Link: University of Iowa

Archive for the ‘Sheila Baker’ Category

Sarah Gardner awarded a 2015 Fight for Sight Summer Student Fellowship

Thursday, June 4th, 2015

Sarah Gardner, and undergraduate major in the Baker Laboratory, was awarded a 2015 Fight for Sight Summer Student Fellowship for her project entitled “Identifying mechanisms of protein targeting essential for the assembly of the photoreceptor ribbon synapse.”

Fight for Sight is a nonprofit organization that provides funding and acknowledgment to promising scientists early in their eye research careers, before they are eligible for government support from the National Institutes of Health. Sarah is joining an exclusive group of over 3,000 Fight for Sight dating back to 1947, many of whom have gone on to become outstanding leaders in eye and vision research and academic ophthalmology. Congratulations, Sarah!

2014 Publications

Monday, February 16th, 2015

The Department’s 2014 publications are now in print and mostly available online.

E. Dale Abel

Riehle C, Abel ED. (2014) Insulin regulation of myocardial autophagy. Circ J. 78(11):2569-76. PMID: 25327953

Pereira RO, Wende AR, Olsen C, Soto J, Rawlings T, Zhu Y, Riehle C, Abel ED. (2014) GLUT1 deficiency in cardiomyocytes does not accelerate the transition from compensated hypertrophy to heart failure. J Mol Cell Cardiol. 72:95-103. DOI: 10.1016/j.yjmcc.2014.02.011. PMID: 24583251

Riehle C, Wende AR, Zhu Y, Oliveira KJ, Pereira RO, Jaishy BP, Bevins J, Valdez S, Noh J, Kim BJ, Moreira AB, Weatherford ET, Manivel R, Rawlings TA, Rech M, White MF, Abel ED. (2014) Insulin receptor substrates are essential for the bioenergetic and hypertrophic response of the heart to exercise training. Mol Cell Biol. 34(18):3450-60. DOI: 10.1128/MCB.00426-14. PMID: 25002528

Wende AR, O’Neill BT, Bugger H, Riehle C, Tuinei J, Buchanan J, Tsushima K, Wang L, Caro P, Guo A, Sloan C, Kim BJ, Wang X, Pereira RO, McCrory MA, Nye BG, Benavides GA, Darley-Usmar VM, Shioi T, Weimer BC, Abel ED. (2014) Enhanced Cardiac Akt/PKB Signaling Contributes to Pathological Cardiac Hypertrophy in Part by Impairing Mitochondrial Function Via Transcriptional Repression of Nuclear-Encoded Mitochondrial Genes. Mol Cell Biol. 35(5):831-46. DOI: 10.1128/MCB.01109-14. PMID: 25535334

Pereira RO, Wende AR, Crum A, Hunter D, Olsen CD, Rawlings T, Riehle C, Ward WF, Abel ED. (2014) Maintaining PGC-1α expression following pressure overload-induced cardiac hypertrophy preserves angiogenesis but not contractile or mitochondrial function. FASEB J. 28(8):3691-702. DOI: 10.1096/fj.14-253823. PMID: 24776744

Fu Q, Xu B, Liu Y, Parikh D, Li J, Li Y, Zhang Y, Riehle C, Zhu Y, Rawlings T, Shi Q, Clark RB, Chen X, Abel ED, Xiang YK. (2014) Insulin inhibits cardiac contractility by inducing a Gi-biased β2-adrenergic signaling in hearts. Diabetes. 63(8):2676-89. DOI: 10.2337/db13-1763. PMID: 24677713

Dai J, Matsui T, Abel ED, Dedhar S, Gerszten RE, Seidman CE, Seidman JG, Rosenzweig A. (2014) Deep sequence analysis of gene expression identifies osteopontin as a downstream effector of integrin-linked kinase (ILK) in cardiac-specific ILK knockout mice. Circ Heart Fail. 7(1):184-93. DOI: 10.1161/CIRCHEARTFAILURE.113.000649. PMID: 24319095

Parra V, Verdejo HE, Iglewski M, Del Campo A, Troncoso R, Jones D, Zhu Y, Kuzmicic J, Pennanen C, Lopez-Crisosto C, Jaña F, Ferreira J, Noguera E, Chiong M, Bernlohr DA, Klip A, Hill JA, Rothermel BA, Abel ED, Zorzano A, Lavandero S. (2014) Insulin stimulates mitochondrial fusion and function in cardiomyocytes via the Akt-mTOR-NFκB-Opa-1 signaling pathway. Diabetes. 63(1):75-88. DOI: 10.2337/db13-0340. PMID: 24009260

Lopez-Izquierdo A, Pereira RO, Wende AR, Punske BB, Abel ED, Tristani-Firouzi M. (2014) The absence of insulin signaling in the heart induces changes in potassium channel expression and ventricular repolarization. Am J Physiol Heart Circ Physiol. 306(5):H747-54. DOI: 10.1152/ajpheart.00849.2013. PMID: 24375641

Caro-Maldonado A, Wang R, Nichols AG, Kuraoka M, Milasta S, Sun LD, Gavin AL, Abel ED, Kelsoe G, Green DR, Rathmell JC. (2014) Metabolic reprogramming is required for antibody production that is suppressed in anergic but exaggerated in chronically BAFF-exposed B cells. J Immunol. 192(8):3626-36. DOI: 10.4049/jimmunol.1302062. PMID: 24616478

Macintyre AN, Gerriets VA, Nichols AG, Michalek RD, Rudolph MC, Deoliveira D, Anderson SM, Abel ED, Chen BJ, Hale LP, Rathmell JC. (2014) The glucose transporter Glut1 is selectively essential for CD4 T cell activation and effector function. Cell Metab. 20(1):61-72. DOI: 10.1016/j.cmet.2014.05.004. PMID: 24930970

Liu T, Kishton RJ, Macintyre AN, Gerriets VA, Xiang H, Liu X, Abel ED, Rizzieri D, Locasale JW, Rathmell JC. (2014) Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis. Cell Death Dis. 5:e1470. DOI: 10.1038/cddis.2014.431. PMID: 25321477

Sheila A. Baker

Pan Y, Laird JG, Yamaguchi DM, Baker SA. (2014) A di-arginine ER retention signal regulates trafficking of HCN1 channels from the early secretory pathway to the plasma membrane. Cell Mol Life Sci. PMID: 25142030

Pearring JN, Lieu EC, Winter JR, Baker SA, Arshavsky VY. (2014) R9AP targeting to rod outer segments is independent of rhodopsin and is guided by the SNARE homology domain. Mol Biol Cell. 25(17):2644-9. DOI: 10.1091/mbc.E14-02-0747. PMID: 25009288

Pan Y, Bhattarai S, Modestou M, Drack AV, Chetkovich DM, Baker SA. (2014) TRIP8b is required for maximal expression of HCN1 in the mouse retina. PLoS One. 9(1):e85850. DOI: 10.1371/journal.pone.0085850. PMID: 24409334

Heather L. Bartlett

Pierick AR, McKane M, Wen KK, Bartlett HL. (2014) Aip1p dynamics are altered by the R256H mutation in actin. J Vis Exp. (89):e51551. DOI: 10.3791/51551. PMID: 25146730

Charles M. Brenner

Brenner C. Boosting NAD to Spare Hearing. Cell Metab. 20(6):926-7. DOI: 10.1016/j.cmet.2014.11.015. PMID: 25470539

Wu BK, Brenner C. Suppression of TET1-Dependent DNA Demethylation Is Essential for KRAS-Mediated Transformation. Cell Rep. 9(5):1827-40. DOI: 10.1016/j.celrep.2014.10.063. PMID: 25466250

Mei SC, Brenner C. (2014) Quantification of protein copy number in yeast: the NAD+ metabolome. PLoS One. 9(9):e106496. DOI: 10.1371/journal.pone.0106496. PMID: 25188219

Wu BK, Mei SC, Brenner C. (2014) RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation. Cell Cycle. 13(20):3222-31. DOI: 10.4161/15384101.2014.950886. PMID: 25485502

Boylston JA, Brenner C. (2014) A knockdown with smoke model reveals FHIT as a repressor of Heme oxygenase 1. Cell Cycle. 13(18):2913-30. DOI: 10.4161/15384101.2014.946858. PMID: 25486479

Brenner C. (2014) Histidine Triad Superfamily. Encyclopedia of Life Sciences, John Wiley & Sons Ltd: Chichester.  DOI: 10.1002/9780470015902.a0020545.pub2.

Brenner C. (2014) Metabolism: Targeting a fat-accumulation gene. Nature. 508(7495):194-5. DOI: 10.1038/508194a. PMID: 24717510

Brenner C. (2014) Understanding Faculty Salaries. ASBMB Today, 3(1):28-29.

