Biochemistry, Biophysics, and Structural Biology Commons^™

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

Mechanistic Determination Of Host Environmental Impacts On Shigella Virulence, Nicholas E. Dickenson

Funded Research Records

No abstract provided.

Recombinant Hagfish Intermediate Filament Proteins Enable Neural Culture Substrates That Promote Neurite Extension And Reduce Oxidative Stress, Justin Jones, Kristin Durrant

Browse all Datasets

This dataset supports the production, characterization, and biological validation of a novel recombinant hagfish intermediate filament (rHIF) protein functionalized with spider silk motifs (rHIF-alpha-GRGGL). The data demonstrates a scalable bioprocess resulting in a 7.76 g/L yield, high structural alpha-helicity (77.2%), and significant support for N2a cells.

Plants Have A Chemical Defense To Protect Themselves From Herbivory, Isis Cordova

Research on Capitol Hill

All plants produce compounds for survival. My work focuses on how plants remember past attacks and whether that memory leads to stronger/faster responses.

The Next Frontier In The Study Of Noncovalent Bonding: Transition Metals, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

As work continues unabated in the study of noncovalent bonding, particularly σ-hole bonds, new challenges have emerged as the participation of transition metals in interactions of this sort is fast becoming appreciated. While there are certain similarities with the halogen, chalcogen, etc, bonds, in which the main group elements participate, there are certain unique properties of these metal atoms that must be analyzed before a complete understanding can be attained. As one example, these atoms tend to act simultaneously as both electron donors and acceptors, a synergistic action that amplifies the overall bond strength. Ideas are expressed in this paper …

Development Of Single Droplet Interface-Specific Sum Frequency Scattering Spectroscopy, Yi Rao

Funded Research Records

No abstract provided.

Enhancing Stability And Emissions In Metal Halide Perovskite Nanocrystals Through Mn2+ Doping, Thi Thu Trinh Phan, Thi Thuy Kieu Nguyen, Trung Kien Mac, Minh Tuan Trinh

Chemistry and Biochemistry Student Research

Metal halide perovskite (MHP) nanocrystals (NCs) offer great potential for high-efficiency optoelectronic devices; however, they suffer from structural softness and chemical instability. Doping MHP NCs can overcome this issue. In this work, we synthesize Mn-doped methylammonium lead bromide (MAPbBr₃) NCs using the ligand-assisted reprecipitation method and investigate their structural and optical stability. X-ray diffraction confirms Mn²⁺ substitution at Pb²⁺ sites and lattice contraction. Photoluminescence (PL) measurements show a blue shift, significant PL quantum yield enhancement, reaching 72% at 17% Mn²⁺ doping, and a 34% increase compared to undoped samples, attributed to effective defect passivation and …

Diets And Environmental Impacts - Generational Outlook, Aspen Hopper, Melanie Jex

Student Research Symposium

How different diets impact the environment: Are we aware?

Determining The Kinetic Basis Of Crispr-Cas12a2 Function, Sobita Kunwar, Thomson Hallmark, Dylan Keiser, Bronson Naegle, Sudeshna Manna, Aaron Thomas, Chase L. Beisel

Student Research Symposium

CRISPR- Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated) systems are bacterial adaptive immune systems that protect bacteria against mobile genetic elements such as viruses and plasmids^1,2.

Solving The Structure Of An Ancestral Protein Tyrosine Phosphatase, Natalie Turcsanski, Edna Armah

Student Research Symposium

Protein tyrosine phosphatases (PTPs) regulate cell signaling by removing phosphate groups from tyrosine residues. Malfunction of these enzymes can lead to diseases such as diabetes and cancer. A conserved feature among PTPs is the catalytic acid loop, essential for phosphate removal. Computational analysis of PTP structures revealed that ancestral PTPs have considerable variation in conformations of this loop, sparking interest in their further study. The Asgard group, identified as ancestral to eukaryotic PTPs, was successfully expressed and purified under optimized conditions. Current efforts focus on optimizing crystallization to obtain larger crystals for structural analysis. This project will investigate the allosteric …

Determining The Function Of Type Iv-B Crispr-Cas Systems, Eric Jenkins, Brendon Guinn

Student Research Symposium

CRISPR-Cas systems are a diverse group of prokaryotic adaptive immune systems that defend against Mobile Genetic Elements (MGEs) such as bacteriophages and plasmids. CRISPR-associated (Cas) proteins bind to guide RNAs (crRNAs) transcribed from a DNA repeat array (CRISPR array) containing spacers complementary to MGEs. Upon infection by a MGE, the Cas protein-crRNA complex binds to the target sequence in the invaders genome and cleaves the nucleic acid.

Activation Of Enkephalinergic Neurons Modulate Pain Within The Brain, Lucy N. Scribner, Oakley M. Statham, Greydon R. Durrant, Callie M. Newson

Student Research Symposium

The endogenous opioid system, consisting of three neuropeptides and canonical receptors, is ubiquitously expressed throughout the brain and is heavily involved in modulating pain[1]. However, research has placed tremendous focus on investigating the receptors of this system, and less attention has been devoted to the peptides. One such opioid peptide, enkephalin, is notably absent within the pain center of the brain, the periaqueductal gray (PAG)[2]. To further understand the role enkephalins play in modulating pain, we aimed to target and activate specific enkephalin-containing neurons that connect to the PAG. By activating these enkephalinergic projections, we hypothesized that this would lead …

A New Crispr System Uses Energy Storage Indiscriminately, Brendon Guinn

Research on Capitol Hill

CRISPR systems are Immune systems used by bacteria to defend against viruses. Recently, tools such as CRISPR Cas9 that are derived from CRISPR systems have been developed as a powerful tool to treat disease. 

Here we are studying a different CRISPR system related to the one used to develop the Cas9 tool. We study this system to discover new proteins that may be used to develop tools to cure diseases and diversify our arsenal of disease-fighting genetic sequences. 

Soil Organic Matter Processes From The Treetops To The Clay Particle: The Role Of Climate, Minerals, And Organic Matter Chemistry In Soil Carbon Accumulation And Stability, Jessica G. Murray

All Graduate Theses and Dissertations, Fall 2023 to Present

Soils store more carbon than plants and the atmosphere, yet release ten times more carbon dioxide (CO₂) to the atmosphere than human activities each year. Small shifts in the balance of soil carbon storage and soil carbon emissions could make climate change less severe, by acting as a sink for the carbon plants pull from the atmosphere, or make climate change worse, by releasing even more planet-warming greenhouse gases. The processes governing whether soils store or release carbon depend on tiny soil microorganisms which convert plant carbon to soil organic matter, releasing CO₂ in the process. In …

A Preliminary Fuzzy Inference System For Predicting Atmospheric Ozone In An Intermountain Basin, John R. Lawson, Seth N. Lyman

Mathematics and Statistics Faculty Publications

High concentrations of ozone in the Uinta Basin, Utah, can occur after sufficient snowfall and a strong atmospheric anticyclone creates a persistent cold pool that traps emissions from oil and gas operations, where sustained photolysis of the precursors builds ozone to unhealthy concentrations. The basin's winter-ozone system is well understood by domain experts and supported by archives of atmospheric observations. Rules of the system can be formulated in natural language ("sufficient snowfall and high pressure leads to high ozone"), lending itself to analysis with a fuzzy-logic inference system. This method encodes human expertise as machine intelligence in a more prescribed …

Assimilating Satellite-Derived Snow Cover And Albedo Data To Improve 3-D Weather And Photochemical Models, Colleen Jones, Huy Tran, Trang Tran, Seth Lyman

