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Archive for February, 2011

Madeline Shea joins Hopkins Society of Scholars

Monday, February 28th, 2011

Congratulations to Madeline A. Shea, who was selected for induction into the Johns Hopkins University Society of Scholars in May, 2011. The Society of Scholars inducts former postdoctoral fellows, postdoctoral degree recipients, house staff and junior or visiting faculty who have served at least a year at Johns Hopkins and thereafter gained marked distinction elsewhere in their fields of physical, biological, medical, social or engineering sciences or in the humanities.

Madeline’s award citation includes the following text:

“In addition to her outstanding contributions to scientific knowledge, many of us know Madeline through her support of the Gibbs Conference and her activities in the Biophysical Society. She earned her PhD in Biophysics in the Jenkins Department in 1984 and continued in the JHU Department of Biology until 1989 as a Postdoctoral Fellow and Associate Research Scientist.

Dr. Shea… is an internationally recognized pioneer in statistical thermodynamic models of complex biological systems. In stark departure from traditional descriptive approaches, her modeling of cellular life processes established an unrivaled paradigm for post-genomic biology in the 21st century. Shea’s early research – initiated at Hopkins – unveiled the workings of the classic genetic switch, bacteriophage lambda. Cited hundreds of times, this study stands as a landmark demonstration that essential aspects of a cell’s life cycle can be quantified from kinetic and statistical thermodynamic information of its constituent macromolecules. As an NSF Presidential Young Investigator she revolutionized biological understandings of calmodulin, an essential human protein critical in the nervous, heart and reproductive systems: her contributions rationalize the mechanisms by which the cooperative network of interactions enable calmodulin proteins to function as sensors, amplifiers and transducers in living cells. Dr. Shea is known for a consummate depth and quantitative clarity. Her investigations explore the very essence of living systems; and her outcomes continue to transform prevailing views of how networks of biological molecules maintain and regulate cellular life.”

Lori Wallrath wins Carver College of Medicine Collegiate Teaching Award

Saturday, February 26th, 2011

Congratulations to Lori Wallrath, winner of a CCOM Collegiate Teaching Award. Through teaching and mentorship, she has influenced the lives of thousands of undergraduates, graduate students, and postdoctoral fellows during her distinguished 13 year career at Iowa. Like many of the very best educators in the College, her teaching excellence flows from her internationally known research program. In the laboratory, she has trained a diverse array of individuals including two high school students, over 30 undergraduates, two junior high school teachers, numerous graduate rotation students, five PhD candidates, five postdoctoral fellows, three technicians, and a faculty member at a primarily undergraduate institution.

2010 Publications

Friday, February 25th, 2011

The Department’s 2010 publications are now in print and mostly available online. There are papers in Cell, Genes & Development, Human Molecular Genetics, JACS, Journal of Immunology, Molecular Cell, Nature, Nature Medicine, Nature Structural & Molecular Biology, PNAS and, and, of course, JBC and Biochemistry.

SHEILA BAKER
Gospe, S.M. 3rd, Baker, S.A., Arshavsky, V.Y. (2010) Facilitative glucose transporter Glut1 is actively excluded from rod outer segments. J Cell Sci 23: 3639-3644. PMID: 20923839

HEATHER BARTLETT
Bartlett, H.L., Escalera, R.B. 2nd, Patel, S.S., Wedemeyer, E.W., Volk, K.A., Lohr, J.L., Reinking, B.E. (2010) Echocardiographic assessment of cardiac morphology and function in Xenopus. Comp Med. 60:107-113. PMID: 20412684

Bartlett, H., Veenstra, G.J., Weeks, D.L. (2010) Examining the cardiac NK-2 genes in early heart development. Pediatr Cardiol. 31:335-41. PMID: 19967350

CHARLES M. BRENNER
Bogan, K.L., Brenner, C. (2010) 5’-Nucleotidases and their new roles in NAD(+) and phosphate metabolism. New J. Chem. 34:845-853.