Huang J, Stewart A, Maity B, Hagen J, Fagan RL, Yang J, Quelle DE, Brenner C, Fisher RA. (2014) RGS6 suppresses Ras-induced cellular transformation by facilitating Tip60-mediated Dnmt1 degradation and promoting apoptosis. Oncogene. 33(27):3604-11. DOI: 10.1038/onc.2013.324. PMID: 23995786

John M. Dagle

Fuller TD, Spracklen CN, Ryckman KK, Knake LA, Busch TD, Momany AM, Murray JC, Dagle JM. (2014) Genetic Variation in CYB5R3 is Associated with Methemoglobin Levels in Preterm Infants Receiving Nitric Oxide Therapy. Pediatr Res. DOI: 10.1038/pr.2014.206. PMID: 25521918

Sampath V, Garland JS, Helbling D, Dimmock D, Mulrooney NP, Simpson PM, Murray JC, Dagle JM. (2014) Anti-Oxidant Response Genes sequence variants and BPD susceptibility in VLBW infants. Pediatr Res. DOI: 10.1038/pr.2014.200. PMID: 25518008

Naderi HM, Murray JC, Dagle JM. (2014) Single mutations in ABCA3 increase the risk for neonatal respiratory distress syndrome in late preterm infants (gestational age 34-36 weeks). Am J Med Genet A. 164A(10):2676-8. DOI: 10.1002/ajmg.a.36660. PMID: 25073622

Ryckman KK, Spracklen CN, Dagle JM, Murray JC. (2014) Maternal factors and complications of preterm birth associated with neonatal thyroid stimulating hormone. J Pediatr Endocrinol Metab. 27(9-10):929-38. DOI: 10.1515/jpem-2013-0366. PMID: 24854527

Hartnett ME, Morrison MA, Smith S, Yanovitch TL, Young TL, Colaizy T, Momany A, Dagle J, Carlo WA, Clark EA, Page G, Murray J, DeAngelis MM, Cotten CM; Genomics Subcommittee. (2014) Genetic variants associated with severe retinopathy of prematurity in extremely low birth weight infants. Invest Ophthalmol Vis Sci. 55(10):6194-203. DOI: 10.1167/iovs.14-14841.PMID: 25118269

Kris A. DeMali

Mahauad-Fernandez WD, DeMali KA, Olivier AK, Okeoma CM. (2014) Bone marrow stromal antigen 2 expressed in cancer cells promotes mammary tumor growth and metastasis. Breast Cancer Res. 16(6):493. PMID: 25499888

DeMali KA, Sun X, Bui GA. (2014) Force transmission at cell-cell and cell-matrix adhesions. Biochemistry. 53(49):7706-17. DOI: 10.1021/bi501181p. PMID: 25474123

Biggs LC, Naridze RL, DeMali KA, Lusche DF, Kuhl S, Soll DR, Schutte BC, Dunnwald M. (2014) Interferon regulatory factor 6 regulates keratinocyte migration. J Cell Sci. 127(Pt 13):2840-8. DOI: 10.1242/jcs.139246. PMID: 24777480

Bays JL, Peng X, Tolbert CE, Guilluy C, Angell AE, Pan Y, Superfine R, Burridge K, DeMali KA. (2014) Vinculin phosphorylation differentially regulates mechanotransduction at cell-cell and cell-matrix adhesions. J Cell Biol. 205(2):251-63. DOI: 10.1083/jcb.201309092. PMID: 24751539

Adrian H. Elcock

Andrews CT, Elcock AH. (2014) COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput. 10(11):5178-5194. PMID: 25400526

Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. (2014) Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev. 114(13):6661-714. DOI: 10.1021/cr400695p. PMID: 24901537

Azzaz AM, Vitalini MW, Thomas AS, Price JP, Blacketer MJ, Cryderman DE, Zirbel LN, Woodcock CL, Elcock AH, Wallrath LL, Shogren-Knaak MA. (2014) Human heterochromatin protein 1α promotes nucleosome associations that drive chromatin condensation. J Biol Chem. 289(10):6850-61. DOI: 10.1074/jbc.M113.512137. PMID: 24415761

Ernesto J. Fuentes

Darnell CL, Wilson JM, Tiwari N, Fuentes EJ, Kirby JR. (2014) Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus. J Bacteriol. 196(17):3160-8. DOI: 10.1128/JB.01866-14. PMID: 24957622

Lokesh Gakhar

Cheguru P, Majumder A, Yadav R, Gopalakrishna KN, Gakhar L, Artemyev NO. (2014) The solution structure of the transducin-α-uncoordinated 119 protein complex suggests occlusion of the Gβ1 γ1 -binding sites. FEBS J. 282(3):550-61. DOI: 10.1111/febs.13161. PMID: 25425538

