Biochemistry, Biophysics, and Structural Biology Commons^™

Characterization Of The Nuclear Pore Complex In Red Alga, Cyanidioschyzon Merolae, Michelle Veronin

Health and Kinesiology Theses

Cyanidioschyzon merolae (C. merolae) is a primitive, unicellular species of red alga that is considered to be one of the simplest self-sustaining eukaryotes. The highly elementary nature of C. merolae makes it an excellent model organism for studying evolution as well as cell function and organelle communication. In our study, we hypothesize that C. merolae contains the minimal assembly of proteins to make up their Nuclear Pore Complexes (NPCs), and hence are the first ancestral NPCs. NPCs are essential for basic nuclear transport in the cell. They are embedded in the double membrane of the nucleus, the …

Oh Chemistry Of Non-Methane Organic Gases (Nmogs) Emitted From Laboratory And Ambient Biomass Burning Smoke: Evaluating The Influence Of Furans And Oxygenated Aromatics On Ozone And Secondary Nmog Formation, Matthew M. Coggon, Christopher Y. Lim, Abigail R. Koss, Kanako Sekimoto, Bin Yuan, Jessica B. Gilman, David H. Hagan, Vanessa Selimovic, Kyle J. Zarzana, Steven S. Brown, James M Roberts, Markus Müller, Robert Yokelson, Armin Wisthaler, Jordan E. Krechmer, Jose L. Jimenez, Christopher Cappa, Jesse H. Kroll, Joost De Gouw, Carsten Warneke

Chemistry and Biochemistry Faculty Publications

Chamber oxidation experiments conducted at the Fire Sciences Laboratory in 2016 are evaluated to identify important chemical processes contributing to the hydroxy radical (OH) chemistry of biomass burning non-methane organic gases (NMOGs). Based on the decay of primary carbon measured by proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS), it is confirmed that furans and oxygenated aromatics are among the NMOGs emitted from western United States fuel types with the highest reactivities towards OH. The oxidation processes and formation of secondary NMOG masses measured by PTR-ToF-MS and iodide-clustering time-of-flight chemical ionization mass spectrometry (I-CIMS) is interpreted using a box model employing …

Total Phenolic And Flavonoid Contents Of Anacyclus Pyrethrum Link Plant Extracts And Their Antioxidant Activity, Hanane Elazzouzi, Nadia Zekri, Touriya Zair, Mohamed Alaoui El Belghiti

Karbala International Journal of Modern Science

In this study, Anacyclus pyrethrm Link (roots) is a medicinal plant from the Asteraceae family, endemic to Morocco and is widely used in traditional medicine; was investigated for their total phenolics, flavonoids contents and antioxidant activities. The quantitative estimation of total flavonoids and phenols by the colorimetric method showed that the extracts were prepared by fractionation of the crude hydromethanolic extract (ethyl acetate and n-butanol). The phenol content of various extracts, estimated by the Folin-Ciocalteu method, was between 1,44 and 12,82 mg EAG / g extract of A. pyrethrum. Moreover, it is clear that ethyl acetate was the …

Structural Basis Of Non-Canonical Transcriptional Regulation By The A-Bound Iron-Sulfur Protein Whib1 In M. Tuberculosis, Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang, Donald F. Becker, Limei Zhang

Department of Biochemistry: Faculty Publications

WhiB1 is amonomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress inM. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 A° -resolution crystal structure of the [4Fe–4S] cluster-bound (holo- )WhiB1 in complex with the C-terminal domain of the 70-family primary sigma factor A of M. tuberculosis containing the conserved region 4 (A 4). Region 4 of the 70-family primary sigma factors is commonly used by transcription factors …

Determination Of Optimal Mild Organic Solvents Of Pdnps For Carbon-Carbon Coupling Reactions, Trina Biswas

Honors College Theses

The synthesis of nanoparticles is an increasingly popular field of interest. The application of nanoparticles is especially popular in the field of nanocatalysts. Metal nanoparticles (NPs) are favorable for catalysis because of the large surface area to volume ratio, which allows them to catalyze a variety of reactions using lesser amounts of active material. As the field of nanoparticle research expands, efforts are being made to create more sustainable approaches to the synthesis of these particles. This research sought to translate the benefits of peptide-based synthesis to organic solvents and use less toxic organic solvents for carbon-carbon coupling reactions, like …

High-Throughput Nano-Scale Characterization Of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography, Alex J. Vecchio, Robert M. Stroud

Department of Biochemistry: Faculty Publications

Structural biology has revealed predicting heterologous expression levels, homogeneity, and stability of a protein from its primary structure are exceedingly difficult. Membrane proteins, in particular, present numerous challenges that make obtaining milligram quantities of quality samples problematic. For structural and functional investigation of these molecules, however, this is what is required. Fluorescence size-exclusion chromatography (F-SEC), a technique where a protein of biological interest is fused to green fluorescent protein (GFP) and monitored, circumvents many bottlenecks inherent to membrane protein structural biology. In vivo expression yields, as well as in vitro homogeneity and stability, can be rapidly evaluated utilizing nanogram quantities …

Alzheimer's And Amyloid Beta: Amyloidogenicity And Tauopathy Via Dyshomeostatic Interactions Of Amyloid Beta, Jordan Tillinghast

Senior Honors Theses

This paper reviews functions of Amyloid-β (Aβ) in healthy individuals compared to the consequences of aberrant Aβ in Alzheimer’s disease (AD). As extraneuronal Aβ accumulation and plaque formation are characteristics of AD, it is reasonable to infer a pivotal role for Aβ in AD pathogenesis. Establishing progress of the disease as well as the mechanism of neurodegeneration from AD have proven difficult (Selkoe, 1994). This thesis provides evidence suggesting the pathogenesis of AD is due to dysfunctional neuronal processes involving Aβ’s synaptic malfunction, abnormal interaction with tau, and disruption of neuronal homeostasis. Significant evidence demonstrates that AD symptoms are partially …

Differential Analysis Of Individual Centruroides Vittatus Venom

Symposium of Student Scholars

Scorpions are well known, venomous arthropods (Class: Arachnida, Order: Scorpiones). Their venom is composed of neurotoxins, proteases and cytotoxic peptides which plays a major role in toxic components such as inflammatory, antimicrobial and hemolytic activity. Venom is key for the survival of scorpions as it is involved in defense against prey and in feeding on predators. Centruroides vittatus (bark scorpion) is commonly found in North America, with habitat ranges from Nebraska to southern Texas. For this study, scorpions were harvested from Laredo, Texas (27˚57’ N, 99˚43’ W), held in captivity for 4 months and fed a consistent diet of Acheta …

Comparative Brain Morphology Of The Greenland And Pacific Sleeper Sharks And Its Functional Implications, Kara E. Yopak, Bailey C. Mcmeans, Christopher G. Mull, Kirk W. Feindel, Kit M. Kovacs, Christian Lydersen, Aaron T. Fisk, Shaun P. Collin

Great Lakes Institute for Environmental Research Publications

In cartilaginous fishes, variability in the size of the brain and its major regions is often associated with primary habitat and/or specific behavior patterns, which may allow for predictions on the relative importance of different sensory modalities. The Greenland (Somniosus microcephalus) and Pacific sleeper (S. pacificus) sharks are the only non-lamnid shark species found in the Arctic and are among the longest living vertebrates ever described. Despite a presumed visual impairment caused by the regular presence of parasitic ocular lesions, coupled with the fact that locomotory muscle power is often depressed at cold temperatures, these sharks remain capable of capturing …

Recruitment Of Polycomb-Group Proteins At Giant In Drosophila Embryos, Elnaz Ghotbi Ravandi

Biological Sciences Theses and Dissertations

Polycomb Group (PcG) proteins are evolutionarily conserved epigenetic transcriptional regulators that maintain the transcriptional repression of silenced genes. PcG mediated silencing is divided into two phases: initiation and maintenance. During the initiation phase, PcG proteins initially recognize and bind to their target genes. Once PcG proteins are recruited to their target genes, they can maintain transcriptional repression through an unlimited number of cell cycles. Most studies on PcG proteins have been focused on the maintenance phase of PcG silencing, and the molecular mechanisms by which PcG proteins are initially recruited to their target genes remained unknown. Two models have been …

Structure And Bioactivity Of A Rationally Designed Nicotinic Acetylcholine Receptor Antagonist Targeting The Alpha-3 Beta-2 Subtype, Leanna Marquart

Boise State University Theses and Dissertations

The work presented in this thesis contributes to ongoing development of an efficient workflow for identification of lead compounds, based on the molecular scaffold of α-conotoxin MII, for drug therapies targeting nicotinic acetylcholine receptors. Nicotinic acetylcholine receptors (nAChRs) are pentameric, ligand-gated ion channels with distribution throughout the central nervous system and are implicated in a variety of neurological diseases including schizophrenia, nicotine addiction, Alzheimer’s disease, and Parkinson’s disease. However, ligand effect on nAChR function is not well understood. Consequently, drug therapies for neurological diseases either do not exist, or have short-lasting efficacy and/or severe side effects. Barriers to the comprehension …

Production And Purification Of Basic Fibroblast Growth Factor Fused To Two Collagen Binding Domains Expressed In E. Coli Bl21 Using Flask And Fed-Batch, Hazim Aljewari

Graduate Theses and Dissertations

Delivering effective and non-toxic doses of bioactive materials that can aid in activating tissue regeneration to wounded tissue has proven to be an enormous challenge. This study was designed to produce a potential therapeutic recombinant protein by fusing two collagen binding domains to basic fibroblast growth factors (bFGF) through a collagenase cleavage site linker, so it can release the bFGF in a wound site by the action of this enzyme. The novel fusion protein was expressed in Escherichia coli BL-21 (E. coli) using traditional flask shaker and fed-batch cultivation. Cell lysate was purified by FPLC using Immobilized metal affinity chromatography …

Investigating Growth Performance And Intestinal Barrier Integrity In Heat-Stressed Modern Broilers And Their Ancestor Jungle Fowl, Travis Tabler

Graduate Theses and Dissertations

Heat stress (HS) has a negative effect on poultry production sustainability due to its adverse consequence on bird welfare, health, growth, and mortality. Although modern broilers have greater gut mass and higher energy use efficiency than unselected birds, they are more vulnerable to HS that induces “leaky gut syndrome,” or increased intestinal permeability. The aim of the current study was to determine the effect of HS on growth performance and gut barrier integrity in three modern broiler lines and their ancestor the Jungle Fowl. Four chicken populations including Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Arkansas Random …

Natural Variation In Yeast Stress Signaling Reveals Multiple Paths To Similar Phenotypes, Amanda N. Scholes

Graduate Theses and Dissertations

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance. Variation in stress sensing and signaling can potentially play a large role in how individuals with different genetic backgrounds are more or less resilient to stress. However, the mechanisms underlying how gene expression variation affects organismal fitness is often obscure.

To understand connections between gene expression variation and stress defense phenotypes, we have been exploiting natural variation in Saccharomyces cerevisiae stress responses using a unique phenotype called acquired …

Multidrug Resistance Regulators Mara, Soxs, Rob, And Rama Repress Flagellar Gene Expression And Motility In Salmonella Enterica Serovar Typhimurium, Srinivas Thota, Lon Chubiz

Biology Department Faculty Works

Production of flagella is costly and subject to global multilayered regulation, which is reflected in the hierarchical control of flagellar production in many bacterial species. For Salmonella enterica serovar Typhimurium and its relatives, global regulation of flagellar production primarily occurs through the control of flhDC transcription and mRNA translation. In this study, the roles of the homologous multidrug resistance regulators MarA, SoxS, Rob, and RamA (constituting the mar-sox-rob regulon in S. Typhimurium) in regulating flagellar gene expression were explored. Each of these regulators was found to inhibit flagellar gene expression, production of flagella, and motility. To different degrees, repression via …

