Biochemistry, Biophysics, and Structural Biology Commons^™

Polymorphisms In Mthfr, Ms And Cbs Genes And Premature Acute Myocardial Infarction In A Pakistani Population, Mohammad Perwaiz Iqbal, Khalida Iqbal, Asal Khan Tareen, Siddiqa Parveen, Naseema Mehboobali, Ghulam Haider, Saleem Perwaiz Iqbal

Department of Biological & Biomedical Sciences

High prevalence of premature coronary heart disease in Pakistanis compared to other populations points towards the genetic predisposition of this population to develop this disease. Since no investigations have been carried out in Pakistan to study the relationship of polymorphisms in genes involved in homocysteine cycle, the objective of the present study was to find out if there is any association of methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C; methionine synthase (MS) A2756G; cystathionine-beta-synthase (CBS) 844ins68, G919A polymorphisms with premature acute myocardial infarction (AMI) in a population of Pakistani patients with this disease. In a cross-sectional study, DNA samples of 143 AMI …

Methods To Assess The Direct Interaction Of C. Jejuni With Mucins, Julie Ann Naughton, Marguerite Clyne, Gina Duggan, Billy Bourke

Books/Book chapters

Studies of the interaction of bacteria with mucus secreting cells can be complemented at a more mechanistic level by exploring the interaction of bacteria with purified mucins. Here we describe a far western blotting approach to show how C. jejuni proteins separated by SDS PAGE and transferred to a membrane or slot blotted directly onto a membrane can be probed biotinylated mucin. In addition we describe the use of novel mucin microarrays to assess bacterial interactions with mucins in a high throughput manner.

Assessing The Risk Of Resistance Evolution, Adult And Larval Susceptibility, And Sublethal Effects After Exposure Of Corn Rootworms To Vacuolar Atpase-A And Snf7 Dsrnas, Adriano Elias Pereira

Department of Entomology: Dissertations, Theses, and Student Research

Corn rootworms are Diabroticite beetles from the genus Diabrotica and include the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, and the northern corn rootworm, D. barberi Smith & Lawrence, as the most important pests in the U.S. Corn Belt. The southern corn rootworm (SCR), D. undecimpunctata howardi Barber, is considered a polyphagous plant pest and feeds in a wide variety of plants including peanuts, cucurbits, soybeans, and especially corn. Resistance to control methods including behavioral resistance to crop rotation and to corn hybrids expressing Bacillus thuringiensis Berliner toxins in WCR has frequently been reported. SCR has been considered a …

A Polyaniline-Based Sensor Of Nucleic Acids, Partha Sengupta, Jared Gloria, Marcus K. Parker, Alex S. Flynt

Faculty Publications

Detection of nucleic acids is at the center of diagnostic technologies used in research and the clinic. Standard approaches used in these technologies rely on enzymatic modification that can introduce bias and artifacts. A critical element of next generation detection platforms will be direct molecular sensing, thereby avoiding a need for amplification or labels. Advanced nanomaterials may provide the suitable chemical modalities to realize label-free sensors. Conjugated polymers are ideal for biological sensing, possessing properties compatible with biomolecules and exhibit high sensitivity to localized environmental changes. In this article, a method is presented for detecting nucleic acids using the electroconductive …

The Biological Function Of Hammerhead Rana Ribozyme In Human Genome, Ibtehal M. A. Awad

Theses

Hammerhead RNA [HHR] sequence originally found in viroids is also detected in many species. HHR are often found in introns of different genes ranging from prokaryotes to

eukaryotes. HHR can form specific tertiary structure that make specific region susceptible to cleavage. However, the role of the HHR is not clear in other life forms. This study aims to

Investigate the role of HHR in the intron 6 of (RECK) gene. Our study shows that when blocking the HHR sequence in the intron6, the production of RECK protein declines which may be due to the effect of HHR in splicing and …

Expression, Purification, And Crystallization Of An Endoxylanase From Bacteroides Vulgatus, Jesslyn Park, Jason Hurlbert

The Winthrop McNair Research Bulletin

Sustainable sources of energy are growing in demand as fossil fuels are rapidly expended. One such energy source is fuel ethanol generated from the fermentation of plant biomass by engineered bacterial biocatalysts. The creation of a biocatalyst capable of converting nearly any plant matter to fuel ethanol requires the identification of novel enzymes capable of degrading specific carbohydrate polymers and cloning these enzymes into a bacterial host. This study seeks to structurally characterize a novel xylanase of glycosyl hydrolase family 30 (GH30) from Bacteroides vulgatus, a bacterium found in the human gut microbiome, via x-ray crystallography. The gene for …

Pyk2 Activates The Nlrp3 Inflammasome By Directly Phosphorylating Asc And Contributes To Inflammasome-Dependent Peritonitis, I-Che Chung, Chun-Nan Ouyang, Sheng-Ning Yuan, Hsin-Pai P. Li, Jeng-Ting Chen, Hui-Ru Shieh, Yu-Jen Chen, David M. Ojcius, Ching-Liang Chu, Jau-Song Yu, Yu-Sun Chang, Lih-Chyang Chen

All Dugoni School of Dentistry Faculty Articles

The inflammasome adaptor protein, ASC, contributes to both innate immune responses and inflammatory diseases via self-oligomerization, which leads to the activation of the protease, caspase-1. Here, we report that the cytosolic tyrosine kinases, FAK and Pyk2, are differentially involved in NLRP3 and AIM2 inflammasome activation. The inhibition of FAK and Pyk2 with RNA interference or chemical inhibitors dramatically abolished ASC oligomerization, caspase-1 activation, and IL-1β secretion in response to NLRP3 or AIM2 stimulation. Pyk2 is phosphorylated by the kinase Syk and relocalizes to the ASC specks upon NLRP3 inflammasome activation. Pyk2, but not FAK, could directly phosphorylate ASC at Tyr146, …

Contribution Of Epithelial Hypoxia Signaling To Pulmonary Fibrosis: Role Of Fak1 And Galectin-1 As Driver Molecules, Jaymin J. Kathiriya

USF Tampa Graduate Theses and Dissertations

Idiopathic Pulmonary Fibrosis (IPF) is a deadly disease of unknown origin, which causes 80,000 deaths every year in the US and Europe combined. Unknown etiology and late diagnosis, combined with limited treatment options, contribute to a dismal survival rate of 3-5 years post diagnosis. Although molecular mechanisms underlying IPF pathogenesis and progression have been studied for over two decades, lack of in vivo models that recapitulate chronic, progressive, and irreversible nature of IPF have contributed to limited therapeutic success in clinical trials. Currently, only two drugs, Pirfenidone and Nintedanib, are approved for IPF treatment in the US, with their efficacy …

Cardiovascular Regulation By Kvβ1.1 Subunit, Jared Tur

USF Tampa Graduate Theses and Dissertations

Heterologous expression systems such as COS-7 cells have demonstrated the profound effects of KCNAB1-3 or Kvβ1-3 proteins on voltage gated potassium channels (Kv) channels. Indeed, in the presence of these β-subunits transiently expressed Kv channels are often modulated in multiple ways. Kv channel membrane expression is often increased in the presence of β-subunits. In addition, non-inactivating Kv currents suddenly become fast-inactivating and fast-inactivating channels become even faster. While much research has demonstrated the profound effects the β-subunits in particular the Kvβ1 subunit have on transiently expressed Kv currents little to date is known of the physiological role it may play. …

Infrared Spectroscopy Of The Nitrogenase Mofe Protein Under Electrochemical Control: Potential-Triggered Co Binding, P. Paengnakorn, Philip A. Ash, Sudipta K. Shaw, Karamatullah Danyal, T. Chen, Dennis R. Dean, Lance C. Seefeldt, Kylie A. Vincent

Chemistry and Biochemistry Faculty Publications

We demonstrate electrochemical control of the nitrogenase MoFe protein, in the absence of Fe protein or ATP, using europium(III/II) polyaminocarboxylate complexes as electron transfer mediators. This allows the potential dependence of proton reduction and inhibitor (CO) binding to the active site FeMo-cofactor to be established. Reduction of protons to H2 is catalyzed by the wild type MoFe protein and Β-98^Tyr→His and Β-^99Phe→His variants of the MoFe protein at potentials more negative than -800 mV (vs. SHE), with greater electrocatalytic proton reduction rates observed for the variants compared to the wild type protein. Electrocatalytic proton reduction is strongly …

P70s6k1 (S6k1)-Mediated Phosphorylation Regulates Phosphatidylinositol 4-Phosphate 5-Kinase Type I Γ Degradation And Cell Invasion, Naser Jafari, Qiaodan Zheng, Liqing Li, Wei Li, Lei Qi, Jianyong Xiao, Tianyan Gao, Cai Huang

Markey Cancer Center Faculty Publications

Phosphatidylinositol 4-phosphate 5-kinase type I γ (PIPKIγ90) ubiquitination and subsequent degradation regulate focal adhesion assembly, cell migration, and invasion. However, it is unknown how upstream signals control PIPKIγ90 ubiquitination or degradation. Here we show that p70S6K1 (S6K1), a downstream target of mechanistic target of rapamycin (mTOR), phosphorylates PIPKIγ90 at Thr-553 and Ser-555 and that S6K1-mediated PIPKIγ90 phosphorylation is essential for cell migration and invasion. Moreover, PIPKIγ90 phosphorylation is required for the development of focal adhesions and invadopodia, key machineries for cell migration and invasion. Surprisingly, substitution of Thr-553 and Ser-555 …

The European Eel Nccβ Gene Encodes A Thiazide-Resistant Na-Cl Cotransporter, Erika Moreno, Consuelo Plata, Alejandro Rodríguez-Gama, Eduardo R. Argaiz, Norma Vázquez, Karla Leyva, Carmen Y. Hernández-Carballo, León Islas, Christopher P. Cutler, Diana Pacheco-Alvarez, Adriana Mercado, Raquel Cariño-Cortés, Gerardo Gamba

Biology: Faculty Publications

The thiazide-sensitive Na-Cl cotransporter (NCC) is the major pathway for salt reabsorption in the mammalian distal convoluted tubule. NCC plays a key role in the regulation of blood pressure. Its inhibition with thiazides constitutes the primary baseline therapy for arterial hypertension. However, the thiazide-binding site in NCC is unknown. Mammals have only one gene encoding for NCC. The eel, however, contains a duplicate gene. NCCα is an ortholog of mammalian NCC and is expressed in the kidney. NCCβ is present in the apical membrane of the rectum. Here we cloned and functionally characterized NCCβ from the European eel. The cRNA …

Pleckstrin Homology (Ph) Domain Leucine-Rich Repeat Protein Phosphatase Controls Cell Polarity By Negatively Regulating The Activity Of Atypical Protein Kinase C, Xiaopeng Xiong, Xin Li, Yang-An Wen, Tianyan Gao

Markey Cancer Center Faculty Publications

The proper establishment of epithelial polarity allows cells to sense and respond to signals that arise from the microenvironment in a spatiotemporally controlled manner. Atypical PKCs (aPKCs) are implicated as key regulators of epithelial polarity. However, the molecular mechanism underlying the negative regulation of aPKCs remains largely unknown. In this study, we demonstrated that PH domain leucine-rich repeat protein phosphatase (PHLPP), a novel family of Ser/Thr protein phosphatases, plays an important role in regulating epithelial polarity by controlling the phosphorylation of both aPKC isoforms. Altered expression of PHLPP1 or PHLPP2 disrupted polarization of Caco2 cells grown in 3D cell cultures …

Mycosins Are Required For The Stabilization Of The Esx-1 And Esx-5 Type Vii Secretion Membrane Complexes, Vincent J. C. Van Winden, Roy Ummels, Sander R. Piersma, Connie R. Jiménez, Konstantin V. Korotkov, Wilbert Bitter, Edith N. G. Houben

Molecular and Cellular Biochemistry Faculty Publications

ABSTRACT Pathogenic mycobacteria contain up to five type VII secretion (T7S) systems, ESX-1 to ESX-5. One of the conserved T7S components is the serine protease mycosin (MycP). Strikingly, whereas MycP is essential for secretion, the protease activity of MycP₁ in Mycobacterium tuberculosis has been shown to be dispensable for secretion. The essential role of MycP therefore remains unclear. Here we show that MycP₁ and MycP₅ of M. marinum have similar phenotypes, confirming that MycP has a second unknown function that is essential for its T7S system. To investigate whether this role is related to proper functioning of …

Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Maintenance Of The Ph Gradient In The Gastric Mucus Layer., Owen Lewis

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Spyb, A Small Heme-Binding Protein, Affects The Composition Of The Cell Wall In Streptococcus Pyogenes, Rebecca J. Edgar, Jing Chen, Sashi Kant, Elena Rechkina, Jeffrey S. Rush, Lennart S. Forsberg, Bernhard Jaehrig, Parastoo Azadi, Veronika Tchesnokova, Evgeni V. Sokurenko, Haining Zhu, Konstantin V. Korotkov, Vijay Pancholi, Natalia Korotkova

Molecular and Cellular Biochemistry Faculty Publications

Streptococcus pyogenes (Group A Streptococcus or GAS) is a hemolytic human pathogen associated with a wide variety of infections ranging from minor skin and throat infections to life-threatening invasive diseases. The cell wall of GAS consists of peptidoglycan sacculus decorated with a carbohydrate comprising a polyrhamnose backbone with immunodominant N-acetylglucosamine side-chains. All GAS genomes contain the spyBA operon, which encodes a 35-amino-acid membrane protein SpyB, and a membrane-bound C3-like ADP-ribosyltransferase SpyA. In this study, we addressed the function of SpyB in GAS. Phenotypic analysis of a spyB deletion mutant revealed increased bacterial aggregation, and reduced sensitivity to β-lactams of the …

Purification Of 26s Proteasomes And Their Subcomplexes From Plants, Richard S. Marshall, David C. Gemperline, Richard D. Vierstra

Biology Faculty Research

The 26S proteasome is a highly dynamic, multisubunit, ATP-dependent protease that plays a central role in cellular housekeeping and many aspects of plant growth and development by degrading aberrant polypeptides and key cellular regulators that are first modified by ubiquitin. Although the 26S proteasome was originally enriched from plants over 30 years ago, only recently have significant advances been made in our ability to isolate and study the plant particle. Here, we describe two robust methods for purifying the 26S proteasome and its subcomplexes from Arabidopsis thaliana; one that involves conventional chromatography techniques to isolate the complex from wild-type …