Link: University of Iowa

Archive for the ‘Miles Pufall’ Category

Karina Kruth, Jessica Maier, and Lacy Barton successfully defended their theses during the 2013-2014 academic year

Wednesday, October 1st, 2014

Karina Kruth, a Biochemistry PhD Student mentored by Dr. Peter Rubenstein, successfully defended her thesis on October 31, 2013, entitled “Effects of three deafness-causing gamma-actin mutations on actin structure and function”. Karina is a post-doctoral fellow with Dr. Miles Pufall at the University of Iowa, Department of Biochemistry.

 

Jessica Maiers, a Molecular and Cellular Biology PhD student mentored by Dr. Kris DeMali, successfully defended her thesis on November 26, 2013, entitled “The role of alpha-catenin and ZO-1 in coupling tight junctions to adherens junctions”. Jessica holds a post-doctoral position with Dr. Vijay Shah at the Mayo Clinic in Rochester,  Minnesota.

 

Lacy Barton, a Biochemistry PhD student mentored by Dr. Pamela Geyer, successfully defended her thesis on July 11, 2014, entitled “Defining the role of a nuclear lamina LEM domain protein in germline stem cells”. Lacy is a post-doctoral fellow with Dr. Ruth Lehmann at New York University in New York.

Congrats Karina, Jessica, and Lacy!

2013 Publications

Saturday, February 1st, 2014

The Department’s 2013 publications are now in print and mostly available online.

Sheila A. Baker

Baker SA, Kerov V. (2013) Photoreceptor inner and outer segments. Curr Top Membr. 72:231-65. DOI: 10.1016/B978-0-12-417027-8.00007-6. PMID: 24210432

Liu X, Kerov V, Haeseleer F, Majumder A, Artemyev N, Baker SA, Lee A. (2013) Dysregulation of Cav 1.4 channels disrupts the maturation of photoreceptor synaptic ribbons in congenital stationary night blindness type 2. Channels (Austin). 7(6). PMID: 24064553

Knoflach D, Kerov V, Sartori SB, Obermair GJ, Schmuckermair C, Liu X, Sothilingam V, Garrido MG, Baker SA, Glösmann M, Schicker K, Seeliger M, Lee A, Koschak A. (2013) Cav1.4 IT mouse as model for vision impairment in human congenital stationary night blindness type 2. Channels (Austin). 7(6). PMID:24051672

Pearring JN, Salinas RY, Baker SA, Arshavsky VY. (2013) Protein sorting, targeting and trafficking in photoreceptor cells. Prog Retin Eye Res. 36:24-51. DOI: 10.1016/j.preteyeres.2013.03.002. PMID: 23562855

Heather L. Bartlett

Ng B, Mathews KD, Bartlett HL. (2013) A 16-week-old infant with failure to thrive and hypotonia. Clin Pediatr (Phila).52(11):1075-8. DOI: 10.1177/0009922813502125. PMID: 24027232

Charles M. Brenner

Mei SC, Brenner C.(2013) NAD as a Genotype-Specific Drug Target. Chem Biol. 20(11):1307-8. DOI: 10.1016/j.chembiol.2013.11.001. PMID: 24267273

Fagan RL, Wu M, Chédin F, Brenner C. (2013) An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes. PLoS One. 8(11):e78752. DOI: 10.1371/journal.pone.0078752. PMID: 24236046

Kennelly PJ, Bond JS, Masters BS, Dennis EA, Brenner C, Raben DM. (2013) Desperately seeking Flexner: time to reemphasize basic science in medical education. Acad Med. 88(10):1405-6. DOI: 10.1097/ACM.0b013e3182a225be. PMID: 24064614

Ghanta S, Grossmann RE, Brenner C. (2013) Mitochondrial protein acetylation as a cell-intrinsic, evolutionary driver of fat storage: Chemical and metabolic logic of acetyl-lysine modifications. Crit Rev Biochem Mol Biol. 48(6):561-74. DOI: 10.3109/10409238.2013.838204. PMID: 24050258

Brenner C. (2013) Demystifying the Chalk Talk. ASBMB Today. 12(8):33-35.

Huang J, Stewart A, Maity B, Hagen J, Fagan RL, Yang J, Quelle DE, Brenner C, Fisher RA. (2013) RGS6 suppresses Ras-induced cellular transformation by facilitating Tip60-mediated Dnmt1 degradation and promoting apoptosis. Oncogene. DOI: 10.1038/onc.2013.324. PMID:23995786

Fagan RL, Cryderman DE, Kopelovich L, Wallrath LL, Brenner C. (2013) Laccaic acid A is a direct, DNA-competitive inhibitor of DNA methyltransferase 1. J Biol Chem. 288(33):23858-67. DOI: 10.1074/jbc.M113.480517. PMID: 23839987

Brenner C. (2013) Rethinking Premedical and Health Professional Curricula in Light of MCAT 2015. Journal of Chemical Education. 90:807-812. DOI:10.1021/ed4002738.

Trammell SAJ & Brenner C. (2013) Targeted, LCMC-Based Metabolomics for Quantitative Measurement of NAD+ Metabolites. Computational and Structural Biotechnology Journal. 4:e201301012. DOI: 10.5936/csbj.201301012.

Bogan KL & Brenner C. (2013) Biochemistry: Niacin/NAD(P). Encyclopedia of Biological Chemistry. W.J. Lennarz & M.D. Lane, eds., 3:172-178, Academic Press.

Brenner C. (2013) Changes in chemistry and biochemistry education: creative responses to medical college admissions test revisions in the age of the genome. Biochem Mol Biol Educ. 41(1):1-4. DOI: 10.1002/bmb.20653. PMID: 23281187

John M. Dagle

Kim J, Stirling KJ, Cooper ME, Ascoli M, Momany AM, McDonald EL, Ryckman KK, Rhea L, Schaa KL, Cosentino V, Gadow E, Saleme C, Shi M, Hallman M, Plunkett J, Teramo KA, Muglia LJ, Feenstra B, Geller F, Boyd HA, Melbye M, Marazita ML, Dagle JM, Murray JC. (2013) Sequence variants in oxytocin pathway genes and preterm birth: a candidate gene association study. BMC Med Genet. 14:77. DOI: 10.1186/1471-2350-14-77. PMID: 23889750

Alleman BW, Bell EF, Li L, Dagle JM, Smith PB, Ambalavanan N, Laughon MM, Stoll BJ, Goldberg RN, Carlo WA, Murray JC, Cotten CM, Shankaran S, Walsh MC, Laptook AR, Ellsbury DL, Hale EC, Newman NS, Wallace DD, Das A, Higgins RD; Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. (2013) Individual and center-level factors affecting mortality among extremely low birth weight infants. Pediatrics. 132(1):e175-84. DOI: 10.1542/peds.2012-3707. PMID: 23753096

Mohamed S, Murray JC, Dagle JM, Colaizy T. (2013) Hyperglycemia as a risk factor for the development of retinopathy of prematurity. BMC Pediatr. 13(1):78. PMID: 23679669

Ryckman KK, Shchelochkov OA, Cook DE, Berberich SL, Copeland S, Dagle JM, Murray JC. (2013) The influence of maternal disease on metabolites measured as part of newborn screening. J Matern Fetal Neonatal Med. 26(14):1380-3. DOI: 10.3109/14767058.2013.791267. PMID: 23550828

Ryckman KK, Dagle JM, Shchelochkov OA, Ehinger N, Poole SD, Berberich SL, Reese J, Murray JC. (2013) Association of amino acids with common complications of prematurity. Pediatr Res. 73(6):700-5. DOI: 10.1038/pr.2013.43. PMID: 23481552

Brandon S. Davies

Young SG, Yang SH, Davies BS, Jung HJ, Fong LG. (2013) Targeting protein prenylation in progeria. Sci Transl Med. 5(171):171ps3. DOI: 10.1126/scitranslmed.3005229. PMID: 23390246

