Biochemistry, Biophysics, and Structural Biology Commons^™

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Hcpr Of Porphyromonas Gingivalis Utilizes Heme To Bind No, Benjamin Belvin

Theses and Dissertations

The obligate anaerobe Porphyromonas gingivalis is the etiological agent responsible for periodontal disease. It must withstand high levels of reactive nitrogen species in the oral cavity generated by the host and other oral flora. The mechanisms allowing for protection against such stress remain poorly understand. HcpR is an FNR-CRP family regulator that has been implicated in regulation of the nitrosative stress response. In this study we characterize the biochemical properties of HcpR. It is a homo-dimer that is composed of 3 domains – a heme-binding domain, dimerization helix, and a DNA-binding domain. Our studies show that HcpR binds the heme …

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 …

Quorum Sensing Molecules For Unicellular Organisms: Spectroscopic And Computational Study Of Conformational Behavior, Daniel Tollefson

Undergraduate Research Symposium

Quorum sensing plays a vital role in unicellular communications. Until recently, it was thought that unicellular bacteria were non-cooperative; that they did not communicate among each other as a larger community. They do, in fact, communicate via small molecules that are created and released into the extracellular environment. Detailed knowledge regarding the interactions of these quorum sensing molecules (QSM) with the molecular and cellular-scale environments can lead to the manipulation of quorum sensing within a population. The function of these molecules requires that they can readily diffuse through the polar environment of aqueous solution and the nonpolar environment of cell …

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 …

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 …

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 …

Expediting Drug Discovery: Fast And Accurate Prediction Of Coupling Constants For Nitrogen Heterocycles, Petr Malek

College of Arts and Sciences Presentations

Nitrogen containing heterocyclic drugs that regulate the JAK-STAT pathway have proven therapeutic usage for a variety of disorders from hematological cancers to rheumatoid arthritis. The synthesis of these drugs to selectively inhibit specific JAK-STAT has become an active area of research for pharmaceutical companies. Nitrogen heterocycles are commonly hydrogen deficient, presenting challenges for their characterization. The method of choice to determine the structure of these novel drugs is Heteronuclear Multiple Bond Correlation (HMBC) Nuclear Magnetic Resonance (NMR) spectroscopy. The limitation of this method is that it requires prior knowledge of the molecular orbital electron density of the molecule to be …

Collagen Xiα1 And The Stem Cell Theory Of Cancer, Cody Roell, Kenneth Weekes, Julia Oxford

College of Arts and Sciences Presentations

Cancer stem cell (CSC) theory hypothesizes that heterogeneity within tumors is not a mere consequence of random mutation and clonal evolution, but results from an intrinsic hierarchy of cells. The KeWe cell line was isolated and characterized in Dr. Oxford’s lab. Characterization has included the determination of conditions for maintenance in cell culture for extended periods of time and using different techniques to count the cells to characterize cellular proliferation rates. Collagen XIα1 can be found throughout the body in a variety of places including tendons, skin, ligaments, interstitial tissue, dentin, blood vessels, the cornea, intervertebral discs, muscle, bone, and …

Ampk Activators Regulate Contractile Function Of Mesenteric Arteries, Victoria Locke

Theses and Dissertations

Vasoconstrictor tone in the splanchnic circulation redistributes blood flow during hemorrhage and resuscitation. A metabolic sensor, 5’adenosine monophosphate-activated protein kinase (AMPK), has been proposed to relax arteries by inhibiting myosin light chain (MLC) kinase (MLCK) and rho kinase (ROCK) activities. Because AMPK activation might be beneficial in re-establishing splanchnic blood flow during resuscitation, we sought to explore the relative ability of AMPK activators (AICAR, A769662, berberine (BBR) and simvastatin (SIMV)) to relax mesenteric artery (MA) contraction. Our data revealed that these drugs caused vasorelaxation when tissues were stimulated either with KCl (producing primarily a Ca2+ dependent contraction) or phenylephrine (PE; …

Comparing And Informing Morphological Species Identifications And Boundaries In Arthropod Gut-Dwelling Protists Using Molecular Phylogenetic Analyses, Mason Hinchcliff, Nicole Reynolds, Eric Tretter, Dustin Heeney, Justin Gause, Tyler Pickell, Prasanna Kandel

College of Arts and Sciences Presentations

Trichomycetes are fungal and protistan symbionts of arthropods and have been found in marine, freshwater, and terrestrial habitats on every continent except Antarctica. Minimally, trichomycetes associate commensally with their immature aquatic hosts (including black flies, mayflies, stoneflies, isopods, and others) attaching to the chitinous lining of the mid or hindgut. Classified with trichomycetes are Paramoebidium, a group of protists which associate in an obligate manner with their hosts. To date, 16 species of Paramoebidium have been identified by morphological approaches. These descriptions have included characterization and discrimination of species based on thallus (body) length and width, differences in the …

Acetobixan, An Inhibitor Of Cellulose Synthesis Identified By Microbial Bioprospecting, Ye Xia, Lei Lei, Chad Brabham, Jozsef Stork, James R. Strickland, Adam Ladak, Ying Gu, Ian Wallace, Seth Debolt

Horticulture Faculty Publications

In plants, cellulose biosynthesis is an essential process for anisotropic growth and therefore is an ideal target for inhibition. Based on the documented utility of small-molecule inhibitors to dissect complex cellular processes we identified a cellulose biosynthesis inhibitor (CBI), named acetobixan, by bio-prospecting among compounds secreted by endophytic microorganisms. Acetobixan was identified using a drug-gene interaction screen to sift through hundreds of endophytic microbial secretions for one that caused synergistic reduction in root expansion of the leaky AtcesA6prc1-1 mutant. We then mined this microbial secretion for compounds that were differentially abundant compared with Bacilli that failed to mimic CBI action …

Designing And Evaluating The Multicom Protein Local And Global Model Quality Prediction Methods In The Casp10 Experiment, Renzhi Cao, Zheng Wang, Jianlin Cheng

Faculty Publications

Background: Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models.

Results: MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based …

Combination Of The Computational Methods: Molecular Dynamics, Homology Modeling And Docking To Design Novel Inhibitors And Study Structural Changes In Target Proteins For Current Diseases, Katherine Cristina Parra

USF Tampa Graduate Theses and Dissertations

In this thesis, molecular dynamics simulations, molecular docking, and homology modeling methods have been used in combination to design possible inhibitors as well as to study the structural changes and function of target proteins related to diseases that today are in the spotlight of drug discovery. The inwardly rectifying potassium (Kir) channels constitute the first target in this study; they are involved in cardiac problems. On the other hand, tensin, a promising target in cancer research, is the second target studied here.

The first chapter includes a brief update on computational methods and the current proposal of the combination of …

Methionine Restriction Extends Lifespan Of Drosophila Melanogaster Under Conditions Of Low Amino-Acid Status, Byung Cheon Lee, Alaattin Kaya, Siming Ma, Gwansu Kim, Maxim V. Gerashchenko, Sun Hee Yim, Zhen Hu, Lawrence G. Harshman, Vadim N. Gladyshev

Lawrence G. Harshman Publications

Reduced methionine (Met) intake can extend lifespan of rodents; however, whether this regimen represents a general strategy for regulating aging has been controversial. Here we report that Met restriction extends lifespan in both fruit flies and yeast, and that this effect requires low amino-acid status. Met restriction in Drosophila mimicks the effect of dietary restriction and is associated with decreased reproduction. However, under conditions of high amino-acid status, Met restriction is ineffective and the trade-off between longevity and reproduction is not observed. Overexpression of InRDN or Tsc2 inhibits lifespan extension by Met restriction, suggesting the role of TOR signalling in …

Solvent Dependent Molecular Mechanics: A Case Study Using Type I Collagen, Heather Harper

USF Tampa Graduate Theses and Dissertations

Being the most abundant protein in the body, by mass, type I collagen provides the building blocks for tissues such as bone, extra-cellular matrix, tendons, cornea, etc[1-3]. The ability of a single protein to create structures with such various mechanical properties is not fully understood. Before one can engineer and assemble a complex tissue, such as cornea, the mechanisms underlying the formation and assembly, mechanical properties, and structure must be investigated and quantified. The work presented herein contains an extensive study of Type I collagen from the molecular to the tissue level.

The engineering of collagenous tissues that mimic the …

Expression, Purification And Characterization Of Soluble Red Rooster Laforin As A Fusion Protein In Escherichia Coli, M. Kathryn Brewer, Satrio Husodo, Vikas V. Dukhande, Mary Beth Johnson, Matthew S. Gentry

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: The gene that encodes laforin, a dual-specificity phosphatase with a carbohydrate-binding module, is mutated in Lafora disease (LD). LD is an autosomal recessive, fatal progressive myoclonus epilepsy characterized by the intracellular buildup of insoluble, hyperphosphorylated glycogen-like particles, called Lafora bodies. Laforin dephosphorylates glycogen and other glucans in vitro, but the structural basis of its activity remains unknown. Recombinant human laforin when expressed in and purified from E. coli is largely insoluble and prone to aggregation and precipitation. Identification of a laforin ortholog that is more soluble and stable in vitro would circumvent this issue.

RESULTS: In this study, we …

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 …

Probing The Effects Of Tbhk2 On Trypanosoma Brucei Growth, Social Growth, And Inhibitor Response, Amber Hackler, William Mcalpine, Yijian Qiu, James Morris

Graduate Research and Discovery Symposium (GRADS)

In sub-Saharan Africa the protozoan parasite, Trypanosoma brucei, continues to be of major concern for the health and economic development of the region. This parasite is known to cause human African trypanosomiasis (HAT or African sleeping sickness) and nagana in livestock such as cattle. Social behaviors, such as colonization and migration, are important in the study of T. brucei because of the way the parasite infects its mammalian host. During the fly bloodmeal, the parasite first passes into the gut but then eventually migrates to the fly salivary glands where it will continue to develop before transmission as a parasitic …

Structural And Functional Analysis Of Harv1 Lipid Binding, Jamie Francisco

Graduate School of Biomedical Sciences Theses and Dissertations

Cardiovascular disease (CVD) has the highest mortality rate worldwide and is considered epidemic in the United States. Statins as the primary and almost sole method of treatment for cholesterol-related CVD, but they have limitations. Proper sterol transport is needed to maintain normal blood lipid levels. Studies have shown that misregulation of lipid trafficking aids in the progression of CVD and in the activation of the unfolded protein response (UPR). Misregulation of lipid and sterol homeostasis also results in the loss of lipid rafts, known cellular signaling hubs and major components of ER associated membrane contact sites. Arv1 is a highly …