Molecular Biology Commons^™

Investigating The Role Of Prmt1 And Arginine Methylation Of Hsp70 In Human Pancreatic Cancer, Liang Wang

Dissertations and Theses (Open Access)

Protein arginine methyltransferase 1 (PRMT1) is the major arginine methyltransferase, which catalyzes the addition of one or two methyl groups to the arginine residues of its substrate proteins. The best-known substrate for PRMT1 is histone, while more and more non-histone proteins are now found to be methylated by PRMT1. Dysregulation of PRMT1 is reported in several human cancer types. However, its biological roles in human pancreatic cancer initiation and development are still unclear. In the first part of this study, I found that the expression level of PRMT1 was elevated in both human and mouse pancreatic cancer tissues in immunohistochemistry …

Characterization Of A Tuberous Sclerosis Complex 2 Variant And Its Interaction Involving The Ras-Related Protein Rheb, Nosaiba Shokr

Graduate Theses and Dissertations

Structure-function relationships of any complex underlie the molecular details of the biological interactions. Rheb, Ras Homology Enriched in Brain, is a Ras-related protein, and it is genetically identified as a molecular switch. Rheb is regulated by cycling between the biologically active GTP and inactive GDP-bound forms. This regulation is partially controlled by an interaction with Tuberous Sclerosis Complex2 (TSC2), a GTPase activating protein (GAP). Upon interaction, TSC2 stimulates Rheb GTP hydrolysis and diminishes the mammalian target of rapamycin (mTOR) pathway. The mTOR pathway is involved in proteins synthesis, cell cycle, and signaling. Mutation in TSC2 causes abnormal activation of Rheb …

The Structural And Functional Properties Of A Double Mutant Of Human Acidic Fibroblast Growth Factor (Hfgf-1), Arwa Mohammed Alghanmi

Graduate Theses and Dissertations

Human acidic Fibroblast Growth Factor 1 (FGF-1), a member of the FGF superfamily, is a potent mitogen and heparin-binding protein involved in a broad spectrum of biological processes, including angiogenesis, cell proliferation, and wound healing. Design of hFGF-1 with an increased thermal stability and an enhanced cell proliferation activity is highly desired for wound healing applications. Herein, we have designed the variant of FGF-1 by substituting two important amino residues in the heparin-binding pocket. The variant was overexpressed in Escherichia coli and was successfully purified to homogeneity using an affinity chromatographic procedure. Far-UV circular dichroism spectroscopic analysis showed that the …

Phylogenetic Diversity Of The Bacterial Communities In Craft Beer, Lindsey Rodhouse

Graduate Theses and Dissertations

The craft beer industry is increasing in popularity in the United States. The craft brewing process typically does not use a pasteurization step, therefore the boiling process is the primary critical control step. Any microorganisms introduced after boiling, or those that are not killed during boiling, are likely to participate in fermentation and persist in the final product. Previous culture-based studies have isolated bacteria and yeast from craft beers at specific time points, but little research has been done on the process as a whole. The objectives of this research are to (1) track bacteria development throughout the brewing process …

A Numerical Study Of The Interaction Between One Dimensional Carbyne Chain And Single Stranded Dna, Zeina Salman

Graduate Theses and Dissertations

resolution at the single nucleotide level when developing DNA sequencers. The purpose of this research was to numerically study the electrical properties associated with the interaction between 1D carbon chain, known as carbyne, and ssDNA. First, the electrical properties of the carbyne chain were calculated. Second, the electrical properties of the carbyne chain were calculated in the presence of different ssDNA bases. Analyzing the differences between the two cases led to determining the effects of these different bases on the electrical properties. The numerical simulation approach conducted in this research was based on the first-principle simulation. The first-principle simulation was …

Elongation Factor P Interactions With The Ribosome Are Independent Of Pausing, Rodney Tollerson Ii, Anne Witzky, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacterial elongation factor P (EF-P) plays a pivotal role in the translation of polyproline motifs. To stimulate peptide bond formation, EF-P must enter the ribosome via an empty E-site. Using fluorescence-based single-molecule tracking, Mohapatra et al. (S. Mohapatra, H. Choi, X. Ge, S. Sanyal, and J. C. Weisshaar, mBio 8:e00300-17, 2017, https://doi.org/10.1128/mBio.00300-17 ) monitored the cellular distribution of EF-P and quantified the frequency of association between EF-P and the ribosome under various conditions. Findings from the study showed that EF-P has a localization pattern that is strikingly similar to that of ribosomes. Intriguingly, EF-P was seen to bind ribosomes more …

Real-Time Sensing Of Single-Ligand Delivery With Nanoaperture-Integrated Microfluidic Devices, W. Elliott Martin, Ning Ge, Bernadeta R. Srijanto, Emily Furnish, C. Patrick Collier, Christine A. Trinkle, Christopher I. Richards

Chemistry Faculty Publications

The measurement of biological events on the surface of live cells at the single-molecule level is complicated by several factors including high protein densities that are incompatible with single-molecule imaging, cellular autofluorescence, and protein mobility on the cell surface. Here, we fabricated a device composed of an array of nanoscale apertures coupled with a microfluidic delivery system to quantify single-ligand interactions with proteins on the cell surface. We cultured live cells directly on the device and isolated individual epidermal growth factor receptors (EGFRs) in the apertures while delivering fluorescently labeled epidermal growth factor. We observed single ligands binding to EGFRs, …

Elucidating The Molecular Parameters And Mechanism Of Homology Searching During Meiosis In Neurospora Crassa, Nicholas Adam Rhoades

Theses and Dissertations

Integration of foreign DNA into a host genome is often detrimental to the host organism, as the DNA is often of viral or transposon origin. Many organisms have established DNA surveillance and genome integrity mechanisms to defend against these harmful DNA insertions. Neurospora crassa, a filamentous fungus belonging to the Ascomycota group, has several DNA defense mechanisms to combat foreign DNA integration to its genome. One such mechanism is Meiotic Silencing of Unpaired DNA (MSUD). During meiosis, this remarkable system can detect unpaired genes on homologous chromosomes during sexual reproduction and silence their expression throughout meiosis. In order for the …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

School of Computing: Faculty Publications

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Modeling Of Dynamic Allostery In Proteins Enabled By Machine Learning, Mohsen Botlani-Esfahani

USF Tampa Graduate Theses and Dissertations

Regulation of protein activity is essential for normal cell functionality. Many proteins are regulated allosterically, that is, with spatial gaps between stimulation and active sites. Biological stimuli that regulate proteins allosterically include, for example, ions and small molecules, post-translational modifications, and intensive state-variables like temperature and pH. These effectors can not only switch activities on-and-off, but also fine-tune activities. Understanding the underpinnings of allostery, that is, how signals are propagated between distant sites, and how transmitted signals manifest themselves into regulation of protein activity, has been one of the central foci of biology for over 50 years. Today, the importance …

Quaternary Interactions And Supercoiling Modulate The Cooperative Dna Binding Of Agt, Manana Melikishvili, Michael G. Fried

Center for Structural Biology Faculty Publications

Human O⁶-alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O⁶-alkylguanine and O⁴-alkylthymine adducts in single-stranded and duplex DNAs. The search for these lesions, through a vast excess of competing, unmodified genomic DNA, is a mechanistic challenge that may limit the repair rate in vivo. Here, we examine influences of DNA secondary structure and twist on protein–protein interactions in cooperative AGT complexes formed on lesion-free DNAs that model the unmodified parts of the genome. We used a new approach to resolve nearest neighbor (nn) and long-range (lr) components from the ensemble-average cooperativity, ω_ave. We found …

Rational Drug Design Directed At Blocking The Initial Signaling Events In Lipopolysaccharide-Induced Sepsis., Christopher A. Tipton

Theses

Systemic Inflammatory Response Syndrome (SIRS) is classified as an immune system response to an infectious state. If left untreated, SIRS leads to sepsis, septic shock, end-organ dysfunction, and death. As a patient progresses through these stages, associations of acute respiratory distress, disseminated intravascular coagulation, and acute renal failure persist, resulting in millions of deaths annually. Lipopolysaccharide (LPS), a bacterial endotoxin, is released into the blood stream, triggering SIRS. LPS is found in the outer cell-wall of Gram-negative bacteria and is responsible for initiation of a devastating cytokine storm. One of the regions of LPS, lipid A, is a polyacylated glucosamine …

Discovering Antibacterial And Anti-Resistance Agents Targeting Multi-Drug Resistant Eskape Pathogens, Renee Fleeman

