Biochemistry, Biophysics, and Structural Biology Commons^™

Structural Characterization Of Feruloylated Arabinoxylan Oligosaccharides Isolated From Rice Bran Fiber, Kan Takahashi

Student Theses and Dissertations

Increased consumption of soluble cereal arabinoxylan (AX), and feruloylated arabinoxylan oligosaccharides (FAXOs) generated from it, may promote healthful gastro-intestinal functioning through modulating the gut microbiota and tuning innate immune response function at the gut epithelium. FAXO compositions isolated from rice bran fiber were characterized for their oligosaccharide mass profiles (MALDI-TOF MS) and monosaccharide compositions (GC-FID). Results indicated gluco-oligosaccharides were covalently associated with the FAXOs. I tested the hypothesis that the association represents a novel intermolecular crosslink between mixed linkage β-glucan and AX in rice caryopsis cell walls. The structural characteristics of gluco-oligosaccharides were analyzed to determine glycosidic linkages (GC-MS) and …

Canvass: A Crowd-Sourced, Natural-Product Screening Library For Exploring Biological Space, Sara E. Kearney, Gergely ZahoráNszky-KőHalmi, Kyle R. Brimacombe, Mark J. Henderson, Caitlin Lynch, Tongan Zhao, Kanny K. Wan, Zina Itkin, Christopher Dillon, Min Shen, Dorian M. Cheff, Tobie D. Lee, Danielle Bougie, Ken Cheng, Nathan P. Coussens, Dorjbal Dorjsuren, Richard T. Eastman, Ruili Huang, Michael J. Iannotti, Surendra Karavadhi, Carleen Klumpp-Thomas, Jacob S. Roth, Srilatha Sakamuru, Wei Sun, Steven A. Titus, Adam Yasgar, Ya-Qin Zhang, Jinghua Zhao, Rodrigo B. Andrade, M. Kevin Brown, Robert B. Grossman

Chemistry Faculty Publications

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The …

Distribution Of Dengue And Zika Virus Igg Immunoglobulin, Madison Smith, Awadalkareem Adam, Anuja Mathew

Senior Honors Projects

Introduction. Dengue Virus (DENV) and Zika Virus (ZIKV) are viruses that belong to the Flavivirus family. They are transmitted by the Aedes aegypti species of mosquitoes. Infection with DENV can result in no symptoms, mild symptoms which include fever, rash, and headache (dengue fever) or more severe symptoms which include hemorrhage, dengue hemorrhagic fever (DHF) and shock, dengue shock syndrome (DSS). ZIKV, until recently caused mild disease but an outbreak in Brazil was associated with fetal complications such as microcephaly or Guillain-Barré syndrome in adults. Due to the similarity between ZIKV and DENV, antibodies (Abs) generated in humans to these …

Generating High-Order Optical And Spin Harmonics From Ferromagnetic Monolayers, G.P. Zhang, M.S. Si, M. Murakami, Y.H. Bai, Thomas George

Chemistry & Biochemistry Faculty Works

High-order harmonic generation (HHG) in solids has entered a new phase of intensive research, with envisioned band-structure mapping on an ultrashort time scale. This partly benefits from a flurry of new HHG materials discovered, but so far has missed an important group. HHG in magnetic materials should have profound impact on future magnetic storage technology advances. Here we introduce and demonstrate HHG in ferromagnetic monolayers. We find that HHG carries spin information and sensitively depends on the relativistic spin–orbit coupling; and if they are dispersed into the crystal momentum k space, harmonics originating from real transitions can be k-resolved and …

