Dr. Daniel Weeks, having served as the Director of Graduate Studies (DGS) for Biochemistry since 2001, is handing the reins of the graduate program to Dr. Ernesto Fuentes. This is a major transition for the Department. Dan is not going anywhere. He is just starting a new 4 year National Institutes of Health R01 award and is serving as the Harold A. Myers Professor in Basic Sciences and has agreed to assist Ernie in his first year as DGS.

As you know, Ernie Fuentes began as an assistant professor in the Department in 2006 after completing his PhD at the University of Illinois at Urbana-Champaign and postdoctoral fellowships at the University of Pennsylvania and the University of North Carolina at Chapel Hill. He was promoted to Associate Professor in 2014. Dr. Fuentes has built national prominence for his work on the structure, dynamics and specificity of PDZ domain-containing proteins. A terrific colleague, Ernie has been heavily invested in the recruitment, retention, and mentorship of underrepresented minorities at the University of Iowa. He has initiated new innovative programs, served as key participant in existing programs, and joined national organizations bringing visibility to the University of Iowa. He was awarded the CCOM Collegiate Teaching Award this past academic year and was just awarded a new R21 from the National Institutes of Health.

Dan began as an assistant professor in the Department in 1987 after completing his PhD at Purdue and postdoctoral fellowship at Harvard. He was promoted to Associate Professor in 1993, Full Professor in 2001, when he assumed the DGS position. He also served as Vice Chair in 2008-2009. Dan is an internationally known nuclei acid biochemist and developmental biologist who has made multiple contributions to vertebrate oocyte development including his latest discovery and characterization of phase-separated protein aggregates in Xenopus nuclei. He has been honored by the JP Long Award for Teaching, the CCOM Collegiate Teaching Award, the CCOM Outstanding Educator Award, the Graduate College Outstanding Mentor Award, the President and Provost Award for Teaching Excellence, the CCOM Faculty Service Award and he was recently appointed the Harold A. Myers Professorship in Basic Sciences. The faculty and graduates of the Biochemistry PhD program are indebted to him for his remarkably effective 17 years of service in leading the program.

Please join us in congratulating Ernie on this appointment and thanking Dan for his terrific service to Biochemistry!

 

Dr. Daniel Weeks has been appointed as the Dr. Harold A. Myers Professor in the Basic Sciences. This three year professorship, effective August 1, 2018, was established to support a PhD faculty member who exhibits exemplary skill and passion for the teaching of medical students and who is a leader in understanding and developing new methods of medical education. This well-deserved honor is a testament to Dr. Week’s outstanding commitment and dedication to the education of graduate students and postdoctoral fellows.

Congratulations to Dr. Daniel Weeks, who was awarded the 2017 Faculty Service Award from the Carver College of Medicine (CCOM). Dr.  Weeks is an internationally known nuclei acid biochemistry and developmental biologist who has had a productive research career and won many teaching awards. Dr. Weeks has dedicated three decades of service to CCOM. His service activities have been diverse and of the highest impact. Thousands of students have benefited from his guidance and educational programming, establishing a strong foundation for their future careers. Of special note is Dr. Weeks’ strong dedication to curriculum development. He served on the Medical Education and Curriculum Committee from 1989-2003 and on the College of Medicine Curriculum Review/Steering Committee from 2014 – present. CCOM’s recent re-accreditation and the success of the New Horizons Curriculum are due in part to his tireless efforts.

 

 

The Department’s 2016 publications are now in print and mostly available online.

E. Dale Abel

Ock S, Lee WS, Ahn J, Kim HM, Kang H, Kim HS, Jo D, Abel ED, Lee TJ, Kim J. (2016) Deletion of IGF-1 Receptors in Cardiomyocytes Attenuates Cardiac Aging in Male Mice. Endocrinology. 157(1):336-45. DOI: 10.1210/en.2015-1709. PMID: 26469138

Ni R, Zheng D, Xiong S, Hill DJ, Sun T, Gardiner RB, Fan GC, Lu Y, Abel ED, Greer PA, Peng T. (2016) Mitochondrial Calpain-1 Disrupts ATP Synthase and Induces Superoxide Generation in Type 1 Diabetic Hearts: A Novel Mechanism Contributing to Diabetic Cardiomyopathy. Diabetes. 65(1):255-68. DOI: 10.2337/db15-0963. PMID: 26470784

Taegtmeyer H, Young ME, Lopaschuk GD, Abel ED, Brunengraber H, Darley-Usmar V, Des Rosiers C, Gerszten R, Glatz JF, Griffin JL, Gropler RJ, Holzhuetter HG, Kizer JR, Lewandowski ED, Malloy CR, Neubauer S, Peterson LR, Portman MA, Recchia FA, Van Eyk JE, Wang TJ. (2016) Assessing Cardiac Metabolism: A Scientific Statement From the American Heart Association. Circulation research. DOI: 10.1161/RES.0000000000000097. PMID: 27012580

Park SY, Rossman MJ, Gifford JR, Bharath LP, Bauersachs J, Richardson RS, Abel ED, Symons JD, Riehle C. (2016) Exercise training improves vascular mitochondrial function. American Journal of Physiology, Heart and Circulatory Physiology. 310(7):H821-9. DOI: 10.1152/ajpheart.00751.2015. PMID: 26825520

Kishton RJ, Barnes CE, Nichols AG, Cohen S, Gerriets VA, Siska PJ, Macintyre AN, Goraksha-Hicks P, de Cubas AA, Liu T, Warmoes MO, Abel ED, Yeoh AE, Gershon TR, Rathmell WK, Richards KL, Locasale JW, Rathmell JC. (2016) AMPK Is Essential to Balance Glycolysis and Mitochondrial Metabolism to Control T-ALL Cell Stress and Survival. Cell metabolism. 23(4):649-62. DOI: 10.1016/j.cmet.2016.03.008. PMID: 27076078

Jaishy B, Abel ED. (2016) Lipids, Lysosomes and Autophagy. Journal of lipid research. DOI: 10.1194/jlr.R067520. PMID: 27330054

O’Neill BT, Lee KY, Klaus K, Softic S, Krumpoch MT, Fentz J, Stanford KI, Robinson MM, Cai W, Kleinridders A, Pereira RO, Hirshman MF, Abel ED, Accili D, Goodyear LJ, Nair KS, Kahn CR. (2016) Insulin and IGF-1 receptors regulate FoxO-mediated signaling in muscle proteostasis. The Journal of clinical investigation. 126(9):3433-46. DOI: 10.1172/JCI86522. PMID: 27525440

Wellberg EA, Johnson S, Finlay-Schultz J, Lewis AS, Terrell KL, Sartorius CA, Abel ED, Muller WJ, Anderson SM. (2016) The glucose transporter GLUT1 is required for ErbB2-induced mammary tumorigenesis. Breast cancer research : BCR. 18(1):131. DOI: 10.1186/s13058-016-0795-0. PMID: 27998284

Trammell SA, Schmidt MS, Weidemann BJ, Redpath P, Jaksch F, Dellinger RW, Li  Z, Abel ED, Migaud ME, Brenner C. (2016) Nicotinamide riboside is uniquely and orally bioavailable in mice and humans. Nature communications. 7:12948. DOI: 10.1038/ncomms12948. PMID: 27721479

Wang Q, Liu Y, Fu Q, Xu B, Zhang Y, Kim S, Tan R, Barbagallo F, West TM, Anderson EJ, Wei W, Abel ED, Xiang YK. (2016) Inhibiting Insulin-Mediated β2AR Activation Prevents Diabetes-Associated Cardiac Dysfunction. Circulation. DOI: 10.1161/CIRCULATIONAHA.116.022281. PMID: 27815373

