Biochemistry, Biophysics, and Structural Biology Commons^™

Geometric Surface Function Of A Giant Marine Virus Cafeteria Roenbergensis Virus, Tiffany H. Blankenship^, Rishabh Jain, Chuan Xiao*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Protein Profiling Of Adenine Nucleoside And Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-Azidoadenosine Analogs As Affinity Based Protein Profiling Probes, Shikha Mahajan

USF Tampa Graduate Theses and Dissertations

Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized …

Binding Efficacy Of Different Polyphenolic Phytochemicals With Β-Lactoglobulin And Human Serum Albumin: Implication For Therapeutics Against Neurodegenerative Diseases, Rene Duran^, Andres Ortiz^, Mahesh Narayan*, Vladik Kreinovich*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Derivation Of Hill's Equation From Scale Invariance, Andres Ortiz^, Vladik Kreinovich*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Interaction Of Trypanosoma Cruzi Sterol 14-Alpha-Demethylase Cyp51 With Ru-Azole Derivatives, Arturo Ortega^, Rosa A. Maldonado*, Roberto A. Sanchez-Delgado, Hugues Ouellet*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Cholesterol Side-Chain Degradation Enzymes Of Mycobacterium Tuberculosis, Brian Villalba^, Itzel Chavarria, Bernardo Terres, Johnathan Abou-Fadel, Rhone A. Mendoza, Hugues Ouellet*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Engineering The Human Immunodeficiency Virus To Infect Drosophila Melanogaster Cells, Laura F. Porras ^, Elizabeth R. Aguilera, Eduardo Urias, Daniel Reyes, Adarsh Saheba, Manuel Llano *

COURI Symposium Abstracts, Spring 2012

HIV continues to infect at pandemic levels despite the significant progress in research, treatment and prevention. Advances in anti-HIV retroviral drugs have led to significant reduction in AIDS-related deaths, delayed the progression of the HIV infection to AIDS and diminished the rates of HIV transmission. However, the current antiretroviral treatment frequently encounters drug-resistant viruses due to the high mutation rate of HIV proteins. Therefore, identification of cellular cofactors of HIV infection is critical to identify new targets for anti-HIV drug development. However, the genetic complexity of mammalian cells imposes additional obstacles to the identification of HIV-1 cellular cofactors. To mitigate …

An Unexpected Function Of The Prader-Willi Syndrome Imprinting Center In Maternal Imprinting In Mice, Mei-Yi Wu, Ming Jiang, Xiaodong Zhang, Arthur L. Beaudet, Ray-Chang Wu

Biochemistry and Molecular Medicine Faculty Publications

Genomic imprinting is a phenomenon that some genes are expressed differentially according to the parent of origin. Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurobehavioral disorders caused by deficiency of imprinted gene expression from paternal and maternal chromosome 15q11–q13, respectively. Imprinted genes at the PWS/AS domain are regulated through a bipartite imprinting center, the PWS-IC and AS-IC. The PWS-IC activates paternal-specific gene expression and is responsible for the paternal imprint, whereas the AS-IC functions in the maternal imprint by allele-specific repression of the PWS-IC to prevent the paternal imprinting program. Although mouse chromosome 7C has a conserved PWS/AS imprinted …

1-Deoxy-D-Xylulose-5-Phosphate Synthase (Dxs) Mechanistic Study And Its Implication In The Development Of Novel Antibiotics And Antimalarials, Sumit Handa

USF Tampa Graduate Theses and Dissertations

Isoprenoids are the largest family of biologically active compounds, synthesized by five carbon subunits namely isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). For long time the mevalonate-dependent (MVA) pathway has been considered as the sole source of IPP and DMAPP, until recently a new non-mevalonte dependent (NMVA) pathway was discovered. This new pathway utilizes entirely different set of enzymes for isoprenoids synthesis and don't have any homologues in humans. NMVA pathway is the only source of isoprenoids for certain eubacteria, parasite and plants. Absence of the NMVA pathway in higher organisms has opened a new platform for the development of …

Flowcell Systems For Single Molecule Detection, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

G9a Interacts With Snail And Is Critical For Snail-Mediated E-Cadherin Repression In Human Breast Cancer, Chenfang Dong, Yadi Wu, Jun Yao, Yifan Wang, Yinhua Yu, Piotr G. Rychahou, B. Mark Evers, Binhua P. Zhou

Molecular and Cellular Biochemistry Faculty Publications

Breast cancers are highly heterogeneous but can be grouped into subtypes based on several criteria, including level of expression of certain markers. Claudin-low breast cancer (CLBC) is associated with early metastasis and resistance to chemotherapy, while gene profiling indicates it is characterized by the expression of markers of epithelial-mesenchymal transition (EMT) - a phenotypic conversion linked with metastasis. Although the epigenetic program controlling the phenotypic and cellular plasticity of EMT remains unclear, one contributor may be methylation of the E-cadherin promoter, resulting in decreased E-cadherin expression, a hallmark of EMT. Indeed, reduced E-cadherin often occurs in CLBC and may contribute …

Cloning And Characterization Of The Cell Wall Acting Enzyme Cd1034 From The Pathogen Clostridium Difficile, Zachary Suter

Honors Projects in Science and Technology

The manifestation of multidrug resistance in bacteria over the past several decades has resulted in one of the foremost challenges in the management of infectious diseases. The question arises, “How do we address this growing problem?” One solution to stem the growing rise in antimicrobial resistance is to investigate new targets, while another approach is to re-examine classical antibacterial targets with a fresh perspective. The aim of this paper is to begin the process of antibacterial development for the pathogen Clostridium difficile by characterizing the cell wall acting glucosaminidase CD1034. It is inunderstanding how CD1034 functions biochemically that it can …

Synthesis Of A Cobalt Complex Of A Sulfonated Binucleating Schiff Base Ligand, Jieun Emily Hwang

Capstone Research Projects

Current synthesis of cobalt (II) complexes of sulfonated binucleating Schiff base ligands requires the reaction be run under nitrogen.1 This research introduces a novel process in which the complex can be prepared in open air. The cobalt (II) complexes are prepared with synthesized 5- sulfosalicylaldehyde, and then analyzed by IR and UV-Vis spectrophotometry.

Section Abstracts: Structural Biology, Biochemisty, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia.

Glycosylation Of Human Cyclooxygenase-2 (Cox-2) Decreases The Efficacy Of Certain Cox-2 Inhibitors., Mary B. Sevigny, Kamara Graham, Esmeralda Ponce, Maggie Louie, Kylie Mitchell

Natural Sciences and Mathematics | Faculty Scholarship

Prostanoids play an important role in a variety of physiological and pathophysiological processes including inflammation and cancer. The rate-limiting step in the prostanoid biosynthesis pathway is catalyzed by cyclooxygenase-2 (COX-2). COX-2 exists as two glycoforms, 72 and 74 kDa, the latter resulting from an additional glycosylation at Asn(580). In this study, Asn(580) was mutated, and the mutant and wild-type COX-2 genes were expressed in COS-1 cells to determine how glycosylation affects the inhibition of COX-2 activity by aspirin, flurbiprofen, ibuprofen, celecoxib, and etoricoxib. Results indicate that certain inhibitors were 2-5 times more effective at inhibiting COX-2 activity when the glycosylation …

The Relationship Between Live Coral And Macroalgae In South Caicos As Influenced By Herbivorous Fishes, Sarah Byce

Honors Theses

Marine life is the basis for most industries in the Turks and Caicos Islands, located on the outskirts of the Caribbean Sea. Few studies have been carried out to assess the current status of reefs in this region, especially those off the shore of South Caicos Island. The AGRRA v.4.0 methodologies were employed create baseline assessments of stony corals, macroalgae and associated fishes and to explore the relationships between these key reef organisms. This study was based on 10 different locations both inside and outside of Marine Protected Areas (MPAs) and including exposed and sheltered reefs in proximity to South …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2015, Norfolk State University, Norfolk, Virginia.

