Biochemistry, Biophysics, and Structural Biology Commons^™

Comprehensive Survey Of The Litter Bacterial Communities In Commercial Turkey Farms, Bishnu Adhikari, Guillermo Tellez-Isaias, Tieshan Jiang, Brian Wooming, Young Min Kwon

Poultry Science Faculty Publications and Presentations

The importance of microbiota in the health and diseases of farm animals has been well-documented for diverse animal species. However, studies on microbiotas in turkey and turkey farms are relatively limited as compared to other farm animal species. In this study, we performed a comprehensive survey of the litter microbiotas in 5 commercial turkey farms in the Northwest Arkansas (H, M, V, K, and R farms) including one farm with positive incidence of cellulitis (R farm). Altogether 246 boot swabs were used for 16S rRNA gene profiling of bacterial communities. At phylum level, 11 major bacterial phyla (≥0.01%) were recovered. …

Stem Cell Technology For Age Related Macular Degeneration Intervention, Laura Valdez

Theses and Dissertations

The main focus of this thesis is to study RPE cell derived from IMR90 induced pluripotent stem cells in various physiological conditions mimicking RPE transplantation rejection. Retinal pigmented epithelium (RPE) cells are located between the choroid and photoreceptors in the eye and they are essential to provide nutrients from blood to rods and cones, as well retinoids of the visual cycle. Vision loss and various ocular diseases are attributable to the degeneration or dysfunction of the RPE cells, leading to blindness. One of the major ocular problem from RPE dysfunction is macular degeneration. Age-related macular degeneration (AMD) can be frequently …

Chloramination Of Iopamidol- And Bromide-Spiked Waters Containing Natural Organic Matter, Nana Osei B Ackerson, Hannah K. Liberatore, Susan D. Richardson, Micheal J. Plewa, Thomas A. Ternes, Stephen E. Duirk

Faculty Publications

Iopamidol (an iodinated X-ray contrast medium) and bromide are precursors in the formation of halogenated disinfection byproducts (DBPs). The interactions of these precursors are vital to elucidate the formation of halogenated DBPs during chloramination. This work investigated the formation of total organic halogen and select individual DBPs in two laboratory-chloraminated source waters containing iopamidol and bromide. Experiments were carried out in batch reactors containing Barberton source water (BSW) and Cleveland BSW (CSW), spiked with iopamidol (5 mu M), bromide (15 mu M), and 100 mu M monochloramine. Total organic iodine concentrations were approximately equal regardless of source water since they …

Editorial: Structure And Function Of Chloroplasts - Volume Ii, Yan Lu, Lu Ning Liu, Rebecca L. Roston, Jurgen Soll, Hongbo Gao

Department of Biochemistry: Faculty Publications

No abstract provided.

Interactions Of The Nlrp3 Inflammasome Complex, Nyasha Makoni

Dissertations

The innate immune system is the first line of defense in response to invasion by pathogens. One of the major pathways in the innate immune system involves a three-protein complex known as the NLRP3 inflammasome. This complex comprises of NLRP3, ASC, and procaspase-1. In response to stimuli, the inflammasome assembles to activate caspase-1 which subsequently facilitates production of interleukin-1β (IL-1β), an inflammatory cytokine. The NLRP3 inflammasome has been implicated in a variety of inflammatory disorders including Alzheimer’s disease (AD). Amyloid beta (Aβ) is the protein that causes AD and Aβ deposits in the brain activate microglia resulting in chronic inflammation. …

Dna Aptamer-Drug Targeting Chemotherapy: Investigation Of Cell Cycle Inhibition Via S15 Aptamer – Norcantharidin Complex, Shannon Fehr

Senior Honors Theses

Lung Cancer is the leading cause of cancer related death in both men and women in the United States (Bray et al., 2018). Cancer treatments are often non-specific and kill many dividing cells within a patient causing unwanted side effects. Norcantharidin (NCTD) is a synthetic FDA approved treatment for cancers including non-small cell lung cancers (NSCLC). NCTD suppresses cell proliferation by inhibiting cells from exiting the G2 phase of the cell cycle. Aptamers are short single-stranded DNA or RNA molecules with ligand directed self-annealing capabilities allowing selective binding to specific targets. This paper will discuss the hypothesized effects of using …

An Investigation Into The Adverse Effects Of Oxidative Stress From Exposure To Bisphenol A And Its Analogues, Rachel Nas

Senior Honors Theses

Oxidative stress is a physiological event caused by an overaccumulation of reactive oxygen species (ROS) within the body. While ROS are a natural by-product of oxygen metabolism, too many can lead to cell and tissue damage and contribute to many etiologies. Bisphenol A (BPA), a component of many plastic products, has been shown to induce oxidative stress. While the industrial usage of BPA usage has lessened, the safety of its replacements is unknown. This paper will primarily discuss ROS and mechanisms of oxidative stress, the usage of BPA and its analogues, etiologies associated with oxidative stress resulting from exposure to …

Biophysical Analysis Of Pseudomonas-Phage Pap3 Small Terminase Suggests A Mechanism For Sequence-Specific Dna-Binding By Lateral Interdigitation., Marzia Niazi, Tyler J. Florio, Ruoyu Yang, Ravi K. Lokareddy, Nicholas A. Swanson, Richard E. Gillilan, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but …

New Methods For Deep Learning Based Real-Valued Inter-Residue Distance Prediction, Jacob Barger

Theses

Background: Much of the recent success in protein structure prediction has been a result of accurate protein contact prediction--a binary classification problem. Dozens of methods, built from various types of machine learning and deep learning algorithms, have been published over the last two decades for predicting contacts. Recently, many groups, including Google DeepMind, have demonstrated that reformulating the problem as a multi-class classification problem is a more promising direction to pursue. As an alternative approach, we recently proposed real-valued distance predictions, formulating the problem as a regression problem. The nuances of protein 3D structures make this formulation appropriate, allowing predictions …

A Co-Opted Steroid Synthesis Gene, Maintained In Sorghum But Not Maize, Is Associated With A Divergence In Leaf Wax Chemistry, Lucas Busta, Elizabeth Schmitz, Dylan K. Kosma, James C. Schnable, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Virtually all land plants are coated in a cuticle, a waxy polyester that prevents nonstomatal water loss and is important for heat and drought tolerance. Here, we describe a likely genetic basis for a divergence in cuticular wax chemistry between Sorghum bicolor, a drought tolerant crop widely cultivated in hot climates, and its close relative Zea mays (maize). Combining chemical analyses, heterologous expression, and comparative genomics, we reveal that: 1) sorghum and maize leaf waxes are similar at the juvenile stage but, after the juvenile-to-adult transition, sorghum leaf waxes are rich in triterpenoids that are absent from maize; 2) biosynthesis …

Data-Driven Modeling Of The Causes And Effects Of Interneuronal Dysfunction In Alzheimer’S Disease And Dravet Syndrome, Carlos Perez

USF Tampa Graduate Theses and Dissertations

One of the defining features of Alzheimer’s disease (AD) is the increased cleavage of the amyloid precursor protein (APP), causing abnormally high levels of the aggregation form of amyloid beta (Aβ ). Many studies have shown that both AD patients and AD mice models exhibit abnormal network activity, including hypersynchronous excitatory neuron behavior, altered brain rhythms, and in some instances epileptic seizures when exposed to high levels of Aβ In particular, strong experimental evidence suggests that it is the small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) rather than the more stable, late stage rigid fibrils (RFs) that cause …

Natalia Shustova Answers Questions About 15 Years Of Research On Covalent Organic Frameworks, Natalia B. Shustova Prof. Dr.

Faculty Publications

No abstract provided.

Pathway-Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan

Biochemistry Publications

No abstract provided.

Genetic Polymorphism Of Bitter Taste Perception In Tempe, Arizona And Its Association With Nutritional Status, Daniel Woodley, Benjamin Cabrera

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modelling Of Temperature Effects On The Afd Neuron Of Caenorhabditis Elegans, Zachary Mobille, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Posttranslational Modification And Protein Disorder Regulate Protein-Protein Interactions And Dna Binding Specificity Of P53, Robin Levy

USF Tampa Graduate Theses and Dissertations

p53 is an intrinsically disordered transcription factor that suppresses tumor development by arresting the cell cycle and promoting DNA repair. p53 deletions or mutations can lead to cancer due to the inability of cells to respond to stress. The protein levels and post-translational modification state of p53 changes in response to cellular stress like DNA damage. Previous studies have shown that p53 can undergo coupled folding and binding with the E3 ubiquitin ligase, Mdm2, and the histone deacetylase, p300. In normal cells, p53 is kept at a low level by Mdm2, which marks it with ubiquitin, targeting p53 for proteasome …

Rapid Evolution Of Aerosol Particles And Their Optical Properties Downwind Of Wildfires In The Western Us, Lawrence I. Kleinman, Arthur J. Sedlacek, Kouji Adachi, Peter R. Buseck, Sonya Collier, Manvendra K. Dubey, Anna L. Hodshire, Ernie Lewis, Timothy B. Onasch, Jeffery R. Pierce, John Shilling, Stephen R. Springston, Jian Wang, Qi Zhang, Shan Zhou, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