Kris A. DeMali

Maiers JL, Peng X, Fanning AS, DeMali KA. (2013) ZO-1 recruitment to α-catenin–a novel mechanism for coupling the assembly of tight junctions to adherens junctions. J Cell Sci. 126(Pt 17):3904-15. DOI: 10.1242/jcs.126565. PMID: 23813953

Johnston JJ, Wen KK, Keppler-Noreuil K, McKane M, Maiers JL, Greiner A, Sapp JC; NIH Intramural Sequencing Center, DeMali KA, Rubenstein PA, Biesecker LG. (2013) Functional analysis of a de novo ACTB mutation in a patient with atypical Baraitser-Winter syndrome. Hum Mutat. 34(9):1242-9. DOI: 10.1002/humu.22350. PMID: 23649928

John E. Donelson

Yao C, Gaur Dixit U, Barker JH, Teesch LM, Love-Homan L, Donelson JE, Wilson ME. (2013) Attenuation of Leishmania infantum chagasi metacyclic promastigotes by sterol depletion. Infect Immun. 81(7):2507-17. DOI: 10.1128/IAI.00214-13. PMID: 23630964

Adrian H. Elcock

Stark AC, Andrews CT, Elcock AH. (2013) Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field. J Chem Theory Comput. 9(9). DOI: 10.1021/ct400008p. PMID: 24223529

Thomas AS, Mao S, Elcock AH. (2013) Flexibility of the bacterial chaperone trigger factor in microsecond-timescale molecular dynamics simulations. Biophys J. 105(3):732-44. DOI: 10.1016/j.bpj.2013.06.028. PMID: 23931321

Randak CO, Dong Q, Ver Heul AR, Elcock AH, Welsh MJ. (2013) ATP and AMP mutually influence their interaction with the ATP-binding cassette (ABC) adenylate kinase cystic fibrosis transmembrane conductance regulator (CFTR) at separate binding sites. J Biol Chem. 288(38):27692-701. DOI: 10.1074/jbc.M113.479675. PMID: 23921386

Frembgen-Kesner T, Elcock AH. (2013) Computer Simulations of the Bacterial Cytoplasm. Biophys Rev. 5(2):109-119. PMID: 23914257

Elcock AH. (2013) A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules. J Chem Theory Comput. 9(7):3224-3239. PMID: 23914146

Zhu S, Travis SM, Elcock AH. (2013) Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study. J Chem Theory Comput. 9(7):3151-3164. PMID: 23914145

Andrews CT, Elcock AH. (2013) Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other. J. Chem. Theory Comput. 9 (10): 4585–4602. DOI: 10.1021/ct400371h

Ernesto J. Fuentes

Willett JW, Tiwari N, Müller S, Hummels KR, Houtman JC, Fuentes EJ, Kirby JR. (2013) Specificity residues determine binding affinity for two-component signal transduction systems. MBio. 4(6):e00420-13. DOI: 10.1128/mBio.00420-13. PMID: 24194534

Joshi M, Gakhar L, Fuentes EJ. (2013) High-resolution structure of the Tiam1 PHn-CC-Ex domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69(Pt 7):744-52. DOI: 10.1107/S1744309113014206. PMID:23832200

Liu Y, Collins C, Kiosses WB, Murray AM, Joshi M, Shepherd TR, Fuentes EJ, Tzima E. (2013) A novel pathway spatiotemporally activates Rac1 and redox signaling in response to fluid shear stress. J Cell Biol. 201(6):863-73. DOI: 10.1083/jcb.201207115. PMID: 23733346

Liu X, Shepherd TR, Murray AM, Xu Z, Fuentes EJ. (2013) The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Structure.21(3):342-54. DOI: 10.1016/j.str.2013.01.004. PMID: 23395182

Lokesh Gakhar

Joshi M, Gakhar L, Fuentes EJ. (2013) High-resolution structure of the Tiam1 PHn-CC-Ex domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69(Pt 7):744-52. DOI: 10.1107/S1744309113014206. PMID: 23832200

Majumder A, Gopalakrishna KN, Cheguru P, Gakhar L, Artemyev NO. (2013) Interaction of aryl hydrocarbon receptor-interacting protein-like 1 with the farnesyl moiety. J Biol Chem. 288(29):21320-8. DOI: 10.1074/jbc.M113.476242. Epub 2013 Jun 4. PMID: 23737531

Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. (2013) The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Dev Cell. 25(5):520-33. DOI: 10.1016/j.devcel.2013.04.007. PMID: 23726974

Darbro BW, Mahajan VB, Gakhar L, Skeie JM, Campbell E, Wu S, Bing X, Millen KJ, Dobyns WB, Kessler JA, Jalali A, Cremer J, Segre A, Manak JR, Aldinger KA, Suzuki S, Natsume N, Ono M, Hai HD, Viet le T, Loddo S, Valente EM, Bernardini L, Ghonge N, Ferguson PJ, Bassuk AG. (2013) Mutations in extracellular matrix genes NID1 and LAMC1 cause autosomal dominant Dandy-Walker malformation and occipital cephaloceles. Hum Mutat. 34(8):1075-9. DOI: 10.1002/humu.22351. PMID: 23674478

Pryor JM, Gakhar L, Washington MT. (2013) Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry. 52(1):254-63. DOI: 10.1021/bi301572z. PMID: 23240687

Liu Y, Bartlett JA, Di ME, Bomberger JM, Chan YR, Gakhar L, Mallampalli RK, McCray PB Jr, Di YP. (2013) SPLUNC1/BPIFA1 contributes to pulmonary host defense against Klebsiella pneumoniae respiratory infection. Am J Pathol. 182(5):1519-31. DOI: 10.1016/j.ajpath.2013.01.050. PMID: 23499554

Pamela K. Geyer

Soshnev AA, Baxley RM, Manak JR, Tan K, Geyer PK. (2013) The insulator protein Suppressor of Hairy-wing is an essential transcriptional repressor in the Drosophila ovary. Development. 140(17):3613-23. DOI: 10.1242/dev.094953. PMID: 23884443

Barton LJ, Pinto BS, Wallrath LL, Geyer PK. (2013) The Drosophila nuclear lamina protein otefin is required for germline stem cell survival. Dev Cell. 25(6):645-54. DOI: 10.1016/j.devcel.2013.05.023. PMID: 23806619

Theresa L. Gioannini

Shirey KA, Lai W, Scott AJ, Lipsky M, Mistry P, Pletneva LM, Karp CL, McAlees J, Gioannini TL, Weiss J, Chen WH, Ernst RK, Rossignol DP, Gusovsky F, Blanco JC, Vogel SN. (2013) The TLR4 antagonist Eritoran protects mice from lethal influenza infection. Nature. 497(7450):498-502. DOI: 10.1038/nature12118. PMID: 23636320

Teghanemt A, Weiss JP, Gioannini TL. (2013) Radioiodination of an endotoxin·MD-2 complex generates a novel sensitive, high-affinity ligand for TLR4. Innate Immun. 19(5):545-60. DOI: 10.1177/1753425913475688. PMID: 23439691

Catherine A. Musselman

Musselman CA, Gibson MD, Hartwick EW, North JA, Gatchalian J, Poirier MG, Kutateladze TG. (2013) Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility. Nat Commun. 4:2969. DOI: 10.1038/ncomms3969. PMID: 24352064

Andrew W. Norris

Olivier AK, Yi Y, Sun X, Sui H, Liang B, Hu S, Xie W, Fisher JT, Keiser NW, Lei D, Zhou W, Yan Z, Li G, Evans TI, Meyerholz DK, Wang K, Stewart ZA, Norris AW, Engelhardt JF. (2013) Abnormal endocrine pancreas function at birth in cystic fibrosis ferrets. J Clin Invest.122(10):3755-68. DOI: 10.1172/JCI60610. PMID:22996690

Lamping KG, Nuno DW, Coppey LJ, Holmes AJ, Hu S, Oltman CL, Norris AW, Yorek MA. (2013) Modification of high saturated fat diet with n-3 polyunsaturated fat improves glucose intolerance and vascular dysfunction. Diabetes Obes Metab.15(2):144-52. DOI: 10.1111/dom.12004. PMID: 22950668

Bryce V. Plapp

Plapp BV, Lee AT, Khanna A, Pryor JM. (2013) Bradykinetic alcohol dehydrogenases make yeast fitter for growth in the presence of allyl alcohol. Chem Biol Interact. 202(1-3):104-10. DOI: 10.1016/j.cbi.2012.11.010. PMID:23200945

Plapp BV, Kedishvili NY, Rižner TL, Maser E, O’Brien PJ. (2013) Chemico-Biological Interactions. Enzymology and molecular biology of carbonyl metabolism 16. Introduction. Chem Biol Interact. 202(1-3):1. DOI: 10.1016/j.cbi.2013.02.004. PMID: 23497822

David H. Price

Guo J, Li T, Price DH. (2013) Runaway transcription. Genome Biol. 14(9):133. PMID: 24079702

Guo J, Price DH. (2013) RNA Polymerase II Transcription Elongation Control. Chem Rev. 113(11):8583-603. DOI: 10.1021/cr400105n. PMID: 23919563

Van Duyne R, Guendel I, Jaworski E, Sampey G, Klase Z, Chen H, Zeng C, Kovalskyy D, El Kouni MH, Lepene B, Patanarut A, Nekhai S, Price DH, Kashanchi F. (2013) Effect of Mimetic CDK9 Inhibitors on HIV-1-Activated Transcription. J Mol Biol. 425(4):812-29. DOI: 10.1016/j.jmb.2012.12.005. PMID: 23247501

Miles A. Pufall

Thomas-Chollier M, Watson LC, Cooper SB, Pufall MA, Liu JS, Borzym K, Vingron M, Yamamoto KR, Meijsing SH. (2013) A naturally occurring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms. Proc Natl Acad Sci USA. 110(44):17826-31. DOI: 10.1073/pnas.1316235110. PMID:24127590

Pufall MA, Kaplan CD. (2013) Mechanisms of eukaryotic transcription. Genome Biol. 14(9):311. PMID: 24079829

Watson LC, Kuchenbecker KM, Schiller BJ, Gross JD, Pufall MA, Yamamoto KR. (2013) The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol. 20(7):876-83. DOI: 10.1038/nsmb.2595. PMID: 23728292

Peter A. Rubenstein

Wen KK, McKane M, Rubenstein PA. (2013) Importance of a Lys113-Glu195 intermonomer ionic bond in F-actin stabilization and regulation by yeast formins Bni1p and Bnr1p. J Biol Chem. 288(26):19140-53. DOI: 10.1074/jbc.M113.474122. PMID: 23653364

Johnston JJ, Wen KK, Keppler-Noreuil K, McKane M, Maiers JL, Greiner A, Sapp JC; NIH Intramural Sequencing Center, Demali KA, Rubenstein PA, Biesecker LG. (2013) Functional analysis of a de novo ACTB mutation in a patient with atypical Baraitser-Winter syndrome. Hum Mutat. 34(9):1242-9. DOI: 10.1002/humu.22350. PMID: 23649928

Lee CY, Lou J, Wen KK, McKane M, Eskin SG, Ono S, Chien S, Rubenstein PA, Zhu C, McIntire LV. (2013) Actin depolymerization under force is governed by lysine 113:glutamic acid 195-mediated catch-slip bonds. Proc Natl Acad Sci USA. 110(13):5022-7. DOI: 10.1073/pnas.1218407110. PMID:23460697

Debra A. Schwinn

Lei B, Schwinn DA, Morris DP. (2013) Stimulation of α1a adrenergic receptors induces cellular proliferation or antiproliferative hypertrophy dependent solely on agonist concentration. PLoS One. 8(8):e72430. DOI: 10.1371/journal.pone.0072430. PMID: 23991110

M. Ashley Spies

Whalen KL, Spies MA. (2013) Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. J Chem Inf Model. 53(9):2349-59. DOI: 10.1021/ci400244x. PMID: 24111836

Subramanyam S, Jones WT, Spies M, Spies MA. (2013) Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction. Nucleic Acids Res. 41(19):9020-32. DOI: 10.1093/nar/gkt691. PMID: 23935068

Whalen KL, Chau AC, Spies MA. (2013) In silico Optimization of a Fragment-Based Hit Yields Biologically Active, High-Efficiency Inhibitors for Glutamate Racemase. ChemMedChem. DOI: 10.1002/cmdc.201300271. PMID:23929705

Spies MA. (2013) Nexus Between Protein–Ligand Affinity Rank-Ordering, Biophysical Approaches, and Drug Discovery. ACS Med. Chem. Lett. 4 (10):895–897. DOI: 10.1021/ml4003502

Maria Spies

Murfuni I, Basile G, Subramanyam S, Malacaria E, Bignami M, Spies M, Franchitto A, Pichierri P. (2013) Survival of the replication checkpoint deficient cells requires MUS81-RAD52 function. PLoS Genet. 9(10):e1003910. DOI: 10.1371/journal.pgen.1003910. PMID: 24204313

Subramanyam S, Jones WT, Spies M, Spies MA. (2013) Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction. Nucleic Acids Res. 41(19):9020-32. DOI: 10.1093/nar/gkt691. PMID: 23935068

Qi Z, Pugh RA, Spies M, Chemla YR. (2013) Sequence-dependent base pair stepping dynamics in XPD helicase unwinding. Elife. 2:e00334. DOI: 10.7554/eLife.00334. PMID: 23741615

Haghighat Jahromi A, Honda M, Zimmerman SC, Spies M. (2013) Single-molecule study of the CUG repeat-MBNL1 interaction and its inhibition by small molecules. Nucleic Acids Res. 41(13):6687-97. DOI: 10.1093/nar/gkt330. PMID:23661680

Masuda-Ozawa T, Hoang T, Seo YS, Chen LF, Spies M. (2013) Single-molecule sorting reveals how ubiquitylation affects substrate recognition and activities of FBH1 helicase. Nucleic Acids Res. 41(6):3576-87. DOI: 10.1093/nar/gkt056. PMID: 23393192

Spies M. (2013) DNA repair: trust but verify. Curr Biol. 23(3):R115-7. DOI: 10.1016/j.cub.2012.12.019. PMID: 23391386

Beyer DC, Ghoneim MK, Spies M. (2013) Structure and Mechanisms of SF2 DNA Helicases. Adv Exp Med Biol. 767:47-73. DOI: 10.1007/978-1-4614-5037-5_3. PMID: 23161006

Wu CG, Spies M. (2013) Overview: what are helicases? Adv Exp Med Biol. 767:1-16. DOI: 10.1007/978-1-4614-5037-5_1. PMID: 23161004

Earle Stellwagen

Stellwagen E, Peters JP, Maher LJ 3rd, Stellwagen NC. (2013) DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. Biochemistry. 52(24):4138-48. DOI: 10.1021/bi400118m. PMID: 23675817

Nancy C. Stellwagen

Stellwagen E, Peters JP, Maher LJ 3rd, Stellwagen NC. (2013) DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. Biochemistry. 52(24):4138-48. DOI: 10.1021/bi400118m. PMID: 23675817

Eric B. Taylor

Gray LR, Tompkins SC, Taylor EB. (2013) Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci. PMID:24363178

Lori L. Wallrath

Fagan RL, Cryderman DE, Kopelovich L, Wallrath LL, Brenner C. (2013) Laccaic acid A is a direct, DNA-competitive inhibitor of DNA methyltransferase 1. J Biol Chem. 288(33):23858-67. DOI: 10.1074/jbc.M113.480517. PMID: 23839987

Barton LJ, Pinto BS, Wallrath LL, Geyer PK. (2013) The Drosophila nuclear lamina protein otefin is required for germline stem cell survival. Dev Cell. 25(6):645-54. DOI: 10.1016/j.devcel.2013.05.023. PMID: 23806619

Zwerger M, Jaalouk DE, Lombardi ML, Isermann P, Mauermann M, Dialynas G, Herrmann H, Wallrath LL, Lammerding J. (2013) Myopathic lamin mutations impair nuclear stability in cells and tissue and disrupt nucleo-cytoskeletal coupling. Hum Mol Genet. 22(12):2335-49. DOI: 10.1093/hmg/ddt079. PMID: 23427149

M. Todd Washington

Dieckman LM, Boehm EM, Hingorani MM, Washington MT. (2013) Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair. Biochemistry. 52(33):5611-9. DOI: 10.1021/bi400378e. PMID: 23869605

Dieckman LM, Washington MT. (2013) PCNA trimer instability inhibits translesion synthesis by DNA polymerase η and by DNA polymerase δ. DNA Repair (Amst). 12(5):367-76. DOI: 10.1016/j.dnarep.2013.02.007. PMID: 23506842

Pryor JM, Gakhar L, Washington MT. (2013) Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry. 52(1):254-63. DOI: 10.1021/bi301572z. PMID:23240687

Ronald J. Weigel

Bhama AR, Smith RJ, Robinson RA, Weigel RJ, Sugg SL, Howe JR, Lal G. (2013) Preoperative evaluation of thyroglossal duct cysts: children versus adults-is there a difference? Am J Surg. PII: S0002-9610(13)00612-0. DOI: 10.1016/j.amjsurg.2013.06.018. PMID: 24246260

Spanheimer PM, Cyr AR, Gillum MP, Woodfield GW, Askeland RW, Weigel RJ. (2013) Distinct Pathways Regulated by RET and Estrogen Receptor in Luminal Breast Cancer Demonstrate the Biological Basis for Combination Therapy. Ann Surg. PMID: 24045439

Lal G, Contreras PG, Kulak M, Woodfield G, Bair T, Domann FE, Weigel RJ. (2013) Human Melanoma cells over-express extracellular matrix 1 (ECM1) which is regulated by TFAP2C. PLoS One. 8(9):e73953. DOI: 10.1371/journal.pone.0073953. PMID: 24023917

Lizarraga IM, Sugg SL, Weigel RJ, Scott-Conner CE. (2013) Review of risk factors for the development of contralateral breast cancer. Am J Surg. 206(5):704-8. DOI: 10.1016/j.amjsurg.2013.08.002. PMID: 24016706

Spanheimer PM, Stoltze AJ, Howe JR, Sugg SL, Lal G, Weigel RJ . (2013) Do giant parathyroid adenomas represent a distinct clinical entity? Surgery. 154(4):714-8; discussion 718-9. DOI: 10.1016/j.surg.2013.05.013. PMID: 23978594

Lizarraga IM, Scott-Conner CE, Muzahir S, Weigel RJ, Graham MM, Sugg SL. (2013) Management of contralateral axillary sentinel lymph nodes detected on lymphoscintigraphy for breast cancer. Ann Surg Oncol. 20(10):3317-22. DOI: 10.1245/s10434-013-3151-y. PMID: 23975295

Carr JC, Spanheimer PM, Rajput M, Dahdaleh FS, Lal G, Weigel RJ, Sugg SL, Liao J, Howe JR. (2013) Discriminating pheochromocytomas from other adrenal lesions: the dilemma of elevated catecholamines. Ann Surg Oncol. 20(12):3855-61. DOI: 10.1245/s10434-013-3142-z. PMID: 23884753

Spanheimer PM, Askeland RW, Kulak MV, Wu T, Weigel RJ. (2013) High TFAP2C/low CD44 expression is associated with an increased rate of pathologic complete response following neoadjuvant chemotherapy in breast cancer. J Surg Res. 184(1):519-25. DOI: 10.1016/j.jss.2013.04.042. PMID: 23764310

Spanheimer PM, Carr JC, Thomas A, Sugg SL, Scott-Conner CE, Liao J, Weigel RJ. (2013) The response to neoadjuvant chemotherapy predicts clinical outcome and increases breast conservation in advanced breast cancer. Am J Surg. 206(1):2-7. DOI: 10.1016/j.amjsurg.2012.10.025. PMID: 23375759

Kulak MV, Cyr AR, Woodfield GW, Bogachek M, Spanheimer PM, Li T, Price DH, Domann FE, Weigel RJ. (2013) Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. Oncogene. 32(34):4043-51. DOI: 10.1038/onc.2012.400. PMID: 22964634

Spanheimer PM, Woodfield GW, Cyr AR, Kulak MV, White-Baer LS, Bair TB, Weigel RJ. (2013) Expression of the RET Proto-oncogene Is Regulated by TFAP2C in Breast Cancer Independent of the Estrogen Receptor. Ann Surg Oncol. 20(7):2204-12. DOI: 10.1245/s10434-012-2570-5. PMID:22878616

Meng Wu

Fagan RL, Wu M, Chédin F, Brenner C. (2013) An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes. PLoS One. 8(11):e78752. DOI: 10.1371/journal.pone.0078752. PMID: 24236046

Storaska AJ, Mei JP, Wu M, Li M, Wade SM, Blazer LL, Sjögren B, Hopkins CR, Lindsley CW, Lin Z, Babcock JJ, McManus OB, Neubig RR. (2013) Reversible inhibitors of regulators of G-protein signaling identified in a high-throughput cell-based calcium signaling assay. Cell Signal. 25(12):2848-55. DOI: 10.1016/j.cellsig.2013.09.007. PMID: 24041654

Yu H, Lin Z, Mattmann ME, Zou B, Terrenoire C, Zhang H, Wu M, McManus OB, Kass RS, Lindsley CW, Hopkins CR, Li M.( 2013) Dynamic subunit stoichiometry confers a progressive continuum of pharmacological sensitivity by KCNQ potassium channels. Proc Natl Acad Sci USA. 110(21):8732-7. DOI: 10.1073/pnas.1300684110. PMID:23650380

Liping Yu

Yu L, Fink BD, Herlein JA, Sivitz WI. (2013) Mitochondrial function in diabetes: novel methodology and new insight. Diabetes. 62(6):1833-42. DOI: 10.2337/db12-1152. PMID: 23328129.

Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. (2013) The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Dev Cell. 25(5):520-33. DOI: 10.1016/j.devcel.2013.04.007. PMID: 23726974.

Yoshida-Moriguchi T, Willer T, Anderson ME, Venzke D, Whyte T, Muntoni F, Lee H, Nelson SF, Yu L, Campbell KP. (2013) SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science. 341(6148):896-9. DOI: 10.1126/science.1239951. PMID: 23929950.

Yu L, Fink BD, Herlein JA, Oltman CL, Lamping KG, Sivitz WI. (2013) Dietary fat, fatty acid saturation and mitochondrial bioenergetics. J Bioenerg Biomembr. PMID: 24121995.

Peterson TA, Yu L, Piper RC. (2013) Backbone and side-chain NMR assignments for the C-terminal domain of mammalian Vps28. Biomol NMR Assign. PMID: 24366722.

2012 Publications

Thursday, July 25th, 2013

The Department’s 2012 publications are now in print and mostly available online.

Heather L. Bartlett

Malloy LE, Wen KK, Pierick AR, Wedemeyer EW, Bergeron SE, Vanderpool ND, McKane M, Rubenstein PA, Bartlett HL. (2012) Thoracic aortic aneurysm (TAAD)-causing mutation in actin affects formin regulation of polymerization. J Biol Chem. 287(34):28398-408. PMID:22753406

Pietra BA, Kantor PF, Bartlett HL, Chin C, Canter CE, Larsen RL, Edens RE, Colan SD, Towbin JA, Lipshultz SE, Kirklin JK, Naftel DC, Hsu DT. (2012) Early predictors of survival to and after heart transplantation in children with dilated cardiomyopathy. Circulation. 126(9):1079-86. PMID: 22800850

Charles M. Brenner

J. Boylston, C. Brenner. (2012) FHIT. Encyclopedia of Signaling Molecules, S. Choi, ed. 68(7):613-616. DOI: 10.1007/978-1-4419-0461-4_68

Brenner C. (2012) Changes in chemistry and biochemistry education: Creative responses to medical college admissions test revisions in the age of the genome. Biochem Mol Biol Educ. PMID:23281187

Brenner C, Ringe D. (2012) Response to the New MCAT: ASBMB Premedical Curriculum. ASBMB Today. 12-14.

Midtkandal RR, Redpath P, Trammell SA, Macdonald SJ, Brenner C, Migaud ME. (2012) Novel synthetic route to the C-nucleoside, 2-deoxy benzamide riboside. Bioorg Med Chem Lett. 22(16):5204-7. PMID:22795628

John M. Dagle

Bream EN, Leppellere CR, Cooper ME, Dagle JM, Merrill DC, Christensen K, Simhan HN, Fong CT, Hallman M, Muglia LJ, Marazita ML, Murray JC. (2012) Candidate gene linkage approach to Identify DNA variants that predispose to preterm birth. Pediatr Res. PMID:23168575

Dagle JM, Murray JC. (2012) Applying deep DNA sequencing to common, complex pediatric traits. Pediatrics. 130(6):e1677-8. PMID: 23166345

Mann PC, Cooper ME, Ryckman KK, Comas B, Gili J, Crumley S, Bream EN, Byers HM, Piester T, Schaefer A, Christine PJ, Lawrence A, Schaa KL, Kelsey KJ, Berends SK, Momany AM, Gadow E, Cosentino V, Castilla EE, López Camelo J, Saleme C, Day LJ, England SK, Marazita ML, Dagle JM, Murray JC. (2012) Polymorphisms in the fetal progesterone receptor and a calcium-activated potassium channel isoform are associated with preterm birth in an Argentinian population. J Perinatol.  PMID: 23018797

Ryckman KK, Cook DE, Berberich SL, Shchelochkov OA, Berends SK, Busch T, Dagle JM, Murray JC. (2012) Replication of clinical associations with 17-hydroxyprogesterone in preterm newborns. J Pediatr Endocrinol Metab. 25(3-4):301-5. PMID: 22768660

Kyser KL, Morriss FH Jr, Bell EF, Klein JM, Dagle JM. (2012)  Improving survival of extremely preterm infants born between 22 and 25 weeks of gestation. Obstet Gynecol. 119(4):795-800. PMID: 22433343

Hajj H, Dagle JM. (2012) Genetics of patent ductus arteriosus susceptibility and treatment. Semin Perinatol. 36(2):98-104. PMID: 22414880

Byers HM, Dagle JM, Klein JM, Ryckman KK, McDonald EL, Murray JC, Borowski KS. (2012) Variations in CRHR1 are associated with persistent pulmonary hypertension of the newborn. Pediatr Res. 71(2):162-7. PMID: 22258127

Ryckman KK, Dagle JM, Kelsey K, Momany AM, Murray JC. (2012) Genetic associations of surfactant protein D and angiotensin-converting enzyme with lung disease in preterm neonates. J Perinatol. 32(5):349-55. PMID: 21960125

Ryckman KK, Feenstra B, Shaffer JR, Bream EN, Geller F, Feingold E, Weeks DE, Gadow E, Cosentino V, Saleme C, Simhan HN, Merrill D, Fong CT, Busch T, Berends SK, Comas B, Camelo JL, Boyd H, Laurie CC, Crosslin D, Zhang Q, Doheny KF, Pugh E, Melbye M, Marazita ML, Dagle JM, Murray JC. (2012) Replication of a genome-wide association study of birth weight in preterm neonates. J Pediatr. 160(1):19-24.  PMID: 21885063

Brandon Davies

Davies BS, Goulbourne CN, Barnes RH 2nd, Turlo KA, Gin P, Vaughan S, Vaux DJ, Bensadoun A, Beigneux AP, Fong LG, Young SG. (2012) Assessing mechanisms of GPIHBP1 and lipoprotein lipase movement across endothelial cells. J Lipid Res. 53(12):2690-7.  PMID:23008484

Gin P, Goulbourne CN, Adeyo O, Beigneux AP, Davies BS, Tat S, Voss CV, Bensadoun A, Fong LG, Young SG. (2012) Chylomicronemia mutations yield new insights into interactions between lipoprotein lipase and GPIHBP1. Hum Mol Genet. 21(13):2961-72. PMID: 22493000

Jung HJ, Coffinier C, Choe Y, Beigneux AP, Davies BS, Yang SH, Barnes RH 2nd, Hong J, Sun T, Pleasure SJ, Young SG, Fong LG. (2012) Regulation of prelamin A but not lamin C by miR-9, a brain-specific microRNA. Proc Natl Acad Sci U S A. 109(7):E423-31. PMID: 22308344

Weinstein MM, Goulbourne CN, Davies BS, Tu Y, Barnes RH 2nd, Watkins SM, Davis R, Reue K, Tontonoz P, Beigneux AP, Fong LG, Young SG. (2012) Reciprocal metabolic perturbations in the adipose tissue and liver of GPIHBP1-deficient mice. Arterioscler Thromb Vasc Biol. 32(2):230-5. PMID: 22173228

Davies BS, Beigneux AP, Fong LG, Young SG. (2012)  New wrinkles in lipoprotein lipase biology. Curr Opin Lipidol. 23(1):35-42. PMID: 22123668

Kris A. DeMali

Peng X, Maiers JL, Choudhury D, Craig SW, DeMali KA. (2012) α-Catenin uses a novel mechanism to activate vinculin. J Biol Chem. 287(10):7728-37. PMID: 22235119

Sloan CM, Quinn CV, Peters JP, Farley J, Goetzinger C, Wernli M, DeMali KA, Ellerbroek SM. (2012) Divergence of Rho residue 43 impacts GEF activity. Small GTPases. 3(1):15-22. PMID:22673745

DeMali KA, Adams J.  (2012) Cell-cell and cell-matrix interactions. Mol Biol Cell, 23:965. DOI:10.1091/mbc.E11-12-0967

Webb DJ, Brown CM, DeMali KA. (2012) Signals Regulating Adhesion DynamicsJournal of Signal Transduction, 2012:785196. DOI: 10.1155/2012/785196

John E. Donelson

Reiling L, Richards JS, Fowkes FJ, Wilson DW, Chokejindachai W, Barry AE, Tham WH, Stubbs J, Langer C, Donelson J, Michon P, Tavul L, Crabb BS, Siba PM, Cowman AF, Mueller I, Beeson JG. (2012) The Plasmodium falciparum erythrocyte invasion ligand Pfrh4 as a target of functional and protective human antibodies against malaria. PLoS One. 7(9):e45253. DOI: 10.1371/journal.pone.0045253. PMID: 23028883

Weirather JL, Wilson ME, Donelson JE. (2012) Mapping of VSG similarities in Trypanosoma brucei. Mol Biochem Parasitol. 181(2):141-52. PMID: 22079099

Adrian H. Elcock

Reinert ZE, Musselman ED, Elcock AH, Horne WS. (2012) A PEG-based oligomer as a backbone replacement for surface-exposed loops in a protein tertiary structure. Chembiochem. 13(8):1107-11. PMID: 22539233

Lokesh Gakhar

Kohlgraf KG, Ackermann AR, Burnell KK, Srikantha RN, Joly SA, Bartlett JA, Gakhar L, Johnson GK, McCray PB Jr, Guthmiller JM, Brogden KA. (2012) Quantitation of SPLUNC1 in saliva with an xMAP particle-based antibody capture and detection immunoassay. Arch Oral Biol. 57(2):197-204. DOI: 10.1016/j.archoralbio.2011.08.013. PMID: 21925642

Mohanty SK, Yu CL, Das S, Louie TM, Gakhar L, Subramanian M. (2012) Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J Bacteriol. 194(15):3872-82. PMID: 22609920

Summers RM, Louie TM, Yu CL, Gakhar L, Louie KC, Subramanian M. (2012) Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J Bacteriol. 194(8):2041-9. PMID: 22328667

Pamela K. Geyer

Hohl AM, Thompson M, Soshnev AA, Wu J, Morris J, Hsieh TS, Wu CT, Geyer PK. (2012) Restoration of topoisomerase 2 function by complementation of defective monomers in Drosophila. Genetics. 192(3):843-56. PMID: 22923380

Soshnev AA, He B, Baxley RM, Jiang N, Hart CM, Tan K, Geyer PK. (2012) Genome-wide studies of the multi-zinc finger Drosophila Suppressor of Hairy-wing protein in the ovary. Nucleic Acids Res. 40(12):5415-31. PMID: 22406832

Theresa L. Gioannini

Rallabhandi P, Phillips RL, Boukhvalova MS, Pletneva LM, Shirey KA, Gioannini TL, Weiss JP, Chow JC, Hawkins LD, Vogel SN, Blanco JC. (2012) Respiratory syncytial virus fusion protein-induced toll-like receptor 4 (TLR4) signaling is inhibited by the TLR4 antagonists Rhodobacter sphaeroides lipopolysaccharide and eritoran (E5564) and requires direct interaction with MD-2. MBio. 3(4). PMID: 22872782

Wendlandt EB, Graff JW, Gioannini TL, McCaffrey AP, Wilson ME. (2012) The role of microRNAs miR-200b and miR-200c in TLR4 signaling and NF-κB activation. Innate Immun. 18(6):846-55. PMID: 22522429

Yu L, Phillips RL, Zhang D, Teghanemt A, Weiss JP, Gioannini TL. (2012) NMR studies of hexaacylated endotoxin bound to wild-type and F126A mutant MD-2 and MD-2·TLR4 ectodomain complexes. J Biol Chem. 287(20):16346-55.  PMID: 22433852

Esparza GA, Teghanemt A, Zhang D, Gioannini TL, Weiss JP. (2012) Endotoxin{middle dot}albumin complexes transfer endotoxin monomers to MD-2 resulting in activation of TLR4. Innate Immun. 18(3):478-91. PMID: 21994253

Piazza, M, Calabrese, V, Damore, G, Cighetti, R, Gioannini, T, Weiss, J, Peri, F. (2012) A synthetic Lipid A mimetic modulates human TLR4 activity.  ChemMedChem. 7: 213-217. PMID:22140087

Yang, D, Postnikov, YV, Li, Y, Tewary, P, de la Rosa, G, Wei, F, Klinman, D, Gioannini, T,Weiss, JP, Furusawa, T, Bustin, M, Oppenheim, JJ.  (2012) High-mobility group nucleosome-binding protein 1 acts as an alarmin and is critical for lipopolysaccharide-induced immune responses.  J. Exp. Med. 209: 157-171. PMID:22184635

Andrew Norris

Olivier AK, Yi Y, Sun X, Sui H, Liang B, Hu S, Xie W, Fisher JT, Keiser NW, Lei D, Zhou W, Yan Z, Li G, Evans TI, Meyerholz DK, Wang K, Stewart ZA, Norris AW, Engelhardt JF. (2012) Abnormal endocrine pancreas function at birth in cystic fibrosis ferrets. J Clin Invest. 122(10):3755-68. PMID: 22996690

Katkhuda R, Peterson ES, Roghair RD, Norris AW, Scholz TD, Segar JL. (2012) Sex-specific programming of hypertension in offspring of late-gestation diabetic rats. Pediatr Res. 72(4):352-61. PMID: 22805998

Hu S, Yao J, Howe AA, Menke BM, Sivitz WI, Spector AA, Norris AW. (2012) Peroxisome proliferator-activated receptor γ decouples fatty acid uptake from lipid inhibition of insulin signaling in skeletal muscle. Mol Endocrinol. 26(6):977-88. PMID: 22474127

Norris AW, Sigmund CD. (2012) A second chance for a PPARγ targeted therapy? Circ Res. 110(1):8-11. PMID: 22223206

Bryce V. Plapp

Plapp BV, Ramaswamy S. (2012) Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Biochemistry. 51(19):4035-48. PMID: 22531044

David H. Price

Van Duyne R, Guendel I, Jaworski E, Sampey G, Klase Z, Chen H, Zeng C, Kovalskyy D, El Kouni MH, Lepene B, Patanarut A, Nekhai S, Price DH, Kashanchi F. (2012) Effect of Mimetic CDK9 Inhibitors on HIV-1-Activated Transcription. J Mol Biol. PMID: 23247501

Kulak MV, Cyr AR, Woodfield GW, Bogachek M, Spanheimer PM, Li T, Price DH, Domann FE, Weigel RJ. (2012) Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. Oncogene. PMID: 22964634

Fujinaga K, Barboric M, Li Q, Luo Z, Price DH, Peterlin BM. (2012) PKC phosphorylates HEXIM1 and regulates P-TEFb activity. Nucleic Acids Res. 40(18):9160-70. PMID: 22821562

Zhou Q, Li T, Price DH. (2012) RNA polymerase II elongation control. Annu Rev Biochem. 81:119-43. PMID: 22404626

Nguyen D, Krueger BJ, Sedore SC, Brogie JE, Rogers JT, Rajendra TK, Saunders A, Matera AG, Lis JT, Uguen P, Price DH. (2012) The Drosophila 7SK snRNP and the essential role of dHEXIM in development. Nucleic Acids Res. 40(12):5283-97. PMID: 22379134

Cheng B, Li T, Rahl PB, Adamson TE, Loudas NB, Guo J, Varzavand K, Cooper JJ, Hu X, Gnatt A, Young RA, Price DH. (2012) Functional association of Gdown1 with RNA polymerase II poised on human genes. Mol Cell. 45(1):38-50. PMID: 22244331

Peterlin BM, Brogie JE, Price DH. (2012) 7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription. Wiley Interdiscip Rev RNA. 3(1):92-103. PMID: 21853533

Li T and Price DH. (2012) Gdown1 – making a link between Mediator and RNA polymerase II elongation control. Transcription, 3(4):177-180. PMID:22771989

Miles Pufall

Serafimova IM, Pufall MA, Krishnan S, Duda K, Cohen MS, Maglathlin RL, McFarland JM, Miller RM, Frödin M, Taunton J. (2012)  Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles. Nat Chem Biol. 8(5):471-6. DOI: 10.1038/nchembio.925. PMID: 22466421

Peter A. Rubenstein

Rubenstein PA, Mayer EA. (2012) Familial visceral myopathies: from symptom-based syndromes to actin-related diseases. Gastroenterology. 143(6):1420-3. PMID:23085350

Malloy LE, Wen KK, Pierick AR, Wedemeyer EW, Bergeron SE, Vanderpool ND, McKane M, Rubenstein PA, Bartlett HL. (2012) Thoracic Aortic Aneurysm (TAAD)-causing Mutation in Actin Affects Formin Regulation of Polymerization. J Biol Chem. (34):28398-408. PMID: 22753406

Glenn NO, McKane M, Kohli V, Wen KK, Rubenstein PA, Bartman T, Sumanas S. (2012) The W-loop of alpha-cardiac actin is critical for heart function and endocardial cushion morphogenesis in zebrafish. Mol Cell Biol. 32(17):3527-40. PMID: 22751927

Kruth KA, Rubenstein PA. (2012) Two deafness-causing (DFNA20/26) actin mutations affect Arp2/3-dependent actin regulation. J Biol Chem. 287(32):27217-26. PMID: 22718764

Michael Schnieders

Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. (2012) Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys. 45(4):427-91. PMID: 23217364

Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P. (2012) The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. J Chem Theory Comput. 8(5):1721-1736. PMID: 22582032

Schnieders MJ, Kaoud TS, Yan C, Dalby KN, Ren P. (2012) Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. Curr Pharm Des. 18(9):1173-85. PMID: 22316156

Debra A. Schwinn

Schwinn DA, Mackensen GB, Brown EN. (2012) Understanding the TXA seizure connection. J Clin Invest. 122(12):4339-41. PMID: 23187134

Arthur Spector

Hu S, Yao J, Howe AA, Menke BM, Sivitz WI, Spector AA, Norris AW. (2012) Peroxisome proliferator-activated receptor γ decouples fatty acid uptake from lipid inhibition of insulin signaling in skeletal muscle. Mol Endocrinol. 26(6):977-88. PMID: 22474127

Maria Spies

Spies M. (2012) There and back again: new single-molecule insights in the motion of DNA repair proteins. Curr Opin Struct Biol. PMID: 23260129

Pugh RA, Wu CG, Spies M. (2012) Regulation of translocation polarity by helicase domain 1 in SF2B helicases. The EMBO Journal. 31, 503 – 514. DOI:10.1038/emboj.2011.412. PMCID: PMC3261565

Eric Taylor

Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen YC, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J. (2012) A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans.Science. 337(6090):96-100. PMID: 22628558

Chen YC, Taylor EB, Dephoure N, Heo JM, Tonhato A, Papandreou I, Nath N, Denko NC, Gygi SP, Rutter J.(2012) Identification of a protein mediating respiratory supercomplex stability. Cell Metab. 15(3):348-60. DOI:10.1016/j.cmet.2012.02.006. PMID: 22405070; PMCID: PMC3302151.

Lori L. Wallrath

Wallrath LL, Elgin SC. (2012) Enforcing silencing: dynamic HP1 complexes in Neurospora. Nat Struct Mol Biol. 19(5):465-7. PMID: 22551706

Dialynas G, Flannery KM, Zirbel LN, Nagy PL, Mathews KD, Moore SA, Wallrath LL. (2012) LMNA variants cause cytoplasmic distribution of nuclear pore proteins in Drosophila and human muscle. Hum Mol Genet. 21(7):1544-56. PMID: 22186027

M. Todd Washington

Dieckman LM, Freudenthal BD, Washington MT. (2012) PCNA Structure and Function: Insights from Structures of PCNA Complexes and Post-translationally Modified PCNA. Subcell Biochem. 62:281-99. PMID: 22918591

Dan L. Weeks

Li YE, Allen BG, Weeks DL. (2012) Using ΦC31 integrase to mediate insertion of DNA in Xenopus embryos. Methods Mol Biol. 2012;917:219-30. DOI: 10.1007/978-1-61779-992-1_13.  PMID: 22956091

Ronald J. Weigel

O’Malley Y, Lal G, Howe JR, Weigel RJ, Komorowski RA, Shilyansky J, Sugg SL. (2012) Invasion in follicular thyroid cancer cell lines is mediated by EphA2 and pAkt. Surgery. 152(6):1218-24. PMID: 23158188

Kulak MV, Cyr AR, Woodfield GW, Bogachek M, Spanheimer PM, Li T, Price DH, Domann FE, Weigel RJ. (2012) Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. Oncogene.  PMID: 22964634

Spanheimer PM, Woodfield GW, Cyr AR, Kulak MV, White-Baer LS, Bair TB, Weigel RJ. (2012) Expression of the RET Proto-oncogene Is Regulated by TFAP2C in Breast Cancer Independent of the Estrogen Receptor. Ann Surg Oncol. PMID:22878616

Larrieux G, Cupp JA, Liao J, Scott-Conner CE, Weigel RJ. (2012) Effect of introducing hematoma ultrasound-guided lumpectomy in a surgical practice. J Am Coll Surg. 215(2):237-43. PMID: 22632911

Spanheimer PM, Weigel RJ. (2012) Management of patients with primary hyperparathyroidism and concurrent thyroid disease: an evolving field. Ann Surg Oncol. 19(5):1428-9. PMID: 22395994

Lal G, Groff M, Howe JR, Weigel RJ, Sugg SL, Lynch CF. (2012) Risk of subsequent primary thyroid cancer after another malignancy: latency trends in a population-based study. Ann Surg Oncol. 19(6):1887-96. PMID: 22227921

Marc S. Wold

Sparks JL, Kumar R, Singh M, Wold MS, Pandita TK, Burgers PM. (2012) Human exonuclease 5 is a novel sliding exonuclease required for genome stability. J Biol Chem. 287(51):42773-83. PMID: 23095756

Hass CS, Chen R, Wold MS. (2012) Detection of posttranslational modifications of replication protein A. Methods Mol Biol. 922:193-204. PMID: 22976188

Lindsey-Boltz LA, Reardon JT, Wold MS, Sancar A. (2012) In vitro analysis of the role of replication protein A (RPA) and RPA phosphorylation in ATR-mediated checkpoint signaling. J Biol Chem. 287(43):36123-31. PMID: 22948311

Hass CS, Lam K, Wold MS. (2012) Repair-specific functions of replication protein A. J Biol Chem. 287(6):3908-18. PMID: 22179778

Meng Wu

Huang F, Zhang H, Wu M, Yang H, Kudo M, Peters CJ, Woodruff PG, Solberg OD, Donne ML, Huang X, Sheppard D, Fahy JV, Wolters PJ, Hogan BL, Finkbeiner WE, Li M, Jan YN, Jan LY, Rock JR. (2012) Calcium-activated chloride channel TMEM16A modulates mucin secretion and airway smooth muscle contraction. Proc Natl Acad Sci U S A. 109(40):16354-9. PMID: 22988107

Mattmann ME, Yu H, Lin Z, Xu K, Huang X, Long S, Wu M, McManus OB, Engers DW, Le UM, Li M, Lindsley CW, Hopkins CR. (2012) Identification of (R)-N-(4-(4-methoxyphenyl)thiazol-2-yl)-1-tosylpiperidine-2-carboxamide, ML277, as a novel, potent and selective K(v)7.1 (KCNQ1) potassium channel activator. Bioorg Med Chem Lett. 22(18):5936-41. PMID: 22910039

Cheung YY, Yu H, Xu K, Zou B, Wu M, McManus OB, Li M, Lindsley CW, Hopkins CR. (2012) Discovery of a series of 2-phenyl-N-(2-(pyrrolidin-1-yl)phenyl)acetamides as novel molecular switches that modulate modes of K(v)7.2 (KCNQ2) channel pharmacology: identification of (S)-2-phenyl-N-(2-(pyrrolidin-1-yl)phenyl)butanamide (ML252) as a potent, brain penetrant K(v)7.2 channel inhibitor. J Med Chem. 55(15):6975-9. PMID: 22793372

Liping Yu

Yu L, Phillips RL, Zhang D, Teghanemt A, Weiss JP, Gioannini TL. (2012) NMR studies of hexaacylated endotoxin bound to wild-type and F126A mutant MD-2 and MD-2·TLR4 ectodomain complexes. J Biol Chem. 287(20):16346-55. PMID: 22433852

Kei-ichiro, I, Yoshida-Moriguchi, T., Hara Y., Anderson, M. E., Yu, L., Campbell K. P. (2012) Dystroglycan function requires xylosyl- and glucuronyltransferase activities of LARGE.  Science. 335: 93-96. PMID: 22223806

Post DM, Yu L, Krasity BC, Choudhury B, Mandel MJ, Brennan CA, Ruby EG, McFall-Ngai MJ, Gibson BW, Apicella MA. (2012) O-antigen and core carbohydrate of Vibrio fischeri lipopolysaccharide: composition and analysis of their role in Euprymna scolopes light organ colonization. J Biol Chem. 287(11):8515-30. DOI: 10.1074/jbc.M111.324012. PMID: 22247546

 

Busy Spring for biochemistry faculty

Wednesday, March 27th, 2013

Biochemistry faculty have been busy this Spring. Dr. Marc Wold gave a seminar at Washington University in January. In February, he attended the Keystone meeting on DNA Replication and Recombination in Banff, Canada.  Dr. Wold chaired the DNA Repair/Recombination Processes Workshop and gave a workshop talk and a poster on his lab’s research.

Dr. David Price spoke at the University of Illinois, Urbana-Champaign on March 1 on the “Mechanisms of RNA Polymerase II Elongation Control: The role of Gdown1 and Myc as non-sequence specific factors.”  Dr. Miles Pufall spoke at Texas A&M University on March 20 and will be presenting a Medical Sciences seminar at Indiana University on April 8 entitled, “The glucocorticoid receptor as signal integrator: understanding treatment resistance in childhood acute lymphoblastic leukemia.”

Dr. Charles Brenner spoke at the Clinical Translation of Epigenetics in Cancer Therapy’s Biennial Workshop and spoke at Duke University’s Sarah W. Stedman Nutrition & Metabolism Center in January.  In February, he was a guest speaker of the Distinguished Scientist Lecture Series hosted by the Institute for Research in Immunology and Cancer at the University of Montreal.  And just before Spring Break, Dr. Brenner represented ASBMB at the AAMC Council of Academic Societies meeting in Ft. Lauderdale.

 

Miles Pufall awarded HCCC seed grant funding

Thursday, November 15th, 2012

A $30,000 seed grant was awarded to Miles Pufall from the Holden Comprehensive Cancer Center’s Institutional Research Grant through the American Cancer Society. The seed grant funding is for one year of Dr. Pufall’s project entitled, “Using genome-wide high-coverage shRNA screening to identify targets of treatment resistance in childhood acute lymphoblastic leukemia.”

Miles Pufall speaks at V Foundation fundraiser

Tuesday, June 12th, 2012

Miles Pufall, a recently named V Foundation Scholar, was a speaker at a benefit gala for cancer research in Cedar Rapids on June 4th. Dr. Pufall gave remarks on his path to becoming a cancer researcher. Also in attendance was Basketball Hall of Fame inductee and ardent supporter of the V Foundation, Dick Vitale, who gave an impassioned speech on the importance of cancer research.

Miles Pufall receives Carver Young Investigator Award

Wednesday, April 25th, 2012

Miles Pufall has been awarded a Carver Young Investigator Award from the Roy J. Carver Charitable Trust for his project, “Understanding glucocorticoid resistance in B cell precursor acute lymphoblastic leukemia.”

This is a three year, $345,000 award to investigate the molecular basis for steroid resistance in acute lymphoblastic leukemia. Dr. Pufall was selected as the sole applicant from the Holden Comprehensive Cancer Center at the University of Iowa. He joins Drs. Lori Wallrath, Adrian Elcock, Todd Washington and Ernesto Fuentes as an early-career recipient of a Carver Trust award.

Department announces hiring of Drs. Maria and M. Ashley Spies

Tuesday, December 20th, 2011

The Department of Biochemistry is pleased to announce the 3rd and 4th faculty hires from the “best available athlete” faculty search initiated in September 2009. In July 2010, Biochemistry welcomed Dr. Sheila Baker from Duke University, an R01 funded investigator focusing on protein localization in vertebrate photoreceptor cells. In July 2011, Biochemistry welcomed Dr. Miles Pufall from University of California, San Francisco, an R00 funded investigator focusing on glucocorticoid receptor function in leukemia. In July 2012, Biochemistry will welcome Dr. Maria Spies and Dr. M. Ashley Spies from University of Illinois. Maria will join the Department as a tenured associate professor. Ashley was jointly recruited by the College of Pharmacy’s Division of Medicinal & Natural Products Chemistry. He will have a 60% appointment as assistant professor in Pharmacy and a 40% appointment in Biochemistry, accompanied by full privileges in both academic units.

Maria Spies, nee Koudrova, a native of St. Petersburg, Russia, is a 1994 BS and a 1996 MS from St. Petersburg State Polytechnic University, and a 2000 PhD from Osaka University. As a post-doctoral fellow with Dr. Stephen Kowalczykowski at University of California, Davis, she obtained a series of high profile results on the RecBCD helicases of E. coli, which were published in Nature, Cell and Molecular Cell. As an assistant professor at Illinois, she has expanded her work to characterize Rad52, Brca1 and several helicases using novel single molecule methods. Her research program has been funded by the American Cancer Society and by an Early Career Award from the Howard Hughes Medical Institute.

Ashley Spies, a native of Kansas, is a 1991 BA, a 1994 MA, and a 1997 PhD from the University of Kansas, where he calculated the intrinsic base-flipping rate constants for DNA and RNA with Dr. Richard Schowen. From 1997 to 2000, as a post-doctoral fellow with Dr. Katsuyuki Tanizawa at Osaka, he worked on quinone biosynthesis. He then joined Dr. Michael Toney’s laboratory at the University of California, Davis, where he developed novel methods to characterize individual steps in the alanine racemase catalytic cycle. As Illinois, he developed an independent research program using computational and experimental approaches to inhibit glutamate racemace, funded by the National Institutes of Health.

Drs. Spies and Spies attribute much of the driving force for their recruitment to the facilities and the collaborative atmosphere available in the Department of Biochemistry. They both collaborate with Drs. Marc Wold and M. Todd Washington on a program project application that focuses on replication, recombination and repair of DNA. In addition, they both collaborate with Dr. David Price and others in a proposed center to perform structural analysis of HIV-host interactions.

Please join me in welcoming the two Spies research groups to the University of Iowa. Expansion of Biochemistry will continue. The Department will begin interviewing candidates for one or more positions focused on diabetes and obesity on January 19.

Pufall wins V Scholar Award

Tuesday, October 11th, 2011

Miles Pufall, a 2011 faculty recruit to the Department of Biochemistry, has been awarded a V Scholar Award from the V Foundation for his project, “B-precursor acute lymphoblastic leukemia: Studying the mechanisms behind Dexamethasone and Prednisone sensitivity in high-risk patients.”

This is a two year, $200,000 award to the most talented new cancer investigators hired by cancer research centers across the US. Proposals are reviewed and awarded by a blue ribbon Scientific Advisory Board. The V Foundation was formed by the late Jim Valvano and ESPN to find cures for cancer.

Highlights of the Annual Retreat

Thursday, September 1st, 2011

The 2011 Biochemistry Annual Retreat, chaired by Lori Wallrath and Lacy Barton, was held on Saturday, August 27 at the Coralville Public Library. Short talks were given in the morning by Kris DeMali, Larry Gray, Lacy Barton, Daniel Weeks,  Todd Washington, Xu Liu, Aaron Ver Heul and Madeline Shea. After lunch, talks were given by Marc Wold, Charles Brenner and Miles Pufall .

The poster session featured 31 posters. Seven awards were given in two divisions. Ashley Angell from the DeMali laboratory and Kristen Syring from the Wallrath laboratory won first and second place in the undergraduate division. In the post-doctoral and staff division, Rebecca Fagan from the Brenner laboratory took first place.  There was a three way tie for second place between Jennifer Bays from the DeMali laboratory, Brett Waite from the Shea laboratory, and Kuo-Kuang Wen from the Rubenstein laboratory.

Two Lois Bigger Gehring Awards  were given to support graduate student travel to research conferences. These awards were given to John Pryor from the Washington laboratory and Alexey Soshnev from the Geyer laboratory.

Thanks to everyone for participating.