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  1. University of Arkansas for Medical Sciences
  2. College of Medicine
  3. Department of Biochemistry and Molecular Biology
  4. Student Highlights
  5. Page 2

Student Highlights

Mary “Allie” Schleiff Student Highlight

Allie is a GPIBS Ph.D. student in the Biochemistry and Molecular Biology track. She is a fourth year student in the laboratory of Dr. Grover Paul Miller.

She graduated from Henderson State University in 2017 with an Honors Bachelor of Science degree in Biochemistry and a minor in Biology, and she received a regulatory sciences certification from the UAMS Department of Environmental and Occupational Health in Spring 2020.

Research Interest Statement

My research focuses on a subset of structurally similar non-steroidal anti-inflammatory drugs (NSAIDs) known as diphenylamine NSAIDs. Diphenylamine NSAIDs are taken more than 15 million times each year in the United States, but roughly 15% of all people administered diphenylamine NSAIDs have a clinically observable case of hepatotoxicity from the compounds. Previous studies identified that diphenylamine hepatotoxicity is dependent upon metabolic bioactivation and varied depending upon minor structural modifications to the diphenylamine structural scaffold, but little work exists to identify the specific mechanisms by which diphenylamines cause hepatotoxicity. I used computational tools to identify potential diphenylamine metabolic bioactivations in seven marketed or withdrawn diphenylamine drugs and experimentally validate these computational results. Thus far, I have discovered that diphenylamine NSAIDs are preferentially bioactivated into quinone-species metabolites in variable amounts and by a variety of cytochrome P450 enzymes dependent upon minor structural modifications to the diphenylamine scaffold. I hope that results from this work can help direct future development of diphenylamine-containing drugs in the future and help identify and stratify patients at-risk following diphenylamine NSAID dosage to promote more personalized patient care.

Something Notable About Time as a Graduate Student

I am so grateful that I was trained as a fresh graduate student by Dr. Dusty Barnette. I was always dropping things, breaking things, and having the same information repeated to me over and over again and Dusty never batted an eye, scolded me, or made me feel like a burden. Specifically, I’m appreciative to him for always getting the tall things off the high shelves for me!

Career Goals

My dream job would be in a contract research organization conducting preclinical and clinical studies for pharmaceutical clients. Once I obtain my PhD, I intend to take a post-doctoral position through the Center for Drug Evaluation and Research (CDER) to enhance my regulatory experience and make myself more marketable!

Experiment or Technique You Would Most Like to Do

Nuclear magnetic resonance is a major technique used frequently in regulatory science and in the pharmaceutical industry, but my only exposure to it was for a week or so as an undergraduate in my Analytical Chemistry course. I was overwhelmed and scared of it then and I still am, though I want to change that!

Fun Fact

Cleaning is legitimately one of my favorite hobbies, so most laboratories stress me out a bit – ha. If I wasn’t working in science, I would want to be a professional home organizer.

Publications

  1. Schleiff, M., Payakachat, S., Schleiff, B., Pinson, A., Flynn, N., Province, D., Boysen, G., Swamidass, S. J., Miller, G. P. “Significance of Multiple Bioactivation Pathways for Meclofenamate as Revealed through Modeling and Reaction Kinetics.”
    • Publication – Accepted, Drug Metabolism and Disposition.
  2. Barnette, D., Schleiff, M., Datta, A., Flynn, N., Swamidass, S. J., Miller, G. P. “Meloxicam Methyl Group Determines Enzyme Specificity for Thiazole Bioactivation Compared to Sudoxicam.”
    • Publication – Accepted, Toxicology Letters.
  3. Pinson, A., Pouncey, D., Schleiff, M., Fantegrossi, W., Prather, P., Radominska-Pandya, A., Boysen, G., Miller, G. P. “Significance of Competing Metabolic Pathways for Synthetic Cannabinoid 5F-APINACA as Revealed through Novel Reaction Kinetics.”
    • Publication – Published, Molecules. DOI: 3390/molecules25204820
  4. Schleiff, M., Russell, L., Gonzalez, E., Bart, A., Broccatelli, F., Humphreys, G., Scott, E., Segall, M., Prasad, B., Hartman, J., Lauschke, V., Nwabufo, C., Takahashi, R., Durmus, S., Nichols, C., Martin, I., and Taub, M., Sodhi, J. “Advances in the Study of Drug Metabolism – Symposium Report of the 12th Meeting of the International Society for the Study of Xenobiotics (ISSX).”
  • Publication – May 2020, Drug Metabolism Reviews. DOI: 1080/03602532.2020.1765793

Grants

I am partially supported by a training grant through the Pharmacology, Toxicology, and Experimental Therapeutics Department in the UAMS Graduate School entitled, “Systems Pharmacology and Toxicology” (T32GM106999).

Awards

  • 2020 Third Place Bhuvan Award for Excellence in Biochemistry Graduate Research – University of Arkansas for Medical Sciences Student Research Day
  • 2020 Top 30 Finalist with Honorarium – Sternfels Prize in Drug Safety Discoveries
  • 2020 Pfizer Society of Toxicology National Conference Student Travel Award – Society of Toxicology Computational Toxicology Specialty Section
  • 2019 First Place Oral Presentation – University of Arkansas for Medical Sciences Graduate Student Association Research Symposium
  • 2019 South Central Chapter Society of Toxicology Regional Conference Travel Award
  • Graduate Student Achievement Award for Selection to the Drug Metabolism Reviews Editorial Board – University of Arkansas for Medical Sciences Fall Research Award Ceremony
  • Graduate Student Achievement Award for Selection to the International Society for the Study of Xenobiotics New Investigator Group – University of Arkansas for Medical Sciences Fall Research Award Ceremony
  • 2019 Outstanding Graduate Student Poster Presentation – Drug Discovery and Development Colloquium
  • 2019 Invited Speaker with Honorarium – Drug Metabolism and Pharmacokinetics Symposium hosted by Genentech
  • 2018 MC-Bios Computational Biology Conference Travel Award – Midsouth Computational Biology and Bioinformatics Society

Filed Under: iBioDS Highlights, Student Highlights

Duah Alkam Student Highlight

Duah is a GPIBS Ph.D. student in the Biochemistry and Molecular Biology track. She is starting her 5th year in the laboratories of Dr. Mark Smeltzer and Dr. David Ussery.

She has a B.S. in Pharmaceutical Sciences and a M.S. in Pharmacology from The Hebrew University of Jerusalem.

Research Interest Statement

Osteomyelitis, or bone infection, is a devastating disease with limited treatment options. My dissertation explores the molecular pathways involved in the pathogenicity of the major cause of osteomyelitis, the bacterial agent Staphylococcus aureus. We draw on genome sequencing technologies coupled with comprehensive bioinformatic analyses to define the genetic landscape of the bacterium during in vivo osteomyelitis. These studies revealed strategies the bacterium employs to survive within the bone while fending off attacks by the host. Targeting these pathways may aid in the development of therapeutics to combat S. aureus infections.

Something Notable about Time as a Graduate Student

There is a pervasive positivity across the UAMS graduate school that I’ve been fortunate to experience through interactions that spanned three departments. My co-mentors exemplified this spirit through their collaboration and commitment to guiding me on topics ranging from the intricate details of Staphylococcus aureus biology to the value of comparative genomics. Equally crucial were the bioinformaticians on our team who taught me how to critically evaluate big data. These interactions have been the highlight of the past four years.

Career Goals

I plan to remain in the genomics/bioinformatics field.

Experiment or Technique You Would Most Like to Do

Anything involving genomic engineering, particularly with CRISPR/Cas9, is always fun.

Fun fact

My husband, Ziad, and I are on a quest to visit every major National Park in the United States – our favorite so far is the Grand Canyon.

Publications

Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, et al. Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. Infect Genet Evol. 2019;75:103965

Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, et al. Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA. Genome Announc. 2017;5(32)

Filed Under: iBioDS Highlights, Student Highlights

Brian Koss student highlight

Brian is a Ph.D. student starting his fifth year in the Biochemistry and Molecular Biology Department in the laboratory of Dr. Alan Tackett.

He has a B.A. in Biochemistry and Molecular Biology from Hendrix College.

Research Interest Statement

My doctoral work focuses on the dynamic interplay between the epigenetic and metabolic pathways used by T cells to sense and respond to environmental pressures. Specifically, I focused on the loss of the histone methyltransferase EZH2 (H3K27me3) in CD8+ T cells, which occurs during solid tumor infiltration and renders T cells dysfunctional. My work revealed loss of H3K27me3 leads to mitochondrial dysfunction and metabolic exhaustion, through a Cdkn2a.ARF-mediated, p53-independent mechanism. Reprogramming T cells to express a gain-of-function EZH2 mutant enhanced inhibition of tumor growth in a model of adoptive T cell therapy. My data suggest manipulation of EZH2 in T cells represents a potential strategy to protect tumor-specific T cells, which is currently unaccounted for in the clinical development of EZH2 inhibitors.

Career Goals

Once I am finished with my PhD, I plan to continue my current work and pursue early independence opportunities.

Experiment or Technique You Would Most Like to Do

This changes from time to time. However, I currently enjoy using proteomic approaches to interrogate protein turnover rates at a proteome level. I believe this approach will give us novel insights into how a cell prepares its proteome for rapid adaptation to environmental conditions.

Fun fact

My wife, Cary, and I have two boys, Bennett (5 years) and Parker (3 years).

Publications

  1. Koss, B.; Shields, B. D; Taylor, E. M.; Storey, A. J.; Byrum, S. D.; et. al. Epigenetic control of Cdkn2a.Arf protects tumor-infiltrating lymphocytes from metabolic-exhaustion. Cancer Research, (accepted).
  2. Trentzsch, M.; Nyamugenda, E.; Miles, T. K.; Griffin, H.; Russell, S.; Koss, B.; Cooney, K. A.; Phelan, K. D.; Tackett A. J., Iyer, S.; Boysen, G.; Baldini, G. Delivery of phosphatidylethanolamine blunts stress in hepatoma cells exposed to elevated palmitate by targeting the endoplasmic reticulum. Cell Death Discovery 6:8 (2020).
  3. Taylor, E.; Koss, B.; Davis L. E.; Tackett, A. J. Histone Modifications as Biomarkers for Immunotherapy. Methods in Molecular Biology 2055:213-228 (2019).
  4. Chiang, T.; Koss, B.; Su, L. J.; Washam, C. L.; Byrum, S. D.; Storey, A.; Tackett, A. J. Effect of sulforaphane and 5-aza-2’-deoxycytidine on melanoma cell growth. Medicines 6, 71 (2019).
  5. Lee, T.; Christov, P. P.; Shaw, S.; Tarr, J. C.; Zhao, B.; Veerasamy, N.; Jeon, K. O.; Mills, J. J.; Bian, Z.; Sensintaffar, J. L.; al. Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors That Demonstrate in Vivo Activity in Mouse Xenograft Models of Human Cancer. Journal of medicinal chemistry 62, 3971–3988 (2019).
  6. Shields, B. D.; Koss, B.; Taylor, E. M.; Storey, A. J.; West, K. L.; Byrum, S. D.; Mackintosh, S. G.; Edmondson, R.; Mahmoud, F.; Shalin, S. C.; Tackett, A. J. Loss of E-Cadherin Inhibits CD103 Antitumor Activity and Reduces Checkpoint Blockade Responsiveness in Melanoma. Cancer Research 79, 1113–1123 (2019).
  7. Ren, Z.; Ahn, J. H.; Liu, H.; Tsai, Y.-H.; Bhanu, N. V; Koss, B.; Allison, D. F.; Ma, A.; Storey, A. J.; Wang, P. PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation. Blood blood-2019000578 (2019).
  8. Shields, B. D.; Mahmoud, F.; Taylor, E. M.; Byrum, S. D.; Sengupta, D.; Koss, B.; Baldini, G.; Ransom, S.; Cline, K.; Mackintosh, S. G. Indicators of responsiveness to immune checkpoint inhibitors. Scientific Reports 7, 807 (2017).
  9. Lee, T.; Bian, Z.; Zhao, B.; Hogdal, L. J.; Sensintaffar, J. L.; Goodwin, C. M.; Belmar, J.; Shaw, S.; Tarr, J. C.; Veerasamy, N.; Matulis, S. M.; Koss, B.; Fischer, M. A.; Arnold, A. L.; Camper, D. V.; Browning, C. F.; Rossanese, O. W.; Budhraja, A.; Opferman, J.; Boise, L. H.; Savona, M. R.; Letai, A.; Olejniczak, E. T.; Fesik, S. W. Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors. FEBS Letters 591, 240–251 (2017). 
  10. Koss, B.; Ryan, J.; Budhraja, A.; Szarama, K.; Yang, X.; Bathina, M.; Cardone, M. H.; Nikolovska-Coleska, Z.; Letai, A.; Opferman, J. T. Defining specificity and on-target activity of BH3-mimetics using engineered B-ALL cell lines. Oncotarget 7, (2016).
  11. Haverkamp, J. M.; Smith, A. M.; Weinlich, R.; Dillon, C. P.; Qualls, J. E.; Neale, G.; Koss, B.; Kim, Y.; Bronte, V.; Herold, M. J.; Green, D. R.; Opferman, J. T.; Murray, P. J. Myeloid-derived suppressor activity is mediated by monocytic lineages maintained by continuous inhibition of extrinsic and intrinsic death pathways. Immunity 41, 947–959 (2014).
  12. Koss, B.; Morrison, J.; Perciavalle, R. M.; Singh, H.; Rehg, J. E.; Williams, R. T.; Opferman, J. T. Requirement for antiapoptotic MCL-1 in the survival of BCR-ABL B-lineage acute lymphoblastic leukemia. Blood 122, 1587–1598 (2013).
  13. Tripathi, P.; Koss, B.; Opferman, J. T.; Hildeman, D. A. Mcl-1 antagonizes Bax/Bak to promote effector CD4(+) and CD8(+) T-cell responses. Cell death and differentiation 20, 998–1007 (2013).
  14. Wang, X.; Bathina, M.; Lynch, J.; Koss, B.; Calabrese, C.; Frase, S.; Schuetz, J. D.; Rehg, J. E.; Opferman, J. T. Deletion of MCL-1 causes lethal cardiac failure and mitochondrial dysfunction. Genes and Development 27, 1351–1364 (2013).
  15. Cohen, N. A.; Stewart, M. L.; Gavathiotis, E.; Tepper, J. L.; Bruekner, S. R.; Koss, B.; Opferman, J. T.; Walensky, L. D. A competitive stapled peptide screen identifies a selective small molecule that overcomes MCL-1-dependent leukemia cell survival. Chemistry and Biology 19, 1175–1186 (2012).
  16. Perciavalle, R. M.; Stewart, D. P.; Koss, B.; Lynch, J.; Milasta, S.; Bathina, M.; Temirov, J.; Cleland, M. M.; Pelletier, S.; Schuetz, J. D.; Youle, R. J.; Green, D. R.; Opferman, J. T. Anti-apoptotic MCL-1 localizes to the mitochondrial matrix and couples mitochondrial fusion to respiration. Nature Cell Biology 14, 575–583 (2012).
  17. Stewart, D. P.; Koss, B.; Bathina, M.; Perciavalle, R. M.; Bisanz, K.; Opferman, J. T. Ubiquitin-independent degradation of antiapoptotic MCL-1. Molecular and cellular biology 30, 3099–3110 (2010).

Complete List of Published Work:

https://www.ncbi.nlm.nih.gov/myncbi/1pihpxbtPQJQh/bibliography/public/

Grants

  • 2019-present NIH/NCI F31 predoctoral fellowship. Epigenetic regulation of metabolic stress pathways in melanoma infiltrating lymphocytes (F31CA232464). 7th percentile. $124,851
  • 2019 Department of Defense Horizon Award. Epigenetic regulation of metabolic stress pathways in melanoma infiltrating lymphocytes. Recommended for funding as alternate.
  • 2017-2018 Systems Pharmacology and Toxicology Graduate Fellowship, a T32 program; University of Arkansas for Medical Sciences.