Evans, C., Bogan, K.L., Song, P., Burant, C.F., Kennedy, R.T., Brenner, C. (2010) NAD+ metabolite levels as a function of vitamins and calorie restriction: evidence for different mechanisms of longevity. BMC Chem Biol. 10:2. PMID: 20175898

JOHN M. DAGLE
Abu-Maziad, A., Schaa, K., Bell, E.F., Dagle, J.M., Cooper, M., Marazita, M.L., Murray, J.C. (2010) Role of polymorphic variants as genetic modulators of infection in neonatal sepsis. Pediatr. Res. 68:323-329. PMID: 20463618

Waleh, N., Hodnick, R., Jhaveri, N., McConaghy, S., Dagle, J., Seidner, S., McCurnin, D., Murray, J.C., Ohls, R., Clyman, R.I. (2010) Patterns of gene expression in the ductus arteriosus are related to environmental and genetic risk factors for persistent ductus patency. Pediatr. Res. 68:292-297.

KRIS DEMALI
Peng, X., Cuff, L.E, Lawton, C.D., DeMali, K.A. (2010) Vinculin regulates cell-surface E-cadherin expression by binding to beta-catenin. J. Cell Sci. 123:567-77. PMID: 20086044

Shepherd, T.R., Klaus, S.M., Liu, X., Ramaswamy, S., DeMali, K.A., Fuentes, E.J. (2010) The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion. J Mol Biol. 398:730-746. PMID: 20361982

JOHN E. DONELSON
DebRoy, S., Keenan, A.B., Ueno, N., Jeronim, S.M., Donelson, J.E., Wilson, M.E. (2010) Leishmania infantum chagasi: A genome-based approach to identification of excreted/secreted proteins. Exp Parasitol. 126:582-591. PMID: 20542033

Yao, C., Li, Y., Donelson, J.E., Wilson, M.E. (2010) Proteomic examination of Leishmania chagasi plasma membrane proteins: Contrast between avirulent and virulent (metacyclic) parasite forms. Proteomics Clin. Appl. 4:4-16. PMID: 21137013

ADRIAN ELCOCK
Elcock, A.H. (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol. 20:196-206. Review. PMID: 20167475

Frembgen-Kesner, T., Elcock, A.H. (2010) Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: The role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys. J. 99:L75-77. PMID: 21044566

McGuffee, S.R., Elcock, A.H. (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput. Biol. 6(3):e1000694. PMID: 20221255

Zhu, S., Elcock, A.H. (2010) A complete thermodynamic characterization of electrostatic and hydrophobic associations in the temperature range 0 to 100 °C from explicit-solvent molecular dynamics simulations. J. Chem. Theory Comput. 6:1293-1306.

ERNESTO J. FUENTES
Ramadugu, S.K., Chung, Y.H., Fuentes, E.J., Rice, K.G., Margulis, C.J. (2010) In silico prediction of the 3D structure of trimeric asialoglycoprotein receptor bound to triantennary oligosaccharide. J. Am. Chem. Soc. 132:9087-9095. PMID: 20540518

Shepherd, T.R., Klaus, S.M., Liu, X., Ramaswamy, S., DeMali, K.A., Fuentes, E.J. (2010) The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion. J. Mol. Biol. 398:730-746. PMID: 20361982

Wen, H., Kim, N., Fuentes, E.J., Mallinger, A., Gonzalez-Alegre, P., Glenn, K. (2010) FBG1 is a promiscuous ubiquitin ligase that sequesters APC2 and causes S-phase arrest. Cell Cycle 9:4506-4517. PMID: 21135578

PAMELA K. GEYER
Dialynas, G., Speese, S., Budnik, V., Geyer, P.K., Wallrath, L.L. (2010) The role of Drosophila Lamin C in muscle function and gene expression. Development 137:3067-3077. PMID: 20702563

THERESA GIOANNINI
Piazza, M., Calabrese, V., Baruffa, C., Gioannini, T., Weiss, J., Peri, F. (2010) The cationic amphiphile 3,4-bis(tetradecyloxy)benzylamine inhibits LPS signaling by competing with endotoxin for CD14 binding. Biochem. Pharmacol. 80:2050-2056. PMID: 20599783

Prohinar, P., Rallabhandi, P., Weiss, J.P., Gioannini, T.L. (2010) Expression of functional D299G.T399I polymorphic variant of TLR4 depends more on coexpression of MD-2 than does wild-type TLR4. J. Immunol. 184:4362-4367. PMID: 20212095

RAMA MALLAMPALLI
Agassandian, M., Chen, B.B., Schuster, C.C., Houtman. J.C., Mallampalli, R.K. (2010) 14-3-3zeta escorts CCTalpha for calcium-activated nuclear import in lung epithelia. FASEB J. 24:1271-1283. PMID: 20007511

Butler, P.L., Mallampalli, R.K. (2010) Cross-talk between remodeling and de novo pathways maintains phospholipid balance through ubiquitination. J. Biol. Chem. 285(9):6246-6258. PMID: 20018880

Gakhar, L., Bartlett, J.A., Penterman, J., Mizrachi, D., Singh, P.K., Mallampalli, R.K., Ramaswamy, S., McCray, P.B. Jr. (2010) PLUNC is a novel airway surfactant protein with anti-biofilm activity. PLoS One 5:e9098. PMID: 20161732

Murthy, S., Ryan, A., He, C., Mallampalli, R.K., Carter, A.B. (2010) Rac1-mediated mitochondrial H2O2 generation regulates MMP-9 gene expression in macrophages via inhibition of SP-1 and AP-1. J. Biol. Chem. 285:25062-25073. PMID: 20529870

Ray, N.B., Durairaj, L., Chen, B.B., McVerry, B.J., Ryan, A.J., Donahoe, M., Waltenbaugh, A,K., O’Donnell, C.P., Henderson, F.C., Etscheidt, C.A., McCoy, D.M., Agassandian, M., Hayes-Rowan, E.C,. Coon, T.A., Butler, P.L., Gakhar, L., Mathur, S.N., Sieren, J.C., Tyurina, Y.Y., Kagan, V.E., McLennan, G., Mallampalli, R.K. (2010) Dynamic regulation of cardiolipin by the lipid pump Atp8b1 determines the severity of lung injury in experimental pneumonia. Nat. Med. 16:1120-1127. PMID: 20852622

PETER L. NAGY
Calva-Cerqueira, D., Dahdaleh, F.S., Woodfield, G., Chinnathambi, S., Nagy, P.L., Larsen-Haidle, J., Weigel, R.J., Howe, J.R. (2010) Discovery of the BMPR1A promoter and germline mutations that cause juvenile polyposis. Hum. Mol. Genet. 19:4654-4662. PMID: 20843829

BRYCE V. PLAPP
Plapp, B.V. (2010) Conformational changes and catalysis by alcohol dehydrogenase. Archives Biochem. & Biophys. 493:3-12. PMID: 19583966

DAVID H. PRICE
Bartkowiak, B., Liu, P., Phatnani, H.P., Fuda, N.J., Cooper, J.J., Price, D.H., Adelman, K., Lis, J.T., Greenleaf, A.L. (2010) CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev. 24:2303-2316. PMID: 20952539

Cojocaru, M., Bouchard, A., Cloutier, P., Cooper, J.J., Varzavand, K., Price, D.H., Coulombe, B. (2010) Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B  J. Biol. Chem. 286:5012-5022. PMID: 21127351

Krueger, B.J., Varzavand, K, Cooper, J.J., Price, D.H. (2010) The mechanism of release of P-TEFb and HEXIM1 from the 7SK snRNP by viral and cellular activators includes a conformational change in 7SK. PLoS One 5:e12335. PMID: 20808803

Price, D.H. (2010) Regulation of RNA polymerase II elongation by c-Myc. Cell 141:399-400. PMID: 20434979

Tahirov, T.H., Babayeva, N.D., Varzavand, K., Cooper, J.J., Sedore, S.C., Price, D.H. (2010) Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465:747-751. PMID: 20535204

MILES PUFALL
Shipp, L.E., Lee, J.V., Yu, C.Y., Pufall, M., Zhang, P., Scott, D.K., Wang, J.C. (2010) Transcriptional regulation of human dual specificity protein phosphatase 1 (DUSP1) gene by glucocorticoids. PLoS One 5:e13754. PMID 21060794

S. RAMASWAMY
Freudenthal, B.D., Gakhar, L., Ramaswamy, S., Washington, M.T. (2010) Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nat. Struct. Mol. Biol. 17:479-484. PMID: 20305653

Gakhar, L., Bartlett, J.A., Penterman, J., Mizrachi, D., Singh, P.K., Mallampalli, R.K., Ramaswamy, S., McCray, P.B. Jr. (2010) PLUNC is a novel airway surfactant protein with anti-biofilm activity. PLoS One 5:e9098. PMID: 20161732

Pashkova, N., Gakhar, L. Winistorfer, S.C., Yu, L., Ramaswamy, S., Piper, R.C. (2010) WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell. 40: 433-443. PMID: 21070969

Shepherd, T.R., Klaus, S.M., Liu, X., Ramaswamy, S., DeMali, K.A., Fuentes, E.J. (2010) The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion. J Mol Biol. 398:730-746. PMID: 20361982

PETER A. RUBENSTEIN
Bergeron, S.E., Zhu, M., Thiem, S.M., Friderici, K.H., Rubenstein, P.A. (2010) Ion-dependent polymerization differences between mammalian beta- and gamma-nonmuscle actin isoforms. J. Biol. Chem. 285:16087-16095. PMID: 20308063

Kudryashov, D.S., Grintsevich, E.E., Rubenstein, P.A., Reisler, E. (2010) A nucleotide state-sensing region on actin. J. Biol. Chem. 285:25591-25601. PMID: 20530485

Wen, K.K., McKane, M., Stokasimov, E., Fields, J., Rubenstein, P.A. (2010) A potential yeast actin allosteric conduit dependent on hydrophobic core residues val-76 and trp-79. J. Biol. Chem. 285:21185-94. PMID: 20442407

MADELINE A. SHEA
Feldkamp, M.D., O’Donnell, S.E., Yu, L., Shea, M.A. (2010) Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin. Proteins 78:2265-2282. PMID: 20544963

O’Donnell, S.E., Yu, L., Fowler, C.A., Shea, M.A. (2010) Recognition of β-calcineurin by the domains of calmodulin: Thermodynamic and structural evidence for distinct roles. Proteins 79:765-86. PMID: 21287611

ARTHUR A. SPECTOR
Fiedorowicz, J.G., Hale, N., Spector, A.A., Coryell, W.H. (2010) Neuroticism but not omega-3 fatty acid levels correlate with early responsiveness to escitalopram. Ann. Clin. Psychiatry 22:157-163. PMID: 20680188

NANCY C. STELLWAGEN
Stellwagen, N.C., Lu, Y.J. (2010) Effect of magnesium ions and temperature on the sequence-dependent curvature of DNA restriction fragments. J Phys. Condens. Matter 22: 494110.

LORI L. WALLRATH
Dialynas, G., Speese, S., Budnik, V., Geyer, P.K., Wallrath, L.L. (2010) The role of Drosophila Lamin C in muscle function and gene expression. Development 137:3067-3077. PMID: 20702563

M. TODD WASHINGTON
Dieckman, L.M., Johnson, R.E., Prakash, S., Washington, M.T. (2010) Pre-steady state kinetic studies of the fidelity of nucleotide incorporation by yeast DNA polymerase delta. Biochemistry 49:7344-7350. PMID: 20666462

Freudenthal, B.D., Brogie, J.E., Gakhar, L., Kondratick, C.M., Washington, M.T. (2010) Crystal Structure of SUMO-Modified Proliferating Cell Nuclear Antigen. J. Mol. Biol. 406:9-17. PMID: 21167178

Freudenthal, B.D., Gakhar, L., Ramaswamy, S., Washington, M.T. (2010) Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nat. Struct. Mol. Biol. 17:479-484. PMID: 20305653

Washington, M.T., Carlson, K.D., Freudenthal, B.D., Pryor, J.M. (2010) Variations on a theme: Eukaryotic Y-family DNA polymerases. Biochim. Biophys. Acta. 1804:1113-1123. Review. PMID: 19616647

DANIEL L. WEEKS
Bartlett, H., Veenstra, G.J., Weeks, D.L. (2010) Examining the cardiac NK-2 genes in early heart development. Pediatr. Cardiol. 31:335-341. PMID: 19967350

Li, Y., Manaligod, J.M., Weeks, D.L. (2010) EYA1 mutations associated with the branchio-oto-renal syndrome result in defective otic development in Xenopus laevis. Biol. Cell. 102:277-292. PMID: 19951260

RONALD J. WEIGEL
Calva-Cerqueira, D., Dahdaleh, F.S., Woodfield, G., Chinnathambi, S., Nagy, P.L., Larsen-Haidle, J., Weigel, R.J., Howe, J.R. (2010) Discovery of the BMPR1A promoter and germline mutations that cause juvenile polyposis. Hum. Mol. Genet. 19:4654-4662. PMID: 20843829

Fang, S.H., Guidroz, J.A., O’Malley, Y., Lal, G., Sugg, S.L., Howe, J.R., Jensen, C.S., Weigel, R.J. (2010) Expansion of a cell population expressing stem cell markers in parathyroid glands from patients with hyperparathyroidism. Ann. Surg. 251:107-113. PMID: 20009751

Gollapalli, V., Liao, J., Dudakovic, A., Sugg, S.L., Scott-Conner, C.E., Weigel, R.J. (2010) Risk factors for development and recurrence of primary breast abscesses. J. Am. Coll. Surg. 211:41-48. PMID: 20610247

Lal, G., Fairchild, T., Howe, J.R., Weigel, R.J., Sugg, S.L., Menda, Y. (2010) PET-CT scans in recurrent or persistent differentiated thyroid cancer: is there added utility beyond conventional imaging? Surgery 148:1082-1089; discussion 1089-90. Review. PMID: 21134537

Woodfield, G.W., Chen, Y., Bair, T.B., Domann, F.E., Weigel, R.J. (2010) Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells. Genes Chromosomes Cancer 49:948-962. PMID: 20629094

MARC S. WOLD
Choi, J.H., Lindsey-Boltz, L.A., Kemp, M., Mason, A.C., Wold, M.S., Sancar, A. (2010) Reconstitution of RPA-covered single-stranded DNA-activated ATR-Chk1 signaling. Proc. Natl. Acad. Sci. USA 107:13660-13665. PMID: 20616048

Haring, S.J., Humphreys, T.D., Wold, M.S. (2010) A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression. Nuc. Acids Res. 38:846-858. PMID: 19942684

Hass, C.S., Gakhar, L., Wold, M.S. (2010) Functional characterization of a cancer causing mutation in human replication protein A. Mol. Cancer Res. 8:1017-1026. PMID: 20587534

Humphreys, T.D., Wold, M.S. (2010) Eukaryotic replication protein A. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester, 2010.

Kemp, M.G., Mason, A.C., Carreira, A., Reardon, J.T., Haring, S.J., Borgstahl, G.E., Kowalczykowski, S.C., Sancar, A., and Wold, M.S. (2010) An alternative form of RPA (aRPA) expressed in normal human tissues supports DNA repair. J. Biol. Chem. 285:4788-4797. PMID: 19996105

Machwe, A., Lozada, E., Wold, M.S., Li, G.M., Orren, D.K. (2010) Molecular Cooperation between the Werner Syndrome Protein and Replication Protein A in Relation to Replication Fork Blockage. J. Biol. Chem. 286:3497-3508. PMID: 21107010

Mason, A.C, Roy, R., Simmons, D.T., Wold, M.S. (2010) Functions of alternative replication protein A in initiation and elongation. Biochemistry 49:5919-5928. PMID: 20545304

LIPING YU
Feldkamp, M.D., O’Donnell, S.E., Yu, L., Shea, M.A. (2010) Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin. Proteins 78:2265-2282. PMID: 20544963

O’Donnell, S.E., Yu, L., Fowler, C.A., Shea, M.A. (2010) Recognition of β-calcineurin by the domains of calmodulin: Thermodynamic and structural evidence for distinct roles. Proteins 79:765-86. PMID: 21287611

Two decades of Biochemistry PhD data

Wednesday, February 23rd, 2011

In a recent post, we provided data on publications per student and time to PhD for those students who began graduate school in the years 2000 through 2005. Our analysis now stretches back to the entering class of 1985.  These 21 entering classes have produced 125 PhDs in Biochemistry plus one PhD in Molecular and Cellular Biology earned in a Biochemistry laboratory.  Of the 126 PhDs, all but one continued his or her education with either medical school or an academic post-doctoral fellowship.  Average time to degree was 5.5 years and average number of publications per PhD thesis was 3.25.  For the first 3 class years, six of the 18 PhDs now hold the title of director of research and eight hold the title of professor.

Year    # students   Pubs/student  Time to degree

1985          8                  3.3                     5.2

1986          8                  3.8                     5.2

1987          2                  2.5                     6.0

1988          7                  3                        5.9

1989         12                2.9                      5.5

1990          8                 2.9                      5.9

1991          4                  4                         5.8

1992          7                 3.1                      5.4

1993          8                 2.5                      5.5

1994          12               3.3                       5.2

1995          8                 3.3                       5.3

1996          6                 2.5                       5.5

1997          2                 2.5                     4.0

1998          4                 2.8                      5.5

1999          1                 8                        7.8

2000         10              3.2                      6.4

2001          2                3.5                       6.5

2002          7               3.7                      5.2

2003          2               4                          5.8

2004          4               3.8                        5.2

2005          4               3.8                        4.8

Two Iowa grads named Fellows of the AAAS

Thursday, February 17th, 2011

This year’s class of Fellows of the American Association for the Advancement of Science includes two Hawkeyes, Professors John York of Duke University and Susan Wente of Vanderbilt University.  York and Wente were both undergraduate biochemistry majors at Iowa, who have had illustrious careers.  John York did his PhD with Phil Majerus at  Washington University, where he established a major presence in inositol phosphate signaling.  He is now a Professor of Pharmacology & Cancer Biology and of Biochemistry and a Howard Hughes Investigator at Duke University.  Susan Wente did her PhD at Berkeley and her post-doctoral work at Rockefeller before joining the faculty at Washington University, where she rose through the ranks.  She then moved to Vanderbilt to chair Cell Biology.  In addition to running her research group on nucleocytoplasmic trafficking, she is now Associate Vice Chancellor for Research and Senior Associate Dean for Biomedical Sciences at the Vanderbilt School of Medicine.  Congratulations to these phenomenal Iowa Biochem majors!

More PhD data from the last decade

Sunday, February 6th, 2011

In a recent post, we reviewed time to degree and placement data for the students who started graduate school in August 2000. Here we summarize data for the cohorts who began graduate school in August 2000 through August 2005.  In the most recent years for which we have complete data, there appears to be a significant trend toward a shorter time to degree with no decline in number of publications per graduate career.  Academic placement of Biochemistry PhDs during the past decade remains at 100%.  Of the 29 Biochemistry PhDs in the data set, five earned MD/PhDs at Iowa and are currently medical residents or University physician scientists, four are PhDs with faculty positions, two are industry scientists who did academic post-docs, and 18 are academic post-docs.  Though it is still early to compute the time our recent graduates will serve as post-docs, it appears that during an era in which time to PhD has been reduced from about 6 years to about 5 years, post-doctoral terms have increased from about 3 years to about 5 years.

Year    # students   Pubs/student  Time to degree  Acad. placement

2000         10                3.2                          6.4                         10

2001          2                 3.5                          6.5                          2

2002          7                 3.7                          5.2                          7

2003          2                 4                             5.8                          2

2004          4                 3.8                          5.2                          4

2005*        4                 3.8                          4.8*                         4

*The 2005 entry class has a 5th student who has not yet graduated.  Thus, mean time to degree will be greater than 4.8 years and the 2005 data are not final.

The 2000 first year graduate class: where are they now?

Saturday, February 5th, 2011

With this year’s first year graduate class now doing their third rotations, we thought it would be a good idea to take a look at the cohort of Biochemistry graduate students who entered a decade earlier.  The ten 2000-2001 first years published 32 papers in graduate school (3.2 per trainee) with an average time to degree of 6.4 years.  All ten conducted an academic post-doctoral fellowship. Seven are currently post-docs, while two have moved on to positions as scientists in industry and one has a faculty position.  Two are at Berkeley, two are at UCLA, two are in Eugene, and there are Iowa PhDs in New York, Missoula, St. Louis and Iowa City. Graduates, if you have updates, we’d love to hear them!

  • Zeynep Akyol was Madeline Shea’s graduate student, working on calmodulin-binding to the NMDA receptor.  She is now a post-doc with Benhur Lee at UCLA, working on viral membrane proteins.
  • Keith Bryan was Peter Rubenstein’s graduate student, working on deafness-associated actin mutations.  He is now a post-doc with Amy Lee in the Physiology Department at Iowa, working on regulation of ion channels in cochlear hair cells.
  • Anne Dickson was Marc Wold’s graduate student, working on replication protein A.  After her post-doctoral fellowship with Mary Wilson in Internal Medicine at Iowa, she took a position as a scientist with Life Technologies, Inc.
  • Debra Ferraro was Andrew Robertson’s graduate student, working on ubiquitin structure and function.  After doing a post-doc with Professor Stanley Perlman in the Microbiology Department at Iowa, she took a faculty position in Chemistry at Maryville University in St. Louis.
  • Jared Helm was John Donelson’s graduate student, working on trypanosome molecular biology.  He is now a post-doc with Professor Jesse Hay at Montana, working on alpha synuclein.
  • Sean McGuffee was Adrian Elcock’s graduate student, working on large scale cytoplasmic modeling.  He is now a post-doc at Memorial Sloan-Kettering Cancer Center, working on structural bioinformatics.
  • Rhonda Newman was Madeline Shea’s graduate student, working on calmodulin domains in allosteric regulation of the ryanodine receptor.  After conducting an NRSA-funded post-doc at Oregon with Dr. Ken Prehoda on membrane-associated guanylate kinases, she took a position as a scientist with Life Technologies, Inc.
  • Yutian Peng was Lois Weisman’s graduate student, working on vacuolar inheritance.  She is now a post-doc with Stefan Westermann at UC Berkeley, working on chromosome segregation.
  • Ling Song was Robert Cohen’s graduate student, working on deubiquitylation.  She is now working on regulated degradation of spindle assembly factors as a post-doc with Michael Rape at UC Berkeley.
  • Geng Wong was Robert Deschenes’s graduate student, working on Ras modification.  He now has a first author Cell paper on regulated RNA import into mitochondria as a post-doc with Carla Koehler at UCLA.

Congratulations to this superb class of Iowa Biochemistry PhDs!  We look forward to providing outcomes data on Biochemistry PhDs who began graduate school in 2001 and beyond.