Biochemistry, Biophysics, and Structural Biology Commons^™

Characterization Of A Catalyst-Based Conversion Technique To Measure Total Particulate Nitrogen And Organic Carbon And Comparison To A Particle Mass Measurement Instrument, Chelsea E. Stockwell, Agnieszka Kupc, Bartlomiej Witkowski, Ranajit K. Talukdar, Yong Liu, Vanessa Selimovic, Kyle J. Zarzana, Kanako Sekimoto, Carsten Warneke, Rebecca A. Washenfelder, Robert J. Yokelson, Ann M. Middlebrook, James M. Roberts

Chemistry and Biochemistry Faculty Publications

The chemical composition of aerosol particles is a key aspect in determining their impact on the environment. For example, nitrogen-containing particles impact atmospheric chemistry, air quality, and ecological N deposition. Instruments that measure total reactive nitrogen (Nr Combining double low line all nitrogen compounds except for N2 and N2O) focus on gas-phase nitrogen and very few studies directly discuss the instrument capacity to measure the mass of Nr-containing particles. Here, we investigate the mass quantification of particle-bound nitrogen using a custom Nr system that involves total conversion to nitric oxide (NO) across platinum and molybdenum catalysts followed by NOĝ'O3 chemiluminescence …

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …

Synthetic Routes To Bromo-Terminated Phosphonate Films And Alkynyl Pyridine Compounds For Click Coupling, Poornima Sunder

Departmental Honors & Graduate Capstone Projects

Click reactions are a highly versatile class of reactions that produce a diverse range of products. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) click reactions require an azide and a terminal alkyne and produce a coupled product that is “clicked” through a triazole ring that can have a variety of substituents. In this work, bromo-terminated phosphonate films on copper oxide surfaces were explored as the platform for click coupling, as the terminal azide needed for the reaction can be generated through an in situ SN2 reaction with a terminal bromo group. The reactions were characterized using model reactions in solution before being conducted …

An N-Terminal Acidic Domain In Β-Amylase2 Is Required For K+ Regulation., Jillian Breault

Senior Honors Projects, 2010-2019

In the chloroplasts of leaf mesophyll cells, β-amylase proteins (BAMs) are responsible for breaking down starch into maltose when the plant cannot undergo photosynthesis. BAM2, which was previously considered inactive, was recently shown to be active under stromal-like levels of salt and has optimal activity at 80mM KCl. In addition, BAM2 is active as a tetramer in vivo and displays sigmoidal kinetics due to a secondary binding site that is responsible for activating BAM2 when bound to starch. A hypothesized tetramer model was created using a homology model of a BAM2 monomer and the configuration of a crystallized sweet potato …

Molecular Mechanism Of Early Amyloid Self-Assembly Revealed By Computational Modeling, Mohtadin Hashemi

Theses & Dissertations

Protein misfolding followed by the formation of aggregates, is an early step in the cascade of conformational changes in a protein that underlie the development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive.

Here, we demonstrate that the hairpin fold, a structure found in the early folding intermediates of amyloid b, induces morphological and stability changes in the aggregates of Aβ(14-23) peptide. We structurally characterized the interactions of monomer and hairpin using extended molecular dynamics (MD) simulations, which revealed a novel intercalated type complex. …

Towards The Identification Of The Molecular Mechanism Responsible For Rpa:Rad52 Complex Formation, Lucas Struble

Theses & Dissertations

Human cells are routinely exposed to DNA-damaging conditions, from both external sources like ionizing radiation and internal sources like normal oxidative metabolism. Damage in the form of double strand breaks (DSBs) is especially problematic. DSBs occurring outside of replication forks can be repaired through two forms of homologous recombination. The first of these is genetic conversion involving either RPA, BRCA1, PALB2, BRCA2, and RAD51, or RPA, RAD52, RAD51, and other unknown factors. The second is single strand annealing involving RPA and RAD52. Familial breast cancers, among numerous others, are characterized by homozygous pathological mutations in the BRCA2 pathway and must …

Inhibition Of Rad52-Based Dna Repair For Cancer Therapy, Mona Al-Mugotir

Theses & Dissertations

Germline BRCA mutations underlay a significant risk for breast and ovarian cancer that increases in age. BRCA mutations are usually associated with the most aggressive subtypes of these cancers such as triple negative breast cancer and high-grade serous ovarian cancer. Conventional chemotherapeutic or hormonal therapies do not address the molecular deficiencies responsible for their resistance and there is a high rate of recurrence. Targeted therapy that can address the unique molecular features in these subtypes of cancer is the only way to cure the disease or, at the very least, improve patients’ quality of life.

Homologous recombination repair is an …

Elucidation Of The Functions Of Neuropilin 2 In Osteoclasts In Promoting Prostate Cancer Bone Metastasis., Navatha S. Polavaram

Theses & Dissertations

Bone metastasis is one of the major clinical concerns that causes skeletal related malignancies and increased mortality. Bone is one of the preferred sites for metastatic prostate cancer. The metastatic prostate cancer cells interact with bone cells (osteoblasts and osteoclasts) resulting in an imbalance in the bone homeostasis leading to increased activation of osteoblasts over osteoclasts. Our preliminary data indicated a non-tyrosine kinase receptor Neuropilin 2 (NRP2) is expressed in osteoclasts induced by metastatic prostate cancer cells and acts as a negative regulator of osteoclast differentiation and function. We hypothesize that prostate cancer -induced NRP2 expression in osteoclasts is necessary …

The Beta-Catenin/Muc1.Ct Interaction In Pancreatic Cancer, Edwin Wiest

Theses & Dissertations

MUC1 is overexpressed in over 90% of pancreatic cancer cases, and its interaction with beta-catenin promotes progression of the disease. Various in vitro and in vivo methods show that beta-catenin and MUC1 interact by way of the cytoplasmic tail of MUC1 (MUC1.CT). This interaction occurs in the membrane of pancreatic cancer cells but is found to a smaller extent in the nucleus as well. Biophysical methods suggest that MUC1 interacts with beta-catenin through a sequence of amino acids in the tail of MUC1 that sit very near the transmembrane domain of MUC1. In pancreatic ductal adenocarcinoma cells, it appears that …

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

Articles

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated with …

Clinical Applications Of Infrared And Raman Spectroscopy: State Of Play And Future Challenges, Matthew Baker, Hugh Byrne, John Chalmers, Peter Gardner, Royston Goodacre, Alex Henderson, Sergei Kazarian, Francis Martin, Julian Moger, Nick Stone, Josep Sule-Suso

Articles

Vibrational spectroscopies, based on Infrared absorption and/or Raman scattering provide a detailed fingerprint of a material, based on the chemical content. Diagnostic and prognostic tools based on these technologies have the potential to revolutionise our clinical systems leading to improved patient outcome, more efficient public services and significant economic savings. However, despite these strong drivers, there are many fundamental scientific and technological challenges which have limited the implementation of this technology in the clinical arena, although recent years have seen significant progress in addressing these challenges. This review examines (i) the state of the art of clinical applications of infrared …

Expression, Purification, And Inhibition Profile Of Dihydrofolate Reductase From The Filarial Nematode Wuchereria Bancrofti, Andrew M. Tobias, Dea Toska, Keith Lange, Tyler Eck, Rohit Bhat, Cheryl A. Janson, David P. Rotella, Ueli Gubler, Nina M. Goodey

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Filariasis is a tropical disease caused by the parasitic nematodes Wuchereria bancrofti and Brugia malayi. Known inhibitors of dihydrofolate reductase (DHFR) have been previously shown to kill Brugia malayi nematodes and to inhibit Brugia malayi DHFR (BmDHFR) at nanomolar concentrations. These data suggest that BmDHFR is a potential target for the treatment of filariasis. Here, protocols for cloning, expression and purification of Wuchereria bancrofti DHFR (WbDHFR) were developed. The Uniprot entry J9F199-1 predicts a 172 amino acid protein for WbDHFR but alignment of this sequence to the previously described BmDHFR shows that this WbDHFR sequence lacks a crucial, conserved 13 …

Analyzing The Effects Of Site-Directed Mutagenesis On The Structure Of Coxsackievirus B3 Genomic Rna, Erin Dimon

Theses/Capstones/Creative Projects

Coxsackievirus B3 (CVB3) is known to cause myocarditis and pancreatitis in humans. The virus has a single stranded RNA genome that codes for 11 different proteins. CVB3 is found to have two serotypes: 28 (virulent and disease causing) and GA (avirulent and not disease causing). Like other members of the Picornaviridae family, CVB3 utilizes the genomic 5’ untranslated region (5’ UTR) to initiate viral replication mechanisms through interactions with host protein factors. Structural variations of the CVB3 5’ UTR are hypothesized to influence the success of such interactions and consequentially determine viral virulence. The aim of this project was to …

Role Of Leptin And Dyslipidemia In Chronic Kidney Disease, Sabeela Noor, Faiza Alam, Syeda Sadia Fatima, Mahnur Khan, Rehana Rehman

