INBRE 2024 Workshops
Saturday, November 9, 10:30 am -11:30 am
Workshop 1: The NIH R15 and SuRE R16 Mechanisms
Jerry Ware, Ph.D., Professor of Physiology and Biophysics, 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 highlights unique factors that distinguish the R15 mechanism from other RPG mechanisms, such as the RO1, where scientific merit and the investigators are major score driving criteria. Funding opportunities, such as the Support for Research Excellence (SuRE) Program and SuRE-First Program (R16s) have been released with AR INBRE PUI faculty successfully obtaining NIH extramural support. Comparing the 2 FOAs and appropriateness for PUI faculty to apply for either will be discussed. 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. Thus, special consideration for how/where to incorporate all three goals into the application will be discussed. The presenter has been part of NIH R15 Special Emphasis Panels and will share experiences with a goal of benefitting interested faculty and providing a perspective on how to write a competitive AREA application. 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.
Workshop 2: Maximizing Research Resources & Communicating Science for Broader Impact
Amy Hopper Swan, Program Director, Arkansas Research Alliance
Location: HILL 202
This interactive workshop will empower undergraduate researchers with the tools they need to both enhance their research productivity and communicate their findings with broader audiences. In the first part, participants will explore the Arkansas Core Facilities Exchange (CFE), a powerful database connecting them to over 350 cutting-edge research assets, from specialized equipment to world-class expertise, all designed to accelerate research and foster statewide collaboration. In the second part, participants will dive into the Message Box-a simple but effective framework developed by COMPASS-to communicate their research clearly and persuasively to funders, collaborators, and the public. By the end of the session, participants will have access to valuable resources and sharpened communication strategies to maximize the impact of their work.
Workshop 3: Training Future and Current Faculty in the Art of Scientific Teaching -> the MoSI Model
Mark Baillie, Ph.D., Associate Professor, UA Little Rock Chemistry Program and STEM Ed Center, UALR
Location: CHEM 147
Helping all of our students succeed in our classes can be extremely challenging. During this interactive 60 minute workshop, participants will engage in a deep dive on inclusive teaching and learn about how we can better support learning across various groups of students. This session is one of the first sessions that faculty and graduate students engage in during the week-long immersive Mobile Summer Institute on Scientific Teaching (MoSI) workshop, a week-long workshop that helps faculty bolster the support and impact for all students, especially those who typically struggle in our courses. This evidence-based workshop is a national model that is implemented around the country, and UA Little Rock has hosted the last 6 years training over 150 faculty.
Workshop 4: Cryo-electron Microscopy
Cody Brazel, Dept. of Chemistry and Biochemistry, UAF
Dylan Girodat, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: CHEM 201
Participant capacity: 12
We are in the era of a resolution revolution in cryo-electron microscopy (cryo-EM) that started in the early 2010s through advancements made in electron microscopy technology. Cryo-EM allows for the near-atomic resolution determination of large macromolecular structures such as those of ribosomes, viruses, or spliceosomes. More recent advances have allowed for the resolution of molecular complexes to atomic resolution, where individual atoms can be directly visualized. One of the main utilities of cryo-EM is the ability to solve structures for molecules that are highly mobile (dynamic) or too large to be solved by other techniques such as X-ray crystallography or NMR. Furthermore, structures of complexes in heterogeneous mixtures can be solved through 3D classification techniques.
This workshop will go over the fundamental theory of Cryo-EM, a hands-on demonstration of how samples are prepared, and how a 3D electron density can be generated from movies of particles. By the end, an attendee will have working knowledge of the Cryo-EM workflow. As an example, attendees will have the chance to use a manual plunger for sample preparation on practice grids.
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
J. Chelsea Stephens, Graduate student in Chemistry and Biochemistry, UAF
Workshop 6: Molecular Modeling
Peter Pulay, PhD, 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: Nanochemistry: Spontaneous Versus Electrochemical Reduction at the Nanoscale
Jingyi Chen, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: DISC 418
Participant capacity: 10
Nanochemistry plays an important role in a wide variety of applications including drug delivery, sensing, environmental remediation, energy storage and conversion. In this workshop, the emphasis focuses on the synthesis of metal at the nanoscale. Two methods will be demonstrated including spontaneous and electrochemical reduction. The optical properties of the metal nanoparticles will be illustrated.
