Karen E. Kirk

Professor of Biology

Specialization

Molecular Genetics and Cell Biology
Infectious Diseases, Genetics, Genomics, and Cancer

Research Interests

Our laboratory studies how telomeres, the chromosome termini, are kept intact.   We want to understand how the telomerase RNA, which supplies the template for the synthesis of telomeric DNA, functions in regulating telomere length.  The telomeres get shorter without this RNA, which is detrimental to all cells, and at a minimum, contributes to cellular aging.  Our research is conducted in model organisms that are quick to reproduce and easy to use, like the filamentous fungus Aspergillus, and thus are great for undergraduates.

Education

Post-doctoral Fellowship, University of California San Fransisco
PhD Molecular Genetics, Rutgers University
BS Chemistry, University of Delaware

Courses Taught

Biology 221: Cell and Molecular Biology
Biology 352: Molecular Genetics
Biology 320: Microbiology
Biology 114: Emerging World Diseases
First-Year Studies 114: Emerging World Diseases
Biology 209: Biology and the Learning Process
Biology 483: Senior Seminar on Cancer and Aging

Articles

Paulius V. Kuprys, P.V.*, Davis, S.M.*, Hauer, T.M.*, Meltser, M.*, Tzfati, Y., Kirk, K.E. (2013) Identification of Telomerase RNAs from Filamentous Fungi Reveals Conservation with Vertebrates and Yeasts.  PLoS ONE 8(3):e58661. doi:10.1371/journal.pone.0058661

Wang, N.*, Rizvydeen, S.*,  Vahedi, M*, Vargas Gonzalez D.*,  Allred, A.*,  Perry, D.*, Mirabito, P.,  Kirk, K.E. (Submitted).  Novel Telomere-Anchored PCR Approach for Studying Sexual Stage Telomeres in Aspergillus nidulans. 

Kirk, K.E., Christ, C.*, McGuire, J.M.*, Paul, A.G.*, Vahedi, M.*, Stuart K.R.  & Cole, E.S. (2008) Abnormal Micronuclear Telomeres Lead to an Unusual Cell Cycle Checkpoint and Defects in Tetrahymena Oral Morphogenesis. Eukaryotic Cell 7:1712-723. doi:10.1128/EC.00393-07

Karen E. Kirk and Jonathan Weiland, (2006) Trekking Through The Human Genome: An Individualized Laboratory Project. American Biology Teacher Online 68:124-130. doi:10.1662/0002-7685(2006)68[124:TTTHGA]2.0.CO;2

McGuire, J.M.*, Gana, J.A., Petcherskaia, M.*, Kirk, K.E. (2003)  Protein Binding to Expanded Telomere Repeats in Tetrahymena Thermophila.  Journal of Eukaryotic Microbiology 50:341-348. doi:10.1111/j.1550-7408.2003.tb00146.x

Petcherskaia, M.*, McGuire, J.M.*, Pherson, J.M.*, Kirk, K.E. (2003) Loss of Cap Structure Causes Mitotic Defect in Tetrahymena thermophila Telomerase Mutants.  Chromosoma 111:429-437. doi:10.1007/s00412-003-0233-9

Jacob, N.K., Kirk, K.E., Price, C.M. (2003)  Generation of Telomeric G Strand Overhangs Involves both G and C Strand Cleavage.  Molecular Cell 11:1021-1032. doi:10.1016/S1097-2765(03)00131-X

Hargrove, B.W., Bhattacharyya, A., Domitrovich, A.M., Kapler G.M., Kirk, K., Shippen, D.E., Kunkel, G.R. (1999) Identification of an Essential Proximal Sequence Element in the Promoter of the Telomerase RNA Gene of Tetrahymena thermophila. Nucleic Acids Research 27:4269-4275. doi: 10.1093/nar/27.21.4269

Blackburn, E.H., Gilley, D., Ware, T., Bhattacharyya, A., Kirk, K.E., Wang, H. (1999) “Studying the Telomerase RNA in Tetrahymena” in Tetrahymena thermophila (Volume 62 of Methods in Cell Biology, ed. Asai, D.J. and Forney, J.D., Academic Press, San Diego, CA).

Kirk, K.E., Harmon, B.P., *Reichardt, I.K., Sedat, J., Blackburn, E.H. (1997) Block in Anaphase Chromosome Separation Due to a Telomerase Template Mutation. Science 275:1478-1481.

