Biochemistry Commons^™

New Tools For Real-Time Study Of Embryonic Development, Lauren M. Browning

Theses and Dissertations in Biomedical Sciences

Embryonic development represents one of the most complex and dynamic cellular processes in biology, and plays vital roles in understanding of functions of embryonic stem cells (ESCs) and design of ESC-based therapy. Conventional assays and fluorescence-based imaging methods have been widely used for the study of embryonic development. These conventional methods cannot effectively provide spatial and temporal resolutions with sufficient sensitivity and selectivity that are required to depict embryonic development in vivo in real-time at single-cell and single-molecule resolutions. In this dissertation, we have developed a wide range of innovative tools for real-time study of embryonic development. These new tools …

(R)-Β-Lysine Modified Elongation Factor P Functions In Translation Elongation, Tammy J. Bullwinkle, S. Betty Zou, Andrei Rajkovic, Steven J. Hersch, Sara Elgamal, Nathaniel Robinson, David Smil, Yuri Bolshan, William Wiley Navarre, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Post-translational modification of bacterial elongation factor P (EF-P) with (R)-β-lysine at a conserved lysine residue activates the protein in vivo and increases puromycin reactivity of the ribosome in vitro. The additional hydroxylation of EF-P at the same lysine residue by the YfcM protein has also recently been described. The roles of modified and unmodified EF-P during different steps in translation, and how this correlates to its physiological role in the cell, have recently been linked to the synthesis of polyproline stretches in proteins. Polysome analysis indicated that EF-P functions in translation elongation, rather than initiation as proposed previously. This was …

Polyphenoloxidase And Perioxidase Activity During Open Air Ripening Storage Of Pineapple (Ananas Comosus L.), Mango (Mangifera Indica) And Papaya (Carica Papaya) Fruits Grown In Dar Es Salaam, Tanzania, Oc Othman

Tanzania Journal of Science

Polyphenoloxidase (PPO) and perioxidase (POD), the enzymes responsible for causing browning and change in texture and flavor of fruits and vegetables, were extracted and measured in harvested mature pineapple (Ananas comosus L.), mango (Mangifera indica) (Viringe and Dodo varieties) and papaya (Carica papaya) fruits during off vine, open air, room temperature ripening storage. The initial (at harvest) average PPO activity values in Δ Optical Density (OD) per minute per cm3 of enzyme solution were 0.00074, 0.00083 and 0.0010 for early, mid and late season pineapple fruits respectively. The initial average PPO activity values in ΔOD/min/ cm3 of enzyme solution were …

A Comparison Of Boltzmann And Gibbs Definitions Of Microcanonical Entropy For Small Systems, Randall B. Shirts

Faculty Publications

Two different definitions of entropy, S= klnW, in the microcanonical ensemble have been competing for over 100 years. The Boltzmann/Planck definition is that W is the number of states accessible to the system at its energy E (also called the surface entropy). The Gibbs/Hertz definition is that W is the number of states of the system up to the energy E (also called the volume entropy). These two definitions agree for large systems but differ by terms of order N^-1 for small systems, where N is the number of particles in the system. For three analytical …

Cloning, Expression, And Characterization Of Ara H 3, A Major Peanut Allergen, Cathryn E. Garvey

LSU New Orleans Theses and Dissertations

Abstract There are eight foods that contribute to food allergies in the western world and peanut is the most common. Currently, there are no medical treatments that can cure an individual of food allergy, so avoidance of the allergic food is the only option. In the United States, there are three immunodominant allergic proteins accountable for patient sensitization to peanut, Arachis hypogea 1, 2, and 3 (Ara h 1, Ara h 2, Ara h 3). Therefore, research into why peanuts are more allergic than other foods that have homologous proteins is critical and may be obtained by studying the structural …

