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Department of Microbiology


College of Liberal Arts and Sciences
University of Illinois at Urbana–Champaign, Champaign, Illinois



Detailed Information

Programs of Study


The Department of Microbiology offers a graduate program leading to a Ph.D. degree. The Ph.D. program emphasizes molecular microbiology, including molecular genetics, microbial physiology, microbial ecology and evolution, pathogenic microbiology, cell biology, virology, and immunology. A Medical Scholars Program leading to an M.D./Ph.D. is also offered.

During the first semester of their first year, students rotate through several laboratories to learn experimental techniques and to choose a research project. By the end of the first semester, students choose a research adviser, and they propose a thesis project during the spring semester of the first year. An oral qualifying exam is given at the end of the second year. Students generally complete their Ph.D. in about five years.

All students teach for at least two semesters as part of their graduate training.

Research Facilities


The Department has all the major equipment and technical expertise needed for modern research, including DNA, protein, antibody, microscopy, and metabolomics core facilities.

Financial Aid


All students admitted to the Ph.D. program receive financial support, including tuition waivers. The starting stipend in 2008–09 was $22,660 per year plus a tuition waiver. Several fellowships, either through the Department or through NIH training grants, are awarded on a competitive basis to outstanding graduate students. Many students are supported by research or teaching assistantships.

Cost of Study


Students should see the Financial Aid section.

Living and Housing Costs


There are many affordable rental options, including modern luxury apartments, loft apartments in downtown areas, and historic houses on tree-lined streets. The University also rents apartments to single or married graduate students (http://www.housing.uiuc.edu). Most residences are within walking or biking distance of the University. For 2008–09, the monthly cost of a one-bedroom apartment ranged from $400 to $500 per month.

Student Group


There are approximately 90 Ph.D. candidates in the Department. Students are selected from a pool of highly qualified national and international applicants, with 10 to 15 students joining the Department each year.

Student Outcomes


Recent graduates have pursued postdoctoral training at some of the best institutions in the United States. Many alumni are currently employed in academia or in scientific positions in the pharmaceutical or biotechnology industries.

Location


The twin cities of Urbana-Champaign lie in the rich Central Illinois prairie about 130 miles south of Chicago. A parklike city with a population of about 130,000, Urbana-Champaign is served by airlines, trains, and interstate highways. Year round, this cosmopolitan community enjoys a wealth of artistic, musical, theatrical, and college sporting events. The city is noted for its live music scene. Urbana-Champaign also offers affordable housing, short commutes, excellent bus service, and outstanding facilities for exercise as well as many lively and congenial places to dine and socialize—and celebrate successes in the lab.

The Department


The Department of Microbiology has been consistently ranked by the National Science Foundation and U.S. News & World Report as one of the best microbiology departments in the United States. The Department encourages close interaction among faculty members and graduate students working in different laboratories. The Department is part of an umbrella program in molecular and cellular biology that encompasses eighty research laboratories.

Applying


Admission to the Ph.D. program in microbiology requires a bachelor’s degree in biological or physical sciences. Applicants should have at least a 3.0 GPA in the last 60 hours of undergraduate work and any graduate work completed. The GRE General Test is also required. Prior research experience is important. MCAT scores are accepted in lieu of GRE scores for applicants to the Medical Scholars Program. For TOEFL scores, a minimum score of 590 (paper-based test), 243 (computer-based test), or 96 (Internet-based test) is required of applicants from countries where English is not the primary language.

Generally, students are only admitted in the fall semester. For full consideration, complete applications should be received by January 15.