Brca1 And Brca2 5′ Noncoding Region Variants Identified In Breast Cancer Patients Alter Promoter Activity And Protein Binding, Leslie J. Burke, Jan Sevcik, Gaetana Gambino, Emma Tudini, Eliseos J. Mucaki, Ben C. Shirley, Phillip Whiley, Michael T. Parsons, Kim De Leeneer, Sara Gutiérrez-Enríquez, Marta Santamariña, Sandrine M. Caputo, Elizabeth Santana Dos Santos, Jana Soukupova, Marketa Janatova, Petra Zemankova, Klara Lhotova, Lenka Stolarova, Mariana Borecka, Alejandro Moles-Fernández, Siranoush Manoukian, Bernardo Bonanni, Stacey L. Edwards, Marinus J. Blok, Thomas Van Overeem Hansen, Maria Rossing, Orland Diez, Ana Vega, Kathleen B.M. Claes, David E. Goldgar, Etienne Rouleau

Biochemistry Publications

© 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc. The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5′ noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency < 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C>T and PAX5 binding to BRCA2:c.-296C …

Epidemiological Studies Of Soybean Vein Necrosis Virus And Potential Resistance Mechanisms To Its Vector Neohydatothrips Variabilis (Beach), Jing Zhou

Graduate Theses and Dissertations

Soybean (Glycine max (L.) Merrill) is one the most important crops in global agriculture with annual production of over 260 million metric tons. As the dependence of a growing global population to soybean has increased, so does the importance of soybean diseases and pests. Over 200 pathogens attack soybean; among them, viruses pose a major threat to the soybean industries accounting for approximately 10% of the annual yield reduction caused by diseases in the past two decades. Soybean vein necrosis virus (SVNV) is a relatively newly discovered virus causing the homonymous disease. The widespread occurrence of the disease in major …

Optimization Of Detergent-Mediated Reconstitution Of Influenza A M2 Protein Into Proteoliposomes, Catherine Hirshfeld Crouch, Margaret H. Bost , '17, Tae H. Kim , '14, Bryan M. Green , '16, Douglas Stuart Arbuckle , '17, Carl H. Grossman, Kathleen P. Howard

Physics & Astronomy Faculty Works

We report the optimization of detergent-mediated reconstitution of an integral membrane-bound protein, full-length influenza M2 protein, by direct insertion into detergent-saturated liposomes. Detergent-mediated reconstitution is an important method for preparing proteoliposomes for studying membrane proteins, and must be optimized for each combination of protein and membrane constituents used. The purpose of the reconstitution was to prepare samples for site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) studies. Our goals in optimizing the protocol were to minimize the amount of detergent used, reduce overall proteoliposome preparation time, and confirm the removal of all detergent. The liposomes were comprised of (1-palmitoyl-2-oleyl-sn-glycero-phosphocholine (POPC) and 1-palmitoyl-2-oleyl-sn-glycero-3-[phospho-rac-(1-glycerol)] …

Functional Consequence Of Psat1 Association On Pkm2'S Inherent Enzymatic Activity., Alexis Avidan Vega

Electronic Theses and Dissertations

Pyruvate kinase M2 (PKM2) is predominantly found in tumors, where it allows the cancer cell to adapt to metabolic conditions through allosteric regulation of its activity. We recently discovered that phosphoserine aminotransferase 1 (PSAT1) associates with and activates PKM2. Here, I sought to affirm PSAT1's ability to increase PKM2 activity through kinetic and association studies of wild-type or mutant PKM2 enzymes. I demonstrate that His-tagged WT and mutant PKM2 enzymes are active, exhibit different kinetics, yet cannot be activated by PSAT1. Comparison studies using untagged WT PKM2 suggest that inclusion of the His-tag disrupts PSAT1 association. In support, pull-down strategies …

Virulence Regulation In Pseudomonas Aeruginosa Via The Alginate Regulators, Algu And Algr, The Posttranscriptional Regulator, Rsma, And The Two-Component System, Algz/R, Sean Stacey

Electronic Theses and Dissertations

Pseudomonas aeruginosa is a Gram-negative bacillus able to colonize a wide variety of environments. In the human host, P. aeruginosa can establish an acute infection or persist and create a chronic infection. P. aeruginosa is able to establish a niche and persist in human hosts by using a wide array of virulence factors used for: movement, killing host cells, and evading immune cells and antibiotics. Understanding virulence factors and their regulation has proved to be an important means of combating the morbidity and mortality of P. aeruginosa as well as the ever-increasing threat of drug resistance. By targeting virulence factors …

