USC.edu

Steven Finkel

Professor of Biological Sciences
Steven Finkel
Email sfinkel@usc.edu Office RRI 319B Office Phone (213) 821-1498

Center, Institute & Lab Affiliations

  • Center for Deep Energy Biosphere Investigations,
  • USC Geobiology,

Education

  • Ph.D. Biological Chemistry, University of California, Los Angeles, 1994
  • B.A. Molecular Biology, University of California, Berkeley, 1987
    • Helen Hay Whitney Foundation Postdoctoral Research Fellow, Microbiology & Molecular Genetics, Harvard Medical School, 1994-1999

  • Tenure Track Appointments

    • Professor, USC Davis School of Gerontology, 2016 –
    • Professor of Biological Sciences, University of Southern California, 2013 –
    • Associate Professor of Biological Sciences, University of Southern California, 2007 – 2013
    • Assistant Professor of Biological Sciences, University of Southern California, 2000 – 2007

    Visiting and Temporary Appointments

    • Reader, The Huntington Library, 2011

    Other Employment

    • Past-President, American Society for Microbiology, 07/01/2022
    • College Dean of Graduate & Professional Education, USC Dornsife College of Letters, Arts & Sciences, 2017
    • Senior Scientist, Center for Dark Energy Biosphere Investigations (C-DEBI), USC, 2015-2022
    • Distinguished Fellow, USC Center for Excellence in Teaching, 2012-2019
    • Dornsife Faculty Fellow, USC Dornsife College of Letters, Arts and Sciences, 2011-2013
    • Deputy Director, USC Center for Excellence in Genomic Science, USC, 2009-2015
    • Fellow, USC Center for Excellence in Teaching, 2009-2012
    • ASM Distinguished Lecturer, American Society for Microbiology, 2009-2011
    • Member, USC/Norris Comprehensive Cancer Center, 2000-2018

  • Summary Statement of Research Interests

    Reseach in Professor Finkel’s laboratory focuses on the long-term survival and evolution of bacteria, including understanding natural systems and applications to electricity production. Among the topics of current study in the laboratory are (1) the mechanisms of survival in many organisms, including population structure at the genetic & genomic level and studies of the GASP (growth advantage in stationary phase) phenotype; (2) the generation of bacterial diversity in different environments, including the roles of error-prone DNA polymerases in generating diversity; (3) the role of DNA-protein interactions in controlling gene expression, organizing the chromosome, and protecting DNA during the stationary phase of the bacterial lifecycle, focusing on the role of the Dps protein, (4) the use of DNA as a nutrient and parallels to natural competence and transformation; (5) the long-term survival ability of bacteria in electricity-generating microbial fuel cells (MFCs) and bioelectrochemical systems (BESs); and mechanisms of survival in severely nutrient- and energy-limited deep subseafloor environments. Model organisms in the laboratory include: Escherichia coli, Shewanella oneidensis, Pseudomonas aeruginosa, Halomonas species and gut microbiota communities.

  • Book Chapters

    • Finkel, S. E. (2012). An accidental evolutionary biologist: GASP, long-term survival and evolution. Microbes and Evolution: The World That Darwin Neve pp. pp.115-122. Washington, DC: ASM Press.
    • Finkel, S. E., Zinser, E., Kolter, R. (2000). Long-term survival and evolution in stationary phase. pp. p. 231-238. Bacterial Stress Responses/ASM.
    • Finkel, S. E., Zinser, E., Gupta, S., Kolter, R. (1998). Life and Death in Stationary Phase. (Vol. 103) pp. 3-16. NATO-ASI Series, Series H: Cell Biology/Springer-Verlag.

    Journal Article

    • Orban, K., Finkel, S. E. (2022). Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein. J. Bacteriol.. Vol. 204 (5), pp. e0003622.
    • Sebatian, H., Finkel, S. E. (2022). Absence of Ribosome Modulation Factor Alters Growth and Competitive Fitness of Escherichia coli. Microbial. Spectr.. Vol. 10 (2), pp. e0223921.
    • Allen, C., Finkel, S. E. (2022). Vibrio harveyi Exhibits the Growth Advantage in Stationary Phase Phenotype during Long-Term Incubation. Microbial. Spectr.. Vol. 10 (1), pp. e0214421.
    • Kingsley, S. F., Seo, Y., Allen, C., Ghanta, K. S., Finkel, S., Tissenbaum, H. A. (2021). Bacterial processing of glucose modulates C. elegans lifespan and healthspan. Sci. Rep.. Vol. 11 (1), pp. 5931.
    • Ratib, N. R., Seidl, F., Ehrenreich, I. M., Finkel, S. E. (2021). Evolution in Long-Term Stationary-Phase Batch Culture: Emergence of Divergent Escherichia coli Lineages over 1,200 Days. mBio. Vol. 12 (1), pp. e03337-20.
    • Kram, K. E., Henderson, A. L., Finkel, S. E. (2020). Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival. mSystems. Vol. 5 (4), pp. e00364-20.
    • Robador, A., Amend, J. P., Finkel, S. E. (2019). Nanocalorimetry Reveals the Growth Dynamics of Escherichia coli Cells Undergoing Adaptive Evolution during Long-Term Stationary Phase. Appl. Environ. Microbial.. Vol. 85 (15), pp. e00968-19.
    • Ferraro, C. M., Finkel, S. E. (2019). Physiological, Genetic, and Transcriptomic Analysis Alcohol-Induced Delay of Escherichia coli Death. Appl Environ Microbiol.. Vol. 85 (2), pp. e02113-18.
    • Westphal, L. L., Lau, J., Negro, Z., Moreno, I. J., Ismail Mohammed, W., Lee, H., Tang, H., Finkel, S. E., Kram, K. E. (2018). Adaptation of Escherichia coli to long-term batch culture in various rich media. Res. Microbiol.. Vol. 169 (3), pp. 145-156.
    • Robador, A., LaRowe, D. E., Finkel, S. E., Amend, J. P., Nealson, K. H. (2018). Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions. Front. Microbiol.. Vol. 9, pp. 109.
    • Kram, K., Geiger, C., Ismail, W., Lee, H., Tang, H., Foster, P., Finkel, S. E. (2017). Adaptation of Escherichia coli to Long-Term Serial Passage in Complex Medium: Evidence of Parallel Evolution. mSystems. Vol. 2 (2), pp. e00192-16.
    • Shroff, N., Xu, S., Acevedo, J., El-Naggar, M., Finkel, S. E. (2017). A Microenvironment for Shewanella oneidensis MR-1 Exists within Graphite Felt Electrodes. J. Electrochem. Soc.. Vol. 164 (3), pp. H3103-H3108.
    • Westphal, L., Sauvey, P., Champion, M., Ehrenreich, I. M., Finkel, S. E. (2016). Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase. mSystems. Vol. 1, pp. e00130-16.
    • Agnello, M., Finkel, S. E., Wong-Beringer, A. (2016). Fitness Cost of Fluoroquinolone Resistance in Clinical Isolates of Pseudomonas aeruginosa Differs by Type III Secretion Genotype. Front Microbiol.. Vol. 4, pp. 1591.
    • Kram, K. E., Finkel, S. E. (2015). Rich Medium Composition Affects Escherichia coli Survival, Glycation, and Mutation Frequency during Long-Term Batch Culture. Applied Environ. Microbiol.. Vol. 81, pp. 4442-4450.
    • Kram, K. E., Finkel, S. E. (2014). Culture volume and vessel affect long-term survival, mutation frequency, and oxidative stress of Escherichia coli. Applied Env. Microbiol.. Vol. 80, pp. 1732-1738.
    • Corzett, C. H., Goodman, M. F., Finkel, S. E. (2013). Competitive Fitness During Feast and Famine: How SOS DNA Polymerases Influence Physiology and Evolution in Escherichia coli. Genetics. Vol. 194, pp. 409-420.
    • Riedel, T. E., Berelson, W. M., Nealson, K. H., Finkel, S. E. (2013). Oxygen Consumption Rates of Bacteria Under Nutrient-Limited Conditions. Applied Environ. Microbiol.. pp. Epub ahead of print.
    • El-Naggar, M. Y., Finkel, S. E. (2013). Live Wires. The Scientist. Vol. 27
    • Yamanaka, K., Minko, I. G., Finkel, S. E., Goodman, M. F., Lloyd, R. S. (2011). The role of high fidelity E. coli DNA polymerase I in the replication bypass of deoxyadenosine DNA-peptide cross-link. J. Bacteriol. Vol. 193, pp. 3815-3821. PubMed Web Address
    • Nealson, K. H., Finkel, S. E. (2011). Electron flow and biofilms. MRS Bulletin. Vol. 36, pp. 380-382.
    • Gonidakis, S., Finkel, S. E., Longo, V. D. (2011). Lifespan extension and paraquat resistance in a ubiquinone-deficient E. coli mutant depend on transcription factors ArcA and TdcA. Aging. Vol. 3, pp. 291-303.
    • Biffinger, J., Fitzgerald, L., Ray, R., Little, B., Lizewski, S., Petersen, E., Ringeisen, B., Sanders, W., Sheehan, P., Pietron, J., Baldwin, J., Nadeau, L., Johnson, G., Ribbens, M., Finkel, S. E., Nealson, K. H. (2011). The utility of Shewanella japonica for microbial fuel cells. Bioresour. Technol.. Vol. 102, pp. 290-297.
    • Pepper, E. D., Farrell, M. J., Nord, G., Finkel, S. E. (2010). Anti-glycation effects of carnosine and other compounds on long-term survival of Escherichia coli. Appl. Environ.Microbiol.. Vol. 76, pp. 7925-7930.
    • Gondakis, S., Finkel, S. E., Longo, V. D. (2010). Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA. Aging Cell. Vol. 9, pp. 868-881.
    • Gonidakis, S., Finkel, S. E., Longo, V. D. (2010). E. coli hypoxia-inducible factor ArcA mediates lifespan extension in a lipoic acid synthase mutant by suppressing acetyle-CoA synthetase. Biol. Chem.. Vol. 391, pp. 1139-1147.
    • Palchevskiy, V., Finkel, S. E. (2009). A role for single-stranded exonucleases in the use of DNA as a nutrient. J. Bacteriol.. Vol. 191, pp. 3712-3716.
    • Biffinger, J. C., Ray, R., Little, B. J., Fitzgerald, L. A., Ribbens, M. A., Finkel, S. E., Ringeisen, B. R. (2009). Simultaneous analysis of physiological and electrical output changes in an operating microbial fuel cell with Shewanella oneidensis. Biotechnol. Bioeng.. Vol. 103, pp. 524-531.
    • Kraigsley, A., Finkel, S. E. (2009). Adaptive evolution in single species biofilms. FEMS Microbiology Letters. Vol. 293, pp. 135-140.
    • Ren, C., Finkel, S. E., Tower, J. (2009). Conditional inhibition of autophagy genes in adult Drosophila impairs immunity without compromising longevity. Exp. Gerontol.. Vol. 44, pp. 228-235.
    • Biffinger, J., Ribbens, M., Pietron, J., Finkel, S. E., Nealson, K. (2009). Characterization of electrochemically active bacteria (EAB) utilizing a high-throughput voltage-based screening assay. Biotechnol. Bioeng.. Vol. 102, pp. 436-444.
    • Kumari, A., Minko, I. G., Harbut, B., Finkel, S. E., Goodman, M. F., Lloyd, R. S. (2008). Replication bypass of interstrand crosslink intermediates by Escherichia coli DNA polymerase IV. J. Biol. Chem.. Vol. 283, pp. 27433-27437.
    • Ren, C., Webster, P., Finkel, S. E., Tower, J. (2007). Increased internal and external bacterial load during Drosophila aging without life span trade-off. Cell Metabolism. Vol. 6, pp. 144-152.
    • Skvortsov, D., Abdueva, D., Stitzer, M. E., Finkel, S. E., Tavaré, S. (2007). Using expression arrays for copy number detection: an example from E. coli. BMC Bioinformatics. Vol. 8, pp. 203.
    • Stevens, M. H., Sanchez, M., Lee, J., Finkel, S. E. (2007). Diversification rates increase with population size and resource concentration in an unstructured habitat. Genetics. Vol. 177, pp. 2243-2250.
    • Pepper, E. D., Farrell, M. J., Finkel, S. E. (2006). Role of penicillin binding protein 1b in competitive stationary phase survival and antibiotic resistance. FEMS Microbiology Letters. Vol. 263, pp. 61-67.
    • Finkel, S. E. (2006). Long-term survival during stationary phase: Evolution and the GASP phenotype. Nature Reviews Microbiology. Vol. 4, pp. 113-120.
    • Finkel, S. E., Petrie, A., Erbe, J. (2005). Use of long-term E. coli cultures to study generation of genetic diversity and teach general microbiology laboratory skills. American Biology Teacher. pp. p.87-92.
    • Nair, S., Finkel, S. E. (2004). Dps protects cells against multiple stresses during stationary phase. Journal of Bacteriology/ASM. Vol. 186, pp. 4192-4198.
    • Farrell, M. J., Finkel, S. E. (2003). The growth advantage in stationary phase phenotype conferred by rpoS mutations is dependent on pH and nutrient source. Journal of Bacteriology/ASM. Vol. 185, pp. 7044-7052.
    • Yeiser, B., Pepper, E. D., Goodman, M. F., Finkel, S. E. (2002). SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness. Proc. Natl. Acad. Sci. USA. Vol. 99, pp. 8737-8741.
    • Finkel, S. E., Kolter, R. (2001). DNA as a nutrient: A novel role for bacterial competence gene homologs. J. Bacteriol.. Vol. 183, pp. 6288-6293.
    • Finkel, S. E., Kolter, R. (1999). Evolution of microbial diversity during prolonged starvation. Proc. Natl. Acad. Sci. USA. Vol. 96, pp. 4023-4027.
    • Mentor, USC-IML Certificate Program, 2007-2008
    • Spotlight Feature, Our paper “Effect of culture medium on long-term survival and generation of genetic diversity in E. coli” was featured in the SPOTLIGHT section of the issue of APPLIED AND ENVIRONMENTAL MICROBIOLOGY where the article appeared, 2013-2014
    • Fellow, American Academy of Microbiology, 2016
    • Albert S. Raubenheimer Outstanding Faculty Award for Excellence in the Areas of Research, Teaching, and Service,, 2019-2020
    • William A. Hinton Research Training Award, American Society for Microbiology, 2017-2018
    • USC Center for Excellence in Teaching, Faculty Fellow, , 2009-2012
    • American Society for Microbiology Branch/Distinguished Lecturer, 2009-2011
    • NIH/NSF Career Development Award, NSF Faculty Early Career Award, 2003-2009
    • USC-Mellon Award for Excellence in Mentoring Undergraduates, 2007-2008
    • Visiting Scholar Award, Alberta Heritage Foundation for Research, 2004-2005

  • Other Advisement or Time Devoted to Students

    • Zlatas Serebnitskiy, Graduate Student, Finkel Lab, Molecular Biology Ph.D. Program, 2023 –
    • Caitlin Nickson, Graduate Student, Finkel Lab, Molecular Biology Ph.D. Program , 2022 –
    • Nicolaus Jakowec, Graduate Student, Finkel Lab, Molecular Biology Ph.D. Program , 2021 –
    • Andrew Janeiro Graduate Student, Finkel Lab, Molecular Biology Ph.D. Program , 2021 –
    • Christopher Corzett, Ph.D., Senior Scientist, Finkel Lab, Molecular & Computational Biology Section , 2017 –
    • Alberto Robador, Ph.D. Research Assistant Professor, Finkel Lab, Molecular Biology & Computational Biology Section , 2016 –

  • Editorships and Editorial Boards

    • Editorial Board, Applied and Environmental Microbiology, 2008 –
    • Editorial Board, Journal of Bacteriology, 2010 – 2021
    • Editor, Research in Microbiology, 2011 – 2014
    • Section Editor, EcoSal: Escherichia coli and Salmonella Cellular & Molecular Biology, 2003 – 2014
    • Editor, Biochemical Journal, 2006 – 2009

    Professional Memberships

    • The Biochemical Society (U.K), 2007 –
    • American Association for the Advancement of Science, 2000 –
    • American Society for Microbiology, 1987 –