Streeter J, Schickling BM, Jiang S, Stanic B, Thiel WH, Gakhar L, Houtman JC, Miller FJ Jr. (2014) Phosphorylation of Nox1 regulates association with NoxA1 activation domain. Circ Res. 115(11):911-8. DOI: 10.1161/CIRCRESAHA.115.304267. PMID: 25228390

Ver Heul AM, Gakhar L, Piper RC, Subramanian R. (2014) Crystal structure of a complex of NOD1 CARD and ubiquitin. PLoS One. 9(8):e104017. DOI: 10.1371/journal.pone.0104017. PMID: 25127239

Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. (2014) Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase. J Phys Chem B. 119(3):906-16. DOI: 10.1021/jp5059963.PMID: 25382260

Pamela K. Geyer

Barton LJ, Wilmington SR, Martin MJ, Skopec HM, Lovander KE, Pinto BS, Geyer PK. (2014) Unique and shared functions of nuclear lamina LEM domain proteins in Drosophila. Genetics. 197(2):653-65. DOI: 10.1534/genetics.114.162941. PMID: 24700158

Theresa L. Gioannini

Gioannini TL, Teghanemt A, Zhang D, Esparza G, Yu L, Weiss J. (2014) Purified monomeric ligand.MD-2 complexes reveal molecular and structural requirements for activation and antagonism of TLR4 by Gram-negative bacterial endotoxins. Immunol Res. 59(1-3):3-11. DOI: 10.1007/s12026-014-8543-y. PMID: 24895101

Resman N, Oblak A, Gioannini TL, Weiss JP, Jerala R. (2014) Tetraacylated lipid A and paclitaxel-selective activation of TLR4/MD-2 conferred through hydrophobic interactions. J Immunol. 192(4):1887-95. DOI: 10.4049/jimmunol.1302119. PMID: 24420921

Catherine A. Musselman

Wang C, Chen Z, Hong X, Ning F, Liu H, Zang J, Yan X, Kemp J, Musselman CA, Kutateladze TG, Zhao R, Jiang C, Zhang G. (2014) The structural basis of urea-induced protein unfolding in β-catenin. Acta Crystallogr D Biol Crystallogr. 70(Pt 11):2840-7. DOI: 10.1107/S1399004714018094. PMID: 25372676

Ezhov RN, Metzel GA, Mukhina OA, Musselman CA, Kutateladze TG, Gustafson TP, Kutateladze AG. (2014) Photoactive Spatial Proximity Probes for Binding Pairs with Epigenetic Marks. J Photochem Photobiol A Chem. 290:101-108. PMID: 25197204

Musselman CA, Khorasanizadeh S, Kutateladze TG. (2014) Towards understanding methyllysine readout. Biochim Biophys Acta. 1839(8):686-93. DOI: 10.1016/j.bbagrm.2014.04.001. PMID: 24727128

Allen HF, Daze KD, Shimbo T, Lai A, Musselman CA, Sims JK, Wade PA, Hof F, Kutateladze TG.(2014) Inhibition of histone binding by supramolecular hosts. Biochem J. 459(3):505-12. DOI: 10.1042/BJ20140145. PMID: 24576085

Andrew W. Norris

Mark AL, Norris AW, Rahmouni K. (2014) Sympathetic inhibition after bariatric surgery. Hypertension. 64(2):235-6. DOI: 10.1161/HYPERTENSIONAHA.114.03183. PMID: 24866141

Baack ML, Wang C, Hu S, Segar JL, Norris AW. (2014) Hyperglycemia induces embryopathy, even in the absence of systemic maternal diabetes: an in vivo test of the fuel mediated teratogenesis hypothesis. Reprod Toxicol. 46:129-36. DOI: 10.1016/j.reprotox.2014.03.013. PMID: 24721120

Norris AW, Bahr TM, Scholz TD, Peterson ES, Volk KA, Segar JL. (2014) Angiotensin II-induced cardiovascular load regulates cardiac remodeling and related gene expression in late-gestation fetal sheep. Pediatr Res. 75(6):689-96. DOI: 10.1038/pr.2014.37. PMID: 24614802

Sui H, Yi Y, Yao J, Liang B, Sun X, Hu S, Uc A, Nelson DJ, Ode KL, Philipson LH, Engelhardt JF, Norris AW. (2014) Quantifying insulin sensitivity and entero-insular responsiveness to hyper- and hypoglycemia in ferrets. PLoS One. 9(3):e90519. DOI: 10.1371/journal.pone.0090519. PMID: 24594704

