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Project Publications: University of California-Davis: Optimizing Bioremediation for Risk Reduction Using Integrated Bioassay, Non-Target Analysis and Genomic Mining Techniques

Superfund Research Program

Optimizing Bioremediation for Risk Reduction Using Integrated Bioassay, Non-Target Analysis and Genomic Mining Techniques

Project Leader: Thomas Michael Young
Co-Investigator: Frank J. Loge
Grant Number: P42ES004699
Funding Period: 2017-2023
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  • Alaimo CP, Li Y, Green PG, Kleeman MJ, Young TM. 2021. Diversity of carbonyl compounds in biogas and natural gas revealed using high-resolution mass spectrometry and nontarget analysis. Environ Sci Technol 55:PMID:34523924
  • Black G, Ho G, Denison MS, Young TM. 2021. Using Estrogenic Activity and Nontargeted Chemical Analysis to Identify Contaminants in Sewage Sludge. Environ Sci Technol 55:6729-6739. doi:10.1021/acs.est.0c07846 PMID:33909413
  • Kim K, Shin H, Wong L, Young TM, Bennett DH. 2021. Evaluating couch polyurethane foam for a potential passive sampler of semivolatile organic compounds. Chemosphere 271:129349. doi:10.1016/j.chemosphere.2020.129349 PMID:33429263 PMCID:PMC7969436
  • Kim K, Shin H, Wong L, Young TM, Bennett DH. 2021. Temporal variability of indoor dust concentrations of semivolatile organic compounds. Indoor Air 31(3):doi:10.1111/ina.12759 PMID:33022817
  • Pinkanjananavee K, Teh SJ, Kurobe T, Lam CH, Tran F, Young TM. 2021. Potential impacts on treated water quality of recycling dewatered sludge supernatant during harmful cyanobacterial blooms. Toxins (Basel) 13(2):99. doi:10.3390/toxins13020099 PMID:33572944
  • Rodgers KM, Bennett DH, Moran R, Knox K, Stoiber T, Gill R, Young TM, Blum A, Dodson RE. 2021. Do flame retardant concentrations change in dust after older upholstered furniture is replaced?. Environ Int 153:doi:10.1016/j.envint.2021.106513 PMID:33770624 PMCID:PMC8154740
  • Wrightwood OM, Hattaway ME, Young TM, Bischel HN. 2021. Assessment of woodchip bioreactor characteristics and their influences on joint nitrate and pesticide removal. ACS ES&T Wat
  • Young TM, Black G, Wong L, Bloszies CS, Fiehn O, He G, Denison MS, Vogel CF, Durbin-Johnson BP. 2021. Identifying toxicologically significant compounds in urban wildfire ash using in vitro bioassays and high-resolution mass spectrometry. Environ Sci Technol 55:3657-3667. doi:10.1021/acs.est.0c06712 PMID:33647203 PMCID:PMC8351470


  • Cui Y, Allmon SD, Siegel JB. 2020. Functional characterization and reclassification of an enzyme previously proposed to be a limonoidUDP-glucosyltransferase. Journal of the Science of Food and Agriculture 9:doi:10.1002/jsfa.10547 PMID:32483918 PMCID:PMC7920543
  • Huang P, Chu SK, Frizzo HN, Connolly MP, Caster RW, Siegel JB. 2020. Evaluating protein engineering thermostability prediction tools using an independently generated dataset. ACS Omega 5:6487-6493. doi:10.1021/acsomega.9b04105 PMID:32258884 PMCID:PMC7114132
  • Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang P, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmstrom L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, O'Conchuir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burma SS, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva D, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. 2020. Macromolecular modeling and design in Rosetta: Recent methods and frameworks. Nat Methods 16:doi:10.1038/s41592-020-0848-2 PMID:32483333
  • Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. 2020. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 11:5130. doi:10.1038/s41467-020-18862-2 PMID:33046702 PMCID:PMC7550611


  • Bertolani SJ, Siegel JB. 2019. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PLoS One 14:15. doi:10.1371/journal.pone.0214126 PMID:30947258 PMCID:PMC6448891
  • Black G, Anumol T, Young TM. 2019. Analyzing a broader spectrum of endocrine active organic contaminants in sewage sludge with high resolution LC-QTOF-MS suspect screening and QSAR toxicity prediction. Environ Sci Process Impacts 21(7):1099-1114. doi:10.1039/c9em00144a PMID:31179481 PMCID:PMC7036296
  • Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. 2019. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat Chem Biol 16:87-94. doi:10.1038/s41589-019-0402-7 PMID:31768035
  • Contreras SC, Bertolani SJ, Siegel JB. 2019. A benchmark for homomeric enzyme active site structure prediction highlights the importance of accurate modeling of protein symmetry. ACS Omega 4:22356-22362. doi:10.1021/acsomega.9b02636 PMID:31909318 PMCID:PMC6941179
  • Gan J, Siegel JB, German JB. 2019. Molecular annotation of food: Towards personalized diet and precision health. Trends Food Sci Technol 21:doi:10.1016/j.tifs.2019.07.016 PMID:33299266 PMCID:PMC7723349 (accepted for publication)
  • Garrido JA, Parthasarathy S, Moschet C, Young TM, McKone TE, Bennett DH. 2019. Exposure assessment for air-to-skin uptake of semivolatile organic compounds (SVOCs) indoors. Environ Sci Technol 53(3):1608-1616. doi:10.1021/acs.est.8b05123 PMID:30525510 PMCID:PMC7036297
  • Jia M, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. 2019. Switching on a Nontraditional Enzymatic Base: Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum. ACS Catal 9:doi:10.1021/acscatal.9b02783 PMID:32489716 PMCID:PMC7266162
  • Mexia N, Koutrakis S, He G, Skaltounis L, Denison MS, Magiatis P. 2019. RETURN TO ISSUEPREVARTICLENEXT Journal Logo A Biomimetic, One-Step Transformation of Simple Indolic Compounds to Malassezia-Related Alkaloids with High AhR Potency and Efficacy. Chem Res Toxicol 32:doi:10.1021/acs.chemrestox.9b00270 PMID:31647221 PMCID:PMC7757739 (accepted for publication)
  • Middleton ER, Talaugon S, Young TM, Wong L, Fluharty S, Reed K, Cosby C, Myers II R. 2019. Bi-directional learning: Identifying contaminants on the Yurok Indian Reservation. Int J Environ Res Public Health 16:pii:E3513. doi:10.3390/ijerph16193513 PMID:31547171 PMCID:PMC6801823
  • Rupiper A, Loge FJ. 2019. Identifying and overcoming barriers to onsite non-potable water reuse in California from local stakeholder perspectives. Resources, Conservation & Recycling: X 4:100018. doi:10.1016/j.rcrx.2019.100018
  • Shin H, Moschet C, Young TM, Bennett DH. 2019. Measured concentrations of consumer product chemicals in California house dust: Implications for sources, exposure, and toxicity potential. Indoor Air 30(1):60-75. doi:10.1111/ina.12607 PMID:31587372 PMCID:PMC6917863


  • Moschet C, Anumol T, Lew BM, Bennett DH, Young TM. 2018. Household dust as a repository of chemical accumulation: new insights from a comprehensive high-resolution mass spectrometric study. Environ Sci Technol 52:2878-2887. doi:10.1021/acs.est.7b05767 PMID:29437387


  • Moschet C, Lew BM, Hasenbein S, Anumol T, Young TM. 2017. LC- and GC-QTOF-MS as complementary tools for a comprehensive micropollutant analysis in aquatic systems. Environ Sci Technol 51(3):1553-1561. doi:10.1021/acs.est.6b05352 PMID:28026950
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