![[Mark Kainz]](../Images/MKainz.JPG)
Mark Kainz (Assistant Professor)
Department of Biology, Colgate
University
Phone: 315.228.7779 Fax: 315.228.7997
E-Mail: MKainz@mail.colgate.edu
Research Interests: Protein and nucleic acid requirements for gene expression and genome replication of tomato spotted wilt virus, a plant and insect infecting virus. [Details]
Teaching Interests: microbiology, molecular biology, virology. [Details]
Mark Kainz
Research Interests:
My research focuses on understanding the mechanisms and regulation of gene expression and genome replication in Tomato spotted wilt virus (TSWV).
TSWV causes disease in many important crops. It is a member of the Bunyavirus group which also includes human pathogens such as the Hantavirus and La Crosse encephalitis virus. Conventional strategies for control of TSWV based on controlling the insect vector of the virus or selecting for natural virus resistance in plants have achieved only limited success. We hope that by understanding the molecular events involved in virus genome replication and gene expression we will provide information for devising novel control strategies.
My research group is attempting to characterize the molecular interactions between the virus RNA genome and viral proteins and between different viral proteins that are required for gene expression and replication. Our approach follows two paths. One involves looking for interactions between purified components in vitro. The other involves screening for interactions between various viral proteins or between viral proteins and host plant proteins by expressing them as fusions with proteins from yeast that regulate expression of a reporter gene in yeast cells. Our goal with this project is to identify potential targets for the development of new control measures.
We have also begun an investigation aimed at understanding the interactions between TSWV and thrips (the insect host and vector of the virus). The virus is able to replicate in the insects but does not cause a disease in the insects. We are seeking to understand if thrips use a posttranscriptional gene silencing (also called RNAi) mechanism to influence the biology of the virus and thereby avoid disease.
The genome of TSWV is divided between three RNA molecules in an ambisense orientation. This arrangement of genes in the viral genome and the technical difficulties associated with introducing foreign genes into plant cells in large numbers are major limitations on our ability to use genetic approaches to understand virus specific processes. We are attempting to reconstitute portions of the TSWV replication cycle in yeast cells which we hope will enable us to use genetic tools to help answer questions regarding mechanisms of the virus replication process.
We collaborate with Dr. Tom German and colleagues at the University of Wisconsin-Madison, Dr. D. Kyle Willis at the UDSA, and with Dr. Pierre Hilson and colleagues at Ghent University in Belgium on these projects.
We have also begun a project in collaboration with Dr. Tim McCay in the Biology department at Colgate aimed at determining the presence and distribution of hantaviruses in rodents in central New York. We are currently developing a PCR base assay to detect hantavirus genomes in blood samples. Once the assay is perfected we will survey local wild rodent communities for the presence and distribution of the viruses in our area.
Teaching Interests:
Biology is an important and an interesting discipline. My goal as a teacher is to communicate the concepts and facts that are central to areas of biology that I teach while at the same time to assist students in appreciating the means by which this understanding is obtained.
Molecules, Cells, and Genes (Biol 212) is one of the foundation courses in the Biology curriculum. The course focuses on life at the cellular, sub-cellular, and molecular levels, how cells communicate with each other, and the means of inheritance of genetic material.. Understanding how a cell receives signals from its environment, processes those signals, and responds to the signal is a major goal of modern biology and of my course.
Microbiology (Biol273) is a course that covers the lifestyles of bacteria and other microbes. These organisms are among the most successful on the planet and understanding their biology should also inform us about aspects of our own biology, about diseases these organisms incite, and about ways that our ecosystem functions.
Virology (Biol 373) is a course that covers the biology of viruses. The study of the different strategies for genome replication and gene expression used by viruses serves as the basis for understanding virus-host interactions and pathogenicity by particular viruses. In addition, understanding viral systems informs us about aspects of biology at the cellular and sub-cellular levels.
Molecular Analysis (Biol 321) is a course that introduces students to the uses of modern molecular techniques for understanding fundamental processes in biology. The lecture portion of the course focuses on understanding the basic principles as well as the uses of techniques such as gene cloning, and the analysis and manipulation of gene expression to the understanding of how cells and organisms function. The laboratory portion of the course consists of a semester long investigative project that applies many of the techniques discussed in lecture toward answering a particular question in biology.
Molecular Biology (Biol 450) is a senior capstone course for students concentrating in Biology and Molecular Biology. The course focuses on understanding, in depth, the processes and regulation of transcription, translation, and DNA replication. The course makes extensive use of the primary scientific literature and provides students the opportunity to gain skill in critical reading of the primary literature.
I also teach in the First Year Seminar program as a part of the Scientific Perspectives Core. My seminar covers viruses and their biology, how viruses and the diseases they cause affect individuals and societies, and how human activity affects range and severity of viral diseases.
Student Research:
Fall 2004
* Bridget Essley: Identification of sequences in the TSWV S RNA that bind N protein with high affinity.
* Alissa Fideli and Chelsey Rhodes: Identification of N protein homotypic interaction regions in the tomato spotted wilt virus N protein.
* Carolyn Baker and Diana Zeledon: Characterization of host cell proteins involved in TSWV replication.
* Jenny Niles: Development of a PCR-based assay to detect hantavirus in rodent populations in central New York.
* Kristin Sinni: Characterization of TSWV glycoprotein processing and intra-virion interactions.
Summer 2004
* Bridget Essley and Kyle Dolan: Identification of sequences in the TSWV S RNA that bind N protein with high affinity.
Spring 2004
* Alice Guo, Maruf Khan, Jamie Timmons, Elke Wagle, Kate Roache, and Alison Soltys: Identification of N protein homotypic interaction regions in the tomato spotted wilt virus N protein.
* Amitabha Gupta: Identification of sequences in the TSWV S RNA that bind N protein with high affinity.
Summer 2002
* Jesse Raab and Christopher Mizzi: Identification of RNA and protein binding regions in the tomato spotted wilt virus N protein.
* Justin Sokolowski: Identification of transcription terminators in the genomes of Mycobacteria species.
Spring 2002
* Robin Pedersen and Stephen Dorkhom: Identification of N protein homotypic interaction regions in the tomato spotted wilt virus N protein.
* Natasha Frederick and Andrea Weiler: Identification of transcription terminators in the genomes of non-enteric bacteria.
* Anna McEvoy: Development of a PCR-based assay to detect hantavirus in rodent populations in central New York.
* Elisha McLam: Identification of sequences in the TSWV S RNA that bind N protein with high affinity.
* Joyce Guerra and Brittany Larkin: Construction of genomic clones of Potato Virus Y.
Fall 2001
* Robin Pedersen: Identification of N protein homotypic interaction regions in the tomato spotted wilt virus N protein.
* Elisha McLam: Identification of sequences in the TSWV S RNA that bind N protein with high affinity.
Spring 2001
* Laura Sweeney and Erin DeRose: Identification of RNA and protein binding regions in the tomato spotted wilt virus N protein.
* Natasha Frederick and Kim Lam: Identification of transcription terminators in the genomes of non-enteric bacteria.
* Catherine Rideaux: Development of a PCR-based assay to detect hantavirus in rodent populations in central New York.
* Susan Burns and Peter Matthews: Identification of host cell proteins involved in replication of tomato spotted wilt virus.
Fall 2000
* Laura Sweeney and Erin DeRose: Identification of RNA and protein binding regions in the tomato spotted wilt virus N protein.
Summer 2000
* Laura Sweeney and Erin DeRose: Identification of RNA and protein binding regions in the tomato spotted wilt virus N protein.
* Natasha Frederick: Identification of transcription terminators in the genomes of non-enteric bacteria.
Spring 2000
* Nick Keiser, Trevor McCroskey, Laura Sweeney, and Andrea Weiler: Identification of RNA and protein binding regions in the tomato spotted wilt virus N protein.
Selected publications:
* indicates Colgate undergraduate student authors
Kainz, M., P. Hilson, L. Sweeney*, E. DeRose*, and T. German (2004) Interaction between Tomato spotted wilt virus N protein monomers involves non-electrostatic forces governed by multiple regions in the primary structure. Phytopathology 94:.759-765.
Kainz, M. and R. Gourse (1998) The C-terminal domain of the alpha subunit of Escherichia coli is required for efficient rho-dependent transcription termination. J. Mol. Biol. 284:1379-1390.
Savery, N., G. Lloyd, M. Kainz, T. Gaal, W. Ross, R. Ebright, R. Gourse, and S. Busby (1998) Transcription activation at class II CRP-dependent promoters: identification of determinants in the c-terminal domain of the RNA polymerase alpha subunit. EMBO J 17:3439-3447.
van Ulsen, P., M. Hillebrand, M. Kainz, R. Collard, L. Zulianello, P. van de Putte, R. Gourse, and N. Goosen (1997) Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and integration host factor-mediated activation of the early promoter of bacteriophage Mu. J.Bact 179:530-537.
Kainz, M. and J.W.Roberts (1995) Kinetics of RNA polymerase initiation and pausing at the lambda late gene promoter. J.Mol.Biol. 254:808-814.
Kainz, M. and J.W. Roberts (1992) Structure of transcription elongation complexes in vivo. Science 255:838-841.
Guo, H.C., M. Kainz, and J.W. Roberts (1991) Characterization of the late-gene regulatory region of phage 21. J.Bact.