The Faculty and Their Research


  • Steven R. Blanke, Ph.D., Illinois at Urbana-Champaign, 1989. Molecular and cellular basis of infection biology and bacterial pathogenesis; bacterial toxins; bacterial persistence during infection; intracellular infection; complex systems and polymicrobial diseases; Helicobacter pylori; gastric ulcer disease and stomach cancer; Bacillus anthracis; novel antimicrobials. Sphingomyelin functions as a novel receptor for Helicobacter pylori VacA: PLoS Pathogens 4(5):e1000073:1–12, 2008 (with Gupta). Helicobacter pylori VacA: A paradigm for toxin multifunctionality. Nat. Rev. Microbiol. 3(4):320–32, 2005 (with Cover). Micro-managing the executioner: Pathogen targeting of mitochondria. Trends Microbiol. 13(2):64–71, 2005. Helicobacter pylori vacuolating cytotoxin enters cells, localizes to the mitochondria, and induces mitochondrial membrane permeability changes correlated to toxin channel activity. Cell Microbiol. 6(2):143–54, 2004 (with Willhite).
  • Isaac K. O. Cann, Ph.D., Mie (Japan), 1994. DNA replication in archaea; enzymes of plant cell wall hydrolysis. Cell sorting protein homologs reveal an unusual diversity in archaeal cell division. Proc.Natl. Acad. Sci. U.S.A. 105(48):18653–4, 2008. Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23. J. Bacteriol. 191(10):3328–38, 2009 (with Dodd et al).
  • John E. Cronan Jr., Ph.D., California, Irvine, 1968. Regulation and mechanisms of lipid metabolism; synthesis of biotin and lipoic acid. Vibrio cholerae FabV defines a new class of enoyl acyl–carrier–protein reductase. J. Biol. Chem. 283:1308–13, 2008 (with Massengo-Tiassé). Genetic interaction between the Escherichia coli AcpT phosphopantetheinyl transferase and the YejM inner membrane protein. Genetics 178:1327–37, 2008 (with De Lay).
  • Stephen K. Farrand, Ph.D., Rochester, 1973. Molecular signaling between bacteria and between bacteria and their hosts; quorum sensing; mechanisms of plasmid transfer. Mutational analysis of TraR: Correlating function with molecular structure of a quorum-sensing transcriptional activator. J. Biol. Chem. 278:13173–82, 2003 (with Luo, Smyth, and Qin). The quorum-sensing system of Agrobacterium plasmids: Its analysis and its utility. Meth. Enzymol. 358:452–84, 2002 (with Qin and Oger). Co-evolution of the agrocinopine opines and the agrocinopine-mediated control of TraR, the quorum-sensing activator of the Ti plasmid conjugation system. Mol. Microbiol. 41:1173–86, 2001 (with Oger). The antiactivator TraM interferes with the autoinducer-dependent binding of TraR to DNA by interacting with the C-terminal region of the quorum-sensing activator. J. Biol. Chem. 275:7713–22, 2000 (with Luo and Qin). Quorum-sensing signal binding results in dimerization of TraR and its release from membranes into the cytoplasm. EMBO J. 19:5212–21, 2000 (with Qin et al.). TraG from RP4 and TraG and VirD4 from Ti plasmids confer relaxosome specificity to the conjugal transfer system of pTiC58. J. Bacteriol. 182:1541–8, 2000 (with Hamilton et al.). Signal-dependent DNA binding and functional domains of the quorum-sensing activator TraR as defined by repressor activity. Proc. Natl. Acad. Sci. U.S.A. 96:9009–14, 1999 (with Luo).
  • Bruce Fouke, Ph.D., SUNY at Stony Brook, 1993. Coral reef and hot spring geomicrobiology: microbe-water-mineral interactions. Microbial biomass: A catalyst for CaCO3 precipitation in advection dominated regimes. Geol. Soc. Am. Bull. 120:442–50, 2008 (with Kandianis, Johnson, Veysey, and Inskeep). Change in zooxanthellae and mucocyte tissue density as an adaptive response to environmental stress by the coral Montastraea annularis. Mar. Biol. 2009 (with Piggot, Sivaguru, Sanford, and Gaskins), in press.
  • Jeffrey F. Gardner, Ph.D., Marquette, 1975. Mechanism of site-specific recombination by bacteriophages and conjugative transposons; mechanisms of protein-DNA interactions; characterization of excisionase proteins. CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges. Nucleic Acids Res. 35:5861–73, 2008 (with Malanowska, Yoneji, and Salyers). The Bacteroides NBU1 integrase performs a homology independent strand exchange to form a Holliday junction intermediate. J. Biol. Chem. 282:31228–37, 2008 (with Rajeev, Segall, and Salyers). Characterization of the integrase of NBU1, a Bacteroides mobilizable transposon. Mol. Microbiol. 61:978–90, 2006 (with Rajeev and Salyers). Characterization of a conjugative transposon integrase, IntDOT. Mol. Microbiol. 60:1228–40, 2006 (with Malanowska and Salyers).