Bryce V. Plapp

Baskar Raj S, Ramaswamy S, Plapp BV. (2014) Yeast alcohol dehydrogenase structure and catalysis. Biochemistry. 53(36):5791-803. DOI: 10.1021/bi5006442. PMID: 25157460

Yahashiri A, Rubach JK, Plapp BV. (2014) Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry. 53(5):881-94. DOI: 10.1021/bi401583f. PMID: 24437493

David H. Price

Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH. (2014) Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biol. 15(10):482. PMID: 25287278

Gu J, Babayeva ND, Suwa Y, Baranovskiy AG, Price DH, Tahirov TH. (2014) Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4. Cell Cycle. 13(11):1788-97. DOI: 10.4161/cc.28756. PMID: 24727379

Guo J, Turek ME, Price DH. (2014) Regulation of RNA polymerase II termination by phosphorylation of Gdown1. J Biol Chem. 289(18):12657-65. DOI: 10.1074/jbc.M113.537662. PMID: 24634214

Mullen Davis MA, Guo J, Price DH, Luse DS. (2014) Functional interactions of the RNA polymerase II-interacting proteins Gdown1 and TFIIF. J Biol Chem. 289(16):11143-52. DOI: 10.1074/jbc.M113.544395. PMID: 24596085

Liu P, Xiang Y, Fujinaga K, Bartholomeeusen K, Nilson KA, Price DH, Peterlin BM. (2014) Release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein (snRNP) activates hexamethylene bisacetamide-inducible protein (HEXIM1) transcription. J Biol Chem. 289(14):9918-25. DOI: 10.1074/jbc.M113.539015. PMID: 24515107

Fowler T, Ghatak P, Price DH, Conaway R, Conaway J, Chiang CM, Bradner JE, Shilatifard A, Roy AL. (2014) Regulation of MYC expression and differential JQ1 sensitivity in cancer cells. PLoS One. 9(1):e87003. DOI: 10.1371/journal.pone.0087003. PMID: 24466310

Miles A. Pufall

Bongers KS, Fox DK, Kunkel SD, Stebounova LV, Murry DJ, Pufall MA, Ebert SM, Dyle MC, Bullard SA, Dierdorff JM, Adams CM. (2014) Spermine Oxidase Maintains Basal Skeletal Muscle Gene Expression and Fiber Size, and Is Strongly Repressed by Conditions that Cause Skeletal Muscle Atrophy. Am J Physiol Endocrinol Metab. 308(2):E144-58. DOI: 10.1152/ajpendo.00472.2014. PMID: 25406264

Peter A. Rubenstein

Bai F, Caster HM, Rubenstein PA, Dawson JF, Kawai M. (2014) Using baculovirus/insect cell expressed recombinant actin to study the molecular pathogenesis of HCM caused by actin mutation A331P. J Mol Cell Cardiol. 74:64-75. DOI: 10.1016/j.yjmcc.2014.04.014. PMID: 24793351

Yamashiro S, Gokhin DS, Sui Z, Bergeron SE, Rubenstein PA, Fowler VM. (2014) Differential actin-regulatory activities of Tropomodulin1 and Tropomodulin3 with diverse tropomyosin and actin isoforms. J Biol Chem. 289(17):11616-29. DOI: 10.1074/jbc.M114.555128. PMID: 24644292

Rubenstein PA, Wen KK. (2014) Insights into the effects of disease-causing mutations in human actins. Cytoskeleton (Hoboken). 71(4):211-29. DOI: 10.1002/cm.21169. PMID: 24574087

Michael J. Schnieders

Park J, Nessler I, McClain B, Macikenas D, Baltrusaitis J, Schnieders MJ. (2014) Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy. J. Chem. Theory Comput. 10 (7): 2781-2791.

Lipparini F, Lagardère L, Stamm B, Cancès E, Schnieders MJ, Ren P, Maday Y, Piquemal J-P. (2014) Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations. J. Chem. Theory Comput. 10 (4): 1638-1651.

Debra A. Schwinn

Schwinn DA. (2014) Team-based patient care. Learning the delicate dance. Iowa Med. 104(3):19. PMID: 25174086

Schwinn DA. (2014) Unlocking the great GME bottleneck. Iowa Med. 104(1):22. PMID: 25167620

Shields RK, Pizzimenti MA, Dudley-Javoroski S, Schwinn DA. (2014) Fostering interprofessional teamwork in an academic medical center: Near-peer education for students during gross medical anatomy. Anat Sci Educ. DOI: 10.1002/ase.1466. PMID: 24888728

Kleine-Brueggeney M, Gradinaru I, Babaeva E, Schwinn DA, Oganesian A. (2014) Alpha1a-adrenoceptor genetic variant induces cardiomyoblast-to-fibroblast-like cell transition via distinct signaling pathways. Cell Signal. 26(9):1985-97. DOI: 10.1016/j.cellsig.2014.05.007. PMID: 24835978

Madeline A. Shea

Newman RA, Sorensen BR, Kilpatrick AM, Shea MA. (2014) Calcium-dependent energetics of calmodulin domain interactions with regulatory regions of the Ryanodine Receptor Type 1 (RyR1). Biophys Chem. 193-194:35-49. DOI: 10.1016/j.bpc.2014.07.004. PMID: 25145833

Wang X, Boyken SE, Hu J, Xu X, Rimer RP, Shea MA, Shaw AS, Andreotti AH, Huang YH. (2014) Calmodulin and PI(3,4,5)P₃ cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production. Sci Signal. 7(337):ra74. DOI: 10.1126/scisignal.2005147. PMID: 25097034

Maria Spies

Ghoneim M, Spies M. (2014) Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. Nano Lett. 14(10):5920-31. DOI: 10.1021/nl502890g. PMID: 25204359

Spies M. (2014) Fulfilling the dream of a perfect genome editing tool. Proc Natl Acad Sci U S A. 111(28):10029-30. DOI: 10.1073/pnas.1408985111. PMID: 24989506

Spies M. (2014) Two steps forward, one step back: determining XPD helicase mechanism by single-molecule fluorescence and high-resolution optical tweezers. DNA Repair (Amst). 20:58-70. DOI: 10.1016/j.dnarep.2014.01.013. PMID: 24560558

Honda M, Okuno Y, Hengel SR, Martín-López JV, Cook CP, Amunugama R, Soukup RJ, Subramanyam S, Fishel R, Spies M. (2014) Mismatch repair protein hMSH2-hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate. Proc Natl Acad Sci U S A. 111(3):E316-25. DOI: 10.1073/pnas.1312988111. PMID: 24395779

Earle Stellwagen

Stellwagen NC, Peters JP, Dong Q, Maher LJ 3rd, Stellwagen E. (2014) The free solution mobility of DNA and other analytes varies as the logarithm of the fractional negative charge. Electrophoresis. 35(12-13):1855-63. DOI: 10.1002/elps.201400040. PMID: 24648187

Nancy C. Stellwagen

Stellwagen NC, Peters JP, Dong Q, Maher LJ 3rd, Stellwagen E. (2014) The free solution mobility of DNA and other analytes varies as the logarithm of the fractional negative charge. Electrophoresis. 35(12-13):1855-63. DOI: 10.1002/elps.201400040. PMID: 24648187

Eric B. Taylor

Gray LR, Tompkins SC, Taylor EB. (2014) Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci. 71(14):2577-604. DOI: 10.1007/s00018-013-1539-2. PMID: 24363178

Lori L. Wallrath

Wallrath LL, Vitalini MW, Elgin SCR. (2014) Heterochromatin: A Critical Part of the Genome. Fundamentals of Chromatin. 529-552.

Azzaz AM, Vitalini MW, Thomas AS, Price JP, Blacketer MJ, Cryderman DE, Zirbel LN, Woodcock CL, Elcock AH, Wallrath LL, Shogren-Knaak MA. (2014) Human heterochromatin protein 1α promotes nucleosome associations that drive chromatin condensation. J Biol Chem. 289(10):6850-61. DOI: 10.1074/jbc.M113.512137. PMID: 24415761

M. Todd Washington

Pryor JM, Dieckman LM, Boehm EM, Washington TM. (2014) Eukaryotic Y-Family Polymerases: A Biochemical and Structural Perspective. Nucleic Acid Polymerases: Nucleic Acids and Molecular Biology. 30: 5-10.

Ronald J. Weigel

Bogachek MV, De Andrade JP, Weigel RJ. (2014) Regulation of Epithelial-Mesenchymal Transition through SUMOylation of Transcription Factors. Cancer Res. 75(1):11-15. PMID: 25524900

Bogachek MV, Park JM, De Andrade JP, Kulak MV, White JR, Wu T, Spanheimer PM, Bair TB, Olivier AK, Weigel RJ. (2014) A Novel Animal Model for Locally Advanced Breast Cancer. Ann Surg Oncol. PMID: 25326397

Xia C, Schroeder MC, Weigel RJ, Sugg SL, Thomas A. (2014) Rate of contralateral prophylactic mastectomy is influenced by preoperative MRI recommendations. Ann Surg Oncol. 21(13):4133-8. DOI: 10.1245/s10434-014-3852-x. PMID: 24934585

