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Identification And Characterization Of Small Compound Inhibitors Of Human Fatp2, Angel Sandoval, Aalap Chokshi, Elliot D. Jesch, Paul N. Black, Concetta C. DiRusso 2010 University of Nebraska-Lincoln

Identification And Characterization Of Small Compound Inhibitors Of Human Fatp2, Angel Sandoval, Aalap Chokshi, Elliot D. Jesch, Paul N. Black, Concetta C. Dirusso

Biochemistry -- Faculty Publications

Fatty acid transport proteins (FATPs) are bifunctional proteins, which transport long chain fatty acids into cells and activate very long chain fatty acids by esterification with coenzyme A. In an effort to understand the linkage between cellular fatty acid transport and the pathology associated with excessive accumulation of exogenous fatty acids, we targeted FATP-mediated fatty acid transport in a high throughput screen of more than 100,000 small diverse chemical compounds in yeast expressing human FATP2 (hsFATP2). Compounds were selected for their ability to depress the transport of the fluorescent long chain fatty acid analogue, C1-BODIPY-C12. Among ...


Transcriptional Defense Response Of The Soybean Plant, Glycine Max, In Reaction To Infestation By The Soybean Aphid, Aphis Glycines, Matthew Edward Studham 2010 Iowa State University

Transcriptional Defense Response Of The Soybean Plant, Glycine Max, In Reaction To Infestation By The Soybean Aphid, Aphis Glycines, Matthew Edward Studham

Graduate Theses and Dissertations

The soybean aphid (Aphis glycines), first spotted in North American fields in 2000, is a major pest of the soybean plant (Glycine max) and can cause millions of dollars in yield losses. The goal of my project was to reveal the transcriptional defense response to soybean aphids in aphid-susceptible soybean plants and aphid-resistant soybean plants with the Rag1 gene. These responses were determined by using Affymetrix GeneChip® Soybean Genome Arrays to characterize transcript levels from leaf tissue collected after one, seven, and twenty-one days of aphid infestation. In addition to the microarray analysis, a bioinformatics tool was developed to determine ...


Interaction Between The Saga Complex And Chromatin Regulates Nucleosome Acetylation And Inducible Gene Transcription, Shanshan Li 2010 Iowa State University

Interaction Between The Saga Complex And Chromatin Regulates Nucleosome Acetylation And Inducible Gene Transcription, Shanshan Li

Graduate Theses and Dissertations

The SAGA family of coactivators is a group of highly conserved histone acetyltransferases that is essential for transcription of genes participating in stress adaptation and developemental processes. Misregulation of SAGA function can lead to developmental diseases and cancer. One important function of SAGA in regulating gene expression is to acetylate nucleosomes at both gene promoters and coding regions. To understand the molecular mechanism of nucleosome acetylation, much work has been done using recombinant Gcn5, the catalytic subunit of SAGA, and histone proteins or peptides. However, little is known about how histones are acetylated by full SAGA complex in the context ...


Transcriptional Regulation Of Proapoptotic Kinase Pkcî´ Expression In Dopaminergic Neurons: Relevance To Gene-Gene And Gene-Environment Interactions In Neurodegeneration, Huajun Jin 2010 Iowa State University

Transcriptional Regulation Of Proapoptotic Kinase Pkcî´ Expression In Dopaminergic Neurons: Relevance To Gene-Gene And Gene-Environment Interactions In Neurodegeneration, Huajun Jin

Graduate Theses and Dissertations

We investigated the mechanisms of transcriptional regulation of the PKCδ gene. By deletion analysis of the ~1.4 kb (-1448 to +1, relative to transcription start site) 5'-flanking sequence of the mouse PKCδ gene, we have identified a basal promoter region, nucleotide -148 to +1, required for sufficient PKCδ transcription in NIE115, MN9D, and N2a cells. We further identified two NFκB binding sites (κB 1, κB 2) as well as a NERF1a site within the basal promoter as key regulatory elements in the mouse PKCδ TATA-less promoter. Subsequent functional studies using site-directed mutation analysis revealed that κB 1, but ...


