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Archive for the ‘Kris DeMali’ Category

The Biochemistry Department has a farewell celebration for Dr. Brenner and the Brenner Lab

Tuesday, July 21st, 2020

Brenner Lab

On July 20, 2020 the Biochemistry Department held a farewell celebration for Dr. Charles Brenner and the Brenner Lab. Join us in wishing our colleagues well on their next opportunities and all their future endeavors.

Dr. Charles Brenner, Chair and DEO of Biochemistry for 11 years, will serve as the inaugural Alfred E Mann Chair of the new Department of Diabetes & Cancer Metabolism within the Beckman Research Institute of the City of Hope National Medical Center in Duarte, California. He will begin August 17th.

Noah Fluharty, Research Intern in the Brenner Lab, will be joining Dr. Brenner’s lab at the City of Hope National Medical Center as lab manager.

Sara B. Mitchell, Research Assistant in the Brenner Lab, will join the Neuroscience PhD program here at the University of Iowa in the Fall.

Mark Schmidt, Research Associate in the Brenner Lab, will be retiring after 17 years of service to the University of Iowa (6 years with Biochemistry). He set the world record on quantitative NAD metabolomes.

Collin Heer, visiting scientist in the Brenner Lab, will complete his PhD in Free Radical and Radiation Biology with Dr. Douglas Spitz. After graduation, Collin will join Dr. Ranjit S. Bindra’s lab at Yale University as a postdoc.

Dr. Tsuyoshi Hattori is finishing his sabbatical here at the University of Iowa and will return to Kanazawa University in Kanazawa, Japan.

Congratulate and support Dr. Kris DeMali, who will serve as interim head on Biochemistry, effective August 14.

Samantha Mackin and Ian McElree awarded Montgomery Scholar’s Prizes

Thursday, May 2nd, 2019

Samantha Makin, an undergraduate major in the Dr. Kris DeMali’s laboratory,  and Ian McElree, an undergraduate in Dr. Chun-Fang Wu’s laboratory in the Department of Biology, have been awarded 2019 Montgomery Biochemistry Scholar’s Prizes for their outstanding research accomplishments and excellent presentations at the Lata Symposium.

This prize was established by mentees, colleagues and friends of Dr. Rex Montgomery, Professor Emeritus of the Department of Biochemistry. Dr. Montgomery began his career at the University of Iowa in 1955, and is admired for his impact as a researcher, teacher and mentor. Dr. Montgomery is an internationally recognized carbohydrate biochemist and textbook author. While on the faculty, he served as Associate Dean for Academic Affairs in the College of Medicine, the Vice President of Research for the University and was the founding director of the University of Iowa Physician Assistant Program. Dr. Montgomery retired in 2005 after more than 50 years on the faculty.


15th Annual Gene F. Lata Undergraduate Research Symposium

Wednesday, April 24th, 2019

Eleven students presented at this year’s Undergraduate Honors Program.  This year marks the fifteenth year for the Gene F. Lata Undergraduate Research Symposium. Please join Professor Marc Wold, Director of Undergraduate Studies and Honors Advisor, in congratulating these 2019 graduates and their research mentors for a job well done.

(front row – left to right): Ariel Kopel, Samantha Mackin, Ashley Segura-Roman, Irini Petros (back row – left to right): Samuel Cole Kitzman, Derek Metzger, Andrew Henry, Lucas Maakestad, Sophia Vogeler

(left) Ian McElree, (right) Jesse Cochran










Jesse Cochran
Mentor: E. Dale Abel
Sex Differences in the Response of C57BL/6 Mice to Ketogenic Diets

Andrew Henry
Mentor: Andrew Norris
Influence of CFTR on Linoleic Acid Metabolism

Samuel (Cole) Kitzman
Mentor: Pamela Geyer
Modeling a premature aging syndrome by a mutant form of Barrier-to-Autointegration Factor (BAF) in Drosophila

Ariel Kopel
Mentor: Sheila Baker
The Role of Synaptic Calcium Channels in Cone Photoreceptors

Lucas Maakestad
Mentor: Todd Washington
Overexpression and Purification of the Fork-Remodeling Enzyme Rad5

Samantha Mackin
Mentor: Kris DeMali
Identifying Mechanisms Coupling Cell Metabolism to Force Transmission

Ian McElree
Mentor: Chun-Fang Wu
Exploration of the rosA Oscillatory ERG Phenotype in Drosophila

Derek Metzger
Mentor: Brandon Davies
Functional Analysis of Human ANGPTL3 Mutants

Irini Petros
Mentor: Dan Weeks
Protein Aggregates in Different Subnucleolar Compartments in Xenopus laevis

Ashley Segura-Roman
Mentor: Brandon Davies
Endothelial Lipase Regulation by ANGPTL3

Sophia Vogeler
Mentor: Charles Brenner
Evaluating the Efficacy of NAD Precursors in Treating Hyperphagia

The symposium also included the presentation of two undergraduate awards (see pictures below), made possible by a gift from Alap Subramanian. The H.G. Wittmann Scholar Award was presented to Derek Metzger (Davies lab) and the H.G. Khorana Scholar Award was presented to Sophia Vogeler (Brenner lab), recognizing their exceptional understanding of biochemistry and its value to society.


Congratulations to everyone named above and all of our 2019 graduates!







Hannah Campbell awarded the People’s Choice Award for Three Minute Thesis challenge

Monday, November 5th, 2018

Hannah Campbell, a graduate student in the DeMali Laboratory, was selected as one of nine finalist for the The University of Iowa’s fifth Three Minute Thesis competition, which challenges graduate students to clearly and concisely articulate complex research to non-specialist audiences.  Hannah was awarded the People’s Choice Award, selected by audience ballot, for her presentation entitled, “Cells that work together, stay together.” Congratulations, Hannah!

Jennifer Bays awarded the 2018 Subramanian Thesis and 2018 Clarence Berg Awards

Wednesday, September 5th, 2018

Dr. Jennifer Bays, a 2017 PhD with Dr. Kris DeMali, has been named the winner of the 2018 Subramanian Award for best PhD thesis in the Department of Biochemistry.  Dr. Bays’ thesis was entitled “Mechanisms of E-cadherin Mechanotransduction.” Jennifer is the 23nd winner of the Subramanian Award, which is made possible by a gift from Dr. Alap Subramanian, a 1964 PhD from the department, who parlayed his training with the late George Kalnitsky, (and with Irving Klotz at Northwestern and both Bernard Davis and Herman Kalckar at Harvard Medical School), into a highly successful career at the Max-Planck-Institut.

Jennifer was also named the winner of the 2018 Clarence Berg Award. The Berg Award is given biennially in honor of our former Professor Clarence P. Berg to the graduate student who demonstrates “scholarship, integrity, cooperativeness, consideration and a willingness to help others.” Clarence P. Berg, an internationally known amino acid biochemist who was a member of the department for 36 years (1932-1968). Dr. Berg is well known as the author of the 1980 book, “The University of Iowa and Biochemistry from their Beginnings.”

Jennifer is currently a postdoctoral fellow in Dr. Christopher Chen’s laboratory at Boston University. Congratulations, Dr. Bays!

Highlights of the 9th Annual Biochemistry Retreat and 70th Anniversary

Wednesday, August 29th, 2018

Over 115 faculty, graduate students, postdoctoral fellows, research staff members, undergraduates, and alumni attended the Department of Biochemistry’s 9th Annual Retreat and 70th Anniversary Celebration on Saturday, August 25, 2018, at the newly rebuilt  Hancher Auditorium.

Invited oral presentations included:

Junmin Peng, PhD., Professor, Departments of Structural Biology and Developmental Neurobiology, and Director of Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital
Title: Omics-based systems biology of human disease
Dr. Peng was a former graduate student in Dr. David Price’s lab, obtaining a PhD in Biochemistry in 1999.

Lois Weisman, PhD, Professor of Cell and Developmental Biology, Life Sciences Institute, University of Michigan
Title: From yeast to humans: Insights into myosin V based transport and phosphoinositide signaling
Dr. Weisman joined the University of Iowa, Department of Biochemistry in 1993.  In 2005, Dr. Weisman moved to her current position at the University of Michigan.

James Kranz, PhD, Director, Drug Product Development, Kiniksa Pharmaceuticals
Title: Biochemistry essentials and biopharmaceutical development: Everything I need to know I first learned from Dryer & Lata “Experimental Biochemistry”
Dr. Kranz received a B.S. in Biochemistry with Honors from the University of Iowa under the mentorship of Dr. Madeline Shea.

This event also included a panel discussion with current and former Department Heads:

Charles Brenner, PhD (2009 – present)
Arthur Spector, MD (1996 – 1998)
Alan Goodridge, PhD (1987 – 1996)

The retreat featured 39 poster presentations.  Winners of the poster presentations were (left to right below):

1st place:  Hannah Campbell (DeMali Lab), Force-induced apoptosis and the mechanoprotective role of PAK2
2nd place: Alicia Ortiz (DeMali Lab), Investigating Metabolic Changes in Response to Force on E-cadherin
3rd place:  Christopher Ball (Price Lab), Human Cytomegalovirus IE2 Differentially Modulates Transcription of Select Viral Transcription Units during Late Infection
4th place:  Kelli Sylvers (Davies Lab), Characterizing the interactions between ANGPTL3, ANGPLT8, and endothelial lipase

Hannah Campbell Recieves AHA Predoctoral Fellowship

Wednesday, July 25th, 2018

Hannah Campbell, Biochemistry graduate student in Dr. Kris DeMali’s lab, has received an American Heart Association Predoctoral Fellowship. Hannah’s proposal entitled, “Force-induced apoptosis and the mechanoprotective role of PAK2” will be funded at the maximum amount for two full years. Hannah’s project is described below.

“All cells experience forces throughout their lifetimes. These forces are sensed by cell surface adhesion receptors and trigger robust actin cytoskeletal rearrangements and growth of the associated adhesion complex to counter the applied forces. This process is known as cell stiffening and is generally thought to be beneficial to the overall health of the cell.  However there are also instances in hypertensive patients and other diseased settings when cells experience supraphysiological forces that initiate cell death.  The key determinants of whether cells survive or die in response to force are not well understood. Here, we show that application of force on E-cadherin activates p21-activated kinase 2 (PAK2). In addition, force recruits PAK2 to the cadherin containing adhesion complex. At this complex, we hypothesize PAK2 serves as a critical component of a signaling cascade culminating in increased contractility and cell stiffening.”

Congrats Hannah!

2017 Faculty Publications

Thursday, March 1st, 2018

The Department’s 2017 publications are now in print and mostly available online.

E. Dale Abel

Pereira RO, Tadinada SM, Zasadny FM, Oliveira KJ, Pires KM, Olvera A, Jeffers J, Souvenir R, Mcglauflin R, Seei A, Funari T, Sesaki H, Potthoff MJ, Adams CM, Anderson EJ, Abel ED. (2017) OPA1 deficiency promotes secretion of FGF21 from muscle that prevents obesity and insulin resistance. EMBO Journal. 36(14):2126-2145.

Rines AK, Chang HC, Wu R, Sato T, Khechaduri A, Kouzu H, Shapiro J, Shang M, Burke MA, Jiang X, Chen C, Rawlings TA, Lopaschuk GD, Schumacker PT, Abel ED, Ardehali H. (2017) Snf1-related kinase improves cardiac mitochondrial efficiency and decreases mitochondrial uncoupling. Nature communications. 8:14095.