Bogachek MV, Chen Y, Kulak MV, Woodfield GW, Cyr AR, Park JM, Spanheimer PM, Li Y, Li T, Weigel RJ. (2014) Sumoylation pathway is required to maintain the basal breast cancer subtype. Cancer Cell. 25(6):748-61. DOI: 10.1016/j.ccr.2014.04.008. PMID: 24835590

Spanheimer PM, Park JM, Askeland RW, Kulak MV, Woodfield GW, De Andrade JP, Cyr AR, Sugg SL, Thomas A, Weigel RJ. (2014) Inhibition of RET increases the efficacy of antiestrogen and is a novel treatment strategy for luminal breast cancer. Clin Cancer Res. 20(8):2115-25. DOI: 10.1158/1078-0432.CCR-13-2221. PMID: 24526731

Cyr AR, Kulak MV, Park JM, Bogachek MV, Spanheimer PM, Woodfield GW, White-Baer LS, O’Malley YQ, Sugg SL, Olivier AK, Zhang W, Domann FE, Weigel RJ. (2014) TFAP2C governs the luminal epithelial phenotype in mammary development and carcinogenesis. Oncogene. 34(4):436-44. DOI: 10.1038/onc.2013.569. PMID: 24469049

Marc S. Wold

Chen R, Wold MS. (2014) Replication protein A: single-stranded DNA’s first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays. 36(12):1156-61. DOI: 10.1002/bies.201400107. PMID: 25171654

Nguyen B, Sokoloski J, Galletto R, Elson EL, Wold MS, Lohman TM. (2014) Diffusion of human replication protein A along single-stranded DNA. J Mol Biol. 426(19):3246-61. DOI: 10.1016/j.jmb.2014.07.014. PMID: 25058683

Sommers JA, Banerjee T, Hinds T, Wan B, Wold MS, Lei M, Brosh RM Jr. (2014) Novel function of the Fanconi anemia group J or RECQ1 helicase to disrupt protein-DNA complexes in a replication protein A-stimulated manner. J Biol Chem. 289(29):19928-41. DOI: 10.1074/jbc.M113.542456. PMID: 24895130

Meng Wu

Wen W, Wang Y, Li Z, Tseng PY, McManus OB, Wu M, Li M, Lindsley CW, Dong X, Hopkins CR. (2014) Discovery and Characterization of 2-(Cyclopropanesulfonamido)-N-(2-ethoxyphenyl)benzamide, ML382: a Potent and Selective Positive Allosteric Modulator of MrgX1. ChemMedChem. 10(1):57-61. DOI: 10.1002/cmdc.201402277. PMID: 25209672

Flaherty DP, Simpson DS, Miller M, Maki BE, Zou B, Shi J, Wu M, McManus OB, Aubé J, Li M, Golden JE. (2014) Potent and selective inhibitors of the TASK-1 potassium channel through chemical optimization of a bis-amide scaffold. Bioorg Med Chem Lett. 24(16):3968-73. DOI: 10.1016/j.bmcl.2014.06.032. PMID: 25017033

Liping Yu

Willer T, Inamori K, Venzke D, Harvey C, Morgensen G, Hara Y, Beltrán Valero de Bernabé D, Yu L, Wright KM, Campbell KP. (2014) The glucuronyltransferase B4GAT1 is required for initiation of LARGE-mediated α-dystroglycan functional glycosylation. Elife. 3. DOI: 10.7554/eLife.03941. PMID: 25279699

Gioannini TL, Teghanemt A, Zhang D, Esparza G, Yu L, Weiss J. (2014) Purified monomeric ligand.MD-2 complexes reveal molecular and structural requirements for activation and antagonism of TLR4 by Gram-negative bacterial endotoxins. Immunol Res. 59(1-3):3-11. DOI: 10.1007/s12026-014-8543-y. PMID: 24895101

Yu L, Fink BD, Herlein JA, Oltman CL, Lamping KG, Sivitz WI. (2014) Dietary fat, fatty acid saturation and mitochondrial bioenergetics. J Bioenerg Biomembr. 46(1):33-44. PMID: 24121995

Fink BD, Herlein JA, Guo DF, Kulkarni C, Weidemann BJ, Yu L, Grobe JL, Rahmouni K, Kerns RJ, Sivitz WI. (2014) A mitochondrial-targeted coenzyme q analog prevents weight gain and ameliorates hepatic dysfunction in high-fat-fed mice. J Pharmacol Exp Ther. 351(3):699-708. DOI: 10.1124/jpet.114.219329. PMID: 25301169

2014 Biochemistry Newsletter now available

Friday, October 31st, 2014

The 2014 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.

Baker Lab Publishes Article in Cellular and Molecular Life Sciences

Monday, August 25th, 2014

Yuan Pan, a senior Biochemistry graduate student, published a first author paper in Cellular and Molecular Life Sciences. This is her second first author paper and her third paper as a graduate student. On this latest work, she was aided by research assistant Joe Laird and BSURF student David Yamaguchi. This is the first scientific paper for David, while Joe has previously published in PNAS.

The paper, “A di-arginine ER retention signal regulates trafficking of HCN1 channels from the early secretory pathway to the plasma membrane,” reports a novel mode of regulating HCN1 channels in the retina. Because these channels are also present throughout the brain and heart, this research might have applications for understanding learning and memory, management of epilepsy and chronic pain, and regulation of heart rate.

An Epub ahead of print version was made available electronically on August 21st.

Congratulations Yuan, Joe, and David!

 

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.

Highlights of the third annual Biochemistry Retreat

Monday, August 27th, 2012

The 2012 Biochemistry Retreat, organized by Lori Wallrath, Todd Washington, John Brogie and Julie Lueth, was held on Saturday, August 24 at the Coralville Public Library. Short talks were given in the morning by Ernesto Fuentes, Karina Kruth (Rubenstein lab), Shyamal Subramanyam (M. Spies lab), Michael Schnieders, Brandon Davies, Charles Brenner, Jessica Maiers (DeMali lab) and Adrian Elcock. After lunch, talks were given by Maria Spies, David Price and Eric Taylor.

The poster session featured 29 posters. Eight total awards were given in three categories: in the undergraduate division, James Bullard (Geyer lab), Melinda Martin (Geyer lab) and Alexander Greiner (Rubenstein lab) won first, second and third, respectively; in the Postdoc/Research Assistant/Associate category, William Jones (M. Spies lab), Jiannan Guo (Price lab) and Christy Mei (Brenner lab) won first, second and third, respectively.

Two Lois Bigger Gehring Awards were given to support graduate student travel to research conferences. Xiaowen Sun (DeMali lab) and Yuan Pan (Baker lab) each won this award for best poster in the graduate student category.

Thanks to everyone for participating.

Next year the retreat will be centered around the Department’s 65th Birthday. Be sure to save the dates: August 23-25, 2013.

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.

Yuan Pan recognized for talk at Midwest Eye Research Symposium

Tuesday, August 2nd, 2011

Congratulations to Yuan Pan, a graduate student in Sheila Baker’s lab, who won an award for her talk at the 4th annual Midwest Eye Research Symposium. This regional vision meeting, held in Iowa City, brings together researchers from across the Midwest and is sponsored by the Institute for Vision Research at the University of Iowa. Yuan’s talk, entitled “Characterization of HCN1 Trafficking in Rod Photoreceptors” was one of three selected from work by graduate students and postdoctoral fellows.

Dean, Marshall, Baker and Shea featured in Press Citizen

Tuesday, July 12th, 2011

Coe College Professor Maria Dean, her student Katelyn Marshall and Biochemistry faculty members Sheila Baker and Madeline Shea were featured in a recent Press Citizen article on the FUTURE program.  Dean and Marshall are spending the summer in Baker’s laboratory as FUTURE Fellows, supported by the Ruth Ann Henriksen Fund in Biochemistry. FUTURE, now in its third year, is directed by Madeline Shea.

Opening of the Pufall laboratory

Friday, July 1st, 2011

Since July 2009, Biochemistry has enjoyed the annual tradition of welcoming a new laboratory to the Department. July, 2009 brought the Brenner group; July, 2010 brought Sheila Baker; and today brought Miles Pufall and his first post-doctoral fellow, Dawne Shelton. Trained by Barbara Graves at University of Utah and Keith Yamamoto of UCSF, Miles brings a research program that will dissect a fundamental problem in biochemistry and a specific problem in leukemogenesis. As he dissects protein-nucleic acid interactions, he seeks to dissect how proteins functions are modulated by changing environmental signals. With his NCI R00 grant, he plans to identify and dissect changes in glucocorticoid induced gene expression in glucocorticoid sensitive and resistant acute lymphoblastic leukemia cells. Dawne and Miles are currently establishing facilities for protein purification and characterization, cell culture, and gearing up to use CCOM facilities in structural biology and genomics.