Department of Biological & Biomedical Sciences

Chronic kidney disease (CKD) patients are at an increased risk of cardiovascular complications and plasma leptin level is elevated in cardio renal syndrome. We wanted to explore leptin levels in patients with different stages of CKD and find its association with risk of cardiovascular disease. This cross-sectional study was conducted in Nephrology Department of Jinnah Post Graduate Medical Centre (JPMC) from January 2014 to September 2014. Group I comprised of controls (GFR=116±8.3, n = 44) acquired from general population, CKD patients were grouped as II, III and IV respectively with GFR; 85.77±9.9 (n = 42), 53.84±9.9 (n=42) and 20.22±8.4 (n …

Genetic Testing And A Real World Case Of Lynch Syndrome, Paige Montanaro

Senior Honors Projects

In recent years, advancements in genetic testing methods have revolutionized the medical field by enhancing the ability to identify persons with an inherited predisposition to cancer. According to the American Society for Clinical Oncology, individuals should undergo genetic testing when he or she meets the following criteria: the individual demonstrates familial history that indicates a predisposition to certain cancers, the test can be adequately interpreted, and the results will aid in the diagnosis, treatment, or management of the patient or additional family members at risk. Genetic testing can be done on samples of hair, skin, blood, amniotic fluid, or other …

Elucidation Of Substrate Binding To Photolyase From Sulfolobus Solfataricus Using Isothermal Titration Calorimetry, Amanda Rose Kuerzi

Theses, Dissertations and Culminating Projects

DNA photolyase is a DNA repair enzyme commonly found across the kingdom of life. Binding studies for the hyperthermophilic photolyase derived from Sulfolobus solfataricus (SsPL) may serve to illuminate how DNA photolyase can adapt over a large temperature range. In the first section of this study, the thermodynamics of substrate binding for SsPL in a choline chloride buffer were determined using isothermal titration calorimetry. Using the Counter-Ion Condensation Concept as a model, ionic strength studies were performed to separate the binding interactions into electrostatic, and nonelectrostatic components. The electrostatic interactions do not appear to make a significant contribution to the …

Guided-Inquiry In Biochemistry Laboratory Course Improves Lab Math Skills, Grishma Deven Patel

Theses, Dissertations and Culminating Projects

Biochemistry graduates pursuing research-related careers must master basic quantitative skills. Laboratory courses present students opportunities to practice lab math skills such as dilution and solution calculations. Employers and researchers have reported inadequate math skills among bioscience graduates and there is a need to evaluate the effectiveness of laboratory teaching approaches in increasing students’ lab math skills. In this threeyear study, we examined the impact of guided-inquiry learning on students’ ability to perform laboratory calculations required for experimental design. An upper-level undergraduate biochemistry laboratory course was divided into sections taught using an inquiry approach where students design their own experiments or …

Ph Sensitivity Of Connexin 50 Hemichannels: H95 And Beyond, Leah Volk

Biology Theses

Gap junction channels formed by connexin proteins are critical for the health and function of the vertebrate lens. It is important to understand how these channels are affected by pH because a pH gradient exists in lens tissue. Intracellular pH (pH_i) is a regulator of gap junction coupling, and different connexins show different sensitivities to pH_i. A “Particle-Receptor” model for pH-dependent channel closure involves the intramolecular interaction between the cytoplasmic tail of the connexin and a region near the mouth of the channel dependent on a highly conserved histidine residue at position 95. While this model …

Investigation Of Catalytic Activity Of Stable Β-Ketoacyl-Acp Substrate Analogs In Quorum Sensing Signal Synthesis, Nhu Lam

Boise State University Theses and Dissertations

Quorum sensing is an intercellular mechanism used by many bacterial pathogens to regulate behaviors, such as motility, virulence, and antibiotic production. Disruption of quorum sensing is shown to be deleterious to bacterial pathogenicity, without causing lethality. In Gram-negative bacteria, acyl-homoserine lactone (AHL or acyl-HSL) signal molecules are synthesized by AHL synthase enzymes using acylated-acyl carrier protein (acyl-ACP) and S-adenosyl-L-methionine (SAM) as their substrates. Pantoea stewartii EsaI, which causes Stewart’s wilt in corn, and Yersinia pestis YspI, which causes bubonic plague are AHL synthases that use 3-oxohexanoyl-ACP and 3-oxooctanoyl-ACP as the acyl-substrate to synthesize 3-oxohexanoyl-HSL and 3-oxooctanoyl-HSL signals, respectively. Unfortunately, the …

