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2013 Publications

  1. Al-Bairuty GA, Shaw BJ, Handy RD, Henry TB. 2013. Histopathological effects of waterborne copper nanoparticles and copper sulphate on the organs of rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology 126:104-115.
  2. Boyle D, Al-Bairuty GA, Henry TB, Handy RD. 2013. Critical comparison of intravenous injection of TiO2 nanoparticles with waterborne and dietary exposures concludes minimal environmentally-relevant toxicity in juvenile rainbow trout Oncorhynchus mykiss. Environmental Pollution 182:70-79.
  3. Boyle D, Al-Bairuty GA, Ramsden CS, Sloman KA, Henry TB, Handy RD. 2013. Subtle alterations in swimming speed distributions of rainbow trout exposed to titanium dioxide nanoparticles are associated with gill rather than brain injury. Aquatic Toxicology 126:116-127.
  4. Brown SD, Utturkar SM, Arkin AP, Deutschbauer AM, Elias DA, Hazen TC, Chakraborty R. 2013. Draft genome sequence for Desulfovibrio africanus strain PCS. Genome Announcements 1:e0014413.
  5. Chourey K, Nissen S, Vishnivetskaya T, Shah M, Pfiffner S, Hettich RL, Loffler FE. 2013. Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site. Proteomics 13:2921-2930.
  6. Curry B, Biggerstaff J, Zemel MB. 2013. Effects of leucine and adipocyte derived microparticles on human peripheral blood monocyte CD11b expression. FASEB Journal 27:e46.
  7. Cusick KD, Sayler GS. 2013. An overview of the marine neurotoxin saxitoxin: genetics, molecular targets, methods of detection, and ecological functions. Marine Drugs 11:991-1018.
  8. Cusick KD, Wetzel RK, Minkin SC, Dodani SC, Wilhelm SW, Sayler GS. 2013. Paralytic shellfish toxins inhibit copper uptake in Chlamydomonas reinhardtii. Environmental Toxicology & Chemistry 32:1388-1395.
  9. DeAngelis KM, Chivian D, Fortney JL, Arkin AP, Simmons B, Hazen TC, Silver WL. 2013. Changes in microbial dynamics during long-term decomposition in tropical forests. Soil Biology & Biochemistry 66:60-68.
  10. DeAngelis KM, D’Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. 2013. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Standards in Genomic Sciences 7:382-398.
  11. Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno YM, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL. 2013. Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environmental Science & Technology 47:10860-10867.
  12. Guo T, Wang Q, Bai W, Zhuang J. 2013. Effect of land use on scouring flow hydraulics and transport of soil solute in erosion. Journal of Hydrologic Engineering 18:465-473.
  13. Guo T, Wang Q, Li D, Zhuang J, Wu L. 2013. Flow hydraulic characteristic effect on sediment and solute transport on slope erosion. Catena 107:145-153.
  14. Hatt JK, Ritalahti KM, Ogles DM, Lebron CA, Loeffler FE. 2013. Design and application of an internal amplification control to improve Dehalococcoides mccartyi 16S rRNA gene enumeration by qPCR. Environmental Science & Technology 47:11131-11138.
  15. Hazen TC. 2013. Deepwater Horizon oil spill: A systems biology approach to an ecological disaster. Abstracts Papers of the American Chemical Society 245.
  16. Hazen TC. 2013. The SuperChip for microbial community structure and function from all environments. Microbial Biotechnology 6:450-452.
  17. Hazen TC, Rocha AM, Techtmann SM. 2013. Advances in monitoring environmental microbes. Current Opinion in Biotechnology 24:526-533.
  18. Henry TB, Wileman SJ, Boran H, Sutton P. 2013. Association of Hg2+ with aqueous (C-60)n aggregates facilitates increased bioavailability of Hg2+ in zebrafish (Danio rerio). Environmental Science & Technology 47:9997-10004.
  19. Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L. 2013. Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philosophical Transactions of the Royal Society of London B: Biological Sciences 368:doi 10.1098/rstb.2012.0322.
  20. Im J, Lee J, Loeffler FE. 2013. Interference of ferric ions with ferrous iron quantification using the ferrozine assay. Journal of Microbiological Methods 95:366-367.
  21. Iyer S, Karig DK, Norred SE, Simpson ML, Doktycz MJ. 2013. Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PLoS ONE 8.
  22. Ji X, Ripp S, Layton AC, Sayler GS, DeBruyn JM. 2013. Assessing long term effects of bioremediation: Soil bacterial communities 14 years after polycyclic aromatic hydrocarbon contamination and introduction of a genetically engineered microorganism. OMICS Journal of Bioremediation and Biodegradation 4:e209, doi: 10.4172/2155-6199.1000209.
  23. Johnson G, Curry B, Cahalan L, Prater R, Beeler M, Gartner M, Biggerstaff J, Cahalan P. 2013. In vitro assessment of blood compatibility: Residual and dynamic markers of cellular activation. Journal of Biomaterials Applications 27:925-936.
  24. Johnson G, Curry B, Cahalan L, Prater R, Biggerstaff J, Hussain A, Gartner M, Cahalan P. 2013. Effects of surface-bound and intravenously administered heparin on cell-surface interactions: inflammation and coagulation. Perfusion-UK 28:263-271.
  25. Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, Zhou J. 2013. Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. FEMS Microbiology Ecology 86:200-214.
  26. Karig DK, Jung S-Y, Srijanto B, Collier CP, Simpson ML. 2013. Probing cell-free gene expression noise in femtoliter volumes. ACS Synthetic Biology 2:497-505.
  27. Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding B, Drozdowska M, Hazen TC, Suflita JM, Morris PJ. 2013. Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Frontiers in Microbiology 4:50.
  28. Krifaton C, Kriszt B, Risa A, Szoboszlay S, Cserháti M, Harkai P, Eldridge M, Wang J, Kukolya J. 2013. Application of a yeast estrogen reporter system for screening zearalenone degrading microbes. Journal of Hazardous Materials 15:244-245.
  29. Lin J, Hunkapiller AA, Layton AC, Yun-Juan C, Robbins KR. 2013. Response of intestinal microbiota to antibiotic growth promoters in chickens. Foodborne Pathogens and Disease 10:331-337.
  30. Linville JL, Rodriguez M, Jr., Mielenz JR, Cox CD. 2013. Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum. Bioresource Technology 147:605-613.
  31. Loffler F, Ritalahti KM, Zinder SH. 2013. Dehalococcoides and reductive dechlorination of chlorinated solvents, p. 39-88. In Stroo HF, Leeson A, Ward CH (ed.), SERDP ESTCP Environmental Remediation Technology vol. Bioaugmentation for Groundwater Remediation. Springer, New York, NY.
  32. Loffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Muller JA, Fullerton H, Zinder SH, Spormann AM. 2013. Dehalococcoides mccartyi gen. nov., sp nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. International Journal of Systematic and Evolutionary Microbiology 63:625-635.
  33. Mailloux BJ, Trembath-Reichert E, Cheung J, Watson M, Stute M, Freyer GA, Ferguson AS, Ahmed KM, Alam MJ, Buchholz BA, Thomas J, Layton AC, Zheng Y, Bostick BC, van Geen A. 2013. Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater. Proceedings of the National Academy of Sciences 110:5331-5335.
  34. Merrifield DL, Shaw BJ, Harper GM, Saoud IP, Davies SJ, Handy RD, Henry TB. 2013. Ingestion of metal-nanoparticle contaminated food disrupts endogenous microbiota in zebrafish (Danio rerio). Environmental Pollution 174:157-163.
  35. Ramsden CS, Henry TB, Handy RD. 2013. Sub-lethal effects of titanium dioxide nanoparticles on the physiology and reproduction of zebrafish. Aquatic Toxicology 126:404-413.
  36. Reinardy HC, Dharamshi J, Jha AN, Henry TB. 2013. Changes in expression profiles of genes associated with DNA repair following induction of DNA damage in larval zebrafish Danio rerio. Mutagenesis 28:601-608.
  37. Reinardy HC, Skippins E, Henry TB, Jha AN. 2013. Assessment of DNA damage in sperm after repeated non-invasive sampling in zebrafish Danio rerio. Journal of Fish Biology 82:1074-1081.