Charles M. Brenner

Trammell SA, Yu L, Redpath P, Migaud ME, Brenner C. (2016) Nicotinamide Riboside Is a Major NAD+ Precursor Vitamin in Cow Milk. J Nutr. 146(5):957-63. DOI: 10.3945/jn.116.230078. PMID: 27052539

Trammell SA, Weidemann BJ, Chadda A, Yorek MS, Holmes A, Coppey LJ, Obrosov A, Kardon RH, Yorek MA, Brenner C. (2016) Nicotinamide Riboside Opposes Type 2 Diabetes and Neuropathy in Mice. Sci Rep. 6:26933. DOI: 10.1038/srep26933. PMID: 27230286

Trammell SA, Schmidt MS, Weidemann BJ, Redpath P, Jaksch F, Dellinger RW, Li Z, Abel ED, Migaud ME, Brenner C. (2016) Nicotinamide riboside is uniquely and orally bioavailable in mice and humans. Nat Commun. 7:12948. DOI: 10.1038/ncomms12948. PMID: 27721479

Ratajczak J, Joffraud M, Trammell SA, Ras R, Canela N, Boutant M, Kulkarni SS, Rodrigues M, Redpath P, Migaud ME, Auwerx J, Yanes O, Brenner C, Cantó C. (2016) NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells. Nat Commun. 7:13103. DOI: 10.1038/ncomms13103. PMID: 27725675

John M. Dagle

Patel PM, Momany AM, Schaa KL, Romitti PA, Druschel C, Cooper ME, Marazita ML, Murray JC, Dagle JM. (2016) Genetic Modifiers of Patent Ductus Arteriosus in Term Infants. J Pediatr.  176:57-61.e1. DOI: 10.1016/j.jpeds.2016.05.066. PMID: 27344223

Smazal AL, Kavars AB, Carlson SJ, Colaizy TT, Dagle JM. (2016) Peripherally inserted central catheters optimize nutrient intake in moderately preterm infants. Pediatr Res. 80(2):185-9. DOI: 10.1038/pr.2016.73. PMID: 27057735

Ryckman KK, Berberich SL, Dagle JM. (2016) Predicting gestational age using neonatal metabolic markers. Am J Obstet Gynecol. 214(4):515.e1-13. DOI: 10.1016/j.ajog.2015.11.028. PMID: 26645954

Sampath V, Helbling D, Menden H, Dimmock D, Mulrooney NP, Murray JC, Dagle JM, Garland JS. (2016) Necrotizing Enterocolitis Is Not Associated With Sequence Variants in Antioxidant Response Genes in Premature Infants. J Pediatr Gastroenterol Nutr. 62(3):420-3. DOI: 10.1097/MPG.0000000000000988. PMID: 26426434

Kaluarachchi DC, Momany AM, Busch TD, Gimenez LG, Saleme C, Cosentino V, Christensen K, Dagle JM, Ryckman KK, Murray JC. (2016) Polymorphisms in NR5A2, gene encoding liver receptor homolog-1 are associated with preterm birth. Pediatr Res. 79(5):776-80. DOI: 10.1038/pr.2016.7. PMID: 26761123

Adrian H. Elcock

Lay WK, Miller MS, Elcock AH. (2016) Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. J Chem Theory Comput. 12(4):1401-7. DOI: 10.1021/acs.jctc.5b01136. PMID: 26967542

Miller MS, Lay WK, Elcock AH. (2016) Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization. J Phys Chem B. 120(33):8217-29. DOI: 10.1021/acs.jpcb.6b01902. PMID: 27052117

Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. (2016) Dynamic binding of replication protein a is required for DNA repair. Nucleic Acids Res. 44(12):5758-72. DOI: 10.1093/nar/gkw339. PMID: 27131385

Clark PL, Elcock AH. (2016) Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis. Nat Struct Mol Biol. 23(7):621-3. DOI: 10.1038/nsmb.3255. PMID: 27384188

Ernesto J. Fuentes

Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. (2016) Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure. 24(12):2053-2066. DOI: 10.1016/j.str.2016.08.019. PMID: 27998539

Lokesh Gakhar

Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. (2016) Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure. 24(12):2053-2066. DOI: 10.1016/j.str.2016.08.019. PMID: 27998539

Ulland TK, Jain N, Hornick EE, Elliott EI, Clay GM, Sadler JJ, Mills KA, Janowski AM, Volk AP, Wang K, Legge KL, Gakhar L, Bourdi M, Ferguson PJ, Wilson ME, Cassel SL, Sutterwala FS.(2016) Nlrp12 mutation causes C57BL/6J strain-specific defect in neutrophil recruitment. Nat Commun. 7:13180. DOI: 10.1038/ncomms13180. PMID: 27779193

Hastie JL, Williams KB, Bohr LL, Houtman JC, Gakhar L, Ellermeier CD. (2016) The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation. PLoS Genet. 12(9):e1006287. DOI: 10.1371/journal.pgen.1006287. PMID: 27602573

Gakhar L, Bassuk AG, Velez G, Khan S, Yang J, Tsang SH, Mahajan VB. (2016) Small-angle X-ray scattering of calpain-5 reveals a highly open conformation among calpains. J Struct Biol. 196(3):309-318. DOI: 10.1016/j.jsb.2016.07.017. PMID: 27474374

Guo Q, Gakhar L, Wickersham K, Francis K, Vardi-Kilshtain A, Major DT, Cheatum CM, Kohen A. (2016) Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry. 55(19):2760-71. DOI: 10.1021/acs.biochem.6b00181. PMID: 27100912

Pamela K. Geyer

Barton LJ, Lovander KE, Pinto BS, Geyer PK. (2016) Drosophila male and female germline stem cell niches require the nuclear lamina protein Otefin. Developmental Biology. 415(1):75-86. PMID: 27174470

Berger F, Geyer PK. (2016) Editorial overview: Genome architecture and expression: Connecting genome composition and nuclear architecture with function. Curr Opin Genet Dev. 37:iv-vi. DOI: 10.1016/j.gde.2016.05.017. PMID: 27292868

Catherine A. Musselman

Musselman CA, Kutateladze TG. (2016) Preparation, Biochemical Analysis, and Structure Determination of Methyllysine Readers. Methods Enzymol. 573:345-62. DOI: 10.1016/bs.mie.2015.12.005. PMID: 27372761

Xing S, Li F, Zeng Z, Zhao Y, Yu S, Shan Q, Li Y, Phillips FC, Maina PK, Qi HH, Liu C, Zhu J, Pope RM, Musselman CA, Zeng C, Peng W, Xue HH. (2016) Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity. Nat Immunol. 17(6):695-703. DOI: 10.1038/ni.3456. PMID: 27111144

Andrew W. Norris

Stump M, Guo DF, Lu KT, Mukohda M, Cassell MD, Norris AW, Rahmouni K, Sigmund CD. (2016) Nervous System Expression of PPARγ and Mutant PPARγ Has Profound Effects on Metabolic Regulation and Brain Development. Endocrinology. 157(11):4266-4275. PMID: 27575030

Yi Y, Norris AW, Wang K, Sun X, Uc A, Moran A, Engelhardt JF, Ode KL. (2016) Abnormal Glucose Tolerance in Infants and Young Children with Cystic Fibrosis. Am J Respir Crit Care Med. 194(8):974-980. PMID: 27447840

Yi Y, Sun X, Gibson-Corley K, Xie W, Liang B, He N, Tyler SR, Uc A, Philipson LH, Wang K, Hara M, Ode KL, Norris AW, Engelhardt JF. (2016) A Transient Metabolic Recovery from Early Life Glucose Intolerance in Cystic Fibrosis Ferrets Occurs During Pancreatic Remodeling. Endocrinology. 157(5):1852-65. DOI: 10.1210/en.2015-1935. PMID: 26862997

Bryce V. Plapp

Plapp BV, Charlier HA Jr, Ramaswamy S. (2016) Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Arch Biochem Biophys. 591:35-42. DOI: 10.1016/j.abb.2015.12.009. PMID:26743849

David H. Price

Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. (2016) Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell. 62(1):34-46. DOI: 10.1016/j.molcel.2016.03.013. PMID: 27058786

Peter A. Rubenstein

Lee CY, Lou J, Wen KK, McKane M, Eskin SG, Rubenstein PA, Chien S, Ono S, Zhu C, McIntire LV. (2016) Regulation of actin catch-slip bonds with a RhoA-formin module.  Sci Rep. 6:35058.  DOI: 1038/srep35058. PMID: 27731359

Jepsen L, Kruth KA, Rubenstein PA, Sept D. (2016) Two Deafness-Causing Actin Mutations (DFNA20/26) Have Allosteric Effects on the Actin Structure.  Biophys J. 111(2):323-32. DOI: 10.1016/j.bpj.2016.06.012. PMID: 27463135

Jepsen L, Kruth KA, Rubenstein PA, Sept D. (2016) Molecular Effects of Deafness Mutations in Actin.  Biophys J. 1110(2):354a.

