INBRE 2025 Workshops
Saturday, November 8, 10:30 am -11:30 am
Workshop 1: Open Discussion – NIH Extramural Funding and Federal Policies Update
Jerry Ware, Ph.D., Program Coordinator of the Arkansas INBRE and Professor of Physiology and Cell Biology, UAMS
Location: HILL 206
The NIH Academic Research Enhancement Award (AREA) program supports faculty research at campuses that have not received significant NIH funding in the past. This workshop and open discussion will briefly introduce the NIH R15 and R16 funding mechanisms, and what distinguishes these awards from other NIH mechanisms, such as the RO1. Both the R15 and R16 have three main goals, 1) to support meritorious science 2) to strengthen the institution’s research environment, and 3) to expose students to research. Discussions will include what reviewers are “coached” to look for during peer review and some of the most common mistakes that can temper reviewer enthusiasm. Special consideration for how/where to incorporate all three goals into the application will be discussed. Current updates and changes to NIH policies will be discussed to ensure faculty are aware of changes to extramural funding opportunities.
Workshop 2: Biodata Science Workshop
Christopher Wardell, UAMS
Location: TBA
Workshop 3: CRISPR-Cas9-mediated Targeted Mutagenesis
Nagayasu Nakanishi, Ph.D., Dept. of Biological Sciences, UAF
Location: FERR 214, 323, and SCEN 122
Participant capacity: 10
CRISPR-Cas9 is a powerful genome editing tool whose applications are rapidly expanding across diverse fields from biomedicine to evolutionary biology. In this workshop, participants will learn how the CRISPR-Cas9 genome editing technology is used to investigate gene function in sea anemones. The hands-on session will involve microinjection of guide RNAs and Cas9 protein into zygotes of sea anemones to generate knockout mutations at a targeted locus.
Workshop 4: Behavioral Neuroscience Approaches
Amy Rosetta Poe, Ph.D., Assistant Professor, Biological Sciences, UAF
Location: SCEN 0606
Participant capacity: 16
The field of behavioral neuroscience involves the application of the principles of biology to study the genetic and developmental mechanisms of behavior. This workshop will provide hands-on experience in examining and quantifying animal behavior. First, I will provide an overview of ways in which behaviors like sleep and feeding can be studied in organisms like Drosophila. Participants will then have the opportunity to learn to identify, analyze, and characterize behaviors at different biological time points using provided movies of freely behaving Drosophila larvae. Participants should bring a phone with a stopwatch feature.
Workshop 5: Preparing for Graduate School
Stefan Kilyanek, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: CHEM 132
This workshop is targeted towards undergraduate students who are considering graduate school as a career. Topics to be discussed will include graduate school expectations and how to prepare for and select the right graduate school and program for you. A panel of faculty and graduate students will be available to share their tips, strategies, insights, and practical advice. We conclude with a Question and Answer session, with the possibility of breaking out into smaller groups based on specific interests.
Panelists:
Tiffany S. Weinkopff, Assistant Professor, Department of Microbiology & Immunology, UAMS
Aaron Kemp, Graduate student in Biomedical Informatics, UAMS
Eston Dunn, Graduate student in Biological Sciences, UAF
Chelsea Stephens, Graduate student in Chemistry and Biochemistry, UAF
Workshop 6: Molecular Modeling
Peter Pulay, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: MAIN 205
Participant capacity: 8 active participants (more people can listen but there are no computer seats for them)
Participants can view the workshop documents here.
This workshop will demonstrate the use of small or personal computers to model molecules, calculate their geometry, infrared and Raman, NMR and VCD spectra, relative stability, NMR chemical shifts, reaction paths and barriers, etc.
The procedure has two steps. First, a qualitatively correct molecular geometry is constructed using a Graphical User Interface and a molecule builder. In the second step, a Quantum Mechanical program allows the determination of wavefunctions, molecular geometries and other properties.
We will use the Parallel Quantum Solutions software developed in Dr. Pulay’s group because a free version is available. Calculations will run on a U of A cloud server at the workshop, but the same programs can be installed free on Windows, Mac and Linux PCs from Dr. Feng Wang’s website.
The 33-page workshop document has a general discussion and describes several exercises (below) in detail. If everything goes well, we will be able to finish the first two.
- Relative stability of the singlet and triplet states of methylene, CH2, and CF2
- Distinguishing 2,3- and 2,5-dihydrofuran by comparing experimental and calculated infrared and NMR spectra
- A molecule with a surprising structure: SF4
- Energetics and reaction path of the cyclobutene thermal ring opening reaction
- Geometry, infrared spectra, and NMR chemical shifts of cyclohexene
Workshop 7: Investigating Metabolism with Multiscale Approaches – From Molecule to Tissue
Timothy J. Muldoon, M.D., Ph.D., Dept. of Biomedical Engineering, Metabolic Imaging and Spectroscopy Core, Arkansas Integrative Metabolic Research Center, UAF
Alan Woessner, Ph.D., Core Manager, Metabolic Imaging and Spectroscopy Core, Arkansas Integrative Metabolic Research Center, UAF
Suresh Thallapuranam, Ph.D., Dept. of Chemistry and Biochemistry, Bioenergetics Core, Arkansas Integrative Metabolic Research Center, UAF
Patience Okoto, Ph.D., Core Manager, Bioenergetics Core, Arkansas Integrative Metabolic Research Center, UAF
Xintao Wu, Ph.D., Dept. of Electrical Engineering and Computer Science, Data Science Core, Arkansas Integrative Metabolic Research Center, UAF
Prateek Verma, Ph.D., Core Manager, Data Science Core, Arkansas Integrative Metabolic Research Center, UAF
Narasimhan Rajaram, Ph.D., Dept. of Biomedical Engineering, Arkansas Integrative Metabolic Research Center, UAF
Location: CHEM 144
The Arkansas Integrative Metabolic Research Center is a NIH-funded COBRE that was established in March 2021 to study metabolism in cells and tissue. As part of the AIMRC, three research cores were established as fee-for-service resources – an imaging and spectroscopy core, a bioenergetics core, and a data science core. This workshop will present the technologies and capabilities available within these three cores for utilization by universities and industry. The imaging and spectroscopy core currently houses state-of-the-art microscopes that allow high-resolution visualization of cell and tissue structure, function, and biomolecular composition. Two-photon microscopy enables quantification of cellular metabolism through endogenous fluorescence intensity and lifetime of the metabolic coenzymes, NADH and FAD. Raman confocal microscopy enables characterization of molecular and chemical structures within intact 3D constructs, such as tissue or engineered cell culture platforms. The bioenergetics core lodges cutting edge technologies to measure various aspects of cellular respiration and real-time metabolic analysis. The sophisticated LC MS q-ToF provides molecule-level information to reliably track metabolic pathways, The Permethion metabolic cage and the Percival/Sage – metabolic cage will provide comprehensive information on the metabolic pathways in both rodents and Drosophila. The Oroboros O2k-FluoRespirometer provides a distinctive high-resolution approach to monitor cellular and mitochondrial respiratory function. In addition, the O2k-FluoRespirometer has the extraordinary capability to measure H2O2 flux, mt-membrane potential, ADP-ATP phosphorylation. Further, the Seahorse XFe8 /24 Analyzers, housed in the bioenergetics core, facilitate the measurement pf key cellular functions such as mitochondrial respiration and glycolysis by measuring the oxygen consumption rate and the extracellular acidification rate of live cells. The data science core provides modern computing and storage servers, develops customized data analytics and AI solutions to center investigators, and provides hands-on training in high performance computing, deep learning based biomedical imaging, and multi-omics data integration and analysis. This workshop will present an overview of each technology currently available in the cores, potential applications, the expertise available from the core directors and technicians, and details on how to access or get trained to use them.
Workshop 8: XRD — New Capabilities for Art Restoration, Pharmaceutical Development, and Structure Determination of Pharmaceutical Targets (Both Small and Large)
Josh Sakon, Ph.D., Professor, Department of Chemistry and Biochemistry, UAF
Location: CHEM 48
Participant Capacity: 10
I strongly encourage participants to bring powder samples (e.g., kidney stones, dyes), small molecules (e.g., sucrose, tartaric acid), or macromolecular crystals (e.g., lysozyme, cytochrome C).
The X-ray diffraction (XRD) system in the X-ray Core Laboratory has long supported statewide research efforts in biomolecular structure determination. With the system replacement funded by the NIH (2022) and ABI (2023), both functionality and usability have been significantly enhanced. The new generation of X-ray detector now produces higher-quality data than was possible with the previous detector, and the updated detector/goniometer software has expanded analytical capabilities.
This upgrade transforms the instrument from one primarily dedicated to protein crystallography into a versatile system that can also generate high-quality small-molecule results. These capabilities ensure the Core Facility remains at the forefront of biomedical research while also providing critical services to additional research laboratories across the state.
During this workshop, we will analyze the samples you bring and review the fundamental theory of XRD and its application to small- and macromolecule structure determination. Powder diffraction will also be demonstrated. Rigaku’s near-noiseless solid-state detector enables extraction of weak signals with greater confidence, even from smaller samples than those currently analyzed at the Smithsonian and Getty Museums. Importantly, this system now provides the ability to identify pigments from paintings or fresco fragments, opening new possibilities in art restoration and cultural heritage research.
Workshop 9: Dancing Bacteria
Yong Wang, Ph.D., Department of Physics, UAF
Location: PHYS 133 and PHYS Lab 115A
Participant capacity: 15
The capability of moving is critical to many bacteria for pursuing nutrients and avoiding hazards. Some bacteria, such as E. coli that naturally exist in human guts, rely on rotating flagella – filaments hooked on motors embedded on cell body – to move in different environments. In this workshop, we will have fun observing the rotation of bacterial flagella and their dancing using fluorescence microscopy.
Workshop 10: Nanopore Technology and their Applications in Detecting DNA and Protein Molecules
Jiali Li, Ph.D., Department of Physics, UAF
Location: PHYS 134 & PHYS Lab 125/124
Participant capacity: 10
Nanopore technology is a recently developed sensing method for analyzing single biomolecules such as DNA, RNA, and proteins in close to their native aqueous solution conditions by measuring changes in electrical current as the molecules pass through a nanometer scale pore. In this workshop, a brief introduction on the principle of nanopore technology and examples of their applications will be given first. Then participants will move to physics labs for demonstrations including (1) silicon nitride nanopore fabrication; (2) a nanopore device sensing DNA/RNA/protein molecules.
Workshop 11: Crystal Growth
Jin Hu, Ph.D., Department of Physics, UAF
Location: PHYS 132 and PHYS Lab 131
Participant capacity: 10
Material science is closely related to our everyday life and the advancement of the modern technology. Synthesize materials is the very first step for fundamental scientific research and technology applications. This workshop will introduce the synthesis of bulk crystals of various important materials.
Workshop 12: Playing with Lasers
Hiro Nakamura, Ph.D., Department of Physics, UAF
Location: NANO 105 and NANO Lab 222
Participant capacity: 15
The workshop will provide hands-on experiences on lasers. We first provide a brief introduction on the type of lasers we use in the lab, and some optical effects such as diffraction. Then participants will move to a physics lab and join a few demonstrations including (1) looking inside a high-power laser; (2) creating higher order patterns from laser beam; (3) make a rainbow using CD, etc.
Facility Tour 1: Department of Chemistry and Biochemistry
Ryan Tian, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: registration desk in FNAR lobby
Facility Tour 2: Arkansas High Performance Computer Center
Raymond Weldon, Dept. of Chemistry and Biochemistry, UAF
Pavel Wolinski, Ph. D. Senior Linux Cluster Administrator, AHPCC
Jaehee Jun, Dept. of Chemistry and Biochemistry, UAF
Location: registration desk in FNAR lobby