OSU Microbiology
Faculty Bios
Faculty Bios

Bacteriophage Ecology and Evolutionary Ecology

Stephen T. Abedon

Stephen T. Abedon


Associate Professor.
Ph.D., University of Arizona, 1990.


Bacteriophage Ecology and Evolutionary Ecology

Bacteriophage, or phage, are the viruses of bacteria. I am interested especially in phage adaptation: How phages can and have optimized their characteristics toward meeting the challenges of growth and survival. My research consists of a combination of theoretical and empirical analyses of phage population growth, and structure, as it occurs within both broth and semi-solid environments. My overall goal is to develop a more-complete theoretical understanding of the constraints acting on phage evolution.

Recent Publications

Calendar, R., Abedon, S.T. (eds) (in press). The Bacteriophages . Second Edition.

Abedon, S.T. (in press). Phage ecology. The Bacteriophages . Second Edition.

Abedon, S.T., Culler, R.R. (2007). Bacteriophage Evolution Given Spatial Constraint. Journal of Theoretical Biology, in press.

Abedon, S.T. (2006). Phage Ecology. In R. Calendar & S.T. Abedon (eds): The Bacteriophages Edition 2, Oxford University Press, pp. 37-46.

Abedon, S.T., LeJeune, J.T. (2005). Why Bacteriophage Encode Exotoxins and Other Virulence Factors. Evolutionary Bioinformatics Online 1:97-110.

Breitbart, M., Rohwer, F., Abedon, S.T. (2005). Phage Ecology and Bacterial Pathogenesis. In M.K. Waldor, D.I. Friedman, & S.L. Adhya (eds): Phages: Their Role in Bacterial Pathogenesis and Biotechnology, ASM Press, Washington, DC, pp. 66-91.

LeJeune J.T, Abedon, S.T., Takemura, K., Christie, N.P. and Sreevatsan, Human S. (2004). Escherichia coliO157:H7-Genetic marker in isolates of bovine origin. Emerging Infect. Dis. 10:1482-1485.

Goodridge, L., Abedon, S.T. (2003). Bacteriophage Biocontrol and Bioprocessing: Application of Phage Therapy to Industry. SIM News , 53:254-262. Click for PDF

Abedon, S.T. , Hyman, P., Thomas, C. (2003). Bacteriophage Latent-Period Evolution as a Response to Bacteria Availability: An Experimental Examination. Applied and Environmental Microbiology , 69:7499-7506. Click for PDF

Gill, J.J., Abedon, S.T. (2003). Bacteriophage Ecology and Plants. APSnet Feature , November 2003, http://www.apsnet.org/online/feature/phages/ . Click for PDF

Abedon, S.T. , Herschler, T. D., Stopar, D. (2001). Bacteriophage latent-period evolution as a response to resource availability. Applied and Environmental Microbiology 67:4233-4241. Click for PDF

Abedon, S.T. (2000). The murky origin of Snow White and her T-even Dwarfs. Genetics 155:481-486. Click for PDF

Abedon, S.T. (1999). Resistance to lysis-inhibition collapse. Genetical Research 74:1-11. Click for PDF

Paddison, P., Gailbreath, K., Dressman, H., Abedon, S.T. , Mosser, E., Neitzel, J., Guttman, B., Kutter, E. (1998) Lysis inhibition and fine-structure genetics in bacteriophage T4. Genetics. 148:1539-1550. Click for PDF

Abedon, S.T. (1994). Lysis and the interaction between free phages and infected cells. The Molecular Biology of Bacteriophage T4. Jim D. Karam, John W. Drake, Kenneth N. Kreuzer, Gisela Mosig, Dwight Hall, Frederick A. Eiserling, Lindsay W. Black, Elizabeth Kutter, Karin Carlson, Eric S. Miller, Eleanor Spicer (eds). Washington, DC ASM Press. pp. 397-405 Click for PDF

Abedon, S.T.(1992). Lysis of lysis-inhibited bacteriophage T4 infected cells. Journal of Bacteriology 174:8073-8080. Click for PDF

Abedon, S.T.(1990). Selection for lysis-inhibition in bacteriophage. Journal of Theoretical Biology 146:501-511. Click for PDF

Abedon, S.T. (1989). Selection for bacteriophage latent period length by bacterial density: A theoretical examination. Microbial Ecology 18:79-88. Click for PDF

Stephen T. Abedon Home Page , Phage Ecology , The Bacteriophages

Faculty Bios

Bacterial Pathogenesis and Genomics.

Robert S. Munson, Jr.


Professor Department of Pediatrics

Bacterial Pathogenesis and Genomics.

Research Summary:
Nontypeable Haemophilus influenzae is an important cause of otitis media in children, and a major cause of lower respiratory disease in children in the developing world. The organism is also associated with exacerbations of chronic bronchitis, and pneumonia in elderly and immunocompromised patients.

Haemophilus ducreyi is the causative agent of chancroid, a sexually transmitted disease. Chancroid ulcers facilitate the transmission of HIV. My laboratory is employing a number of genetic and immunological approaches in order to assess the role of outer membrane proteins, toxins and adhesins in the pathogenesis of Haemophilus disease.

My laboratory is also interested in global regulation of expression of virulence determinants. We also have a major interest in bacterial genomics. Recently, we completed the sequence of the genome of H. ducreyi and we are currently annotating the sequence.

Recent Publications

Sun, S., Schilling, B., Tarantino, L., Tullius, M. V., Gibson, B. W. and Munson, R. S., Jr. (2000). Cloning and characterization of the lipooligosaccharide galactosyltransferase II gene of Haemophilus ducreyi. J Bacteriol 182 (8): 2292-8.

Young, R. S., Fortney, K., Haley, J. C., Hood, A. F., Campagnari, A. A., Wang, J., Bozue, J. A., Munson, R. S., Jr. and Spinola, S. M. (1999). Expression of sialylated or paragloboside-like lipooligosaccharides are not required for pustule formation by Haemophilus ducreyi in human volunteers. Infect Immun 67 (12): 6335-40.

Bozue, J. A., Tullius, M. V., Wang, J., Gibson, B. W. and Munson, R. S., Jr. (1999). Haemophilus ducreyi produces a novel sialyltransferase. Identification of the sialyltransferase gene and construction of mutants deficient in the production of the sialic acid-containing glycoform of the lipooligosaccharide. J Biol Chem 274 (7): 4106-14.

Cope, L. D., Lumbley, S., Latimer, J. L., Klesney-Tait, J., Stevens, M. K., Johnson, L. S., Purven, M., Munson, R. S., Jr., Lagergard, T., Radolf, J. D. and Hansen, E. J. (1997). A diffusible cytotoxin of Haemophilus ducreyi. Proc Natl Acad Sci U S A 94 (8): 4056-61.

Palmer, K. L. and Munson, R. S., Jr. (1995). Cloning and characterization of the genes encoding the hemolysin of Haemophilus ducreyi. Mol Microbiol 18 (5): 821-30

Faculty Bios

Peptide and Protein Design, Antigenic and Immunogenic Determinants, Peptide & Protein Folding

Pravin T. P. Kaumaya

Pravin T. P. Kaumaya


Ph.D., 1981, Portsmouth School of Pharmacy, England

Peptide and Protein Design, Antigenic and Immunogenic Determinants, Peptide & Protein Folding.

