Biochemistry, Biophysics, and Structural Biology Commons^™

Assessment Of Salmonella Enterica Biofilms And Expression Differences Among Serovars, Zhaohao Shi

Graduate Theses and Dissertations

Biofilms are communities of microorganisms associated by a matrix of extracellular polymers. In this state, microorganisms occupy an ecological niche distinct from their free-floating, planktonic counterparts. Also, biofilm bacteria become biologically unique as they form communities and lose motility. The acquisition of these physiological attributes enables the biofilm to persist through harsh environmental conditions, including antimicrobial induced stress and to resist sanitization efforts. Because of these features, biofilms can rapidly disseminate across numerous surfaces and as they establish, become challenging to remove. This is a particular issue for the food industry as processing plants offer favorable conditions for biofilm formation …

Investigation Of Electrolytic Flocculation For Microalga Scenedesmus Sp Using Aluminum And Graphite Electrodes, Shihong Liu, Husam A. Abu Hajar, Guy Riefler, Ben J. Stuart

Civil & Environmental Engineering Faculty Publications

Electrolytic flocculation using non-sacrificial electrodes with flocculants added was studied on harvesting Scenedesmus sp. In order to optimize the operating conditions of the electrolytic flocculation process and to quantify the amount of flocculants added, aluminum electrodes were first used in the process. It was found that under optimal conditions, the microalgae removal efficiency using aluminum electrodes could reach 98.5%, while 34.2 mg L^-1 of aluminum ions were released during the process. Different metal electrodes were also studied, but high microalgae removal efficiency was witnessed only using aluminum electrodes, indicating the influence of the aluminum ion in flocculation. When non-sacrificial …

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 …

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, …

Lipid Extraction From Spirulina Sp. And Schizochytrium Sp. Using Supercritical Co2 With Methanol, Shihong Liu, Husam A. Abu Hajar, Guy Riefler, Ben J. Stuart

Civil & Environmental Engineering Faculty Publications

Microalgae are one of the most promising feedstocks for biodiesel production due to their high lipid content and easy farming. However, the extraction of lipids from microalgae is energy intensive and costly and involves the use of toxic organic solvents. Compared with organic solvent extraction, supercritical CO₂ (SCCO₂) has demonstrated advantages through lower toxicity and no solvent-liquid separation. Due to the nonpolar nature of SCCO_2, polar organic solvents such as methanol may need to be added as a modifier in order to increase the extraction ability of SCCO₂. In this paper, pilot scale lipid …

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 …

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 …

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 …

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 …

Investigating Autophagy Dysfunction Induced By A Parkinson's Disease-Causing Mutation In Vps35, Abir Ashfakur Rahman

Boise State University Theses and Dissertations

Parkinson’s Disease (PD) is an idiopathic disorder with no known cure. With number of cases steadily rising around the world, it is imperative to turn to the underlying cellular and molecular mechanisms of the disease manifestation and neurodegeneration to craft novel modes of therapy. VPS35 is one of the few genes that have identified and definitively linked to familial PD. The particular mutation that has been associated is known to cause dysfunction of a key cellular process known as autophagy. This process is primarily responsible for clearance of unwanted, damaged or misfolded proteins, among other things. Our study reveals an …

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 …

Role Of P300 Zz Domain In Chromatin Association And Histone Acetylation, Yongming Xue

Dissertations and Theses (Open Access)

Transcription is strictly regulated by numerous factors including transcription coactivators. The p300 protein and its close paralogue CREB-binding protein (CREBBP, aka CBP) are well-known transcriptional coactivators that have intrinsic lysine acetyltransferase activity. The functions of p300/CBP largely rely on their capabilities to bind to chromatin and to acetylate the histone substrates. However, the molecular mechanisms underlying the regulation of these processes are not fully understood.

Through combination of various biochemical, biophysical and molecular approaches, we show that the ZZ-type zinc finger (ZZ) domain of p300 functions as a histone reader that specifically binds the N-terminal tail of histone H3. Crystal …

A Role For Epac1 And Epac2 In Nociceptor Hyperexcitability And Chronic Pain After Spinal Cord Injury, Samantha Berkey

Dissertations and Theses (Open Access)

Chronic pain is a major complaint of those living with spinal cord injury (SCI), affecting 65-80% of the SCI population, but the treatment options remain limited or non-existent. The cAMP sensor EPAC has previously been shown to play a key role in chronic inflammatory and neuropathic pain, though the contribution from each of its two main isoforms, EPAC1 and EPAC2, is unclear. Here I test the hypothesis that both EPAC1 and EPAC2 play a key role in the maintenance of persistent nociceptor hyperexcitability and chronic pain after SCI.

Using both a T9 SCI mouse model and a T10 SCI rat …

Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri

Electronic Theses and Dissertations

SABP2 (Salicylic Acid Binding Protein 2) plays a vital role in the salicylic acid signaling pathway of plants both regarding basal resistance and systemic acquired resistance against pathogen infection. SIP-428 (SABP2 Interacting Protein-428) is a Silent information regulator 2 (SIR2) like deacetylase enzyme that physically interacts with SABP2 in a yeast two-hybrid interaction and confirmed independently by a GST pull-down assay. We demonstrated that SIP- 428 is an NAD+ dependent SIR2 deacetylase enzyme. Transgenic tobacco plants silenced in SIP- 428 expression via RNAi showed enhanced basal resistance to microbial pathogens. Moreover, these SIP-428-silenced lines also exhibited a robust induction of …

Characterization Of Acyltransferases And Wrinkled Orthologs Involved In Tag Biosynthesis In Avocado, Md Mahbubur Rahman

Electronic Theses and Dissertations

Triacylglycerols (TAG) or storage oils in plants are utilized by humans for nutrition, production of biomaterials and fuels. Since nonseed tissues comprise the bulk biomass, it is pertinent to understand how to improve their TAG content. Typically, the final step in TAG biosynthesis is catalyzed by diacylglycerol (DAG) acyltransferases (DGAT) and/or phospholipid: diacylglycerol acyltransferases (PDAT), which also determine the content and composition of TAG. Besides enzymatic regulation of TAG synthesis, transcription factors such as WRINKLED1 (WRI1) play a critical role during fatty acid synthesis. In this study, mesocarp of Persea americana, with > 60% TAG by dry weight and oleic …

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 …

Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright

Electronic Theses and Dissertations

Organisms adapt to their environments by adjusting their biochemistry and physiology; such adaptation is limited by resource availability and physiological constraints. The freshwater crustacean Daphnia magna inhabits a wide range of environments and must survive and reproduce within a range of temperatures. One limit to low-temperature adaptation is thought to be the availability of unsaturated fatty acids necessary to maintain proper fluidity of cellular membranes. D. magna maintained at 10 ºC on a diet poor in unsaturated fatty acids have been observed to produce clutches that fail to develop. However, this has not been observed on a diet rich in …

Genetic And Genomic Analyses Of Bacterial Responses To Different Stress Environments, Sakshi Rampal

Graduate Theses and Dissertations

Bacteria encounter a plethora of environmental stresses and have evolved different mechanisms to recognize and respond to various harmful conditions. Understanding and elucidating common themes as well as unique aspects of the molecular mechanisms underlying stress adaptation is important and can provide valuable strategies for applications. This study focuses on stress responses in three different bacteria, namely, Acidothermus cellulolyticus, Mycobacterium smegmatis and Escherichia coli. The thermophilic and acidophilic organism A. cellulolyticus was used as a model system to understand the effects of lignin phenolic acids on cellulolytic bacteria. Lignin phenolic acids pose a significant challenge to microbial deconstruction of lignocellulosic …

A Simple Metabolic Switch May Activate Apomixis In Arabidopsis Thaliana, David Alan Sherwood

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Apomixis, asexual or clonal seed production in plants, can decrease the cost of producing hybrid seed and enable currently open pollinated crops to be converted to more vigorous and higher yielding hybrids that can reproduce themselves through their own seed. Sexual reproduction may be triggered by a programmed stress signaling event that occurs in both the meiocyte, just prior to meiosis, and later in the egg just prior to embryo sac maturation. The prevention of stress signaling and the activation of a pro-growth signal prior to meiosis triggered apomeiosis, the first half of apomixis. The same approach was used prior …

Ca2+ - Induced Structural Change Of Multi-Domain Collagen Binding Segments Of Collagenases Colg And Colh From Hathewaya Histolytica, Christopher Eric Ruth

Graduate Theses and Dissertations

Hathewaya histolytica, previously renamed as Clostridium histolyticum, secretes at least two collagenases, ColH and ColG, that allow for degradation of extracellular matrices of animal tissue. Hathewaya histolytica virulence factors are proposed to undergo domain rearrangement upon secretion from the bacteria to the host. In order to accomplish this, collagenases seek the least ordered regions in collagen to efficiently disassemble the fibril. Two types of domains, Polycystic Kidney Disease-like (PKD) and Collagen Binding Domain (CBD), direct the collagenases ability to disassemble the fibril. Calcium dependent structural change have been reported to increase in thermal stability and in tighter collagen binding for …

Investigation Of The Molecular Mechanisms Of The Shigella Type Iii Secretion System Tip Complex, Abram R. Bernard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Shigella are bacteria that are responsible for millions of infections and hundreds of thousands of deaths every year. The emergence of antibiotic resistant Shigella adds to the potentially devastating effect that these bacteria can have on human health. Shigella flexneri utilize specialized molecular machinery called the Type III secretion system to infect humans and cause disease. Research of this machinery promises to provide the knowledge, tools, and direction for the development of new avenues to combat shigellosis. This dissertation presents studies of two Shigella proteins, invasion plasmid antigens C and D (IpaC and IpaD). These proteins are part of a …

Differentiation Of Oligodendrocytes For Myelination In The Nervous System, Krishna Deo Sharma

Student Theses and Dissertations

Differentiation of neural stem cells (NSCs) into large a number of oligodendrocytes (ODCs) for transplantation therapy has been a challenge. Evidence indicates that NSC differentiation is influenced by the interaction of the stem cells and their extracellular environment such as extracellular matrix (ECM), and soluble factors, such as growth factors and hormones. We tested if (1) well planned sequential addition of a combination of soluble factors increase the population of NSCs differentiating into ODCs and (2) a natural ECM (e.g, matrigel) promotes ODC differentiation better than poly-D-lysine (PDL). Embryonic rat NSCs were propagated in the presence of basic fibroblast growth …

A Gcn5-Related N-Acetyltransferase (Gnat) Capable Of Acetylating Polymyxin B And Colistin Antibiotics In Vitro, Mateusz P. Czub, Brian Zhang, M. Paul Chiarelli, Karolina A. Majorek, Layton Joe, Pryemyslaw J. Prebski, Alina Revilla, Weiming Wu, Daniel P. Becker, Wladek Minor, Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

Deeper exploration of uncharacterized Gcn5-related N-acetyltransferases has the potential to expand our knowledge of the types of molecules that can be acylated by this important superfamily of enzymes and may offer new opportunities for biotechnological applications. While determining native or biologically relevant in vivo functions of uncharacterized proteins is ideal, their alternative or promiscuous in vitro capabilities provide insight into key active site interactions. Additionally, this knowledge can be exploited to selectively modify complex molecules and reduce byproducts when synthetic routes become challenging. During our exploration of uncharacterized Gcn5-related N-acetyltransferases from Pseudomonas aeruginosa, we identified such an …

Metformin, Oxidative Stress, And Infertility: A Way Forward, Rehana Rehman, Syed Hani Abidi, Faiza Alam

Department of Biological & Biomedical Sciences

No abstract provided.

Molecular Fossils From Phytoplankton Reveal Secular Pco2 Trend Over The Phanerozoic, Caitlyn R. Witkowski, Johan W. H. Weijers, Brian S. Blais, Stefan Schouten, Jaap S. Sinninghe Damsté

Science and Technology Department Faculty Journal Articles

Past changes in the atmospheric concentration of carbon dioxide (PCO2) have had a major impact on earth system dynamics; yet, reconstructing secular trends of past PCO2 remains a prevalent challenge in paleoclimate studies. The current long-term PCO2reconstructions rely largely on the compilation of many different proxies, often with discrepancies among proxies, particularly for periods older than 100 million years (Ma). Here, we reconstructed Phanerozoic PCO2 from a single proxy: the stable carbon isotopic fractionation associated with photosynthesis (Ɛp) that increases as PCO2 increases. This concept has been widely applied to alkenones, but here, we …

Ms In Cytopathology, Joanna Burkhardt

Library Impact Statements

No abstract provided.

A Rapid And Sensitive System For Recovery Of Nucleic Acids From Mycobacteria Sp. On Archived Glass Slides, Balkis A. Talip, William J. Snelling, Roy D. Sleator, Colm Lowery, James S.G. Dooley

Department of Biological Sciences Publications

The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM …

Decreasing Phosphatidylcholine On The Surface Of The Lipid Droplet Correlates With Altered Protein Binding And Steatosis, Laura Listenberger, Elizabeth Townsend, Cassandra Rickertsen, Anastasia Hains, Elizabeth Brown, Emily G. Inwards, Angela K. Stoeckman

Chemistry Faculty Publications

Alcoholic fatty liver disease (AFLD) is characterized by an abnormal accumulation of lipid droplets (LDs) in the liver. Here, we explore the composition of hepatic LDs in a rat model of AFLD. Five to seven weeks of alcohol consumption led to significant increases in hepatic triglyceride mass, along with increases in LD number and size. Additionally, hepatic LDs from rats with early alcoholic liver injury show a decreased ratio of surface phosphatidylcholine (PC) to phosphatidylethanolamine (PE). This occurred in parallel with an increase in the LD association of perilipin 2, a prominent LD protein. To determine if changes to the …

Mitochondrial Metabolism In Major Neurological Diseases, Zhengqiu Zhou, Grant L. Austin, Lyndsay E. A. Young, Lance A. Johnson, Ramon Sun

Molecular and Cellular Biochemistry Faculty Publications

Mitochondria are bilayer sub-cellular organelles that are an integral part of normal cellular physiology. They are responsible for producing the majority of a cell’s ATP, thus supplying energy for a variety of key cellular processes, especially in the brain. Although energy production is a key aspect of mitochondrial metabolism, its role extends far beyond energy production to cell signaling and epigenetic regulation–functions that contribute to cellular proliferation, differentiation, apoptosis, migration, and autophagy. Recent research on neurological disorders suggest a major metabolic component in disease pathophysiology, and mitochondria have been shown to be in the center of metabolic dysregulation and possibly …