Michael J. Schnieders

Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P. (2016) Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Phys Chem Chem Phys. 18(44):30261-30269. PMID: 27254477

Bu F, Borsa NG, Jones MB, Takanami E, Nishimura C, Hauer JJ, Azaiez H, Black-Ziegelbein EA, Meyer NC, Kolbe DL, Li Y, Frees K, Schnieders MJ, Thomas C, Nester C, Smith RJ. (2016) High-Throughput Genetic Testing for Thrombotic Microangiopathies and C3 Glomerulopathies. J Am Soc Nephrol. 27(4):1245-53. DOI: 10.1681/ASN.2015040385. PMID: 26283675

DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, Schnieders MJ, Lentz SR, Tucker BA, Mullins RF, Scheetz TE, Stone EM, Slusarski DC. (2016) Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Hum Mol Genet. 25(1):44-56. DOI: 10.1093/hmg/ddv446. PMID: 26494905

Nessler IJ, Litman JM, Schnieders MJ. (2016) Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals. Phys Chem Chem Phys. 18(44):30313-30322. PMID: 27524378

Debra A. Schwinn

Schwinn DA. (2016) EDUCATE TO TRANSFORM: THE ART OF DEVELOPING CURIOUS MINDS. Trans Am Clin Climatol Assoc. 127:259-271. PMID: 28066058

M. Ashley Spies

Hengel SR, Malacaria E, Folly da Silva Constantino L, Bain FE, Diaz A, Koch BG, Yu L, Wu M, Pichierri P, Spies MA, Spies M. (2016) Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells. Elife. 5. pii: e14740. DOI: 10.7554/eLife.14740. PMID: 27434671

Maria Spies

Spies M, Chemla YR. (2016) Single-molecule enzymology: fluorescence-based and high-throughput methods. Methods in enzymology. Elsevier. 581. ISSN 0076-6879

Boehm EM, Powers KT, Kondratick CM, Spies M, Houtman JC, Washington MT. (2016) The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1. J Biol Chem. 291(16):8735-44. DOI: 10.1074/jbc.M115.697938. PMID: 26903512

Boehm EM, Spies M, Washington MT. (2016) PCNA tool belts and polymerase bridges form during translesion synthesis. Nucleic Acids Res. 44(17):8250-60. DOI: 10.1093/nar/gkw563. PMID: 27325737

Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. (2016) Dynamic binding of replication protein a is required for DNA repair.  Nucleic Acids Res. 44(12):5758-72. DOI: 10.1093/nar/gkw339. PMID: 27131385

Bain FE, Wu CG, Spies M. (2016) Single-molecule sorting of DNA helicases. Methods. 108:14-23. DOI: 10.1016/j.ymeth.2016.05.009. PMID: 27223403

Hengel SR, Malacaria E, Folly da Silva Constantino L, Bain FE, Diaz A, Koch BG, Yu L, Wu M, Pichierri P, Spies MA, Spies M. (2016) Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells. Elife. 5. pii: e14740. DOI: 10.7554/eLife.14740. PMID: 27434671

Subramanyam S, Ismail M, Bhattacharya I, Spies M. (2016) Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. Proc Natl Acad Sci U S A. 113(41):E6045-E6054. PMID: 27671650

Wu CG, Spies M. (2016) G-quadruplex recognition and remodeling by the FANCJ helicase. Nucleic Acids Res. 44(18):8742-8753. PMID: 27342280

Boehm EM, Subramanyam S, Ghoneim M, Washington MT, Spies M. (2016) Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol. 581:105-145. DOI: 10.1016/bs.mie.2016.08.019. PMID: 27793278

Eric B. Taylor

Gray LR, Rauckhorst AJ, Taylor EB. (2016) A Method for Multiplexed Measurement of Mitochondrial Pyruvate Carrier Activity. J Biol Chem. 291(14):7409-17. DOI: 10.1074/jbc.M115.711663.PMID: 26823462

Rauckhorst AJ, Taylor EB. (2016) Mitochondrial pyruvate carrier function and cancer metabolism. Curr Opin Genet Dev. 38:102-109. DOI: 10.1016/j.gde.2016.05.003. Review. PMID: 27269731

Lori L. Wallrath

Wallrath LL, Bohnekamp J, Magin TM. (2016) Cross talk between the cytoplasm and nucleus during development and disease. Curr Opin Genet Dev. 37:129-36. DOI: 10.1016/j.gde.2016.03.007. PMID: 27110666

Bohnekamp J, Cryderman DE, Thiemann DA, Magin TM, Wallrath LL. (2016) Using Drosophila for Studies of Intermediate Filaments. Methods Enzymol. 568:707-26. DOI: 10.1016/bs.mie.2015.08.028. PMID: 26795490

M. Todd Washington

Boehm EM, Powers KT, Kondratick CM, Spies M, Houtman JC, Washington MT. (2016) The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1. J Biol Chem. 291(16):8735-44. DOI: 10.1074/jbc.M115.697938. PMID: 26903512

Boehm EM, Gildenberg MS, Washington MT. (2016) The Many Roles of PCNA in Eukaryotic DNA Replication. Enzymes. 39:231-54. DOI: 10.1016/bs.enz.2016.03.003. PMID: 27241932

Boehm EM, Spies M, Washington MT. (2016) PCNA tool belts and polymerase bridges form during translesion synthesis. Nucleic Acids Res. 44(17):8250-60. DOI: 10.1093/nar/gkw563. PMID: 27325737

Kondratick CM, Boehm EM, Dieckman LM, Powers KT, Sanchez JC, Mueting SR, Washington MT. (2016) Identification of New Mutations at the PCNA Subunit Interface that Block Translesion Synthesis. PLoS One. 11(6):e0157023. DOI: 10.1371/journal.pone.0157023. PMID: 27258147

Boehm EM, Washington MT. (2016) R.I.P. to the PIP: PCNA-binding motif no longer considered specific: PIP motifs and other related sequences are not distinct entities and can bind multiple proteins involved in genome maintenance. Bioessays. 38(11):1117-1122. DOI: 10.1002/bies.201600116. PMID: 27539869

Washington MT. (2016) DNA Polymerase Fidelity: Beyond Right and Wrong. Structure. 24(11):1855-1856. DOI: 10.1016/j.str.2016.10.003. PMID: 27806256

Boehm EM, Subramanyam S, Ghoneim M, Washington MT, Spies M. (2016) Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol. 581:105-145. DOI: 10.1016/bs.mie.2016.08.019. PMID: 27793278

Daniel l. Weeks

Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJ. (2016) Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development (Cambridge, England). 143(8):1340-50. PMID: 26952988

Hayes MH, Weeks DL. (2016) Amyloids assemble as part of recognizable structures during oogenesis in Xenopus. Biology open. 5(6):801-6. PMID: 27215327

