Title: Mechanisms of Chemotherapy-Induced Cognitive Impairment
PI: Antiño R. Allen, PhD
Associate Professor
Division of Radiation Health
UAMS – College of Pharmacy
Chemotherapy-induced cognitive impairment, colloquially termed as ‘chemobrain’, is a poorly understood phenomenon affecting a highly variable proportion of both male and female cancer patients as well as survivors of all ages and many chemotherapy regimens. Chemobrain symptoms can persist for years post-chemotherapy, and some patients never regain their previous quality of life. Using genetic models and pharmacologic approaches, our work examines how the changes in the neuronal microenvironment e.g. inflammation, oxidative stress affects neurogenesis and cognitive function after exposure to Breast Cancer and Juvenile Acute Lymphoblastic Leukemia chemotherapy.
Lab Website: https://pharmacy.uams.edu/team/antino-r-allen/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/14wyModil-65l/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: Yes
Dr. Adam Wolfe SRI Bio
Title: Targeting DNA Repair to Overcome Radiation Resistance in Pancreatic Cancer
PI: Adam Wolfe, MD, PhD
Assistant Professor
Department of Radiation Oncology
UAMS – College of Medicine
The Wolfe Lab investigates DNA repair pathways leading to treatment resistance to radiation therapy, novel DNA damage radiation biomarkers, and the development of novel DNA repair targets to improve responses to radiation therapy. We are interested in understanding the molecular drivers of radiation resistance. Our main disease of focus is pancreatic cancer. We utilize genetic and proteomic approaches to address the fundamental mechanisms of genetic alterations in cancer cells, resulting in heightened DNA repair leading to radiation resistance. We have developed relevant in vitro and in vivo models of human cancer that mimic the disease phenotype in the patients.
Lab Website: adamwolfelab.com
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/12Sv-7rbjMxQNU/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: No
Dr. Alicia K. Byrd Bio
Title: Mechanisms of genome maintenance by HELB
PI: Alicia K. Byrd, PhD
Assistant Professor
Department of Biochemistry and Molecular Biology
UAMS – College of Medicine
HELB is a DNA helicase whose overexpression is associated with reduced survival in glioma but increased survival in melanoma. HELB is involved in DNA repair and cancer therapy resistance. DNA repair affects genome instability, which is a hallmark of cancer cells. Despite this, the mechanisms by which HELB affects genome instability are not well defined. Using cellular and in vitro approaches, our lab is studying the molecular mechanism by which HELB increases genome stability after stalling of DNA replication.
Lab Website: https://medicine.uams.edu/biochemistry/faculty/primary/alicia-k-byrd-ph-d/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/alicia.byrd.1/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: No
Dr. Analiz Rodriguez
PI: Analiz Rodriguez MD, PhD
Associate Professor (effective 7/1/22)
Department of Neurosurgery
The Rodriguez lab investigates glioblastoma and metastatic brain tumors. Patients with these tumors typically have less than a year and a half to live after diagnosis. The laboratory uses next generation sequencing and proteomics to identify novel targets and understand tumor progression. Patient-derived organoid models are also used to validate candidate targets and understand brain tumor growth. Dr. Rodriguez is also interested in health care disparities and how to improve access to surgical interventions for brain tumor patients.
Lab Website: https://neurosurgery.uams.edu/rodriguez-lab/
My NCBI: https://pubmed.ncbi.nlm.nih.gov/?term=analiz+rodriguez&sort=date
Pre-requisite courses: No
Bioinformatics Students: Yes
Dr. Darin E. Jones Bio
PI: Darin E. Jones, PhD
Associate Professor
Department of Pharmaceutical Sciences
UAMS – College of Pharmacy
We develop small molecule inhibitors and chemical tool compounds of essential proteins involved in DNA repair to provide a greater understanding of the mechanisms of DNA repair and of chemotherapeutic drug resistance. We have identified selective inhibitors of poly(ADP-ribose) glycohydrolase (PARG), a monogenic enzyme that removes the poly(ADP-ribose) posttranslational modification of proteins modified by PARP1. A genetic knockdown of PARG sensitizes cells to DNA damage and phenocopies the effects of PARP1 enzymatic inhibitors in BRCA-deficient cells. In this project, we improve the potency and selectivity of small molecule PARG inhibitors through structure-guided chemical synthesis and testing in vitro, and advance selected compounds to preclinical trials of tumor killing activity in cultured cells and xenograft models of breast and ovarian cancer.
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/darin.jones.1/bibliography/public/
Pre-requisite courses: Organic chemistry
Bioinformatics Students: Yes
Dr. Karl W. Boehme Bio
Title: Viruses and the type-1 interferon response
PI: Karl W. Boehme, Ph.D.
Associate Professor
Department of Microbiology & Immunology
UAMS – College of Medicine
Type-1 interferons are a component of the innate immune system that are critical for controlling viruses. Viral infection causes the production of type-1 interferons, which interfere with viral replication and limit viral disease. We use mammalian orthoreovirus (reovirus) as a model to uncover how viruses trigger the type-1 interferon response during infection, as well as how viruses overcome type-1 interferon responses to replicate efficiently. Ongoing work in the lab combines genetic, biochemical, and cell biological approaches to investigate these questions in cell culture. We also explore the role of type-1 interferons in viral disease using mice as a small animal model.
Lab Website: https://medicine.uams.edu/mbim/faculty/primary/karl-boehme-ph-d/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/karl.boehme.1/bibliography/public/
Pre-requisite courses: No
Bioinformatics students: No
Karl Boehme, Ph.D.
Associate Professor
Department of Microbiology & Immunology
University of Arkansas for Medical Sciences
Little Rock, AR 72205
Phone (501) 686-5189
Email: kwboehme@uams.edu
Dr. Nukhet Aykin-Burns
TITLE: Determining efficacy of tocotrienols against lead toxicity.
PI: Nukhet Aykin-Burns, PhD
Associate Professor,
Department of Pharmaceutical Sciences
UAMS – College of Pharmacy
The neurotoxicity of lead has been well established through numerous studies. However, the cellular processes of lead neurotoxicity, as well as techniques to prevent or reverse cellular damage after lead exposure, remain unknown. Oxidative stress plays a primary role in lead-induced neurotoxicity, thus antioxidants should assist in reviving lead-exposed cells. This project will explore different isoforms of tocotrienols as antioxidant agents in PC-12 cells after lead exposure. Selective oxidative stress parameters, including glutathione (GSH), glutathione disulfide (GSSG) and mitochondrial function will be measured in PC-12 cells exposed to various concentrations of lead acetate.
STUDENT’S RESPONSIBILITIES-DUTIES IN THE PROPOSED PROJECT:
The student will be responsible for learning sterile tissue culture technique and methods to measure oxidative stress markers using spectrophotometry and extracellular flux analysis
Lab website: https://pharmacy.uams.edu/team/nukhet-aykin-burns/
Pre-requisite courses: No
Biomedical informatics Students: Yes
Dr. Robert Eoff Bio
Title: Mechanisms of DNA damage tolerance in response to replication stress
PI: Robert L. Eoff, PhD
Professor
Department of Biochemistry and Molecular Biology
UAMS – College of Medicine
Barriers to DNA replication can arise from endogenous and exogenous sources. Cells have evolved a variety of mechanisms that allow timely resumption of impaired fork progression. Our laboratory studies the molecular mechanisms that allow tolerance of endogenous fork barriers, such as G-quadruplexes (G4), and bypass of DNA damage induced by exogenous agents, such as genotoxic cancer therapies (e.g., ionizing radiation and chemotherapy). We are interested in determining the molecular features and biochemical properties that govern these processes. We are also focused on understanding how cells choose between translesion DNA synthesis (TLS) and other replication stress response (RSR) mechanisms. A long-term goal is to leverage our knowledge of the RSR as a means of developing new therapeutic strategies for the treatment of glioblastoma and other deadly forms of cancer.
Lab website: https://medicine.uams.edu/biochemistry/faculty/primary/eoff/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/robert.eoff.1/bibliography/public/
Pre-requisite courses: No
Bioinformatics students: No
Dr. Roy Morello SRI BIO
Title: Study of connective tissue diseases caused by alterations in collagens.
PI: Roy Morello, Ph.D.
Associate Professor
Department of Physiology & Cell Biology, Orthopaedic Surgery, and Division of Genetics
UAMS – College of Medicine
Summary: My research interests consist in genetic aspects and pathogenesis of human disease, with a focus on skeletal dysplasias and in the biology and function of collagens. We use laboratory mice with the objective to learn from the animal model and make correlations with relevant aspects of human disease to gain mechanistic insights of biological function. I have developed significant experience in the phenotypic, histological, imaging and molecular characterization of skeletal and non-skeletal defects in a variety of mouse models that phenocopy human syndromes, including Osteogenesis imperfecta (OI) but also Nail-Patella (NPS) and Ehlers-Danlos syndrome (EDS). The current focus is to study the impact of type I collagen alterations on the skeleton and the respiratory system in mouse models of OI.
Lab/PI website: https://medicine.uams.edu/physiology/faculty/primary-faculty/roy-morello/
My NBCI: https://www.ncbi.nlm.nih.gov/myncbi/1x1wyxj-kowks/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: Yes
Dr. Rupak Pathak Bio
Title: Sensitizing cancer cells to radiation with mevalonate pathway inhibitors
PI: Rupak Pathak, PhD
Assistant Professor
Division of Radiation Health
UAMS – College of Pharmacy
Radiation therapy effectively suppresses tumor growth, but concurrently cause damage to the normal healthy tissues. Normal tissue toxicity is one of the major dose-limiting factors. Therefore, strategies for radiation dose reduction are required without compromising its therapeutic efficacy. Mevalonate pathway inhibitors limit cholesterol biosynthesis and are used to treat cardiovascular diseases. Our preliminary data shows mevalonate pathway inhibitors suppress proliferation of various cancer cells. Here, we seek to determine whether various mevalonate pathway inhibitors enhances the potency of radiation to control cancer cell proliferation and define the underlying molecular mechanisms.
