INBRE Summer Program 2024
Summer Research Fellowships for Undergraduate Students – Plot your course for the future...Explore a Summer Fellowship in Biomedical Research
Dates of Summer Program: May 20, 2024 – July 26, 2024
Application Deadline: February 9, 2024
APPLY HERE
Looking for a summer research experience? Paid summer research fellowships are available for undergraduate students who are rising juniors or seniors. Selected students will work on a project relevant to human health led by a faculty member at either the University of Arkansas, or the University of Arkansas for Medical Sciences. The scope of the projects range from laboratory based research to clinical studies using human subjects. A major goal of the INBRE Summer Student Research Fellowship Programs is to involve Arkansas students from groups traditionally underrepresented in science in a stimulating research experience. The Arkansas INBRE offers two 10-week summer research programs tailored to students with STEM majors (e.g., biology, chemistry, physics, engineering, computer science, mathematics, and related disciplines) who are considering careers in biomedical research.
Mentors in the Department of Chemistry and Biochemistry
Biophysical and Biochemical Approaches to Study Ras-Related Protein Interactions (1UARK)
Paul D. Adams, Ph.D.
Department of Chemistry and Biochemistry
Our research interests are focused on understanding structure and function of Ras-related
proteins involved in signal transduction processes involved in the onset of diseases
such as cancer and COPD. The Ras proteins presently being studied in the laboratory
include Cdc42 (Cell division cycle 42) and Rheb (Ras homology enriched in brain),
both of which are involved in a wide range of cellular processes including cell cycle
progression, cytoskeletal organization, protein trafficking, and secretion. The goal
of our research is to develop approaches to study molecular details of these proteins,
and their interaction with effectors. We use several biophysical and biochemical techniques,
including site-directed mutagenesis, multi-dimensional NMR spectroscopy for use in
protein structure determination as well as dynamics, steady-state and time-resolved
fluorescence spectroscopy, isothermal titration calorimetry, differential scanning
calorimetry, protein expression and purification procedures, circular dichroism spectroscopy,
structural analysis of proteins using molecular dynamics simulations in our approaches.
Dr. Adams Website
Pre-requisite courses: None
Bioinformatics students: Yes
Nanoparticles Interact with Bacterial Cells (28UARK)
Jingyi Chen, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
The antibiotic resistance becomes an imminent issue in the treatment of bacterial
infections. Metal nanoparticles have been used as alternative antimicrobial agents.
The most well-known example is the antimicrobial effect of metal nanoparticles. Studies
have suggested serval antimicrobial mechanisms of metal nanoparticles including membrane
damage, DNA condensation and malfunction, release of metal ions, free radical generations,
and loss of ATP production; however, these findings were based on the ensemble measurements
and the results remain controversial. We address the controversies by developing methodologies
for studying individual biomolecules (i.e., proteins, DNA, and membrane lipids) with
temporal and spatial resolutions in single live cells and by measuring the dependence
of nanoparticles’ effectiveness on particle shapes and surface modifications. Dr. Chen’s Lab
Pre-requisite courses: None
Bioinformatics students: Yes
Functional Optical Spectroscopy and Microscopy Imaging in Material and Biological
Science(32UARK)
Bin Dong, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
Our research team is interested in in-situ measurement of nanoscale dynamics in functional
materials and biological systems by optical spectro-microscopy imaging methods. Our
work enables us to better understand important processes such as receptor-mediated
endocytosis, heterogeneous catalysis and structural, morphological changes in nanomaterials
(e.g., nanoparticles, thin layered materials), etc. Understanding these processes
will profoundly impact designing better drug delivery vehicles, catalysts, and functional
materials. For more details, please visit us at DongLab.
Pre-requisite courses: None
Bioinformatics students: Yes
Studying Bacteria and Cancers by Synthetic Biology (30UARK)
Chenguang Fan, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
The research interest in our group includes protein chemistry, bacterial pathogenesis,
cancer biology, and synthetic biology. The major approach is to use genetic code expansion
technique to incorporate noncanonical amino acids into proteins for different studies:
1) Protein chemistry: developing noncanonical amino acid incorporation systems for
labeling proteins, studying post-translational modifications, and mapping protein-protein
interaction networks. 2) Pathogen infections: applying the genetic code expansion
technique in pathogens. Specific topics include studying effects of post-translational
modifications in Salmonella toxicity, exploring host targets of Salmonella toxins,
and designing small molecules to block Salmonella metabolic organelle functions. 3)
Cancer biology: applying the genetic code expansion technique in cancer research,
studying phosphorylation and acetylation identified in a variety of cancer cells.