Ronald J. Weigel

De Andrade JP, Park JM, Gu VW, Woodfield GW, Kulak MV, Lorenzen AW, Wu VT, Van Dorin, SE, Spanheimer PM, Weigel RJ. (2016) EGFR Is Regulated by TFAP2C in Luminal Breast Cancer and Is a Target for Vandetanib. Molecular Cancer Therapeutics. 15:503-11. PMID: 26832794

Bogachek MV, Park JM, De Andrade JP, Lorenzen AW, Kulak MV, White JR, Gu VW, Wu VT, Weigel RJ. (2016) Inhibiting the SUMO Pathway Represses the Cancer Stem Cell Population in Breast and Colorectal Carcinomas. Stem Cell Reports. 7:1140-1151. PMID: 27916539

Rosengart TK, Kent KC, Bland KI, Britt LD, Eberlein TJ, Gewertz BL, Hunter JG, Lillemoe KD, Pellegrini CA, Schulick RD, Stain SC, Weigel RJ. (2016) Key Tenets of Effective Surgery Leadership: Perspectives from the Society of Surgical Chairs Mentorship Sessions. JAMA Surg. 151:768-70. PMID: 27096328

Thomas A, Weigel RJ, Lynch CF, Spanheimer PM, Breitbach EK, Schroeder MC (2016). Incidence, Characteristics and Management of Recently Diagnosed, Microscopically Invasive Breast Cancer by Receptor Status: Iowa SEER 2000-2013. American Journal of Surgery. pii: S0002-9610(16)30504-9. DOI: 10.1016/j.amjsurg.2016.08.008.

Marc S. Wold

Myler LR, Gallardo IF, Zhou Y, Gong F, Yang SH, Wold MS, Miller KM, Paull TT, Finkelstein IJ. (2016) Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins. Proc Natl Acad Sci U S A. 113(9):E1170-9. DOI: 10.1073/pnas.1516674113. PMID: 26884156

Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. (2016) Dynamic binding of replication protein a is required for DNA repair.  Nucleic Acids Res. 44(12):5758-72. DOI: 10.1093/nar/gkw339. PMID: 27131385

Meng Wu

Hengel SR, Malacaria E, Folly da Silva Constantino L, Bain FE, Diaz A, Koch BG, Yu L, Wu M, Pichierri P, Spies MA, Spies M. (2016) Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells. Elife. 5. pii: e14740. DOI: 10.7554/eLife.14740. PMID: 27434671

Liping Yu

Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. (2016) Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure. 24(12):2053-2066. DOI: 10.1016/j.str.2016.08.019. PMID: 27998539

Fink BD, Bai F, Yu L, Sivitz WI. (2016) Impaired utilization of membrane potential by complex II-energized mitochondria of obese, diabetic mice assessed using ADP recycling methodology.  Am. J. Physiol. Regul. Integr. Comp. Physiol. 311, R756-R763.  DOI: 10.1152/ajpregu.00232.2016. PMID: 27558314

Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. (2016) Structure of protein O-mannose kinase reveals a unique active site architecture.  eLife. 5, e22238.  DOI: 10.7554/eLife.22238. PMID: 27879205

Briggs DC, Yoshida-Moriguchi T, Zheng T, Venzke D, Anderson ME, Strazzulli A, Moracci M, Yu L, Hohenester E, Campbell KP. (2016) Structural basis of laminin binding to the LARGE glycans on dystroglycan. Nat. Chem. Biol. 12(10), 810-814. DOI:10.1038/nchembio.2146. PMID: 27526028

Hengel SR, Malacaria E, Folly da Silva Constantino L, Bain FE, Diaz A, Koch BG, Yu L, Wu M, Pichierri P, Spies MA, Spies M. (2016) Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells. Elife. 5. pii: e14740. DOI: 10.7554/eLife.14740. PMID: 27434671

Trammell SA, Yu L, Redpath P, Migaud ME, Brenner C. (2016) Nicotinamide Riboside Is a Major NAD+ Precursor Vitamin in Cow Milk. J Nutr. 146(5):957-63. DOI: 10.3945/jn.116.230078. PMID: 27052539

Bai F, Fink BD, Yu L, Sivitz WI. (2016) Voltage-dependent regulation of complex II energized mitochondrial oxygen flux. PLoS One. 11(5):e0154982. DOI:10.1371/journal.pone.0154982. PMID: 27153112

Mishanina TV, Yu L, Karunaratne K, Mondal D, Corcoran JM, Choi MA, Kohen A. (2016) An unprecedented mechanism of nucleotide methylation in organisms containing thyX. Science. 351 (6272), 507-510.  DOI:

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

Congratulations to Professor Dan Weeks, who has been selected as the recipient of the 2015-16 Graduate College Outstanding Faculty Mentor Award: Biological and Life Sciences.

In his nomination letter, Dr. Charles Brenner wrote “For the past 28 years Professor Weeks, an internationally known nucleic acid biochemist and developmental biologist, has demonstrated exemplary mentoring of doctoral students. His mentorship has influenced thousands of undergraduates, graduates, and medical students who have gone on to enjoy productive careers in academia, industry and policy.” He continued, “Professor Weeks has served as Director of Graduate Studies for the Department of Biochemistry for over a decade. His devotion to each and every student collectively makes our graduate program a huge success.”

Professor Weeks will be recognized at the Graduate College Outstanding Mentor Award Recognition and Reception on May 4, 2016.

The Department’s 2015 publications are now in print and mostly available online.

E. Dale Abel

Jaishy B, Zhang Q, Chung HS, Riehle C, Soto J, Jenkins S, Abel P, Cowart LA, Van Eyk JE, Abel ED. (2015) Lipid-induced NOX2 activation inhibits autophagic flux by impairing lysosomal enzyme activity. J Lipid Res. 56(3):546-61. DOI: 10.1194/jlr.M055152. PMID: 25529920

Winkler EA, Nishida Y, Sagare AP, Rege SV, Bell RD, Perlmutter D, Sengillo JD, Hillman S, Kong P, Nelson AR, Sullivan JS, Zhao Z, Meiselman HJ, Wenby RB, Soto J, Abel ED, Makshanoff J, Zuniga E, De Vivo DC, Zlokovic BV. (2015) GLUT1 reductions exacerbate Alzheimer’s disease vasculo-neuronal dysfunction and degeneration. Nat Neurosci. 18(4):521-30. DOI: 10.1038/nn.3966. PMID: 25730668

Koentges C, König A, Pfeil K, Hölscher ME, Schnick T, Wende AR, Schrepper A, Cimolai MC, Kersting S, Hoffmann MM, Asal J, Osterholt M, Odening KE, Doenst T, Hein L, Abel ED, Bode C, Bugger H. (2015) Myocardial mitochondrial dysfunction in mice lacking adiponectin receptor 1. Basic Res Cardiol. 110(4):37. DOI: 10.1007/s00395-015-0495-4. PMID: 25982881

Ilkun O, Wilde N, Tuinei J, Pires KM, Zhu Y, Bugger H, Soto J, Wayment B, Olsen C, Litwin SE, Abel ED. (2015) Antioxidant treatment normalizes mitochondrial energetics and myocardial insulin sensitivity independently of changes in systemic metabolic homeostasis in a mouse model of the metabolic syndrome. J Mol Cell Cardiol. 85:104-16. DOI: 10.1016/j.yjmcc.2015.05.012. PMID: 26004364

Rasmussen TP, Wu Y, Joiner ML, Koval OM, Wilson NR, Luczak ED, Wang Q, Chen B, Gao Z, Zhu Z, Wagner BA, Soto J, McCormick ML, Kutschke W, Weiss RM, Yu L, Boudreau RL, Abel ED, Zhan F, Spitz DR, Buettner GR, Song LS, Zingman LV, Anderson ME. (2015) Inhibition of MCU forces extramitochondrial adaptations governing physiological and pathological stress responses in heart. Proc Natl Acad Sci USA. 112(29):9129-34. DOI: 10.1073/pnas.1504705112. PMID: 26153425