Awards

  • 2020 Sanofi Scholar-in-Training Award. American Association for Cancer Research (AACR), San Diego, CA
  • 2020 Keystone Symposia Scholarship. Emerging Cellular Therapies: Cancer and Beyond. Banff, AB Canada
  • 2019 Cancer Institute Member Spotlight. University of Arkansas for Medical Sciences, Little Rock AR.
  • 2019 Graduate School Outstanding Achievement Award. University of Arkansas for Medical Sciences, Little Rock AR.
  • 2018 Immuno-Oncology Innovation Award, Miltenyi Biotec. Fully paid travel to AACR 2018 and $2500 for research.

Filed Under: iBioDS Highlights, Student Highlights

Megan Reed Student Highlight

Megan is a Ph.D. student in her 5th year in the Biochemistry and Molecular Biology Department. She joined the laboratory of Dr. Robert Eoff for her research studies.

She has a B.S. in Biology with a dual minor in Chemistry and Psychology from Henderson State University.

Research Interest Statement

My project involves elucidating various mechanisms that glioblastoma brain tumors use to tolerate, repair and ultimately survive chemotherapeutic intervention. We are most interested in investigating the alternate functions of the DNA damage tolerance polymerase kappa (hpol k) and how these responses aid in tumor survival. Overexpression of this polymerase has been linked to tumor recurrence and resistance to standard-of-care chemotherapeutics. Understanding the possible ways that hpol k promotes these outcomes could help develop more effective treatments for glioblastoma patients.

Something Notable about Time as a Graduate Student

A fun fact about the Eoff lab is we are all left handed. We have this running joke that a requirement to join the lab is you must be left handed.

In all seriousness though I would say I have really enjoyed being part of the Biochemistry Department. I have built life-long friendships and have received tremendous support not only from my primary advisor but from many of the labs in this department. I like to joke that I am the department’s graduate student as I have pretty much gone to every lab at one time or another asking for experimental advice or to borrow reagents. My graduate school experience wouldn’t have been as successful if it was not for the faculty, postdocs and students that make up the Biochemistry Department.

Career Goals

Once I am finished with my PhD, I plan to pursue post-doctoral research in a lab focused on developing 3D tumor model systems. My long term goal is to conduct research using these model systems to help predict patient drug response, thereby opening up access to personalized chemotherapeutic treatments that are currently unavailable to most cancer patients.

Experiment or Technique You Would Most Like to Do

I really enjoy immunofluorescence microscopy. I don’t think I will ever get tired of taking beautifully colored fluorescent images.

Fun fact

I enjoy spending time with family, friends and hiking with my dog Brain.

Publications

Bostian, A. C., Maddukuri, L. M., Reed, M. R., Savenka, T., Hartman, J. H., Davis, L., Pouncey, D.L., Miller, G.P., and Eoff, R. L. Kynurenine signaling increases DNA polymerase kappa and promotes genomic instability in glioblastoma cells. Chem. Res. Toxicol. 2016, 29(1): 101-8.

Byrd, A. K., Zybailov, B. L., Maddukuri, L., GAO, J., Marecki, J. C., Jaiswal, M., Bell, M. R., Griffin, W.C., Reed, M. R., Chib, S., Mackintosh, S. G., MacNicol, A. M., Baldini, G., Eoff, R. L., and Raney, K. D. Evidence that G-quadruplex DNA accumulates in the cytoplasm and participates in stress granule assembly in response to oxidative stress. J. Biol. Chem. 2016, 24(3): 432-36.

Zafar, M. K., Maddukuri, L., Ketkar, A., Penthala, N.R., Reed, M. R., Eddy, S., Crooks, P. A., and Eoff, R. L. A small-molecule inhibitor of human DNA polymerase h potentiates the effects of cisplatin in tumor cells. Biochemistry. 2018, 57(7): 1262-73.

West, K. L., Kelliher, J. L., Xu, Z., An, L., Reed, M. R., Eoff, R. L., Wang, J., Huen, M. S. Y., and Leung, J. W. C.  LC8/DYNLL1 is a 53BP1 effector and regulates checkpoint activation. Nucleic Acids Res. 2019, 47(12): 6236-6249.

Ketkar, A., Maddukuri, L., Penthala, N. R., Reed, M. R., Zafar, M. K., Crooks, P. A., and Eoff, R. L. Inhibition of human DNA polymerases eta and kappa by indole-derived molecules occurs through distinct mechanisms. ACS Chem Biol. 2019, 14(6): 1337-1351.

Reed, M. R., Maddukuri, L., Ketkar, A., Byrum, S. D., Zafar, M. K., Bostian, A. C. L., Tackett, A. J., and Eoff, R. L. Inhibition of tryptophan-2,3-deoxygenate impairs DNA damage tolerance and repair in glioma cells. (In preparation)

Patents

U.S. Provisional Patent Application No.: 62/792,226

Title: Naphthoyl, napthalenylmethyl, and naphthalenysulfonyl indole aminoguanidine analogs as DNA polymerase kappa inhibitors targeting glioblastoma.

