Biochemistry Commons^™

Estrogenic Effects On A Protandrous Hermaphroditic Species: Amphiprion Percula, Randall Burns, Katie Dose

Undergraduate Research Symposium

Estrogen concentrations are increased in aquatic environments due to the addition of pharmaceutical drugs (i.e. birth control) through runoff water. This manipulates maturation of sexes within many species that inhabit aquatic enviornments, including fresh and marine habitats. Amphiprion percula exhibit a hierarchal system behavioral pattern, which determines the social status of individuals within a group. Multiple clown anemonefish, A. percula were studied via a controlled environment and hierarchal succession was observed under estrogenic additions. From this study, data on sex change of a hermaphroditic protandrous species was observed under the influence of three concentrations of natural estrogen. Based on sex …

Localization And Expression Level Of Vascular Endothelial Growth Factor After Partial Hepatectomy Of Wky Rats, Adam Kronebusch, Tyler Koonst

Undergraduate Research Symposium

Inflammation and fibrosis are indicative of liver regeneration following injury and chronic liver diseases, such as cirrhosis and hepatocellular carcinoma. The formation of new vasculature via the process of angiogenesis is vital to the pathological progression of liver regeneration and these diseases. Thus, inhibiting the process of angiogenesis could have the potential to stop or slow the progression of chronic liver diseases. Vascular endothelial growth factor (VEGF) is the most potent and specific growth factor for initiating the process of angiogenesis, making it a prime target to inhibit angiogenesis. Bevacizumab is an antibody that binds to VEGF, inhibiting it from …

Rubidium Uptake In Isolated Rat Cardiomyocytes, Jooyoung Lee, Jaekook Sim, Karleen Doering

Undergraduate Research Symposium

The element rubidium is known to have similar biological impact as K+ ions and some studies have shown that heart tissue takes up rubidium through K+ channels and Na+/K+ ATPase pumps. The purpose of the research was to confirm whether or not rubidium was transported into individual cardiomyocytes. Rubidium may be used as a marker to study different physiological functions of K+ and its channels and pumps. The methods used are mainly two parts: isolation of single heart cells and treatment with rubidium. Isolated heart cells were obtained by anesthetizing a rat, extracting the heart, and infusing its aorta with …

Effect Of Artificial Sweeteners On The Renin-Angiotensin System In Rats, Jacob Ball

Undergraduate Research Symposium

Normal abundant dietary sugars such as fructose and glucose can contribute to hypertension and other health issues. To avoid these health complications, many individuals use artificial sweeteners. An equivalent intake of some artificial sweeteners also can lead to hypertension. However, Stevia, a sweetener that is isolated from a Paraguayan plant, was shown in relevant literature to decrease blood pressure in both rat specimens and humans. The general purpose of this research project was to study the effect of Stevia and glucose on the expression of two key components of the renin-angiotensin-aldosterone system (RAAS): prorenin receptor (PRR) and angiotensin receptor type …

Trail-R1 Is A Negative Regulator Of Pro-Inflammatory Responses And Modulates Long-Term Sequelae Resulting From Chlamydia Trachomatis Infections In Humans, Mufadhal Al-Kuhlani, James Rothchild, Sukumar Pal, Luis M. De La Maza, Sander Ouberg, Servaas A. Morré, Deborah Dean, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

The immune system eliminates Chlamydia trachomatis infection through inflammation. However, uncontrolled inflammation can enhance pathology. In mice, TNF-related apoptosis-inducing ligand receptor (TRAIL-R), known for its effects on apoptosis, also regulates inflammation. In humans, the four homologues of TRAIL-R had never been investigated for effects on inflammation. Here, we examined whether TRAIL-R regulates inflammation during chlamydial infection. We examined TRAIL-R1 single nucleotide polymorphisms (SNPs) in an Ecuadorian cohort with and without C. trachomatis infections. There was a highly significant association for the TRAIL+626 homozygous mutant GG for infection vs no infection in this population. To confirm the results observed in the …

A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Cheryl Bailey, Students And Tas In Genomics Education Partnership Courses

Department of Biochemistry: Faculty Publications

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge.We have developed a bioinformatics project that provides a coursebased research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment …

Developing An Unstructured Model To Investigate The Effect Of Ethanol On Product Yields For Glucose And Xylose Cofermentation In Saccharomyces Cerevisiae 424a (Lnh-St), Shane D. Clingenpeel

Open Access Theses

Production of bio-ethanol from lignocellulose requires the efficient fermentation of glucose and xylose, even in the presence of inhibitors. The desired product, ethanol itself, will inhibit the fermentation. A further understanding of how ethanol affects the organism is critical to overcoming its inhibition.

This thesis evaluated the effect of ethanol on the cofermentation of glucose and xylose in two different cases. The first case had an unstructured model created for Saccharomyces cerevisiae 424A (LNH-ST), a genetically modified strain of yeast capable of cofermenting glucose and xylose. The differential equations were based around sugar consumption, and the product yields were investigated …

Redox Regulation Of Protein Translation In Eukaryotes, Maxim Gerashchenko

Department of Biochemistry: Dissertations, Theses, and Student Research

Gene expression may be controlled at multiple levels, e.g., through genomic architecture, transcription and translation. In the current work, we focused on regulation of protein synthesis. Historically, the investigation of the regulation of gene expression at the level of translation lagged behind the transcriptional control because of the lack of accessible high-throughput methods. Our research has begun with the finding of the use of alternative non-AUG start codon in thioredoxin-glutathione reductase (TGR), a selenoprotein involved in redox control during male reproduction. The use of this codon, CUG, relies on the Kozak consensus sequence and ribosomal scanning mechanism. However, the CUG …

Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison

OES Theses and Dissertations

Sucrose gradient centrifugation and Field-flow fractionation (FFF) are two different particle separation methods that overcome the problems of similar size microorganisms clumping together during standard filtration methods. FFF separates particles based on size and density via the parabolic velocity profile of laminar flow in a ribbon-like channel. The sucrose method separates particles via centrifugation in a density gradient. Both techniques worked well in separating eukaryotic from prokaryotic microbes, with the preferred method depending on the type and relative abundance of organisms to be separated. Minicells were separated from mother cells in transformed Escherichia coli cultures, heterotrophic flagellates (e.g., Diplonema papillatum …

Exploration Of Mutations In Erythroid 5-Aminolevulinate Synthase That Lead To Increased Porphyrin Synthesis, Erica Jean Fratz

USF Tampa Graduate Theses and Dissertations

5-Aminolevulinate synthase (ALAS; EC 2.3.1.37) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the first committed step of heme biosynthesis in animals, the condensation of glycine and succinyl-CoA yielding 5-aminolevuliante (ALA), CoA, and CO2. Murine erythroid-specific ALAS (mALAS2) variants that cause high levels of PPIX accumulation provide a new means of targeted, and potentially enhanced, photosensitization. Transfection of HeLa cells with expression plasmids for mALAS2 variants, specifically for those with mutated mitochondrial presequences and a mutation in the active site loop, caused significant cellular accumulation of PPIX, particularly in the membrane. Light treatment of HeLa cells expressing mALAS2 variants revealed …

Combined Metal-Enhanced Fluorescence-Surface Acoustic Wave (Mef-Saw) Biosensor, Samuel Morrill

USF Tampa Graduate Theses and Dissertations

Immunofluorescence assays are capable of both detecting the amount of a protein and the location of the protein within a cell or tissue section. Unfortunately, the traditional technique is not capable of detecting concentrations on the nanoscale. Also, the technique suffers from non-specific attachment, which can cause false-positives, as well as photobleaching when detecting lower concentrations is attempted. There is also a time constraint problem since the technique can take from many hours to a few days in some cases.

In this work, metal-enhanced fluorescence (MEF) is used to lower the detection limit and reduce photobleaching. Unfortunately, MEF also increases …

Stoichiometries And Affinities Of Interacting Proteins From Concentration Series Of Solution Scattering Data: Decomposition By Least Squares And Quadratic Optimization, Himanshu Chandola, Tim E. Williamson, Bruce A. Craig, Alan M. Friedman, Chris Bailey-Kellogg

Dartmouth Scholarship

In studying interacting proteins, complementary insights are provided by analyzing both the association model (the stoichiometry and affinity constants of the intermediate and final complexes) and the quaternary structure of the resulting complexes. Many current methods for analyzing protein interactions either give a binary answer to the question of association and no information about quaternary structure or at best provide only part of the complete picture. Presented here is a method to extract both types of information from X-ray or neutron scattering data for a series of equilibrium mixtures containing the initial components at different concentrations. The method determines the …

Desorption Electrospray Ionization Mass Spectrometry Imaging: Instrumentation, Optimization And Capabilities, Manan Dhunna

Theses and Dissertations

Desorption Electrospray Ionization Mass spectrometry Imaging (DESI-MSI) is an area of great interest and a promising tool in the field of chemical imaging. It is a powerful, label-free technique, which can determine, map and visualize different molecular compounds on a sample surface. The amount of information acquired in a single DESI-MSI experiment is enormous compared to other techniques, as it can simultaneously detect different compounds with their spatial distribution on the surface. The experiment can be used to produce two-dimensional and three-dimensional images. Chapter 2 focuses on the design and optimization of the setup for performing DESI-MS imaging on various …

Facile Synthesis And Characterization Of A Thermally Stable Silica-Doped Alumina With Tunable Surface Area, Porosity, And Acidity, Maryam Khosravi Mardkhe

Theses and Dissertations

Mesoporous γ-Al2O3 is one of the most widely used catalyst supports for commercial catalytic applications. The performance of a catalyst strongly depends on the combination of textural, chemical and physical properties of the support. Pore size is essential since each catalytic system requires a unique pore size for optimal catalyst loading, diffusion and selectivity. In addition, high surface area and large pore volume usually result in higher catalyst loading, which increases the number of catalytic reaction sites and decreases reaction time. Therefore, determination of surface area and porosity of porous supports is critical for the successful design and optimization of …

Structural Insights Into The Interaction Between A Potent Anti-Inflammatory Protein, Viral Cc Chemokine Inhibitor (Vcci), And The Human Cc Chemokine, Eotaxin-1, Nai-Wei Kuo, Yong-Guang Gao, Megan Schill, Nancy Isern, Cynthia Dupureur, Patricia Liwang

Chemistry & Biochemistry Faculty Works

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N …

Structures Of The Puta Peripheral Membrane Flavoenzyme Reveal A Dynamic Substrate-Channeling Tunnel And The Quinone-Binding Site, Harkewal Singh, Benjamin W. Arentson, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of L-proline to L-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. Located at the inner membrane of Gram-negative bacteria, PutAs play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. Here, we report seven crystal structures of the 1,004- residue PutA from Geobacter sulfurreducens, along with determination of the protein oligomeric state by small-angle X-ray scattering and kinetic characterization of substrate channeling and quinone reduction. The structures reveal …

Low Doses Of Colony-Stimulating Factors Lead To Resolution Of Neutropenia In Cancer Patients Through Increased Levels Of Dihydrofolate Reductase, Mohammad Perwaiz Iqbal, Ikram Ali Burney

Department of Biological & Biomedical Sciences

Low doses of granulocyte- colony stimulating factor (G-CSF) and granulocyte macrophage- colony stimulating factor (GM-CSF) have been shown to be beneficial in reducing duration of systemic antibiotic therapy and in-patient hospitalization by decreasing the period of neutropenia in cancer patients undergoing chemotherapy. Since the underlying mechanism is unclear, the aim of this study was to investigate whether the administration of G-CSF and GM-CSF in two different doses (low dose and standard dose) would result into resolution of neutropenia with concomitant increase in multiple forms of dihydrofolate reductase (DHFR, a pivotal enzyme in the pathway of de novo DNA synthesis). Thirty …

Survivin: Regulation By Yy1 And Role In Pancreatic Cancer Combination Therapy, Nicholas R. Galloway

Loma Linda University Electronic Theses, Dissertations & Projects

Despite significant clinical and basic science advancements, cancer remains a devastating disease that affects people of all ages, races, and background. Survivin, the fourth most common transcript found in cancer cells, is a protein that is thought to be involved in the enhanced proliferation, survival, and metastasis of cancer cells. Therefore understanding how this gene is regulated is potentially of vital importance to improving cancer management and therapy. Our work has identified a novel transcriptional regulator of survivin called Yin Yang 1 (YY1). YY1 is a transcription factor that has been observed to activate some gene promoters and repress others, …

Global Analysis Of Lysine Acetylation Suggests The Involvement Of Protein Acetylation In Diverse Biological Processes In Rice (Oryza Sativa)., Babi Ramesh Reddy Nallamilli, Mariola J. Edelmann, Xiaoxian Zhong, Feng Tan, Hana Mujahid, Jian Zhang, Bindu Nanduri, Zhaohua Peng

CALS Publications

Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa). We identified 60 lysine acetylated sites on 44 proteins of diverse …

Genome-Wide Rnai Ionomics Screen Reveals New Genes And Regulation Of Human Trace Element Metabolism, Mikalai I. Malinouski, Nesrin M. Hasan, Yan Zhang, Javier Seravalli, Jie Lin, Andrei Avanesov, Svetlana Lutsenko, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Trace elements are essential for human metabolism and dysregulation of their homoeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundamental differences in the regulation of different trace elements. Specifically, selenium levels are controlled through the selenocysteine machinery and expression of abundant selenoproteins; copper balance is affected by lipid metabolism and requires …