Ph-Induced Folding Of The Caspase-Cleaved Par-4 Tumor Suppressor: Evidence Of Structure Outside Of The Coiled Coil Domain, Andrea M. Clark, Komala Ponniah, Meghan S. Warden, Emily M. Raitt, Andrea C. Yawn, Stephen M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, …

Harnessing The Physical Properties Of Zno Nanoparticles For Biological Applications And Factors That Impact Zno Nanoparticle Toxicity, Joshua Eixenberger

Boise State University Theses and Dissertations

The production of materials at the nanoscale leads to novel properties and has made the field of nanotechnology a part of everyday life. Numerous applications of nanomaterials have led to their use in electronics, optics, and medicine. However, creating materials at such a small size brings them on the same scale as many biomolecules and cellular components, altering their interactions with biological systems. This can lead to unintended biological impacts as many nanomaterials are considerably more toxic than their bulk counterpart material. ZnO nanoparticles (nZnO) are particularly interesting in this context. The FDA classifies ZnO as a generally recognized as …

The Goldilocks Approach: A Review Of Employing Design Of Experiments In Prokaryotic Recombinant Protein Production, Barry Ryan, Albert Uhoraningoga, Gemma K. Kinsella, Gary T. .. Henehan

Articles

The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem statistical models, such as Design of Experiments (DoE), have been used to optimise recombinant protein production. This review explores the application of DoE in the production of recombinant proteins, focusing on prokaryotic expression systems with a specific emphasis on media composition and …

Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani

Graduate Theses and Dissertations

This dissertation presents a collection of studies that investigate the genetic and epigenetic associations to ascites phenotype in broiler chickens. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome PHS. It is a multi-factorial syndrome caused by interactions between genetic, physiological, environmental, and managemental factors. It was estimated that ascites accounts for losses of about US$1 billion annually worldwide and for over 25% of broilers mortality. Although traditional and molecular genetic methods in the selection and in performance improvements, has greatly reduced ascites frequency, yet it has not …

The First In Vivo Human Methionine Sulfide Proteome And The Impact Of Smoking, Abdullah Qassab

Graduate Theses and Dissertations

Reactive oxygen species are naturally generated within the human body and they are known to modulate signaling pathway and mediate other physiological activities. However, excessive generation of ROS and the inability of body defense system in detoxifying them results in the so called “oxidative stress”. Methionine has powerful antioxidant properties due to the presence of electronegative sulfur in its structure. Therefore, Met is readily oxidized, and methionine sulfoxide has been linked to several pathological conditions.

The urinary proteome is an attractive candidate for the discovery of biomarkers to diagnose and classify health conditions because of the non-invasive collection procedure. However, …

Coagulation Factor Xiiia: Biochemical Properties Underlying Physiological Function., Boris Anokhin

Electronic Theses and Dissertations

Factor XIIIA (FXIIIA) is a transglutaminase that crosslinks intra- and extracellular protein substrates. The oligomeric state of active FXIIIA remains controversial, and the present work commenced with addressing this issue. The results of size exclusion chromatography and analytical ultracentrifugation confirmed a dimeric state for zymogen and, for the first time, indicated a monomeric state for the active FXIIIA in solution. Comparing sedimentation properties of proteolytically and nonproteolytically activated FXIIIA suggested conformational and functional differences between the two forms. Those differences were further assessed in a series of catalytic activity studies. Kinetic analysis revealed affinity for the glutamine substrate was higher …

Localization Of Sip470, A Plant Lipid Transfer Protein In Nicotiana Tabacum, Shantaya Andrews

Electronic Theses and Dissertations

SABP2-interacting protein 470 (SIP470), a non-specific lipid transfer protein (nsLTP), was discovered in a yeast two-hybrid screening using SABP2 as bait and tobacco leaf proteins as prey. SABP2 is an important enzyme in systemic acquired resistance that converts salicylic acid to methyl salicylate. Localization studies are an important aspect to understanding the biological function of proteins. nsLTPs are generally considered apoplastic proteins and has been localized intracellularly and extracellularly. Transient expression shows highest expression of SIP470-eGFP at 2 days post infiltration into Nicotiana benthamiana. Confocal microscopy showed localization near the periphery of the cell. Subcellular localization using differential centrifugation showed …

Heteroleptic Nickel Complexes Of A Bulky Bis(Carbene)Borate Ligand, Jorge L. Martinez, Wei-Tsung Less, Maren Pink, Chun-Hsing Chen, Jeremy M. Smith

Chemistry: Faculty Publications and Other Works

Bis(carbene)borate ligand transfer to the nickel nitrosyl synthon Ni(NO)(PPh3)2Br provides the new nickel nitrosyl complex Ph2B(t BuIm)2Ni(NO)(PPh3). The solid state structure reveals a trigonal pyramidal nickel ion with a very long bond to the apical PPh3 ligand. The complex reversibly dissociates PPh3 in solution to afford three‐coordinate Ph2B(t BuIm)2Ni(NO), with NMR data providing evidence for PPh3 binding at low temperatures. Ligand transfer to Ni(PMe3)2Cl2 provides the square planar complex, Ph2B(t BuIm)2Ni(PMe3)Cl, which shows no evidence for rearranging to the form a homoleptic complex with two bis(carbene)borate ligands. This complex is a suitable synthon for the [Ph2B(t BuIm)2Ni]+ fragment, as demonstrated …

Developing Ultra-High Throughput Sequencing Based Assay For Ligase Ribozymes For The Study Of Evolutionary Innovations, James Collet

Boise State University Theses and Dissertations

The study of evolutionary innovations, or novel traits, is integral to understanding evolution yet is poorly understood. By studying the regions between genotype networks that produce the same phenotype, we can better characterize the process by which innovation occurs. The overarching goal of this study is to assign fitness values to the overlapping genotype network of two catalytic RNA molecules, or ribozymes. Properly characterizing this region requires the study of thousands of individual sequences, which is achievable through the use of high-throughput sequencing analysis. This thesis focuses on developing assays for one of the ribozymes, the ligase ribozyme. Due to …

The Study Of Alcoholic Liver Diseases, Seun Emmanuel Owoseni

Electronic Theses and Dissertations

Excessive alcohol consumption is the primary contributing factor in the development of alcoholic liver diseases (ALD). Nicotine contained in tobacco is a major addictive alkaloid, which enhances the effects of ALDs. The major enzyme involved in nicotine metabolism is cytochrome P450 2A5 (CYP2A5) which is produced in the liver. Alcohol can stimulate the CYP2A5 enzyme. We utilized cyp2a5-/- knockout mice in this research to examine the effects of CYP2A5.

The cyp2a5-/- mice and wild-type (WT) mice were fed liquid ethanol diet with or without nicotine to induce ALD. Nicotine enhancing effects on ALD were observed in WT mice but not …

Data On Spectrum-Based Fluorescence Resonance Energy Transfer Measurement Of E. Coli Multidrug Transporter Acrb, Yuguang Cai, Thomas E. Wilkop, Yinan Wei

Chemistry Faculty Publications

This paper presented the dataset of correction parameters used in the determination of the energy transfer efficiencies from the spectrum-based fluorescence resonance energy transfer (FRET) measurement in a trimeric membrane protein AcrB. The cyan fluorescent protein (CFP) and yellow fluorescent protein (YPet) were used as the donor and acceptor, respectively. Two AcrB fusion proteins were constructed, AcrB-CFP and AcrB-YPet. The proteins were co-expressed in Escherichia coli cells, and energy transfer efficiency were determined in live cells. To obtain reliable energy transfer data, a complete set of correction parameters need to be first determined to accommodate for factors such as background …