Inventors: Robert L. Eoff, Peter Crooks, Narsimha Penthala, Amit Ketkar, Leena Maddukuri, and Megan Reed

BV Reference No.: 2019-09

Awards

2017: First place overall, for poster presentation at UAMS Student Research Day

2017: First place, Bhuvan award for excellence in biochemistry

2020: First place overall, for poster presentation at UAMS Student Research Day

2020: Second place, Bhuvan award for excellence in biochemistry

Filed Under: Student Highlights

Dustyn Barnette Student Highlight

Dustyn is a Ph.D. Student in his 5th year in the Biochemistry and Molecular Biology Department. He joined the laboratory of Dr. Grover P. Miller for his research studies.

He has a B.S. in Biology from Ouachita Baptist University with minors in chemistry and art.

Research Interest Statement

A major obstacle in drug development is the occurrence of drug-induced liver injury (DILI).  DILI can cause drugs to be rejected for market approval, or it can be idiosyncratic, meaning that it may not be discovered until after market approval.

The focus of my graduate research is to study metabolic activation of drugs to form toxic metabolites, which is one of the possible causes of idiosyncratic DILI.  I am interested in the development and use of in vitro systems and computational models to serve as alternatives to in vivo trials for predicting and investigating mechanisms of drug induced hepatotoxicity.  I have conducted thorough analyses of metabolic pathways of three marketed drugs (warfarin, terbinafine, and meloxicam) with special focus on pathways that contribute to bioactivation or detoxification.  Through these efforts, I am working to establish the mechanisms that explain the idiosyncratic DILI observed for some drugs.  The clinical application of this mechanistic knowledge is to be able to predict which patients will be vulnerable to DILI based on factors that affect metabolism such as genetics, environmental exposures, and drug-drug interactions.

Something Notable about Time as a Graduate Student

Last spring, I got to go to Baltimore to present my research at the annual Society of Toxicology meeting.  Of course, the very first thing I did when I got there is take the metro train from the airport to the convention center.  When the train got to my final stop, I walked over to the door ready to get off.  I had no idea that this station was closed for construction, and the train was only stopping there because it had to wait on a crossing.  No worries though, I found this all out very quickly after the train suddenly lurched ahead again, sending my unsuspecting self toppling like a flailing rag doll straight onto the lap of some random guy sitting next to the door.  Sometimes, to only way to learn things is the hard way.

Career Goals

Once I get my Ph.D. I want to enroll in a post-doctoral position in a government research lab.  Long term, I want my career to facilitate the development, improvement, and use of in vitro systems and computational models as alternatives to in vivo for predicting and investigating mechanisms of drug induced hepatotoxicity.

Experiment or Technique You Would Most Like to Do

I always enjoy when I get to use fluorescent compounds to chemically label the metabolites that I’m studying.  There is something very fulfilling about working with brightly colored samples.

Fun fact

I like to hike.  One of my favorite trails in Arkansas is the Lost Valley Trail near Ponca.  At the hike’s end there’s a big cave with a waterfall in it, but my favorite part is actually around the halfway point.  There’s a little cave located a couple hundred feet off the main trail that my cousins and I just stumbled upon by chance one time.  You have to crawl to get into it, but once you’re in, you get to see dozens of little aquatic invertebrate fossils all over the walls and ceiling.  It looks very cool!

Publications

Comprehensive kinetic and modeling analyses revealed CYP2C9 and 3A4 determine terbinafine metabolic clearance and bioactivation.  Dustyn A. Barnette, Mary A. Davis, Noah Flynn, Anirudh S. Pidugu, S. Joshua Swamidass, and Grover P. Miller.  Biochemical Pharmacology.  October 9, 2019.  doi: 10.1016/j.bcp.2019.113661, PMID: 31605674.

CYP2C19 and 3A4 dominate metabolic clearance and bioactivation of terbinafine based on computational and experimental approaches.  Mary A. Davis, Dustyn A. Barnette, Noah R. Flynn, Anirudh S. Pidugu, S. Joshua Swamidass, Gunnar Boysen, Grover P. Miller.  Chemical Research in Toxicolgoy.  2019 Apr 10. doi: 10.1021/acs.chemrestox.9b00006, PMID: 30925039.

Lamisil (terbinafine) toxicity: Determining pathways to bioactivation through computational and experimental approaches. Dustyn A. Barnette, Mary A. Davis, Na L. Dang, Anirudh S. Pidugu, Tyler Hughes, S. Joshua Swamidass, Gunnar Boysen, Grover P. Miller.  Biochemical Pharmacology.  August 2018, 156, 10-21.  doi:  https://doi.org/10.1016/j.bcp.2018.07.043, PMID: 30076845.

Stereospecific Metabolism of R- and S-Warfarin by Human Hepatic Cytosolic Reductases.  Dustyn A. Barnette, Bryce P. Johnson, Dakota L. Pouncey, Robert Nshimiyimana, Linda Desrochers, Thomas E. Goodwin, Grover P. Miller.  Drug Metabolism and Disposition.  September 2017, 45 (9) 1000-1007.  doi: https://doi.org/10.1124/dmd.117.075929, PMID: 28646078.

Exposure cessation during adulthood did not prevent immunotoxicity caused by developmental exposure to low-level trichloroethylene in drinking water.  Kathleen M. Gilbert, Shasha Bai, Dustyn Barnette, and Sarah J. Blossom.  Toxicological Sciences.  March 2017, 157 (2): 429-437.  doi:10.1093/toxsci/kfx061, PMID: 28369519.

