Biochemistry, Biophysics, and Structural Biology Commons^™

Increased Geranylgeranylated K-Ras Contributes To Antineoplastic Effects Of Farnesyltransferase Inhibitors., Mandy A. Hall

Dissertations & Theses (Open Access)

The Ras family of small GTPases (N-, H-, and K-Ras) is a group of important signaling mediators. Ras is frequently activated in some cancers, while others maintain low level activity to achieve optimal cell growth. In cells with endogenously low levels of active Ras, increasing Ras signaling through the ERK and p38 MAPK pathways can cause growth arrest or cell death. Ras requires prenylation – the addition of a 15-carbon (farnesyl) or 20-carbon (geranylgeranyl) group – to keep the protein anchored into membranes for effective signaling. N- and K-Ras can be alternatively geranylgeranylated (GG’d) if farnesylation is inhibited but are …

Development And Evaluation Of A Mouse Neocortical Cells Neurodevelopment Assay To Assess The Effects Of Pyrethroids, Stephanie I. Savino

Pell Scholars and Senior Theses

Pyrethroid insecticides have been used for more than 40 years and account for 25% of the global insecticide market with household, agricultural and public health applications. With increasing use of pyrethroids over recent years, human exposure to these chemicals is likely. The acute toxicity of pyrethroids to mammalian adults has been documented as moderately toxic by the U.S. Environmental Protection Agency. However, little evidence is available regarding the potential toxicological effects of pyrethroids on mammalian neurodevelopment. In this study, a neurodevelopment assay was developed for future investigation of potential pyrethroid effects on the neuronal development of Mus musculus neocortical cells.

Regulation Of Protein Degradation In The Heart By Amp-Activated Protein Kinase, Kedryn K. Baskin, Kedryn K. Baskin

Dissertations & Theses (Open Access)

The degradation of proteins by the ubiquitin proteasome system is essential for cellular homeostasis in the heart. An important regulator of metabolic homeostasis is AMP-activated protein kinase (AMPK). During nutrient deprivation, AMPK is activated and intracellular proteolysis is enhanced through the ubiquitin proteasome system (UPS). Whether AMPK plays a role in protein degradation through the UPS in the heart is not known. Here I present data in support of the hypothesis that AMPK transcriptionally regulates key players in the UPS, which, under extreme conditions can be detrimental to the heart. The ubiquitin ligases MAFbx /Atrogin-1 and MuRF1, key regulators of …

An Investigation Of Trypanosoma Brucei Hexokinases: Localization, Oligomerization, And Inhibition, April Joice

All Dissertations

Trypanosoma brucei is the causative agent of African sleeping sickness in humans and nagana in livestock. The parasite inhabits multiple environmental niches including the bloodstream of the mammalian host and the mid-gut of the tsetse fly vector. While in the bloodstream of its mammalian host, the organism depends solely on glycolysis for production of ATP. My studies focus on the first enzyme in glycolysis, hexokinase.
T. brucei has two hexokinases, TbHK1 and TbHK2 that are 98.5% identical at the nucleotide level. The hexokinases are expressed in the glycosomes of both procyclic form and bloodstream form parasites. Glycosomes are peroxisome-like organelles …

The Role Of Traf2 In Zebrafish, Bradie N. Manion

Honors College

Tumor necrosis factor (TNF) receptor associated factor 2 (Traf2) is suspected to be involved in the anti-apoptotic pathways of the innate immune system in the zebrafish. The expression of three different forms of Traf2, 2a1, 2a2, and 2b, was knocked down in pairs using antisense morpholino oligonucleotides in zebrafish embryos. A rescue was attempted by knocking down a potential receptor for the Traf2 to pathway. After infection with snakehead rhabdovirus (SHRV), mortality was quantified and the apoptotic effects of each of the Traf2 genes was assessed. Cell death was quantified using the TUNEL technique. The findings indicated that at least …

Structural And Mechanistic Investigations Of Phosphothreonine Lyase Class Of Enzymes, Alok Gopalkrishna Shenoy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation and dephosphorylation are a highly pervasive mechanism in biology that is used by the cell to modulate enzymes and proteins. The presence of a phosphate group can activate or deactivate an enzyme. The phosphate group is linked to a protein by a phosphoester bond that is known to be highly stable in cytoplasmic pH range. Thus the breaking and formation of these bonds need to be effected by enzymes.

Recent discovery of the activity carried out by certain virulence related proteins (OspF released by Shigella and SpvC released by Salmonella) have resulted in a necessity to create a new …

Activation Of The Carbon Concentrating Mechanism By Co2 Deprivation Coincides With Massive Transcriptional Restructuring In Chlamydomonas Reinhardtii, Andrew J. Brueggeman, Dayananda S. Gangadharaiah, Matyas F. Cserhati, David Casero, Donald P. Weeks, Istvan Ladunga

Department of Biochemistry: Faculty Publications

A CO₂-concentrating mechanism (CCM) is essential for the growth of most eukaryotic algae under ambient (392 ppm) and very low (ppm) CO₂ concentrations. In this study, we used replicated deep mRNA sequencing and regulatory network reconstruction to capture a remarkable scope of changes in gene expression that occurs when Chlamydomonas reinhardtii cells are shifted from high to very low levels of CO₂ (£100 ppm). CCM induction 30 to 180 min post-CO₂ deprivation coincides with statistically significant changes in the expression of an astonishing 38% (5884) of the 15,501 nonoverlapping C. reinhardtii genes. Of these genes, …

Capturing More Light: Phycobilisome Characterization For Increased Hydrogen Production Efficiency, Paul Abraham Willard

Masters Theses

Alternative energy and biofuels are a growing area of research. The demand for more and clean energy is ever increasing, but the current technology is inefficient, expensive, and incapable of meeting the demands of the current market. Hydrogen is a potential future fuel, as it is both clean and renewable, but its formation through conventional means is costly and inefficient. Photosynthesis can be utilized for the formation of hydrogen, which can then serve as a convenient and renewable biofuel. Photosynthetic hydrogen evolution is observed in vitro, but the current photosystem design is not very versatile and optimized to use …

Genetic Basis Of Flocculation In Azospirillum Brasilense., Priyanka Satish Mishra

Masters Theses

Azospirillum brasilense is a class of rhizobacteria capable of nitrogen fixation, root colonization and hence promoting host plant growth. The bacteria posses cell interaction behaviors like clumping and flocculation that contribute the survival of the organism in nutrient limited conditions. Change in the cell surface adhesive properties allows the cells to progress from free swimming to clumping and finally flocculation. Less is known about the genetic regulation of these processes with flcA being the only transcriptional regulator known so far to directly control flocculation. Recent evidence suggesting that Che1, a chemotaxis like signal transduction pathway controls the cell behavior clumping …

A Fast Response Highly Selective Probe For The Detection Of Glutathione In Human Blood Plasma, Yixing Guo, Xiaofeng Yang, Lovemore Hakuna, Aabha Barve, Jorge O. Escobedo, Mark Lowry, Robert M. Strongin

Chemistry Faculty Publications and Presentations

A fluorescent probe for glutathione (GSH) detection was developed. Our study indicates a possible mechanism which couples a conjugate addition and micelle-catalyzed large membered ring formation/elimination sequence. This method enables excellent selectivity towards GSH over other biological thiols such as cysteine (Cys) and homocysteine (Hcy). The proposed method is precise with a relative standard deviation (R.S.D) lower than 6% (n = 3) and has been successfully applied to determine GSH in human plasma with recoveries between 99.2% and 102.3%.

Designing An "Information-Experience" Using Creativity Science Theory And Tools, Stephanie Belhomme

Creativity and Change Leadership Graduate Student Master's Projects

An “information-experience” encapsulated by a technological/digital audio-visual tool presents data and potentially meaningful information to prompt actionable knowledge concerning: “unspoken creative process elements;” their profound impacts on both how well our “physiology of creativity” functions; but also on how well foundational creative thinking and behavioral prerequisites (energy, motivation, imagination, and ownership) are leveraged.

The product: 1) introduces the user to one component of the CPS (Creative Problem Solving) Facilitation Process - Exploring the Challenge; 2) features a content specific component which prompts exploration of the many correlations between societal, organizational / community, human physiological / behavioral data, and the direct …

1. Improving The Yield Of Biodiesel From Microalgae And Other Lipids. 2. Studies Of The Wax Ester Biosynthetic Pathway And Potential Biotechnological Application, Bradley D. Wahlen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The production of biofuels and oleochemicals from renewable sources offers an opportunity to reduce our dependence on fossil fuels. The work contained in this dissertation has focused on developing and improving methods for the production of biodiesel from non-traditional feedstocks and understanding biosynthetic pathways that result in the production of oleochemicals and fuels.

Pure vegetable oil can account for 70-80% of the total cost of biodiesel production. Many low-cost oils contain high amounts of free fatty acids, which are unsuitable for base-catalyzed transesterification. Herein an approach is described that efficiently accomplishes the simultaneous esterification and transesterification of both free fatty …

Development Of An Assay To Screen For Novel Proteins From Bacillus Thuringiensis With Antibacterial Activity, Auriole T. Tamegnon

Theses and Dissertations - UTB/UTPA

Bacillus thuringiensis (Bt) produces the non specific Cyt protein and the specific Cry protein. Past research has shown these proteins are toxic to insects, red blood cells, cancer cells, and some bacteria. While many antibacterial substances are known to exist, efforts to find new ones still continue. In this project we used Bt 6-2-56 (containing a novel filament associated parasporal body which appears non-toxic to insects and protozoan) and Bt 4Q13 (which has been shown to have activity against E. coli and S. aureus) to develop a simple, easy, scalable assay in a 96 well Microtitre plate to look for …

Genome-Wide Identification Of Conditionally Essential Genes In Salmonella Typhimurium Using Tn-Seq Method, Anita Khatiwara

Graduate Theses and Dissertations

ABSTRACT

As more whole genome sequences become available, there is an increasing need for high-throughput methods that link genes to phenotypes and facilitate discovery of new gene functions. The objective of this study was to develop a high-throughput method to study gene functions in bacteria and use this method to study gene functions of S. enterica serotype Typhimurium (S. Typhimurium) under various environmental conditions encountered during its life cycle. Chapter I of this dissertation reviews the history and evolution of functional genomics in bacteria with focus on Salmonella, along with the recent techniques available. Chapter II, deals with the development …

Characterization Of Novel Histone H2b Mutants Associated With Chromosome Segregation Defects In Saccharomyces Cerevisiae, Thiruchelvam Rajagopal

Graduate Theses and Dissertations

Histones are small basic proteins that associate with DNA to form the basic unit of chromatin, the nucleosome. Histones H3 and H4 form a tetramer that is bound by two H2A-H2B dimers to form the histone octamer, to which approximately 146 bp of DNA wrap around to form the nucleosome. High resolution structural information and recent advances in the understanding of histone post-translational modifications have illuminated the many regulatory functions chromatin exerts in the cell, from the transcriptional control of gene expression to chromosome segregation. However, the specific role that histones play in these processes is not well understood. Previous …

The Time-Course Of The Effects Of Growth Hormone During Zebrafish (Danio Rerio) Auditory Hair Cell Regeneration, Yajie Wang

Masters Theses & Specialist Projects

Growth hormone (GH) was upregulated in the zebrafish inner ear following sound exposure in a previous study. To identify the specific role of GH in hair cell regeneration and the possible cellular mechanisms of this regeneration, groups of zebrafish were divided into baseline (no sound exposure, no injection), buffer-injected and GH-injected groups. Buffer- and GH-injected fish were exposed to a 150 Hz tone at a source level of 179 dB re 1 μPa root mean squared (RMS) for 36 h. Phalloidin-staining was used to assess the effects of GH on hair cell bundle density; BrdU-labeling was used to assess the …

Stromal-Epithelial Interactions Modulate Cross Talk Between Prolactin Receptor And Her2/Neu In Breast Cancer, Cong Xu

All Dissertations

The tumor microenvironment is a crucial factor in breast tumorigenesis. Tumor epithelial cells maintain 3D structure in tumor stroma and they interact with soluble factors secreted by stromal cells such as cancer associated fibroblasts (CAFs) or directly with the extracellular matrix (ECM). Recent studies have shown that the hormone prolactin (PRL) promotes the proliferation and survival of breast cancer cells in part via the transactivation of human epidermal growth factor receptor 2 (HER2), also known as Neu in rodents. A PRL receptor (PRLR) antagonist, G129R, has been demonstrated not only to be able to directly inhibit PRLR activation but also …

Structure Of The Catalytic Chain Of Methanococcus Jannaschii Aspartate Transcarbamoylase In A Hexagonal Crystal Form: Insights Into The Path Of Carbamoyl Phosphate To The Active Site Of The Enzyme, Jacqueline Vitali, Aditya K. Singh, Alexei S. Soaresb, Michael J. Colaneri

Physics Faculty Publications

Crystals of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6₃22, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K⁺ ion as …

A Leishmania Mitogen Activated Protein Kinase As A Potential Anti-Parasitic Drug Target : Purification, Characterization And Inhibitor Interactions, Aysenur Sayakci

Theses, Dissertations and Culminating Projects

The disease, Leishmaniasis, is caused by the protozoal parasite Leishmania, which is transmitted by the bite of an infected Phlebotomine female sandfly. It is a significant health problem in tropical regions of the world and new therapeutic approaches for treating this disease are urgently needed.

Protozoal MAPKs (Mitogen Activated Protein Kinases) play important roles in parasite viability and infectivity and as such, represent viable drug targets. It has been demonstrated that LmxMPKl is an essential MAPK required for the parasite to establish infection and for proliferation of the amastigote stage (the mammalian stage of the parasite) of the parasite. In …

Conformational Motions Associated With Ligand Binding In Dihydrofolate Reductase From Bacillus Stearothermophilus, Mayam Tobilola Alapa

Theses, Dissertations and Culminating Projects

A fluorescently-labeled, conformationally-sensitive Bacillus stearothermophilus (Bs) dihydrofolate reductase (DHFR) (C73A/S131C_MDCC DHFR) was developed and used to investigate kinetics and protein conformational motions associated with methotrexate (MTX) binding. This construct bears a covalently attached fluorophore, N-[2-(lmaleimidyl) ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC) attached at a distal cysteine, introduced by mutagenesis. The probe is sensitive to the local molecular environment, reporting on changes in the protein structure associated with ligand binding. Intrinsic tryptophan fluorescence of the unlabeled Bs DHFR construct (C73A/S131C DHFR) also showed changes upon MTX association. Stopped-flow analysis of all data can be understood by invoking the presence of two native state DHFR …