Chemistry and Biochemistry Faculty Publications

During wintertime temperature inversion episodes, ozone in the Uinta Basin sometimes exceeds the standard of 70 ppb set by the US Environmental Protection Agency. Since ozone formation depends on sunlight, and less sunlight is available during winter, wintertime ozone can only form if snow cover and albedo are high. Researchers have encountered difficulties replicating high albedo values in 3-D weather and photochemical transport model simulations for winter episodes. In this study, a process to assimilate MODIS satellite data into WRF and CAMx models was developed, streamlined, and tested to demonstrate the impacts of data assimilation on the models’ performance. Improvements …

Metal Assisted O2-Dependent Carbon-Carbon Bond Cleavage Of Β-Diketones And Flavonols, Stephen N. Anderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Almost everything we interact with on a daily basis has been synthesized by chemists ranging from plastics, food preservatives, and medications. The diversity of synthetic molecules are achieved by the formation of new bonds between existing molecules and/or through the cleaving of bonds found in a molecule. There are uncountable amount of conditions reported to facilitate chemical reactions which all depend on the nature of molecules being used and the environment it is used in.

In recent years, more attention has been paid to identify chemical reactions that can use more environmentally favorable conditions and reduce the use of limited …

A Structural Role For Tryptophan In Proteins, And The Ubiquitous Trp CΔ1—H&Centerdot;&Centerdot;&Centerdot;O=C (Backbone) Hydrogen Bond, Michal Szczygiel, Urszula Derewenda, Steve Scheiner, Wladek Minor, Zygmunt S. Derewenda

Chemistry and Biochemistry Faculty Publications

Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the N^ε—H group, which is a potent donor in canonical hydrogen bonds, and a polarized C^δ1—H group, which is capable of forming weaker, noncanonical bonds. Due to adjacent electron-withdrawing moieties, C—H···O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, C^α groups (adjacent to the carbonyl and amino groups of flanking peptide …

Ancient Nitrogenases Are Atp Dependent, Derek F. Harris, Holly R. Rucker, Amanda K. Garcia, Zhi-Yong Yang, Scott D. Chang, Hannah Feinsilber, Betül Kaçar, Lance C. Seefeldt

Chemistry and Biochemistry Faculty Publications

Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg²⁺, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the N₂-reducing enzyme nitrogenase. The Proterozoic ancestor is predicted to be ~540–2,300 million years old, post-dating the Great Oxidation Event. Growth …

An Investigation Of Protein Arginine Methyltransferase 1 Substrate Recognition Through Ribonucleoprotein Modifications, Isabella Beverly Lonardo

Undergraduate Honors Capstone Projects

Just as humans need to communicate with each other, our cells have a series of processes that allows them to communicate from one to another. Protein Arginine Methyltransferase I is an enzyme that helps mediate cellular communication by selectively binding to target proteins and performing chemistry that has broad-reaching downstream effects. However, the mechanisms that underly PRMT1 selectivity have yet to be elucidated. This study uses alterations to a series of known targets, called ribonucleoproteins, to identify some of the characteristics that govern recognition by the PRMT1 enzyme. I have made significant progress in the creation, expression, and purification of …

Testing Resilience Of Microalgae Biofilms When Exposed To Hydrothermal Liquefaction Aqueous Phase, Davis Riley Haag

Undergraduate Honors Capstone Projects

There are a multitude of experimental and processing techniques in the bioenergy field that produce sustainable and carbon negative to carbon neutral methods of converting renewable resources into biologically based hydrocarbons. One example of a process is hydrothermal liquefaction (HTL) which specializes in converting wet biomass into biocrude oil. One reason that these processes are not used outside experimental testing is due to the high cost of performing these processes. There is potential to move these processes to larger scale testing and eventually industrial adaptation if breakthroughs are made to offset the process expenses. There is a waste product produced …

Mechanical Properties Of Natural Osmia Lignaria Silk And Recombinant Expression Of The Silk Proteins, Jackson Morley

Undergraduate Honors Capstone Projects

The use of petroleum-based plastic and the subsequent waste has led researchers to explore alternatives in the form of biopolymers. Spider silk and hagfish intermediate filaments show the potential to be advantageously utilized in textile and biomedical industries. Bee silk is a sparsely studied biopolymer that has shown potential to be added to these other impressive biopolymers. Osmia lignaria, is a solitary bee native to the western United States. Silk from these bees can be isolated while the larvae are spinning their silk. The silk from these bees has been mechanically tested for strength, stress, strain, and elasticity. Cocoon …

Relation Between Halogen Bond Strength And Ir And Nmr Spectroscopic Markers, Akhtam Amonov, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C–X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded …

C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) is examined by quantum chemical means. The Si···O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C···O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite …

Ranchsatdb: A Genome-Wide Simple Sequence Repeat (Ssr) Markers Database Of Livestock Species For Mutant Germplasm Characterization And Improving Farm Animal Health, Naveen Duhan, Simardeep Kaur, Rakesh Kaundal

Plants, Soils and Climate Student Research

Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface …

Growth, Morphological, And Biochemical Responses Of Four Native Species To Salinity Stress, Asmita Paudel, Youping Sun

Plants, Soils, and Climate Faculty Publications

Native plants are of great value in landscape maintenance. Despite their importance in the landscape, the salt tolerance of most native plants has received little attention. The present research was designed to assess morphological, physiological, and biochemical responses of four Utah-native plants [Arctostaphylos uva-ursi (kinnikinnick), Cercocarpus ledifolius (curl-leaf mountain mahogany), Cercocarpus montanus ‘Coy’ (alder-leaf mountain mahogany), and Shepherdia ×utahensis ‘Torrey’ (hybrid buffaloberry)] at different salinity levels. Each species was irrigated with a nutrient solution at an electrical conductivity (EC) of 1.2 dS·m^-1 (control) or saline solutions at ECs of 5.0 or 10.0 dS·m^-1 for 8 …

Discovery And Characterization Of A Prophage Encoded Anti-Crispr Against The Type Iv-A Crispr System, Andrew Williams

Student Research Symposium

CRISPR Systems are adaptive immune systems in bacteria used to defend against mobile genetic elements such as bacteriophages, or bacterial viruses, and plasmids. They use a protein complexed with a guide RNA to target the protein to a foreign invader and neutralize it by cleaving its genetic information. In order to survive and keep infecting bacteria, bacteriophages likewise have developed machinery used to inhibit CRISPR immunity in the form of anti-CRISPR (Acr) proteins. The type IV-A system is a recently discovered and characterized system by the Jackson lab. It has been shown to defend against plasmids, but further data on …

Cycloaddition Of Aryldiazoacetates With Terminal Alkynes And Nitriles Via A Bioinspired Cobalt Complex, Liming Tan

Student Research Symposium

In this study, we present a novel method for the efficient cycloaddition of aryl diazoacetates with both terminal alkynes and nitriles, employing a bioinspired cobalt complex as a catalyst. Our findings indicate that terminal alkynes react with aryl diazoacetates to yield a cyclopropenation product through a 2+1 cycloaddition reaction. Meanwhile, nitriles react with aryl diazoacetates to produce an oxazole product via a 2+3 cycloaddition reaction. These results have significant implications for the development of new synthetic routes towards cyclopropenation and oxazole compounds.

Developing Cancer Treatments With A One-Two Punch Of A Metal And Carbon Monoxide, Joel Ashton

Research on Capitol Hill

Carbon monoxide (CO) has unique therapeutic properties including anti-cancer effects. Flavonols such as 3-hydroxyflavone can release CO upon exposure to visible light. Gallium(III) also has anti-cancer properties and can replace Fe(III) in biological processes. This research was focused on synthesizing a family of complexes with gallium(III) bound to 3-hydroxyflavone and similar ligands which can hopefully combine the anti-cancer properties of both gallium and CO. These complexes follow a simple synthesis and the flavonols are easily modified to optimize their properties. Several of these complexes have been made with varying degrees of solubility. Each of these complexes have been confirmed to …

Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …