Members of the Levin Lab

Levin Lab
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Emory University
Dept. of Biology
1510 Clifton Road
Atlanta, GA 30322

Office: 404-727-2826
Lab: 404-727-2956
Fax: 404-727-2880

EcLF

Members of the Levin Lab

Pierre Ankomah MD/PhD. Student BA (Biochemistry and Molecular Biology) from Franklin & Marshall College. My general research interests are the evolution of antibiotic resistance and the population dynamics of infectious diseases and their treatment.


Omar Cornejo PhD. Student e-mail: ocornej@emory.edu BA Biology Universidad Simón Bolívar (Caracas, Venezuela). MS in Ecology Instituto Venezolano de Investigaciones Científicas (Caracas, Venezuela). Research interests: Population genetics, molecular evolution, and population dynamics of diseases I am mainly interested in understanding the relative roles of recombination, mutation and selection in shaping genetic variation in and determining the genetic structure of populations of microorganism, and especially microbes responsible for infectious diseases. I see this subject as having the virtues of being central to our understanding of the population genetics of microbes and at the same time having practical value for understanding and ideally controlling existing and emerging infectious diseases. I believe that a combination of experimental studies in the laboratory, mathematical modeling, and retrospective analyses of DNA sequence data will enable us to understand the relative importance of these evolutionary processes in generating and maintaining genetic variation in microbial populations and shaping their genetic structure.	Publications Cornejo, O.E., D. Rozen, R.M. May and B.R. Levin (2008) Oscillations in continuous culture populations of Streptococcus pneumoniae: Population dynamics and the evolution of clonal suicide (Proceeding Royal Society B, On Line FirstCite (doi:10.1098/rspb.2008.1415)[PDF] [Supplemental On Line Material] Cornejo, OE, and AA Escalante. 2006. The origin and age of Plasmodium vivax. Trends in Parasitology 22(12): 558-563.[PDF] Escalante, AA., Cornejo, OE, Freeland, DE, Poe, AE, Durrego, E, Collins, WE, and AA Lal. 2005. A monkey’s tale: The origin of Plasmodium vivax as a human malaria parasite. Proceedings of the National Academy of Sciences 102(6): 1980-1985. [PDF] Escalante, AA, Cornejo, OE, Rojas, A, Udhayakumar, V, and AA Lal. 2004. Assessing the effect of natural selection in malaria parasites. Trends in Parasitology 20(8): 388-395. [PDF]


Kim Garner Lab Manager - Technician extraordinare B.S., Agricultural Science (1999), Tennessee State University M.S., Animal Science (Microbiology) (2002), University of Tennessee, Knoxville MPH, Environmental and Occupational Health (anticipated 2009), Emory University	Publications in addition to the three from this Lab. Ebner P, K. Garner and A.G. Mathew. June 2004. Class I integrons in various Salmonella enterica isolated from animals and identification of genomic island SGI1 in Salmonella enterica var. Meleagridis. Journal of Antimicrobial Chemotherapy 53(6):1004-9 Mathew AG.,Garner KN, Ebner PD, Saxton AM, Clift RE, Liamthons S. Fall 2005. Effect of antibiotic use in sows on resistance of E.coli and Salmonells enterica Typhimurium in their offspring. Foodborne Pathog. Dis. 2(3):212-20



Pål Johnsen Visiting Associate Professor Department of Pharmacy University Education : 2000-2004: MSc (Cand. Scient)/PhD (Doctor Scient.) Department of Medical Biology/University Hospital of North Norway (UNN), University of Tromsø , Norway . Professor Arnfinn Sundsfjord's laboratory. 2004-2007: Post Doc Department of Pharmacy, University of Tromsø, Norway. Professor Kaare M. Nielsen Lab. My research interests are microbial evolution and population dynamics with an emphasis on horizontal gene transfer, its evolution and role in the adaptation of bacteria their current and novel environments. I am also interested in the different population processes involved in persistence of antibiotic resistant bacteria after the removal of antimicrobial drug selective pressures. My research whilst "vacationing" in Bruce Levin's Lab include theoretical and experimental studies of the population dynamics of Bacillus subtilis and the conditions responsible for the evolution and maintenance of competence and transformation.	Publications Johnsen, P.J., D. Dubnau, and B. R. Levin (2009) Episodic Selection and the Maintenance of Competence and Natural Transformation in Bacillus subtilis (GENETIC S, In Press) [PDF] Johnsen P. J ., G. S. Simonsen, Ø. Olsvik, T. Midtvedt, and A. Sundsfjord. 2002. Stability, persistence, and evolution of plasmid-encoded VanA glycopeptide resistance in enterococci in the absence of antibiotic selection in vitro and in gnotobiotic mice. Microb. Drug. Resist . 8: 161-170. Johnsen P. J ., J. I. Østerhus, H. Sletvold, M. Sørum, H. Kruse, K. Nielsen, G. S. Simonsen, and A. Sundsfjord. 2005. Persistence of animal and human glycopeptide resistant enterococci on two Norwegian poultry farms formerly exposed to avoparcin is associated with a widespread plasmid-mediated vanA-element within a polyclonal Enterococcus faecium population. Appl. Environm. Microbiol. 71: 159-168. Sletvold H., P. J. Johnsen, G. S. Simonsen, B. Aasnes, A. Sundsfjord, and K. M. Nielsen. 2007. Comparative DNA analysis of two vanA plasmids from Enterococcus faecium strains isolated from poultry and a poultry farmer in Norway. Antimicrob. Agents Chemother. 51: 736-9. Sørum M., P. J. Johnsen, B. Aasnes, T. Rosvoll, H. Kruse, A. Sundsfjord, and G. S. 2006. Simonsen.Colonisation, persistence, and molecular characterisation of glycopeptide resistant enterococci (GRE) in Norwegian poultry and poultry farmers three to eight years after the ban of avoparcin. Appl. Environm. Microbiol. 72: 516-521. Nielsen K. M., P. J. Johnsen, and J. D. Van Elsas. Gene transfer and microevolution in soil. 2007, in: Modern Soil Microbiology 2 nd ed. CRC Press, Boca Raton, Chapt. 3, pp. 55-81. Dahl K. H., D. D. Mater, M.J. Flores, P. J. Johnsen, T. Midtvedt, G. Corthier, and A. Sundsfjord. 2007. Transfer of plasmid and chromosomal glycopeptide resistance determinants occurs more readily in the digestive tract of mice than in vitro and exconjugants can persist stably in vivo in the absence of glycopeptide selection. J. Antimicrob. Chemother. 59: 478-86. Nielsen K. M., P. J. Johnsen , D. Bensasson, and D. Daffonchio. 2007. Release and persistence of extracellular DNA in the environment. Environ. Biosafety Res. In Press


Elisa Margolis MD/Ph.D. Student BA Brown University I have a broad interest in evolutionary medicine and have been engaged in exploring the evolutionary question of why infectious diseases make people sick. While evolutionary biologists have come up with many reasons why diseases make people sick they can not account for two observations: most pathogens rarely cause damage and the damage of many pathogens is ultimately due to the host's own immune response. I am interested in exploring the implications of these observations on the evolution of virulence. In order to test why most pathogens rarely cause disease I have tested whether within-host evolution occurs during colonization of commensal bacteria, whereby in the colonizing population an invasive strain evolves and is responsible for bacteremias. I am also exploring the evolutionary consequences of immune over-responses, in particular the formation of bacterial abscesses as an immune response which hinders clearance and provides a refugee for bacteria.	Publications Margolis, E. (2009) Hydrogen peroxide mediated interference competition by Streptococcus pneumoniae has no significant effect on Staphylococcal nasal colonization of neonatal rats J. Bact. 191: 571-575 [PDF] Handel, A, E. Margolis and B.R. Levin (2008) Exploring the role of the immune response in preventing antibiotic resistance(Theoretical Biology 1095-8541 Electronic – E published ahead of print) [PDF] Margolis, E. and B. R. Levin (2008) The evolution of bacteria-host interactions: virulence and the immune over-response. IN “ Introduction to the Evolutionary Biology of Bacterial and Fungal Pathogens ” J-A. Gutteriez and F.M. Baquero Editors (ASM Press) - Also to be published in an Institute of Medicine (IOM) workshop report in honor of Joshua Lederberg [PDF] Margolis, E. and B.R. Levin 2007 Within–Host Evolution for the Invasiveness of Commensal Bacteria: an experimental study of bacteremias resulting from Haemophilus influenzae nasal carriage, Journal of Infectious Disease 175: 1069-1075 [PDF]


Klas Ifeanyi Udekwu Postdoctoral Research Associate Background My graduate studies were in the department of Cell and Molecular Biology in Uppsala University, Sweden. My Master's research was on tRNA identity under the supervision of Professor Leif Kirsebom. The title of my PhD dissertation which I did under the direction of Professor E Gerhart Wagner is “Functional characterization of the small Antisense RNA MicA in Escerichia coli”. In that investigation, I discovered the target of a (then) newly identified small RNA with the help of global screening methodology. My collaborators and I then characterized the mode of interaction and post-transcriptional control exerted by this antisense RNA on its target, a long-lived mRNA encoding the OmpA outer membrane porin. I went on to chart the transcriptional profile of this small RNA in response to various disfavourable environmental conditions and showed it to be under exclusive control of the membrane stress-related sigma factor, σE. My postdoctoral research involves the application of the tools of population and molecular biology to improving the success of antibiotic treatment and understanding the mechanisms of antibiotic action. My current research includes theoretical, in vitro and laboratory animal experiments. Of particular concern in these studies are the effects of the density and physiological state of Staphylococcus aureus on the in vitro pharmacodyanamics of antibiotics of different classes their their implications for therapy. The results of my studies have raised a number of questions about the mechanisms by which antibiotics of different classes kill and/or inhibit the growth of bacteria and their response to stress which I will also be addressing.	Publications Udekwu, K,; N. Parrish, P. Ankomah, , F. Baquero and BR Levin (2009) Functional Relationship Between Cell Density and the Efficacy of Antibiotics (Journal of Antimicrobial Chemotherapy, In Press). [PDF] Udekwu et al., 2005. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA, Genes & Development 1;19(19):2355-66. Udekwu & Wagner, 2007. Sigma E controls biogenesis of the antisense RNA MicA, Nucleic Acids Research 35(4):1279-88


Yan Wei Ph.D. Student 1999-2003 B.S. in Biological Sciences Beijing Forestry University, China 2003-2004 M.Sc in Biological Science University of Bath, UK I am interested in population dynamics of bacteria and phage. While almost all of my research is in vitro and most of my time is spent in the Laboratory, as noted by my photo I sometime go into the real world. My PhD dissertation research is on the population dyanmics of Vibrio cholerae and its lytic phage and the role of these viruses in regulating the densities of populations of these bacteria and the effects of resistance to these phage on the fitness and virulence of these bacteria. Of particular concern in this investigation is the potential role of these viruses in controlling outbreaks of cholera in humans (see Jensen et al. 200, Proc. Nat. Acad. Sci. US103:4652-4657and the associated references). Alhough I I am not planning to consider the contribution of camels to the ecology of V. cholereae and its phage, in my microcosm studies I'm considering the role of different copepods and other zooplankton with V. cholerae interact.	As you can see, I also like camels... and I am trying to inoculate bacteria in them (BUT, DO NOT TELL ANYBODY) Publications Buckling A, Wei Y, Massey RC, Brockhurst MA, Hochberg ME (2006)Antagonistic coevolution with parasites increases the cost of host deleterious mutations. Proc. R. Soc. London, Ser. B 273(1582):45-9. [PDF]