Link: University of Iowa

2009 Publications

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.

CHARLES M. BRENNER
Belenky, P., Christensen, K.C., Gazzaniga, F., Pletnev, A.A., Brenner, C. (2009) Nicotinamide riboside and nicotinic acid riboside salvage in fungi and mammals. Quantitative basis for Urh1 and purine nucleoside phosphorylase function in NAD+ metabolism. J. Biol. Chem. 284:158-164. PMID: 19001417

Bogan, K.L., Evans, C., Belenky, P., Song, P., Burant, C.F., Kennedy, R.T., Brenner, C. (2009) Identification of Isn1 and Sdt1 as glucose and vitamin-regulated NMN and NaMN 5′-nucleotidases responsible for production of nicotinamide riboside and nicotinic acid riboside. J. Biol. Chem. 284:34861-34869. PMID: 19846558

Gazzaniga, F., Stebbins, R., Chang, S.Z., McPeek, M.A., Brenner, C. (2009) Microbial NAD metabolism: lessons from comparative genomics. Microbiol. Mol. Biol. Rev. 73:529-541. PMID: 19721089

JOHN M. DAGLE
Dagle, J.M., Lepp, N.T., Cooper, M.E., Schaa, K.L., Kelsey, K.J.P., Orr, K.L., Caprau, D., Zimmerman, C.R., Steffen, K.M., Johnson, K.J., Marazita, M.L., and Murray, J.C. (2009) Determination of genetic predisposition to patent dactus arteriosus in preterm infants. Pediatrics 123:1116-1123. PMID: 19336370

Mohamed, S., Schaa, K., Cooper, M.E., Ahrens, E., Alvarado, A., Colaizy, T., Marazita, M.L., Murray, J.C., and Dagle, J.M. (2000) Genetic contributions to the development of retinopathy of prematurity. Pediatric Res. 65:193-197. PMID: 18787502

KRIS DEMALI
Wen, K.-K., Rubenstein, P.A., and DeMali, K.A. (2009) Vinculin nucleates actin polymerization and modifies actin filament structure. J. Biol. Chem. 284:30463-30473. PMID: 19736312

Johnson, J.L., Winterwood, N., DeMali, K.A, and Stipp, C.S. (2009) Tetraspanin CD151 regulates RhoA activation and the dynamic stability of carcinoma cell-cell contacts. J. Cell Sci. 122:2263-2273. PMID: 19509057

JOHN E. DONELSON
Helm, J.R., Hertz,-Fowler, C., Aslett, M., Berriman, M., Sanders, M., Quail, M.A., Soares, M.B., Bonaldo, M.F., Sakurai, T., Inoue, N., and Donelson, J.E. (2009) Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. Mol. Biochem. Parasitol. 168:34-42. PMID: 19559733

Helm, J.R., Wilson, M.E., and Donelson J.E. (2009) Differential expression of a protease gene family in African trypanosomes. Mol. Biochem. Parasitol. 163:8-18. PMID: 18848586

ADRIAN ELCOCK
Brandt, F., Etchells, S.A., Ortiz, J.O., Elcock, A.H., Hartl, F.U., and Baumeister, W. (2009) The native 3D organization of bacterial polysomes. Cell 136:261-271. PMID: 19167328

Frembgen-Kesner, T., and Elcock, A.E. (2009) Striking effects of hydrodynamic interactions on the stimulated diffusion and folding of proteins. J. Chem. Theory. and Comput. 5:242-256. 10.1021/ct800499p

ERNESTO J. FUENTES
Law, A.B., Fuentes, E.J., and Lee, A.L. (2009) Conservation of side-chain dynamics within a protein family. J. Am. Chem. Soc. 131:6322-6323. PMID: 19374353

Petit, C.M., Zhang, J., Sapienza, P.J., Fuentes, E.J., and Lee, A.L. (2009) Hidden dynamic allostery in a PDZ domain. PNAS 106:18249-18254. PMID: 19828436

PAMELA K. GEYER
Schulze, S.R., Curio-Penny, B., Speese, S., Dialynas, G., Cryderman, D.E., McDonough, C.W., Nalbant, D., Petersen, M., Budnik, V., Geyer, P.K., and Wallrath, L.L. (2009) A comparative study of Drosophila and human A-type lamins. PLoS One 4:e7564. PMID: 19855837

THERESA GIOANNINI
Piazza, M., Yu, L., Teghanemt, A., Gioannini, T., Weiss, J, and Peri, F. (2009) Evidence of a specific interaction between new synthetic antisepsis agents and CD14. Biochemistry 48:12337-12344. PMID: 19928913

Va l, J., Oblak, A., Gioannini, T.L., Weiss, J.P., and Jerala, R. (2009) Novel roles of lysines 122, 125, and 58 in functional differences between human and murine MD-2. J. Immunol. 183:5138-5145. PMID: 19783674

Resman, N., Vasl, J., Oblak, A., Pristovsek, P., Gioannini, T.L., Weiss, J.P., and Jerala, R. (2009) Essential roles of hydrophobic residues in both MD-2 and toll-like receptor 4 in activation by endotoxin. J. Biol. Chem. 284:15052-15060. PMID: 19321453

Trompette, A., Divanovic, S., Visintin, A., Blanchard, C., Hegde, R.S., Madan, R., Thorne, P.S., Wills-Karp, M., Gioannini, T.L., Weiss, J.P., and Karp, C.L. (2009) Allergenicity resulting from functional mimicry of a Toll-like receptor complex protein. Nature 457:585-588. PMID: 19060881

RAMA MALLAMPALLI
Butler, P.L. and Mallampalli, R.K. (2009) Cross-talk between remodeling and de novo pathways maintains phospholipid balance through ubiquitination. J Biol Chem. [Epub ahead of print] PMID: 20018880

Agassandian, M., Chen, B.B., Schuster, C.C., Houtman, J.C., Mallampalli, R.K. (2009) 14-3-3[zeta] escorts CCT[alpha] for calcium-activated nuclear import in lung epithelia. FASEB J. [Epub ahead of print] PMID: 20007511

Chen, B.B. and Mallampalli R.K. (2009) Masking of a nuclear signal motif by monoubiquitination leads to mislocalization and degradation of the regulatory enzyme cytidylyltransferase. Mol. Cell Biol. 29:3062-3075. PMID: 19332566

REX MONTGOMERY
Yang, B.Y., Ding, Q., and Montgomery, R. (2009) Preparation and physical properties of chitin fatty acids esters. Carbohydrate Research 344:336-342. PMID: 19091309

PETER L. NAGY
Lenert, P., Yasuda, K., Busconi, L., Nelson, P., Fleenor, C., Ratnabalasuriar, R.S., Nagy, P.L., Ashman, R.F., Rifkin, I.R., and Marshak-Rothstein, A. (2009) DNA-like class R inhibitory oligonucleotides (INH-ODNs) preferentially block autoantigen-induced B-cell and dendritic cell activation in vitro and autoantibody production in lupus-prone MRL-Faslpr/lpr mice in vivo. Arthritis Res. & Ther. 11:R79. PMID: 19476613

Nagy, P.L. and Price D.H. (2009) Formaldehyde-assisted isolation of regulatory elements. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1:400-406.

BRYCE V. PLAPP
Pal, S., Park, D.H., Plapp, B.V. (2009) Activity of yeast alcohol dehydrogenases on benzyl alcohols and benzaldehydes: characterization of ADH1 from Saccharomyces carlsbergensis and transition state analysis. Chem. Biol. Interact. 178:16-23. PMID: 19022233

DAVID H. PRICE
Price, D,H. (2009) Guest Editor’s Introduction. Controlling which genes are transcriptionally expressed is key to the generation and maintenance of the repertoire of cell types needed to support the mammalian lifestyle. Methods 48:321-322. PMID: 19654069

Cheng, B., and Price, D.H. (2009) Isolation and functional analysis of RNA polymerase II elongation complexes. Methods 48:346-352. PMID: 19409997

Nagy, P.L. and Price D.H. (2009) Formaldehyde-assisted isolation of regulatory elements. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1:400-406.

S. RAMASWAMY
Barren, B., Gakhar, L., Muradov, H., Boyd, K.K., Ramaswamy, S., Artemyev, N.O. (2009) Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. EMBO J. 28:3613-22. PMID: 19798052

Freudenthal, B.D., Gakhar, L., Ramaswamy, S., and Washington, M.T. (2009) A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions. Acta Crystallogr. D63:560-566. PMID: 19465770

PETER A. RUBENSTEIN
Stokasimov, E., and Rubenstein, P.A. (2009) Actin isoform specific conformational differences observed with HD exchange and mass spectrometry. J. Biol. Chem. 284:25421-25430. PMID: 19605362

Morín, M., Bryan, K.E., Mayo-Merino, F., Goodyear, R., Mencía, A., Modamio-Høybjør, S., del Castillo, I., Cabalka, J.M., Richardson, G., Moreno, F., Rubenstein, P.A., and Moreno-Pelayo, M.A. (2009) In vivo and in vitro effects of two novel gamma-actin (ACTG1) mutations that cause DFNA20/26 hearing impairment. Hum. Mol. Genet. 18 3075-3089. PMID: 19477959

Bryan, K.E. and Rubenstein, P.A. (2009) Allele-specific effects of human deafness (gamma)-actin mutations (DFNA20/26) on the actin/cofilin interaction. J. Biol. Chem. 284:18260-18269. PMID: 19419963

Wen, K.K. and Rubenstein, P.A., (2009) Differential regulation of actin polymerization and structure by yeast formin isoforms. J. Biol. Chem. 284:16776-16783. PMID: 19386598

Scoville, D., Stamm, J.D., Altenbach, C., Shvetosov, A., Kokabi, K., Rubenstein, P.A., Hubbell, W.L., and Reisler, E. (2009) Effects of binding factors on structural elements in F-actin. Biochemistry 48:370-378. PMID: 19113841

Wen, K.-K., Rubenstein, P.A., and DeMali, K.A. (2009) Vinculin nucleates actin polymerization and modifies actin filament structure. J. Biol. Chem. 284:30463-30473. PMID: 19736312

MADELINE A. SHEA
O’Donnell, S.E., Newman, R.A., Witt, T.J., Hultman, R., Froehlig, J.R., Christensen, A.P., and Shea, M.A. (2009) Thermodynamics and conformational change governing domain-domain interactions of calmodulin. Methods in Enzymology 466:503-526. 10.1016/S0076-6879(09)66021-3

Evans, T.I. and Shea, M.A. (2009) Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII. Proteins 76:47-61. PMID: 19089983

ARTHUR A. SPECTOR
Bianco, R.A., Agassandian, K., Cassell, M.D., Spector, A.A., and Sigmund, C.D. (2009) Characterization of transgenic mice with neuron-specific expression of soluble epoxide hydrolase. Brain Res. PMID: 19643090

Spector, A.A. (2009) Arachidonic acid cytochrome P450 epoxygenase pathway. J. Lipid Res. 50:S52-56. PMID: 18952572

EARLE STELLWAGEN
Dong, Q., Stellwagen, E., and Stellwagen, N.C. (2009) Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 48:1047-1055. PMID: 19154116

Stellwagen, N.C. and Stellwagen, E. (2009) Effect of the matrix on DNA electrophoretic mobility. J. Chromatogr. A. 1216:1917-1929. PMID: 19100556

NANCY C. STELLWAGEN
Stellwagen, N.C. (2009) Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution. Electrophoresis 30:S188-195. PMID: 19517510

Dong, Q., Stellwagen, E., and Stellwagen, N.C. (2009) Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 48:1047-1055. PMID: 19154116

Stellwagen, N.C. and Stellwagen, E (2009) Effect of the matrix on DNA electrophoretic mobility. J. Chromatogr. A. 1216:1917-1929. PMID: 19100556

LORI L. WALLRATH
Schulze, S.R., Curio-Penny, B., Speese, S., Dialynas, G., Cryderman, D.E., McDonough, C.W., Nalbant,D., Petersen, M., Budnik, V., Geyer, P.K., and Wallrath, L.L. (2009) A comparative study of Drosophila and human A-type lamins. PLoS One 4:e7564. PMID: 19855837

Hines, K.A., Cryderman, D.E., Flannery, K.M., Yang, H., Vitalini, M.W., Hazelrigg, T., Mizzen, C.A., and Wallrath, L.L. (2009) Domains of heterochromatin protein 1 required for Drosophila melanogaster heterochromatin spreading. Genetics 182:967-977. PMID: 19487560

M. TODD WASHINGTON
Freudenthal, B.D., Gakhar, L., Ramaswamy, S., and Washington, M.T. (2009) A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions. Acta Cryst. D63:560-566. PMID: 19465770

Washington, M.T., Carlson, K.D., Freudenthal, B.D., and Pryor, J.M. (2009) Variations on a theme: Eukaryotic Y-family DNA polymerases. Biochimica et Biophysics Acta [Epub ahead of print]. PMID: 19616647

DANIEL L. WEEKS

Bartlett, H. and Weeks, D.L. (2009) Lessons from the lily pad: Using Xenopus to understand heart disease. Drug Discovery Today 5:141-146. PMID: 19802378

RONALD J. WEIGEL
Johnson, M.T., Guidroz, J.A., Smith, B.J., Graham, M.M., Scott-Conner, C.E.H., Sugg, S.L., and Weigel, R.J. (2009) A single institutional experience of factors affecting successful identification of sentinel lymph node in breast cancer patients. Annual Meeting of the Central Surgical Association 146:671-676. PMID: 19789026

Lal, G., Hashimi, S., Smith, B.J., Lynch, C.F., Zhang, L., Robinson, R.A., and Weigel, R.J. (2009) Extracellular matrix 1 (ECM1) expression is a novel prognostic marker for poor long-term survival in breast cancer: A hospital-based cohort study in Iowa. Ann. Sug. Oncol. 16:2280-22887. PMID: 19521735

Calva, D., O’Dorisio, T.M., O’Dorisio, M.S., Lal, G., Sugg, S., Weigel, R.J., and Howe, J.R. (2009) When is prophylactic thyroidectomy indicated for patients with RET codon 609 mutations? Ann. Surg. Oncol. 16:2237-2244. PMID: 19472011

Woodfield, G.W., Hitchler, M.J., Chen, Y., Domann, F.E., and Weigel, R.J. (2009) Interaction of TFAP2C with the estrogen rectpors-alpha promoter is controlled by chromatin structures. Clin. Cancer Res. 15:3672-3679. PMID: 19458056

Spanheimer, P.M., Graham, M.M., Sugg, S.L., Scott-Conner, C.E.H., and Weigel, R.J. (2009) Measurement of uterine radiation exposure from lymphoscintigrophy indicates safety of sentinel lymph node biopsy during pregnancy. Ann. Surg. Oncol. 16:1143-1147. PMID: 19267158

MARC S. WOLD

Dickson, A.M., Krasikova, Y., Pestryakov, P., Lavrik, O., and Wold, M.S. (2009) Essential functions of the 32 kDA subunit of yeast replication protein A. Nuc. Acids Res. 37:2313-2326. PMID: 19244309

Mason, A.C., Haring, S.J., Pryor, J.M., Staloch, C.A., Gan, T.F., and Wold, M.S. (2009) An alternative form of replication protein a prevents viral replication in vitro. J. Biol. Chem. 284:5324-5331. PMID: 19116208

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