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Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller 2010 University of Connecticut - Storrs

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Publications

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein ...


Neuroprotection With Anesthetics In Two Models Of Cerebral Ischemia, Rafael Eduardo Chaparro-Buitrago 2010 University of South Florida

Neuroprotection With Anesthetics In Two Models Of Cerebral Ischemia, Rafael Eduardo Chaparro-Buitrago

Graduate Theses and Dissertations

Neuroprotection with anesthetics has been studied for many decades; important advances in this field have modified the way Anesthesiologists treat patients in the operating room. Animal models have played an important role in the study of ischemia in the operating room. Recent studies have demonstrated that the effect of anesthetics seems to be different in different animal models. We decided to evaluate anesthetics in a well-known model of cerebral ischemia and also in hypotensive models designed by us. We used a model of cerebral ischemia (MCAO) to test anesthetics neuroprotective effect in a two-week period. Then, we used a model ...


T10c12 Conjugated Linoleic Acid Causes Delipidation In 3t3-L1 Adipocytes And Mice, shan jiang 2010 University of Nebraska - Lincoln

T10c12 Conjugated Linoleic Acid Causes Delipidation In 3t3-L1 Adipocytes And Mice, Shan Jiang

Theses and Dissertations in Animal Science

T10c12 conjugated linoleic acid (t10c12 CLA) causes the reduction of triglyceride contents in adipocytes. T10c12 CLA’s delipidation effect is associated with decreased nutrient uptake, adipogenesis, lipogenesis, and increased energy expenditure, lipolysis, fatty acid oxidation in adipocytes. However, the molecular mechanisms of CLA’s delipidation effects are still unknown. AMP-activated protein kinase (AMPK), a central regulator of cellular energy levels, is activated by an increase in the cellular AMP:ATP ratio or various cellular stresses. We demonstrated that t10c12 CLA activated AMPK in 3T3-L1 adipocytes, leading to inhibition of anabolic biosynthesis and increase of energy expenditure. Strong activation of AMPK ...


Ribosomal Rna Mutations That Inhibit The Activity Of Transfer-Messenger Rna Of Stalled Ribosomes, Jacob N. Crandall 2010 Brigham Young University - Provo

Ribosomal Rna Mutations That Inhibit The Activity Of Transfer-Messenger Rna Of Stalled Ribosomes, Jacob N. Crandall

All Theses and Dissertations

In eubacteria, stalled ribosomes are rescued by a conserved quality-control mechanism involving transfer-messenger RNA (tmRNA) and its protein partner SmpB. Mimicking a tRNA, tmRNA enters stalled ribosomes, adds Ala to the nascent polypeptide, and serves as a template to encode a short peptide that tags the nascent protein for destruction. To further characterize the tagging process, we developed two genetic selections that link tmRNA activity to cell death. These negative selections can be used to identify inhibitors of tagging or to identify mutations in key residues essential for ribosome rescue. Little is known about which ribosomal elements are specifically required ...


Dynamics On Multiple Timescales In The Rna-Directed Rna Polymerase From The Cystovirus Φ6, Zhen Ren, Hsin Wang, Ranajeet Ghose 2010 CUNY City College

Dynamics On Multiple Timescales In The Rna-Directed Rna Polymerase From The Cystovirus Φ6, Zhen Ren, Hsin Wang, Ranajeet Ghose

Publications and Research

The de novoinitiating RNA-directed RNA polymerase (RdRP), P2, forms the central machinery in the infection cycle of the bacteriophage ϕ6 by performing the dual tasks of replication and transcription of the double-stranded RNA genome in the host cell. By measurement and quantitative analysis of multiple-quantum spin-relaxation data for the δ1 positions of Ile residues that are distributed over the 3D-fold of P2, we find that the enzyme is dynamic both on the fast (ps–ns) and slow (µs–ms) timescales. The characteristics of several motional modes including those that coincide with the catalytic timescale (500–800/s) are altered ...


Phosphorylation Of Su(Var)3–9 By The Chromosomal Kinase Jil-1, Joern Boeke, Catherine Regnard, Weili Cai, Jorgen Johansen, Kristen M. Johansen, Peter B. Becker, Axel Imhof 2010 Ludwig Maximilians University of Munich

Phosphorylation Of Su(Var)3–9 By The Chromosomal Kinase Jil-1, Joern Boeke, Catherine Regnard, Weili Cai, Jorgen Johansen, Kristen M. Johansen, Peter B. Becker, Axel Imhof

Biochemistry, Biophysics and Molecular Biology Publications

The histone methyltransferase SU(VAR)3–9 plays an important role in the formation of heterochromatin within the eukaryotic nucleus. Several studies have shown that the formation of condensed chromatin is highly regulated during development, suggesting that SU(VAR)3–9's activity is regulated as well. However, no mechanism by which this may be achieved has been reported so far. As we and others had shown previously that the N-terminus of SU(VAR)3–9 plays an important role for its activity, we purified interaction partners from Drosophila embryo nuclear extract using as bait a GST fusion protein containing ...


Inhibiting Mirna In Caenorhabditis Elegans Using A Potent And Selective Antisense Reagent, Genhua Zheng, Victor R. Ambros, Wen-hong Li 2010 University of Texas Southwestern Medical Center

Inhibiting Mirna In Caenorhabditis Elegans Using A Potent And Selective Antisense Reagent, Genhua Zheng, Victor R. Ambros, Wen-Hong Li

Program in Molecular Medicine Publications and Presentations

BACKGROUND: Antisense reagents can serve as efficient and versatile tools for studying gene function by inhibiting nucleic acids in vivo. Antisense reagents have particular utility for the experimental manipulation of the activity of microRNAs (miRNAs), which are involved in the regulation of diverse developmental and physiological pathways in animals. Even in traditional genetic systems, such as the nematode Caenorhabditis elegans, antisense reagents can provide experimental strategies complementary to mutational approaches. Presently no antisense reagents are available for inhibiting miRNAs in the nematode C. elegans.

RESULTS: We have developed a new class of fluorescently labelled antisense reagents to inhibit miRNAs in ...


Aspergillus Fumigatus Stimulates The Nlrp3 Inflammasome Through A Pathway Requiring Ros Production And The Syk Tyrosine Kinase, Najwane Saïd-Sadier, Eduardo V. Padilla, Gordon Langsley, David M. Ojcius 2010 University of California, Merced

Aspergillus Fumigatus Stimulates The Nlrp3 Inflammasome Through A Pathway Requiring Ros Production And The Syk Tyrosine Kinase, Najwane Saïd-Sadier, Eduardo V. Padilla, Gordon Langsley, David M. Ojcius

Dugoni School of Dentistry Faculty Articles

Invasive aspergillosis (IA) is a life-threatening disease that occurs in immunodepressed patients when infected with Aspergillus fumigatus. This fungus is the second most-common causative agent of fungal disease after Candida albicans. Nevertheless, much remains to be learned about the mechanisms by which A. fulmigatus activates the innate immune system. We investigated the inflammatory response to conidia and hyphae of A. fumigatus and specifically, their capacity to trigger activation of an inflammasome. Our results show that in contrast to conidia, hyphal fragments induce NLRP3 inflammasome assembly, caspase-1 activation and IL-1β release from a human monocyte cell line. The ability of Aspergillus ...


Computational Protein Design: Advances In The Design And Redesign Of Biomolecular Nanostructures, Jeffery G. Saven 2010 University of Pennsylvania

Computational Protein Design: Advances In The Design And Redesign Of Biomolecular Nanostructures, Jeffery G. Saven

Departmental Papers (Chemistry)

Computational protein design facilitates the continued development of methods for the design of biomolecular structure, sequence and function. Recent applications include the design of novel protein sequences and structures, proteins incorporating nonbiological components, protein assemblies, soluble variants of membrane proteins, and proteins that modulate membrane function.


Synthesis Of Cifidabco And Mannose Co-Functionalized G(4)-Pamam Dendrimer For Use In Antibiotics, Harrison VanKoten 2010 Carroll College, Helena, MT

Synthesis Of Cifidabco And Mannose Co-Functionalized G(4)-Pamam Dendrimer For Use In Antibiotics, Harrison Vankoten

Chemistry and Physics Undergraduate Theses

Synthesis of C16DABCO and mannose co-functionalized G(4)-PAMAM dendrimer is expected to yield a useful antimicrobial that is effective in binding to mannose specific lectins on bacterial fimbriae. Thus far, mannose has been attached to the dendrimer with near complete functionalization. C16DABCO and mannose cofunctionalized G(4)-PAMAM dendrimer have been synthesized, but not in sufficient quantities to allow examination of its the antibacterial properties. Future work includes optimizing the final synthesis and performing toxicity studies.


The Effects Of Glycosylation On Prion Protein Conversion, Christopher Casebeer 2010 Carroll College, Helena, MT

The Effects Of Glycosylation On Prion Protein Conversion, Christopher Casebeer

Life and Environmental Sciences Undergraduate Theses

Glycosylation of the prion protein may be experimentally altered through expression in different insect cell lines. The presence or absence of several terminal sugars may or may not have an effect on the conversion efficiency of the prion protein into its infectious form. The main focus of this research was to characterize the prion protein as it is produced in two varying insect cell lines that are able to glycosylate proteins to different extents. Glycosidase treatment demonstrated that the expressed prion protein was glycosylated. Lectin blotting was used to assess the presence or absence of terminal sugar moieties existing on ...


The Development Of A Quantitative Assay To Measure The Effects Of Protein Disulfide Isomerase On Prion Protein Misfolding, Lauren Vogl 2010 Carroll College, Helena, MT

The Development Of A Quantitative Assay To Measure The Effects Of Protein Disulfide Isomerase On Prion Protein Misfolding, Lauren Vogl

Life and Environmental Sciences Undergraduate Theses

The objective ofthis project was to develop a quantitative assay to measure the misfolding ofprion proteins that can be used to assess the effects of Protein Disulfide Isomerase (PDI) on the misfolding process ofthe Chronic Wasting Disease (CWD) prion protein. CWD is a spongiform encephalopathy native to animals in the family Cervidae, which includes whitetail deer, mule deer, elk and moose. CWD is caused by the misfolding ofprion proteins. Qualitative observations from previous studies indicate that disulfide bond rearrangement might be a rate limiting step in the misfolding process. There is a need to be able to quantitate the amount ...


Characterization And Normalization Of Rat Salivary Cholinesterase, Elise Klohe 2010 Carroll College, Helena, MT

Characterization And Normalization Of Rat Salivary Cholinesterase, Elise Klohe

Life and Environmental Sciences Undergraduate Theses

Cholinesterase (ChE) is an enzyme which allows neurons to return to a resting state by hydrolyzing the neurotransmitter acetylcholine. Organophosphate pesticides, which are commonly used in agriculture, inhibit the activity of ChE. The inhibition of ChE activity in plasma and red blood cells is used as a biomarker for human pesticide exposure. Currently, salivary ChE activity is being examined as a non-invasive biomarker; however little is known about baseline ChE activity in saliva. In order to characterize baseline salivary ChE, saliva was collected from 5 adult male SpragueDawley rats, salivary ChE was measured using the Ellman assay, and total salivary ...


Effect Of Membrane Cholesterol Levels And Allelic Variation On Prion Conversion, Ross Hartman 2010 Carroll College, Helena, MT

Effect Of Membrane Cholesterol Levels And Allelic Variation On Prion Conversion, Ross Hartman

Life and Environmental Sciences Undergraduate Theses

Chronic Wasting Disease (CWD) is caused by an accumulation of misfolded prion proteins (PrPsc) and subsequent plaque formation in the central nervous system. CWD is horizontally transferable; misfolded prions from one animal can enter another and cause normal prion proteins (PrPc) to misfold. This misfolding process is termed prion conversion. In natural deer populations an allelic variation in the prion gene is thought to confer resistance to CWD. Wild type mule deer are serine (S) homozygotes at codon 225. Mule deer that are Serine/ Phenyalanine (S/F) heterozygotes exhibit resistance to prion infection. In this study the F encoding allele ...


An Entrepreneurial Approach To Librarianship, Flora G. Shrode, Jennifer R. Duncan, Wendy Holliday 2010 Utah State University

An Entrepreneurial Approach To Librarianship, Flora G. Shrode, Jennifer R. Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking ...


An Entrepreneurial Approach To Librarianship, Flora G. Shrode, Jennifer R. Duncan, Wendy Holliday 2010 Utah State University

An Entrepreneurial Approach To Librarianship, Flora G. Shrode, Jennifer R. Duncan, Wendy Holliday

Flora Shrode

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking ...


Section Abstracts: Structural Biology, Biochemistry, And Biophysics, 2010 Old Dominion University

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 88th Annual Meeting of the Virginia Academy of Science, May 20-21, 2015. James Madison University, Harrisonburg, Virginia.


Section Abstracts: Biology With Microbiology And Molecular Biology, 2010 Old Dominion University

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 88th Annual Meeting for the Virginia Academy of Science, May 20-21, 2010, James Madison University, Harrisonburg, VA.


The Effects Of Cocaine And Ecstasy On Cardiac Myocytes And The Intact Myocardium, David A. Tiangco 2010 Old Dominion University

The Effects Of Cocaine And Ecstasy On Cardiac Myocytes And The Intact Myocardium, David A. Tiangco

Theses and Dissertations in Biomedical Sciences

Cocaine and ecstasy are widely used illicit drugs. Both drugs have undergone intense scrutiny as information regarding their side-effects has become available. One important yet incomplete area of investigation pertains to their effects on the heart. The purpose of the current studies was to test the hypothesis that exposure to cocaine or ecstasy will adversely affect cellular homeostasis and normal heart function. Cultured cardiac myocytes (H9c2) and New Zealand White rabbits (Oryctolagus cuniculus) were used to measure the responses to various concentrations of cocaine or ecstasy at both the cellular and intact organ system levels. We observed that cocaine and ...


Characterization Of Glycation Sites On Human Serum Albumin Using Mass Spectrometry, Omar S. Barnaby 2010 University of Nebraska-Lincoln

Characterization Of Glycation Sites On Human Serum Albumin Using Mass Spectrometry, Omar S. Barnaby

Student Research Projects, Dissertations, and Theses - Chemistry Department

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation ...


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