Zhang Y, Xie L, Gunasekar SK, Tong D, Mishra A, Gibson WJ, Wang C, Fidler T, Marthaler B, Klingelhutz A, Abel ED, Samuel I, Smith JK, Cao L, Sah R. (2017) SWELL1 is a regulator of adipocyte size, insulin signalling and glucose homeostasis. Nature Cell Biology. 19(5):504-517.

Park SJ, Gavrilova O, Brown AL, Soto JE, Bremner S, Kim J, Xu X, Yang S, Um JH, Koch LG, Britton SL, Lieber RL, Philp A, Baar K, Kohama SG, Abel ED, Kim MK, Chung JH. (2017) DNA-PK Promotes the Mitochondrial, Metabolic, and Physical Decline that Occurs During Aging. Cell Metabolism. 25(5):1135-1146.e7.

Fidler TP, Middleton E, Rowley JW, Boudreau LH, Campbell RA, Souvenir R, Funari T, Tessandier N, Boilard E, Weyrich AS, Abel ED. (2017) Glucose Transporter 3 Potentiates Degranulation and Is Required for Platelet Activation, Arteriosclerosis, Thrombosis, and Vascular Biology. Arterioscler Thromb Vasc Biol. 37(9):1628-1639.

Fidler TP, Campbell RA, Funari T, Dunne N, Balderas Angeles E, Middleton EA, Chaudhuri D, Weyrch AS, Abel ED. (2017) Deletion of GLUT1 and GLUT3 Reveals Multiple Roles for Glucose Metabolism in Platelet and Megakaryocyte Function. Cell Reports. 20(4):881-894.

Wende AR, Kim J, Holland W, Wayment BE, O’Neill BT, Tuinei J, Brahma MK, Pepin ME, McCrory MA, Luptak I, Halade GV, Litwin SE, Abel ED. (2017) Glucose transporter 4 (GLUT4) deficient hearts develop maladaptive hypertrophy in response to physiologic or pathologic stresses., American journal of physiology. Heart and circulatory physiology.

Steinhorn B, Sartoretto JL, Sorrentino A, Romero N, Kalwa H, Abel ED, Michel T. (2017) Insulin-dependent metabolic and inotropic responses in the heart are modulated by hydrogen peroxide from NADPH-oxidase isoforms NOX2 and NOX4. Free radical biology & medicine. 113:16-25.

Tsushima K, Bugger H, Wende AR, Soto J, Jenson GA, Tor AR, McGlauflin R, Kenny HC, Zhang Y, Souvenir R, Hu XX, Black CL, Pereira RO, Lira VA, Spitzer K, Sharp TL, Shoghi KI, Sparagna GC, Rog-Zielinska EA, Kohl P, Khalimonchuk O, Schaffer JE, Abel ED. (2017) Mitochondrial Reactive Oxygen Species in Lipotoxic Hearts Induces Post-Translational Modifications of AKAP121, DRP1 and OPA1 That Promote Mitochondrial Fission. Circulation research.

Pires KM, Buffolo M, Schaaf C, David Symons J, Cox J, Abel ED, Selzman CH, Boudina S. (2018) Activation of IGF-1 receptors and Akt signaling by systemic hyperinsulinemia contributes to cardiac hypertrophy but does not regulate cardiac autophagy in obese diabetic mice. Journal of molecular and cellular cardiology. 113:39-50.

Nabeebaccus AA, Zoccarato A, Hafstad AD, Santos CX, Aasum E, Brewer AC, Zhang M, Beretta M, Yin X, West JA, Schröder K, Griffin JL, Eykyn TR, Abel ED, Mayr M, Shah AM. (2017) Nox4 reprograms cardiac substrate metabolism via protein O-GlcNAcylation to enhance stress adaptation. JCI insight. 2(24).

Ted Abel

G Kronberg, M Bridi, T Abel, M Bikson, LC Parra. (2017)  Direct current stimulation modulates LTP and LTD: activity dependence and dendritic effects. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10:1, 51-85.

G Kronberg, M Bridi, T Abel, LC Parra. (2017) Electric Fields Boost LTP in Vitro. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10:1, e14-e15.

JC Kreutzmann, JC Tudor, CC Angelakos, T Abel. (2017) The Impact of Sleep Deprivation on Molecular Mechanisms of Memory Consolidation in Rodents. Cognitive Neuroscience of Memory Consolidation, 75-85.

AJ Park, R Havekes, X Fu, R Hansen, JC Tudor, L Peixoto, Z Li, YC Wu, SG Poplawski, JM Baraban, T Abel (2017) Learning induces the translin/trax RNase complex to express activin receptors for persistent memory. Life, 6.

H Schoch, AS Kreibich, SL Ferri, RS White, D Bohorquez, A Banerjee, RG Port, HC Dow, L Cordero, AA Pallathra, H Kim, H Li, WB Biker, S Hirano, RT Schultz, K Borgmann-Winter, CG Hahn, D Feldmeyer, GC Carlson, T Abel, ES Brodkin. (2017) Sociability deficits and altered amygdala circuits in mice lacking Pcdh10, an autism associated gene. Biological psychiatry 81 (3), 193-202.

V Luczak, KT Blackwell, T Abel, JA Girault, N Gervasi. (2017) Dendritic diameter influences the rate and magnitude of hippocampal cAMP and PKA transients during β-adrenergic receptor activation. Neurobiology of learning and memory 138, 10-20.

CC Angelakos, AJ Watson, WT O’Brien, KS Krainock, T Nickl‐Jockschat, T Abel. (2017) Hyperactivity and male‐specific sleep deficits in the 16p11. 2 deletion mouse model of autism. Autism Research 10 (4), 572-584.

A Günther, V Luczak, T Abel, A Baumann. (2017) Caspase-3 and GFAP as early markers for apoptosis and astrogliosis in shRNA-induced hippocampal cytotoxicity. Journal of Experimental Biology 220 (8), 1400-1404.

MS Bridi, JD Hawk, S Chatterjee, S Safe, T Abel. Pharmacological Activators of the NR4A Nuclear Receptors Enhance LTP in a CREB/CBP-Dependent Manner. Neuropsychopharmacology 42 (6), 1243.

AV Ciernia, EA Kramár, DP Matheos, R Havekes, TJ Hemstedt, CN Magnan, K Sakata, A Tran, S Azzawi, A Lopez, R Dang, W Wang, B Trieu, J Tong, RM Barrett, RJ Post, P Baldi, T Abel, G Lynch, MA Wood. (2017) Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling. Learning & Memory 24 (5), 199-209.

R Havekes, T Abel. (2017) The tired hippocampus: the molecular impact of sleep deprivation on hippocampal function. Current opinion in neurobiology 44, 13-19.

P Mews, G Donahue, AM Drake, V Luczak, T Abel, SL Berger. (2017) Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory. Nature 546 (7658), 381.

J Jȩdrzejewska-Szmek, V Luczak, T Abel, KT Blackwell. (2017) β-adrenergic signaling broadly contributes to LTP induction. PLoS computational biology 13 (7), e1005657.

J Li, W Zhang, H Yang, DP Howrigan, B Wilkinson, T Souaiaia, OV Evgrafov, G Genovese, VA Clementel, JC Tudor, T Abel, JA Knowles, BM Neale, K Wang, F Sun, MP Coba. (2017) Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. Nature neuroscience 20 (8), 1150.

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.

J.L. Wilsbacher, M. Cheng, D. Cheng, S.A.J. Trammell, Y. Shi, J. Guo, S.L. Koeniger, P.J. Kovar, Y. He, S. Jagadeeswaran, H.R. Heyman, B.K. Sorensen, R.F. Clark, T.M. Hansen, K.L. Longenecker, D. Raich,  A.V. Korepanova, D.L. Towne, V.C. Abraham, H. Tang, S.M. McLoughlin, M.L. Curtin, M.R. Michaelides, D. Maag, F.G. Buchanan, W. Gao, S.H. Rosenberg, C. Brenner & C. Tse. (2017) Discovery and Characterization of Novel, Orally Bioavailable Non-substrate and Substrate NAMPT Inhibitors. Molecular Cancer Therapeutics, v. 16, pp. 1236-1245.

M.V. Hamity, S.R. White, R.Y. Walder, M.S. Schmidt, C. Brenner & D.L. Hammond. (2017) Nicotinamide Riboside, a Form of Vitamin B3 and NAD+ Precursor, Relieves the Nociceptive and Aversive Dimensions of Paclitaxel-induced Peripheral Neuropathy in Female Rats. Pain, v. 158, pp. 962–972.

Fletcher, J. Ratajczak, C.L. Doig, L.A. Oakey, R.Callingham, G. da Silva Xavier, A. Garten, Y.S. Elhassan, P. Redpath, M.E. Migaud, A. Philp, C. Brenner, C. Canto & G.G. Lavery. (2017) Nicotinamide Riboside Kinases Display Redundancy in Mediating Nicotinamide Mononucleotide and Nicotinamide Riboside Metabolism in Skeletal Muscle Cells. Molecular Metabolism, v. 6.

Vaur, B. Brugg, M. Mericskay, Z. Li, M.S. Schmidt, D. Vivien, C. Orset, E. Jacotot, C. Brenner & E. Duplus. (2017) Nicotinamide riboside, a form of vitamin B3, protects against excitotoxicity-induced axonal degeneration. FASEB Journal.

S.Thakur & C. Brenner. (2017) KRAS-driven miR-29b Expression is Required for Tumor Suppressor Gene Silencing. Oncotarget, v.8(43), pp. 74755-74766.

Sato, G. Solanas, F.O. Peixoto, L. Bee, A. Symeonidi, M.S. Schmidt, C. Brenner, S. Masri, S.A. Benitah & P. Sassone-Corsi. (2017) Circadian Reprogramming Identifies Metabolic Pathways of Aging. Cell, v. 170(4), pp. 664-677.

John M. Dagle

Sampath V, Bhandari V, Berger J, Merchant D, Zhang L, Ladd M, Menden H, Garland J, Ambalavanan N, Mulrooney N, Quasney M, Dagle J, Lavoie PM, Simpson P, Dahmer M. (2017) A Functional ATG16L1 (T300A) Variant is Associated with Necrotizing Enterocolitis in Premature Infants. Pediatr Res, 81(4):582-588.

Boghossian NS, Do BT, Bell EF, Dagle JM, Brumbaugh JE, Stoll BJ, Vohr BR, Das A, Shankaran S, Sanchez PJ, Wyckoff MH, Bethany Ball M, Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network. (2017) Efficacy of pharmacologic closure of patent ductus arteriosus in small-for-gestational-age extremely preterm infantsEarly Human Development. 113:10-17.

Kaluarachchi DC, Smith CJ, Klein JM, Murray JC, Dagle JM, Ryckman KK. (2017) Polymorphisms in urea cycle enzyme genes are  associated with persistent pulmonary hypertension of the newborn. Pediatr Res. 83(1-1):142-147.

Smith CJ, Ryckman KK, Bahr TM, Dagle JM. Polymorphisms in CYP2C9 are associated with response to indomethacin among neonates with patent ductus arteriosus. Pediatr Res. 82(5):776-780.

Morrow LA, Wagner BD, Ingram DA, Poindexter BB, Schibler K, Cotten CM, Dagle J, Sontag MK, Mourani PM, Abman SH. Antenatal Determinants of Bronchopulmonary Dysplasia and Late Respiratory Disease in Preterm InfantsAm J Respir Crit Care Med. 196(3):364-374.

Noonan M, Turek JW, Dagle J, McElroy SJ. (2017) Intraoperative High-Frequency Jet Ventilation Is Equivalent to Conventional Ventilation During Patent Ductus Arteriosus Ligation. World J Pediatr Congenit Heart Surg. 8(5):570-574.

Brandon Davies

Cushing EM, Chi X, Sylvers KL, Shetty SK, Potthoff MJ, Davies BSJ. (2017) Angiopoietin-like 4 directs uptake of dietary fat away from adipose during fasting. Mol Metab. 6(8):809–818.

Chi X, Britt EC, Shows HW, Hjelmaas AJ, Shetty SK, Cushing, EM, Li W, Dou A, Zhang R, Davies BSJ. (2017) ANGPTL8 promotes the ability of ANGPTL3 to bind and inhibit lipoprotein lipase. Mol Metab. 6(10):1137-1149.

Kris DeMali

Bays JL, DeMali KA. It takes energy to resist force. Cell Cycle. 16(19):1733-1734.

Bays JL, Campbell HK, Heidema C, Sebbagh M, DeMali KA. Linking E-cadherin mechanotransduction to cell metabolism through force-mediated activation of AMPK.Nat Cell Biol. 19(6):724-731.

Bays JL, DeMali KA. (2017) Vinculin in cell-cell and cell-matrix adhesions.Cell Mol Life Sci. 74(16):2999-3009.

Campbell HK, Maiers JL, DeMali KA. (2017) Interplay between tight junctions & adherens junctions. Exp Cell Res. 358(1):39-44.

Adrian H. Elcock

Andrews, CT, Campbell, BA, Elcock, AH. (2017) Direct comparison of amino acid and salt interactions with double-stranded and single-stranded DNA from explicit-solvent molecular dynamics simulations. J. Chem. Theory Comput. 13, 1794-1811.

Miller, MS, Lay, WK, Li, S, Hacker, WC, An, J, Ren, J, Elcock, AH. (2017) Reparameterization of protein force field nonbonded interactions guided by osmotic coefficient measurements from molecular dynamics simulations. J. Chem. Theory Comput. 13, 1812-1826.

Lay, WK, Miller, MS, Elcock, AH. (2017) Reparameterization of solute-solute interactions for amino acid-sugar systems using isopiestic osmotic pressure molecular dynamics simulations. J Chem. Theory Comput. 13, 1874-1882.

Hacker, WC, Li, S, Elcock, AH. (2017) Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome. Nucleic Acids Res. 45, 7541-7554.

Ernesto J. Fuentes

Mignon D., Panel N., Chen X., Fuentes E.J. and Simonson T. (2017) Computational design of the Tiam1 PDZ domain and its ligand binding. J Chem Theory Comput. 13(5):2271-2289.

Xu Z., Gakhar L., Bain F.E., Spies M. and Fuentes E.J. (2017) Tiam1 auto-inhibition by the N-terminal PHn-CC-Ex domain. J Biol Chem. 292(43):17777-17793.

Panel N., Sun Y.J., Fuentes E.J.* and Simonson T*. (2017) A simple PB/LIE free energy function accurately pre-dicts the peptide binding specificity of the Tiam1 PDZ domain. Front Mol Biosci. 4:65.

Lokesh Gakhar

Vance NR, Gakhar L, Spies MA. (2017) Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach. Angew Chem Int Ed Engl. 56(46):14443-14447.

Xu Z, Gakhar L, Bain FE, Spies M, Fuentes EJ. (2017) The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain. J Biol Chem. 292(43):17777-17793.

Yadav RP, Gakhar L, Yu L, Artemyev NO. (2017) Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. Proc Natl Acad Sci U S A. 114(32):E6536-E6545.

Pamela K. Geyer

Baxley, R.M., Bullard, J.D, Klein, M.W., Fell, A.G., Morales-Rosado, J.A., Duan, T. and Geyer, P.K. (2017) Deciphering the DNA code for the function of the Drosophila polydactyl zinc-finger protein Suppressor of Hairy-wing. Nucl. Acid Res., 45(8):4463-4478

Catherine A. Musselman

Gatchalian J, Wang X, Ikebe J, Cox KL, Tencer AH, Zhang Y, Burge NL, Di L, Gibson MD, Musselman CA, Poirier MG, Kono H, Hayes JJ, Kutateladze TG. (2017) Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat Commun. 8(1):1489.

Tencer AH, Cox KL, Di L, Bridgers JB, Lyu J, Wang X, Sims JK, Weaver TM, Allen HF, Zhang Y, Gatchalian J, Darcy MA, Gibson MD, Ikebe J, Li W, Wade PA, Hayes JJ, Strahl BD, Kono H, Poirier MG, Musselman CA, Kutateladze TG. (2017) Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell Rep. 21(2):455-466.

Morrison EA, Sanchez JC, Ronan JL, Farrell DP, Varzavand K, Johnson JK, Gu BX, Crabtree GR, Musselman CA. (2017) DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes. Nat Commun. 8:16080.

Flenker KS, Burghardt EL, Dutta N, Burns WJ, Grover JM, Kenkel EJ, Weaver TM, Mills J, Kim H, Huang L, Owczarzy R, Musselman CA, Behlke MA, Ford B, McNamara JO 2nd. (2017) Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity.  Mol Ther. 25(6):1353-1362.

Andrew W. Norris

Sun X, Yi Y, Xie W, Liang B, Winter MC, He N, Liu X, Luo M, Yang Y, Ode KL, Uc A, Norris AW, Engelhardt JF.  (2017) CFTR Influences Beta Cell Function and Insulin Secretion Through Non-Cell Autonomous Exocrine-Derived FactorsEndocrinology. 158(10):3325-3338.

Coryell WH, Langbehn DR, Norris AW, Yao JR, Dindo LN, Calarge CA. (2017) Polyunsaturated fatty acid composition and childhood adversity: Independent correlates of depressive symptom persistence. Psychiatry Res. 256:305-311.

Bryce V. Plapp

K Kim and BV Plapp. (2017) Inversion of Substrate Stereoselectivity of Horse Liver Alcohol Dehydrogenase by Substitutions of Ser-48 and Phe-93. Chem. Biol. Interact. 276,77-87.

BV Plapp, BR Savarimuthu, DJ Ferraro, JK Rubach, EN Brown, and S Ramaswamy. (2017) Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry. 56, 3632-3646.

David H. Price

Bosque, A., Nilson, K.A., Macedo, A.B., Spivak, A.M., Archin, N., Van Wagoner, R.M., Martins, L.J., Novis, C.L., Szaniawski, M.A., Ireland, C.M., Margolis, D.M, Price, D.H., Planelles, V. (2017) Benzotriazoles reactivate latent HIV-1 through inactivation of STAT5 SUMOylation. Cell Reports, 18:1324-1334.

Brogie, J.E and Price D.H. (2017) Reconstitution of a functional 7SK snRNP. Nucleic Acids Res. 45(11):6864-6880.

Nilson, K.A., Lawson, C.K., Mullen, N.J., Ball, C.B., Spector, B.M., Meier, J.L., Price, D.H. (2017) Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome. Nucleic Acids Res. 45(19):11088-11105.

Mullen, NJ and Price DH. (2017) Hydrogen peroxide yields mechanistic insights into human mRNA capping enzyme function. PLoS ONE, 12(10):e0186423.

Miles Pufall

Rollins DA, Kharlyngdoh JB, Coppo M, Tharmalingam B, Mimouna S, Guo Z, Sacta MA, Pufall MA, Fisher RP, Hu X, Chinenov Y, Rogatsky I. (2017) Glucocorticoid-induced phosphorylation by CDK9 modulates the coactivator functions of transcriptional cofactor GRIP1 in macrophages. Nat Commun. 8(1):1739.

Pufall MA. (2017) Defining Native Enhancer Function. Cell Syst. 5(4):310-312.

Michaelson JJ, Shin MK, Koh JY, Brueggeman L, Zhang A, Katzman A, McDaniel L, Fang M, Pufall M, Pieper AA. (2017) Neuronal PAS Domain Proteins 1 and 3 Are Master Regulators of Neuropsychiatric Risk Genes. Biol Psychiatry. 82(3):213-223.

Kruth KA, Fang M, Shelton DN, Abu-Halawa O, Mahling R, Yang H, Weissman JS, Loh ML, Müschen M, Tasian SK, Bassik MC, Kampmann M, Pufall MA. (2017) Suppression of B-cell development genes is key to glucocorticoid efficacy in treatment of acute lymphoblastic leukemia.  Blood. 129(22):3000-3008.

Chan LN, Chen Z, Braas D, Lee JW, Xiao G, Geng H, Cosgun KN, Hurtz C, Shojaee S, Cazzaniga V, Schjerven H, Ernst T, Hochhaus A, Kornblau SM, Konopleva M, Pufall MA, Cazzaniga G, Liu GJ, Milne TA, Koeffler HP, Ross TS, Sánchez-García I, Borkhardt A, Yamamoto KR, Dickins RA, Graeber TG, Müschen M. (2017) Metabolic gatekeeper function of B-lymphoid transcription factors.  Nature. 542(7642):479-483.

Peter A. Rubenstein

Niederhoffer EC, Cline SD, Osheroff N, Simmons JM, Diekman AB, Franklin DS, Abali EE, Bateman RC Jr, Fontes JD, Lindsley JE, Pearson D, Rubenstein PA, Slaughter CA, Bernstein JA, Hyland KM, Park VM, Sobering AK, Weiler TA, Dasgupta S. (2017) Teaching Biochemistry and Genetics to Students of Dentistry, Medicine, and Pharmacy 6thInternational Conference of the Association of Biochemistry Educators (ABE) Clearwater Beach, FL, USA, May 7-11, 2017. Med Sci Educ. 27(4):855-859.

Michael J. Schnieders

Lansdon LA, Bernabe HV, Nidey N, Standley J, Schnieders MJ, Murray JC. (2017) The Use of Variant Maps to Explore Domain-Specific Mutations of FGFR1. J Dent Res. 96(11):1339-1345.

Simpson A, Avdic A, Roos BR, DeLuca A, Miller K, Schnieders MJ, Scheetz TE, Alward WL, Fingert JH. (2017) LADD syndrome with glaucoma is caused by a novel gene.  Mol Vis. 23:179-184.

Madeline Shea

*Hovey, L., *Fowler, C.A., Mahling, R., Lin, Z., Miller, M.S. Marx, D.C., Yoder, J.B., Kim, E.H.,Tefft, K.M., Waite, B.C., Feldkamp, M.D., Yu, L., Shea, M.A. (2017) Calcium Triggers Reversal of Calmodulin on Nested Anti-Parallel Sties in the IQ Motif of the Neuronal Voltage- Dependent Sodium Channel NaV1.2 . Biophysical Chemistry, 224:1-19.

Fowler, C.A., Núñez Hernandez, M., O’Donnell, S.E., Yu, L., and Shea, M.A. (2017) Backbone and Side-Chain Resonance Assignments of (Ca2+)4-Calmodulin Bound to Beta Calcineurin A CaMBD Peptide. Biomolecular NMR Assignments, 11:275–28

Mahling, R., Kilpatrick, A. M., and Shea, M.A. Backbone resonance assignments of complexes of human voltage-dependent sodium channel NaV1.2 IQ motif peptide bound to apo calmodulin and to the C-domain fragment of apo calmodulin. Biomolecular NMR Assignments, 11:297–303.

M. Ashley Spies

Vance, N.R, Gakhar, L., and Spies, M.A. (2017) Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery ApproachAngew Chem Int Ed. Eng. 56(46):14443-14447.

Hengel, S.R., Spies, M.A.*, and Spies, M.* (2017) Small-Molecule Inhibitors Targeting DNA Repair and DNA Repair Deficiency in Research and Cancer Therapy. Cell Chem. Bio. 24(9):1101-1119.

Maria Spies

Hengel, S.R., Spies, M.A.*, and Spies, M.* (2017) Small-Molecule Inhibitors Targeting DNA Repair and DNA Repair Deficiency in Research and Cancer Therapy. Cell Chem. Bio. 24(9):1101-1119.

Caldwell CC, Spies M. (2017) Helicase SPRNTing through the nanopore. Proc Natl Acad Sci U S A. 114(45):11809-11811.

Xu Z., Gakhar L., Bain F.E., Spies M. and Fuentes E.J. (2017) Tiam1 auto-inhibition by the N-terminal PHn-CC-Ex domain. J Biol Chem. 292(43):17777-17793.

Spies M, Smith BO. (2017) Protein-nucleic acids interactions: new ways of connecting structure, dynamics and function. Biophys Rev. 9(4):289-291.

Spies M. (2017) A time for promiscuity in a eukaryotic recombinase. J Biol Chem. 292(26):11136-11137.

Nancy C. Stellwagen

Stellwagen NC. (2017) Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory. J Phys Chem B. 121(9):2015-2026.

Eric B. Taylor

Rauckhorst AJ, Gray LR, Sheldon RD, Fu X, Pewa AD, Feddersen CR, Dupuy AJ, Gibson-Corley KN, Cox JE, Burgess SC, Taylor EB. (2017) The mitochondrial pyruvate carrier mediates high fat diet-induced increases in hepatic TCA cycle capacity. Mol Metab. 6(11):1468-1479.

Vigueira PA, McCommis KS, Hodges WT, Schweitzer GG, Cole SL, Oonthonpan L, Taylor EB, McDonald WG, Kletzien RF, Colca JR, Finck BN. (2017) The beneficial metabolic effects of insulin sensitizers are not attenuated by mitochondrial pyruvate carrier 2 hypomorphism. Exp Physiol. 102(8):985-999.

DeZwaan-McCabe D, Sheldon RD, Gorecki MC, Guo DF, Gansemer ER, Kaufman RJ, Rahmouni K, Gillum MP, Taylor EB, Teesch LM, Rutkowski DT. (2017) ER Stress Inhibits Liver Fatty Acid Oxidation while Unmitigated Stress Leads to Anorexia-Induced Lipolysis and Both Liver and Kidney Steatosis. Cell Rep. 19(9):1794-1806.

Taylor EB. (2017) Functional Properties of the Mitochondrial Carrier System. Trends Cell Biol. 27(9):633-644.

M. Todd Washington

Zhoa, L. and Washington, M. T. (2017) Translesion synthesis: Insights into the selection and switching of DNA polymerases. Genes, 8(1), e24.

Liu, J., Ede, C., Wright, W. D., Gore, S. K., Jenkins, S. S., Freudenthal, B. D., Washington, M. T., Veaute, X., and Heyer, W. D. (2017) Srs2 promotes synthesis-dependent strand annealing by disruptiong DNA polymerase delta-extending D-loops. eLife 6, e22195.

Powers, K. T. and Washington, M. T. (2017) Analyzing the catalytic activities and interactions of eukaryotic translesion synthesis. Methods Enzymol. 592, 329-356.

Ronald J. Weigel

De Andrade JP, Lorenzen AW, Wu VT, Bogachek MV, Park JM, Gu VW, Sevenich CM, Cassady VC, Beck AC, Kulak MV, Robinson RA, Lal G, Weigel RJ. (2017) Targeting the SUMO pathway as a novel treatment for anaplastic thyroid cancer. Oncotarget. 8(70):114801-114815.

Wu VT, Lorenzen AW, Beck AC, Reid VJ, Sugg SL, Howe JR, Pollard JH, Lal G, Weigel RJ. (2017) Comparative analysis of radioactive iodine versus thyroidectomy for definitive treatment of Graves disease. Surgery. 161(1):147-155.

Gómez-Contreras P, Ramiro-Díaz JM, Sierra A, Stipp C, Domann FE, Weigel RJ, Lal G. (2017) Extracellular matrix 1 (ECM1) regulates the actin cytoskeletal architecture of aggressive breast cancer cells in part via S100A4 and Rho-family GTPases. Clin Exp Metastasis. 34(1):37-49.

Thomas A, Weigel RJ, Lynch CF, Spanheimer PM, Breitbach EK, Schroeder MC. (2017) Incidence, characteristics, and management of recently diagnosed, microscopically invasive breast cancer by receptor status: Iowa SEER 2000 to 2013. Am J Surg. 214(2):323-328.

Marc S. Wold

Zhang, H., Gan, H., Wang, Z. Lee, J-H., Zhou, H. Ordog, T., Wold, M.S., Ljungman, M., Zhang, Z. (2017) RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells. Molecular Cell 65, 272-282.