Crystal Structures And Kinetics Of Monofunctional Proline Dehydrogenase Provide Insight Into Substrate Recognition And Conformational Changes Associated With Flavin Reduction And Product Release, Min Luo, Benjamin W. Arentson, Dhiraj Srivastava, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline dehydrogenase catalyzes the FAD-dependent oxidation of proline to Δ1- pyrroline-5- carboxylate, which is the first step of proline catabolism. Here, we report the structures of proline dehydrogenase from Deinococcus radiodurans in the oxidized state complexed with the proline analog L-tetrahydrofuroic acid and in the reduced state with the proline site vacant. The analog binds against the si face of the FAD isoalloxazine and is protected from bulk solvent by the α8 helix and the β1-α1 loop. The FAD ribityl chain adopts two conformations in the E-S complex, which is unprecedented for flavoenzymes. One of the conformations is novel for …

Selection Of Trna Charging Quality Control Mechanisms That Increase Mistranslation Of The Genetic Code, Srujana S. Yadavalli, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer RNA (tRNA) pairs by aminoacyl-tRNA synthetases (aaRSs) and inaccurate selection of aminoacyl-tRNAs by the ribosome. Many aaRSs actively edit non-cognate amino acids, but editing mechanisms are not evolutionarily conserved, and their physiological significance remains unclear. To address the connection between aaRSs and mistranslation, the evolutionary divergence of tyrosine editing by phenylalanyl-tRNA synthetase (PheRS) was used as a model. Certain PheRSs are naturally error prone, most notably a Mycoplasma example that displayed a low level of specificity consistent with elevated mistranslation of the proteome. Mycoplasma PheRS was found …

Microfluidic Devices With Integrated Sample Preparation For Improved Analysis Of Protein Biomarkers, Pamela Nsang Nge

Theses and Dissertations

Biomarkers present a non-invasive means of detecting cancer because they can be obtained from body fluids. They can also be used for prognosis and assessing response to treatment. To limit interferences it is essential to pretreat biological samples before analysis. Sample preparation methods include extraction of analyte from an unsuitable matrix, purification, concentration or dilution and labeling. The many advantages offered by microfluidics include portability, speed, automation and integration. Because of the difficulties encountered in integrating this step in microfluidic devices most sample preparation methods are often carried out off-chip. In the fabrication of micro-total analysis systems it is important …

Spatial Patterns Of Mercury In Atmospheric Deposition, Soils And Lake Biota In The Adirondack Park, New York, Xue Yu

Civil and Environmental Engineering - Dissertations

Mercury (Hg), as a trace element cycling in the environment, poses a serious health threat to both humans and wildlife due to its toxicity. Atmospheric deposition is the main source of Hg to most remote environments. The Adirondack Park in New York State of the United States receives moderate Hg deposition, and is a region characterized by relatively high concentrations of Hg in the terrestrial and especially aquatic biota. It is important to understand the mechanisms that contribute to the sensitivity of this region to Hg inputs. In my research, studies of the spatial patterns of Hg in atmospheric deposition, …

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Knockout Of The 15 Kda Selenoprotein Protects Against Chemically-Induced Aberrant Crypt Formation In Mice, Petra A. Tsuji, Bradley A. Carlson, Salvador Naranjo-Suarez, Min-Hyuk Yoo, Xue-Ming Xu, Dmitri E. Fomenko, Vadim Gladyshev, Dolph L. Hatfield, Cindy D. Davis

Department of Biochemistry: Faculty Publications

Evidence suggests that selenium has cancer preventive properties that are largely mediated through selenoproteins. Our previous observations demonstrated that targeted down-regulation of the 15 kDa selenoprotein (Sep15) in murine colon cancer cells resulted in the reversal of the cancer phenotype. The present study investigated the effect of Sep15 knockout in mice using a chemically-induced colon cancer model. Homozygous Sep15 knockout mice, and wild type littermate controls were given four weekly subcutaneous injections of azoxymethane (10 mg/kg). Sep15 knockout mice developed significantly (pGBP-1 in humans has been associated with a highly significant, increased five-year survival rate in colorectal cancer patients. In …

Functional Analysis Of Drosophila Integrator Complex In Snrna 3' End Processing, Jiandong Chen

Dissertations and Theses (Open Access)

Uridine-rich small nuclear RNAs (U snRNAs) play essential roles in eukaryotic gene expression by facilitating the removal of introns from mRNA precursors and the processing of the replication-dependent histone pre-mRNAs. Formation of the 3’ end of these snRNAs is carried out by a poorly characterized, twelve-membered protein complex named Integrator Complex.

