Molecular Biology Commons^™

Phase Diagram Of Water Confined By Graphene, Zhenghan Gao, Nicolas Giovambattista, Ozgur Sahin

Publications and Research

The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in …

Investigation Of Alcohol-Induced Changes In Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics, Crystina Leah Kriss

USF Tampa Graduate Theses and Dissertations

Alcohol liver disease (ALD) is a major health concern throughout the world. Currently, in the United States, 17 million people suffer from alcoholism, of which 1.4 million people are receiving treatment [1, 2]. The link between ethanol metabolism, reactive oxygen species (ROS) and liver injury in ALD has been well characterized over the last couple decades [3-10]. Ethanol metabolism relies on the availability of the cofactor NAD+ for the oxidation of ethanol into acetate, consequently causing alterations in redox potential. Redox dysfunction within the mitochondria can affect multiple pathways important in maintaining cellular homeostasis. Chapter 1 provides an introduction to …

The Role Of Phosphohistidine Phosphatase 1 In Ethanol-Induced Liver Injury, Daniel Richard Martin

USF Tampa Graduate Theses and Dissertations

Chronic liver diseases, which includes alcoholic liver disease (ALD), are consistently among the top 15 leading causes of death in the United States. ALD is characterized by progression from a normal liver to fatty liver disease (hepatic steatosis), which can lead to cirrhosis, alcoholic hepatitis, and liver failure. We have identified a novel role of phosphohistidine signaling, mediated through phosphohistidine phosphatase 1 (PHPT1), in the onset of hepatic steatosis. We have identified PHPT1 as a target of selective oxidation following acute ethanol exposure as well as being downregulated following chronic ethanol exposure. We mapped the oxidative modification site and developed …

Whole Tart Cherry Improves Disease Activity Index In Rat Model Of Dextran Sulfate Solution – Induced Ulcerative Colitis By Downregulating The Janus 1 And Janus 3 Kinases And Tnf - Alpha, Johana Alexandra Coronel

LSU Master's Theses

Ulcerative colitis (UC) is a disabling inflammatory bowel disease. UC is characterized by chronic, relapsing inflammation of the colon and rectum. Current treatments such as monoclonal antibodies against TNF-α, IL-6, IL-12/p40, adhesion molecules, Janus kinases (JAK) inhibitors have side effects or lose their effects over time. Alternative approaches with fewer side effects for patients are needed. Montmorency tart cherries (Prunus cerasus) are a good source of anti-inflammatory flavonoids. We hypothesized that regular consumption whole tart cherry (TC) standardized to its major anthocyanin content, namely cyanidin-3-glucosyl-rutinoside, would be effective in reducing inflammation in UC. The aim of this research was to …

Cloning, Purification, And Preliminary Dna-Binding And Unfolding Results For The Dna Polymerase I From The Psychrophile Psychromonas Ingrahamii, John Tod Baker

LSU Master's Theses

Psychromonas ingrahamii is a psychrophilic bacterium that lives in Arctic polar sea ice and grows at a temperature range of -12 to 10º C. This bacterium resides within veins inside the ice where the salinity is high, resulting in a freezing point depression and liquid water. The large fragment of DNA polymerase I from Psychromonas ingrahamii, called Klenpin, has been cloned, expressed, and purified in our laboratory. Although enzyme kinetic studies have been performed on a few psychrophilic enzymes, the thermodynamics of ligand binding and of protein stability have not been well studied for this class of extremophilic proteins. …

Elastin-Like Polypeptide Fusion Tag As A Protein-Dependent Solubility Enhancer Of Cysteine-Knot Growth Factors, Tamina L. Johnson

USF Tampa Graduate Theses and Dissertations

Elastin-like peptide (ELP) fusions promote therapeutic delivery and efficacy. Recombinant proteins, like neurotrophins, lack bioavailability, have short in vivo half-lives, and require high manufacturing costs. Fusing recombinant proteins with genetically encodable ELPs will increase bioavailability, enhance in vivo solubilization, as well as provide a cost-effective method for purification without the need for chromatography. During expression of neurotrophin-ELP (N-ELP) fusions, dense water-insoluble aggregates known as inclusion bodies (IBs) are formed. Inclusion bodies are partially and misfolded proteins that usually require denaturants like Urea for solubilization. Strong denaturants arrest ELPs stimuli-responsive property and increase unwanted aggregation, making purification difficult, yet possible. The …

Ef-P Post-Translational Modification Has Variable Impact On Polyproline Translation In Bacillus Subtilis, Anne Witzky, Katherine R. Hummels, Rodney Tollerson Ii, Andrei Rajkovic, Lisa A. Jones, Daniel B. Kearns, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is a ubiquitous translation factor that facilitates translation of polyproline motifs. In order to perform this function, EF-P generally requires posttranslational modification (PTM) on a conserved residue. Although the position of the modification is highly conserved, the structure can vary widely between organisms. In Bacillus subtilis, EF-P is modified at Lys³² with a 5-aminopentanol moiety. Here, we use a forward genetic screen to identify genes involved in 5-aminopentanolylation. Tandem mass spectrometry analysis of the PTM mutant strains indicated that ynbB, gsaB, and ymfI are required for modification and that yaaO, yfkA, and …

Breaking Conventions: Ohrr, A Transcriptional Regulator From Burkholderia Thailandensis, Anuja Rajiv Pande

LSU Doctoral Dissertations

Organic peroxides (OPs) are highly toxic oxidants. They directly react with cellular macromolecules rendering them inactive. Soil bacteria live in an oxidative environment rich in OPs from plant exudates and other xenobiotic compounds. Bacteria also face a burst of organic peroxides (lipid peroxides) in the macrophages during host invasion. Prokaryotes sense oxidative changes in environment and modulate their gene expression as an adaptive response for survival. MarR (multiple antibiotic resistance regulators) proteins enable bacteria to respond to such stress. Resistance to organic oxidants has been hypothesized to help bacteria survive in presence of disinfectants. This increases nosocomial infection rate.

Bacteria …

Monitoring And Quantifying Tetracycline Resistance Genes In A Swine Waste Anaerobic Digester Over A 100-Day Period, Melanie Couch

Masters Theses & Specialist Projects

Unregulated use of growth promoting antibiotics like Tetracyclines in agricultural feeds is becoming an increasing problem in antibiotic resistance. Undigested antibiotics leads to significant concentrations in livestock waste. These concentrations provide continuous selection pressure for the development of antibiotic resistance genes in the environment. Antibiotic resistance related deaths are projected to surpass cancer related deaths by 2050 making antibiotic resistance a pressing public health issue. The purpose of this study is to determine the abundance and persistence of tetracycline (tet) resistance genes in swine waste over a period of 100 days in an anaerobic digester system. Tet(A), tet(B), tet(G), tet(M), …

Molecular Cloning And Functional Analysis Of Salt Overly Sensitive (Sos) Pathway Genes From Local Plants Of The United Arab Emirates, Mariam Obaid Saeed Abdalla Alzaabi

Biology Theses

Salinity is one of the major abiotic stresses that lead to extreme reduction in crop productivity worldwide. Increased soil and water salinity is a major issue in UAE’s agriculture. Some plants however have adapted to grow in high saline conditions, i.e. halophytes. Unfortunately, most crops are glycophytes and cannot tolerate high salinity. During salinity stress, expression of numerous genes is altered to protect the plants. Understanding the differences in gene structure between halophytes and glycophytes could provide insights into developing transgenic crops that can thrive in salinity conditions. The Salt Overly Sensitive (SOS) pathway is a key mechanistic cascade controlling …

Transcriptomic Analysis On Hepatocellular Carcinoma Model In Response To Safranal Treatment, Badriya Mahmood Ahmed Baig

Biology Theses

Unsolved riddle of cancer remains a major global health concern particularly in hepatocellular carcinoma (HCC) which is among the leading causes of cancer related death worldwide. Saffron (Crocus sativus L.) and its bioactive phytochemicals possess promising anti-cancer activities. One of these phytochemicals, safranal, has demonstrated potent anti-cancer activities against different types of cancers. Yet, its association with liver cancer remains under documented. This study investigated HCC response to safranal’s treatment via transcriptomic approach. Safranal was found to be involved in mitochondrial dysfunction, induced oxidative stress and increased reactive oxygen species (ROS) production leading to cell death. Interestingly, safranal has …

Advancing Professional Development Strategies For Chemistry And Biochemistry Undergraduates, Christian A. Brown

Senior Theses

In the Department of Chemistry and Biochemistry at the University of South Carolina (the Department), most curriculum-driven professional development is reserved for third- and fourth-year students. Classroom learning occurs at all levels, but the context comes late. Early exposure to career options and hands-on training is imperative for undergraduates to obtain maximum experiential learning. The purpose of this project is to advance the current professional development strategies of the Department, specifically targeting second- and third-year students. The study surveyed students' current involvement in professional development activities. The data on extracurricular experience and post-graduation interest was used to design a workshop …

Enhancement Of Fast Scan Cyclic Voltammetry Detection Of Dopamine With Tryptophan, Sarah E. Thompson

