Graduate Program in Biological Chemistry

Students & Alumni

Student picture The Graduate Program in Biological Chemistry accepts three to seven highly qualified students each year. Currently our program is home to 33 students. Students who have earned Ph.D. degrees have gone on to prestigious postdoctoral positions at Harvard, the California Institute of Technology, and other renowned institutions. Our students are high achievers who have a demonstrated commitment to research.

Many of our students have won awards for the research they conducted here. Chia Che Chang and Brian Geisbrecht won the Paul Ehrlich Research Prize. Xian-Zhong Xu won the Shanoff Award as well as a national award, the 2000 Harold Weintraub Graduate Student Award. Jianwu Bai won the David Israel Macht Award and the 2001 Harold Weintraub Award. Daniel Cohen was awarded a Howard Hughes Medical Institutes Graduate Research Fellowship. Debra Silver won the 2002 Harold Weintraub Award and the 2003 Howard and Carol Macht Award. Seung-Jae Lee won the 2003 Mette Strand Award. In 2006, Tao Wang won the Paul Ehrlich Research Prize. If you are an outstanding student who is interested in a world class graduate education in an intense research environment, you should apply to the Graduate Program in Biological Chemistry.

Selected discoveries published by students in the Graduate Program in Biological Chemistry:

1997 | 1998 | 1999 | 2000 | 2001 | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008

2008

Zhao, Z., Lindsay, M.E., Roy Chowdhury, A., Robinson, D.R., Englund, P.T. (2008) "p166, a link between the trypanosome mitochondrial DNA and flagellum, mediates genome segregation." EMBO. Jan 9;27(1):143-54.

Chowdhury, A.R., Zhao, Z., Englund PT. (2008) "Effect of hydroxyurea on procyclic Trypanosoma brucei: an unconventional mechanism for achieving synchronous growth." Eukaryotic Cell. Feb;7(2):425-8.

2007

Kane, L.A., Priori, S.G., Napolitano, C., Arking, D.E., and Van Eyk, J.E. (2007)“Genetics, Genomics and Proteomics in Sudden Cardiac Death.” Cardiac Arrest: the science and practice of resuscitation medicine (2nd ed). Cambridge University Press .

Agnetti, G., Kane, L.A., Guarnieri, C., Caldarera, C.M. and Van Eyk, J.E. (2007) “Proteomic technologies in the study of kinases: Novel tools for the investigation of PKC in the heart.” Pharmacological Research Jun;55(6):511-22.

2006

Kane L.A., Neverova I., Van Eyk J.E. (2006) “Subfractionation of heart tissue: the "in sequence" myofilament protein extraction of myocardial tissue.” Methods in molecular biology ;357:87-90.

Kane, L.A., Yung, C.K., Agnetti, G., Neverova, I. and Van Eyk, J.E. “Optimization of paper bridge loading for 2-DE analysis in the basic pH region: Application to the mitochondrial subproteome.” Proteomics. (2006) Nov;6(21):5683-7.

Arrell, D.K., Elliott, S.T., Kane, L.A., Guo, Y., K,o Y.H., Pedersen, P.L., Robinson, J., Murata, M., Murphy, A.M., Marban, E., Van Eyk, J.E. “Proteomic analysis of pharmacological preconditioning: novel protein targets converge to mitochondrial metabolism pathways.” Circulation Research. (2006) Sep 29;99(7):706-14.

Booth, A.M., Fang, Y., Fallon, J.K., Yang, J.M., Hildreth, J.E., Gould, S.J. (2006) Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane. The Journal of cell biology. 172:923-935. [Abstract]

Chen, C. , Saxena, A.K., Simcoke, W.N., Garboczi, D.N., Pedersen, P.L., Ko, Y.H. (2006) Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism. J Biological Chemistry. [Abstract]

Kwon, Y. , Montell, C. (2006) Dependence on the Lazaro phosphatidic acid phosphatase for the maximum light response. Current Biology. [Abstract]

Liu, K. , Nagase, H., Huang, C.G., Calamita, Agre, P. (2006) Purification and functional characterization of aquaporin-8. Biology of the Cell 98:153–161. [Abstract]

Kim, S., Wong, P., Coulombe, P.A. (2006) A keratin cytoskeletal protein regulates protein synthesis and epithelial cell growth. Nature. 441:362-365

2005

Bernot, K.M., Lee, C.H., Coulombe, P.A. (2005) A small surface hydrophobic stripe in the coiled-coil domain of type I keratins mediates tetramer stability. J Cell Biol. 168:965-974. [Abstract]

Chen, H., Cohen, D.M., Choudhury, D.M., Kioka, N., Craig, S.W. (2005) Spatial distribution and functional significance of activated vinculin in living cells. J Cell Biol. 169:459-470. [Abstract]

Cohen, D.M. , Chen, H., Johnson, R.P., Choudhury, B., Craig, S.W. (2005) Two distinct head-tail interfaces cooperate to suppress activation of vinculin by talin. J Biol Chem. 280:17109-17117. [Abstract]

Fang, Q. , Shortle, D. (2005) A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 60:90-96. [Abstract]

Fang, Q. , Shortle, D. (2005) Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions. Proteins 60:97-102. [Abstract]

Hu, Z. , Cha, S.H., van Haasteren, G., Wang, J., Lane, M.D. (2005) Effect of centrally administered C75, a fatty acid synthase inhibitor, on ghrelin secretion and its downstream effects. Proc Natl Acad Sci U S A. 102:3972-3977. [Abstract]

Hu, Z. , Dai, Y., Prentki, M., Chohnan, S., Lane, M.D. ( 2005) A role for hypothalamic malonyl-CoA in the control of food intake. J Biol Chem. 280:39681-39683. [Abstract]

Kalume, D.E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Kumar, N. Pandey, A. (2005) Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 6:128. [Abstract]

Lee, H. , Caterina, M.J. (2005) TRPV channels as thermosensory receptors in epithelial cells. Pflugers Arch. 451:160-167. [Abstract]

Lee, H. , Iida, T., Mizuno, A., Suzuki, M., Caterina, M.J. (2005) Altered thermal selection behavior in mice lacking transient receptor potential vanilloid 4. J Neurosci. 25:1304-1310. [Abstract]

Liu, B., Liu, Y., Motyka, S.A., Agbo, E.E., Englund, P.T. (2005) Fellowship of the rings: the replication of kinetoplast DNA. Trends Parasitol. 21:363-369. [Abstract]

Liu, K. , Kozono, D., Kato, Y., Agre, P., Hazama, A., Yasui, M. (2005) Conversion of aquaporin 6 from an anion channel to a water-selective channel by a single amino acid substitution. Proc Natl Acad Sci U S A. 102:2192-2197 [Abstract]

Liu, Y. , Motyka, S.A., Englund, P.T. (2005) Effects of RNA interference of Trypanosoma brucei structure-specific endonuclease-I on kinetoplast DNA replication. J Biol Chem. 280:35513-35520. [Abstract]

Wang, T.,Jiao, Y., Montell, C. (2005) Dissecting independent channel and scaffolding roles of the Drosophila transient receptor potential channel. J Cell Biol. 171:685-94. [Abstract]

Wang, T. , Montell, C. (2005) Rhodopsin formation in Drosophila is dependent on the PINTA retinoid-binding protein. J Neurosci. 25:5187-5194. [Abstract]

Wang, T. , Xu, H., Oberwinkler, J., Gu, Y., Hardie, R.C., Montell, C. (2005) Light activation, adaptation, and cell survival functions of the Na+/Ca2+ exchanger, CalX. Neuron 45:367-378. [Abstract]

2004

Bakolitsa, C., Cohen, D.M., Bankston, L.A., Bobkov, A.A., Cadwell, G.W., Jennings, L., Critchley, D.R., Craig, S.W., Liddington, R.C. (2004) Structural basis for vinculin activation at sites of cell adhesion. Nature 430:583-586. [Abstract]

Chen, C. , Ko, Y.H., Delannoy, M., Ludtke, S.J., Chiu, W., Pedersen, P.L. (2004) Mitochondrial ATP synthasome: three-dimensional structure by electron microscopy of the ATP synthase in complex formation with carriers for P i and ADP/ATP. J Biol Chem. 279:31761-31768. [Abstract]

Chung, M.K., Lee, H., Mizuno, A., Suzuki, M., Caterina, M.J. (2004) 2-aminonethoxydiphenyl borate activates and sensitizes the heat-gated ion channel TRPV3. J Neurosci. 24:5177-5182. [Abstract]

Chung, M.K., Lee, H., Mizuno, A., Suzuki, M., Caterina, M.J. (2004) TRPV3 and TRPV4 mediate warmth-evoked currents in primary mouse keratinocytes. J Biol Chem. 279:21569-21575. [Abstract]

Coulombe, P.A., Tong, X., Mazzalupo, S., Wang, Z., Wong, P. (2004) Great promises yet to be fulfilled: defining keratin intermediate filament function in vivo. Eur J Cell Biol. 83:735-746. Review. [Abstract]

Fang, Y. , Morrell, J.C., Jones, J.M., Gould, S.J. (2004) PEX3 functions as a PEX19 docking factor in the import of class I peroxisomal membrane proteins. J Cell Biol. 164:863-875. [Abstract]

Lee, S.J., Xu, H., Montell, C. (2004) Rhodopsin kinase activity modulates the amplitude of the visual response in Drosophila. Proc Natl Acad Sci U S A. 101:11874-11879. [Abstract]

Motyka, S.A., Zhao, Z., Gull, K., Englund, P.T. (2004) Integration of pZJM library plasmids into unexpected locations in the Trypanosoma brucei genome. Mol Biochem Parasitol. 134:163-167. [Complete Article]

Tong, X. , Coulombe, P.A. (2004) A novel mouse type I intermediate filament gene, keratin 17n (K17n), exhibits preferred expression in nail tissue. J Invest Dermatol. 122:965-70. [Abstract]

Xu, H. , Lee, S.J., Suzuki, E., Dugan, K.D., Stoddard, A., Li, H.S., Chodosh, L.A., Montell, C. (2004) A lysosomal tetraspanin associated with retinal degeneration identified via a genome-wide screen. EMBO J. 23:811-822. [Abstract]

2003

Chung, M.K., Lee, H., Caterina, M.J. (2003) Warm temperatures activate TRPV4 in mouse 308 keratinocytes. J Biol Chem. 278:32037-32046. [Abstract]

Fang, Q. , Shortle, D. (2003) Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments. Proteins 53:486-490. [Abstract]

Gao, S. , Lane, M.D. (2003) Effect of the anorectic fatty acid synthase inhibitor C75 on neuronal activity in the hypothalamus and brainstem. Proc Natl Acad SciU S A. 100:5628-5633. [Abstract]

Hu, Z. , Cha, S.H., Chohnan, S., Lane, M.D. (2003) Hypothalamic malonyl-CoA as a mediator of feeding behavior. Proc Natl Acad SciU S A. 100:12624-12629. [Abstract]

Lee, M.G. , Pedersen, P.L. (2003) Glucose metabolism in cancer: importance of transcription factor-DNA interactions within a short segment of the proximal region of the type II hexokinase promoter. J Biol Chem. 278:41047-41058. [Abstract]

Lee, S.J., Xu, H. , Kang, L.W., Amzel, L.M., Montell, C. (2003) Light adaptation through phosphoinositide-regulated translocation of Drosophila visual arrestin. Neuron 39:121-132. [Abstract]

Li, X. , Gould, S.J. (2003) The dynamin-like GTPase DLP1 is essential for peroxisome division and is recruited to peroxisomes in part by PEX11. J Biol Chem. 278:17012-17020. [Abstract]

Tong, X. , Coulombe, P.A. (2003) Mouse models of alopecia: identifying structural genes that are baldly needed. Trends Mol Med. 9:79-84. [Abstract]

2002

Bai, J. , Montell, D.J. (2002) Eyes absent, a key repressor of polar cell fate during Drosophila oogenesis, Development 129:5377-5388. [Abstract]

Li, X. , Gould, S.J. (2002) PEX11 promotes peroxisome division independently of peroxisome metabolism. J Cell Biol. 156:643-651. [Abstract]

Li, X. , Baumgart, E., Morrell, J.C., Jimenez-Sanchez, G., Valle, D., Gould S.J. (2002) PEX11 b deficiency is lethal and impairs neuronal migration but does not abrogate peroxisome function. Mol Cell Biol. 22:4358-4365. [Abstract]

Wang, Z. , Drew, M.E., Morris, J.C., Englund, P.T. (2002) Asymmetrical division of the kinetoplast DNA network of the trypanosome. Embo J. 21:4998-5005. [Abstract]

Zeidan, Q., Strauss, M., Porras, N., Anselmi, G. (2002) Differential long-term subcellular responses in heart and liver to adriamycin stress. Exogenous L-carnitine cardiac and hepatic protection.
Journal of submicroscopic cytology and pathology. 34(3):315-21.

2001

Lee, S.J. ,Montell, C. (2001) Regulation of the rhodopsin protein phosphatase, RDGC, through interaction with calmodulin. Neuron 32:1097-1106. [Abstract]

Liu, Y. , Montell, D.J. (2001) Jing: a downstream target of slbo required for developmental control of border cell migration. Development 128:321-330. [Abstract]

Ma, L. , Yamada, S., Wirtz, D., Coulombe, P.A. (2001) A “hot-spot” mutation alters the mechanical properties of keratin filament networks. Nature Cell Biology 3:503-506. [Abstract]

Silver, D. , Montell, D.J. (2001) Paracrine signaling through the JAK/STAT pathway activates invasive behavior of ovarian epithelial cells in Drosophila. Cell107:831-841. [Abstract]

Wang, Z. , Englund, P.T. (2001) RNA interference of a trypanosome topoisomerase II causes progressive loss of mitochondrial DNA. Embo J. 20:4674-4683. [Abstract]

Xu, X.Z.S. , Moebius, F., Gill, D.L., Montell, C. (2001) Regulation of melastatin, a TRP-related protein, through interaction with a cytoplasmic isoform. Proc Natl Acad Sci U S A. 98:10692-10697. [Abstract]

2000

Bai, J. , Uehara, Y., Montell, D.J. (2000) Regulation of invasive cell behavior by Taiman, a Drosophila protein related to AIB1, a steroid receptor coactivator amplified in breast cancer. Cell.103:1047-1058. [Abstract]

Hoffert, J.D. , Leitch, V., Agre, P., King, L.S. (2000) Hypertonic induction of aquaporin-5 expression through an ERK-dependent pathway. J Biol Chem. 275:9070-9077. [Abstract]

Wang, Z. , Morris, J.C., Drew, M.E., Englund, P.T. (2000) Inhibition of Trypanosoma brucei gene expression by RNA interference using an integratable vector with opposing T7 promoters. J Biol Chem. 275:40174-40179. [Abstract]

Xu, X.Z.S. , Chien, F., Butler, A., Salkoff, L., Montell, C. (2000) TRP g , a Drosophila TRP-related subunit, forms a regulated cation channel with TRPL. Neuron 26:647-657. [Abstract]

1999

Chang, C.C. , Warren, D.S., Sacksteder, K.A., Gould, S.J. (1999) PEX12 interacts with PEX5 and PEX10 and acts downstream of receptor docking in peroxisomal matrix protein import. J Cell Biol. 147:761-774. [Complete Article]

Geisbrecht, B.V. , Gould, S.J. (1999) The human PICD gene encodes a cytoplasmic and peroxisomal NADP +-dependent isocitrate dehydrogenase. J Biol Chem. 274:30527-30533. [Complete Article]

Geisbrecht, B.V. , Liang, X., Morrell, J.C., Schulz, H., Gould, S.J. (1999) The mouse gene PDCR encodes a peroxisomal D 2 , D 4 -dienoyl-CoA reductase. J Biol Chem. 274:25814-25820. [Complete Article]

Liu, Y. , Bjorkman, J., Urquhart, A., Wanders, R.J., Crane, D.I., Gould, S.J. (1999) PEX13 is mutated in complementation group 13 of the peroxisome-biogenesis disorders. Am J Hum Genet. 65:621-634. [Abstract]

Liu, Y. , Montell, D.J. (1999) Identification of mutations that cause cell migration defects in mosaic clones. Development 126:1869-1878. [Complete Article]

Ma, L. , Xu, J., Coulombe, P.A., Wirtz, D. (1999) Keratin filament suspensions show unique micromechanical properties. J Biol Chem. 274:19145-19151. [Complete Article]

1998

Geisbrecht, B.V. , Collins, C.S., Reuber, B.E., Gould, S.J. (1998) Disruption of a PEX1-PEX6 interaction is the most common cause of the neurologic disorders Zellweger syndrome, neonatal adrenoleukodystrophy, and infantile Refsum disease. Proc Natl Acad Sci U S A. 95:8630-8635. [Complete Article]

Xu, X.Z.S. , Choudhury, A., Li, X., Montell, C. (1998) Coordination of an array of signaling proteins through homo- and heteromeric interactions between PDZ domains and target proteins. J Cell Biol. 142:545-555. [Complete Article]

Xu, X.Z.S. , Wes, P.D., Chen, H., Li, H.S., Yu, M., Morgan, S., Liu, Y., Montell, C. (1998) Retinal targets for calmodulin include proteins implicated in synaptic transmission. J Biol Chem. 273:31297-31307. [Complete Article]

1997

Chang, C.C. , Lee, W.H., Moser, H., Valle, D., Gould, S.J. (1997) Isolation of the human PEX12 gene, mutated in group 3 of the peroxisome biogenesis disorders. Nat Genet. 15:385-388. [Abstract]

Xu, X.Z.S. , Li, H.S., Guggino, W.B., Montell, C. (1997) Coassembly of TRP and TRPL produces a distinct store-operated conductance. Cell 89:1155-1164. [Abstract]

top