Life Sciences Commons^™

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 …

The Role Of Inositol Polyphosphate-4-Phosphatase Type Ii B (Inpp4b) In Obese Models And Endocrine Cancers, Manqi Zhang

FIU Electronic Theses and Dissertations

INPP4B is a dual-specificity phosphatase and a tumor suppressor in prostate and breast cancers. Progression of the prostate and breast cancers depends on the androgen receptor (AR) or estrogen receptor alpha (ERα) signaling, respectively. In this work we demonstrated that INPP4B reprograms ERα transcriptional activity in breast cancer. INPP4B maintains expression and protein levels of progesterone receptor (PR), an ERα direct target gene required for mammary gland development. Consistently we demonstrated that Inpp4b knockout severely impairs lateral branching in the mammary gland of maturing virgin females. In advanced prostate cancer, activation and transcriptional reprogramming of AR frequently coincides with the …

Production Of Dynein And Kinesin Motor Ensembles On Dna Origami Nanostructures For Single Molecule Observation, Jingjie Hu, Nathan Derr

Biological Sciences: Faculty Publications

Summary

The goal of this protocol is to form ensembles of molecular motors on DNA origami nanostructures and observe the ensemble motility using total internal reflection fluorescence microscopy.

Abstract

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and others. Many of these functions require motors to operate in ensembles. Despite a wealth of knowledge about the mechanisms of individual cytoskeletal motors, comparatively less is known about the mechanisms and emergent behaviors of motor ensembles, examples of which include changes to ensemble processivity and velocity with changing motor number, location, …

Iron-Sulfur Cluster Assembly; In Vivo Analysis Of The Methanogenic Suf System, Evan Dunkle

LSU Master's Theses

Iron-sulfur (Fe-S) clusters are among the most ancient and prevalent of all biological cofactors. Their assembly into associated proteins is a tightly regulated process with many organisms employing multiple cluster assembly pathways. Much is known about Fe-S cluster assembly in aerobic organisms such as Escherichia coli (E. coli) but little is known in regards to cluster assembly in more ancient organisms such as methanogens. Methanogens are members of the domain of Archaea and are defined by their ability to generate methane as a byproduct of their main energy generating pathway. Methanogens also have significantly higher Fe-S cluster content …

Study Of Blood Viscosity With Added Sodium Nitrate And Temperature Variance: A Potential Therapy To Regulate Blood Flow After Induced Hypothermia, Brianna Munnich

Pence-Boyce STEM Student Scholarship

The human body has natural systems for vasodilation which are fueled by nitric oxide production, but in cases of cardiac disfunction and stress nitric oxide can be inhibited. In this study, nitric oxide was studied as a mediator for the blood rush experienced from the warming after induced hypothermia. Nitric oxide (NO) was introduced through sodium nitrate, which was aimed to reduce the speed and turbulence of blood flow through interaction between NO and the active site of hemoglobin. A viscometer was used to examine the rate of blood flow, while the temperature was varied to simulate the conditions of …

Electrostatically Localized Proton Bioenergetics: Better Understanding Membrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In Mitchell's chemiosmotic theory, membrane potential Δψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ([H-⁺_L] + ⁿΣ _i=1 [M⁽ⁱ⁺⁾_L]) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane …

The Influence Of Hibernation Temperature On Deiodinase 2 In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis), Kalera Stratton

Dissertations and Theses

Environmental cues such as day length and temperature contribute to timing of biological rhythms in seasonal breeders. Life-history transitions such as spring emergence from hibernation, migration, or mating must be coordinated with environmental conditions or survival is compromised. Therefore, there must be chemical signaling pathways in the brain that transduce seasonally-changing sensory inputs into signals that initiate a hormonal cascade, culminating in reproductive behavior. The relative importance of environmental cues to reproductive timing varies with species, time of year, and sex, and the mechanisms driving these differences remain unknown. The role of photoperiod in regulating reproductive behavior has been explored …

Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder

Chemistry and Biochemistry Faculty Publications

Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PAS^_WT has a much less negative Brønsted coefficient (ß_{leaving group} ^obs-Enz=-0.33) than the uncatalyzed reaction (ß_{leaving group} ^obs=-1.81). This situation is diminished when cationic active site groups are exchanged for alanine. …

Structural Studies On Calcium/Calmodulin-Dependent Activation Of Eukaryotic Elongation Factor 2 Kinase, Kwangwoon Lee

Dissertations, Theses, and Capstone Projects

Eukaryotic elongation factor 2 kinase (eEF-2K) is a key modulator of the rate of protein synthesis. Activated by calcium-loaded calmodulin (Ca²⁺-CaM), eEF-2K phosphorylates its only known physiological substrate, eEF-2, on a specific threonine residue (Thr-56). Phosphorylated eEF-2 has reduced affinity for the ribosome, and results in a significant decrease in the rate of translation elongation. Modulation of the rate of translation elongation plays a crucial role in proteostasis – adequate regulation of protein synthesis, protein folding, and protein degradation that greatly influences cellular growth and survival. Binding of Ca²⁺-CaM triggers activation of eEF-2K and remains intact …

Microglia Are Both A Source And Target Of Extracellular Cyclophilin A, Gurkiran Kaur Flora, Ryan S. Anderton, Bruno P. Meloni, Gilles J. Guillemin, Neville W. Knuckey, Gabriella Macdougall, Vance Matthews, Sherif Boulos

Health Sciences Papers and Journal Articles

Glioblastoma (GBM) are lethal primary brain tumours whose pathogenesis is aided, at least partly, via a pro-tumorigenic microenvironment. This study investigated whether microglia, a cell component of the GBM microenvironment, mediates pro-tumorigenic properties via the action of cyclophilin A (CypA), a potent secretable chemokine and cytoprotectant that signals via the cell surface receptor, CD147. To this end, intracellular and secreted CypA expression was assessed in human primary microglia and BV2 microglial cells treated with the endotoxin, lipopolysaccharide (LPS) and the oxidative stress inducer, LY83583. We report that human primary microglia and BV2 microglia both express CypA and CD147, and that …

Identification Of Antibiotic Ge37468a From Pseudonocardia Symbionts Of Trachymyrmex Septentrionalis Ants, Krithika Rao

Scripps Senior Theses

In response to the growing rates of antibiotic resistance in human bacterial pathogens, this study explores the natural products involved in the defensive symbiosis between actinobacteria and fungus-growing ants to uncover new potential antibiotics. This study also seeks to understand the function of natural antibiotics in their ecological contexts, especially those involved in defensive symbioses. Defensive symbiosis can be a beneficial platform for discovering useful antibiotics, because antibiotics in these relationships must be able to selectively inhibit enemies without harming hosts, and are therefore likely more specific and less toxic. Pseudonocardia sp. associated with Trachymyrmex septentrionalis ants demonstrated antibiotic activity …

Blubber Transcriptome And Proteome Responses To Repeated Adrenocorticotropic Hormone Administration In A Marine Mammal, Jared Deyarmin

University of the Pacific Theses and Dissertations

Chronic physiological stress impacts animal fitness by catabolizing metabolic stores and suppressing reproduction and immunity. This can be especially deleterious for capital breeding carnivores, such as marine mammals, which rely on lipid stores accrued during intensive foraging to sustain prolonged periods of fasting associated with reproduction. Therefore, chronic stress may cause a decrease in fitness in these animals, leading to population declines and potentially detrimental shifts in food web dynamics as a result. However, the impacts and indicators of chronic stress in animals are currently poorly understood. To identify downstream mediators of repeated stress responses in marine mammals, adrenocorticotropic hormone …

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 …

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 …

Characterization Of The Roles Of Ppp1r15a (Gadd34) And Ppp1r15b (Crep) In Er Stress-Induced Apoptosis In Vivo, Danielle Hicks

University of the Pacific Theses and Dissertations

Failure to balance synthesis, folding and degradation of secreted proteins results in the accumulation of unfolded proteins in the endoplasmic reticulum, termed ER stress. Cells respond to ER stress by activating a signaling pathway known as the unfolded protein response (UPR). The UPR induces phosphorylation of eIF2α to attenuate global protein translation, allowing the ER to clear misfolded proteins. Opposing this function, eIF2α phosphatases contain a catalytic subunit, Protein Phosphatase 1, and either of two homologous scaffolding subunits, GADD34 and CReP. Inhibition of eIF2α phosphatases has been shown to prolong UPR signaling and promote survival in many cells types and …

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 …

Application And Comparison Of Active Learning Implementation Methods In Biochemistry Education, Dylan Thibaut

Honors Undergraduate Theses

Biochemistry has continued to be one of the most complex and important subjects in science education. The purpose of this research is to investigate active learning implementation methods in a Biochemistry I context to determine the most effective means of preparing current science undergraduates. Two Biochemistry I classes over two semesters were analyzed in this study, with class A using a variable active learning schedule and class B using a consistent active learning schedule. Four aspects were analyzed to determine active learning validity: perception of different active learning properties, standardized final exam grades, class grade, and teaching implementation. The consistent …

Stabilization Of Dna I-Motif Structures By 7-Aminoactinomycin D, An Anti-Tumor Drug, Justin Lane Parmely

Electronic Theses and Dissertations

Alternative DNA structures are likely to form from Watson-Crick B-form DNA when antitumor drug known to bind DNA loops -- can affect the iM structure. Our results demonstrate as an i-motif (iM). While both structures are known to exist in vivo they are energetically uphill can utilize intercalating cytosine-cytosine base pairing to form a four-stranded structure known controlled by alternative DNA structures like G4s and iMs. especially during processes that involve superhelical duress. A guanosine rich strand can form a facilitate their stabilization. In this report we present data on how 7-aminoactinomycin D -- an formation. Earlier it was believed …

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 …

Structural Investigation Of Bcsc: Insight Into Periplasmic Transport During Cellulose Export, William Scott, Joel T. Weadge

Theses and Dissertations (Comprehensive)

A biofilm can be defined by a community of microbes coexisting within a self-produced protective polymeric matrix. Exopolysaccharide (EPS) is a key component in biofilms and a contributor to their virulence and pathogenicity. The cellulose bacterial synthesis complex is one such EPS system that is found in many Enterobacteriaceae,including Escherichia coli and Salmonella spp., and is responsible for the production and secretion of the EPS cellulose. BcsC is the periplasmic protein responsible for the export of the exopolysaccharide cellulose and was the focus of this research. Sequence homology comparisons and structural predictions between BcsC, and the previously characterized alginate …

Erk3 Negatively Regulates The Il-6/Stat3 Signaling Via Socs3, Astha Shakya

Browse all Theses and Dissertations

Mitogen activated protein kinases (MAPKs) are Ser/Thr kinases that relay the extracellular signal into intracellular responses and regulate several biological responses. They are classified into conventional MAPKs and atypical MAPKs. Extracellular signal regulated kinase 3 (ERK3) is an atypical MAPK that has a single phospho-acceptor site (Ser 189) in its activation motif instead of the canonical Thr-Xaa-Tyr (TXY) motif of conventional MAPK like ERK1/2. ERK3 comprises of a unique C terminal tail and a central C34 domain that further distinguishes it from ERK1/2. Moreover, compared to ERK1/2, much less is known about the upstream activators and the downstream targets of …

Genotyping For Response To Physical Training, Stacy Simmons

Browse all Theses and Dissertations

Understanding the inter-individual variability in physical fitness performance has been the focus of scientific research for decades especially in the United States military. Injury and physical inadequacy cost the U.S military millions of dollars every year. The project PHITE (Precision High Intensity Training through Epigenetics) was funded to investigate this personal complex trait by combing the genetic and epigenetic (non-shared environmental factors) contributions into a single model for physical training response. This project is set up as having 150 male and female recruits between the ages of 18-27 years old. Each participant is randomly put blind into either a high …

∆Np63Α Positively Regulates Erk3 Expression In Non-Melanoma Skin Cancer, Eid Salem Alshammari

Browse all Theses and Dissertations

Non-melanoma skin cancer (NMSC) is a group of skin cancer that includes basal cell carcinoma of the skin (BCC), squamous cell carcinoma of the skin (SCC), actinic keratoses, a precursor to SCC, and other rare cutaneous carcinomas. p63, a member of the p53 gene family, is an important regulator for epithelial tissue growth and development. ∆Np63α, a main isoform of p63, is highly expressed in NMSC and plays essential roles in NMSCs development. Extracellular signal-regulated kinase 3 (ERK3) is an atypical member of the MAPK family. It possesses a single phosphorylation site (serine 189) in its activation loop, which makes …