Lab Website: https://pharmacy.uams.edu/team/rupak-pathak/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/
Pre-requisite courses: No
Bioinformatics Students: Yes
Dr. Ruud P.M. Dings
Title: The role of tumor vasculature in carcinogenesis and treatment
PI: Ruud P.M. Dings, Ph.D, M.Sc. (He/Him)
Assistant Professor
Department of Radiation Oncology
UAMS – College of Medicine
The primary goal of our lab is to enhance our understanding of vascular biology to discover and develop improved methods for cancer treatment. Our major research interest is the tumor microenvironment, with emphasis on the crosstalk between the immune system and the tumor vasculature. Our objective is to identify and delineate unexplored mechanisms to positively contribute to the vascular biology field and improve treatment strategies. We use multi-disciplinary techniques that include cellular and molecular biology approaches (e.g. aseptic techniques, flow cytometry, PCR, ELISA and others) using patient samples and mouse models to decipher cancer initiation and progression, and the treatment thereof.
Lab Website: Ruud P.M. Dings lab website
My NCBI: NCBI Ruud P.M. Dings
Pre-requisite courses: No, but Biology, Immunology, and/or Chemistry is desired.
Bioinformatics Students: Yes
Dr. Tremaine Williams SRI BIO
Project title: Quantifying Clinical Team Social Network Influences on Care of Patients with Multimorbidity
PI: Tremaine Williams. Ed.D.
Assistant Professor,
Department of Biomedical Informatics
UAMS – College of Medicine
Broadly, Dr. Williams’ research focuses on testing interventions addressing the organizational and behavioral determinants of clinical information quality on multimorbidity patient care outcomes with the target of improving the design and usability of the electronic medical record. Nationally, 81% of Americans age 65 years and older and 50% of Americans age 45 to 65 are living with multiple chronic conditions (MCC). MCC prevalence in Arkansas has been ranked as the second highest of all 50 states among adults between the ages of 18 to 45. The state of MCCs not only poses a critical risk for individual health, but it is increasingly recognized as a risk to value-based care and population health due to the enormous care-related costs. With regard to spending, the top five percent of medically complex patients account for nearly 50 percent of the nation’s spending on health care. Through this project, we examine patient care team networks [social network analysis] as predictors of care outcomes [hospitalizations, Days-at-home/Days-between-hospitalizations, high cost encounters] to evaluate predictors of risk and increased care utilization. Outcomes drive the development and refinement of computational tools that support clinical management and mitigation of risk.
Pre-requisite courses: No
Biomedical informatics Students: Yes
Dr. Michael Bauer, PhD
Project title: Multi-omic Approaches Towards Understanding Cancer Biology
PI: Michael Bauer, PhD
Assistant Professor,
Department of Biomedical Informatics
UAMS – College of Medicine
My work focuses on furthering the understanding of cancer biology with the inclusion of multiple types of molecular data. These data types include epigenetic information, whole genome and RNA sequencing and using bioinformatic approaches to combine these genomic modalities to get a more complete picture of the cancer biology. Recent work has involved investigating the largely unexplored process of alternative splicing and lncRNA and their role in Multiple Myeloma. To that end, I am looking to incorporate third-generation sequencing, also known as long-read sequencing, which as the name denotes sequence considerably longer DNA and RNA fragments. These long sequences enable unambiguous identification of rare or novel transcripts, gene fusion events, and complex genomic rearrangements without the need for assembly. Additionally, long read sequencing can capture base modifications of both DNA and RNA, which provides a mechanism to interrogate both epigenomics and epitranscriptomics along with genomics and transcriptomics. Together with this cutting-edge technology and cell-lines, mouse models and patient data I will apply multi-omic analysis to get answers to important cancer biology questions such as mechanism of drug resistance, relapse, and patient risk stratification.
Lab Website: https://medicine.uams.edu/dbmi/team/michael-bauer-ph-d/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/michael.bauer.1/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: Yes
Dr. Eva C. Diaz Fuentes, M.D., Ph.D., MMsc
Project title: Physical fitness, nutrition, and sleep in relation to childhood development
PI: Eva C. Diaz Fuentes
Assistant Professor,
Department of Pediatrics, Department of Nutrition Section
UAMS – College of Medicine
Physical activity and nutrition are major determinants of health and childhood development. My research focuses on evaluating the complex interactions of nutrition, physical fitness, and sleep in relation with childhood health and development. Human studies involving school age are ongoing at the Arkansas Children’s Nutrition Center (ACNC). Our studies aim to evaluate how physical fitness, nutrition, and sleep impact metabolic and bioenergetic health of children. Study participants attend ACNC where measures of physical fitness (body composition, strength, aerobic capacity, etc.), physical activity, sleep, bioenergetics, indirect calorimetry, and metabolic health are conducted in the clinical and laboratory settings. There is opportunity to do data analysis if of interest.
Lab Website:https://medicine.uams.edu/pediatrics/people/eva-c-diaz-fuentes-m-d-mmsc/
My NCBI: https://www.ncbi.nlm.nih.gov/myncbi/eva%20carolina.diaz.1/bibliography/public/
Pre-requisite courses: No
Bioinformatics Students: Yes