  • James A. Imlay, Ph.D., Berkeley, 1987. Mechanisms by which oxidants damage cells; cellular defenses against oxidative stress. Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli. Mol. Microbiol. 72(4):844–58, 2009 (with Anjem and Varghese). The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity. Proc. Natl. Acad. Sci. U.S.A. 106(20):8344–9, 2009 (with Macomber). Cellular defenses against superoxide and hydrogen peroxide. Annu. Rev. Biochem. 77:755–76, 2008.
  • Andrei Kuzminov, Ph.D., Novosibirsk (Russia), 1990. Chromosomal fragmentation: mechanisms, repair, and avoidance in Escherichia coli. Patterns of chromosomal fragmentation due to uracil-DNA incorporation reveal a novel mechanism of replication-dependent double-strand breaks. Mol. Microbiol. 68:202–15, 2008 (with Kouzminova). The mutT defect does not elevate chromosomal fragmentation in Escherichia coli because of the surprisingly low levels of MutM/MutY-recognized DNA modifications. J. Bacteriol. 189:6976–88, 2007 (with Rotman). The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision. J. Biol. Chem. 281:22635–46, 2006 (with Amado).
  • William W. Metcalf, Ph.D., Purdue, 1991. Molecular, genetic, and biochemical analysis of methanogenic archaea and phosphorus metabolism in bacteria. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat. Chem. Biol. 3:480–5, 2007 (with Blodgett et al.). Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway. Proc. Natl. Acad. Sci. U.S.A. 102:10664–9, 2005 (with Welander).
  • Charles G. Miller, Ph.D., Northwestern, 1968. Mechanisms of intracellular protein breakdown and proteolytic modification. DapE can function as an aspartyl peptidase in the presence of Mn2+. J. Bacteriol. 185:4748–54, 2003 (with Broder). Structure of peptidase T from Salmonella typhimurium. Eur. J. Biochem. 269:443–50, 2002 (with Häkansson).
  • Gary J. Olsen, Ph.D., Colorado, 1983. Genome analysis; gene expression in the Archaea; evolution of genes and genomes; microbial ecology. Critical evaluation of two commonly-used primers for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 74:2461–70, 2008 (with Frank et al.). Genomic minimalism in the early diverging, intestinal parasite, Giardia lamblia. Science 317:1921–6, 2007 (with Morrison et al.). The RAST Server: Rapid annotations using subsystems technology. BMC Genom. 9:75, 2008 (with Aziz et al.). A whole-genome approach to identifying protein binding sites: Promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 36:6948–58, 2008 (with Li et al.).
  • Peter A. B. Orlean, Ph.D., Cambridge, 1982. Glycolipid anchoring of protein; structure and function of membrane-bound glycosyltransferases; cell wall biogenesis in yeast and pathogenic fungi. GPI anchoring of protein in yeast and mammalian cells or: How we learned to stop worrying and love glycophospholipids. J. Lipid Res. 48:993–1011, 2007 (with Menon). In vivo characterization of the GPI assembly defect in yeast mcd4-174 mutants and bypass of the Mcd4p-dependent step in mcd4a cells. FEMS Yeast Res. 7:78–83, 2007 (with Wiedman, Fabre, B. Taron, and C. Taron).
  • Abigail A. Salyers, Ph.D., George Washington, 1969. Interaction of colonic bacteria with host; molecular microbial ecology; genetics of obligate anaerobes; polysaccharide uptake and catabolism by Bacteroides; conjugative transposons of Bacteroides. Unexpected effect of a Bacteroides conjugative transposon, CTnDOT, on chromosomal gene expression in its bacterial host. Mol. Microbiol. 64:1562–71, 2007 (with Moon and Sonnenburg). A Bacteroides conjugative transposon, CTnERL, can transfer a portion of itself by conjugation without excising from the chromosome. J. Bacteriol. 188:1169–74, 2006 (with Whittle and Shoemaker). Characterization of a conjugative transposon integrase, IntDOT. Mol. Microbiol. 60:1228–40, 2006 (with Malanowska and Gardner). Revenge of the Microbes. Washington, D.C.: ASM Press, 2005 (with Whitt).