Meng Wu

Qu C, Ding M, Zhu Y, Lu Y, Du J, Miller M, Tian J, Zhu J, Xu J, Wen M, Er-Bu A, Wang J, Xiao Y, Wu M, McManus OB, Li M, Wu J, Luo HR, Cao Z, Shen B, Wang H, Zhu MX, Hong X. (2017) Pyrazolopyrimidines as Potent Stimulators for Transient Receptor Potential Canonical 3/6/7 Channels. J Med Chem. 60(11):4680-4692.

Liping Yu

Fowler, C.A., Núñez Hernandez, M., O’Donnell, S.E., Yu, L., and Shea, M.A. (2017) Backbone and Side-Chain Resonance Assignments of (Ca2+)4-Calmodulin Bound to Beta Calcineurin A CaMBD Peptide. Biomolecular NMR Assignments, 11:275–280.

Yadav RP, Gakhar L, Yu L, Artemyev NO. (2017) Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. Proc Natl Acad Sci U S A. 114(32):E6536-E6545.

B. Fink, F. Bai, L. Yu, and W. Sivitz. (2017) Regulation of ATP production: dependences on calcium concentration and respiratory state. American Journal of Physiology – Cell Physiology, 313, C146-C153. DOI: 10.1152/ajpcell.00086.2017.

L. Yu, R.P. Yadav, and N.O. Artemyev. (2017) NMR resonance assignments of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) in complex with a farnesyl ligand. Biomol. NMR Assign., 11, 111-115. DOI: 10.1007/s12104-017-9730-2.

*Hovey, L., *Fowler, C.A., Mahling, R., Lin, Z., Miller, M.S. Marx, D.C., Yoder, J.B., Kim, E.H.,Tefft, K.M., Waite, B.C., Feldkamp, M.D., Yu, L., Shea, M.A. (2017) Calcium Triggers Reversal of Calmodulin on Nested Anti-Parallel Sties in the IQ Motif of the Neuronal Voltage-Dependent Sodium Channel NaV1.2 . Biophysical Chemistry, 224:1-19.

2017 IDT & Smith-Gehring Graduate Fellowships

Wednesday, July 5th, 2017

The IDT and Smith-Gehring Graduate Fellowships are awarded to three of the most meritorious second year Biochemistry graduate students based on academic and research achievements.

The 2017 IDT Graduate Fellows are Kelli Sylvers and Christopher Ball:

Ms. Kelli Sylvers had a productive first year in the graduate program and made significant scientific progress. Her rotation work has already contributed to one research paper. Ms. Sylvers grew up in Coon Rapids, Minnesota and graduated with a B.S in Biochemistry and a B.A in Biology from The College of St. Scholastica (Duluth, MN) in spring 2016. Ms. Sylvers is training in the laboratory of Dr. Brandon Davies. Her research involves the characterization of two circulating factors, ANGPTL3 and ANGPTL8, that regulate lipid metabolism. ANGPTL3 and ANGPTL8 form a complex that inhibits lipoprotein lipase, the enzyme responsible for delivering triglycerides from the bloodstream to tissue. ANGPTL3, and possibly ANGPTL8, can also inhibit endothelial lipase, a major regulator of HDL.  Moreover, targeting ANGPTL3 and ANGPTL8 can therapeutically lower plasma lipids, which may reduce the risk of cardiac disease. The goals of Ms. Sylvers research are to understand the interactions between ANGPTL3 and ANGPTL8, characterize the mechanisms by which they inhibit lipoprotein lipase and endothelial lipase, and to identify small molecules that can disrupt the action of ANGPTL3 and ANGPTL8 complexes.

Mr. Christopher Ball had an outstanding first year. He earned over a 4.0 average in his classes for the two semesters and performed in an exemplary manner during his three rotations. During his rotations, he got up to speed quickly in each of the three very different research environments and was able to contribute intellectually to each project. Having a good idea is easier than putting that idea into practice, but Mr. Ball is able to fully translate his imagination into experiments that work. Mr. Ball entered Dr. David Price’s lab in the Spring and has begun several projects aimed at understanding the regulation of transcription by human RNA polymerase II. He is utilizing both biochemical and molecular approaches. Key to his success is his soft spoken thoughtfulness coupled with a drive to succeed. Mr. Ball will attend the Cold Spring Harbor Lab meeting on Transcriptional Mechanisms in the Fall where he will present some of his first results demonstrating a rapid increase in transcribing RNA polymerase II in cells under oxidative stress.

The 2017 Smith-Gehring Graduate Fellow is Alicia Ortiz:

Ms. Alicia Ortiz joined the Biochemistry Department in the Fall of 2016 after having been actively engaged in microbiology research at University of Nebraska at Lincoln.  Upon her recruitment to the University of Iowa, Alicia was named an Alfred P. Sloan Scholar, a fellowship awarded to promote the doctoral training of deserving US citizens from minority backgrounds.  As a first year student in the Biochemistry graduate program, Ms. Ortiz excelled accumulating an impressive academic and research credentials.  As a consequence of her successes, she was awarded a position on the Predoctoral Training Grant in the Pharmacological Sciences.  This is an NIH-funded institutional training program that promotes the interdisciplinary training of graduate students.  Ms. Ortiz will carry out her dissertation work in the laboratory of Dr. Kris DeMali and will focus her research efforts on understanding how epithelial cells sense and transmit forces in normal and cancer cells.

Congratulations to the 2017 IDT & Smith-Gehring Graduate Fellows!

Kris DeMali receives 2017 Honors Thesis Mentor Award

Wednesday, May 3rd, 2017

Dr. Kris DeMali was selected as the 2017 Honors Thesis Mentor Award recipient. Each year the University of Iowa Honors Program selects a single faculty member to recognize with this honor, which is driven by student nominations. Dr. DeMali will be recognized at the Honors Commendation Ceremony on May 12, 2017.