Liao X, Zhang R, Lu Y, Prosdocimo DA, Sangwung P, Zhang L, Zhou G, Anand P, Lai L, Leone TC, Fujioka H, Ye F, Rosca MG, Hoppel CL, Schulze PC, Abel ED, Stamler JS, Kelly DP, Jain MK. (2015) Kruppel-like factor 4 is critical for transcriptional control of cardiac mitochondrial homeostasis. J Clin Invest. 125(9):3461-76. DOI: 10.1172/JCI79964. PMID: 26241060

Bharath LP, Ruan T, Li Y, Ravindran A, Wan X, Nhan JK, Walker ML, Deeter L, Goodrich R, Johnson E, Munday D, Mueller R, Kunz D, Jones D, Reese V, Summers SA, Babu PV, Holland WL, Zhang QJ, Abel ED, Symons JD. (2015) Ceramide-Initiated Protein Phosphatase 2A Activation Contributes to Arterial Dysfunction In Vivo. Diabetes. 64(11):3914-26. DOI: 10.2337/db15-0244. PMID: 26253611

Ho PC, Bihuniak JD, Macintyre AN, Staron M, Liu X, Amezquita R, Tsui YC, Cui G, Micevic G, Perales JC, Kleinstein SH, Abel ED, Insogna KL, Feske S, Locasale JW, Bosenberg MW, Rathmell JC, Kaech SM. (2015) Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses. Cell. 162(6):1217-28. DOI: 10.1016/j.cell.2015.08.012. PMID: 26321681

Ock S, Lee WS, Ahn J, Kim HM, Kang H, Kim HS, Jo D, Abel ED, Lee TJ, Kim J. (2015) Deletion of IGF-1 Receptors in Cardiomyocytes Attenuates Cardiac Aging in Male Mice. Endocrinology. 157(1):336-45. DOI: 10.1210/en.2015-1709. PMID: 26469138

Ni R, Zheng D, Xiong S, Hill DJ, Sun T, Gardiner RB, Fan GC, Lu Y, Abel ED, Greer PA, Peng T. (2015) Mitochondrial Calpain-1 Disrupts ATP Synthase and Induces Superoxide Generation in Type 1 Diabetic Hearts: A Novel Mechanism Contributing to Diabetic Cardiomyopathy. Diabetes. 65(1):255-68. DOI: 10.2337/db15-0963. PMID: 26470784

Noh J, Wende AR, Olsen CD, Kim B, Bevins J, Zhu Y, Zhang QJ, Riehle C, Abel ED.( 2015) Phosphoinositide dependent protein kinase 1 is required for exercise-induced cardiac hypertrophy but not the associated mitochondrial adaptations. J Mol Cell Cardiol. 89(Pt B):297-305. DOI: 10.1016/j.yjmcc.2015.10.015. PMID: 26476238

Sheila A. Baker

Pan Y, Laird JG, Yamaguchi DM, Baker SA. (2015) An N-Terminal ER Export Signal Facilitates the Plasma Membrane Targeting of HCN1 Channels in Photoreceptors. Invest Ophthalmol Vis Sci. 56(6):3514-21. DOI: 10.1167/iovs.15-16902. PMID: 26030105

Laird JG, Pan Y, Modestou M, Yamaguchi DM, Song H, Sokolov M, Baker SA. (2015) Identification of a VxP Targeting Signal in the Flagellar Na(+) /K(+) -ATPase. Traffic. 16(12):1239-53. DOI: 10.1111/tra.12332. PMID: 26373354

Cao Y, Sarria I, Fehlhaber KE, Kamasawa N, Orlandi C, James KN, Hazen J, Gardner MR, Farzan M, Lee A, Baker SA, Baldwin K, Sampath AP, Martemyanov KA. (2015) Mechanism for selective synaptic wiring of rod photoreceptors into the retinal circuitry and its role in vision. Neuron. 87(6):1248-60. PMID: 26402607

Charles M. Brenner

Trammell SA, Brenner C. (2015) NNMT: A Bad Actor in Fat Makes Good in Liver. Cell Metab. 22(2):200-1. DOI: 10.1016/j.cmet.2015.07.017. PMID: 26244929

Mei SC, Brenner C. (2015) Calorie restriction-mediated replicative lifespan extension in yeast is non-cell autonomous. PLoS Biol. 13(1):e1002048. DOI: 10.1371/journal.pbio.1002048. PMID: 25633578

John M. Dagle

Waleh N, Barrette AM, Dagle JM, Momany A, Jin C, Hills NK, Shelton EL, Reese J, Clyman RI. (2015) Effects of Advancing Gestation and Non-Caucasian Race on Ductus Arteriosus Gene Expression. J Pediatr. 167(5):1033-1041.e2. DOI: 10.1016/j.jpeds.2015.07.011. PMID: 26265282

Sampath V, Helbling D, Menden H, Dimmock D, Mulrooney NP, Murray JC, Dagle JM, Garland JS. (2015) Necrotizing Enterocolitis is Not Associated with Sequence Variants in Anti-Oxidant Response Genes in Premature Infants.J Pediatr Gastroenterol Nutr. PMID: 26426434

Ryckman KK, Berberich SL, Dagle JM. (2015) Predicting gestational age by the use of neonatal metabolic markers. Am J Obstet Gynecol. pii: S0002-9378(15)02401-1. DOI: 10.1016/j.ajog.2015.11.028. PMID: 26645954

Kaluarachchi DC, Momany AM, Busch TD, Gimenez LG, Saleme C, Cosentino V, Christensen K, Dagle JM, Ryckman KK, Murray JC. (2015) Polymorphisms in NR5A2, gene encoding liver receptor homolog-1 are associated with preterm birth. Pediatr Res. DOI: 10.1038/pr.2016.7. PMID: 26761123

Brandon S. Davies

Beigneux AP, Fong LG, Bensadoun A, Davies BS, Oberer M, Gårdsvoll H, Ploug M, Young SG. (2015) GPIHBP1 missense mutations often cause multimerization of GPIHBP1 and thereby prevent lipoprotein lipase binding. Circ Res. 116(4):624-32. DOI: 10.1161/CIRCRESAHA.116.305085. PMID: 25387803

Chi X, Shetty SK, Shows HW, Hjelmaas AJ, Malcolm EK, Davies BS. (2015) Angiopoietin-like 4 Modifies the Interactions between Lipoprotein Lipase and Its Endothelial Cell Transporter GPIHBP1.J Biol Chem. 290(19):11865-77. DOI: 10.1074/jbc.M114.623769. PMID: 25809481

Kris A. DeMali

Jannie K, Ellerbroek SM, Zhou DW, Chen S, Crompton DJ, Garcia AJ, DeMali KA (2015) Vinculin-dependent actin bundling regulates cell migration and traction forces. Biochem. J. 465 (3) 383-393. DOI: 10.1042/BJ20140872. PMID: 25358683

Adrian H. Elcock

Li S, Elcock AH. (2015) Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins. J Phys Chem Lett. 6(11):2127-33. DOI: 10.1021/acs.jpclett.5b00654. PMID: 26266514

Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL. (2015) Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore. ACS Nano. 9(9):9050-61. DOI: 10.1021/acsnano.5b03053. PMID: 26302243

Brown RF, Andrews CT, Elcock AH. (2015) Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment. J Chem Theory Comput. 11(5):2315-28. DOI: 10.1021/ct501170h.PMID:26574427

Frembgen-Kesner T, Andrews CT, Li S, Ngo NA, Shubert SA, Jain A, Olayiwola OJ, Weishaar MR, Elcock AH. (2015) Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. J Chem Theory Comput. 11(5):2341-54. DOI: 10.1021/acs.jctc.5b00038. PMID: 26574429

Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA, Campbell BA, Brown RF, Guo C, Schrodt M, Liu YT, Elcock AH. (2015) Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. J Chem Theory Comput. 11(3):1315-29. DOI: 10.1021/ct5010966. PMID: 26579777

Schrodt MV, Andrews CT, Elcock AH. (2015) Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput. 11(12):5906-17. DOI: 10.1021/acs.jctc.5b00899. PMID: 26580891

Lokesh Gakhar

Yadav RP, Majumder A, Gakhar L, Artemyev NO. (2015) Extended conformation of the proline-rich domain of human aryl hydrocarbon receptor-interacting protein-like 1: implications for retina disease. J Neurochem. 135(1):165-75. DOI: 10.1111/jnc.13223. PMID: 26139345

Wert KJ, Bassuk AG, Wu WH, Gakhar L, Coglan D, Mahajan M, Wu S, Yang J, Lin CS, Tsang SH, Mahajan VB. (2015) CAPN5 mutation in hereditary uveitis: the R243L mutation increases calpain catalytic activity and triggers intraocular inflammation in a mouse model. Hum Mol Genet. 24(16):4584-98. DOI: 10.1093/hmg/ddv189. PMID: 25994508

Bassuk AG, Yeh S, Wu S, Martin DF, Tsang SH, Gakhar L, Mahajan VB. (2015) Structural modeling of a novel CAPN5 mutation that causes uveitis and neovascular retinal detachment. PLoS One. 10(4):e0122352. DOI: 10.1371/journal.pone.0122352. PMID: 25856303

Feldkamp MD, Gakhar L, Pandey N, Shea MA. (2015) Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. Proteins. 83(5):989-96. DOI: 10.1002/prot.24781. PMID: 25694384

Cho C, Chande A, Gakhar L, Bakaletz LO, Jurcisek JA, Ketterer M, Shao J, Gotoh K, Foster E, Hunt J, O’Brien E, Apicella MA. (2015) Role of the nuclease of nontypeable Haemophilus influenzae in dispersal of organisms from biofilms. Infect Immun. 83(3):950-7. DOI: 10.1128/IAI.02601-14. PMID: 25547799

Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. (2015) 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, Soshnev AA, Geyer PK. (2015) Networking in the nucleus: a spotlight on LEM-domain proteins. Curr Opin Cell Biol. 34:1-8. DOI: 10.1016/j.ceb.2015.03.005.PMID: 25863918

Catherine A. Musselman

Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG. (2015) Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1. Structure. 23(2):312-21. DOI: 10.1016/j.str.2014.11.013. PMID: 25579814

Andrew W. Norris

Uc A, Olivier AK, Griffin MA, Meyerholz DK, Yao J, Abu-El-Haija M, Buchanan KM, Vanegas Calderón OG, Abu-El-Haija M, Pezzulo AA, Reznikov LR, Hoegger MJ, Rector MV, Ostedgaard LS, Taft PJ, Gansemer ND, Ludwig PS, Hornick EE, Stoltz DA, Ode KL, Welsh MJ, Engelhardt JF, Norris AW. (2015) Glycaemic regulation and insulin secretion are abnormal in cystic fibrosis pigs despite sparing of islet cell mass. Clin Sci (Lond). 128(2):131-42. DOI: 10.1042/CS20140059. PMID: 25142104

Morgan DA, McDaniel LN, Yin T, Khan M, Jiang J, Acevedo MR, Walsh SA, Ponto LL, Norris AW, Lutter M, Rahmouni K, Cui H. (2015) Regulation of glucose tolerance and sympathetic activity by MC4R signaling in the lateral hypothalamus. Diabetes. 64(6):1976-87. DOI: 10.2337/db14-1257. PMID: 25605803

Gordon EE, Reinking BE, Hu S, Yao J, Kua KL, Younes AK, Wang C, Segar JL, Norris AW. (2015) Maternal Hyperglycemia Directly and Rapidly Induces Cardiac Septal Overgrowth in Fetal Rats. J Diabetes Res. 2015:479565. DOI: 10.1155/2015/479565. PMID: 26064981

Gray LR, Sultana MR, Rauckhorst AJ, Oonthonpan L, Tompkins SC, Sharma A, Fu X, Miao R, Pewa AD, Brown KS, Lane EE, Dohlman A, Zepeda-Orozco D, Xie J, Rutter J, Norris AW, Cox JE, Burgess SC, Potthoff MJ, Taylor EB. (2015) Hepatic Mitochondrial Pyruvate Carrier 1 Is Required for Efficient Regulation of Gluconeogenesis and Whole-Body Glucose Homeostasis. Cell Metab. 22(4):669-81. DOI: 10.1016/j.cmet.2015.07.027. PMID: 26344103

Sawatzke AB, Norris AW, Spyropoulos F, Walsh SA, Acevedo MR, Hu S, Yao J, Wang C, Sunderland JJ, Boles Ponto LL. (2015) PET/CT imaging reveals unrivaled placental avidity for glucose compared to other tissues. Placenta. 36(2):115-20. DOI: 10.1016/j.placenta.2014.12.009. PMID: 25555498

Bryce V. Plapp

Plapp BV, Leidal KG, Murch BP, Green DW. (2015) Contribution of liver alcohol dehydrogenase to metabolism of alcohols in rats. Chem Biol Interact. 234:85-95. DOI: 10.1016/j.cbi.2014.12.040. PMID: 25641189

David H. Price

Nilson KA, Guo J, Turek ME, Brogie JE, Delaney E, Luse DS, Price DH. (2015) THZ1 Reveals Roles for Cdk7 in Co-transcriptional Capping and Pausing. Mol Cell. 59(4):576-87. DOI: 10.1016/j.molcel.2015.06.032. PMID: 26257281

Miles A. Pufall

Fontana MF, Baccarella A, Pancholi N, Pufall MA, Herbert DR, Kim CC. (2015) JUNB is a key transcriptional modulator of macrophage activation. J Immunol. 194(1):177-86.DOI: 10.4049/jimmunol.1401595. PMID: 25472994

Sasse SK, Zuo Z, Kadiyala V, Zhang L, Pufall MA, Jain MK, Phang TL, Stormo GD, Gerber AN. (2015) Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem. 290(32):19756-69. DOI: 10.1074/jbc.M115.668558. PMID: 26088140

Pufall MA. (2015) Glucocorticoids and Cancer. Adv Exp Med Biol. 872:315-33. DOI: 10.1007/978-1-4939-2895-8_14. PMID: 26216001

Peter A. Rubenstein

Rubenstein PA, Wen KK. (2015) Mutant vascular actin is a TAAD misbehaving. Proc Natl Acad Sci USA. 112(31):9500-1. DOI: 10.1073/pnas.1512086112. PMID: 26204915

Michael J. Schnieders

Bu F, Borsa NG, Jones MB, Takanami E, Nishimura C, Hauer JJ, Azaiez H, Black-Ziegelbein EA, Meyer NC, Kolbe DL, Li Y, Frees K, Schnieders MJ, Thomas C, Nester C, Smith RJ. 92015) High-Throughput Genetic Testing for Thrombotic Microangiopathies and C3 Glomerulopathies. J Am Soc Nephrol. pii: ASN.2015040385. PMID:26283675

LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WT, Fenn TD, Washington MT, Schnieders MJ. (2015) Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophys J. 109(4):816-26. DOI: 10.1016/j.bpj.2015.06.062. PMID: 26287633

Booth KT, Azaiez H, Kahrizi K, Simpson AC, Tollefson WT, Sloan CM, Meyer NC, Babanejad M, Ardalani F, Arzhangi S, Schnieders MJ, Najmabadi H, Smith RJ. (2015) PDZD7 and hearing loss: More than just a modifier. Am J Med Genet A. 167(12):2957-65. DOI: 10.1002/ajmg.a.37274. PMID: 26416264

DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, Schnieders MJ, Lentz SR, Tucker BA, Mullins RF, Scheetz TE, Stone EM, Slusarski DC. (2015) Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Hum Mol Genet. 25(1):44-56. DOI: 10.1093/hmg/ddv446. PMID: 26494905

Lagardère L, Lipparini F, Stamm B, Schnieders MJ, Cances E, Ren P, Maday Y, Piquemal J. (2015) Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Towards Massively Parallel Computations Using Smooth Particle Mesh Ewald. Journal of Chemical Theory and Computation. 11(6):2589–2599.