Evaluation of virulence and antimicrobial resistance in Salmonella enterica serovar Enteritidis isolates from humans and chicken- and egg-associated sources. Jing Han, Kuppan Gokulan, Dustyn Barnette, Sangeeta Khare, Anthony W. Rooney, Joanna Deck, Rajesh Nayak, Rossina Stefanova, Mark E. Hart, and Steven L. Foley. Foodborne Pathogens and Disease. December 2013, 10 (12): 1008-1015. doi:10.1089/fpd.2013.1518, PMID: 24102082.

Awards

UAMS Graduate Student Association Research Symposium – Third Place for Poster Presentations (Fall 2019)

Arkansas Academy of Sciences Conference – Third Place for Biochemistry/Chemistry Oral Presentation (Spring 2016)

Filed Under: iBioDS Highlights, Student Highlights

Tresor Mukiza Recognized for Research Publication

Tresor Mukiza, a Ph.D. student at UAMS, received high honors for his first-author publication in the November issue of the journal Genetics. The editors selected the paper to be featured in a Highlight, and cover art for the article was displayed on the journal home page during the month of publication.

“This is a notable accomplishment,” said Wayne Wahls, Ph.D., professor of Biochemistry and Molecular Biology and mentor for Mukiza’s doctoral dissertation research. “It reflects the high quality of Tresor’s research and the importance of his findings to the scientific community.”

In humans, the wrong number of chromosomes (aneuploidy) is the leading cause of spontaneous pregnancy loss, intellectual disability, and congenital birth defects such as Down syndrome.  This stems from errors in chromosome segregation during meiosis, which produces the reproductive cells (sperm and eggs) of the parents.  Because the fundamental features of meiosis are conserved from fungi to humans, the Wahls’ laboratory uses an exceptionally powerful model organism, the fission yeast S. pombe, to study molecular mechanisms of meiosis.

In their paper, Mukiza and his co-authors Reine Protacio, Ph.D., Mari Davidson, Ph.D., Walter Steiner Ph.D., and Wayne Wahls, Ph.D. report that DNA sequence elements and their binding proteins remodel the structure of chromosomes to regulate the distribution of homologous recombination during meiosis. “This provides important clues about the meiotic origins of aneuploidy,” said Mukiza, “because correctly positioned homologous recombination is essential for the proper segregation of chromosomes in meiosis.”

Mukiza earned a bachelor’s degree in biology with a minor in chemistry, Magna Cum Laude with Distinction in Biology, from Hendrix College. He was just awarded his Ph.D. degree in biochemistry and molecular biology from UAMS.  Mukiza’s dissertation research was supported by a $1.2 million grant to Wahls from the National Institute of General Medical Sciences, which is the basic science institute within the National Institutes of Health.

Filed Under: Student Highlights

Andrea Edwards Student Highlight

Andrea is a Ph.D. Student in her 5th year in the Interdisciplinary Biomedical Sciences Program. She joined the laboratory of Dr. Kevin Raney in the Biochemistry and Molecular Biology Department for her research studies.

She has a B.S. in Biology from the University of Arkansas at Fort Smith.

Research Interest Statement

I study G-Quadruplexes which are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes. Proto-oncogenes normally regulate cell proliferation and growth but transition to oncogenes when mutated or overexpressed, promoting tumorigenesis. The prominence of G-Quadruplexes in proto-oncogenes suggests they serve an important regulatory role in the cell. Interestingly, G-Quadruplexes are highly susceptible to oxidative stress. Thus, it is important that there is a repair mechanism in place to protect these important structures. Poly (ADP-ribose) Polymerase -1 (PARP-1) binds various DNA structures and responds to DNA damage. In response, PARP-1 is enzymatically activated and covalently modifies repair enzymes or chromatin-associated proteins with polymers of ADP-ribose (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. During my research studies, I found that PARP-1 binds several G-Quadruplex structures. However, only a subset of G-Quadruplexes promote PARP-1 activity. The G-Quadruplex-forming sequence found in the proto-oncogene c-KIT promoter enzymatically activates PARP-1. I found that the loop-forming characteristics of the c-KIT G-Quadruplex sequence regulate PARP-1 catalytic activity. Eliminating the loop features reduced PARP-1 activity. Interestingly, oxidized G-Quadruplexes have been shown to form unique, looped structures to signal repair and also regulate gene expression. I found that oxidized G-Quadruplexes stimulate significant PARP-1 activity. These results support a PARP-1 and G-Quadruplex interaction, potentially linked to DNA repair and gene regulatory functions.

Something Notable about Time as a Graduate Student

At this institution, I met people that have given me great advice that I will cherish and carry with me throughout life.

Career Goals

I would like to work at St. Jude for my post-doctoral research. I have interests in teaching and also have a newfound interest in precision medicine. A dream job of mine would be to develop novel cancer therapeutics or provide knowledge that could be implemented into making better therapies.

Experiment or Technique You Would Most Like to Do

I am really interested in working with animal models such as mice. I would also like to work with patient tumor samples, performing techniques such as immunohistochemistry to identify tumorigenic markers.

Fun fact

I love to cook and try new dishes. I play piano and I’m currently learning to play by ear. I love riding four-wheelers and banshees on the farm.