Blackburn, E.H., Bhattacharyya, A., Gilley, D., Kirk, K.E., Krauskopf, A., Prescott, J.P., Strahl, C., Ware, T. (1997) The Telomere and Telomerase: How Do They Interact? Telomeres and Telomerase, Ciba Foundation Symposia (1997) 211:2-13.

Kirk, K.E., Blackburn, E.H. (1995) Unusual sequence Arrangement in the Telomeres of the Germ-Line Micronucleus in Tetrahymena thermophila. Genes & Development 9:59-71. doi:10.1101/gad.9.1.59

Kirk, K.E., Morris, N.R. (1993) Either alpha-tubulin Isogene Product is Sufficient for Microtubule Function During All Stages of Growth and Differentiation in Aspergillus nidulans. Molecular and Cellular Biology 13:4465-4476. doi:10.1128/MCB.13.8.4465

Kirk, K.E., Morris, N.R. (1991) The tubB alpha-tubulin Gene is Essential for Sexual Development in Aspergillus nidulans. Genes and Development 5:2014-2023. doi:10.1101/gad.5.11.2014

Crane, M.S.J., Goggin, B., Pellegrino, R.M., Ravino, O.J., Lange, C., Karkhanis, Y.D., Kirk, K.E., Chakraborty, P.R. (1991) Cross-Protection Against Four Species of Chicken coccidia with a Single Recombinant Antigen. Infection and Immunity 59:1271-1277.

Kirk-Mason, K.E., Turner, M.J., Chakraborty, P.R. (1989) Evidence for Unusually Short mRNA Leaders and Characterization of Tubulin Genes in Giardia lamblia. Molecular and Biochemical Parasitology 36: 87-99. doi:10.1016/0166-6851(89)90204-1

Kirk-Mason, K.E., Turner, M.J., Chakraborty, P.R. (1988) Cloning and Sequence of beta-tubulin cDNA from Giardia lamblia. Nucleic Acids Research 16:2733.

Tocci, M.J., Hutchinson, N.I., Cameron, P.M., Kirk, K.E., Norman, D., Chin, J., Rupp, E.A., Limjuco, G.A., Bonilla, V., Schmidt, J. (1987) Expression in Escherichia coli of Fully Active Recombinant Human IL 1: Comparison with Native Human IL 1. Journal of Immunology 138:1109-1114.

Bhogal, B.S., Nollstadt, K., Kirk, K.E., Karkhanis, Y.D., Jacobson, E. (1987) Induction of Antibody and Cellular Immune Responses in Chickens Against Eimeria tenella by Anti-Idiotype. Avian Immunology, Alan R. Liss, New York, NY, 307-320.

Research Grants and Awards

National Science Foundation Research in Undergraduate Institutions Award, $266,000 (2010, 3 years).  Exceptionally Short Telomeres in Filamentous Fungi and The RNA That Makes Them.

National Science Foundation Major Research Instrumentation Award, $94,000 (2001). Acquisition of Multi-Imaging System for Use at an Undergraduate Institution.

National Science Foundation CAREER Award, $500,000 (1999, 5 years). Telomere Dynamics in Research and Education.

William L. Dunn Award for Outstanding Teaching and Scholarly Promise (1999).

National Institutes of Health AREA Award, $75,000 (awarded 1999, but voluntarily declined)

March of Dimes Foundation Basil O’Connor Starter Scholar Award, $100,000 (awarded 1999, but voluntarily declined)

National Institutes of Health Postdoctoral Research Training Grant (1995-96)

American Cancer Society Postdoctoral Research Fellowship (1992-95)

Merck Predoctoral Research Fellowship (1989-90)

Popular Work

Kirk, K.E. “From genes to traits,” MacMillan Science Library encyclopedia set, Biology (2001).

Lake Forest Hospital (March, 2002) in conjunction with Lake Forest Public Library “The Human Genome Project”

Recent Talks and Posters

American Society for Cell Biology Annual Meeting (December, 2011)
“Identifying the First Telomerase RNA in a Filamentous Fungus ”
Poster presented by undergraduate coauthor in Denver, Colorado.

Cold Spring Harbor Telomeres and Telomerase Meeting (April, 2011)
“Using a novel telomere-anchored PCR approach to determine telomere length and to search for a telomerase RNA gene in Aspergilli ”
Poster presented by undergraduate coauthor in Cold Spring Harbor, NY.

American Society for Cell Biology Annual Meeting (December, 2010)
“Novel Anchored Telomere PCR Approach for Studying Rare Telomeres in Aspergillus nidulans”
Poster presented by undergraduate coauthor in Philadelphia, PA.

Cold Spring Harbor Telomeres and Telomerase Meeting (April, 2009)
“Measuring the Exceptionally Short Telomeres of Aspergillus nidulans”
Poster presented by undergraduate coauthor in Cold Spring Harbor, NY.

American Society for Cell Biology Annual Meeting (December, 2008)
“Telomere Length in Meiotic Aspergillus nidulans”
Poster presented by undergraduate coauthor in San Francisco, CA.

American Association for the Advancement of Science (February, 2008) “Scientists Partnering with Educators: Why and How? Panelist to discuss how scientists benefit from such a partnership with the Science Education Partnership at University of California San Francisco. Boston, MA

American Society for Cell Biology Annual Meeting (December, 2007) “Telomere length regulation in Aspergillus nidulans”  Poster presented by undergraduate coauthors in Washington, D.C

American Society for Cell Biology Annual Meeting (December, 2003)
“Micronuclear telomere loss and cell division arrest in telomerase mutants”
Poster presented by undergraduate coauthor in San Francisco, CA.

FASEB Ciliate Molecular Biology Meeting (July, 2003)
“Massive telomere loss and cell division defects in telomerase mutants,” platform speaker
“Protein binding to expanded telomere repeats in Tetrahymena thermophila,” poster presentation by undergraduate coauthor
FASEB Summer Research Conference, Saxtons River, VT.

Cold Spring Harbor Telomeres and Telomerase Meeting (April, 2003)
“Protein binding to expanded telomere repeats in Tetrahymena thermophila,” and “Cell cycle defects in T. thermophila telomerase mutants.”
Both posters presented by undergraduate coauthors at Cold Spring Harbor, NY.

Midwest Protozoology Meeting (April, 2002)
“T. thermophila proteins bind differentially to telomere sequence variants in vitro”
Talk presented by undergraduate coauthor at Lake Forest College, Lake Forest, IL.
“Length regulation and processing mechanisms at Tetrahymena telomeres,” coauthor of talk
“Analysis of cell division arrest in T. thermophila telomerase mutants,” poster coauthored and presented by undergraduate

DNA Replication Meeting (September, 2001)
“Regulation of G-overhang structure at Tetrahymena telomeres”
Co-author of platform presentation by Naduparambil J., Kirk, K., and Price, C.
Cold Spring Harbor, NY.

Midwest Protozoology Meeting (April, 2001) “Does phenotype severity of Tetrahymena telomerase template mutants correlate to protein binding affinity?” Platform speaker, University of Chicago, Chicago, IL

Telomeres and Telomerase Meeting (March, 2001) “Does phenotype severity of Tetrahymena telomerase template mutants correlate to protein binding affinity?” Poster presented at Cold Spring Harbor, NY.

Kalamazoo College (October, 2000) “Mutating telomeres and inducing senescence (in an unsuspecting microbe)” Biology Departmental Seminar, Kalamazoo, MI.

Midwest Protozoology Meeting (April, 2000) “Phenotype of T. thermophila telomerase mutants,” platform speaker and “Using mutations to explore developmental dependencies in Tetrahymena thermophila,” Co-author of keynote talk with E. Cole, K. Stuart, T. Marsh, D. Romero, and K. Kirk, Purdue University, West Lafayette, IN.

Chicago Medical School (January, 2000) “Telomere mutants in Tetrahymena: An ageless Story” Molecular and Cellular Biology Departmental Seminar, North Chicago, IL.

University of Illinois Chicago (November, 1999) “Telomere mutants in Tetrahymena: An ageless Story” Cellular and Developmental Biology Departmental Seminar, Chicago, IL.

Ciliate Molecular Biology Meeting (August, 1999) “Micronuclear anaphase arrest in T. thermophila telomerase template mutants” FASEB Summer Research Conference, Saxtons River, VT.

St. Olaf College (November, 1998) Biology Departmental Seminar, Northfield, MN.

Ciliate Molecular Biology Meeting (July, 1997) FASEB Summer Research Conference, Copper Mountain, CO.