Design Of Mononuclear Nonheme Enzyme For Oxygen Activation, Joel John Rempillo

Renée Crown University Honors Thesis Projects - All

Natural enzymes are complex systems with intricate folds and binding pockets, which recognize specific substrates and position them ideally for catalysis. Large size and complexity of enzymes prevent their study and use as industrial catalysts. On the other hand, de novo designed models of enzymes often use simple and stable protein scaffold, which streamlines mechanistic studies and allows industrial applications. In this work, we use previously designed four-helix bundle as a protein framework to incorporate 2-His-1- carboxylate motif often found in non-heme enzymes. Such coordination environment provides ligands to bind iron(II) and leaves three additional coordination sites to accommodate substrate …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

Evidence For Organelle-Like Extracellular Vesicles From A Parasite Of Drosophila And Their Function In Suppressing Host Immunity, Mary Heavner

Dissertations, Theses, and Capstone Projects

Parasitic wasps act as keystone species in natural ecosystems. Adept at suppressing immunity of their insect hosts, these natural enemies of insect pests are used for biocontrol in many parts of the world. Female parasitic wasps of the closely-related species Leptopilina heterotoma (Lh), a generalist of many Drosophilia flies, and Leptopilina boulardi (Lb), a specialist on flies of the melanogaster subgroup, produce venom and virus-like particles (VLPs) in their long gland-reservoir complexes, a secretory organ connected to ovipositors. Venom and VLPs are deposited, along with wasp eggs, into the body of the wasp’s larval fly host …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Functional And Structural Impact Of The Loss Of The Leucine-Rich Repeat Protein Lrit1 In The Mouse Retina., Catherine Ann Cobb

Electronic Theses and Dissertations

Mutations in genes encoding the leucine-rich repeat (LRR) proteins nyctalopin and LRIT3 lead to complete congenital stationary night blindness because they are critical to depolarizing bipolar cell function in the retina. LRIT3 has two closely related family members, LRIT1 and LRIT2. In silico analyses of publicly available RNA-Seq data showed that Lrit1 was highly expressed in the retina. Here I describe the expression pattern and impact of loss of LRIT1 on retinal function. To enable these studies, we used CRISPR/Cas9 technology to create an Lrit1^-/- mouse line. Retinal morphology and morphometry analyses showed no gross changes in retinal structure …

The Effects Of Passive Integrated Transponder Tagging On Cortisol Release In The Gulf Killifish, Fundulus Grandis, Ariel Marcelo Hernandez

Senior Honors Theses

Due to its ease of use, low cost, and essentially limitless number of unique codes, PIT tagging has become the favored technique for tagging individuals in biological studies. However, studies employing PIT tagging generally assume that stress due to the implantation and presence of a PIT tag has no influence on the experimental results. This study investigated the effects of PIT tagging on levels of the stress hormone cortisol in the Gulf Killifish, Fundulus grandis, an estuarine fish of the Gulf of Mexico that is prone to daily or seasonal environmental stressors. Cortisol was measured non-invasively by extracting and …

Functional Similarity Of Prd-Containing Virulence Regulators In Bacillus Anthracis, Malik Raynor

Dissertations and Theses (Open Access)

Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the …

Nanoscale Organization Of The Small Gtpase Rac1, Kelsey Maxwell

Dissertations and Theses (Open Access)

Rac1 is a small, guanine-nucleotide binding protein that cycles between an inactive GDP-bound and active GTP-bound state to regulate actin-mediated motility, migration, and adhesion. Plasma membrane (PM) localization is essential for its biological activity. Rac1 PM targeting is directed by a C-terminal membrane anchor that encompasses a geranylgeranyl-cysteine-methyl-ester, palmitoyl, and a polybasic domain (PBD) of contiguous lysine and arginine residues. Using high-resolution imaging combined with spatial mapping analysis, I found that Rac1 forms nanoclusters on the PM. Cycling between the GTP- and GDP-bound states, Rac1 forms nanoclusters that are non-overlapping, consequently undergoing guanine nucleotide-dependent spatial segregation. I further found that …

Calvin Avenue Basin Project Description And Analysis, Calvin University

Faculty and Professional Research

The existing detention basin, Calvin Avenue Basin was modified in 2017 to include a two-stage ditch, level spreaders, and micro- and macrotopography with the goal of reducing the volume of stormwater leaving the basin, resulting in less stormwater, less flashiness, and improved water quality in the downstream, impaired waterway of Silver Creek. The total storage increase at a reference elevation of 690 is 348,615 gallons (1.07 acre-feet) for all modifications (two-stage ditch and microtopography). This equates to 4.35 million gallons of stormwater that will be stored and slowly released. Of this, 2.46 million gallons of stormwater will be infiltrated annually. …