Research efforts in my laboratory are primarily based on exploiting the immune system’s exquisite specificity which offers one of the simplest and most effective ways to prevent and control disease. To achieve our goals a multidisciplinary research approach is being pursued which is at the interface of chemistry and biology with special emphasis on modulation of the immune response. We have and are continuing to develop innovative approaches to antigen specific vaccination as well as developing immunotherapies for cancer and autoimmune diseases. Therefore, we are actively pursuing an interdisciplinary approach to testing a novel multi-epitope cancer vaccine that bridges the synthetic, preclinical, and clinical elements of vaccine development. Several long term objectives include: 1) developing a widely applicable vaccine targeting the HER-2 oncoprotein (breast/ovarian/tumor/cancer vaccine and to gain understanding of immune response to self peptides in normal and pathologic conditions, 2) developing a widely applicable blockade strategy targeting costimulatory molecules (CD28:B7, CD40:CD40L) and also to elucidate the underlining mechanisms in downregulating immune responses as well as to gain understanding the biological active conformation of these peptide mimics and how they interact with the costimulatory molecules, 3) developing a B cell and T-cell vaccine for the retrovirus – HTLV-I (the causative agent of Adult T-cell Leukemia).

For peptide vaccines to become a practical reality, rationally designed, highly engineered synthetic constructs must incorporate enough antigenic determinants to elicit all three arms of the immune system. Novel vaccines designed to stimulate both antibody and T cell responses against human tumors are urgently required. It is critical to identify general rules for the definition of immunogenicity so that vaccine optimization is rational rather than empirical. Identification of the biologically relevant epitopes, devising strategies to engineer conformationally dependent sequences¸ adopting ways to increase the immunogenicity in an outbred population, delivering the immunogen in a safe and efficacious vehicle, developing animal models are at the basis of our approaches to developing new anticancer and retroviral vaccines. With these factors in mind, we have developed strategies for the design of PEPTIDE VACCINES that can provide optimal B cell, T helper cell and cytotoxic T cell responses. Our approach for the design of peptide vaccines with improved binding affinities, titers, and enhanced immunity a priori relies on the engineering of structured peptides which mimic antibody recognition sites and approaches to bypass MHC “restriction” of the T cell response. The immune responses (B-cell and T cell) to these peptides are then extensively studied to correlate biological or immunological reactivity with structure. This process of design, synthesis, structural characterization and immunological testing may point to a general strategy for tailoring peptide vaccines with more useful antigenic and immunogenic characteristics. Empirical and computational approaches are applied to the engineering and synthesis of complex peptide sequences designed to adopt well defined -secondary and three dimensional structures. A variety of biophysical techniques (CD, FTIR, SAXS, NMR, MS and X-Ray crystallography) are used to extensively characterize the chemical and structural properties of the synthetic peptides.

On the other spectrum of our research goals, overwhelming experimental evidence has emerged in recent years concerning the impact of costimulatory signals for complete T cell activation and has allowed investigators to develop new strategies for immune intervention, both for suppression of the immune system and for stimulation of the immune system. Attempts to block T cell costimulation as a therapeutic strategy in autoimmunity and transplantation have gained tremendous momentum. We are developing novel immunotherapeutic strategies that take advantage of normal mechanisms of tolerance to self antigen for immune intervention both for suppression of the immune system (autoimmune diseases (Multiple Sclerosis) and transplantation) and for stimulation of the immune system (vaccines). Our focus has been directed towards developing novel peptide mimics of ligand-binding regions of several costimulatory molecules (CD28:B7 and CD40:CD40L) in an attempt to block T cell costimulation pathways by use of retro-inverso (RI) modification of peptides that preserves the parent peptide overall topology and provides at the same time stability to proteolysis, leading to derivatives with prolonged half-life in vitro and in vivo. Blocking T cell costimulation as a therapeutic strategy in autoimmunity and transplantation is a major thrust in our laboratories.

Recent Publications

Kaumaya, P.T.P., Berndt, K., Heindorn, D., Trewhella, J., Kezdy, F.J. and Goldberg, E. (1990) Synthesis and Biophysical Characterization of Topographic Immunogenic Determinants with aa Topologies. Biochemistry, 29,13-23.

Kaumaya, P.T.P., VanBuskirk, A., Goldberg, E. and Pierce, S.K. (1992) Design and Immunological Properties of Topographic Immunogenic Determinants of a Protein Antigen (LDH-C4) as Vaccines. J. Biol. Chem., 267, 6338-6346.

Kaumaya, P.T.P., Seo, Y.H., Kobs, S., Ngua, l., Sheridan, J. and Stevens, V. (1993) Peptide vaccines incorporating a “promiscuous” T cell epitope bypass certain haplotype restricted immune responses and provide broad spectrum immunogenicity. J. Molec. Recog. 6, 81-94.

Kobs-Conrad, S., Lee, H., DiGeorge, A.M. and Kaumaya, P.T.P. (1993) Engineered Topographic Determinants with ab, bab, and baba Topologies show High Affinity Binding to Native Protein Antigen LDH-C4. J. Biol. Chem., 268, 25285-25295.

Lairmore, M.D., DiGeorge, A.M., Conrad, S.F., Trevino, A. and Kaumaya, P.T.P. (1995) HTLV-I Peptides Constructs incorporating Promiscuous T cell epitopes overcome genetic restriction, elicit neutralizing antibodies and T cell help. J. Virol.,69 (10),6077-6089

Kaumaya, P.T.P. (1996) Synthetic Peptide Vaccines: Dream or Reality. In Peptides in Immunology (Schneider, C.H., Ed.) Wiley and Sons, Ltd., pp. 117-148

Bakaletz, L. O., Leake, E. R., Billy, J. M., and Kaumaya, P. T. P. (1997) Relative Immunogenicity and Efficacy of Two Synthetic Chimeric Peptides of Fimbrin as Vaccinogens against Nasopharyngeal Colonization by Nontypeable Haemophilus Influenzae in the Chinchilla. Vaccine 15 (9), 955-961.

Dakappagari, N.K., Douglas, D.B., Triozzi, P.L., Stevens, V.C., and Kaumaya, P.T.P. (2000) Prevention of Mammary Tumors with a Chimeric HER-2 B-cell Epitope Peptide Vaccine. Cancer Research 60, 3782-3789

Frangione, M., Albretch, B., Dakappagari, N., Rose, T., Brooks, C.L., Schwendeman, S.P., Lairmore, M.D., and Kaumaya, P.T.P. (2001) Enhanced Immunogenicity of a Conformational Epitope of Human T-Lymphotropic Virus Type 1 using a Novel Chimeric Peptide. Vaccine 19, 1068-1081

Frangione-Beebe, M., Rose, T., Kaumaya, P.T.P., and Schwendeman, S.P. (2001) Microencapsulation of a Synthetic Peptide for HTLV-1 in Biodegradable Poly(D,L-lactise-co-glycolide) Microspheres using a Novel Encapsulation Technique. J. of Microencapsulation 18 (5), 663-677

Srinivasan, M., Wardrop, R.M., Whitacre, C., and Kaumaya, P.T.P. (2001) A Retro-Inverso Peptide Mimic of CD28 Encompassing the MYPPPY Motif Adopts a Polyproline Type II Helix and Inhibits Encaphalitogenic T cell in Vitro. J. Immunol 167:578-585

Roshni Sundaram, Christopher M Walker, and Pravin T.P. Kaumaya. (2001) Evaluation of HTLV-1 Cytotoxic T-cell Epitopes in HLA-A2.1 Transgenic Mice. In Peptides: The Wave of the Future (Eds Houghten R.A and Lebl, M) Kluwer Academic Publisher, Dordrecht, Netherlands. In Press

Pravin T.P. Kaumaya, John Pyles and Naveen Dakappagari. (2001) A combination of HER-2 peptide epitope vaccines mediate superior biological effects. In Peptides: The Wave of the Future (Eds Houghten R.A and Lebl, M) Kluwer Academic Publisher, Dordrecht, Netherlands. In Press

Sundaram, R., Dakappagari., and Pravin T.P. Kaumaya. (2002) Synthetic Peptides as Cancer Vaccine. Bioplolymers 66 (3),200-216

Sundaram, R, Yiping Sun, C.Walker, F.A.Lemonnier, S.Jacobson, and Pravin T.P. Kaumaya. (2003) A Novel HTLV-1 Epitope CTL Peptide Construct Elicits Robust Cellular Immune Responses in HLA-A*0201 Transgenic ß2 M, Db Double Knockout Mice. Vaccine 21, 2767-2781

Dakappagari, N., Parihar,R., J.Pyles, W.E. Carson, and Pravin T.P. Kaumaya. (2003) A Chimeric Multi HER-2 B cell epitope Peptide Vaccine mediates Superior Anti-tumor Responses. J. Immunol. 170:4242-4253

Utano Tomaru, Yoshihisa Yamano, Masahiro Nagai, Dragan Maric, Pravin T.P. Kaumaya, William Biddison, and Steven Jacobson. (2003) Acquisition of Peptide/HLA-GFP Complexes by Virus-Specific T Cells Differentiate Stages of T Cell Maturation Associated with The Outcome of Chronic Viral Infections. Nature Medicine 9(4), 469-475.