During the first phase of the Biomass Burn Operational Project (BBOP) field campaign, conducted in the Pacific Northwest, the DOE G-1 aircraft was used to follow the time evolution of wildfire smoke from near the point of emission to locations 2-3.5 h downwind. In nine flights we made repeated transects of wildfire plumes at varying downwind distances and could thereby follow the plume's time evolution. On average there was little change in dilution-normalized aerosol mass concentration as a function of downwind distance. This consistency hides a dynamic system in which primary aerosol particles are evaporating and secondary ones condensing. Organic …

Evaluation Of Anti-Cancer Function In Natural Killer Cells Generated From Rat Hematopoietic Stem Cells, Alireza Pirahmadian

Student Works (2020-2029)

Natural killer cells (NK) cells are lymphocytes and they are the most important key constituent of mammalian immune system against cancer tumour cells. The genome of NK cells is categorically divided to inhibitory and activator genes that code ligands on the surface of NK cells. Indeed, these ligands are cancer tumour cells destroyer arms of the NK cells. On the other hand, hematopoietic stem cells (HSCs) are the origin of all blood cells, derives from BM and mature to immune cells. NK cells cannot defeat CTCs on their own. The main reason is their population (numbers are low), they cannot …

New Mechanisms That Control Fact Histone Chaperone And Transcription-Mediated Genome Stability, Angelo Vincenzo De Vivo Diaz

USF Tampa Graduate Theses and Dissertations

The Role of deubiquitinating enzymes (DUBs) in transcription, replication and genome integrity is not one that has been extensively researched. OTU DUBs are a particular class of enzyme with very little known about them.OTUD5 is a cysteine protease in the OTU family responsible to processing lysine 48 and lysine 63 ubiquitin chains. Recently, it has been implicated in to play a role in transcription through its binding partner UBR5. OTUD5 has also been shown to interact with proteins such as PDCD5 and p53, potentially have great importance in cell fate. In this study, I describe new discovered functions for OTUD5 …

White Matter Plasticity In Anxiety: Disruption Of Neural Network Synchronization During Threat-Safety Discrimination, Jia Liu, Ekaterina Likhti, A. Duke Shereen, Tracy A. Dennis-Tiwary, Patricia Casaccia

Advanced Science Research Center

Recent evidence highlighted the importance of white matter tracts in typical and atypical behaviors. White matter dynamically changes in response to learning, stress, and social experiences. Several lines of evidence have reported white matter dysfunction in psychiatric conditions, including depression, stress- and anxiety-related disorders. The mechanistic underpinnings of these associations, however, remain poorly understood. Here, we outline an integrative perspective positing a link between aberrant myelin plasticity and anxiety. Drawing on extant literature and emerging new findings, we suggest that in anxiety, unique changes may occur in response to threat and to safety learning and the ability to discriminate between …

Chicoreus Brunneus Seashells As A Catalyst In Rice Bran Biodiesel Production, Hoora Mazaheri

Student Works (2020-2029)

Environmental pollution and the declining global supply of accessible fossil fuels are the key drivers to search for alternative energy sources. This study focused on developing a “green” and sustainable heterogenous calcium oxide (CaO) catalyst from Chicoreus Brunneus shells for biodiesel production from rice bran oil (RBO). Coastal people frequently collect these shells for food and shell crafts. Thus, by using seashell wastes, cost-efficient catalysts can be achieved for the biodiesel industry. The shells were calcinated, washed and dried to produce pure CaO catalyst. After that, CaO was converted into calcium methoxide (Ca(OCH3)2) and followed by loading onto zeolite support …

Origins Of Amyloid Oligomers And Novel Approaches For Their Detection, Jeremy Barton

USF Tampa Graduate Theses and Dissertations

Alzheimer’s disease, type II diabetes, and other amyloid diseases are known to be associated with the formation of amyloid aggregates. It has been thoroughly researched whether amyloid fibrils or oligomers are the main culprit for these diseases, and recent evidence has connected oligomers as the most disease relevant aggregate species. However, many difficulties have arose in confirming this hypothesis. Techniques for oligomer detection are often limited in their sensitivity, and in many cases are unable to distinguish oligomers from rigid fibrils. Additionally, the role oligomer splay in fibril assembly is still unclear, and has led to the belief that different …

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. …

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 …

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 …

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 …

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 …

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 …