Udp-Glucose Dehydrogenase As A Novel Field-Specific Candidate Biomarker Of Prostate Cancer, Dali Huang, George P. Casale, Jun Tian, Subodh M. Lele, Vladimir M. Pisarev, Melanie A. Simpson, George P. Hemstreet III 2010 University of Nebraska Medical Center, Omaha, NE

Udp-Glucose Dehydrogenase As A Novel Field-Specific Candidate Biomarker Of Prostate Cancer, Dali Huang, George P. Casale, Jun Tian, Subodh M. Lele, Vladimir M. Pisarev, Melanie A. Simpson, George P. Hemstreet Iii

Biochemistry -- Faculty Publications

Uridine diphosphate (UDP)-glucose dehydrogenase (UGDH) catalyzes the oxidation of UDP-glucose to yield UDP-glucuronic acid, a precursor for synthesis of glycosaminoglycans and proteoglycans that promote aggressive prostate cancer (PC) progression. The purpose of our study was to determine if the UGDH expression in normal appearing acini (NAA) from cancerous glands is a candidate biomarker for PC field disease/effect assayed by quantitative fluorescence imaging analysis (QFIA). A polyclonal antibody to UGDH was titrated to saturation binding and fluorescent microscopic images acquired from fixed, paraffin-embedded tissue slices were quantitatively analyzed. Specificity of the assay was confirmed by Western blot analysis and ...


Development Of Ultra-Sensitive Fluorescence Photoamplification Assays For The Detection Of Molecular Recognition Events, Tiffany Priscilla Gustafson 2010 University of Denver

Development Of Ultra-Sensitive Fluorescence Photoamplification Assays For The Detection Of Molecular Recognition Events, Tiffany Priscilla Gustafson

Electronic Theses and Dissertations

During the course of this research a novel method which couples the molecular recognition-triggered photoamplification chain in diaryl ketone adducts of dithiane with a "turn-off" or "turn-on" fluorescence-based assay for the detection of biological targets and ligands, regardless of their nature, through a molecular recognition event has been developed. This research has included several key steps, the most significant being: (1) the design of fluorophore adducts or dyads which recover fluorescence upon photocleavage for a "turn-on" assay and the identification of fluorophores which are quenched upon the photochemical release of a quencher for a "turn off" assay; (2) Optimization of ...


Programmable Diagnostic Devices Made From Paper And Tape, Andres W. Martinez, Scott T. Phillips, Zhihong Nie, Chao-Min Cheng, Emanuel Carrilho, Benjamin J. Wiley, George M. Whitesides 2010 Harvard University

Programmable Diagnostic Devices Made From Paper And Tape, Andres W. Martinez, Scott T. Phillips, Zhihong Nie, Chao-Min Cheng, Emanuel Carrilho, Benjamin J. Wiley, George M. Whitesides

Chemistry and Biochemistry

This paper describes three-dimensional microfluidic paper-based analytical devices (3-D μPADs) that can be programmed (postfabrication) by the user to generate multiple patterns of flow through them. These devices are programmed by pressing single-use ‘on’ buttons, using a stylus or a ballpoint pen. Pressing a button closes a small space (gap) between two vertically aligned microfluidic channels, and allows fluids to wick from one channel to the other. These devices are simple to fabricate, and are made entirely out of paper and double-sided adhesive tape. Programmable devices expand the capabilities of μPADs and provide a simple method for controlling the movement ...


Biochemical Characterization Of Suppressor Of Ikk-Ε And Nak-Associated Protein 1, Jonathan Forbes 2010 Virginia Commonwealth University

Biochemical Characterization Of Suppressor Of Ikk-Ε And Nak-Associated Protein 1, Jonathan Forbes

Theses and Dissertations

Innate immunity provides the first line of defense against invading pathogen by recognizing and mounting a response to the pathogenic challenge. Among the cellular mechanisms of the innate immune response, Toll-like receptor 3 (TLR3) recognizes viral dsRNA and signals subsequent production of type-I interferon. The TLR3:interferon signaling cascades contains a kinase complex composed of two kinases and a scaffold protein, NAK-associated protein 1 (NAP1). The role of NAP1 in modulating kinase activation or regulation is unknown. A key inhibitory protein identified in the TLR3:interferon pathway, silencer of inhibitor of κBα kinase ε (SIKE), blocks the activity of this ...