4) Synthetic biology: utilizing naturally designed protein complexes in bacteria as
nano-bioreactors for biofuel and chemical compound production. Fan Lab
Pre-requisite courses: None
Bioinformatics students: Yes
Bioanalytical Chemistry on a Small Scale (6UARK)
Ingrid Fritsch, Ph.D.
Department of Chemistry and Biochemistry
The unifying theme of our research program is the development of multifunctional,
miniaturized analytical devices with integrated components on a single substrate.
Such “labs-on-a-chip” have promise in revolutionizing sample preparation, chemical
analysis, and chemical synthesis. A wide variety of applications are possible, including
on-site analysis of environmental samples (e.g. cyanobacteria), analysis of key components
in the body or body fluids (e.g. neurotransmitters), and synthesis and purification
of materials (such as therapeutic peptides) on a small scale. To carry out this work,
our activities are interdisciplinary in nature. We investigate chemistry in the limit
of ultrasmall volumes (nanoliters to picoliters), near materials having ultrasmall
features (submicron patterning), and with new approaches to manipulate liquids in
an automated way (microfluidics). In addition, we study the means of interfacing inorganic
electrodes and micro/nanostructures with assemblies of organic and biologically- important
molecules. Computer simulations are used as a complementary tool to further investigate
these systems. Fritsch Research Group
Pre-requisite courses: None
Bioinformatics students: Yes
Dissecting Essential Motions of Molecular Nanomachines in Health and Disease (33UARK)
Dylan Girodat, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
The Girodat lab is interested in the process of protein synthesis initiation regulation
mechanisms in prokaryotic organisms and how it is inhibited by antibiotics. Protein
synthesis is the target of roughly half of all antibiotics and is facilitated by the
ribonucleoprotein complex known as the ribosome. For protein synthesis to be commenced
the small and large subunits must be joined together on a messenger RNA encoding a
protein. Intricate rearrangements of ribosomal segments known as inter-subunit bridges
are required to facilitate subunit joining. The Girodat lab focuses on studying the
structural dynamics of subunit joining using cryo-electron microscopy, molecular simulations,
and pre-steady state kinetics. These approaches provide detailed mechanistic understandings
of ribosomal subunit joining that underpins an essential process in gene expression.
Studying these mechanisms in the presence of antibiotics provides valuable insights
into how these antibiotics act to inhibit ribosomal subunit joining. Another aspect
of the Girodat lab’s research is to study the structural impact of ribosomal variations
that lead to human disease known as ribosomopathies. The Girodat lab uses cryo-electron
microscopy to solve structures of variant ribosomes to understand the structural and
functional impact of disease-causing mutations.
Pre-requisite courses: None
Bioinformatics students: Yes
Carbon nanomaterial functionalization and applications (27UARK)
Maggie He, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
Carbon nanomaterials such as carbon nanotubes (CNTs) and graphene have outstanding
mechanical, electrical, optical, and biological properties. These unique properties
have enabled various applications from electrode materials to sensors and biomedical
devices. Functionalization plays an important role in tailoring these nanomaterials’
properties and functions through the anchoring of chemical groups, macromolecules,
or biomolecules. Our research focuses on developing new methods for the functionalization
of CNTs and graphene using organic chemistry and exploring their utility in material
and biological applications. Because our research is interdisciplinary, students have
the opportunity to learn diverse techniques in organic synthesis as well as materials
characterization. He Group Website
Pre-requisite courses: None
Bioinformatics students: Yes
Biomolecular Simulations (26UARK)
Mahmoud Moradi, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
Research in Moradi Lab (Biomolecular Simulations Group) is centered around two inter-related questions: (i) how do proteins function by changing
their conformation and undergoing concerted motions? and (ii) how can we simulate
these functionally important conformational changes at an atomic level? We develop
and employ various molecular dynamics based simulation techniques to tackle both problems.
Answering these questions would shed light on the structure-function relationships
in proteins, and could improve our understanding of disease at a molecular level.
