Biochemistry, Biophysics, and Structural Biology Commons^™

Regulation Of The Shigella Flexneri Icsp Gene And H-Ns Dependent Repression, Rosa Ojeda, Amanda Wigley, Dustin Harrison, Helen Wing

Undergraduate Research Opportunities Program (UROP)

The gram negative bacterium Shigella flexneri is known to cause dysentery in humans and primates. In order to help prevent the spread of shigellosis, gene regulation must be understood. Studies show that the virulence genes in S .flexneri are thermo regulated. At 30°C histone-like nucleoid structuring protein (H-NS) represses transcription of virulence genes and at 37°C VirB derepresses virulence genes. One of the genes that contribute to the virulence of S. flexneri is icsP. My project focuses on the regulation of the S. flexneri icsP gene and has two main goals. The first is to identify the sequence of H-NS …

The Formation And Stability Of Radical-Molecule And Radical-Radical Complexes And Their Importance In Atmospheric Processes, Jared M. Clark

Theses and Dissertations

This research explores the role that radical-molecule complexes play in the chemistry of Earth's atmosphere. The formation of such complexes can have direct and pronounced effects on the reaction and product outcome of atmospheric chemical reactions. Some attention is also given to the formation of radial-radical pre-reactive complexes in the HO + ClO system. Peroxy radicals (RO2) can form stable complexes with polar compounds such as H2O, NH3, and CH3OH. For the simplest RO2 radical, HO2, complex formation (e.g., HO2-H2O, HO2-NH3, and HO2-722;CH3OH) gives rise to a significant increase in the HO2 self-reaction rate constant. Although this phenomenon has been …

Development Of Lps Antagonistic Therapeutics: Synthesis And Evaluation Of Glucopyranoside-Spacer-Amino Acid Motifs, Sophon Kaeothip, Geeta Paranjape, Shana Terrill, Aileen Bongat, Maria Udan, Teerada Kamkhachorn, Hope Johnson, Michael Nichols, Alexei Demchenko

Chemistry & Biochemistry Faculty Works

No abstract provided.

Characterization Of The Desorption Electrospray Ionization Mechanism Using Microscopic Imaging Of The Sample Surface, Michael Craig Wood

Theses and Dissertations

Desorption electrospray ionization (DESI) is an ambient ionization technique for mass spectrometry. This solvent based desorption ion source has wide applicability in surface analysis with minimal sample preparation. Interest in improving detection limits, broadening applications, and increasing the spatial resolution for chemical imaging has led to studies of the DESI mechanism. An inverted microscope has been used to image interactions between the DESI spray and test analytes on a glass surface. Microscopic images recorded with millisecond time resolution have provided important insights into the processes governing analyte transport and desorption. These insights are the basis of a rivulet-based model for …

Identification And Characterization Of Enzymes Involved In The Biosynthesis Of Different Phycobiliproteins In Cyanobacteria, Avijit Biswas

LSU New Orleans Theses and Dissertations

A multi-plasmid, co-expression system was used to recreate the biosynthetic pathway for phycobiliproteins from the cyanobacterium Synechococcus sp. PCC 7002 in E. coli. This system efficiently produced chromophorylated allophycocyanin (ApcA/ApcB), -phycocyanin, and -phycocyanin. This system was used to demonstrate that CpcS-I and CpcU proteins are both required attaching PCB to allophycocyanin subunits ApcD (AP-B) and ApcF (18). The N-terminal, AP-like domain of ApcE (LCM99) was produced in soluble form and shown to have intrinsic bilin lyase activity. In addition, this system was used to chromophorylated CpcA from Synechococystis sp. PCC 6803 with a non-cognate bilin; PEB with the aid …

Ferritin Diversity: Mechanistic Studies, Disease Implications, And Materials Chemistry, Robert Joseph Hilton

Theses and Dissertations

The study of ferritin includes a rich history of discoveries and scientific progress. Initially, the composition of ferritin was determined. Soon, it was shown that ferritin is a spherical, hollow protein. Eventually, over several decades of research, the structure and some function of this interesting protein was elucidated. However, the ferritin field was not completely satisfied. Today, for example, researchers are interested in refining the details of ferritin function, in discovering the role of ferritin in a variety of diseases, and in using ferritin for materials chemistry applications. The work presented in this dissertation highlights the progress that we have …

The Characterization Of Avian Polyomavirus, Satellite Tobacco Mosaic Virus, And Bacteriophage Cw02 By Means Of Cryogenic Electron Microscopy, Peter S. Shen

Theses and Dissertations

Viruses are the most abundant biological entity in the biosphere and are known to infect hosts from all domains of life. The aim of my work is to identify conserved and non-conserved features among the capsid structures of related and divergent icosahedral viruses via cryogenic electron microscopy, sequence analysis, molecular modeling, and other techniques. Bird polyomaviruses often cause severe disease in their hosts whereas mammalian polyomaviruses generally do not. Avian polyomavirus is a type of bird polyomavirus with an unusually broad host range compared to the restricted tropism of other polyomaviruses. Although most polyomaviruses have a conserved, rigid capsid protein …

Physiologically-Based Pharmacokinetic Modeling For Predicting Drug-Drug Interactions, David M. Ng, Ali Navid

STAR Program Research Presentations

Dynamics of interactions between the drugs caffeine and ciprofloxacin are predicted using physiologically-based pharmacokinetic (PBPK) modeling. Pharmacokinetic means the model determines where the drugs are distributed in the body over time. Physiologically-based means the anatomy and physiology of the human body is reflected in the structure and functioning of the model. Multiple drugs can interact to increase or decrease their beneficial and/or undesired effects. This is important because some common substances, such as caffeine in coffee and soft drinks, are actually drugs that affect the body. By implementing the model as a computer program, it is relatively straightforward to perform …

Discovery Of An Apoptosis Inducing Ligand For Burkitt Lymphoma, Carolyn Laymon, Kyla Bradylong, Mary Saunders, David Olivos, Kit Lam

STAR Program Research Presentations

One-bead two-compound (OB2C) combinatorial chemistry libraries enable the discovery of novel synthetic compounds which can be used to evoke specific signaling response in cells. The library configuration is composed of a fixed known cell adhesion ligand and a random chemical library displayed on the surface of Tentagel beads. The cell adhesion ligand binds to specific receptors located on the surface of cells enabling the random immobilized chemical molecules on each bead resin bead to evoke specific cellular responses such as apoptosis or cell death. To validate this concept, a OB2C combinatorial library comprised of an α4β1 integrin targeting ligand, LLP2A, …

Interspecies Comparison Of Αii-Spectrin Abundance Between Chinook Salmon And Steelhead, Brielle D. Kemis, Ann L. Miracle, Katie A. Wagner, Christa M. Woodley

STAR Program Research Presentations

Salmonids, such as Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss), are a staple economic, recreational, tribal, and environmental resource, yet many populations are unsustainable. This study was part of a broad scale effort to monitor the impact of downstream migration obstacles on juvenile salmonid health and survival, which is an essential step towards increasing Smolt-to-Adult Return ratios (SARs). The objective of this study was to determine if juvenile Chinook salmon and steelhead exhibit differing quantities of alphaII-Spectrin Breakdown Products (SBDPs) over two consecutive spring migration periods, indicative of neurogenesis rate and/or biological response to head …

Forward Osmosis Bag: Ground Testing The Prospect Of Using Alternative Water Sources For Drinking Water, Michaela Marie Brant, Ariella Yendler, Mona Hammoudeh, Michael T. Flynn

STAR Program Research Presentations

On the STS-135 Space Shuttle mission, to be launched July 8, 2011, a forward osmosis bag (FOB) study will be conducted. At NASA Ames this summer, the ground truth testing is being conducted for results comparisons. The FOB technology is derived from a commercial product, the X-Pack water filter. Forward osmosis operates by utilizing an established concentration gradient across a semi-permeable membrane to move water molecules from one side of the membrane to the other. This concept is exploited to harvest drinking water from grey water sources such as urine, sea water, or vehicle water. In this experiment, potassium chloride …

Computational Identification Of Protein Catalytic Sites: Tests, Validation, Dan Kirshner, Jerome Nilmeier, Felice Lightstone

STAR Program Research Presentations

This project is one element of the analysis “pipeline” to characterize an organism that previously has not been well-studied. Once a protein of unknown structure has been computationally modeled (based on its sequence similarity to proteins with solved structures), then catalytic sites are identified on the model by comparison to a library of known sites. This work tested the identification algorithms with a set of proteins that have known structures and catalytic sites.

Sound Production In Two Loricariid Catfishes, Amanda Lynn Webb

Masters Theses & Specialist Projects

Many families of catfish produce sounds via pectoral spine stridulation and/or swim bladder compression using sonic muscles attached to the swim bladder. The sound production capabilities and characteristics in Loricariidae, the largest catfish family, have not been well examined. Sounds produced by two loricariid catfish species, Macrotocinclus affinis and Pterygoplichthys gibbiceps were recorded. Both species produce broad band calls via pectoral spine stridulation. These species produce sounds by rubbing the ridges of the dorsal process of the pectoral spine base against the groove of the pectoral girdle. Call duration was generally shorter in M. affinis (2-15 ms) as opposed to …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

Stimulator Of Neurotropic Effects Determining The Mechanism Of Action Of The Ms-818 Compound Through Protein Identification By Affinity Chromatography And Sds-Page, Charlene Seraphina Dass

HIM 1990-2015

The MS-818 compound is used in the proliferation process of neuronal cells and many biological activities that accompany this process such as astrocyte differentiation, inhibition of neuronal apoptosis, and fraction repairs. We do know the effects of this compound, but the mechanism of action remained uncertain until now. To determine the pathway of this compound, NT2 cells were cultured and lysed to isolate the proteins. Affinity Chromatography was performed in order to immobilize the MS-818 compound to a Hi-Trap NHS column. The NT2 protein sample was injected through the column and eluted with a MS-818 concentrated, high salt content elution …

Synthesis Of A Chemical Probe For Identification Of Ger Receptor Proteins Of Bacillus Anthracis, Hyelee Lee

UNLV Theses, Dissertations, Professional Papers, and Capstones

Bacillus anthracis,a gram positive, endospore-forming, rod-shaped, aerobic bacterium, is the causative agent of anthrax. A key step in the pathogenic cycle is the spore germination, where the dormant spore transforms into a metabolically active cell. This allows B. anthracis to proliferate and secrete toxins. It is believed that spore germination is triggered when small molecules, known as germinants, are recognized by germination (Ger) receptor proteins located in the inner membrane of spores. Most Ger proteins are encoded by tricistronic operons, resulting in three distinct products, the A-, B-, C-subunits. Genomic sequencing showed that B. anthracis has seven ger receptor …

Developmental Deregulation And Tumorigenesis Inhibition In 14-3-3zeta Knockout Mouse, Jun Yang

Dissertations and Theses (Open Access)

Cancer is second leading cause of death in the United States. Improving cancer care through patient care, research, education and prevention not only saves lives, but reduces health care cost as well. Breast cancer is the most leading cause of cancer incidence and cancer related death in women of the United States. 14-3-3s are a family of conserved proteins ubiquitously expressed in all eukaryotic organisms. They form complexes with hundreds of proteins by binding to specific phospho-serine/threonine containing motifs. In this way they regulate a variety of cellular processes and are involved in many human diseases especially cancer to our …

Significance Of Increased Tissue Transglutaminase In Hormone Refractory Prostate Cancer, Amy L. Han

Dissertations and Theses (Open Access)

The progression of hormone responsive to hormone refractory prostate cancer poses a major clinical challenge in the successful treatment of prostate cancer. The hormone refractory prostate cancer cells exhibit resistance not only to castrate levels of testosterone, but also to other therapeutic modalities and hence become lethal. Currently, there is no effective treatment available for managing this cancer. These observations underscore the urgency to investigate mechanism(s) that contribute to the progression of hormone-responsive to hormone-refractory prostate cancer and to target them for improved clinical outcomes.

Tissue transglutaminase (TG2) is a multifunctional pro-inflammatory protein involved in diverse physiological processes such as …

Uptake And Metabolism Of 5’-Amp In The Erythrocyte Play Key Roles In The 5’-Amp Induced Model Of Deep Hypometabolism, Isadora Daniels

Dissertations and Theses (Open Access)

UPTAKE AND METABOLISM OF 5’-AMP IN THE ERYTHROCYTE PLAY KEY ROLES IN THE 5’-AMP INDUCED MODEL OF DEEP HYPOMETABOLISM

Publication No. ________

Isadora Susan Daniels, B.A.

Supervisory Professor: Cheng Chi Lee, Ph.D.

Mechanisms that initiate and control the natural hypometabolic states of mammals are poorly understood. The laboratory developed a model of deep hypometabolism (DH) initiated by uptake of 5’-adenosine monophosphate (5’-AMP) into erythrocytes. Mice enter DH when given a high dose of 5’-AMP and the body cools readily. Influx of 5’-AMP appears to inhibit thermoregulatory control. In a 15°C environment, mice injected with 5’-AMP (0.5 mg/gw) enter a Phase …

Mechanism Of Transcriptional Suppression Of A Phytochrome A Epiallele In Arabidopsis Thaliana, Gulab D. Rangani

Graduate Theses and Dissertations

Cytosine methylation in DNA is an integral part of epigenetically controlled regulatory networks in eukaryotes. Both plants and vertebrates display DNA methylation in the gene coding region; however, its role in gene expression is not well understood. Gene promoter, on the other hand, remains largely unmethylated. Acquisition of methylation in promoter results in transcriptional suppression of the gene. The goal of this research is to study the effect of coding region methylation in gene expression using a unique gene model, phyA'. phyA' is a transcriptionally suppressed epiallele of the Arabidopsis thaliana Phytochrome A gene, which contains methylation in CG sites …