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Archive for the ‘S. Ramaswamy’ Category

2016 Biochemistry Newsletter now available

Friday, November 4th, 2016

2016_newslettercoverimageThe 2016 Biochemistry @ Iowa newsletter is hot off the presses and available for download. Alumni and friends should receive a hard copy in the mail this week. If you would like to be added to our mailing list, please send your contact information to biochem@uiowa.edu. While you are at it, feel free to send us your news and updates! Previous newsletters are also available online.

Dr. Subramanian Ramaswamy receives 2015 UIRF Inventors Award

Wednesday, May 4th, 2016

Dr. Subramanian Ramaswamy, Adjunct Professor of Biochemistry, has received a 2015 University of Iowa Research Foundation Inventors Award. In 2015, the UI Research Foundation and Dr. Subramanian, secured an option agreement with Spyryx Biosciences, Inc. for Dr. Subramanian’s technology“PLUNC-A Secreted Protein of Respiratory Epithelia and Salivary Glands With Surfactant Activity.”

2015 Biochemistry Newsletter now available

Tuesday, October 20th, 2015

Cover_2015_newsletterThe 2015 Biochemistry @ Iowa newsletter is hot off the presses and available for download. Alumni and friends should receive a hard copy in the mail this week. If you would like to be added to our mailing list, please send your contact information to biochem@uiowa.edu. While you are at it, feel free to send us your news and updates! Previous newsletters are also available online.

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

Susan O’Donnell wins the Clarence Berg Award

Monday, August 30th, 2010

Susan O’Donnell, who recently completed her PhD with Madeline Shea, has been named the winner of the 2010 Clarence Berg Award. This prize is given every other year to a student who demonstrates “scholarship, integrity, cooperativeness, consideration and a willingness to help others.” Dr. O’Donnell was an American Heart Association-funded graduate student who focused on the structural and thermodynamic bases for recognition of calcineurin by calmodulin domains. Previously, Susan was the winner of the 2006 Usha Balakrishnan Award for best poster presented at the annual meeting of the Center for Biocatalysis and Bioprocessing. She also presented her work in a plenary session of the 2007 Gibbs Conference on Biothermodynamics and received a 2008 Biophysical Society Student Research Achievement Award as well as an inaugural Gehring Award last fall.

Dr. O’Donnell is currently a post-doctoral fellow with Robert Deschenes at University of South Florida.

Susan is the 21st winner of the Berg Award, which was established by former students of Professor Berg, an internationally known amino acid biochemist who was a member of the department for 39 years. Dr. Berg is well known as the author of the 1980 book, The University of Iowa and Biochemistry from their Beginnings.

Prior winners of the Berg Award are:

Structure of Monoubiquitylated PCNA

Tuesday, March 23rd, 2010

The proliferating cell nuclear antigen (PCNA) is a trimeric, ring-shaped protein that slides along DNA to promote replication. When DNA is damaged, a replicative polymerase is replaced by a translesion polymerase in a process that involves addition of a single ubiquitin modification to each PCNA monomer. How this modification changes the appearance and function of PCNA was not understood until Todd Washington’s laboratory developed an ingenious trick. (more…)

S. Ramaswamy named Dean of inStem in Bangalore

Wednesday, February 17th, 2010

S. Ramaswamy, a faculty member in Biochemistry since 2000, has been named Senior Professor and Dean of inStem, the Institute for Stem Cell Science and Regenerative Medicine in Bangalore, India. inStem, which has been written up in Science and Forbes, represents a massive Indian investment in basic and applied stem cell research. The Department is extremely proud of Rams as a leader of this exciting endeavor and wishes him and his family the very best.

2009 Publications

Wednesday, December 30th, 2009

The Department’s 2009 publications are now in print and mostly available online. There are papers in Nature, Cell, PNAS, EMBO J, JACS, Genetics, Methods in Enzymology, Methods, Mol Biochem Parasitol, Nucleic Acids Res, PLoS One, Human Molecular Genetics, Pediatrics, J Cell Sci, J Immunology, J Lipids Res, Clinical Cancer Res, and, of course, JBC and Biochemistry. (more…)

Sedore wins 2009 Subramanian Best Doctoral Dissertation Award

Tuesday, September 1st, 2009

Congratulations to Stanley Sedore, winner of the 2009 Best Doctoral Dissertation Award, sponsored by Alap Subramanian. Dr. Sedore’s thesis entitled, “Gene-specific control of P-TEFb by HIV,” was performed under the supervision of David Price. He is now finishing medical school at the Carver College of Medicine as an MD/PhD student. (more…)