Genetic Regulation Of Bovine Milk Fatty Acid Composition: Improving The Healthfulness Of Milk Through Selection, Rafael Nafikov 2010 Iowa State University

Genetic Regulation Of Bovine Milk Fatty Acid Composition: Improving The Healthfulness Of Milk Through Selection, Rafael Nafikov

Graduate Theses and Dissertations

The current study was designed to identity polymorphisms in the genes involved in milk lipid biosynthesis to provide animal breeders with tools that allow selection of animals producing milk with healthier fatty acid composition. High concentrations of saturated fatty acids (SFA) in human diets are known to increase plasma cholesterol concentrations and, as a result, increase the risk of developing cardiovascular diseases (CVD), the number one cause of death worldwide. Because bovine milk is one of the primary sources of SFA and individual atherogenic fatty acids such as palmitic (16:0) and myristic (14:0) in human diets the improvement ...


Electroporation-Mediated Delivery Of A Naked Dna Plasmid Expressing Vegf To The Porcine Heart Enhances Protein Expression, W. G. Marshall Jr., B. A. Boone, J. D. Burgos, S. I. Gografe, M. K. Baldwin, M. L. Danielson, M. J. Larson, D. R. Caretto, Y. Cruz, B. Ferraro, L. C. Heller, K. E. Ugen, M. J. Jaroszeski, R. Heller 2010 Old Dominion University

Electroporation-Mediated Delivery Of A Naked Dna Plasmid Expressing Vegf To The Porcine Heart Enhances Protein Expression, W. G. Marshall Jr., B. A. Boone, J. D. Burgos, S. I. Gografe, M. K. Baldwin, M. L. Danielson, M. J. Larson, D. R. Caretto, Y. Cruz, B. Ferraro, L. C. Heller, K. E. Ugen, M. J. Jaroszeski, R. Heller

Bioelectrics Publications

Gene therapy is an attractive method for the treatment of cardiovascular disease. However, using current strategies, induction of gene expression at therapeutic levels is often inefficient. In this study, we show a novel electroporation (EP) method to enhance the delivery of a plasmid expressing an angiogenic growth factor (vascular endothelial growth factor, VEGF), which is a molecule previously documented to stimulate revascularization in coronary artery disease. DNA expression plasmids were delivered in vivo to the porcine heart with or without coadministered EP to determine the potential effect of electrically mediated delivery. The results showed that plasmid delivery through EP significantly ...


Increased Perfusion And Angiogenesis In A Hindlimb Ischemia Model With Plasmid Fgf-2 Delivered By Noninvasive Electroporation, B. Ferraro, Y. L. Cruz, M. Baldwin, D. Coppola, R. Heller 2010 Old Dominion University

Increased Perfusion And Angiogenesis In A Hindlimb Ischemia Model With Plasmid Fgf-2 Delivered By Noninvasive Electroporation, B. Ferraro, Y. L. Cruz, M. Baldwin, D. Coppola, R. Heller

Bioelectrics Publications

Gene therapy approaches delivering fibroblast growth factor-2 (FGF-2) have shown promise as a potential treatment for increasing blood flow to ischemic limbs. Currently, effective noninvasive techniques to deliver plasmids encoding genes of therapeutic interest, such as FGF-2, are limited. We sought to determine if intradermal injection of plasmid DNA encoding FGF-2 (pFGF) followed by noninvasive cutaneous electroporation (pFGFE+) could increase blood flow and angiogenesis in a rat model of hindlimb ischemia. pFGFE+ or control treatments were administered on postoperative day 0. Compared to injection of pFGF alone (pFGFE-), delivery of pFGFE+ significantly increased FGF-2 expression for 10 days. Further, the ...


Frustrated Drift Of An Anchored Scroll-Wave Filament And The Geodesic Principle, Marcel Wellner, Christian W. Zemlin, Arkady M. Pertsov 2010 Old Dominion University

Frustrated Drift Of An Anchored Scroll-Wave Filament And The Geodesic Principle, Marcel Wellner, Christian W. Zemlin, Arkady M. Pertsov

Bioelectrics Publications

We investigate anchored scroll-wave filaments in an excitable medium whose diffusivity matrix, including its determinant, is spatially nonuniform. The study is motivated by cardiological applications where scroll-wave behavior in the presence of diffusivity gradients is believed to play an important role in the development of severe arrhythmias. A diffusivity gradient is expected to make the filament drift, unless drift is prevented ("frustrated") by anchoring to localized defects in the propagation medium. The resulting stationary filament is a geodesic curve, as demonstrated here in the case of a nonzero but constant gradient. That is, the diffusivity matrix has a determinant that ...