  38. Reinardy HC, Scarlett AG, Henry TB, West CE, Hewitt LM, Frank RA, Rowland SJ. 2013. Aromatic naphthenic acids in oil sands process-affected water, resolved by GCxGC-MS, only weakly induce the gene for vitellogenin production in zebrafish (Danio rerio) larvae. Environmental Science & Technology 47:6614-6620.
  39. Reinardy HC, Syrett JR, Jeffree RA, Henry TB, Jha AN. 2013. Cobalt-induced genotoxicity in male zebrafish (Danio rerio), with implications for reproduction and expression of DNA repair genes. Aquatic Toxicology 126:224-230.
  40. Scarlett AG, Reinardy HC, Henry TB, West CE, Frank RA, Hewitt LM, Rowland SJ. 2013. Acute toxicity of aromatic and non-aromatic fractions of naphthenic acids extracted from oil sands process-affected water to larval zebrafish. Chemosphere 93:415-420.
  41. Skerker JM, Leon D, Price MN, Mar JS, Tarjan DR, Wetmore KM, Deutschbauer AM, Baumohl JK, Bauer S, Ibanez AB, Mitchell VD, Wu CH, Hu P, Hazen T, Arkin AP. 2013. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates. Molecular Systems Biology 9:doi 10.1038/msb.2013.30.
  42. Somenahally AC, Mosher JJ, Yuan T, Podar M, Phelps TJ, Brown SD, Yang ZK, Hazen TC, Arkin AP, Palumbo AV, Van Nostrand JD, Zhou J, Elias DA. 2013. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. PLoS ONE 8:e83909.
  43. Spier C, Stringfellow WT, Hazen TC, Conrad M. 2013. Distribution of hydrocarbons released during the 2010 MC252 oil spill in deep offshore waters. Environmental Pollution 173:224-230.
  44. Vishnivetskaya TA, Fisher LS, Brodie GA, Phelps TJ. 2013. Microbial communities involved in biological ammonium removal from coal combustion wastewaters. Microbial Ecology 66:49-59 doi: 10.1007/s00248-012-0152-5.
  45. Xu T, Close DM, Sayler GS, Ripp S. 2013. Genetically modified whole-cell bioreporters for environmental assessment. Ecological Indicators 28:125-141.
  46. Xu T, Close D, Webb J, Price S, Ripp S, Sayler G. 2013. Continuous, real-time bioimaging of chemical bioavailability and toxicology using autonomously bioluminescent human cell lines. In Southern SO (ed.), Proc. SPIE 8723, Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring III, 872310 (May 29, 2013), Baltimore, MD.
  47. Xu T, Close D, Webb J, Ripp S, Sayler G. 2013. Autonomously bioluminescent mammalian cells for continuous and real-time monitoring of cytotoxicity. Journal of Visualized Experiments e50972, doi:10.3791/50972.
  48. Yan J, Im J, Yang Y, Loffler FE. 2013. Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity. Philosophical Transactions of the Royal Society B-Biological Sciences 368:doi 10.1098/rstb.2012.0320.
  49. Yang Y-F, Wang Q-J, Zhuang J. 2013. Estimating hydraulic parameters of stony soils on the basis of one-dimensional water absorption properties. Acta Agriculturae Scandinavica Section B-Soil and Plant Science 63:304-313.
  50. Yoon S, Sanford RA, Loffler FE. 2013. Shewanella spp. use acetate as an electron donor for denitrification but not ferric iron or fumarate reduction. Applied and Environmental Microbiology 79:2818-2822.
  51. Zhang H, Lenaghan SC, Connolly MH, Parker LE. 2013. Zebrafish larva locomotor activity analysis using machine learning techniques, Proceedings of the 12th International Conference on Machine Learning and Applications, Miami, FL, December 4-7.
  52. Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME Journal 7:1790-1802.
  53. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson D, Fortenberry D, Holland M, Burr S, Shannon WD, Sodergren EJ, Weinstock GM. 2013. Biogeography of the ecosystems of the healthy human body. Genome Biology 14:R1. doi:10.1186/gb-2013-14-1-r1.
  54. Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J. 2013. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Environmental Science & Technology 47:9841-9849.