Biochemistry, Biophysics, and Structural Biology Commons^™

Hif-2 Regulation Of Amino Acid Transporter Expression In Hepatocellular Carcinoma Cells, Jason A. Misurelli

Graduate Research Theses & Dissertations

Hypoxia represents a major driver of the cancer phenotype in solid tumors, especially those of hepatic origin. Low oxygen availability triggers a complex cellular response which alters metabolism and promotes cellular invasion. Growing evidence suggests the amino acid glutamine, an important molecular currency for both energy producing reactions and biosynthetic pathways, plays an enhanced role in cancer cells under hypoxia. Hypoxia-inducible factors (HIFs) are transcription factors crucial for regulating the cellular response to low oxygen. Family member HIF-1 has been well studied, however, recent evidence suggests HIF-2 may have a regulatory role in amino acid transport and metabolism under hypoxia. …

Impact Of Conformational Change, Solvation Environment, And Post-Translational Modification On Desulfurization Enzyme 2'-Hydroxybiphenyl-2-Sulfinate Desulfinase (Dszb) Stability And Activity, Landon C. Mills

Theses and Dissertations--Chemical and Materials Engineering

Naturally occurring enzymatic pathways enable highly specific, rapid thiophenic sulfur cleavage occurring at ambient temperature and pressure, which may be harnessed for the desulfurization of petroleum-based fuel. One pathway found in bacteria is a four-step catabolic pathway (the 4S pathway) converting dibenzothiophene (DBT), a common crude oil contaminant, into 2-hydroxybiphenyl (HBP) without disrupting the carbon-carbon bonds. 2’-Hydroxybiphenyl-2-sulfinate desulfinase (DszB), the rate-limiting enzyme in the enzyme cascade, is capable of selectively cleaving carbon-sulfur bonds. Accordingly, understanding the molecular mechanisms of DszB activity may enable development of the cascade as industrial biotechnology. Based on crystallographic evidence, we hypothesized that DszB …

Illuminating Dna Packaging In Sperm Chromatin: How Polycation Lengths, Underprotamination And Disulfide Linkages Alters Dna Condensation And Stability, Daniel Kirchhoff

Theses and Dissertations--Chemistry

During spermiogenesis, somatic chromatin is remodeled and a vast majority (> 90%) of DNA histones are replaced by short arginine-rich peptides called protamines. This compaction is immense, with protamine-DNA self-assembly in sperm chromatin resulting in a final volume roughly 1/6th of a somatic nucleus. This near crystalline organization of the DNA in sperm is thought crucial both for the transport of the paternal genes as well as for the protection of genetic information as sperm chromatin is transcriptionally inactive and all DNA repair mechanisms are shut down.

Chapter 1 will include an overview of the topics discussed in this document, …

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or …

Functions Of Dfrp And Other Drg Pathway Genes In The Moss Physcomitrella Patens, Robert James Srygler

Graduate Research Theses & Dissertations

GTP binding proteins (G proteins) are molecular switches that regulate many aspects of physiology in all cells. DRG1 and DRG2 (Developmentally Regulated GTP-binding proteins) have been found in all eukaryotes examined. Amino acid identity across eukaryotes is about 65% within an orthologous group and 55% between paralogs of a single species. Although DRGs are likely involved in some aspect of translation regulation, details of their precise cellular functions are not known.

In addition to DRGs there are other genes/proteins that comprise the “DRG pathway.” DFRPs (DRG Family Regulatory Proteins) have been shown to physically and genetically interact with DRGs. Previous …

Multi-Scale Computational Studies Of Calcium (Ca2+) Signaling, Bin Sun

Theses and Dissertations--Chemistry

Ca²⁺ is an important messenger that affects almost all cellular processes. Ca²⁺ signaling involves events that happen at various time-scales such as Ca²⁺ diffusion, trans-membrane Ca²⁺ transport and Ca²⁺-mediated protein-protein interactions. In this work, we utilized multi-scale computational methods to quantitatively characterize Ca²⁺ diffusion efficiency, Ca²⁺ binding thermodynamics and molecular bases of Ca²⁺-dependent protein-protein interaction. Specifically, we studied 1) the electrokinetic transport of Ca²⁺ in confined sub-µm geometry with complicated surfacial properties. We characterized the effective diffusion constant of Ca²⁺ in a cell-like environment, which helps to understand …