In the effort to understand Integrator Complex function in the formation of the snRNA 3’ end, we performed a functional RNAi screen in Drosophila S2 cells to identify protein factors required for snRNA 3’ end formation. This screen was conducted by using a fluorescence-based reporter that elicits GFP expression …

Biochemical Characterization Of Binding Partners Of Two Hsp70 Co-Chaperones In Saccharomyces Cerevisiae, Jacob Verghese

Dissertations and Theses (Open Access)

Cells are exposed to a variety of environmental and physiological changes including temperature, pH and nutrient availability. These changes cause stress to cells, which results in protein misfolding and altered cellular protein homeostasis. How proteins fold into their three-dimensional functional structure is a fundamental biological process with important relevance to human health. Misfolded and aggregated proteins are linked to multiple neurodegenerative diseases, cardiovascular disease and cystic fibrosis. To combat proteotoxic stress, cells deploy an array of molecular chaperones that assist in the repair or removal of misfolded proteins.

Hsp70, an evolutionarily conserved molecular chaperone, promotes protein folding and helps maintain …

A Study On The Function Of 14-3-3sigma In Regulating Cancer Energy Metabolism, Liem M. Phan, Liem M. Phan

Dissertations and Theses (Open Access)

Metabolic reprogramming has been shown to be a major cancer hallmark providing tumor cells with significant advantages for survival, proliferation, growth, metastasis and resistance against anti-cancer therapies. Glycolysis, glutaminolysis and mitochondrial biogenesis are among the most essential cancer metabolic alterations because these pathways provide cancer cells with not only energy but also crucial metabolites to support large-scale biosynthesis, rapid proliferation and tumorigenesis. In this study, we find that 14-3-3σ suppresses all these three metabolic processes by promoting the degradation of their main driver, c-Myc. In fact, 14-3-3s significantly enhances c-Myc poly-ubiquitination and subsequent degradation, reduces c-Myc transcriptional activity, and down-regulates …

Tumour Inflammasome-Derived Il-1b Recruits Neutrophils And Improves Local Recurrence-Free Survival In Ebv-Induced Nasopharyngeal Carcinoma, Lih-Chyang Chen, Li-Jie Wang, Nang-Ming Tsang, David M. Ojcius, Chia-Chen Chen, Chun-Nan Ouyang, Chuen Hsueh, Ying Liang, Kai-Ping Chang, Chiu-Chin Chen, Yu-Sun Chang

All Dugoni School of Dentistry Faculty Articles

Inflammasomes sense infection and cellular damage and are critical for triggering inflammation through IL-1β production. In carcinogenesis, inflammasomes may have contradictory roles through facilitating antitumour immunity and inducing oncogenic factors. Their function in cancer remains poorly characterized. Here we show that the NLRP3, AIM2 and RIG-I inflammasomes are overexpressed in Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC), and expression levels correlate with patient survival. In tumour cells, AIM2 and RIG-I are required for IL-1β induction by EBV genomic DNA and EBV-encoded small RNAs, respectively, while NLRP3 responds to extracellular ATP and reactive oxygen species. Irradiation and chemotherapy can further activate AIM2 …

Reversible Inhibition Of Chlamydia Trachomatis Infection In Epithelial Cells Due To Stimulation Of P2x4 Receptors, Matthew A. Pettengill, Camila Marques-Da-Silva, Maria Luisa Avila, Verissa W. Lam, Ikechukwu Ollawa, Ali Abdul-Sater, Robson Coutinho-Silva, Georg Hacker, David M. Ojcius, Suellen D'Arc Dos Santos Oliveira