Masters Theses

Dysregulation of dopamine release is a pathological effect of common neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease. Fast scan cyclic voltammetry (FSCV) has been used as an analytical tool to investigate the role of dopamine in these diseases, and in relation to drug addiction and reward behavior. Methods to improve the sensitivity of FSCV have involved modifying the surface of the carbon electrodes used for dopamine detection, altering the potential waveform, and changing the structure of the carbon sensor. Here, the amino acid tryptophan was investigated as a potential surface modification for increased dopamine detection. This study serves as …

Anti-Colon Cancer Effect Of Origanum Majorana Essential Oil, Asma Nasser Rashed Alrashedi

Biology Theses

Plants have been shown to be an excellent source of new drugs, including anticancer agents. Origanum majorana commonly known as marjoram is a plant that is known to possess different therapeutic values including antioxidant andantimicrobial activities.

Our research team has previously tested the ethanolic extract of O. majorana on triple negative breast cancer and published the findings. The ethanolic extract promoted mitotic arrest at G2/M phase, induced apoptosis as well as inhibition of migration and metastasis. The promising potential of the ethanolic extract encouraged us to test the effects of O. majorana essential oil on human colon cancer cell lines. …

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin …

Increased Liver Tumor Formation In Neutral Sphingomyelinase-2-Deficient Mice, Liansheng Zhong, Ji Na Kong, Michael B. Dinkins, Silvia Leanhart, Zhihui Zhu, Stefka D. Spassieva, Haiyan Qin, Hsuan-Pei Lin, Ahmed Elsherbini, Rebecca Wang, Xue Jiang, Mariana N. Nikolova‑Karakashian, Guanghu Wang, Erhard Bieberich

Physiology Faculty Publications

Sphingolipids are key signaling lipids in cancer. Genome-wide studies have identified neutral SMase-2 (nSMase2), an enzyme generating ceramide from SM, as a potential repressor for hepatocellular carcinoma. However, little is known about the sphingolipids regulated by nSMase2 and their roles in liver tumor development. We discovered growth of spontaneous liver tumors in 27.3% (9 of 33) of aged male nSMase2-deficient (fro/fro) mice. Lipidomics analysis showed a marked increase of SM in the tumor. Unexpectedly, tumor tissues presented with more than a 7-fold increase of C₁₆-ceramide, concurrent with upregulation of ceramide synthase 5. The fro/fro liver tumor, …

Insights Into The Cellular Trafficking Of Perilipin 5, Hannah M. Bailey

Undergraduate Honors Thesis Projects

Perilipins are a family of five proteins found on the surface of lipid storage droplets in nearly all tissues. These proteins act as cofactors for lipases and scaffolding for other proteins involved in lipid metabolism. In addition to the lipid droplet surface, members of the perilipin family have been found in the cytosol, endoplasmic reticulum, plasma membrane and mitochondria. The localization of these proteins is in part due to the phosphorylation state of the perilipin in question. Many other biological processes occur through kinase pathways, which have numerous cellular outcomes. Recently, perilipin 5 has been shown to localize to the …

Profiling Prostate Cancer Therapeutic Resistance, Cameron A. Wade, Natasha Kyprianou

Urology Faculty Publications

The major challenge in the treatment of patients with advanced lethal prostate cancer is therapeutic resistance to androgen-deprivation therapy (ADT) and chemotherapy. Overriding this resistance requires understanding of the driving mechanisms of the tumor microenvironment, not just the androgen receptor (AR)-signaling cascade, that facilitate therapeutic resistance in order to identify new drug targets. The tumor microenvironment enables key signaling pathways promoting cancer cell survival and invasion via resistance to anoikis. In particular, the process of epithelial-mesenchymal-transition (EMT), directed by transforming growth factor-β (TGF-β), confers stem cell properties and acquisition of a migratory and invasive phenotype via resistance to anoikis. Our …

Role Of Pu.1 And C/Ebpα In Remodelling The Interleukin (Il)-1Β Enhancer-Promoter Interaction, Woohyun Cho, Soon-Duck Ha, Sung Ouk Kim

Western Research Forum

Background: IL-1b is a potent inflammatory cytokine promptly expressed in activated myeloid immune cells. Among various transcription factors, PU.1 and CCAAT/enhancer-binding protein alpha (C/EBPa) play a key role in the lineage commitment of myeloid cells. To date, however, the exact mechanisms by which these lineage-determining transcription factors employ to regulate the expression of myeloid-specific genes remains elusive; thus, this study explores the role of PU.1 and C/EBPa in remodelling the chromatin conformation that allows ample production of IL-1b.

Methods: To examine the mechanism of these lineage-determining transcription factors, production of IL-1b and enhancer-promoter interactions were analyzed in non-myeloid B16-BL6 cells …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot …