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2020 Publications

  1. Abramov AA, Vishnivetskaya TA, Rivkina EM. Are permafrost microorganisms as old as permafrost? FEMS Microbiology Ecology 10.1093/femsec/fiaa260, in press.
  2. Artal MC, Pereira KD, Luchessi AD, Okura VK, Henry TB, Marques-Souza H, Umbuzeiro GD. 2020. Transcriptome analysis in Parhyale hawaiensis reveal sex-specific responses to AgNP and AgCl exposure. Environmental Pollution 260:e113963.
  3. Bai XY, Zhu XF, Jiang HB, Wang ZQ, He CG, Sheng LX, Zhuang J. 2020. Purification effect of sequential constructed wetland for the polluted water in urban river. Water 12.
  4. Boyle D, Catarino AI, Clark NJ, Henry TB. 2020. Polyvinyl chloride (PVC) plastic fragments release Pb additives that are bioavailable in zebrafish. Environmental Pollution 263, doi: 10.1016/j.envpol.2020.114422.
  5. Bubier JA, Philip VM, Quince C, Campbell J, Zhou Y, Vishnivetskaya T, Duvvuru S, Hageman Blair R, Ndukum J, Donohue KD, Foster CM, Mellert DJ, Weinstock G, Culiat CT, O’Hara B, Palumbo AV, Podar M, Chesler EJ. 2020. A microbe associated with sleep revealed by a novel systems-genetic analysis of the microbiome in collaborative cross mice. Genetics 10.1534/genetics.119.303013:genetics.303013.2019.
  6. Chakraborty S, Molugu TR, Doktorova M, Heberle FA, Scott HL, Kelley EG, Nagao M, Dzikovski BG, Standaert RF, Barrera FN, Katsaras J, Khelashvili G, Brown MF, Ashkar R. 2020. Stiffening of phosphocholine membranes by cholesterol. Biophysical Journal 118:86A-86A.
  7. Chen G, Fisch AR, Gibson CM, Mack EE, Seger ES, Campagna SR, Loffler FE. 2020. Mineralization versus fermentation: Evidence for two distinct anaerobic bacterial degradation pathways for dichloromethane. ISME Journal doi:10.1038/s41396-019-0579-5.
  8. Chen J, Yang L, Chen X, Ripp S, Radosevich M, Zhuang J. Bacterial mobility facilitated by soil depth and intact structure. Soil and Tillage Research, in press.
  9. Conway M, Brumbaugh A, Xu T, Young A, Close D, Ripp S. 2020. Overview of in vivo imaging methods and instrumentation. In Barroso MM, Intes X (ed.), Imaging from cells to animals in vivo. CRC Press, doi: 10.1201/9781315174662.
  10. Conway M, Xu T, Kirkpatrick A, Ripp S, Sayler G, Close D. 2020. Real-time tracking of stem cell viability, proliferation, and differentiation with autonomous bioluminescence imaging. BMC Biology 18, doi: 10.1186/s12915-020-00815-2.
  11. Dai Y, Zhuang J, Chen X. 2020. Synergistic effects of unsaturated flow and soil organic matter on retention and transport of PPCPs in soils. Environmental Research 191:110135.
  12. Din G, Hassan A, Rafiq M, Hasan F, Badshah M, Khan S, Chen G, Ripp S, Shah AA. 2020. Characterization of organic acid producing Aspergillus tubingensis FMS1 and its role in metals leaching from soil. Geomicrobiology Journal 37:336-344.
  13. Dove NC, Rogers TJ, Leppanen C, Simberloff D, Fordyce JA, Brown VA, LeBude AV, Ranney TG, Cregger MA. 2020. Microbiome variation across two hemlock species with hemlock woolly adelgid infestation. Frontiers in Microbiology 11:e1528.
  14. Heberle FA, Doktorova M, Scott HL, Skinkle A, Lyman ER, Waxham N, Levental I. 2020. Direct imaging of nanoscale lipid organization in probe-free biomimetic membranes. Biophysical Journal 118:386A-386A.
  15. Huangfu YC, Essington ME, Hawkins SA, Walker FR, Schwartz JS, Layton AC. 2020. Testing the sediment fingerprinting technique using the SIAR model with artificial sediment mixtures. Journal of Soils and Sediments 10.1007/s11368-019-02545-7.
  16. Huo L, Yang Y, Lv Y, Li X, Löffler FE, Yan J. 2020. Complete genome sequence of Sulfurospirillum strain ACSTCE, a tetrachloroethene-respiring anaerobe isolated from contaminated soil. Microbiology Resource Announcements 9:e00941-20.
  17. Kucharzyk KH, Meisel JE, Kara-Murdoch F, Murdoch RW, Higgins SA, Vainberg S, Bartling CM, Mullins L, Hatzinger PB, Loffler FE. 2020. Metagenome-guided proteomic quantification of reductive dehalogenases in the Dehalococcoides mccartyi-containing consortium SDC-9. Journal of Proteome Research 19:1812-1823.
  18. Liang XL, Zhang YY, Wommack KE, Wilhelm SW, DeBruyn JM, Sherfy AC, Zhuang J, Radosevich M. 2020. Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity. Soil Biology & Biochemistry 144.
  19. Liu JG, Scanlon BR, Zhuang J, Varis O. 2020. Food-energy-water nexus for multi-scale sustainable development. Resources Conservation and Recycling 154.
  20. Miao RH, Guo MX, Zhao XY, Gong ZQ, Jia CY, Li XJ, Zhuang J. 2020. Response of soil bacterial communities to polycyclic aromatic hydrocarbons during the phyto-microbial remediation of a contaminated soil. Chemosphere 261.
  21. Moon J-W, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole Ii FL, Lui LM, Adams BG, De León KB, Brewer SS, Williams DE, Lowe KA, Rodriguez M, Mehlhorn TL, Pfiffner SM, Chakraborty R, Arkin AP, Wall JD, Fields MW, Adams MWW, Stahl DA, Elias DA, Hazen TC. 2020. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere 255:e126951.
  22. Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kampfer 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, de los Santos PE, 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, Loffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedros-Alio 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. 2020. Roadmap for naming uncultivated Archaea and Bacteria (vol 5, pg 987, 2020). Nature Microbiology 10.1038/s41564-020-00827-2.
  23. Patsiou D, del Rio-Cubilledo C, Catarino AI, Summers S, Fahmi AM, Boyle D, Fernandes TF, Henry TB. 2020. Exposure to Pb-halide perovskite nanoparticles can deliver bioavailable Pb but does not alter endogenous gut microbiota in zebrafish. Science of the Total Environment 715:e136941.
  24. Rivkina EM, Fedorov-Davydov DG, Zakharyuk AG, Shcherbakova VA, Vishnivetskaya TA. 2020. Free iron and iron-reducing microorganisms in permafrost and permafrost-affected soils of northeastern Siberia. Eurasian Soil Science 53:1455-1468.
  25. Scott HL, Skinkle A, Kelley EG, Waxham N, Levental I, Heberle FA. 2020. On the mechanism of bilayer separation by extrusion; or, why your large unilamellar vesicles are not really unilamellar. Biophysical Journal 118:388A-388A.
  26. Shen CY, Jin Y, Zhuang J, Li TT, Xing BS. 2020. Role and importance of surface heterogeneities in transport of particles in saturated porous media. Critical Reviews in Environmental Science and Technology 50:244-329.
  27. Sun EW-H, Hajirezaie S, Dooner M, Vishnivetskaya TA, Layton A, Chauhan A, Pfiffner SM, Whyte LG, Onstott TC, Lau MCY. 2020. Thaumarchaea genome sequences from a high Arctic active layer. Microbiology Resource Announcements 9:e00326-20.
  28. Sun HH, Lee J, Chen XJ, Zhuang J. 2020. Estimating soil water retention for wide ranges of pressure head and bulk density based on a fractional bulk density concept. Scientific Reports 10.
  29. Toro-Gonzalez M, Dame AN, Foster CM, Millet LJ, Woodward JD, Rojas JV, Mirzadeh S, Davern SM. 2020. Quantitative encapsulation and retention of Th-227 and decay daughters in core-shell lanthanum phosphate nanoparticles. Nanoscale 12:9744-9755.
  30. Vad J, Dunnett F, Liu F, Montagner CC, Roberts JM, Henry TB. 2020. Soaking up the oil: Biological impacts of dispersants and crude oil on the sponge Halichondria panicea. Chemosphere 257:e127109.
  31. Vishnivetskaya TA, Almatari AL, Spirina EV, Wu X, Williams DE, Pfiffner SM, Rivkina EM. 2020. Insights into community of photosynthetic microorganisms from permafrost. FEMS Microbiology Ecology 10.1093/femsec/fiaa229.
  32. Xing YN, Chen X, Wagner RE, Zhuang J, Chen XJ. 2020. Coupled effect of colloids and surface chemical heterogeneity on the transport of antibiotics in porous media. Science of the Total Environment 713.
  33. Xu S, Shen CY, Zhang XY, Chen XJ, Radosevich M, Wang SQ, Zhuang J. 2020. Mobility of cellulose nanocrystals in porous media: Effects of ionic strength, iron oxides, and soil colloids. Nanomaterials 10:e348.
  34. Xu T, Young A, Narula J, Sayler G, Ripp S. 2020. High-throughput analysis of endocrine disrupting compounds using BLYES and BLYAS bioluminescent yeast bioassays p. 29-41. In Ripp S (ed.), Methods in Molecular Biology – Bioluminescent Imaging, vol. 2081. Humana, New York, NY.
  35. Yip D, Kirkpatrick A, Xu T, Masi T, Stephenson S, Ripp S, Close D. 2020. Continuous and real-time in vivo autobioluminescent imaging in a mouse model, p. 191-201. In Ripp S (ed.), Methods in Molecular Biology – Bioluminescent Imaging, vol. 2081. Humana, New York, NY.
  36. Yu JL, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu ZR, Abbott AG, Staton ME. 2020. Distinctive gene expression patterns define endodormancy to ecodormancy transition in apricot and peach. Frontiers in Plant Science 11:e180.
  37. Zajic J, Ripp S, Trogl J, Kuncova G, Pospisilova M. 2020. Repetitive detection of aromatic hydrocarbon contaminants with bioluminescent bioreporters attached on tapered optical fiber elements. Sensors 20:e3237.