INBRE 2023 Workshops
Saturday, November 4, 10:30 am -11:30 am
Workshop 1: The NIH R15 and SuRE R16 Mechanisms
Jerry Ware, PhD, 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. New funding opportunities, the Support for Research Excellence (SuRE) Program and SuRE-First Program (R16s) have been released with the first-ever submission deadline of September 2021. 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 recent 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: Cryo-electron Microscopy
Dylan Girodat, PhD, Dept. of Chemistry and Biochemistry, UAF
Location: GEAR 101
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 splicesome. 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 for how a 3D electron density can be generated from movies of particles. By the end an attendee will be able to have working knowledge of the workflow for single particle 3D reconstruction. As an example, the workshop will go through the single particle reconstruction of the large protein beta-galactosidase.
Workshop 3: Preparing for Graduate School
Stefan Kilyanek, PhD, Dept. of Chemistry and Biochemistry, UAF
Location: CHEM 132
This workshop is targeted towards under-graduate 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:
Julie Stenken, 21st Century Chair in Proteomics & Professor, Dept. of Chemistry and Biochemistry, UAF
Kusum Naithani, Graduate coordinator and Associate Professor, Dept. of Biological Sciences, UAF
Adnan Ali Khalaf Alrubaye, Associate Director of Graduate Program in Cell and Molecular Biology, UAF
Karl Boehme, Associate Professor, Department of Microbiology & Immunology, UAMS
Aaron Kemp, Graduate student in Biomedical Informatics, UAMS
Amanda Raley, Graduate student in Chemistry and Biochemistry, UAF
Eston Dunn, Graduate student in Biological Sciences, UAF
Colette Robinson, Graduate student in Cell and Molecular Biology, UAF
Workshop 4: 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 5: XRD New Capability for Art Restoration, Pharmaceutical Development, and Structure Determination of Pharmaceutical Targets Both Small and Large
Josh Sakon, PhD, Dept. of Chemistry and Biochemistry, UAF
Location: CHEM 48
Participant capacity: 10
I strongly encourage you to bring powder samples (kidney stones, dyes, etc.), small molecules (sucrose, tartaric acid, etc.), or macromolecule crystals (lysozyme, cytochrome C, etc.).
The X-ray diffraction system, in the X-ray Core laboratory has played a role in the statewide research efforts in the structure determination of biomolecules. XRD replacement funded in 2021 by NIH will increase the functionality and usability of the system. The new generation of X-ray detector produces higher quality data than what can be done with the older X-ray detector and the software that now comes with the detector/goniometer. The instrument extends the capacity of the instrument from being a system dedicated to protein crystallography to one that is capable of also generating high-quality small molecule results, which can help the core facility to stay at the cutting edge of biomedical research, as well as provide needed service to additional research labs in the state.
Let’s solve the samples you have. Also the fundamental theory for XRD and small/macromolecule structure determination will be discussed. Powder samples can also be analyzed by the instrument. Rigaku’s near noiseless solid-state detector will enable the extraction of weak with better confidence from smaller samples than the systems currently used at Smithsonian and Getty Museums. The instrument gained ability to identify pigments from paintings or fresco particles.
Workshop 6: CRISPR-Cas9-mediated targeted mutagenesis
Nagayasu Nakanishi, PhD, Dept. of Biological Sciences, UAF
Location: FERR 214, 323, and SCEN122
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 7: Data Science Help Desk for the Arkansas INBRE
Phil H. Williams, PhD, Dept. of Information Science, UALR
Location: HILL 202
A data Science Help Desk has been created using Spiceworks. Users can easily request help with projects in a variety of data science areas. These include general data science as well as Bioinformatics specific solutions. Examples include, machine learning, high performance computing (HPC), RNA-seq analysis, internet of things (IoT), Linux OS, scripting in R, python and bash, systems integration, systems automation, and Cloud computing.
The Help Desk enhances our ability to track trends in client needs and the solutions.
For help with data science, email your request to: help@arinbre-datahelp.on.spiceworks.com
Workshop 8: Investigating Metabolism with Multiscale Approaches: From Molecule to Tissue
Timothy J. Muldoon, MD, PhD, Dept. of Biomedical Engineering, Metabolic Imaging and Spectroscopy Core, Arkansas Integrative Metabolic Research Center, UAF
Narasimhan Rajaram, PhD, Dept. of Biomedical Engineering, Metabolic Imaging and Spectroscopy Core, Arkansas Integrative Metabolic Research Center, UAF
Suresh Thallapuranam, PhD, 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 9: Confocal Microscopy
Payal Sanadhya, PhD
Fiona Goggin, PhD, 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 10: Dancing Bacteria
Yong Wang, PhD, 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 11: Quantifying the Dynamics of Cell Division of Bacteria and Yeast at Single Cell
Pradeep Kumar, PhD, 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 12: Physics REU and Graduate Application
Reeta Vyas, PhD, Dept. of Physics, UAF
Location: PHYS 134
Participant capacity: 15
In this workshop participants will learn about Physics REU at UA, career options for physics graduates, dos and don’ts of the application process for Physics Graduate Programs in the US – importance of and preparation for GRE, course work, recommendation letters, assistantships, etc.
Workshop 13: Build a Robot at the MonArk Quantum Foundry
Hugh Churchill, PhD, Department of Physics, UAF
Location: NANO 105
Participant capacity: 16
Workshop participants will assemble a sample transfer robot and use it to collect treats as they explore robotics, cartesian motion control, microcontroller programming, and automation similar to 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, PhD, Dept. of Chemistry and Biochemistry, UAF
Location: meet in Hillside foyer