Publications

Jun Gao, Alicia K. Byrd, Boris L. Zybailov, John C. Marecki, Michael J. Guderyon, Andrea D. Edwards, Shubeena Chib, Kirk L. West, Zachary J. Waldrip, Samuel G. Mackintosh, Zhaofeng Gao, Andrea A. Putnam, Eckhard Jankowsky and Kevin D. Raney, “DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA.” Chemical Communications., Vol. 55, pg. 4467-4470, 2019.
https://www.ncbi.nlm.nih.gov/pubmed/30855040

Andrea D. Edwards, Alicia K. Byrd, John C. Marecki, and Kevin D. Raney, “G-Quadruplex loops regulate PARP-1 activation.” In preparation.

Grants

Southern Regional Education Board Dissertation Fellowship

Awards

UAMS 1st place 2019 Bhuvan Award for Excellence in Biochemistry Graduate Research

ASBMB 2019 Graduate Student Travel Award for Experimental Biology Meeting Orlando, Florida

Conference Series LLC Ltd. Molecular Biology and Nucleic Acids Conference Toronto, Ontario, Canada-Student Poster award 2018

Filed Under: Student Highlights

Tresor O. Mukiza Student Highlight

Tresor is a Ph.D. Student in his fifth year in the Biochemistry and Molecular Biology Department in the laboratory of Dr. Wayne Wahls.

Tresor Mukiza
(Image credit: Reine Protacio)

He has a B.A. in Biology with a Chemistry minor from Hendrix College.

Research Interest Statement

The wrong number of chromosomes, called aneuploidy, is the leading cause of spontaneous pregnancy loss, intellectual disability, and congenital birth defects such as Down syndrome (trisomy 21). These aneuploidies stem from errors during meiosis in one of the parents, which generates their reproductive cells (sperm and eggs). A meiotic process called homologous recombination plays a crucial role in placing the correct number of chromosomes into reproductive cells.

My Ph.D. dissertation is focused on how meiotic recombination is correctly positioned in the genome, which is required for the faithful segregation of chromosomes. By studying five different classes of recombination hotspots in the fission yeast Schizosaccharomyces pombe, I provided new insight into the underlying mechanisms. Diverse, cis-acting regulatory modules (different transcription factors and their binding sites) each function through shared chromatin remodeling pathways that help provide the basal recombination machinery access to its DNA substrates within chromatin. This work helps us to understand broadly conserved mechanisms that create reproductive cells, and it provides insight into the underlying causes of Down syndrome and miscarriage.

Something Notable about Time as a Graduate Student

I enjoyed the collaborative environment in the BCMB department where students and faculty members are willing to help each other.

Career Goals

I want to do a postdoctoral fellowship and continue doing research while also teaching.

Experiment or Technique You Would Most Like to Do

I love analyzing chromatin structure of specific chromosomal regions using micrococcal nuclease to digest non-nucleosomal DNA. Nicely phased nucleosomes flanked by nucleosome-depleted promoters or linker DNA make the most beautiful figures in my opinion. I would love to try to look at an entire genome chromatin structure in various conditions by coupling micrococcal nuclease and deep-sequencing the resulting mononucleosomal DNA.

Fun fact

I am from Rwanda and studied in French before coming to the USA for college. After the first week of classes in college, my chemistry teacher said we would have a quiz at the beginning of the next class period. So that next Monday, I found out that a quiz is a small test the hard way. Although I miserably failed, I will never forget what a quiz is. I love playing soccer, although my advanced age has considerably slowed me down.

Publications

Mukiza TO, Protacio RU, Davidson MK, Steiner WW, Wahls WP. Five DNA sequences activate meiotic recombination hotspot via chromatin remodeling. Genetics. 2019.
https://www.ncbi.nlm.nih.gov/pubmed/31511300

Ketkar A, Voehler M, Mukiza T, Eoff RL. Residues in the RecQ C-terminal Domain of the Human Werner Syndrome Helicase are involved in unwinding g-quadruplexes DNA. Journal of Biological Chemistry. 2017.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336152/

Awards

Best oral presentation by a graduate student at the American Society of Microbiology-South East Region, Little Rock, AR.

Academic All-America Team for Division III college soccer

Filed Under: Student Highlights

Graduate Student Explores Potential of Handheld DNA/RNA Sequencers in Outbreaks

By Amy Widner

 Imagine there’s an outbreak of an infectious disease. Could health officials on the ground harness the power of new handheld DNA and RNA sequencers to monitor outbreaks in real-time and quickly contain them?

This question lies at the heart of research published in the journal Infection, Genetics and Evolution by UAMS Biochemistry and Molecular Biology track graduate student Duah Alkam. She and her advisers from the College of Medicine Department of Biomedical Informatics and the Department of Microbiology and Immunology collaborated with the Arkansas Department of Health to look at specimens collected during a 2016 mumps outbreak in Northwest Arkansas.

It took the Human Genome Project 13 years to complete the first sequence of a human genome in 2003. As sequencers became available for purchase, they were large, expensive and slow.

Alkam holding tech in palm of hand
Alkam used the the Oxford Nanopore Technologies MinION to sequence the samples in her study.Amy Widner

That has changed. Alkam used a device called the Oxford Nanopore Technologies MinION to sequence each sample in a matter of hours. To offload the data, she simply connected the MinION through a USB port to a laptop.

“You see results on your computer in real time,” Alkam said. “It’s fast, affordable and simple. The idea is that something like this might be useful during an outbreak, especially in a rural setting. If you can quickly identify a strain, you’re that much closer to understanding the origin of the outbreak, which may help contain it and protect the at-risk population.”

The new challenge for scientists is how to interpret the massive amount of data produced by these powerful sequencers. That is where the relatively new field of biomedical informatics comes in.

“Biomedical informatics allows us to look at genomes within a matter of hours and compare them, pinpointing connections and what might be important about these datasets,” Alkam said. “In this way, biomedical informatics is sort of the bridge between raw data and relevant information.”

In this case, Alkam was able to determine the unique characteristics of the specific variation of the mumps virus that was behind the 2016 outbreak. They used a computational technique called immunoinformatics to plot a “family tree” of sorts for the virus.

“We found that it was very similar to a strain that started an outbreak in Massachusetts around the same time in 2016, and it was also related to another strain that spread in Washington state, which may suggest that all three outbreaks originated from the same strain.”

While Alkam’s experiment was not conducted during an active outbreak, she and her advisers believe the results demonstrate great promise for the technique to be applied in the real world. Earlier in 2019, other scientists in the Department of Bioinformatics collaborated with researchers around the world for the first demonstration that the MinION could be used for the rapid genetic sequencing of multiple human viruses.

“The possibility of infectious disease outbreaks in health care settings and communities is something that unites us across the globe. We’re all vulnerable,” said Se-Ran Jun, Ph.D., Alkam’s adviser for the project and an assistant professor in biomedical informatics. “So at UAMS, it’s exciting each time we demonstrate how we can harness the power of new sequencing technology, big data science and analytics, and high performance computing in biomedical informatics to offer solutions.”

The project was funded with a grant to Jun from the UAMS for Translational Research Institute.

Alkam is a student in the UAMS Graduate School’s Graduate Program in Interdisciplinary Biomedical Sciences (GPIBS). Her other advisers are David Ussery, Ph.D., a professor in the Department of Biomedical Informatics; and Mark Smeltzer, Ph.D., a professor in the Department of Microbiology and Immunology.

Filed Under: iBioDS Highlights, Student Highlights

Eugene Nyamugenda Student Highlight

Eugene Nyamugenda

Eugene is a Ph.D. Student in his 5th year in the Biochemistry and Molecular Biology Department in the laboratory of Dr. Giulia Baldini.

He has a B.A. in Biochemistry and Molecular Biology from Hendrix College.

Research Interest Statement

The hypothalamus plays a central role in maintaining healthy energy homeostasis. The arcuate nucleus (ARC) of the hypothalamus receives anorexigenic signals from the periphery mediated by increased circulating leptin and insulin, which bind to receptors expressed by proopiomelanocortin (POMC) neurons in the ARC. When activated, POMC neurons release α-Melanocyte stimulating hormone (α-MSH). In the paraventricular nucleus (PVN), α-MSH binds to the melanocortin-4 receptor (MC4R) to signal decreased food intake and increased energy expenditure. Single-minded-1 (Sim1) neurons in the PVN include the population of MC4R neurons. My research uses mice to study the effect of obesity by a high-fat (HF) diet on the PVN neurons expressing Sim1 transcription factor and MC4R.  When mice are fed HF diet, they have increased body weight as a result of increased caloric intake. We found that exposure to HF diet induces loss of Sim1 neurons in the PVN and, in male mice, loss of POMC neurons and α-MSH abundance.  Because there are no reliable commercial antibodies that can detect MC4R, we generated a knock-in mouse line expressing HA-tagged MC4R (MC4R-HA) by using CRISPR/Cas9 technology to detect MC4R protein. We found that HF diet induces injury to MC4R neurons in the PVN as indicated by loss of MC4R protein, decreased mitochondrial abundance, and mitochondrial network size. The data suggest that HF diet induces loss of MC4R protein rather than of MC4R neurons, suggesting that expression of MC4R could be a target for anti-obesity therapy.

Something Notable about Time as a Graduate Student

Overall my time in graduate school has been excellent. I would say that I happened to fall into the right group of people. The life lesson I learned is never to translate a joke. The chances are either the joke is not funny, none understands it, or you will offend someone.

Career Goals

I want to do a postdoctoral fellowship for a few years and look for opportunities in biotech and pharmaceutical companies.

Experiment or Technique You Would Most Like to Do

I like to do many experiments. I love making DNA constructs. It excites me. If my labmates wanted to subclone anything, I would volunteer to do it.

Fun fact

When I grew up, my mother treated every ailment with a specific type of food (she still does). When I got sick in boarding school, I asked permission to go home. She would cook food for me, and the next day I would feel better and go back to school. Food is still my over-the-counter medicine today.  If you see me sick, the first treatment to give me is food (enough of it).

Publications

Nyamugenda E, Cox AB, Pierce JB, Banning RC, Huynh ML, May C, Marshall S, Turkal CE, Duina AA. Charged residues on the side of the nucleosome contribute to normal Spt16-gene interactions in budding yeast. Epigenetics. 2018; 13(1):1-7. doi: 10.1080/15592294.2017.1418132. Epub 2018 Feb 8. PMID: 29271283

Nyamugenda E, Trentzsch M, Russell S, Miles T, Boysen G, Phelan KD, Baldini G. Injury to hypothalamic Sim1 neurons is a common feature of obesity by exposure to a high-fat diet in male and female mice. J Neurochem. 2019 Apr; 149(1):73-97. doi: 10.1111/jnc.14662. Epub 2019 Feb 11. PMID: 30615192

Awards

Rwanda Presidential Scholarship

Filed Under: Student Highlights

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