John McDonald, Professor and Associate Dean for Biology Program Development
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
Cancer Biology:
In the McDonald lab, we are taking an integrated systems approach to the study of cancer. This means that we view cancer not as a defect in any particular gene or protein, but as a de-regulated cellular/inter-cellular process. An understanding of such complex processes requires the implementation of an experimental approach that can provide an integrative holistic or "systems" view of intra- and inter-cellular process. We employ a number high-throughput genomic (e.g., microarray) and proteomic (e.g., MASS SPEC) technologies to gather systems data on the status of cancer cells. We strive to integrate into our research program, the exceptional strengths that exist at Georgia Tech in the fields of engineering and the computational sciences. The primary focus of our current research is ovarian cancer and our overall goals are: 1) the development of a reliable and accurate diagnostic test for ovarian cancer, 2) the development of a molecular-based objective and precise classification system for ovarian cancers, and 3) the development of new and effective treatments for ovarian cancer.
Representative recent publications in Cancer Biology:
Guan W, Zhou M, Hampton CY, Benigno BB, Walker D, Gray A, McDonald JF. and Facundo, FM. 2009. Ovarian Cancer Detection from Metabolomic Liquid Chromatography/Mass Spectrometry Data by Support Vector Machines.BMC Bioinformatics. Aug 2009. 10:259-274.
Blackburn W, Dickerson E, Smith M, McDonald JF, Lyon A.2009. Peptide-Functionalized Nanogels for Targeted siRNA Delivery. Bioconjugate Chemistry Apr 2 [Epub ahead of print].
Mezencev R, Kutschy P, Salayová A, Updegrove T, McDonald JF. 2009.The design, synthesis and anticancer activity of new nitrogen mustard derivatives of natural indole phytoalexin 1-methoxyspirobrassinol. Neoplasma, 56(4): 321-330
Carpendo RL, Bratt-Leal AM, Marklein RA, Seamen SA, Bowen NJ, McDonald JF, McDevitt TC. 2009.Homogeneous and organized differentiation within embyoid bodies induced by microsphere-mediated delivery of small molecules. Biomaterials, 30(13) :2507-15.
Scharer CD, Laycock N, Osunkoya AO, Logani S, McDonald JF, Benigno BB, Moreno CS. 2008. Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells. J Transl Med, Dec 11.6:79.
Arakaki A, Skolnick J, McDonald JF. 2008.Marker metabolites can be thereapeutic as well. Nature, Nov 27. 456 (7221): 443.
Dickerson, E.B., Dreaden, E.C, Huang, X., Chu, X., Pushpanketh, S., McDonald, J.F and El-Sayed, M.A. 2008. Gold nanorod assisted near infrared plasmonic photothermal therapy (PPTT) of HSC-3 tumors in mice. Cancer Lett. Sep 28.269 (1): 57-66.
Mezencev, R., Kutschy,P. Salayova, A. Curillová, Z., Mojzis, J., Pilatová, M. and McDonald, J.F. 2008. Anticancer properties of 2-piperidyl analogues of the natural indole phytoalexin 1-methoxyspirobrassinol. Chemotherapy, Sep 4. 54 (5) : 372-78.
Scarberry, K., Dickerson,E.B., McDonald, J.F. and Zhang, Z.J. 2008.Targeting and extraction of cancer cells in vitro and in vivo using magnetic nanoparticle-peptide conjugates. J. Am. Chem. Soc., Aug 6; 130 (31):10258-62.
Abbott K.L., Nairn, A.V., Hall, E.M., Horton, M.B., McDonald, J.F., Moremen, K.W. , Dinulescu, D.W. and Pierce, M. 2008. Focused glycomic analysis for the N-linked glycan biosynthetic pathway in ovarian cancer, Proteomics . Aug 2008; 8 (16): 3210-20.
Transposable Elements and Genome Evolution
The McDonald lab has long pioneered efforts to elucidate the evolutionary significance of transposable elements. Once considered "junk DNA" of little or no biological significance, transposable elements are today widely recognized as major players in bringing about evolutionary change. Our laboratory integrates methods of computational and molecular biology to test hypotheses on the contribution of transposable elements to gene and genome evolution. Current interests are focused on the role of retrotransposons in the evolution of epigenetic phenomena and on the role of retrotransposons in human evolution.
Representative recent publications in Evolutionary Biology
Arora, G., Polavarapu, N. and McDonald, J.F.2009.Did Natural Selection for Increased Cognitive Ability in Humans Lead to an Elevated Risk of Cancer? Med. Hypotheses Apr 29 [Epub ahead of print] .
Matyunina, L.V., Bowen N.J. and McDonald ,J.F. 2008. LTR retrotransposons and dosage compensation in Drosophila. 2008 BMC Mol. Biol. Jun 2008 9:55.
Huda A., Polavarapu N. , Jordan I. K. and McDonald J.F. 2008. Endogenous Retroviruses of the Chicken Genome, Biology Direct, 3:9
Polavarapu N., Marino-Ramirez, L., Landsman, D., McDonald, J.F. and Jordan, I.K. 2008. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA, BMC Genomics May 17 9 : 226.
Piriyapongsa J., Polavarapu N., Borodovsky M., McDonald J.F. 2007. Exonization of the LTR transposable elements in human genome. BMC Genomics. Aug 28; 8(1); 291.
Polavarapu, N., Bowen, N. and McDonald, J.F. 2006. Identification and characterization of chimpanzee LTR retrotransposons. J. Virology 80: 4640-2. 6.Fablet M., McDonald J.F., Biemont C. and Vieira, C. 2006. Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans.Gene 375:54-62.
Polavarapu N, Bowen N.J. and McDonald J.F.2006. Newly identified families of human endogenous retroviruses. J Virol.May;80(9):4640-2.
Herrera, R. J. ,Lowery, R. Alfonso, A., McDonald, J.F. and Luis, J. 2006. Ancient retroviral insertions among human populations. J. Human Genetics 51(4): 353-62.
Ganko, E., Greene, C., Lewis, J., Bhattacharjee, V. and McDonald, J.F. 2006 LTR retrotransposon-gene associations in D. melanogaster. J Mol Evol. 62: 111-120.
De Barry. J., Ganko, E. and McDonald, J.F. 2006. The contribution of LTR retrotransposons sequences to gene evolution in Mus musculus. Mol Biol Evol . 23: 479-481.