  • Joanna L. Shisler, Ph.D., Emory, 1996. Poxvirus evasion of immune responses; viral proteins that inhibit the NF-?B transcription factor. Poxviral regulation of the host NF-?B response: The vaccinia virus M2L protein inhibits induction of NF-?B activation via an ERK2 pathway in virus-infected human embryonic kidney cells. J. Virol. 80:8676, 2006 (with Gedey, Jin, and Hinthong). The MC 160 protein expressed by the dermatotropic Molluscum contagiosum virus prevents tumor necrosis factor alpha-induced host NF-?B activation via inhibition of the I kappa kinase complex. J. Virol. 80:578, 2006 (with Nichols).
  • James M. Slauch, Ph.D., Princeton, 1990. Molecular mechanisms of Salmonella pathogenesis. Phagocytic superoxide specifically damages an extracytoplasmic target to inhibit or kill Salmonella. PLos One 4(3):e4975, 2009 (with Craig). The Salmonella SPI1 type three secretion system responds to periplasmic disulfide bond status via the flagellar apparatus and the RcsCDB system. J. Bacteriol. 190:87–97, 2008 (with Lin and Rao). Fur regulates expression of the Salmonella SPI1 type three secretion system by post-transcriptionally controlling expression of HilD. J. Bacteriol. 190:476–86, 2008 (with Ellermeier).
  • Richard I. Tapping, Ph.D., McMaster, 1995. Genetic basis of host resistance to Yersinia pestis. Infect. Immun. 77(1):367–73, 2009; Infect. Immun.76(9):4092–9, 2008; J. Biol. Chem. 282(43):31197–205, 2007; Eur. J. Immunol. 37(8):2059–62, 2007; J. Immunol. 178(12):7520–4, 2007; J. Immunol. 178(10):6387–94, 2007.
  • Carin K. Vanderpool, Ph.D., Minnesota, 2003. Molecular biology and genetics of small RNA-regulated bacterial stress responses; physiology of sugar-phosphate stress in Escherichia coli; biochemistry of novel family of transcription factors. A novel dual function for a bacterial small RNA: SgrS performs basepairing-dependent regulation and encodes a functional polypeptide. Proc. Natl. Acad. Sci. U.S.A. 104:20454–9, 2007. Physiological consequences of small RNA–mediated regulation of glucose-phosphate stress. Curr. Opin. Micro. 10(2):146–51, 2007. The novel transcription factor SgrR coordinates the response to glucose-phosphate stress. J. Bacteriol. 189(6):2238–48, 2007 (with Gottesman).
  • Rachel J. Whitaker, Ph.D., Berkeley, 2004. Evolutionary ecology in microbial populations; population genomics in natural microbial communities with a focus on Archaea; geomicrobiology and microbial ecology. Allopatric origins of microbial species. Phil. Trans. Roy. Soc. Lond. B 361(1475):1975–84, 2006. Population genomics in natural microbial communities. Trends Ecol. Evol. 21(9):508–16, 2006 (with Banfield); doi:10.1016/j.tree.2006.07.001. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol. Biol. Evol. 22:2354–61, 2005. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–8, 2003 (with Grogan and Taylor).
  • Brenda A. Wilson, Ph.D., Johns Hopkins, 1989. Bacterial toxin interaction with host cells. Proc. Natl. Acad. Sci. U.S.A. 106:7179–84, 2009; J. Biol. Chem. 283:23288–94, 2008; J. Biol. Chem. 283:17009–19, 2008; Protein Sci. 17:1–5, 2008; Cell. Microbiol. 9:2485–96, 2007. Anti-toxin therapeutics. Toxicon 53:392–9, 2009; Toxicon 51:597–605, 2008; Infect. Immun. 73:6998–7005, 2005; Curr. Opin. Biotechnol. 13:267, 2002. Host-microbial ecosystems. J. Clin. Microbiol. 47:1181–9, 2009; Appl. Environ. Microbiol. 74:2461–70, 2008.
  • Carl R. Woese, Ph.D., Yale, 1953. Molecular evolution of prokaryotes; structure and function of protein translation apparatus. Biology’s next revolution. Nature 445:369, 2007 (with Goldenfeld). A new biology for a new century. Microbiol. Mol. Biol. Rev. 68:173–186, 2004. On the nature of global classification. Proc. Natl. Acad. Sci. U.S.A. 89:2930–4, 1992 (with Whellis and Kandler).

Correspondence and Information


University of Illinois at Urbana-Champaign
Department of Microbiology
B103 Chemical and Life Sciences Laboratory, MC-110
601 South Goodwin Avenue
Urbana, Illinois 61801-3709
Email: gradinfo@mcb.uiuc.edu