Debra A. Schwinn

Levine AS, Alpern RJ, Andrews NC, Antman K, Balser JR, Berg JM, Davis PB, Fitz JG, Golden RN, Goldman L, Jameson JL, Lee VS, Polonsky KS, Rappley MD, Reece EA, Rothman PB, Schwinn DA, Shapiro LJ, Spiegel AM. (2015) Research in academic medical centers: two threats to sustainable support. Sci Transl Med. 7(289):289fs22. DOI: 10.1126/scitranslmed.aac5200. PMID: 26019216

Morris DP, Lei B, Longo LD, Bomsztyk K, Schwinn DA, Michelotti GA. (2015) Temporal Dissection of Rate Limiting Transcriptional Events Using Pol II ChIP and RNA Analysis of Adrenergic Stress Gene Activation. PLoS One. 10(8):e0134442. DOI: 10.1371/journal.pone.0134442. PMID: 26244980

Gradinaru I, Babaeva E, Schwinn DA, Oganesian A. (2015) Alpha1a-Adrenoceptor Genetic Variant Triggers Vascular Smooth Muscle Cell Hyperproliferation and Agonist Induced Hypertrophy via EGFR Transactivation Pathway. PLoS One. 10(11):e0142787. DOI: 10.1371/journal.pone.0142787. PMID: 26571308

Madeline A. Shea

Feldkamp MD, Gakhar L, Pandey N, Shea MA. (2015) Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. Proteins. 83(5):989-96. DOI: 10.1002/prot.24781. PMID: 25694384

M. Ashley Spies

Dean SF, Whalen KL, Spies MA. (2015) Biosynthesis of a Novel Glutamate Racemase Containing a Site-Specific 7-Hydroxycoumarin Amino Acid: Enzyme-Ligand Promiscuity Revealed at the Atomistic Level. ACS Cent Sci. 1(7):364-373. PMID: 26539562

Marsden AE, King JM, Spies MA, Kim OK, Yahr TL. (2015) Inhibition of Pseudomonas aeruginosa ExsA DNA-Binding Activity by N-Hydroxybenzimidazoles. Antimicrob Agents Chemother. 60(2):766-76. DOI: 10.1128/AAC.02242-15. PMID: 26574012

Maria Spies

Spies M, Fishel R. (2015) Mismatch repair during homologous and homeologous recombination. Cold Spring Harb Perspect Biol. 7(3):a022657. DOI: 10.1101/cshperspect.a022657. PMID: 25731766

Earle Stellwagen

Stellwagen E, Dong Q, Stellwagen NC. (2015) Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts. Biophys J. 108(9):2291-9. DOI: 10.1016/j.bpj.2015.01.044. PMID: 25954886

Stellwagen E, Stellwagen NC. (2015) Electrostatic coupling between DNA and its counterions modulates the observed translational diffusion coefficients. Anal Chem. 87(17):9042-6. DOI: 10.1021/acs.analchem.5b02230. PMID: 26218420

Nancy C. Stellwagen

Stellwagen E, Dong Q, Stellwagen NC. (2015) Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts. Biophys J. 108(9):2291-9. DOI: 10.1016/j.bpj.2015.01.044. PMID: 25954886

Stellwagen E, Stellwagen NC. (2015) Electrostatic coupling between DNA and its counterions modulates the observed translational diffusion coefficients. Anal Chem. 87(17):9042-6. DOI: 10.1021/acs.analchem.5b02230. PMID: 26218420

Eric B. Taylor

Gray LR, Sultana MR, Rauckhorst AJ, Oonthonpan L, Tompkins SC, Sharma A, Fu X, Miao R, Pewa AD, Brown KS, Lane EE, Dohlman A, Zepeda-Orozco D, Xie J, Rutter J, Norris AW, Cox JE, Burgess SC, Potthoff MJ, Taylor EB. (2015) Hepatic Mitochondrial Pyruvate Carrier 1 Is Required for Efficient Regulation of Gluconeogenesis and Whole-Body Glucose Homeostasis. Cell Metab. 22(4):669-81. DOI: 10.1016/j.cmet.2015.07.027. PMID: 26344103

Lori L. Wallrath

Bohnekamp J, Cryderman DE, Paululat A, Baccam GC, Wallrath LL, Magin TM. (2015) A Drosophila Model of Epidermolysis Bullosa Simplex. J Invest Dermatol. 135(8):2031-9. DOI: 10.1038/jid.2015.129. PMID: 25830653

Dialynas G, Shrestha OK, Ponce JM, Zwerger M, Thiemann DA, Young GH, Moore SA, Yu L, Lammerding J, Wallrath LL. (2015) Myopathic lamin mutations cause reductive stress and activate the nrf2/keap-1 pathway. PLoS Genet. 11(5):e1005231. DOI: 10.1371/journal.pgen.1005231. PMID: 25996830

Bohnekamp J, Cryderman DE, Thiemann DA, Magin TM, Wallrath LL. (2015) Using Drosophila for Studies of Intermediate Filaments. Methods Enzymol. 568:707-26. DOI: 10.1016/bs.mie.2015.08.028. PMID: 26795490

M. Todd Washington

Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. (2015) Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response. Structure. 23(4):724-33. DOI: 10.1016/j.str.2015.02.008. PMID: 25773143

LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WT, Fenn TD, Washington MT, Schnieders MJ. (2015) Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophys J. 109(4):816-26. DOI: 10.1016/j.bpj.2015.06.062. PMID: 26287633

Ronald J. Weigel

Borcherding N, Kusner D, Kolb R, Xie Q, Li W, Yuan F, Velez G, Askeland R, Weigel RJ, Zhang W. (2015) Paracrine WNT5A Signaling Inhibits Expansion of Tumor-Initiating Cells. Cancer Res. 75(10):1972-82. DOI: 10.1158/0008-5472.CAN-14-2761. PMID: 25769722

Lizarraga I, Schroeder MC, Weigel RJ, Thomas A. (2015) Surgical Management of Breast Cancer in 2010-2011 SEER Registries by Hormone and HER2 Receptor Status. Ann Surg Oncol. 22 Suppl 3:566-72. DOI: 10.1245/s10434-015-4591-3. PMID: 25956579

Spanheimer PM, Lorenzen AW, De Andrade JP, Kulak MV, Carr JC, Woodfield GW, Sugg SL, Weigel RJ. (2015) Receptor Tyrosine Kinase Expression Predicts Response to Sunitinib in Breast Cancer. Ann Surg Oncol. 22(13):4287-94. DOI: 10.1245/s10434-015-4597-x. PMID: 25971960

Weigel RJ. (2015) 2015 Presidential Address–Society of Surgical Oncology: The Next 75 Years. Ann Surg Oncol. 22(8):2455-61. DOI: 10.1245/s10434-015-4638-5. PMID: 26033181

Weigel RJ, Upchurch GR Jr, Eberlein TJ, Lucas CE. (2015) Presidential Forum Discussion: Development of Surgical Scientists. Ann Surg. 262(4):555-62. DOI: 10.1097/SLA.0000000000001400. PMID: 26366534

Lizarraga IM, Weigel RJ. (2015) Axillary lymph node dissection for breast cancer: Primum non nocere. Eur J Surg Oncol. 41(8):955-7. DOI: 10.1016/j.ejso.2015.05.006. PMID: 26071786

Meng Wu

Schreiber SL, Kotz JD, Li M, Aubé J, Austin CP, Reed JC, Rosen H, White EL, Sklar LA, Lindsley CW, Alexander BR, Bittker JA, Clemons PA, de Souza A, Foley MA, Palmer M, Shamji AF, Wawer MJ, McManus O, Wu M, Zou B, Yu H, Golden JE, Schoenen FJ, Simeonov A, Jadhav A, Jackson MR, Pinkerton AB, Chung TD, Griffin PR, Cravatt BF, Hodder PS, Roush WR, Roberts E, Chung DH, Jonsson CB, Noah JW, Severson WE, Ananthan S, Edwards B, Oprea TI, Conn PJ, Hopkins CR, Wood MR, Stauffer SR, Emmitte KA; NIH Molecular Libraries Project Team. (2015) Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes. Cell. 161(6):1252-65. DOI: 10.1016/j.cell.2015.05.023. PMID: 26046436

Wongrakpanich A, Wu M, Salem AK. (2015) Correlating intracellular nonviral polyplex localization with transfection efficiency using high-content screening. Biotechnol Prog. 31(6):1685-92. DOI: 10.1002/btpr.2146. PMID: 26193826

Wu M, Li M. (2015) Resonant waveguide grating for monitoring biomolecular interactions. Methods Mol Biol. 1278:139-52. DOI: 10.1007/978-1-4939-2425-7_8. PMID: 25859947

Zhu Y, Lu Y, Qu C, Miller M, Tian J, Thakur DP, Zhu J, Deng Z, Hu X, Wu M, McManus OB, Li M, Hong X, Zhu MX, Luo HR. (2015) Identification and optimization of 2-aminobenzimidazole derivatives as novel inhibitors of TRPC4 and TRPC5 channels. Br J Pharmacol. 172(14):3495-509. DOI: 10.1111/bph.13140. PMID: 25816897

Li J, Crowley ST, Duskey J, Khargharia S, Wu M, Rice KG. (2015) Miniaturization of gene transfection assays in 384- and 1536-well microplates. Anal Biochem. 470:14-21. DOI: 10.1016/j.ab.2014.10.001. PMID: 25448623

Ennis EA, Wright J, Retzlaff CL, McManus OB, Lin Z, Huang X, Wu M, Li M, Daniels JS, Lindsley CW, Hopkins CR, Blakely RD. (2015) Identification and characterization of ML352: a novel, noncompetitive inhibitor of the presynaptic choline transporter. ACS Chem Neurosci. 6(3):417-27. DOI: 10.1021/cn5001809. PMID: 25560927

Wen W, Wang Y, Li Z, Tseng PY, McManus OB, Wu M, Li M, Lindsley CW, Dong X, Hopkins CR. (2015) 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

Liping Yu

Yu L, Fink BD, Sivitz WI. (2015) Simultaneous quantification of mitochondrial ATP and ROS production. Methods Mol Biol. 1264:149-59. DOI: 10.1007/978-1-4939-2257-4_14. PMID: 25631011

Dialynas G, Shrestha OK, Ponce JM, Zwerger M, Thiemann DA, Young GH, Moore SA, Yu L, Lammerding J, Wallrath LL. (2015) Myopathic lamin mutations cause reductive stress and activate the nrf2/keap-1 pathway. PLoS Genet. 11(5):e1005231.DOI: 10.1371/journal.pgen.1005231. PMID: 25996830

Rasmussen TP, Wu Y, Joiner ML, Koval OM, Wilson NR, Luczak ED, Wang Q, Chen B, Gao Z, Zhu Z, Wagner BA, Soto J, McCormick ML, Kutschke W, Weiss RM, Yu L, Boudreau RL, Abel ED, Zhan F, Spitz DR, Buettner GR, Song LS, Zingman LV, Anderson ME. (2015) Inhibition of MCU forces extramitochondrial adaptations governing physiological and pathological stress responses in heart. Proc Natl Acad Sci USA. 112(29):9129-34. DOI: 10.1073/pnas.1504705112. PMID: 26153425

 

Professor Dan Weeks has been chosen by the Council on Teaching as one of this year’s recipients of the President and Provost Award for Teaching Excellence. For the past 28 years Professor Weeks, an internationally known nucleic acid biochemist and developmental biologist, has demonstrated sustained contributions to teaching at the University of Iowa. His teaching has influenced thousands of undergraduates, graduates, and medical students who have gone on to enjoy productive careers in academia, industry and policy.

Professor Weeks will be honored at the 2016 University Faculty and Staff Awards Banquet this fall.

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

The FUTURE in Biomedicine program, founded in 2009 by Madeline Shea, is developing a statewide network of scientist-educators and a pipeline of prospective students for our graduate and clinical program. The 7th annual program brought 25 faculty Fellows and students from primarily undergraduate institutions in Iowa to conduct research and pursue collaborations with UI faculty through summer laboratory work and weekly professional development activities. The Fellows also received support to use our state-of-the-art research core facilities such as those in genomics, crystallography and NMR.

Of the 13 Faculty Fellows, four worked with host professors in Biochemistry. Dr. Gary Coombs from Waldorf College worked on the role of lamins in regulating muscle function and metabolism with Professor Lori Wallrath. Dr. Heriberto Hernandez from Grinnell College worked on the role of thermodynamics in the formulation of pharmaceuticals with Assistant Professor Mike Schnieders. Dr. Hernandez was supported by the Ruth Ann Henriksen Fellowship that honors Dr. Henriksen, a Ph.D. graduate of our department who pursued her academic career at East Carolina University. Two Fellows from Drake University – Adina Kilpatrick in Physics and Jerry Honts in Biology – pursued a joint collaboration on Tetrahymena calcium-binding proteins with Professor Madeline Shea.

Two additional Faculty Fellows are Biochemistry Alumni – Dr. Ugur Akgun, now on the Physics faculty at Coe College had been a postdoctoral fellow with Shahram Khademi, and Dr. Heidi Sleister in Biology at Drake University was a former BSURF student.

In addition, Ms. Dulce Chavez from St. Mary-of-the-Woods was the first recipient of the Gioannini Summer Undergraduate Research Fellowship honoring our former colleague Dr. Theresa L. Gioannini, who held a joint appointment in Biochemistry. Mr. Adam Page, of Kirkwood Community College, conducted research with Professor E. Dale Abel, a joint appointee in Biochemistry, and Adam’s participation in the activities of the FUTURE in Biomedicine program were arranged by Ms. Juanita Limas, the faculty Director of the LSAMP program at Kirkwood who earned her B.S. in Biochemistry doing research with Professor Lori Wallrath.

Members of the Department of Biochemistry featured prominently in the weekly activities of the FUTURE in Biomedicine program. These included a session when Professor Dan Weeks described preparation for our Ph.D. programs, a workshop on “3-D Printing in Research and Education” presented jointly by UI Biochemistry Assistant Professor Miles Pufall and Jerry Honts of Drake University, and a Career Panel on making the transition from postdoctoral fellow to teaching faculty, including two Biochemistry postdocs – Dr. Lynne Dieckman formerly in the Musselman laboratory and Dr. Casey Andrews in the Elcock laboratory. In the prior academic year, Dr. Andrews had a mentored semester-long teaching experience at Loras College with 2014 FUTURE Fellow Adam Moser.

The research being conducted in partnerships developed through the FUTURE in Biomedicine program is being published in peer-reviewed journals, and presented at national conferences. This reciprocal network is encouraging excellent candidates to apply to our training opportunities and openings for research assistants and postbac internships. The FUTURE program is committed to advancing closer ties with our alumni in the years ahead.