USF Tampa Graduate Theses and Dissertations

Antibiotic resistance has been a developing problem for mankind in recent decades and multi-drug resistant bacteria are now encountered that are resistant to all treatment options available. In 2014, the World Health Organization announced that this problem is driving us towards a “post-antibiotic era” that will change the face of modern medicine as we know it. If lack of novel antibiotic development and FDA approval continues, by the year 2050, 10 million people will die each year to an antimicrobial resistant bacterial infection. With lack of pharmaceutical industry involvement in developing novel antibiotics, the responsibility now lies within the academic …

The Chondrocyte Channelome: A Novel Ion Channel Candidate In The Pathogenesis Of Pectus Deformities, Anthony J. Asmar

Biological Sciences Theses & Dissertations

Costal cartilage is a type of rod-like hyaline cartilage connecting the ribs to the sternum. The chest wall deformities pectus excavatum (PE) and pectus carinatum (PC) involve displacement of the sternum causing a depression or protrusion of the chest. There is little knowledge about costal cartilage and pectus deformities with much of its understanding based on assumptions from articular cartilage. Chondrocytes are subjected to a constantly changing environment with fluctuations in pH and osmolarity. Ion channels detect these changes and in turn regulate proliferation, differentiation, and extracellular matrix production. Using ion channel qPCR arrays, we produced expression profiles for normal, …

Il-18 Polymorphisms Contribute To Hepatitis B Virus-Related Cirrhosis And Hepatocellular Carcinoma Susceptibility In Chinese Population: A Case-Control Study., Zhi-Jun Dai, Xing-Han Liu, Meng Wang, Yan Guo, Wenge Zhu, Xiao Li, Shuai Lin, Tian Tian, Kang Liu, Yi Zheng, Peng Xu, Tianbo Jin, Xiaopeng Li

Biochemistry and Molecular Medicine Faculty Publications

IL-18 polymorphisms influence the transcriptional activity of the IL-18 gene and associated with various diseases. However, their relationships with hepatitis B virus-related liver diseases had not reached a consensus. So we conducted this case-control study with a view to clarifying the association. We included four groups: healthy controls, chronic hepatitis B virus (CHB) carriers, liver cirrhosis (LC) and hepatocellular carcinoma (HCC) groups with each group of 250 persons. Odd ratios (ORs) and 95% confidence intervals (95%CIs) with or without adjustment were calculated. Haplotype analysis was also performed. The results showed people carrying rs187238 CG genotype had a lower risk of …

Safety And Potential Efficacy Of Gemfibrozil As A Supportive Treatment For Children With Late Infantile Neuronal Ceroid Lipofuscinosis And Other Lipid Storage Disorders., Kyeongsoon Kim, Hynda K Kleinman, Hahn-Jun Lee, Kalipada Pahan

Biochemistry and Molecular Medicine Faculty Publications

Neuronal Ceroid Lipofuscinosis (NCL), also known as Batten disease, is a group of genetically distinct lysosomal disorders that mainly affect the central nervous system, resulting in progressive motor and cognitive decline primarily in children. Multiple distinct genes involved in the metabolism of lipids have been identified to date with various mutations in this family of diseases. There is no cure for these diseases but some new therapeutic approaches have been tested that offer more hope than the standard palliative care. Many of the therapeutic advances require invasive procedures but some progress in slowing the disease has been found and more …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Sivasai Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Selected Works Temporary Series

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Departmental Papers (Biology)

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

A Lipid Binding Structure And Functional Analysis Of Human Arv1, Jessie Lee Cunningham

Graduate School of Biomedical Sciences Theses and Dissertations

Metabolic Syndrome (MetS) is a combination of risk factors that can over time increase the probability of developing diseases, including cardiovascular disease, type 2 diabetes, non-alcoholic fatty liver disease (NAFLD), and non-alcoholic steatohepatitis (NASH). Acyl-coenzyme-A: cholesterol O-acyl transferase related enzyme required for viability-1, abbreviated as Arv1, is an evolutionarily conserved putative lipid binding protein. Several studies have implicated hArv1 as a critical regulator of lipid transport and trafficking.

Recent work using an Arv1 knock out (KO) mouse model have established a clear link between Arv1 function and the progression of MetS and NAFLD/NASH [unpublished data] [1]. Overall, studies show that …

Endocrine And Metabolic Effects Of Consuming Sugar-Sweetened Beverages: Preclinical And Clinical Studies", Peter Havel

Science Seminar Series

Peter J. Havel of the School of Veterinary Medicine at UC Davis will speak on his research on Endocrine and Metabolic Effects of Consuming Sugar-Sweetened Beverages: Preclinical and clinical studies at this Science Seminar Series lecture.