Dual Activities Of Plant Cgmp-Dependent Protein Kinase And Its Roles In Gibberellin Signaling And Salt Stress., Qingwen Shen, Xinqiao Zhan, Pei Yang, Jing Li, Jie Chen, Bing Tang, Xuemin Wang, Xuemin Wang, Yueyun Hong

Biology Department Faculty Works

Cyclic GMP (cGMP) is an important regulator in eukaryotes, and cGMP-dependent protein kinase (PKG) plays a key role in perceiving cellular cGMP in diverse physiological processes in animals. However, the molecular identity, property, and function of PKG in plants remain elusive. In this study, we have identified PKG from plants and characterized its role in mediating the gibberellin (GA) response in rice (Oryza sativa). PKGs from plants are structurally unique with an additional type 2C protein phosphatase domain. Rice PKG possesses both protein kinase and phosphatase activities, and cGMP stimulates its kinase activity but inhibits its phosphatase activity. One of …

Mammal Species Inventory Using Various Trapping Methods In Zone 4 Of Billy Barquedier National Park, Belize During Rainy Season, Mersady Redding

Animal Science Undergraduate Honors Theses

Belize is a small country, but it is extremely ecologically diverse. Based on the few studies conducted in Belize, the abundance of mammals is low but diversity is high. Particular findings note the number and identity of species differed between four sites in the Maya Mountains of Belize, indicating that a data set from a single site is not representative of the Neotropical region. Insufficient data is available to estimate current species richness of many areas in Belize, including Billy Barquedier National Park (BBNP). The objective of this study was to explore trapping and documentation methods of terrestrial mammals in …

Mechanisms And Consequences Of Myb Gene Activation In Salivary Gland Tumors, Candace Frerich

Biomedical Sciences ETDs

Salivary gland adenoid cystic carcinoma (ACC) is an aggressive tumor with a tendency to infiltrate surrounding nerves and metastasize to distant sites. The standard treatment often fails to control local tumor recurrence and distant metastases and no approved targeted therapeutic options exist for these tumors. The goal of our studies was to reveal the molecular mechanisms driving ACC tumor development and novel drug targets to improve patient morbidity and mortality.

We first analyzed clinical and RNA-sequencing (RNA-seq) data for 68 formalin-fixed paraffin-embedded (FFPE) ACC tumor samples and described previously unappreciated molecular heterogeneity that predicts patient outcome. The poor outcome subgroup …

Impact Of Metazooplankton Filter Feeding On Escherichia Coli Under Variable Environmental Conditions, Niveen S. Ismail, Brittney M. Blokker, Tyler R. Feeney, Ruby H. Kohn, Jingyi Liu, Vivian E. Nelson, Mariah C. Ollive, Sarah B. L. Price, Emma J. Underdaha

Engineering: Faculty Publications

The fecal indicator bacterial species Escherichia coli is an important measure of water quality and a leading cause of impaired surface waters. We investigated the impact of the filter-feeding metazooplankton Daphnia magna on the inactivation of E. coli. The E. coli clearance rates of these daphnids were calculated from a series of batch experiments conducted under variable environmental conditions. Batch system experiments of 24 to 48 h in duration were completed to test the impacts of bacterial concentration, organism density, temperature, and water type. The maximum clearance rate for adult D. magna organisms was 2 ml h1 organism1. Less than …

A Seascape Genetics Approach To Studying Genetic Differentiation In The Bull Kelp Nereocystis Luetkeana, Lily G. Gierke