We are particularly interested in the study of large-scale conformational changes
of proteins such as channels, transporters, membrane insertases, and viral fusion
proteins including influenza hemagglutinin and coronavirus spike protein. Moradi Lab
Pre-requisite courses: No
Bioinformatics students: Yes
3-Dimensional Structural Analysis of Protein-Ligand Complexes (17UARK)
Joshua Sakon, Ph.D.
Department of Chemistry and Biochemistry
Detailed structural studies of medically relevant proteins can reveal subtle features
concerning the interaction of the protein and its binding partners. From this information,
lead compounds may be developed using structure-based drug design methodology. Techniques
include protein isolation, protein crystallization and structural characterization
using x-ray crystallography. Dr. Sakon Website
Pre-requisite courses: None
Bioinformatics students: Yes
In Vivo Microdialysis Sampling Studies for Monitoring Signaling Molecules (18UARK)
Julie Stenken, Ph.D.
Department of Chemistry & Biochemistry Chemical Biology
Our bioanalytical chemistry laboratory focuses on making direct measurements as well
as improving the ability to make measurements within awake and freely moving mammalian
systems. Microdialysis sampling is a widely used and successful sample collection
method to obtain analytically-clean samples from very complex matrices such as mammalian
tissues, bioreactors, or environmental samples. There are numerous potential projects
that could be tailored for students and faculty within the Arkansas INBRE program.
Our current major focus has been aimed towards improving peptide and protein sampling
using the microdialysis sampling approach. Systems of interest include: 1. Detection
of cytokines and matrix metalloproteinases in situ within wound sites. 2. Modulation
of cytokines and MMPs during wound healing. 3. Measurement of neuropeptides related
to addiction. 4. Measurement of peptides and proteins (e.g., insulin, leptin) related
to obesity and metabolic syndrome. Common analytical techniques frequently used in
this laboratory include ELISA, HPLC, flow cytometry-based immunoassays, and mass spectrometry.
Pre-requisite Courses: Freshmen Chemistry
Bioinformatics Students: Yes
Glycosidase Mechanisms, Structure and Function (20UARK)
Susanne Striegler, Ph.D.
Department of Chemistry & Biochemistry
The prevalence of glycoside hydrolases in progression and pathology of multiple diseases
marks these enzymes as frequent targets during drug development. Glycosides are crucial
in many cell-to-cell recognitions including bacterial and viral infections, fertilization,
and disease recognition. The complex interactions of glycosides with protein receptors
or hydrolases are important for the understanding of underlying recognition processes.
Along these lines, we examined galactonoamidines as transition state analogs of beta-galactosidases
to elucidate important binding interactions in the active sites, enzyme conformations
that support inhibitor binding and the role of proton donors and nucleophiles. In
this project we use biochemical methods for protein expression and purification, spectroscopic
evaluation of enzyme function and structure that are supported by molecular docking
and modeling studies. Dr. Striegler Website
Pre-requisite courses: None
Bioinformatics students: No
Structure, Function and Interactions of Cytokines (21UARK)
Suresh Kumar Thallapuranam, Ph.D.
Department of Chemistry and Biochemistry
My research group is focused on understanding the structure, function, folding and
interaction(s) of fibroblast growth factors (FGFs). Using protein engineering techniques,
we are currently engaged in developing a new class of FGFs which have higher thermal
stability and enhanced wound healing activity. In addition, the molecular mechanisms
underlying the activation of the FGF receptor(s) are being investigated. Another
focus of my research group is to decipher the molecular events involved in the endoplasmic
reticulum- Golgi independent, non-classical secretion of cytokines such as, FGF(s),
vascular endothelial growth factor, and interleukins. We are also actively working
on in silico modeling of 3D structures of proteins and protein-ligand interactions.
We use a wide array of structural biology, molecular biology, cell biology and computational
techniques in our research. Dr. Thallapuranam Website
Pre-requisite courses: None
Bioinformatics students: Yes
Computational Modeling of Chemical and Biophysical Systems. (25UARK)
Feng Wang, Ph.D.
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville
The Wang laboratory uses supercomputing resources to model interesting problems of
chemical and biophysical significance. Projects include but not limited to materials
under extreme conditions, crystallization of polymorphs, biomass conversion for sustainable
energy, and physical properties of pharmaceutical compounds and small peptides.
Pre-requisite courses: Calculus I or equivalent
Bioinformatics students: Yes