Structure Of The Proline Utilization A Proline Dehydrogenase Domain Inactivated By N-Propargylglycine Provides Insight Into Conformational Changes Induced By Substrate Binding And Flavin Reduction, Dhiraj Srivastava, Weidong Zhu, William H. Johnson Jr., Christian P. Whitman, Donald F. Becker, John J. Tanner 2010 University of Missouri-Columbia

Structure Of The Proline Utilization A Proline Dehydrogenase Domain Inactivated By N-Propargylglycine Provides Insight Into Conformational Changes Induced By Substrate Binding And Flavin Reduction, Dhiraj Srivastava, Weidong Zhu, William H. Johnson Jr., Christian P. Whitman, Donald F. Becker, John J. Tanner

Biochemistry -- Faculty Publications

Proline utilization A (PutA) from Escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. Previous studies have shown that the binding of proline in the proline dehydrogenase (PRODH) active site and subsequent reduction of the FAD trigger global conformational changes that enhance PutA-membrane affinity. These events cause PutA to switch from its repressor to enzymatic role, but the mechanism by which this signal is propagated from the active site to the distal membrane-binding domain is largely unknown. Here, it ...


Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly 2010 Iowa State University

Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly

Chemical and Biological Engineering Publications

A gene encoding a glycoside hydrolase family 44 (GH44) protein from Clostridium acetobutylicum ATCC 824 was synthesized and transformed into Escherichia coli.The previously uncharacterized protein was expressed with a C-terminal His tag and purified by nickel-nitrilotriacetic acid affinity chromatography. Crystallization and X-ray diffraction to a 2.2-Å resolution revealed a triose phosphate isomerase (TIM) barrel-like structure with additional Greek key and β-sandwich folds, similar to other GH44 crystal structures. The enzyme hydrolyzes cellotetraose and larger cellooligosaccharides, yielding an unbalanced product distribution, including some glucose. It attacks carboxymethylcellulose and xylan at approximately the same rates. Its activity on carboxymethylcellulose is ...


Genetic Connections Between Neurological Disorders And Cholesterol Metabolism, Ingemar Bjorkhem, Valerio Leoni, Steve Meaney 2010 Karolinska Institute

Genetic Connections Between Neurological Disorders And Cholesterol Metabolism, Ingemar Bjorkhem, Valerio Leoni, Steve Meaney

Articles

Cholesterol is an essential component of both the peripheral and central nervous systems of mammals. Over the last decade, evidence has accumulated that disturbances in cholesterol metabolism are associated with the development of various neurological conditions. In addition to genetically defined defects in cholesterol synthesis, which will be covered in another review in this Thematic Series, defects in cholesterol metabolism (cerebrotendinous xanthomatosis) and intracellular transport (Niemann Pick Syndrome) lead to neurological disease. A subform of hereditary spastic paresis (type SPG5) and Huntington's disease are neurological diseases with mutations in genes that are of importance for cholesterol metabolism. Neurodegeneration is ...


Role Of Muscle C-Jun Nh2-Terminal Kinase 1 In Obesity-Induced Insulin Resistance, Guadalupe Sabio, Norman J. Kennedy, Julie Cavanagh-Kyros, Dae Young Jung, Hwi Jin Ko, Helena Ong, Tamera Barrett, Jason K. Kim, Roger J. Davis 2010 University of Massachusetts Medical School

Role Of Muscle C-Jun Nh2-Terminal Kinase 1 In Obesity-Induced Insulin Resistance, Guadalupe Sabio, Norman J. Kennedy, Julie Cavanagh-Kyros, Dae Young Jung, Hwi Jin Ko, Helena Ong, Tamera Barrett, Jason K. Kim, Roger J. Davis

Davis Lab Publications

Obesity caused by feeding of a high-fat diet (HFD) is associated with an increased activation of c-Jun NH(2)-terminal kinase 1 (JNK1). Activated JNK1 is implicated in the mechanism of obesity-induced insulin resistance and the development of metabolic syndrome and type 2 diabetes. Significantly, Jnk1(-)(/)(-) mice are protected against HFD-induced obesity and insulin resistance. Here we show that an ablation of the Jnk1 gene in skeletal muscle does not influence HFD-induced obesity. However, muscle-specific JNK1-deficient (M(KO)) mice exhibit improved insulin sensitivity compared with control wild-type (M(WT)) mice. Thus, insulin-stimulated AKT activation is suppressed in muscle, liver, and ...


Functional Cooperation Of The Proapoptotic Bcl2 Family Proteins Bmf And Bim In Vivo, Anette Hubner, Julie Cavanagh-Kyros, Mercedes Rincon, Richard Flavell, Roger J. Davis 2010 University of Massachusetts Medical School

Functional Cooperation Of The Proapoptotic Bcl2 Family Proteins Bmf And Bim In Vivo, Anette Hubner, Julie Cavanagh-Kyros, Mercedes Rincon, Richard Flavell, Roger J. Davis

Davis Lab Publications

Bcl2-modifying factor (Bmf) is a member of the BH3-only group of proapoptotic proteins. To test the role of Bmf in vivo, we constructed mice with a series of mutated Bmf alleles that disrupt Bmf expression, prevent Bmf phosphorylation by the c-Jun NH(2)-terminal kinase (JNK) on Ser(74), or mimic Bmf phosphorylation on Ser(74). We report that the loss of Bmf causes defects in uterovaginal development, including an imperforate vagina and hydrometrocolpos. We also show that the phosphorylation of Bmf on Ser(74) can contribute to a moderate increase in levels of Bmf activity. Studies of compound mutants ...


The Role Of Igf-1 And Notch Signaling In Thoracic Malignancies., Sandra Eliasz 2010 Loyola University Chicago

The Role Of Igf-1 And Notch Signaling In Thoracic Malignancies., Sandra Eliasz

Dissertations

Thoracic malignancies are one of the deadliest of all cancers, being the leading cause of cancer death in the Western world. Thoracic malignancies arise from different tissues; however the most common are of epithelial (commonly referred to as non-small cell lung cancer, or NSCLC), neuroendocrine (small cell lung cancer, or SCLC) and mesothelial origin (malignant mesothelioma, or MM). The DNA oncogenic virus Simian Virus 40 (SV40) has been shown to cooperate with environmental oncogenic fibers in the onset of MM. Insulin like growth factor-1 (IGF-1) signaling plays a central role in all thoracic malignancies and in the process of SV40-mediated ...


New Cyclophanes As Supramolecular Scaffolds: The Synthesis Of Tribenzo-1,4,7-Triazacyclononatriene., Andria M. Panagopoulos 2010 Loyola University Chicago

New Cyclophanes As Supramolecular Scaffolds: The Synthesis Of Tribenzo-1,4,7-Triazacyclononatriene., Andria M. Panagopoulos

Dissertations

Supramolecular chemistry involves the formation of complex molecular entities that have the capacity to participate in specific molecular recognition of guest molecules. A commonly employed scaffold in supramolecular chemistry is the trimeric crown-shaped molecule cyclotriveratrylene (CTV). CTV has been studied extensively for its capability of binding a number of smaller organic and organometallic guests within its bowl-shaped cleft and has been used as a building block enabling the construction of more complex cryptophanes. The goal of this research is the synthesis and characterization of a novel cyclophane, tribenzo-1,4,7-triazacyclononene and derivatives thereof. These new cyclophanes should have greater versatility ...


Epsvr And Epmeta: Prediction Of Antigenic Epitopes Using Support Vector Regression And Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang 2010 Jacobs University Bremen

Epsvr And Epmeta: Prediction Of Antigenic Epitopes Using Support Vector Regression And Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang

Faculty Publications in the Biological Sciences

Background: Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - currently there are only a few discontinuous epitope prediction servers available, though discontinuous peptides constitute the majority of all B-cell antigenic epitopes. The small number of structures for antigen-antibody complexes limits the development of reliable discontinuous epitope prediction methods and an unbiased benchmark to evaluate developed methods.

Results: In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta is a meta ...


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