E, Yan J, Swift C, Wagner DD, Chourey K, Hettich RL, Ritalahti KM, Loeffler FE. 2014. Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring Chloroflexi. Applied and Environmental Microbiology 80:808-818.
  33. Pedersen K, Bengtsson A, Edlund J, Rabe L, Hazen T, Chakraborty R, Goodwin L, Shapiro N. 2014. Complete genome sequence of the subsurface, mesophilic sulfate-reducing bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announcements 2:doi 10.1128/genomeA.00509-14.
  34. Petersen EJ, Henry TB, Zhao J, MacCuspie RI, Kirschling TL, Dobrovolskaia MA, Hackley V, Xing B, White JC. 2014. Identification and avoidance of potential artifacts and misinterpretations in nanomaterial ecotoxicity measurements. Environmental Science & Technology 48:4226-4246.
  35. Piceno YM, Reid FC, Tom LM, Conrad ME, Bill M, Hubbard CG, Fouke BW, Graff CJ, Han J, Stringfellow WT, Hanlon JS, Hu P, Hazen TC, Andersen GL. 2014. Temperature and injection water source influence microbial community structure in four Alaskan North Slope hydrocarbon reservoirs. Frontiers in Microbiology 5:doi 10.3389/fmicb.2014.00409.
  36. Sha K, Choi S-H, Im J, Lee GG, Loeffler F, Park JH. 2014. Regulation of ethanol-related behavior and ethanol metabolism by the corazonin neurons and corazonin receptor in Drosophila melanogaster. PLoS ONE 9:doi 10.1371/journal.pone.0087062.
  37. Shi W, Menn FM, Xu T, Zhuang ZT, Beasley C, Ripp S, Zhuang J, Layton AC, Sayler GS. 2014. C60 reduces the bioavailability of mercury in aqueous solutions. Chemosphere 95:324-328.
  38. Stelling SC, Techtmann SM, Utturkar SM, Alshibli NK, Brown SD, Hazen TC. 2014. Draft genome sequence of Thalassotalea sp. strain ND16A isolated from Eastern Mediterranean sea water collected from a depth of 1,055 meters. Genome Announcements 2:doi 10.1128/genomeA.01231-14.
  39. Trexler R, Solomon C, Brislawn CJ, Wright JR, Rosenberger A, McClure EE, Grube AM, Peterson MP, Keddache M, Mason OU, Hazen TC, Grant CJ, Lamendella R. 2014. Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania. Frontiers in Microbiology 5:doi 10.3389/fmicb.2014.00522.
  40. Twining BS, Nodder SD, King AL, Hutchins DA, LeCleir GR, DeBruyn JM, Maas EW, Vogt S, Wilhelm SW, Boyd PW. 2014. Differential remineralization of major and trace elements in sinking diatoms. Limnology and Oceanography 59:689-704.
  41. Vishnivetskaya T, Chauhan A, Layton A, Pfiffner S, Huntemann M, Copeland A, Chen A, Kyrpides NC, Markowitz V, Palaniappan K, Ivanova NN, Mikhailova N, Ovchinnikova G, Andersen EW, Pati S, Stamatis D, Reddy TBK, Shapiro N, Nordberg HP, Cantor MN, Hua XS, Woyke T. 2014. Draft genome sequences of ten strains of the genus Exiguobacterium. Genome Announcements 2:e01058-01014.
  42. Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE, Pfiffner SM, Biggerstaff JP, Stackhouse BT, Phelps TJ, Whyte L, Sayler GS, Onstott TC. 2014. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiology Ecology 87:217-230.
  43. Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, DeSantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS. 2014. Microbial biogeography across a full-scale wastewater treatment plant transect: Evidence for immigration between coupled processes. Applied Microbiology and Biotechnology 98:4723-4736.
  44. Welsh A, Chee-Sanford JC, Connor LM, Loffler FE, Sanford RA. 2014. Refined NrfA phylogeny improves PCR-based nrfA gene detection. Applied and Environmental Microbiology 80:2110-2119.
  45. Wilkins MJ, Daly R, Mouser PJ, Trexler R, Wrighton KC, Sharma S, Cole DR, Biddle JF, Denis E, Fredrickson JK, Kieft TL, Onstott TC, Petersen L, Pfiffner SM, Phelps TJ, Schrenk MO. 2014. Trends and future challenges in sampling the deep terrestrial biosphere. Frontiers in Microbiology 5:doi 10.3389/fmicb.2014.00481.
  46. Woo HL, Ballor NR, Hazen TC, Fortney JL, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Jansson J, Kimbrel J, DeAngelis KM. 2014. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Standards in Genomic Sciences 9:19.
  47. Woo HL, Hazen TC, Simmons BA, DeAngelis KM. 2014. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Systematic and Applied Microbiology 37:60-67.
  48. Woo HL, Utturkar S, Klingeman D, Simmons BA, DeAngelis KM, Brown SD, Hazen TC. 2014. Draft genome sequence of the lignin-degrading Burkholderia sp. strain LIG30, isolated from wet tropical forest soil. Genome Announcements 2:e00637-14.
  49. Xu T, Close D, Smartt A, Ripp S, Sayler G. 2014. Detection of organic compounds with microbial bioluminescent bioassays, p. 111-151. In Thouand G, Marks R (ed.), Bioluminescence: Fundamentals and Applications in Biotechnology. Springer, New York, NY.
  50. Xu T, Perry N, Chauhan A, Sayler G, Ripp S. 2014. Microbial indicators for monitoring pollution and bioremediation, p. 115-132. In Das S (ed.), Microbial Biodegradation and Bioremediation. Elsevier, New York, NY.
  51. Xu T, Ripp S, Sayler G, Close D. 2014. Expression of a humanized viral 2A-mediated lux operon efficiently generates autonomous bioluminescence in human cells. PLoS ONE 9:e96347.
  52. Zhou JZ, Deng Y, Zhang P, Xue K, Liang YT, Van Nostrand JD, Yang YF, He ZL, Wu LY, Stahl DA, Hazen TC, Tiedje JM, Arkin AP. 2014. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences U. S. A. 111:E836-E845.