Biochemistry, Biophysics, and Structural Biology Commons^™

Salt Dependence Of Thermodynamic Stability Of A Cold-Active Dna Polymerase I Fragment, Xinji Zhu

LSU Doctoral Dissertations

P. ingrahamii is a halo-psychrophilic bacterium isolated from Arctic sea ice. We have cloned and purified the large fragment of the cold-active DNA polymerase I from P. ingrahamii, named Klenpin. The objective of this project is to directly compare the thermodynamic stability of Klenpin, and the salt dependence of that stability, with Klenow and Klentaq; two homologous polymerases from a mesophile (E. coli) and a thermophile (Thermus aquaticus).

We first examined the effects of salts on the thermal stability (Tm) of Klenpin and Klenow across the Hofmeister series. Significantly different trends were observed on …

Hysteretic Behavior In Voltage-Gated Channels, Carlos A. Villalba-Galea, Alvin T. Chiem

School of Pharmacy Faculty Articles

An ever-growing body of evidence has shown that voltage-gated ion channels are likely molecular systems that display hysteresis in their activity. This phenomenon manifests in the form of dynamic changes in both their voltage dependence of activity and their deactivation kinetics. The goal of this review is to provide a clear definition of hysteresis in terms of the behavior of voltage-gated channels. This review will discuss the basic behavior of voltage-gated channel activity and how they make these proteins into systems displaying hysteresis. It will also provide a perspective on putative mechanisms underlying hysteresis and explain its potential physiological relevance. …

Prevalence Of Brca1 And Brca2 Mutations Among Breast And Ovarian Cancer Patients In Northern Emirates, Zahra Ahmed Mohammed Saeed

Theses

Breast Cancer (BC) is the most common cancer and the second most cause of death among women. Mutations in BRCA1 and BRCA2 genes confer high susceptibility to both breast and ovarian cancer. However, data on the prevalence of the BRCA1/2 mutations among breast and ovarian cancer patients is limited. The genetic component of breast cancer in the UAE is largely unknown and no study has evaluated the BRCA mutations status in breast and ovarian cancer patients in the UAE population. This retrospective study aimed to establish mutation frequencies of the BRCA genes in breast and ovarian cancer patients from the …

Evaluation Of The Genetic And Structural Variations Of Camel Hemoglobin, Amanat Ali

Dissertations

The single-humped Arabian camel (Camelus dromedarius) thrives in the hot arid Arabian desert. Many unique adaptations permit it to accomplish this. Camel erythrocytes or red blood cells (RBCs) have a peculiar elliptical shape and are amenable to large variations in physical conditions resulting from dehydration and rehydration cycles. The oxygen transport protein hemoglobin is found abundantly in RBCs and is also believed to behave differently in camels. While several physiological and biochemical studies have been performed on camel hemoglobin, very little is known about genetic and structural adaptions in this protein. The camel genome harbors several unique variations …

Dissecting The Regulatory Network Of Sphingolipid Biosynthesis In Plants, Ariadna Gonzalez-Solis

Department of Biochemistry: Dissertations, Theses, and Student Research

Sphingolipids are a diverse group of lipids recognized as important components of cellular membranes and regulators of processes during development and in response to environmental stresses. Serine palmitoyltransferase (SPT) catalyzes the first step in sphingolipid biosynthesis and is a primary regulatory point for homeostasis. ORM proteins have been identified as negative regulators of SPT activity, however the mechanistic details of the regulation are only beginning to be understood. In this work, we show that ORM1 and ORM2 are essential for life cycle completion in Arabidopsis thaliana. Furthermore, the study of a structural ORM1 variant provided information about a transmembrane …

Presence Of The Hppd Inhibitor Sensitive 1 Gene And AlsS653n Mutation In Weedy Oryza Sativa Sensitive To Benzobicyclon, Chad Brabham, Jason K. Norsworthy, Fidel Gonzalez-Torralva

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha⁻¹, SC formulation) at 30 days after treatment (DAT). …

Gcn5: The Quintessential Histone Acetyltransferase, Vikki M. Weake

Department of Biochemistry Faculty Publications

In this Special Issue, we bring together many of the original researchers involved in the initial studies to identify and characterize Gcn5, together with leaders from the field who have contributed to our understanding of this quintessential histone acetyltransferase. First, Jim Brownell and David Allis describe the discovery of Gcn5 [8], followed by Brittany Albaugh and John Denu who highlight key structural and catalytic attributes of Gcn5 as the defining member of the Gcn5-related N-acetyltransferase (GNAT) protein superfamily [15]. Next, Michael Sack and colleagues describe a protein that is closely related to Gcn5, Gcn5L1, which lacks intrinsic histone acetylation activity …

In Vitro Invistigation Of The Heterodimerization Between Angiotensin Ii And Thrombin Receptors, Isra Mansur Al Zamel

Biology Theses

The renin angiotensin system (RAS) through its hormone angiotensin (AngII) and the protease thrombin are two major physiological regulators of vascular and renal functions. RAS is involved in the regulation of blood pressure and water-electrolytes hemostasis, while thrombin has a crucial role in platelets activation and thrombosis. The interplay between these two systems at the physiological and the pathophysiological levels has been documented in many studies. However, such an interplay at the pharmacological level between the AngII and thrombin receptors still has not been explored. Our study aimed to explore the interplay between the AngII type 1 receptor (AT1R) and …

Molecular And Physiological Assessment Of Salinity Stress Tolerance In Transgenic Arabidopsis Lines Expressing A Solanum Tuberosum Ribosome-Binding Protein, Onoud Rashed Saeed Ali Alyammahi

Biology Theses

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily associated with translation of mRNA leading to protein synthesis. Additionally, some of these proteins are known to play critical role in plants RNA metabolism during stress responses, growth, and development. In this study, transgenic Arabidopsis plants expressing a ribosomal protein S27 (hereafter D26) isolated from Solanum tuberosum was subjected to NaCl-induced salinity stress conditions, to evaluate their putative stress resistance. Transgenic plants were exposed to high salinity stress, induced by 200 mM NaCl and physiological and biochemical assays were performed. The D26 transgenic plants demonstrated improved plant height and …

Donor And Transplant Candidate Selection For Solid Organ Transplantation During The Covid-19 Pandemic, N Thao N Galvan, Nicolas F Moreno, Jay E Garza, Susan Bourgeois, Marion Hemmersbach-Miller, Bhamidipati Murthy, Katherine Timmins, Christine A O'Mahony, James Anton, Andrew Civitello, Puneet Garcha, Gabe Loor, Kenneth Liao, Alexis Shaffi, John Vierling, Rise Stribling, Abbas Rana, John A Goss

Faculty, Staff and Students Publications

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus responsible for a worldwide pandemic has forced drastic changes in medical practice in an alarmingly short period of time. Caregivers must modify their strategies as well as optimize the utilization of resources to ensure public and patient safety. For organ transplantation, in particular, the loss of lifesaving organs for transplantation could lead to increased waitlist mortality. The priority is to select uninfected donors to transplant uninfected recipients while maintaining safety for health care systems in the backdrop of a virulent pandemic. We do not yet have a standard approach to evaluating …

Improving Therapeutic Potential Of Non-Viral Minimized Dna Vectors, Lirio M Arévalo-Soliz, Cinnamon L Hardee, Jonathan M Fogg, Nathan R Corman, Cameron Noorbakhsh, Lynn Zechiedrich

Faculty, Staff and Students Publications

The tragic deaths of three patients in a recent AAV-based X-linked myotubular myopathy clinical trial highlight once again the pressing need for safe and reliable gene delivery vectors. Non-viral minimized DNA vectors offer one possible way to meet this need. Recent pre-clinical results with minimized DNA vectors have yielded promising outcomes in cancer therapy, stem cell therapy, stem cell reprograming, and other uses. Broad clinical use of these vectors, however, remains to be realized. Further advances in vector design and production are ongoing. An intriguing and promising potential development results from manipulation of the specific shape of non-viral minimized DNA …

Biomechanical And Biophysical Properties Of Breast Cancer Cells Under Varying Glycemic Regimens, Diganta Dutta, Xavier-Lewis Palmer, Jose Ortega-Rodas, Vasundhara Balraj, Indrani Ghosh Dastider, Surabhi Chandra

Electrical & Computer Engineering Faculty Publications

Diabetes accelerates cancer cell proliferation and metastasis, particularly for cancers of the pancreas, liver, breast, colon, and skin. While pathways linking the 2 disease conditions have been explored extensively, there is a lack of information on whether there could be cytoarchitectural changes induced by glucose which predispose cancer cells to aggressive phenotypes. It was thus hypothesized that exposure to diabetes/high glucose alters the biomechanical and biophysical properties of cancer cells more than the normal cells, which aids in advancing the cancer. For this study, atomic force microscopy indentation was used through microscale probing of multiple human breast cancer cells (MCF-7, …

Chronic Ulcers And Malnutrition In An African Patient\, Timothy G Singer, Monica A Bray, Audrey Chan, Saki Ikeda, Brittany Walters, Maren Y Fuller, Carla Falco

Faculty, Staff and Students Publications

An 11-year-old female with a congenitally malformed left hand, sickle-cell trait, asthma, and history of appendicitis was transferred from Zambia for evaluation and treatment of widespread suppurative and ulcerative skin lesions that typically appeared following trauma to her skin. The ulcers first presented 3 years earlier but had markedly worsened in the 9 months prior to transfer, spreading circumferentially on her extremities and abdomen at the site of an appendectomy. They were painful and did not resolve with multiple courses of intravenous (IV) antibiotics and close management by a Pediatric Infectious Disease specialist working for a non-governmental organization (NGO) in …

Identification Of Inherited And De Novo Exomic Variations In An Emirati Family With Neurodevelopmental Disorders, Asmaa Samir Muhammed Abdelaziz Refaey

Biology Theses

Neurodevelopmental disorders (NDDs) are a heterogenous group of disorders that affect children at any point of development and lead to mental and motor function deficits. Often, the underlying cause could be genetic and inherited. This study investigated possible genetic variations that could have led to these neurological abnormalities and other genetic disorders in an Emirati family. Whole exome sequencing (WES) was used to sequence the protein-coding regions of the genome to identify potential de novo and inherited variants that are associated with disorders in this family.

WES of DNA from the parents and ten children were performed. Several variants were …

Use Of Florpyrauxifen-Benzyl In Non-Flooded Rice Production Systems, Hannah Wright, Jason K. Norsworthy, Trenton L. Roberts, Robert C. Scott, Jarrod T. Hardke, Edward E. Gbur

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The lack of a flood on rice (Oryza sativa) levees and in furrow-irrigated rice creates a favorable environment for terrestrial weeds like Palmer amaranth (Amaranthus palmeri S. Wats) to emerge and quickly overtake the crop for a longer portion of the year than in flooded rice culture. Florpyrauxifen-benzyl is a new auxin herbicide labeled for use in rice that has activity on both grasses and broadleaf weeds, as well as certain sedges. Field experiments were conducted to determine the efficacy of florpyrauxifen-benzyl in a non-flooded environment. Experiments were conducted in 2017 and 2018 at the Lon Mann …

Polydopamine Antioxidant Hydrogels For Wound Healing Applications, Naphtali A. O'Connor, Abdulhaq Syed, Madeline Wong, Josiah Hicks, Greisly Nunez, Andrei Jitianu, Zach Siler, Marnie Peterson

Publications and Research

Antioxidants are known to improve the wound healing process and are researched as a therapeutic strategy to treat chronic wounds. Dopamine is a known neurotransmitter with antioxidant properties that can be polymerized to form polydopamine (PDA). Herein, polydopamine is demonstrated as an antioxidant biomaterial. In prior work, we developed methodology to prepare hydrogels by crosslinking polysaccharides with polyamines via epichlorohydrin and NaOH. Using this previously developed methodology, dextran hydrogels crosslinked with polydopamine were prepared. Darkening of the gels indicated the increasing incorporation of polydopamine within the hydrogels. In addition to basic pH, polydopamine can be formed by reaction with polyethylene …

In Vitro Antioxidant Activities Of Ethanol, Ethyl Acetate And N-Hexane Extracts Of Mangifera Indica Leaves, Yunusa O. Ibrahim, Musa B. Busari, Ruqayyah S. Yusuf, Rabiat U. Hamzah

Tanzania Journal of Science

Mangifera indica leaves have been in use in folk medicine since ancient time, for the treatment and/or management of numerous health complications. In this study, total phenols and flavonoids contents, as well as in vitro antioxidant activities of ethanol, ethyl acetate and n-hexane extracts of M. indica leaves were determined and compared. The in vitro antioxidant activities were determined using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power, and inhibition of lipid peroxidation assays, respectively. The total phenols were found to be present in the descending order of; ethanol extract > ethyl acetate extract > n-hexane extract, while flavonoids were observed …

Effect Of Ceratonia Siliqua And Cucurbita Pepo Seeds Extracts On Spermatogenesis In Male Mice, Nour Elakhdar, Roweida Bawab, Jamilah Borjac

BAU Journal - Health and Wellbeing

Worldwide, a percentage close to 50% of infertility cases is due to male-related problems including spermatogenesis defects, the process that determines sperm cells’ number and thus male fertility. Spermatogenesis is controlled by different hormones including the luteinizing hormone (LH), the follicle stimulation hormone (FSH), and testosterone. LH stimulates the Leydig cells to synthesize testosterone. FSH acts synergistically with testosterone. There is no current efficient treatment for spermatogenesis defects and people are reverting to natural remedies among which are the pumpkin and carob seeds. This study aims to evaluate the effects of pumpkin and carob seeds’ aqueous extracts on spermatogenesis and …

Antibacterial Action Of Graphene Oxide Towards Bacteria And Its Toxicological Effects On Human Epidermal Keratinocytes, Thiruchelvi Pulingam

Student Works (2020-2029)

The antibacterial nature of graphene oxide (GO) has stimulated wide interest in the medical field. Although the antibacterial activity of GO towards bacteria has been well studied, a deeper understanding of the mechanism of action of GO is still lacking. The objectives of the study were to characterize the physicochemical properties of GO, to determine the antibacterial and antibiofilm activity and the mechanistic action of GO against Gram-positive Staphylococcus aureus and Enterococcus faecalis and Gram-negative Escherichia coli and Pseudomonas aeruginosa, to determine the synergistic behaviour of GO with selected antibiotics against bacterial cells in suspension and biofilm and to determine …

Population Genetics Of Rhizophora Apiculata In Peninsular Malaysia Using Microsatellite Markers, Amelia Azman

Student Works (2020-2029)

Rampant illegal logging, overharvesting and deforestation coupled with climate change, pose significant threats to the natural stands of Rhizophora apiculata, or locally known as Bakau Minyak; one of the most economically and ecologically important species of mangroves in Peninsular Malaysia. Despite being a dominant mangrove species, the reduction in the number of R. apiculata in its habitat has resulted in concerns over the long-term survival potential of the species. In Malaysia, genetic information to develop effective guidelines for the conservation and management of mangrove species has been lacking, and hence, further research should be conducted to fill this gap. The …

New Mechanisms That Regulate Dna Double-Strand Break-Induced Gene Silencing And Genome Integrity, Dante Francis Deascanis

USF Tampa Graduate Theses and Dissertations

Proliferating cells are constantly threatened by genotoxic stressors that can potentially lead to genomic instability. Breaks in the DNA, namely double-strand breaks, are detrimental sources of damage that must be repaired to maintain genomic integrity and prevent potential tumorigenesis. Here we discuss a gene silencing mechanism flanking damaged chromatin. Gene silencing and transcriptional repression at damaged DNA are necessary to prevent potential genomic aberrations from occurring through conflicts with the DNA repair machinery. BMI1, a core polycomb protein in the polycomb repressive complex 1 (PRC1) has been known to play a role in gene silencing at damaged chromatin. However, the …

Curie Temperature Engineering In A Novel 2d Analog Of Iron Ore (Hematene) Via Strain, Renu Singla, Timothy A. Hackett, Sarvesh Kumar, Jyotsna Sharma, Manish K. Kashyap

Department of Biochemistry: Faculty Publications

As a newly exfoliated magnetic 2D material from hematite, hematene is the most far-reaching ultrathin magnetic indirect bandgap semiconductor. We have carried out a detailed structural analysis of hematene via prefacing strain by means of first-principles calculations based on density functional theory (DFT). Hematene in the pristine form emerges out to be a magnetic semiconductor with a bandgap of 1.0/2.0 eV for the majority/minority spin channel. The dependence of magnetic anisotropy energy (MAE), T_C, and the bandgap on compressive and tensile strains has been scanned exclusively. It is examined that T_C depends firmly on the compressive strain …

From Regulation Of Secondary Metabolites To Increased Virulence Under Sublethal Dosage Of Antibiotics: An Unprecedented Role Of Global Regulator, Mftr, In Burkholderia Thailandensis, Sudarshan Singh Thapa

LSU Doctoral Dissertations

The rise of multi-drug resistant bacteria combined with a decreasing pool of effective antibiotics has placed an increasing need for the development of novel antibiotics. Bacterial natural products or secondary metabolites have been the greatest source for development of novel antibiotics. The genus Burkholderia has recently emerged as a source of promising compounds with antibacterial, antifungal, and anti-cancer activities. Bacterial secondary metabolites provide added advantage to bacteria under stressful environments such as during host infection, evading predators or nutrient deficient conditions. However, genes involved in synthesis of these novel compounds remain silent under normal laboratory growth, creating a hurdle in …

Axonal Blockage With Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Numerous neurological dysfunctions are characterized by undesirable nerve activity. By providing reversible nerve blockage, electric stimulation with an implanted electrode holds promise in the treatment of these conditions. However, there are several limitations to its application, including poor bio-compatibility and decreased efficacy during chronic implantation. A magnetic coil of miniature size can mitigate some of these problems, by coating it with biocompatible material for chronic implantation. However, it is unknown if miniature coils could be effective in axonal blockage and, if so, what the underlying mechanisms are. Here we demonstrate that a submillimeter magnetic coil can reversibly block action potentials …

The Impacts Of Membrane Modulators On Membrane Material Properties At Microscopic And Nanoscopic Levels, Chinta Mani Aryal

USF Tampa Graduate Theses and Dissertations

Peptide-membrane interactions depict the cell’s response to an external molecule. This is a critical event to evaluate the peptide’s function and effect as well as the response of target molecule. The understanding of the mechanism of action of peptide in a molecular level is important, for example, this may be useful in developing the therapeutic strategy. Peptides are the functional macromolecules which are actively researched among bio-related fields. Model membrane systems that mimic the real cell have been useful platform to test the perturbation upon peptide addition. In this thesis, we investigate the membrane modulation behavior of three peptides (modulators) …

Fine-Tuning Of Alanyl-Trna Synthetase Quality Control Alleviates Global Dysregulation Of The Proteome, Paul Kelly, Arundhati Kavoor, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have …

Antioxidant Carbon Nanoparticles Inhibit Fibroblast-Like Synoviocyte Invasiveness And Reduce Disease Severity In A Rat Model Of Rheumatoid Arthritis, Mark R Tanner, Redwan Huq, William K A Sikkema, Lizanne G Nilewski, Nejla Yosef, Cody Schmitt, Carlos P Flores-Suarez, Arielle Raugh, Teresina Laragione, Pércio S Gulko, James M Tour, Christine Beeton

Faculty, Staff and Students Publications

Reactive oxygen species have been involved in the pathogenesis of rheumatoid arthritis (RA). Our goal was to determine the effects of selectively scavenging superoxide (O2•−) and hydroxyl radicals with antioxidant nanoparticles, called poly(ethylene glycol)-functionalized hydrophilic carbon clusters (PEG-HCCs), on the pathogenic functions of fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA) and on the progression of an animal model of RA. We used human FLS from patients with RA to determine PEG-HCC internalization and effects on FLS cytotoxicity, invasiveness, proliferation, and production of proteases. We used the pristane-induced arthritis (PIA) rat model of RA to assess the benefits of …

Role Of Ceramide-1 Phosphate In Regulation Of Sphingolipid And Eicosanoid Metabolism In Lung Epithelial Cells, Brittany A. Dudley

USF Tampa Graduate Theses and Dissertations

Ceramide 1-Phosphate (C1P) is a sphingolipid metabolite which plays a large role in inflammation, cell survival and proliferation¹. C1P is known to have both pro- and anti-apoptotic roles in lung cancer cells, governed by ceramide kinase (CERK), upstream of precursor ceramide (Cer)². Previous work reveals C1P serves as the liaison between sphingolipid and eicosanoid synthesis, by decreasing the dissociation rate of group IVA cytosolic PLA₂ (cPLA_2α) from the Golgi membrane, C1P directly activates this phospholipase for downstream eicosanoid synthesis and subsequent inflammatory response³. CERK has been discovered to modulate eicosanoid synthesis, …

Graphene-Based Electrochemical Aptasensor For The Detection Of Salmonella Typhimurium, Shalini Muniandy

Student Works (2020-2029)

Recent foodborne outbreaks in multiple locations necessitate the continuous development of highly sensitive and specific biosensors that offer rapid and sensitive detection of foodborne pathogens. The emergence of electrochemical aptasensor which is a compact analytical device with a combination of an aptamer as the biorecognition element integrated on the transducer surface created a breakthrough in the detection of foodborne bacterial pathogens. Graphene has emerged as a promising nanomaterial for reliable detection of pathogenic bacteria due to its exceptional properties such as high electrical conductivity, large surface to volume ratio, high mechanical strength and its unique interactions with DNA bases of …

Impact Of Uv-Induced Ozone And Low-Energy Ar+-Ion Cleaning On The Chemical Structure Of Cu(In,Ga)(S,Se)2 Absorber Surfaces, Victor R. Van Maris, Dirk Hauschild, Thomas P. Niesen, Patrick Eraerds, Thomas Dalibor, Jörg Palm, Monika Blum, Wanli Yang, Clemens Heske, Lothar Weinhardt

Chemistry and Biochemistry Faculty Research

Dry buffer layer deposition techniques for chalcopyrite (CIGSSe)-based thin-film solar cells lack the surface-cleaning characteristics of the commonly used CdS or Zn(O,S) wet-chemical bath deposition. A UV-induced ozone and/or a low-energy Ar+-ion treatment could provide dry CIGSSe surface cleaning steps. To study the impact of these treatments, the chemical surface structure of a CIGSSe absorber is investigated. For this purpose, a set of surface-sensitive spectroscopic methods, i.e., laboratory-based x-ray photoelectron spectroscopy and x-ray-excited Auger electron spectroscopy, is combined with synchrotron-based soft x-ray emission spectroscopy. After treatment times as short as 15 s, the UV-induced ozone treatment decreases the amount of …