Workshop 8: Getting Started on Scorpion & Spider Genomics
Douglas Rhoads, Ph.D., University Professor, Dept. of Biological Sciences, UAF
Location: SCEN 0408
We have recently published manuscripts on genome assembly and annotation for a scorpion species endemic to Arkansas. We are now working to do assemblies for two spiders. In this workshop we will provide advice and experiences. We will answer your questions on genomics based on our experiences with genomics in snakes, chickens, arthropods, and bacteria.
Workshop 9: 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 10: 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
Narasimhan Rajaram, Ph.D., Dept. of Biomedical Engineering, Metabolic Imaging and Spectroscopy Core, Arkansas Integrative Metabolic Research Center, UAF
Suresh Thallapuranam, Ph.D., Dept. of Chemistry and Biochemistry, 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, two research cores were established as fee-for-service resources – an imaging and spectroscopy core and a bioenergetics core. This workshop will present the technologies and capabilities available within these two 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. Recently acquired, our Raman confocal microscope 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 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. 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 11: Confocal Microscopy
Payal Sanadhya, Ph.D.
Fiona Goggin, Ph.D., Department of Entomology and Plant Pathology, UAF
Location: AGRI 315 and AGRI 225
Confocal laser scanning microscopy (CSLM) is one of the most widely-used imaging techniques in biology. Through detection of naturally-occurring or artificially-added fluorescent chemicals (fluorophores), it allows the three-dimensional imaging of living tissues in real time, giving us a window into the structure, chemistry, and physiological functioning of these tissues. The Arkansas Bioimaging Core Facility at the University of Arkansas houses a state-of-the-art Leica Stellaris 8 microscope with a white light laser and Tausense technology for analysis of photon arrival time. These features provide enhanced sensitivity, reduced background noise, and the capacity to detect and distinguish a wider range of fluorophores than traditional confocal microscopes. This workshop will provide an introduction to the capabilities of the Stellaris 8 microscope and a tour of the Bioimaging Core Facility, which is available to investigators state-wide. Participants who wish to bring their own samples should contact Fiona Goggin: fgoggin@uark.edu.
Workshop 12: Quantifying the Dynamics of Cell Division of Bacteria and Yeast at Single Cell
Pradeep Kumar, Ph.D., Department of Physics, UAF
Location: PHYS 132 and PHYS Lab 126
Participant capacity: 15
The workshop will provide hands-on experience on working with yeast and bacterial cells under a microscope, and the methods to quantify their cell division dynamics. First, we will provide a brief introduction of the phase contrast microscopy and its usage in Biology. Participants will have the opportunity to learn to build and automate an autofocus system using a microscope and Arduino processor to capture focused long time-lapse movies of bacteria and yeast growing on a nutrient microchamber. Participants will then use a combination of image processing tools and obtained time-lapse movies to analyze and quantify cell division.
Workshop 13: Crystal Growth
Jin Hu, Ph.D., Department of Physics, UAF
Location: PHYS 133 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 14: 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.
Workshop 15: Build a Robot at the MonArk Quantum Foundry
Hugh Churchill, Ph.D., Department of Physics, UAF
Josh Goss, MonArk NSF Quantum Foundry, UAF
Location: NANO Lobby, NANO 105/Lab
Participant capacity: 16
Workshop participants will use a sample transfer robot to collect starburst treats as they explore robotics, cartesian motion control, microcontroller programming, and automation using similar tools built at the MonArk Quantum Foundry to move semiconductor device chips through our fabrication pipeline. Participants will learn about the activities of the MonArk NSF Quantum Foundry that seeks to use robots and artificial intelligence to automate and accelerate the fabrication of quantum devices based on atomically thin two-dimensional materials. Time permitting, we will conclude with short tour of the MonArk Quantum Foundry Lab located in NANO 325, 731 W Dickson, Fayetteville, Arkansas.
Facility Tour 1: Department of Chemistry and Biochemistry
Ryan Tian, Ph.D., Dept. of Chemistry and Biochemistry, UAF
Location: meet in Hillside foyer
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
Location: meet in Hillside foyer