Sundaram, R., Beebe, M., and Kaumaya, P.T.P. (2004) Structural and Immunogenicity analysis of chimeric B-cell epitope constructs derived from gp46 and gp21 subunits of the env glycoproteins of HTLV-1. J. Peptide Res., 63, 132-140

Roshni Sundaram, Marcus P. Lynch , Sharad V. Rawale, Yiping Sun, Merdud Kazanji and Pravin T.P. Kaumaya. (2004) Denovo Design of Peptide Immunogens that Mimic the Coiled Coil Region of Human T-cell Leukemia Virus Type-1 gp21 Transmembrane Subunit for Induction of Native Protein Reactive Neutralizing Antibodies. J. Biol Chem., April 1, Epub ahead of Print); 279 (23) 24141-24151

Roshni Sundaram, Sharad Rawale , Naveen Dakappagari, Donn Young, Christopher M Walker, Francois Lemonnier, Steven Jacobson and Pravin T.P. Kaumaya. (2004) Protective Efiicacy of Multiepitope HLA-A*0201 restricted CTL Peptide construct against challenge with HTLV-1 TAX recombinant vaccinia virus. J. Acquir. Immune Defic. Syndr. 37 (3), 1329-1339

Roshni Sundaram, Melanie Beebe and Pravin T.P. Kaumaya (2004) Structural and Immunogenicity analysis of Chimeric B-cell epitope constructs derived from the gp46 and gp21 subunits of the env proteins of HTLV-1. J. Peptide Res. 63, 1-9

Naveen K. Dakappagari, Kenneth D. Lute, Sharad Rawale, Joan T. Steele, Stephanie D. Allen, Gary Phillips, R. Todd Reilly, and Pravin T.P. Kaumaya (2005) Conformational HER-2/neu B-Cell Epitope Peptide Vaccine Designed to Incorporate Two Native Disulfide Bonds Enhances Tumor Cell Binding and Antitumor Activities. J.Biol Chem (manuscript in press)

Faculty Bios

The Role of MHC-Restricted Antigen Presentation in the Immune Response Against Invading Microbial Pathogens and Tumors

Paula Wolf Bryant

Assistant Professor
Ph.D. – Baylor College of Medicine, 1988-1993
Postdoctoral fellowship – Harvard Medical School, 1993-2000

The role of MHC-restricted antigen presentation in the immune response against invading microbial pathogens and tumors.

The focus of research in my laboratory is the role of MHC-restricted antigen presentation in the immune response against invading microbial pathogens and tumors. To eliminate infected or transformed cells, the immune system must be capable of specifically recognizing antigen. Antigen-specific receptors on T lymphocytes recognize antigen only after it has been processed into small fragments or peptides, and presented on the cell surface bound in the peptide-binding cleft of major histocompatibility complex (MHC) class I and class II molecules. MHC class II molecules acquire peptide in the enodcytic pathway, and present their cargo to CD4+ T helper cells.

My research thus far has examined the machinery required to load class II molecules with antigenic peptides in healthycells of the mouse. Shortly after synthesis in the ER, MHC class II ab-dimers interact with a third glycoprotein, the invariant chain (Ii). Sorting signals in the cytoplasmic tail of Ii target class II molecules to their site of peptide binding in the endocytic pathway. As class II-Ii complexes traverse the endocytic route Ii is sequentially degraded by the combined action of cysteine- and aspartyl-proteases. Upon completion, a small fragment of Ii, CLIP, remains bound in the peptide-binding groove of class II. The final cleavage of Ii into CLIP is performed by the cysteine proteases Cathepsin S (Cat S) in B cells, dendritic cells macrophages, and Cathepsin L (Cat L) in Thymic Epithelial Cells. To complete peptide binding, most class II alleles require interaction with yet another accessory molecule, the nonclassical class II-dimer, DM. Interaction of DM with class II facilitates exchange of CLIP for antigenic peptides.

The requirements for DM and Cat S/L in class II peptide loading were defined by examining mice in which the genes encoding these accessory molecules were ‘knocked out’. These studies only examined antigen presentation in the uninfected host. Little is known about the role of class II-restricted antigen presentation in eliminating invading pathogens or tumors, and in resolution of disease, which is the current focus of my laboratory. Pathogens have developed means to escape immune recognition and destruction. How do microbes (i.e., mycobacterium) modify or abrogate the antigen presentation pathways of the host to avoid immune recognition and attack? Likewise, T cell tolerance is emerging as one of the leading mechanisms by which tumor cells evade immune recognition. Reactivity’s of CD4+ T cells that are restricted by MHC class II molecules have been documented against melanomas, lymphomas, colon cancers, and breast cancers. What is the antigen processing machinery used by tumor cells to process and present melanoma-associated antigens via class II molecules to CD4+ T cells? How does class II conformation influence acquisition and presentation bacterial-derived or tumor-derived antigens? What are the components of class II-restricted antigen presentation used by the host to elicit a T cell-mediated immune response against microbes, and against tumors? These questions are currently being addressed in my laboratory by using the various antigen presentation-deficient mice as infectious disease and tumor progression models.

Recent Publications

Wolf Bryant, P., Feibeger, E., Lennon-Duménil, A -M. Driessen, C., and H. L. Ploegh. (2001). Peptide loading of H-2-I-Ab molecules in the absence of Cat S is strictly DM-dependent. Submitted.

Lennon-Duménil, A -M., Bryant, R. A. R., Bikoff, E. R., Ploegh, H. L., and P. Wolf Bryant. (2001). The p41 Isoform of Invariant Chain is a Chaperone for Cathepsin L. EMBO J. in press.

Hsu, P. -N., Wolf Bryant, P., Sutkowski, N., McLellan, B., Ploegh, H. L., and B. T. Huber. (2001). Association of MMTV superantigen with MHC class II during biosynthesis. J. Immunol. 166: 3309-14.

Sant, A. J., Beeson, C., McFarland, H. F., Cao, B., Ceman, S., Bryant, P. W., and S. Wu. (1999). Individual hydrogen bonds play a critical role in MHC class II:peptide interactions: implications for the dynamic aspects of class II trafficking and DM-mediated peptide exchange. Immunol. Reviews. 172:239-53.

Wolf Bryant, P., Ceman, S., Sant, A. J., and H. L. Ploegh. (1999). Deviant trafficking of I-Ad mutant molecules is reflected in their peptide binding properties. Eur. J. Immunol. 9: 2729-39.

Driessen, C., Bryant, R. A. R., Lennon-Dumenil, A -M., Villadangos, J. A., Bryant, P. W., Shi, G. -P., Chapman, H. A., and H. L. Ploegh. (1999). Cathepsin S controls the trafficking and maturation of MHC class II molecules in dendritic cells. J. Cell Biol. 147:775-90.