Theses and Dissertations

The brown alga Nereocystis luetkeana is a foundation species found from Alaska to California. In the Salish Sea, N. luetkeana is declining, but little is known about its population structure. We explored N. luetkeana 1) allelic dissimilarity and richness using seven microsatellite markers, and 2) tested models of gene flow in the Salish Sea using a hydrodynamic transport model. Our results suggest that the N. luetkeana distribution is comprised of four genetic co-ancestry groups that are geographically coherent, apart from the separation of the Strait of Georgia/Puget Sound by the Strait of Juan de Fuca. Our model supported that environmental …

A Novel Switch-Like Function Of Delta-Catenin In Dendrite Development, Ryan Baumert

Dissertations & Theses (Open Access)

The formation of neuronal networks in the brain is tightly regulated, and dependent on the morphology of dendrites, the branch-like signal-receiving structures extending from neurons. Disruptions in dendrite development, or dendritogenesis, can lead to the atypical neuronal connectivity associated with multiple neurodevelopmental diseases. My research addresses molecular processes that underlie dendritogenesis via analysis of a pair of novel interactions involving the protein delta-catenin.

In neurons, delta-catenin localizes to dendrites and synapses, where it functions in their development and maintenance. Structurally, delta-catenin possesses a central Armadillo domain and a C-terminal PDZ-binding motif. This motif associates with PDZ domain-containing proteins, and is …

Xenobiotic Exposure Requires Mitochondrial Metabolism For Redox Homeostasis And Survival In Astrocytes, Jordan Rose

Department of Biochemistry: Dissertations, Theses, and Student Research

Astrocytes are integral components of glutamatergic neurotransmission, providing essential metabolic processes for neuronal homeostasis and acting as the first line of defense against xenobiotics crossing the blood brain barrier. Arsenic is a xenobiotic with widespread natural and industrial prevalence, and has been linked to impaired neurodevelopment and neuronal death. Given the integrated metabolic nature of astrocytes and neurons, we sought to explore how arsenic impacts astrocyte metabolism in order to better understand the mechanisms of xenobiotic toxicity in the mammalian brain.

We demonstrate that astrocyte viability depends upon de novoglutathione (GSH) synthesis during arsenic exposure, and sub-lethal arsenic exposure …

Characterization Of The Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor, Tyler Degener

Theses/Capstones/Creative Projects

The mannose-6-phosphate/insulin-like growth factor II (M6P/IGF2) receptor is a transmembrane protein known to sequester growth factors from the extracellular matrix. This behavior suggests a mechanism of tumor suppression. Structurally, the receptor’s extracellular region is segmented into 15 homologous repeats, which are divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. What is notable about the triplets is their propensity to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose of this experiment is to characterize these domain interactions. Using a urea …

Cpsa Protein-Protein Interactions In Group B Streptococcus, Ben Tero

Honors College

Group B Streptococcal (GBS) infections pose a great threat to mortality in neonates. Neonates are often exposed to GBS both before, during, and after delivery, which can cause a range of health problems including meningitis, sepsis, or stillbirth. One of the major virulence factors that contributes to the infectivity of the pathogen is the bacterial capsule. The capsule is a polysaccharide matrix surrounding the cell which helps in the evasion of host defenses, and penetration into normally sterile sites like the bloodstream. The highly conserved GBS protein CpsA has been shown to regulate expression of the capsule. The objective of …

Targeting The Γ-Aminobutyric Acid A Receptor (Gabaar) To Alleviate Inflammation For Asthma And Neuropathic Pain, Amanda Nicole Nieman

Theses and Dissertations

The γ-Aminobutyric Acid A Receptor (GABAAR) is a ligand-gated, pentameric chloride channel composed of subunits that include α1-6, β1-3, γ1-3, δ, ε, π, θ, ρ1-3.1-2 The most common arrangement includes two α subunits, two β subunits, and a γ subunit.3 This receptor includes two binding sites for the endogenous ligand γ-aminobutyric acid (GABA) between the α and β subunits and a binding site between the α and γ subunit for benzodiazepines, a large family of positive allosteric modulators.4-5

Benzodiazepines are one of the most prescribed classes of pharmaceuticals to treat anxiety, insomnia, and epilepsy as well as for muscle relaxation.6-7 …

Comparison Study Of Mold Growth Resistance Of Plastic Based Material Flooring (Pbm Flooring) And Ceramic Tile Flooring, Jyothi Rangineni, Jeremy Tzeng

Publications

Clemson University Department of Biological Sciences and Tile Council of North America Product Performance Testing Laboratory evaluated whether ceramic tile and Plastic Based Material (PBM¹) flooring support mold growth when exposed to fungal spores.

Mold grows in moisture-rich environments and requires only minimal sources of nutrition to support growth. It has long been identified to cause damage to buildings and construction materials and its presence in buildings has been connected to many major health concerns with various studies and reviews published on this matter.²

The method used to evaluate mold growth was ASTM G21-96 (2015).³ This …

Discovery Of Genomic Variations By Whole-Genome Resequencing Of The North American Araucana Chicken, Rooksana E. Noorai, Vijay Shankar, Nowlan H. Freese, Christopher M. Gregorski, Susan C. Chapman

Publications

Gallus gallus (chicken) is phenotypically diverse, with over 60 recognized breeds, among the myriad species within the Aves lineage. Domestic chickens have been under artificial selection by humans for thousands of years for agricultural purposes. The North American Araucana (NAA) breed arose as a cross between the Chilean “Collonocas” that laid blue eggs and was rumpless and the “Quetros” that had unusual tufts but with tail. NAAs were introduced from South America in the 1940s and have been kept as show birds by enthusiasts since then due to several distinctive traits: laying eggs with blue eggshells, characteristic ear-tufts, a pea …

Effects Of The Dihydrouracil Lesion On Dna Using 1h/31p 1d And 2d Solution Nmr, Benjamin M. Boyd

MSU Graduate Theses

The effects of the dihydrouracil lesion in DNA were studied using two dimensional NMR spectroscopy. The sequence used was based off of the Drew-Dickerson Dodecamer, with the cytosine in the three position replaced by a dihydrouracil. All of the nonexchangeable proton chemical shifts, with the exception of the H2, H5’, and H5’’, of the lesioned DNA were identified using NOESY spectra and then compared to the chemical shift values of the Drew Dickerson Dodecamer. The largest differences in chemical shifts were observed in the nucleotides neighboring the lesion, both within the strand and on the opposite strand. The imino exchangeable …

Factors Related To Adverse Mental Health Condition Of Demented Family Caregivers: A Study In West Bengal, India, Ipsita Basu, Susmita Mukhopadhyay

Journal Articles

Dementia caregiving is a unique and the caregivers faces extreme challenges which affect care-giver's mental health adversely. Family caregiving towards elderly individuals with dementia is becoming widespread. The study aims to evaluate the mental health status of dementia family caregivers and some related factors that affect their mental health condition. Present cross sectional study includes a total of 134 family caregivers. Socio-demographic and caregiving related data were collected using pre-tested questionnaires. Standardized questionnaires were used to collect data on caregivers' mental health traits (measured in terms of level of stress and anxiety), level of psychosocial distress, support they provided and …

Exploration Of Ataxia Telangiectasia And Rad3-Related’S (Atr’S) Role In Cell Death Regulation: Implications In Development, Cancer, And Stroke, Brian Cartwright

Electronic Theses and Dissertations

From gametogenesis until death an organism’s genome is under constant bombardment from endogenous and exogenous sources of DNA damage. To maintain genomic integrity amid this damage, cells have evolved responses which allow them to either preserve viability for recovery or initiate self-destructive pathways depending on the severity of DNA damage. One protein involved in initiating and carrying out these responses is the protein kinase ataxia telangiectasia and Rad3-related (ATR). ATR is known primarily for its regulatory role in initiating the checkpoint-signaling cascade following DNA damage and replicative stress. These signaling events lead to cell cycle arrest, DNA repair, or apoptosis …