All Dugoni School of Dentistry Faculty Articles

Bacterial infections of the mucosal epithelium are a major cause of human disease. The prolonged presence of microbial pathogens stimulates inflammation of the local tissues, which leads to changes in the molecular composition of the extracellular milieu. A well-characterized molecule that is released to the extracellular milieu by stressed or infected cells is extracellular ATP and its ecto-enzymatic degradation products, which function as signaling molecules through ligation of purinergic receptors. There has been little information, however, on the effects of the extracellular metabolites on bacterial growth in inflamed tissues. Millimolar concentrations of ATP have been previously shown to inhibit irreversibly …

Characterization Of Beryllium As A Novel Agent To Study Cell Cycle Arrest And Cellular Senescence, Priyatham Gorjala

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cancer cells evade senescence, apoptosis, and other constraints on proliferation, often via mutation of the p53 tumor suppressor gene (TP53). Normal human lung fibroblasts have been shown to enter premature senescence upon exposure to beryllium. In these cells, BeSO₄ stabilizes p53 protein, increases p21 gene expression, induces senescence-associated β-galactosidase activity and causes cell proliferation arrest. In the present study, we have investigated whether BeSO₄ is able to induce similar effects in cancer cells that have wildtype p53. We have demonstrated that beryllium salt at low concentration can induce molecular changes in the p53 signaling pathway leading to cell …

Trim24-Regulated Estrogen Response Is Dependent On Specific Histone Modifications In Breast Cancer Cells, Teresa T. Yiu

Dissertations and Theses (Open Access)

In this dissertation, I discovered that function of TRIM24 as a co-activator

of ERα-mediated transcriptional activation is dependent on specific histone

modifications in tumorigenic human breast cancer-derived MCF7 cells. In the first

part, I proved that TRIM24-PHD finger domain, which recognizes unmethylated

histone H3 lysine K4 (H3K4me0), is critical for ERα-regulated transcription.

Therefore, when LSD1-mediated demethylation of H3K4 is inhibited, activation of

TRIM24-regulated ERα target genes is greatly impaired. Importantly, I

demonstrated that TRIM24 and LSD1 are cyclically recruited to estrogen

responsive elements (EREs) in a time-dependent manner upon estrogen

induction, and depletion of their expression exert corresponding time-dependent

effect …

Regulation Of The Lipid Raft Localization Of The Gal/Galnac Lectin, An Adhesin On The Surface Of The Human Protozoan Parasite, Entamoeba Histolytica, Amanda Goldston

All Dissertations

Lipid rafts, sterol- and sphingolipid-rich membrane microdomains, have been shown to control virulence in a variety of parasites including Entamoeba histolytica, an intestinal parasite that causes dysentery and liver abscess. Parasite cell surface receptors, such as the Gal/GalNAc lectin, facilitate attachment to host cells and extracellular matrix. The Gal/GalNAc lectin binds to galactose or N-acetylgalactosamine residues on host components, and is composed of heavy (Hgl), intermediate (Igl), and light (Lgl) subunits. Although Igl is constitutively localized to lipid rafts, Hgl and Lgl transiently associate with this compartment in a cholesterol-dependent fashion. Exposure to bonafide Gal/GalNAc lectin ligands is associated with …

A Genetic, Transgenic, And Transcriptomic Analysis Of Larval Salivary Gland Physiology In Drosophila Melanogaster, Elana A. Paladino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cholesterol is the precursor to a unique class of lipophilic signaling molecules called steroid hormones that initiate the development of sexual characteristics, reactions to stress, and maintenance of metabolism, among many other functions. Although much progress has been made in understanding the function of these signaling hormones, we do not fully understand how a single steroid can cause many distinct, tissue-specific responses. Drosophila melanogaster is an effective model for understanding steroid hormone action because of its simplicity. The steroid molting hormone 20-hydroxyecdysone (hereafter, 20E) is the primary active steroid in Drosophila and mediates not only larval molts and the emergence …