Biology

John McDonald, Professor and Chair

Ph.D., Genetics, University of California Davis, 1977

Phone: 404-894-3735, 404-385-6630
Fax: (404) 894-0519
Office: CE 201 / IBB 3314

Research Interests

Genome evolution and cancer research

Current Research

Retrotransponons and Evolution

Retrotransposons are the most abundant and wide spread class of eukaryotic transposable elements. For example, retrotransposons constitute ~10% of the Drosophila genome, ~20% of the rice genome, ~40% of the human genome, ~50% of the maize genome and >90% of the genome of some lilies. Our laboratory is interested in understanding the mechanisms underlying retroelement evolution and the impact these elements have had on the evolution of the host genomes in which they reside. We combine molecular biology and computational genomics to address these questions in a variety of organisms ranging from yeast to humans.

Cancer

Our laboratory's interests in retrotransposons extends to the role these elements may play in the alteration of chromatin structure and other epigenetic changes associated with tumorgenesis. In collaboration with the Ovarian Cancer Institute (Atlanta), we are engaged in efforts to identify molecular markers of early staged ovarian cancers using microarray (Affymetrix), 2-D gel and mass spectrometry (MALDI-TOF) technologies. We are also nterested in analyzing the molecular responses of different stages and classes of tumors to chemotherapy and in understanding the molecular basis of chemotherapy resistance.

Selected Publications

Bowen, N., P. Wade and J. F. McDonald. (2006) The Role of Pax8 in the Mesenchymal to Epithelial Transition of Ovarian Mesothelium into Epithelial Ovarian Carcinomas. Gynecologic Oncology (in press).

Polavarapu, N., N. Bowen and J. F. McDonald 2006. Identification and characterization of chimpanzee LTR retrotransposons. J. Virology (in press).

Herrera, R. J. , R. Lowery, A. Alfonso, J. F. McDonald and J. Luis..( 2006). Ancient retroviral insertions among human populations. J. Human Genetics (in press).

Ganko, E., C. Greene, J. Lewis, V. Bhattacharjee and J. F. McDonald. (2006) LTR retrotransposon-gene associations in D. melanogaster. J Mol Evol. 62: 111-120.

De Barry. J., E. Ganko and J. F. McDonald. (2006). The contribution of LTR retrotransposons sequences to gene evolution in Mus musculus. Mol Biol Evol . 23: 479-481.

McDonald, J.F., Matzke, M.A. and A.J. Matzke. (2005). Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenet Genome Res. 110: 242-249.

Franchini, L.F., E.W. Ganko, J.F. McDonald. 2004. Retrotransposon-gene Mol. Biol. Evol. 21(7):1323-1331. 2004

Menendez L, Benigno BB, McDonald JF. 2004. L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas. Mol Cancer., Apr 26;3(1):12.

Gao, L, McCarthy EM, Ganko EW, McDonald JF. 2004. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics, 5:18. PubMed / Journal Website

McCarthy, E.M., and J.F. McDonald. 2004. LTR Retrotransposons of Mus musculus. Genome Biology, 5:R14.