Xylan Metabolism By Caulobacter Crescentus, Viet Bui

Masters Theses

Bacteria present unique opportunities to explore the molecular mechanisms of nutrient acquisition processes at single cell level under various experimental conditions. Caulobacter crescentus is a gram-negative oligotrophic environmental bacterium with adaptive physiological responses, such as slow growth or complete arrest of cell cycle, presence of sessile and motile progenies with the sessile cells growing stalk to enhance nutrient uptake for growth in low-nutrient conditions. Details of plant polysaccharide-derived carbon compound, such as cellobiose, maltose, and xylose utilization by C. crescentus can be found but molecular details or mechanisms of polysaccharide utilization, such as xylan, has not been reported. Database analyses …

Assessing The Effects Of Antioxidants On Oxidative Stress In Triple-Negative Breast Cancer Cells Via Protein Carbonylation, Dalton Sheffield

Honors Theses

Breast cancer is a highly complex, heterogeneous disease, and potential effective treatment options are being continuously researched in order to provide a method of halting cancer growth and metastasis. One area in particular involves alleviating oxidative stress within cancer cells. Oxidative stress is generally defined as an imbalance between oxidant and antioxidant species in favor of the oxidants. Cancer cells use this oxidative stress to initiate carcinogenesis in cells through different mechanisms, and protein carbonylation is a primary biomarker used to quantify oxidative stress levels. Antioxidant compounds are those used to alleviate oxidative stress within cells. Here breast cancer cells …

Protein Templated Silver Nanoclusters, Greyson Keel

Honors Theses

Nanoclusters are smaller than their nanoparticle counterparts and have unique properties. Most research has been done on gold nanoclusters, but silver nanoclusters are said to be more robust. During the process of trying to create nanoclusters, several methods in the procedure were changed when gathering data: determining a successful silver concentration, working with the correct buffer, mixing gold and silver metals together, observing the effects of pH, and finding a good reducing agent. After experimenting with those changes, a successful protocol was adapted and modified from literature (Journal of Materials Chemistry, 2011, 21, 11205-11212) to produce the protein-templated Ag clusters. …

Screening Of Human Serum/Plasma Using Vibrational Spectroscopy For Early Disease Diagnostics And Therapeutic Drug Monitoring, Drishya Rajan Parachalil [Thesis]

Doctoral

Analysis of analytes present in the blood stream can potentially deliver crucial information on patient health and indicate the presence of numerous pathologies. Existing clinical techniques for this analysis can, however, be costly and time-consuming. The potential of Raman spectroscopic analysis of human plasma and/or serum for diagnostic purposes has been widely investigated and, increasingly, its feasibility for clinical translation has been explored. However, as the concentration of many analytes in plasma/serum is relatively low, to date such analysis has commonly been performed on air-dried drops deposited on substrates, leading to inhomogeneity and inconsistencies. This study explores the potential of …

Novel Methods For The Inactivation Of Cruzain For The Prevention And Treatment Of Chagas Disease, Veronica Gonzalez

Open Access Theses & Dissertations

Chagas Disease, also known as American Trypanosomiasis, is endemic to Latin American and is gradually making its way to other countries. The disease is caused by Trypanosoma cruzi, a protozoan parasite that causes lesions and inflammation of organs including the heart, esophagus, and colon. Over 30% of people infected will develop heart disease which can be fatal if untreated. While no vaccine is yet available, research is currently being conducted in finding new treatments for the disease. One target is an enzyme that is believed to help the progression of the disease. Cruzain, a cysteine protease expressed as a pro-enzyme, …

Characterization Of The Effects Of Sex And Estrogen Receptor Signaling On Antigen-Specific T Cells For Immunotherapy, Flor Cecilia Navarro Negredo

Dissertations

Adoptive cell transfer (ACT) immunotherapy using antigen (Ag)-specific T cells is partially effective treating several malignancies but numerous challenges remain in order to improve its therapeutic potential. The roles of host factors, such as sex hormone receptor signaling, that can affect the T cell anti-tumor function remain understudied. The work performed in this dissertation characterized the role of estrogen signaling on T cell function in vitro, and during ACT immunotherapy against hepatocellular carcinoma (HCC) in vivo. Estrogen signaling through ERa enhanced the expression and secretion of Type I effector cytokines including IFNg, TNFa, and Granzyme B in male and female …

Yczr, A New Case Of Plp-Dependent Mocr/Gabr Type Transcription Regulator In Klebsiella Pneumonia, Yuanzhang Zheng

Dissertations

Increasing number of genes encoding PLP-dependent transcription regulators, MocR/GabR type regulators, have been identified in various bacterial genomes. However, only a handful of them, including MocR, PdxR and GabR have been studied experimentally. They control different aspects of the bacterial metabolism. Only GabR has reported crystallographic structures. MocR/GabR regulators possess a chimeric structure consisted of a WHTH DNA binding domain and an Aminotransferase-like regulation domain, which can bind PLP as an effector in transcription regulation. Such a chimeric construct presents an interesting case in molecular evolution. The regulation domains of All MocR/GabR type regulators loss their catalytic capacity during evolution …

Unravelling The D1r-D2r Heteromer, Margaret M. Champion

Master's Theses and Doctoral Dissertations

Dopamine receptors D1R and D2R form a heterooligomeric complex with signaling properties distinct from the individual receptors. Aberrant expression of this protein-protein complex is linked to the etiology of various neuropsychiatric diseases. Formation of the D1R-D2R heteromer is thought to be dependent upon electrostatic interactions occurring between the carboxyl tail of D1R and the third intracellular loop of D2R. Using this interaction site as template, I synthesized several peptides designed to disrupt the minimal area of the D1R-D2R interaction interface and tested these using whole cell lysates of human brain tissue and dopamine receptor constructs. I report that a synthetic …

Aligning Best Practices In Student Success And Career Preparedness: An Exploratory Study To Establish Pathways To Stem Careers For Undergraduate Minority Students, Kimberly D. Kendricks, Anthony A. Arment, K. V. Nedunuri, Cadance A. Lowell

Journal of Research in Technical Careers

Undergraduate minority retention and graduation rates in STEM disciplines is a nationally recognized challenge for workforce growth and diversification. The Benjamin Banneker Scholars Program (BBSP) was a five-year undergraduate study developed to increase minority student retention and graduation rates at an HBCU. The program structure utilized a family model as a vehicle to orient students to the demands of college. Program activities integrated best K-12 practices and workforce skillsets to increase academic preparedness and career readiness. Findings revealed that a familial atmosphere improved academic performance, increased undergraduate research, and generated positive perceptions of faculty mentoring. Retention rates among BBSP participants …

Functional Analysis Of Bacillus Anthracis Aspartate Transcarbamoylase And Dihydroorotase, Katelyn Leigh Schwager Silva

Wayne State University Theses

There are many enzymes required for efficient and proper pyrimidine biosynthesis. The two that are most important and were discussed in this thesis are aspartate transcarbamoylase (ATCase) and dihydroorotase (DHOase). Both play an important role in not only pyrimidine biosynthesis production, but also mechanistic regulation of de novo synthesis. Anthrax is an infection caused by Bacillus anthracis. Here we studied ATCase and DHOase in Bacillus Anthracis. In this thesis we understood the effects of the enzymes ATCase and DHOase on pyrimidine biosynthesis. Adequate inhibitors of these enzymes would result in cell death and could pose as a cure to infection …

Eralpha Isoforms Modulate The Tumorigenicity Of 24r,25(Oh)2d3 In Estrogen-Responsive Cancer, Anjali Verma

Theses and Dissertations

Over 200,000 cases of breast cancer are diagnosed every year. Nearly 20% of these patients supplement their diets with some form of vitamin D. This high frequency of vitamin D supplement use may be due in part to research suggesting that cancer patients with higher serum vitamin D₃ levels have better prognoses than patients with low serum vitamin D_3. However, double-blind clinical trials on the efficacy of vitamin D₃ supplementation in breast cancer have been inconclusive. A recent meta-analysis showed evidence of reduced cancer recurrence in patients taking vitamin D₃ supplements who had ‘estrogen receptor positive’ …

Cyclophilin A As A Molecular Switch Regulating Prolactin Receptor Mediated Signaling, Mammary Tumorigenesis And Metastasis, Shawn Hakim

Theses and Dissertations

Prolactin (PRL) and its receptor (PRLr) have been implicated in the development and progression of human breast cancer. PRL activates its receptor and induces activation of proximal Janus kinase 2 (Jak2) for signal transduction. Here, we sought to determine the role of PRLr-associated peptidyl-prolyl isomerase, cyclophilin A (CypA), in modulating structure/function relationships of the PRLr. It was demonstrated that CypA mediated PRL-induced conformational change of the CFP- and -YFP tagged forms of the PRLr cytoplasmic-tail, whereas CypA inhibition by NIM811 (N-methyl-4-isoleucine cyclosporin) or knockdown blocked the conformational change of the PRLr assessed by Fluorescence Resonance Energy Transfer (FRET) signal or …

Adaptation Of The Streptococcal Collagen-Like Protein 1, Scl1, Of Group A Streptococcus To Recognize Fibronectin Type Iii Repeats, Dudley H. Mcnitt

Graduate Theses, Dissertations, and Problem Reports (ETD)

Background: Group A Streptococcus (GAS) is responsible more than 700 million infections worldwide each year. Most of these infections start with initial colonization of the throat and skin, which is augmented by surface adhesins. The streptococcal collagen-like protein 1 (Scl1) is a major adhesin expressed by GAS that contains an N-terminal sequence-variable (V) domain, protruded away from the cell surface by the collagen domain. The Scl-V domain is comprised of three pairs of anti-parallel α-helices interconnected by surface-exposed loops. For attachment, GAS adhesins require a portal of entry, such as a wound or breach in the epithelium, to enter …

Regulation Of The Long Non-Coding Rna Fam83h-As1 By Human Papillomavirus In Cervical Cancer, Jamie Ann Barr Ph.D.

Graduate Theses, Dissertations, and Problem Reports (ETD)

Non-coding RNAs (NcRNAs), such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been found to be involved in a variety of critical biological processes, and dysregulation of ncRNAs have been involved with several human diseases including cancer.

High-risk human papillomavirus (HPV) infection is one of the first events in the process of carcinogenesis in cervical and a subset of head and neck cancers. The expression of the viral oncoproteins E6 and E7 is essential in this process by inactivating the tumor suppressor proteins p53 and Rb, respectively, in addition to their interactions with other host proteins and regulation of …

Measuring The Impact Of Oesophagectomy On Physical Functioning And Physical Activity Participation: A Prospective Study, E.M. Guinan, A.E. Bennett, Suzanne Doyle, Luke O'Neill, J. Gannon, G. Foley, J.A. Elliott, J. O'Sullivan, J.V. Reynolds, J. Hussey

Articles

Background: Oesophagectomy remains the only curative intervention for oesophageal cancer, with defined nutritional and health-related quality of life (HR-QOL) consequences. It follows therefore that there is a significant risk of decline in physical wellbeing with oesophagectomy however this has been inadequately quantified. This study prospectively examines change in physical functioning and habitual physical activity participation, from presurgery through 6-months post-oesophagectomy. Methods: Patients scheduled for oesophagectomy with curative intent were recruited. Key domains of physical functioning including exercise tolerance (six-minute walk test (6MWT)) and muscle strength (hand-grip strength), and habitual physical activity participation, including sedentary behaviour (accelerometry) were measured presurgery (T0) …

Decadal Biomass Increment In Early Secondary Succession Woody Ecosystems Is Increased By Co2 Enrichment, Anthony Walker, Martin G. De Kauwe, Blinda E. Medlyn, Sonke Zaehle, Colleen M. Iversen, Shinichi Asao, Bertrand Guenet, Anna Harper, Tonas Hickler, Bruce A. Hungate, Atul K. Jain, Yiqi Luo, Xingjie Lu, Meng Lu, Kristina Luus, J. Patrick Megonigal, Ram Oren, Edmund Ryan, Shijie Shu, Alan Talhelm, Ying-Ping Wang, Jeffrey M. Warren, Christian Werner, Jianyang Xia, Bai Yang, Donald R. Zak, Richard J. Norby

Articles

Increasing atmospheric CO2 stimulates photosynthesis which can increase net primary production (NPP), but at longer timescales may not necessarily increase plant biomass. Here we analyse the four decade-long CO2-enrichment experiments in woody ecosystems that measured total NPP and biomass. CO2 enrichment increased biomass increment by 1.05 ± 0.26 kg C m−2 over a full decade, a 29.1 ± 11.7% stimulation of biomass gain in these early-secondary-succession temperate ecosystems. This response is predictable by combining the CO2 response of NPP (0.16 ± 0.03 kg C m−2 y−1) and the CO2-independent, linear slope between biomass increment and cumulative NPP (0.55 ± 0.17). …

Structural Characterization Of Black Widow Spider Dragline Silk Proteins Crp1 And Crp4, Mikayla Shanafelt

University of the Pacific Theses and Dissertations

Spider dragline silk is a biomaterial with outstanding material properties, possessing high-tensile strength and toughness. In nature, dragline silk serves a central role during spider locomotion and web construction. Today, scientists are racing to elucidate the molecular machinery governing silk extrusion, attempting to translate this knowledge into a mimicry process in the laboratory to create synthetic fibers for a wide range of different applications. During extrusion, it has been established that biochemical and mechanical forces govern spidroin folding, aggregation, and assembly. In black widow spiders, at least 7 different proteins have been identified as constituents of dragline silk fibers. These …

Evaluating Methods Of Obtaining Male Pheromone From Hymenochirus Sp. Using Analytical Chemistry, Vincent Wing-Kun Leung

University of the Pacific Theses and Dissertations

Male Hymenochirus sp. frogs are known to release pheromone that attracts females of the same species. Four methods for collecting secretions containing pheromone in Hymenochirus sp. were tested: norepinephrine injection, gonadotropin-releasing hormone injection, homogenization of gland tissue, and electrostimulation of the skin over the breeding gland area. The samples collected were analyzed using high-performance liquid chromatography (HPLC) and mass spectrometry. The HPLC chromatograph for the male norepinephrine sample contained a peak at 6.4 min that was not in the female norepinephrine sample HPLC chromatograph. The male norepinephrine sample mass spectrum had a peak of m/z 292.0 not in the female …

Knob-Socket Investigation Of Stability And Specificity In Alpha-Helical Secondary And Quaternary Packing Structure, Taylor Renee Rabara

University of the Pacific Theses and Dissertations

The novel knob-socket (KS) model provides a construct to interpret and analyze the direct contributions of amino acid residues to the stability in α-helical protein structures. Based on residue preferences derived from a set of protein structures, the KS construct characterizes intra- and inter-helical packing into regular patterns of simple motifs. The KS model was used in the de novo design of an α-helical homodimer, KSα1.1. Using site-directed mutagenesis, KSα1.1 point mutants were designed to selectively increase and decrease stability by relating KS propensities with changes to α-helical structure. This study suggests that the sockets from the KS Model can …

Investigating The Effect Of Rutaecarpine On The Benzo[A]Pyrene-Induced Dna Damage In Vitro, You Li

University of the Pacific Theses and Dissertations

Benzo[a]pyrene (BaP), is one of the most potent mutagens and carcinogens known. It requires metabolic activation through cytochrome P450 (CYP)1A1 to yield the ultimate carcinogenic metabolite, benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE). BPDE can bind to DNA and form predominantly covalent (+) trans adducts at the N2 position of guanine causing DNA damage. Rutaecarpine (RTC) is an herbal medicine that has been used to treat several diseases such as headache, hypertension, gastrointestinal disorders, amenorrhea, and anti-inflammation. It has also been reported as a potent inducer of CYP enzymes, including CYP1A1, and CYP1A2. The mechanisms underlying up-regulation of CYP1A1 by RTC is dependent on aryl …

Functional Characterization Of Accessory Proteins And Novel Activities In Direct And Indirect Trna Aminoacylation, Udumbara Menike Rathnayake

Wayne State University Dissertations

Indirect tRNA aminoacylation is essential for most bacteria and archaea, particularly when these species do not have genes encoding asparaginyl- and/or glutaminyl-tRNA synthetase (AsnRS and GlnRS). In the absence of AsnRS, the first step in Asn-tRNAAsn synthesis involves misacylation of tRNAAsn with aspartate to produce Asp-tRNAAsn; this reaction is catalyzed by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS). Subsequently, in bacteria, an amidotransferase called GatCAB converts Asp-tRNAAsn to Asn-tRNAAsn. An analogous, two-step processes exist to produce Gln-tRNAGln. In this case, a non-discriminating glutamyl-tRNA synthetase (ND-GluRS) misacylates tRNAGln to produce Glu-tRNAGln, which is then converted to Gln-tRNAGln by GatCAB. The central hub of …

The Match-Play Sprint Performance Of Elite Senior Hurlers During Competitive Games, Damien Young, Giuseppe Coratella, Shane Malone, Kieran Collins, Laurent Mourot, Marco Beato

Articles

The typical sprint profile in elite hurling has yet to be established. The purpose of this study was to investigate the sprinting demands of elite hurling competition and characterize the sprinting patterns of different playing positions. GPS (10-Hz, STATSports Viper) were used to collect data from 51 hurlers during 18 games. The total sprint (≥22 km·h^-1) distance (TSD), the number of sprints (NOS) classified as length (<20 >m, ≥20 m) and relative speed thresholds (90%), the between-sprint duration and the number of repeated-sprint bouts (≥2 sprints in ≤60 s) were analyzed. The NOS was 22.2 ± 6.8 accumulating …

Development Of A Biomarker Panel For Identifying Stressed Marine Mammals, Laura Pujade

University of the Pacific Theses and Dissertations

Increasing anthropogenic disturbance in marine ecosystems such as fishing, oil-drilling, and noise pollution can have detrimental effects on the reproduction and survival of apex predators such as marine mammals. Stress activates the hypothalamic-pituitary-adrenal (HPA) axis, resulting in increased circulating glucocorticoid (GCs) hormones, which alter expression of target genes encoding metabolic enzymes and other mediators of stress. Prolonged HPA axis stimulation may increase catabolism of nutrient stores and suppress immune and reproductive functions, impacting the fitness of marine mammals. GCs measurements are used to identify wild animals experiencing stress. However, these measurements may not be sensitive enough to distinguish between an …

Relationship Of Sociodemographic Factors With Serum Levels Of Vitamin D In A Healthy Population Of Pakistan, Khalida Iqbal, Najmul Islam, Naseema Mehboobali, Ali Asghar, Saleem Perwaiz Iqbal, Mohammad Perwaiz Iqbal

Department of Biological & Biomedical Sciences

High prevalence of vitamin D deficiency has been reported from Pakistan. Association of sociodemographic factors with vitamin D status has received little attention in this region. Therefore, we embarked on investigating the relationship of sociodemographic factors with vitamin D levels in a healthy Pakistani population. Venous blood from 226 healthy participants (age range 19-69 years) was collected and analyzed for serum concentrations of 25(OH) vitamin D [25(OH)D] and other related biomarkers. Demographic characteristics of the study participants were collected. Vitamin D deficiency (25(OH)D levels less than 20 ng/ml) was found to be 75% in this cohort. Gender, sunlight exposure and …