Rodgers, J. R., Levitt, J., M., Cresswell, P., Lindahl, K. F., Mathis, D., Monaco, J. T., Singer, D. S., Ploegh, H. L., and P. Wolf Bryant. (1999). A nomenclature solution to mouse MHC confusion. J. Immunol. 162: 6294.

Wolf, P. R., Tourne, S., Miyazaki, T., Benoist, C., Mathis, D., and H. Ploegh. (1998). The phenotype of H-2M deficient mice is dependent on the class II molecules expressed. Eur. J. Immunol. 28: 2605-2618.

Wilson, N. A., Wolf, P., Ploegh, H., Ignatowicz, L., Kappler, J., and P. Marrack. (1998). Invariant chain can bind MHC class II at a site other than the peptide binding groove. J.Immuol. 161:4777-84.

Tourne, S., Miyazaki, T., Wolf, P., Ploegh, H., Benoist, C., and D. Mathis. (1997). Functionality of major histocompatibility complex class II molecules in mice doubly deficient for invariant chain and H-2M complexes. Proc. Natl. Acad. Sci. USA. 94: 9255-60.

Miyazaki, T., Wolf, P., Tourne, S., Waltzinger, C., Dierich, A., Barois, N., Ploegh, H., Benoist, C., and D. Mathis. (1996). Mice lacking H-2M complexes, enigmatic elements of the MHC class II peptide-loading pathway. Cell. 84: 531-41.

Riese, R. J., Wolf, P. R., Bromme, D., Natkin, L. R., Villadangos, J. A., Ploegh, H. L., and H. A. Chapman. (1996). Essential role for cathepsin S in MHC class II-associated invariant chain processing and peptide loading. Immunity. 4: 357-66.

Wolf, P. R., and H. L. Ploegh. (1995). How MHC class II molecules acquire peptide cargo: Biosynthesis and trafficking through the endocytic pathway. Annu. Rev. Cell Dev. Biol. 11: 267-306.

Wolf, P. R., and H. L. Ploegh. (1995). DM exchange mechanism. Nature. 376: 464-65.

Wolf, P. R., and R. G. Cook. (1995). The class I-b molecule Qa-1 forms heterodimers with H-2Ld and a novel 50-kD glycoprotein encoded centromeric to I-Eb. J. Exp. Med. 181: 657-68.

Wolf, P. R., and R. G. Cook. (1990). The TL region gene 37 encodes a Qa-1 antigen. J. Exp. Med. 172: 1795-1804.

Faculty Bios

Pathogenicity of Gram-negative Pathogens.

Neil R. Baker

Neil R. Baker


Associate Professor,
Ph.D., University of Maryland, 1975.

Pathogenicity of gram-negative pathogens.

My research is primarily concerned with secondary pathogens of the respiratory tract. Pseudomonas aeruginosa, has been of particular concern because of the high mortality rates associated with hospital-acquired infections and the high incidence in cystic fibrosis patients. More recently we have expanded our interests to other Gram-negative bacteria.

Recent investigations have concerned identification of the receptors on eukaryotic cells for bacteria. The primary interest has been identification of receptors for Pseudomonas aeruginosa. Two classes of receptors have been identified. We are currently trying to identify the bacterial adhesins responsible for the binding. At least two adhesins have been characterized: pili and flagella. The role of pili has been documented by several investigators. How flagella may function as an adhesin is less clear, but our results indicate that it is required for adherence. We have hypothesized that after the organisms have attached to cells by contractile pili, they are brought to the cell surface where secondary adhesins create a stronger attachment. Flagellin appears to be a major secondary adhesin.

An exciting finding that may be related to the targeting of the flagellin is posttranslational modification of flagellin. A segment of DNA located downstream of the flagellin gene appears to be involved in the modification of flagellin. This process is distinct from the phosphorylation of flagellin that has been noted by others, and may involve glycosylation–a rare event in bacteria. The regulation and significance of the modificationare a major areas of focus.

An new area of investigation is genetic immunization to prevent the occurence of secondary infection following traumatic injury. Preliminary data using the P. aeruginosa flagellin gene in a eucaryotic expression system indicates that we can induce a strong immune response to bacterial antigens following injection of the plasmid DNA. Current studies are concentrating on defining the optimum conditions for immunization and determining the efficacy of these vaccines.

Recent Publications


Baker, N. and Verran, J. (2004). The future of Microbiology Laboratory Classes: Wet, dry or in combination. Nature Rev. Microbiol. 2 :338-342.
Denis-Mize KS, Price BM, Baker N.R., Galloway DR. 2000. Analysis of immunization with DNA encoding Pseudomonas aeruginosa exotoxin A. FEMS Immunol Med Microbiol. 27:147-54.
Wahl, S. and Baker, N.R. Identification of a locus involved in the posttranslational modification of flagellin from Pseudomonas aeruginosa. Molecular Microbiology – In preparation

Wahl, S. and Baker, N.R. Analysis of type a flagellin from Pseudomonas aeruginosa strain PAO1. In preparation.

Baker, N.R., Gehring, K. and Wahl, S. Evidence for a direct role of flagellin in the adherence of Pseudomonas aeruginosa to glycosphingolipids. In preparation.

Baker, N. R. 1992. Mucosal adherence of Pseudomonas aeruginosa. In R.B.Fick (ed.), Pseudomonas aeruginosa the opportunist: pathogenesis and disease. CRC Press, Inc.

Baker, N.R., V. Minor, C. Deal, M.S. Shahrabadi, D.A. Simpson, and D.E.Woods. 1991. Pseudomonas aeruginosaexoenzyme-S is an adhesin. Infect.Immun. 59:2859-2863.

Baker, N. R. 1991. The role of exoenzyme-S in the adherence of Pseudomonas aeruginosa. Pediat. Pulmon. S6: 136-137.

Baker, N.R., G. Hansson, H. Leffler, G. Riise, and C. Svanborg-Eden. 1990.Glycosphingolipid receptors for Pseudomonas aeruginosa. Infect. Immun.58:2361-2366

Faculty Bios

Microbial Genomics, Emphasizing the Molecular Biology of Polysaccharide Degradation and Bacterial Adhesion to Plant Surfaces.

Mark Morrison


Associate Professor
Ph.D., University of Illionois, 1991

Microbial genomics, emphasizing the molecular biology of polysaccharide degradation and bacterial adhesion to plant surfaces.

An obligatory step in cellulose degradation by anaerobic bacteria is the adhesion of the bacterium to the polysaccharide. In many anaerobic bacteria the adhesion protein, and the enzymes required for polysaccharide hydrolysis, are organized into a complex and interesting structure called the cellulosome. The genetics and biochemical characteristics of cellulosomes are quite diverse, but very little is known about the events underpinning the synthesis and assembly of these interesting complexes. My laboratory is currently examining the production and characteristics of these complexes in a variety of anaerobic cellulolytic and non-cellulolytic bacteria. My lab is also interested in the adhesion of bacteria to plant surfaces, and we have identified a novel form of cellulose-binding protein, produced by the gram-positive, cellulose-degrading anaerobe Ruminococcus albus. This protein is a member of the Pil-protein family, and is very similar to the type 4 fimbrial proteins of Gram-negative, pathogenic bacteria. These studies have provided new insights into the adhesion of bacteria to plant surfaces, and call attention to the likely existence of genetically analogous adhesion determinants in both pathogenic and non-pathogenic bacteria. A number of cellulose-degrading microorganisms are now the subject of genome sequencing projects, which will facilitate a more global analysis of the genetics and molecular biology controlling this key process in the cellulose degradation.

My laboratory is also studying the microbial interactions that support optimal rates and extent of cellulose degradation. One example is the requirement by Ruminococcus albus for micromolar amounts of phenylacetic and phenylpropionic acids, which stimulate the formation of cellulosome-like complexes and maximal rates of cellulose degradation. Other members of the microbial community produce these phenyl-substituted fatty acids, and my laboratory is currently investigating how R. albus responds to these compounds, by using techniques such as differential display RT-PCR and proteomics. A second example is the synergistic association between cellulose-degrading eubacteria and methanogenic archaea, via the process known as interspecies hydrogen transfer. Many cellulose-degrading bacteria will produce hydrogen during fermentation, which permits the bacterium to produce additional ATP by substrate-level phosphorylation, and affords faster rates of growth and cellulose degradation. However, the cellulose-degrading bacteria are dependent on the consumption of hydrogen by autotrophic methanogens to maintain this energetically favorable pathway of fermentation. Now that the genomes of several methanogens and cellulose-degrading bacteria have been completely sequenced, it will be possible to investigate this synergistic association more completely. An ultimate goal for our research is to use genomics and related methods to understand the molecular details of these microbial interactions and improve the bioconversion of cellulosic wastes into useful products such as ethanol.

Recent Publications

Morrison, M. and Miron, J. 2000. MiniReview: Adhesion to cellulose by Ruminococcus albus: a combination of cellulosomes and Pil-proteins? FEMS Microbiol. Letts. 185: 109-115

Heng, N.C.K., Bateup, J.M., Loach, D.M., Wu, X., Jenkinson, H.F., Morrison, M. and Tannock, G.W. 1999. The influence of different functional elements of plasmid pGT232 on the maintenance of recombinant plasmids in Lactobacillus reuteri populations in vitro and in vivo. Appl. Environ. Microbiol. 65: 5378-5385.

Larson, M.A. and Morrison, M. 1999. Application of the differential display RT-PCR technique to examine conditional gene expression in Ruminococcus albus. In: Bell, C.R. et al. (Eds.) Microbial Biosystems: New Frontiers. Proc. 8th Int. Symp. Microb. Ecol

Pegden, R. S., Larson, M.A., Grant, R.J., and Morrison, M. 1998. Adherence of the gram-positive bacterium Ruminococcus albus to cellulose, and identification of a novel form of cellulose-binding protein which belongs to the Pil-family of proteins. J. Bacteriol. 180: 5921-5927.

White, B.A., Cann, I.K.O., Mackie, R.I., and Morrison, M. 1997. Cellulase and xylanase genes from ruminal bacteria. Domain analysis suggests a non-cellulosome model for organization of the cellulase complex. pp. 69-80. In: Onodera, R. et al. (Eds.) “Rumen Microbes and Digestive Physiology of Ruminants ” Japan Scientific Societies Press, Tokyo, Japan.

Faculty Bios

Associate Professor

Juan D. Alfonzo


B.S., Indiana University- Bloomington, IN
Ph.D., Indiana University- Bloomington, IN
Post-doctoral Research, University of California, Los Angeles

The Alfonzo Lab

Editing & Modification of tRNA: Roles in Mitochondrial Biogenesis and Disease.

We are interested in RNA processing events that are unique to trypanosomes and could be exploited as targets for the design of therapies against protozoan diseases. To date, the Protozoa are responsible for the infection and death of millions of people worldwide. I am especially interested in two facets of RNA processing in trypanosomes: tRNA editing and tRNA modification.

The Mechanism of tRNA Editing

RNA editing involves any process by which the information content of a given transcript (mRNA, tRNA, etc.) is changed so that it will differ from that encoded in the genome. RNA editing occurs by a variety of chemically distinct post-transcriptional mechanisms including nucleotide insertion, deletions, base deaminations, and nucleotide exchange (to name a few) and plays an important role in the regulation of gene expression. In trypanosomes, I discovered that the nucleus-encoded tRNATrp undergoes an essential cytosine to uridine editing of the wobble position of the anticodon upon importation into the mitochondrion. Most notable, the deamination of cytosine to uridine at the anticodon allows the decoding of UGA codons as tryptophan. We are interested in the mechanism of tRNA editing and plan to use a genetic and biochemical approach to achieve a complete structure/function analysis of this process in trypanosomes

The Modifications of tRNA and Contribution to Mitochondrial Function

The functional importance of RNA modifications is evident from the large number of phylogenetically conserved modifications that occur in various cellular RNAs. Little is known about the role and extent of RNA modifications in early divergent eukaryotes. In addition, there are increasing numbers of reports linking tRNA modifications with mitochondrial diseases. I plan to use trypanosomes as a model system to study the role that specific tRNA modifications play in mitochondrial function. These studies will be the basis for examining the role site-specific tRNA modifications plays in mitochondrial function. The long-term goal is to utilize the exquisite specificity of these editing and modification enzymes for the long-term applications in gene therapy in humans.

In general, the emphasis of my laboratory will focus on the translation of RNA structure into RNA function in a biological system. Specifically, I hope to dissect the pathways involved in tRNA maturation, including editing and modification, to address issues involving molecular recognition. I firmly believe this research will not only uncover useful knowledge of basic cellular processes, but also provides the added incentive of great overall implications towards applications in medicine.

Faculty Bios

Biochemistry, Molecular Biology, Molecular Ecology, Archaea.

  F. Robert Tabita

Professor; Ohio Eminent Scholar of Microbiology
Professor, Natural Resources
Professor, Plant Biology
Director, Plant-Microbe Genomics Facility
Director, Plant Molecular Biology/Biotechnology Program
Ph.D., Syracuse University, 1971.


Biochemistry, molecular biology, molecular ecology, archaea.

My laboratory is concerned with the molecular regulation, biochemistry,and enzymology of carbon dioxide assimilation.  All organisms require CO2 and many enzyme-catalyzed reactions employ CO2 as a reactant for processes as important and varied as carbohydrate metabolism, lipid biosynthesis,and the production of important metabolic intermediates for the cell. With the realization that many microorganisms require CO2 in order to elicit pathogenesis, it is not surprising that CO2metabolism and its control has great health relevance.  Carbon dioxide may also be employed as the sole source of carbon by a large and diverse group of organisms on this planet.  For this reason, CO2 fixation is a process that is associated with global issues of agricultural productivity, carbon cycling, and industrial productivity.  CO2 is also recognized as the chief green house gas and has been implicated in the general warming of the earth’s biosphere.  For all these reasons,research on various aspects of CO2 fixation control, biochemistry,and ecology have attracted wide interest.  The following pages summarize our ongoing and future efforts to probe various aspects of this issue.

Molecular Regulation

We are specifically interested in how CO2 fixation structural genes are regulated in bacteria and various eukaryotic organisms. The bulk of our work over the years has concentrated on two or three model systems, both of which enable organisms to use CO2 as the sole source of carbon for growth.  One system, the Calvin-Bassham-Benson (CBB) reductive pentose phosphate pathway, is undoubtedly the means by which most organic matter is produced on earth.  For these studies, we have concentrated on the metabolically versatile nonsulfur purple bacteria, especially Rhodobacter sphaeroides , Rhodobacter capsulatus , and Rhodopseudomonas palustris . In these organisms, we have found that the structural ( cbb ) genes are clustered in distinct operons, some of which are localized in different genetic elements, as in R. sphaeroides .  In this organism, the entire cbb regulon is under the control of a specific transcriptional regulator gene, cbbR , whose product, CbbR, positively controls the transcription of the two major operons required for CO2 fixation. CbbR must be activated in the cell, probably after binding a specific effector molecule, in order to turn on transcription.  We are currently studying aspects of the biochemistry of CbbR so that we can understand how the cell is able to convert this constitutively synthesized protein to the activated state.  Unlike R. sphaeroides, there are two cbbR genes in R. capsulatus , each of which specifically regulates its cognate cbb operon.   Current studies indicate that several factors, in addition to CbbR, impinge on control in these organisms.  Of particular note is a global two-component signal transduction system that integrates the control of CO2 assimilation with the nitrogen fixation ( nif ) system and other processes important for energy generation.  Indeed, molecular signals are apparently received at the surface of the cell, undoubtedly reflecting the redox state of some signal molecule (? in Fig. 1), thus stimulating a membrane-bound sensor kinase (RegB/PrrB) to become autophosphorylated. RegB~P then transfers its phosphate to a response regulator protein, RegA/PrrA; the phosphorylated form of this molecule (RegB~P) then binds to DNA, affecting transcription.  This has become a fairly complicated regulatory system, as good evidence for the presence of other regulator molecules has also been obtained.  An interesting aspect of our studies on cbb control was the finding that the nitrogen fixation ( nif ) system, and its control, is intimately involved, with the Reg (Prr) system important for this interaction.  Indeed, knocking out the cbb system, under conditions where CO2 is normally used as an electron acceptor and not a carbon source, causes both organisms to derepress nitrogenase synthesis and the nifHDK genes, so that reducing equivalents may now be dissipated as a result of the H+-reducing hydrogenase activity of nitrogenase.  Thus, the organism exquisitely controls how it handles environmental signals related to carbon and nitrogen metabolism.  Our current model for this complex regulatory process is summarized below for R. sphaeroides (Fig. 1); basically this conceptual model holds for R. capsulatus andR. palustris as well. Note, manipulating the regulation of this system allows the organisms to produce copious quantities of hydrogen gas, a biofuel of enormous significance.


Fig. 1. Conceptual model showing the interplay of various factors involved in signal transduction and regulation of cbb gene expression in R. sphaeroides . The link between the CO2 ( cbb ) and nitrogen regulatory system, including the nitrogen fixation ( nif ) genes is shown. Primary signals are received at the cytoplasmic membrane. This is thought to affect the redox potential of some key component (?) influencing RegB/PrrB autophosphorylation and the subsequent formation of RegA~P (PrrA~P). RegA~P (PrrA~P) interacts directly with the cbb and nif operator-promoter regions (Dubbs and Tabita, submitted for publication). Positive regulation is thus conferred both by the CbbR protein and RegA~P(PrrA~P), the phosphorylated response regulator of the Reg (Prr) two-component regulatory system. CbbR is converted to CbbR (the transcriptionally active form of this molecule), presumably by virtue of binding a coinducer molecule produced under CO2 fixation conditions or other growth conditions that favor cbb transcription. The expression of glnB is affected by the cbb system (Qian and Tabita 1998) with glnB influencing nif derepression through the Ntr system and NifA. Blockage of the CBB pathway results in hydrogen evolution by virtue of the hydrogenase activity of the derepressed nitrogenase complex (Joshi and Tabita 1996).The nitrogenase complex and its inherent hydrogenase activity thus serves to remove excess reducing equivalents not dissipated in strains unable to use CO2 as an electron acceptor. p, refers to promoter-operator regions that are activated in a positive manner (+).  From Tabita (1999).


The Rhodopseudomomas palustris Microbial Cell Project/Genomes to Life Program

OSU recently initiated a new program to study mechanisms by which a single organism controls the ability to regulate many aspects of metabolism simultaneously ( http://www.osu.edu/researchnews/archive/micromet.htm ). For this purpose, the Department of Energy awarded a large grant to a consortium of investigators from seven institutions to begin the Rhodopseudomonas palustris Microbial Cell Project. Ohio State, with F. R. Tabita, the Principal Investigator, is the lead institute of the consortium.This project involves the genetically tractable and metabolically versatile organism, Rhodopseudomonas palustris , whose entire genomic sequence was recently completed. Postgenomic approaches will be used to determine how the organism regulates the ability to produce useful forms of energy while also removing greenhouse gases (such as carbon dioxide) and degrading toxic compounds. Rps. palustris is metabolically similar, but more versatile than other nonsulfur purple bacteria ( Rhodobacter ) under study in the laboratory (see above).


A. RubisCO

We are deeply involved in efforts to determine how the structure influences the function of key enzymes and proteins important for CO2 fixation.  How the activity of these proteins is regulated in the cell is also of prime importance to our laboratory.  Over the years, we have primarily focused on RubisCO, which is the key enzyme of the CBB pathway.  This enzyme is a very poor catalyst, yet it is the protein that actually fixes the bulk of CO2 on this planet.  This is probably why RubisCO is the most abundant protein found on earth, making aspects of its biochemistry and molecular control (see above) so topical.  The major issue that we study is the basis by which RubisCO discriminates between CO2 and O2 , two gaseous substrates that compete for the active same active site on the protein. This is a very important issue as O2normally prevents efficient CO2 fixation. Despite a wealth of structural and mechanistic information, it is still not clear how closely related RubisCO molecules possess different specificities for CO2 and O2 .  Taking a combined molecular biological and chemical approach we are attacking this problem by constructing novel mutant enzymes, and have developed prokaryotic genetic selection procedures to facilitate these efforts (Smith and Tabita 2003).  An added bonus has been the finding, from genomic sequencing studies, that anoxic hyperthermophilic archaea contain RubisCO genes.  We have recently found that at least some of these putative RubisCO sequences encode for bona fide RubisCO activity.  As these enzymes are derived from organisms that never encounter molecular oxygen, these proteins are proving to be very interesting; i.e., they serve as model systems to understand how the active site of RubisCO may have evolved. The structure of the Methanococcus jannaschii and Archaeoglobus fulgidus RubisCO enzymes have been modeled (Fig. 2), providing a ready system for current and future structure-function studies of the archaeal enzyme. More recently, we have shown that these enzymes actually produce physiologically significant RubisCO proteins (Finn and Tabita 2003) and we have elucidated the probable role of this enzyme in archaea.


Fig. 2. Tertiary structure prediction of archaeal RubisCO molecules. The predicted tertiary structure of the M. jannaschii sequence (A) and the A. fulgidus 2 sequence (B) is compared to the known structure of (C), the Synechococcus large subunit.  The Synechococcus small subunit is also shown to the lower left of the structure (in amber).  Label sizes and shading reflect the distance from the viewer, smaller and darker being further from the viewer. The main features are highlighted as follows: yellow = active site residues within 3.3 � of the bound transition state analogue CABP in the Synechococcus enzyme, and the equivalent residues in the M. jannaschii and A. fulgidus sequences; red = loop-6; cyan = highly divergent ?-helix-6 residues; purple = residues that appear to be absent in the M. jannaschii and A. fulgidussequences (eight residues at the N-terminus of the Synechococcus enzyme were not resolved in the structure determination and therefore are not shown here).  Mg 2 + is represented as a green sphere and CABP as a ball and stick model in C.  From Watson et al. (1999)


B. Other CBB Enzymes

Other enzymes of the CBB pathway are also under study.  RubisCO activase is an enzyme that catlyzes the removal of inhibitory phosphorylated compounds from the active site of RubisCO. Another key enzyme of the pathway that is studied is phosphoribulokinase, the enzyme that catalyses the formation of the substrate for RubisCO.  Transketolase and pentose 5-phosphate-3-epimerase are two enzymes whose genes, cbbT and cbbE , respectively, are found in the cbb regulon (Fig.1).  These two enzymes catalyze important 5-carbon sugar phosphate transformations and are also studied. Transketolase has particularly been the focus of recent studies, in which the involvement of a specific cysteine residue in cofactor binding was elucidated (Bobst and Tabita submitted)

C. RTCA Cycle Enzymes

We also study another model CO2 fixation system, the reductive tricarboxylic acid (RTCA) pathway, in which several interesting and unique CO2 fixation catalysts are focal points. This is a pathway found in many bacteria and eukaryotic CO2 fixing organisms, and many of the key reactions are important in archaea as well. Virtually nothing is known of the molecular regulation of the RTCA cycle and we have recently developed an interesting model system, the green sulfur bacterium Chlorobium tepidum , for these studies. This organism, unlike other organisms that use this pathway, has a fairly well defined genetic system and the organism grows rapidly. We have recently isolated all the relevant and important enzymes of this pathway, including pyruvate synthase, alpha-ketoglutarate synthase, ATP-citrate lyase, and PEP carboxylase, along with several important electron carriers including rubredoxin, two ferredoxins, and two cytochromes. The structural genes for these proteins have all been isolated and we have begun to study aspects of the molecular regulation of this interesting CO2 fixation process. The key CO2 fixation catalysts are redox sensitive proteins which show interesting and novel interactions with electron carriers such as rubredoxin (Fig. 3). This work has recently been published in the Journal of Biological Chemistry (Yoon et al. 1999; 2001) and other manuscripts are in preparation.

Fig. 3. EPR spectrum of C. tepidum rubredoxin before (A) and after (B) reduction with pyruvate ferredoxin oxidoreductase/pyruvate synthase.

An interesting aspect of our work with C. tepidum was the finding of an unusual RubisCO-like protein (RLP) which is involved with sulfur metabolism and the stress response (Hanson and Tabita 2001, 2003).

Molecular Ecology

We have collaborated with marine scientists at the University of South Florida to understand how the regulation of key CO2 fixation genes, like the RubisCO genes, are controlled in the oceans. This work, a combination of ship-board and laboratory investigations, is devoted to a primary problem, namely the sequestration of CO2 in the environment. Procedures for the direct examination of RubisCO transcripts in the open ocean were developed and applied to the global CO2 fixation problem. As these studies unfolded, it became possible to identify organisms which contribute to active CO2 fixation and sequestration by amplifying and sequencing specific RubisCO transcripts via RT-PCR technology. These studies have been performed in concert with physiological and biochemical studies with marine cyanobacteria and algae, such that a coherent picture of how carbon dioxide assimilation may be controlled in these organisms, both in the environment and in the laboratory.

We also have a collaboratine project to ascertain the role and study the significance of a RubisCO in hydrothermal vent archaeal extremophiles. These studies promise to provide much information as to how CO2 fixation pathways may evolve in potential extraterrestial systems .


Applied Studies

Knowledge of the biochemistry and molecular control of CO2 fixation has stimulated us to use this knowledge to consider the possibility that useful compounds of economic and industrial importance might be synthesized using this cheap and ubiquitous gas as the starting material. In one study, we have considered the possibilty that CO2 might be converted to ethanol using a genetically engineered strain with the requisite genes. Other offshoots of this technology are also being developed for the production of value-added products.


Future Studies

In addition to continuing the molecular, biochemical, and ecological efforts described above, we are embarking on new approaches to learn how CO2 fixation control relates to the overall regulation of metabolism in representative organisms. Taking advantage of the many genomes that have been sequenced from CO2 -fixing prokaryotes, including bacteria and archaea which are studied in our laboratory, we have initiated studies employing microarray and proteomics technology to investigate the global expression of CO2 -responsive genes in these organisms. This technology promises to allow us the capability of identifying a large complement of genes important for CO2 fixation that we would not normally identify with standard procedures. Moreover, since we have mutants at our disposal that are known to influence carbon assimilation, it should be feasible to greatly improve our efforts to examine overlapping metabolic schemes. Finally, it is our intention to use this technology to examine genes that are turned on during CO2 -dependent pathogenesis in selected organisms of health significance.

Faculty Bios

Jessica Dyszel

Jessica Dyszel

I received my Bachelors degree in microbiology from Southern Illinois University. As an undergraduate I worked in an independent food-testing laboratory assisting in research projects and performing routine testing. Working as a laboratory technician furthered my interest in microbiology and prompted me to attend graduate school. When searching for a university to attend, the balanced program at Ohio State stood out. The diversity of the professors, their backgrounds, and research made the program very attractive when compared to other schools. During a campus visit I met many of the professors and graduate students and was surprised by the overall friendliness and enthusiasm of the department. After I joined the department, lab rotations allowed me to explore various fields and interests as well as meet more of the students and professors.

In 2002 I joined the lab of Brian Ahmer. Currently I am working on the identification of genes regulated by SdiA, a LuxR homolog, in Salmonella typhimurium. One of the greatest advantages to being at a large university is access to equipment and facilities, that an individual lab could not support. The classes that I have taken are constantly under revision to include the most recent information and involve the students in the process. I am sure that the education that I receive from the department will serve me well in the future.

Faculty Bios

Environmental and Industrial Microbiology

Olli H. Tuovinen

Olli H. Tuovinen


Ph.D., University of London, 1973

Environmental and Industrial Microbiology.

Several projects are underway in my laboratory that combine microbial metabolism and ecology with environmental disciplines. Examples of current studies include (1) the biodegradation of pesticides and polynuclear aromatic hydrocarbons, (2) microbial ecology and biogeochemistry of acid mine drainage, (3) microbial solubilization and weathering of minerals, and (4) microbial processes in landfills.
(1) Biodegradation is by far the single most important factor in the attenuation of pesticides in soils. Biodegradation rates vary with bioavailability and presence of organisms with degradative capabilities in soils and subsurface environments. We have previously investigated the degradation of phenoxyalkanoic acid and chloroacetamide herbicides and our current focus is on the pre-emergent weed killer atrazine. This compound has a symmetric, N-heterocyclic aromatic structure and has no known natural analog in the nature.
Annual applications of atrazine are known to enhance biodegradation rates in agricultural soils, and this acclimation effect has also been reported for many other herbicides. Biodegradation rate constants and the corresponding half-lives may vary by two orders of magnitude between soils with different histories of atrazine application, including reference soils with no prior exposure. Such kinetic differences reflect phenotypic and genotypic variation in soil microbial communities.
Complete biodegradation of atrazine involves dehalogenation, N-dealkylation, deamination, and ring-cleavage steps. Several genes of the atrazine degradative pathways have been described in the literature. The genes provide the basis for the characterization of soil microbial communities by molecular techniques such as DNA probes and PCR amplification, cloning, and sequencing. In addition to agricultural soils, we have also used these approaches for describing atrazine-degrading microbial communities in natural and constructed wetlands.
Biodegradation is also most important in the natural attenuation of polynuclear aromatic hydrocarbons; these compounds are highly nonpolar and sorb on soil and sediment particles. The scope in our studies is to assess the biodegradation potential of polynuclear aromatic hydrocarbons in compost materials and in sediments impacted by hydrocarbon pollution and stormwater runoff. The biodegradation potential yields useful information for assessing the fate and kinetics of the biodegradation of these compounds in environments impacted by anthropogenic sources. Such information may be useful in designing bioremediation strategies for solid waste materials.
(2) Mine drainage constitutes a serious water pollution problem in many metal and coal mine areas. Treatment methods of acid mine water include constructed wetland systems to remove acidity and metal ions. Our approach to elucidating microbial ecology in constructed acid mine wetlands has been based on using 16S rDNA-based techniques. With emphasis on non-culturable approaches, we have use PCR amplification with universal and genus/species specific phylogenetic primers, cloning and sequencing, RFLP, DGGE, and FISH to characterize microbial communities in a constructed wetland system treating acid coal mine water. Geochemical and mineralogical changes with time have been described by analysis of pore water and iron precipitates in aerobic and anaerobic zones of the constructed wetland.
(3) The dominant bacterial groups in constructed mine drainage wetland systems are aerobic, iron- and sulfur-oxidizing bacteria. These acidophilic bacteria are also involved in the oxidative dissolution of sulfide minerals in ore deposits and coal refuse piles. A long-term study in my laboratory has been to characterize dissolution processes using research-grade minerals as well as ores and concentrates. These bacteria have application for processing of copper-, uranium-, and precious metal-containing ore materials in the mining industry. We have also shown that anaerobic sulfate reducing-bacteria can also be involved in biogeochemical transformations by using solid-phase electron acceptors.
(4) Microbial processes in conventional landfills are usually limited by low moisture content. This dry tomb technology of landfill management is contrasted by landfill bioreactor approaches, which aim to accelerate waste decomposition and landfill gas production through leachate circulation. Our studies in landfill bioreactor technology are aimed at optimizing environmental conditions conducive to anaerobic microbial activities and assessing nutrient deficiency conditions for landfill materials.
Projects in my laboratory have prospective in remediation and other applications with interdisciplinary approaches, but the foundations are firmly based on microbial biochemistry, ecology, and physiology. Many of the research problems under study in my laboratory involve biogeochemical redox reactions, interfacial reactions, and molecular ecological approaches that help design microbiological strategies competitive in environmental investigations.


Recent Publications

Hao, Y., W.A. Dick, and O.H. Tuovinen. 2002. PCR amplification of 16S rDNA sequences in Fe-rich sediment of coal refuse drainage. Biotechnology Letters 24:1049-1053.


Nicomrat, D., W.A. Dick, and O.H. Tuovinen. 2002. Molecular bacterial ecology of Fe(III)-precipitates in a constructed wetland treating acid coal mine water. Paper No. 614. In: Transactions of the 17th World Congress of Soil Science, p. 614-1 to 614-9. Bangkok, Thailand.


Ostrofsky, E.B., J.B. Robinson, S.J. Traina, and O.H. Tuovinen. 2002. Analysis of atrazine-degrading microbial communities in soils using most-probable-number enumeration, DNA hybridization, and inhibitors. Soil Biology and Biochemistry 34:1449-1459.


Anderson , K.L., K.A. Wheeler, J.B. Robinson, and O.H. Tuovinen. 2002. Atrazine mineralization potential in two wetlands. Water Research 36:4785-4794.


Bevilaqua, D., A.L.L.L. Leite, O. Garcia Jr., and O.H. Tuovinen. 2002. Oxidation of chalcopyrite by Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans in shake flasks. Process Biochemistry 38:589-594.


Stamper, D.M., M. Radosevich, K.B. Hallberg, S.J. Traina, and O.H. Tuovinen. 2002. Ralstonia basilensis M91-3, a denitrifying soil bacterium capable of using s -triazines as nitrogen sources. Canadian Journal of Microbiology 48:1089-1098.


Karnachuk, O.V., S.Y. Kurochkina, D. Nicomrat, Y.A. Frank, D.A. Ivasenko, E.A. Phyllipenko, and O.H. Tuovinen. 2003. Copper resistance in Desulfovibrio strain R2. Antonie van Leeuwenhoek 83:99-106.


Carlstrom, C.J., and O.H. Tuovinen. 2003. Mineralization of phenanthrene and fluoranthene in yardwaste compost. Environmental Pollution 124:81-91.


Li, Y., W.A. Dick, and O.H. Tuovinen. 2003. Evaluation of fluorochromes for imaging bacteria in soil. Soil Biology and Biochemistry 36:737-744.


Liu, Q., K.M. Mancl, and O.H. Tuovinen. 2003. Biomass accumulation and carbon utilization in layered sand filter biofilm systems receiving milkfat/detergent mixtures. Bioresource Technology 89:275-279.


Kang, Y.W., K. M. Mancl and O.H. Tuovinen. 2003. Biological treatment of turkey processing wastewater with coarse/fine sand filtration. In: Animal, Agricultural and Food Processing Wastes (Proceedings of the Ninth International Symposium), p. 44-49. American Society of Agricultural Engineers, St. Joseph, MI.


Xi, J., K.M. Mancl, and O.H. Tuovinen. 2003. Transformations and accumulation of carbon in gavel/sand filters treating cheese processing wastewater. In: Animal, Agricultural and Food Processing Wastes (Proceedings of the Ninth International Symposium), p. 341-349. American Society of Agricultural Engineers, St. Joseph, MI.


Radosevich, M., and O.H. Tuovinen. 2004. Microbial degradation of atrazine in soils, sediments and surface waters. In: Pesticide decontamination and detoxification (ACS Symposium Series No. 863) (J.J. Gan, P.C. Zhu, S.D. Aust, and A.T. Lemley, Eds.), p. 129-139. American Chemical Society, Washington, D.C.


Li, Y., W.A. Dick, and O.H. Tuovinen. 2004. Fluorescence microscopy for visualization of soil microorganisms � a review. Biology and Fertility of Soils 39:301-311.


�tyriakov�, I., T.M. Bhatti, J.M. Bigham, I. �tyriak, A. Vuorinen, and O.H. Tuovinen. 2004. Weathering of phlogopite by Bacillus cereus and Acidithiobacillus ferrooxidans. Canadian Journal of Microbiology 50:213-219.


Rowan, M.A., K. M. Mancl, and O.H. Tuovinen. 2004. Clogging incidence of drip irrigation emitters distributing effluents of differing levels of treatment. In: On-site Wastewater Treatment X(Proceedings of the Tenth National Symposium on Individual and Small Community Sewage Systems), p. 84-91. American Society of Agricultural Engineers, St. Joseph, MI.


Xi, J., K.M. Mancl, and O.H. Tuovinen. 2005. Carbon transformation during sand filtration of cheese processing wastewater. Applied Engineering in Agriculture 21:271-274.


Karnachuk, O.V., N.V. Pimenov, S.K. Yusupov, Y.A. Frank, A.H. Kaksonen, J.A. Puhakka, M.V. Ivanov, E.B. Lindstr�m, and O.H. Tuovinen. 2005. Sulfate reduction potential in sediments in the Norilsk mining area, northern Siberia. Geomicrobiology Journal 22:11-25.


Kang, Y.K., K.M. Mancl, and O. H. Tuovinen. 2005. Feasibility of renovating turkey processing wastewater using fixed film bioreactors. In: Proceedings of the 14th Annual Technical Education Conference, 9 p. National Onsite Wastewater Recycling Association, Cleveland, OH.


Gaur, R.S., L. Cai, K.M. Mancl, and O.H. Tuovinen. 2005. Pretreatment of animal fat through coarse sand filters. In: Proceedings of the 14th Annual Technical Education Conference, 10 p. National Onsite Wastewater Recycling Association, Cleveland, OH.


Rowan, M., K.M. Mancl, and O.H. Tuovinen. 2005. Performance of drip irrigation emitters distributing primary and secondary wastewater effluent. In: Proceedings of the 14th Annual hnical Education Conference, 9 p. National Onsite Wastewater Recycling Association, Cleveland, OH.


Rzhepishevska, O.I., E.B. Lindstr�m, O.H. Tuovinen, and M. Dopson. 2005. Bioleaching of sulfidic tailing samples with a novel, vacuum-positive pressure driven bioreactor. Biotechnology and Bioengineering 92:559-567.


Stamper, D.M., J.A. Krzycki, D. Nicomrat, S.J. Traina, and O.H. Tuovinen. 2005. Ring-cleaving cyanuric acid amidohydrolase activity in the atrazine-mineralizing Ralstonia basilensis M91-3. Biocatalysis and Biotransformation 23:387-396.


Nicomrat, D., W.A. Dick, and O.H. Tuovinen. 2006. Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage. Microbial Ecology, in press.


Wang, H., J.M. Bigham, and O.H. Tuovinen. 2006. Formation of schwertmannite and its transformation to jarosite in the presence of acidophilic iron-oxidizing microorganisms. Materials Science and Engineering C, in press.