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 …

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 …

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 …

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 …

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 …

Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan

Computer Science Faculty Publications

Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins. …

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 …

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 …

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 …

Global Acetylation Dynamics In The Heat Shock Response Of Saccharomyces Cerevisiae, Rebecca E. Hardman

Graduate Theses and Dissertations

All organisms face a constant barrage of environmental stresses. Single-cell organisms such as Saccharomyces cerevisiae, or common Baker’s yeast, must rely solely on cellular responses in order to survive. This response must occur in a rapid and highly coordinated manner to quickly inhibit all unnecessary processes and shuttle all available resources to those necessary for survival. One method that cells utilize for rapid protein regulation is the use of post-translational modifications. Enzymes within the cell add or remove a variety of chemical modifications, thus altering the local chemical environment of a protein. This creates a conformational change in the protein …

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 …

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 …

Probing Of Carbohydrate-Protein Interactions Using Galactonoamidine Inhibitors, Jessica B. Pickens

Graduate Theses and Dissertations

Glycoside hydrolases are ubiquitous and one of the most catalytically proficient enzymes known, and thus understanding their mechanisms are crucial. Most research has focused on the interaction of the glycon of substrates and their inhibitors within the active site of glycoside hydrolases. The inhibitors employed to probe these interactions generally had small aglycons (i.e. a hydrogen atom, amidines, small aliphatic groups, or benzyl groups). Here, the interactions of the aglycon with glycoside hydrolases are examined by probing the active sites with a library of 25 galactonoamidines. The studies described in this dissertation aim to increase the understanding of stabilization of …

Toward Understanding The Mechanism Of Protein Targeting In The Chloroplast Signal Recognition Particle Pathway, Mercede Furr

Graduate Theses and Dissertations

Protein targeting is a vital cellular function. The signal recognition particle (SRP) pathway is a universally conserved targeting system present in the cytosol and used to co-translationally target many proteins to the inner membrane of prokaryotes and the endoplasmic reticulum of eukaryotes. The chloroplast has a homologous SRP system which post-translationally targets light harvesting chlorophyll binding proteins (LHCPs) to the thylakoid membrane for integration. The chloroplast SRP (cpSRP) is a heterodimer with a 54 kDa subunit equivalent to SRP54 in the canonical pathway. In addition, cpSRP contains a novel 43 kDa subunit which is a unique and irreplaceable component. cpSRP43 …

The Curious Case Of Nad-Cleaving Nudix Hydrolases, Atreyei Ray

Theses and Dissertations

Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds (x). These enzymes have catalytic activity on a wide range of substrates such as dNTPs (both canonical and their oxidized forms), nucleotide sugars, alcohols, dinucleoside polyphosphates, dinucleotide cofactors, and nucleoside diphosphates linked to RNA. The bacterial genome encodes around 13, while the human genome encodes for 22 such nudix proteins.

The E. coli genome encodes for a mutT mutator gene, the progenitor of the family expressing the MutT pyrophosphohydrolase (NudA) protein (Treffers et al., 1954; Bhatnagar et al., 1988). The enzyme …

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 …

Analyzing Multigene Stacking And Genome Editing Strategies In Rice, Bhuvan Pathak

Graduate Theses and Dissertations

Crop improvement through biotechnology is an integrated effort, incorporating multiple approaches like integration of genes, editing of native genes, and removal of selection marker genes. Before streamlining the protocols, the efficiency and feasibility of the individual approach and their components must be tested. This study evaluated following approaches: 1) stacking an array of genes into a single locus by site-specific integration via Cre-lox recombination in rice, 2) determining the efficiency of I-SceI and the CCR5-ZFN in the targeted excisions of gene fragments in rice and Arabidopsis, and 3) determining the efficiency of CRISPR/Cas9 in generating targeted mutations for genome editing …

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 …

Electropermeabilization Does Not Correlate With Plasma Membrane Lipid Oxidation, Olga Michel, Andrei G. Pakhomov, Maura Casciola, Jolanta Saczko, Julita Kulbacka, Olga N. Pakhomova

Bioelectrics Publications

The permeabilized condition of the cell membrane after electroporation can last minutes but the underlying mechanisms remain elusive. Previous studies suggest that lipid peroxidation could be responsible for the lasting leaky state of the membrane. The present study aims to link oxidation within the plasma membrane of live cells to permeabilization by electric pulses. We have introduced a method for the detection of oxidation by ratiometric fluorescence measurements of BODIPY-C11 dye using total internal reflection fluorescence (TIRF) microscopy, limiting the signal to the cell membrane. CHO-K1 cells were cultured on glass coverslips coated with an electroconductive indium tin oxide (ITO) …

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 …