Validation On Sodium Channel Dependence By Electrical Stimulation-Induced Dopamine Release, Alice E. Hernandez ^, Mabel N. Terminel, Edward Castaneda *

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Elucidation Of The Pax/Six Gene Regulatory Network In Ephydatia Muelleri, Anna Rued

Honors Theses

The evolution of gene regulatory networks accounts for much of the diversity we observe in the animal kingdom. In particular, the Pax/Six/Eya/Dac gene network has been known to play critical roles in development of all bilaterians and cnidarians. However, this network has not been characterized in Porifera. These studies focus on tracing the evolutionary history of the PSED network back to the most basal organism in the metazoan phylogeny through demonstrating the presence of a direct gene regulatory network between PaxB and Six1/2 orthologs in sponges. To this end, putatitve Six1/2 cis- regulatory elements were identified while the PaxBprd transcription …

Alteration In 5ht1a Receptor Activity From A Prenatal Exposure To Dexamethasone In A Stressed And Non-Stressed Adult Male Rat, Darshan S. Shah

Honors Theses

Synthetic glucocorticoids (GC) are used as a clinical therapeutic to stimulate lung development in fetuses that present the risk of preterm delivery. Previous studies have shown that a prenatal exposure to Dexamethasone (DEX) causes a disturbance in normal GC mediation of neuritic outgrowth, cell signaling, and serotonergic systems. Our hypothesis is that a prenatal exposure to DEX during the third trimester of pregnancy alters 5HT1A receptor function. Pregnant dams were injected daily with 150μg/ml/kg of DEX from gestation day 14 through 19. Control dams were treated with and equal volume of saline. Swim stress followed by elevated plus maze testing …

The Optimization Of A One-Pot Heteroconjugate Addition-Oxidation-Diels-Alder Reaction, Christina Vivelo

Honors Theses

Ynoate esters are ideal reagents for one-pot reactions due to their ability to undergo multiple addition reactions in one flask. Ethyl propiolate undergoes a heteroconjugate addition reaction with aromatic thiol nucleophiles, producing an enoate which is then oxidized by m-CPBA and is able to undergo a Diels–Alder reaction with cyclopentadiene. The work presents the optimization of a three-step heteroconjugate addition-oxidation-Diels–Alder reaction to yield cyclic compounds favoring endo stereochemistry, which may be used in further synthesis of biologically active compounds such as (+)-Methyl-5-epi-Shikimate or Deipeptyl-IV-Peptidase inhibitor.

The Role Of Histidines In Neurosteroid Binding Of Nmda Glun2b And D Subunits, Sarah Rhoads

Honors Theses

Implicit in cellular mechanisms essential for learning and memory, NMDA receptors are heterotetrameric members of the family of ionotropic glutamate receptors. Activation of the glutamate-specific receptor subunits results in the opening of ion channels, triggering an excitatory pathway, which can be moderated by certain endogenous and exogenous compounds. Previous research with the endogenous neurosteroids pregnenolone sulfate (PS) and 3α-hydroxy-5-β-20-one sulfate (PregS) have indicated that the binding of these neurosteroids to NMDA receptors containing the four A-D isoforms of the GluN2 subunit affects current flow through them1. Binding of PS to NMDA receptors containing GluN2A or GluN2B subunits causes an increased …

Determination Of The Atomic Resolution Structure Of A Dna Polymerase I Isolated From Rhodothermus Marinus, Natalie S. Omattage

Honors Theses

DNA polymerase I employs a multistep mechanism for sorting correctly paired nucleotides from mismatches. We aim to characterize reaction intermediates during nucleotide selection to better understand how this class of enzymes achieves high DNA replication fidelity. DNA polymerase I from R. marinus contains an unusual and disruptive proline in the mobile O helix near the active site. To characterize this enzyme, the structure of the large (5´-to-3´ exo-deficient) fragment of the R. marinus DNA polymerase I (RF) was solved to 2.95 Å (R = 0.234) using multi-wavelength anomalous dispersion. Alignment …

Understanding The Auto-Regulation Of Leukotriene Biosynthesis A Model Of Inactivation For 5-Lipoxgenase, Erin E. Schexnaydre

Honors Capstones

No abstract provided.

Evolution Finds Shelter In Small Spaces, Niles Lehman

Chemistry Faculty Publications and Presentations

When RNA is replicated in cell-free systems, a ubiquitous problem is the hijacking of the system by short parasitic RNA sequences. In this issue of Chemistry & Biology, Bansho et al. show that compartmentalization into water-in-oil droplets can ameliorate this problem, but only if the droplets are small. This result helps to both recapitulate abiogenesis and optimize synthetic biology.

Refers to: Bansho, Yohsuke, et al. "Importance of Parasite RNA Species Repression for Prolonged Translation-Coupled RNA Self-Replication." Chemistry & Biology 19.4 (2012): 478-487.

Nonosecond Pulsed Electric Field Induced Changes In Dielectric Properties Of Biological Cells, Jie Zhuang

Electrical & Computer Engineering Theses & Dissertations

Nanosecond pulsed electric field induced biological effects have been a focus of research interests since the new millennium. Promising biomedical applications, e.g. tumor treatment and wound healing, are emerging based on this principle. Although the exact mechanisms behind the nanosecond pulse-cell interactions are not completely understood yet, it is generally believed that charging along the cell membranes (including intracellular membranes) and formation of membrane pores trigger subsequent biological responses, and the number and quality of pores are responsible for the cell fate. The immediate charging response of a biological cell to a nanosecond pulsed electric field exposure relies on the …

Nano- And Micro-Second Electrical Pulsing Of B16-F10 Mouse Melanoma Cells: Plasma Membrane And Sub-Cellular Organelle Changes, Yiling Chen

Theses and Dissertations in Biomedical Sciences

High electric field-treated cells are permeable to molecular dye through either opening of pores in the plasma membrane or other unknown processes which can disturb the membrane in an organized way. However, direct morphological evidence is lacking and responses of intracellular organelles are not clear. We used traditional chemical fixatives and biochemical techniques to capture cell membrane and organelle changes immediately after pulsing with high voltage electric field application. Different pulse durations, nanosecond (ns) and microsecond (µs), and field magnitudes, 60 kV/cm and 1.2 kV/cm, were applied to mouse melanoma B16-F10 cells. Two different ns durations (60 and 300 ns) …

Design Of In Vivo Assays For Study Of Transport, Biocompatibility And Toxicity Of Nanoparticles, Kerry Jean Lee

Theses and Dissertations in Biomedical Sciences

This dissertation focuses on the design of new in vivo assays for study of transport, biocompatibility and toxicity of nanoparticles (NPs) in zebrafish embryos. We synthesized and purified spherical silver (Ag) NPs with diameters, ranging from 12 to 95 nm, that are stable (non-aggregated) in egg-water media. We developed new imaging approaches to characterize the sizes of single Ag NPs in zebrafish embryos at nanometer resolution by measuring their size-dependent plasmonic spectra and scattering intensity using dark-field optical microscopy and spectroscopy (DFOMS). We used single Ag NPs because they exhibit the high quantum yield (QY) of Rayleigh scattering and resist …

The Dietary Isoprenoid Perillyl Alcohol Inhibits Telomerase Activity In Prostate Cancer Cells, Tabetha Sundin

Theses and Dissertations in Biomedical Sciences

This is the first evidence that a plant-derived compound–perillyl alcohol regulates telomerase activity via the mammalian target of rapamycin (mTOR) pathway in prostate cancer cells. Telomerase–the enzyme responsible for immortalizing cells through telomeric repeats addition–is de-repressed early in an aspiring cancer cell. We hypothesized that perillyl alcohol regulates hTERT (human telomerase reverse transcriptase) at the translational and post-translational levels via its effects on the mTOR pathway. A rapid suppression of telomerase activity was detected in prostate cancer cell lines (PC-3 and DU145) in response to biologically-relevant concentrations and short incubations of perillyl alcohol or the mTOR inhibitor—rapamycin.

Western blot analysis …

Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family, Panagis Filippakopoulos, Sarah Picaud, Maria Mangos, Tracy Keates, Jean-Philippe Lambert, Dalia Barsyte-Lovejoy, Ildiko Felletar, Rudolf Volkmer, Susanne Muller, Tony Pawson, Anne-Claude Gingras, Cheryl H. Arrowsmith, Stefan Knapp

Biochemistry and Molecular Medicine Faculty Publications

Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations …