Open Access. Powered by Scholars. Published by Universities.®

Biochemistry, Biophysics, and Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

12,473 Full-Text Articles 26,200 Authors 1,658,542 Downloads 249 Institutions

All Articles in Biochemistry, Biophysics, and Structural Biology

Faceted Search

12,473 full-text articles. Page 418 of 428.

Coupling Into Waveguide Evanescent Modes With Applications In Electron Paramagnetic Resonance, Jason Walter Sidabras 2010 Marquette University

Coupling Into Waveguide Evanescent Modes With Applications In Electron Paramagnetic Resonance, Jason Walter Sidabras

Master's Theses (2009 -)

The use of analytical and numerical techniques in solving the coupling of evanescent modes in a microwave waveguide through slots can be optimized to create a uniform magnetic field excitation on axis within a waveguide. This work has direct applications in Electron Paramagnetic Resonance (EPR) where a 100~kHz time-varying magnetic field is incident on a sample contained in a microwave cavity. Typical cavity designs do not take into consideration the uniformity of the 100~kHz field modulation and assume it to be uniform enough over the sample region from quasi-static principles. This work shows otherwise and uses Ansoft (Pittsburgh ...


Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt 2010 Old Dominion University

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new ...


From The Valleys To The Mountains: The Biographic History Of Antelope Squirrels, Bats, And Chipmunks In Western North America, Stacy James Mantooth 2010 University of Nevada Las Vegas

From The Valleys To The Mountains: The Biographic History Of Antelope Squirrels, Bats, And Chipmunks In Western North America, Stacy James Mantooth

UNLV Theses, Dissertations, Professional Papers, and Capstones

Genetic differentiation within and between species often coincides with significant geological or climatic changes that have shaped the sizes and locations of their geographic ranges and altered the connectivity between populations over time. Across western North America, many endemic taxa experienced high levels of initial divergence associated with geological transformations of the Neogene, with subsequent diversification and geographic structuring of populations associated with climatic changes during the Quaternary. As such, we can use a combination of molecular markers and genetic analyses to effectively examine the evolutionary and biogeographic histories of populations, species, and regional biotas whose signatures of differentiation are ...


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 ...


The Genomics Education Partnership: Successful Integration Of Research Into Laboratory Classes At A Diverse Group Of Undergraduate Institutions, Christopher D. Shaffer, Consuelo Alvarez, Cheryl Bailey, Daron Barnard, Satish Bhalla, Chitra Chandrasekaran, Vidya Chandrasekaran, Hui-Min Chung, Douglas R. Dorer, Chunguang Du, Todd T. Eckdahl, Jeff L. Poet, Donald Frohlich, Anya L. Goodman, Yuying Gossner, Charles Hauser, Laura L.M. Hoopes, Diana Johnson, Christopher J. Jones, Marian Kaehler, Nighat Kokan, Olga R. Kopp, Gary A. Kuleck, Gerard McNeil, Robert Moss, Jennifer L. Myka, Alexis Nagengast, Robert Morris, Paul J. Overvoorde, Elizabeth Shoop, Susan Parrish, Kelynne Reed, E. Gloria Regisford, Dennis Revie, Anne G. Rosenwald, Ken Saville, Stephanie Schroeder, Mary Shaw, Gary Skuse, Christopher Smith, Mary Smith, Eric P. Spana, Mary Spratt, Joyce Stamm, Jeff S. Thompson, Matthew Wawersik, Barbara A. Wilson, Jim Youngblom, Wilson Leung, Jeremy Buhler, Elaine R. Mardis, David Lopatto, Sarah C.R. Elgin 2010 Washington University in St. Louis

The Genomics Education Partnership: Successful Integration Of Research Into Laboratory Classes At A Diverse Group Of Undergraduate Institutions, Christopher D. Shaffer, Consuelo Alvarez, Cheryl Bailey, Daron Barnard, Satish Bhalla, Chitra Chandrasekaran, Vidya Chandrasekaran, Hui-Min Chung, Douglas R. Dorer, Chunguang Du, Todd T. Eckdahl, Jeff L. Poet, Donald Frohlich, Anya L. Goodman, Yuying Gossner, Charles Hauser, Laura L.M. Hoopes, Diana Johnson, Christopher J. Jones, Marian Kaehler, Nighat Kokan, Olga R. Kopp, Gary A. Kuleck, Gerard Mcneil, Robert Moss, Jennifer L. Myka, Alexis Nagengast, Robert Morris, Paul J. Overvoorde, Elizabeth Shoop, Susan Parrish, Kelynne Reed, E. Gloria Regisford, Dennis Revie, Anne G. Rosenwald, Ken Saville, Stephanie Schroeder, Mary Shaw, Gary Skuse, Christopher Smith, Mary Smith, Eric P. Spana, Mary Spratt, Joyce Stamm, Jeff S. Thompson, Matthew Wawersik, Barbara A. Wilson, Jim Youngblom, Wilson Leung, Jeremy Buhler, Elaine R. Mardis, David Lopatto, Sarah C.R. Elgin

Biochemistry -- Faculty Publications

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than ...


A Comparison Of Three Computer-Based Methods Used To Determine Emg Signal Amplitude, Doug Renshaw 2010 University of Texas of the Permian Basin

A Comparison Of Three Computer-Based Methods Used To Determine Emg Signal Amplitude, Doug Renshaw

Doug Renshaw

No abstract provided.


Structure-Function Characterization Of The Extreme C-Terminus Of Apolipoprotein A-V, Kasuen Mauldin, Brian L. Lee, Martha Oleszczuk, Brian D. Sykes, Robert O. Ryan 2010 San Jose State University

Structure-Function Characterization Of The Extreme C-Terminus Of Apolipoprotein A-V, Kasuen Mauldin, Brian L. Lee, Martha Oleszczuk, Brian D. Sykes, Robert O. Ryan

Kasuen Mauldin

No abstract provided.


Systematic Discovery Of Regulatory Motifs In Fusarium Graminearum By Comparing Four Fusarium Genomes, Lokesh Kumar, Andrew Breakspear, Corby Kistler, Li-Jun Ma, Xiaohui Xie 2010 University of Massachusetts - Amherst

Systematic Discovery Of Regulatory Motifs In Fusarium Graminearum By Comparing Four Fusarium Genomes, Lokesh Kumar, Andrew Breakspear, Corby Kistler, Li-Jun Ma, Xiaohui Xie

Li-Jun Ma

Background

Fusarium graminearum (Fg), a major fungal pathogen of cultivated cereals, is responsible for billions of dollars in agriculture losses. There is a growing interest in understanding the transcriptional regulation of this organism, especially the regulation of genes underlying its pathogenicity. The generation of whole genome sequence assemblies for Fg and three closely related Fusarium species provides a unique opportunity for such a study.

Results

Applying comparative genomics approaches, we developed a computational pipeline to systematically discover evolutionarily conserved regulatory motifs in the promoter, downstream and the intronic regions of Fg genes, based on the multiple alignments of sequenced Fusarium ...


Computational Design And Elaboration Of A De Novo Heterotetrameric Α-Helical Protein That Selectively Binds An Emissive Abiological (Porphinato)Zinc Chromophore, H Christopher Fry, Andreas Lehmann, Jeffery G. Saven, William F. DeGrado, Michael J. Therien 2010 University of Pennsylvania

Computational Design And Elaboration Of A De Novo Heterotetrameric Α-Helical Protein That Selectively Binds An Emissive Abiological (Porphinato)Zinc Chromophore, H Christopher Fry, Andreas Lehmann, Jeffery G. Saven, William F. Degrado, Michael J. Therien

Departmental Papers (Chemistry)

The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of [(DPP)Zn:A(His):B(Thr)](2) is provided by UV/visible and circular dichroism spectroscopies ...


Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti 2010 Dartmouth College

Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti

Open Dartmouth: Faculty Open Access Scholarship

In plants and animals, cryptochromes function as either photoreceptors or circadian clock components. We have examined the cryptochrome from the filamentous fungus Neurospora crassa and demonstrate that Neurospora cry encodes a DASH-type cryptochrome that appears capable of binding flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF). The cry transcript and CRY protein levels are strongly induced by blue light in a wc-1-dependent manner, and cry transcript is circadianly regulated, with a peak abundance opposite in phase to frq. Neither deletion nor overexpression of cry appears to perturb the free-running circadian clock. However, cry disruption knockout mutants show a small phase delay ...


Efficient Activation Of Reconstructed Rat Embryos By Cyclin-Dependent Kinase Inhibitors, Robin L. Webb, Kirk A. Findlay, Michael A. Green, Tina L. Beckett, M. Paul Murphy 2010 University of Kentucky

Efficient Activation Of Reconstructed Rat Embryos By Cyclin-Dependent Kinase Inhibitors, Robin L. Webb, Kirk A. Findlay, Michael A. Green, Tina L. Beckett, M. Paul Murphy

Molecular and Cellular Biochemistry Faculty Publications

Background

Over the last decade a number of species, from farm animals to rodents, have been cloned using somatic cell nuclear transfer technology (SCNT). This technique has the potential to revolutionize the way that genetically modified animals are made. In its current state, the process of SCNT is very inefficient (<5% success rate), with several technical and biological hurdles hindering development. Yet, SCNT provides investigators with powerful advantages over other approaches, such as allowing for prescreening for the desired level of transgene expression and eliminating the excess production of undesirable wild-type animals. The rat plays a significant role in biomedical research, but SCNT has been problematic for this species. In this study, we address one aspect of the problem by evaluating methods of activation in artificially constructed rat embryos.

Principal Findings

We demonstrate that treatment with a calcium ionophore (ionomycin) combined with a variety of cyclin-dependent kinase inhibitors is an effective way to activate rat embryos. This is in contrast to methods developed for the mouse embryo, which tolerates much less specific chemical treatments. Methods developed to activate mouse ...


Antimicrobial And Antioxidant Activities Of Essential Oil And Methanol Extract Of Jasminum Sambac From Djibouti, Fatou Abdoul-Latif, Prosper Edou, François Eba, Nabil Mohamed, Adwa Ali, Samatar Djama, Louis-Clément Obame, Mamoudou Hama DICKO 2010 University of Djibouti

Antimicrobial And Antioxidant Activities Of Essential Oil And Methanol Extract Of Jasminum Sambac From Djibouti, Fatou Abdoul-Latif, Prosper Edou, François Eba, Nabil Mohamed, Adwa Ali, Samatar Djama, Louis-Clément Obame, Mamoudou Hama Dicko

Pr. Mamoudou H. DICKO, PhD

The essential oil of jasminum sambac from Djibouti was subjected to screening for their possible antioxidant activity by two complementary test systems, namely DPPH free radical scavenging and beta-carotene-linoleic acid assays. Butylated hydroxytoluene (BHT) was used as positive control in both test systems. In the DPPH test system, the IC50 value of essential oil and methanol extract were respectively 7.43 and 2.30 μg/ml. In the beta-carotene-linoleic acid system, oxidation was effectively inhibited by Jasminum sambac, the RAA value of essential oil and methanol extract were respectively 96.6 and 93.9%. When compared to BHT, the essential ...


A Monomeric Variant Of Insulin Degrading Enzyme (Ide) Loses Its Regulatory Properties, Eun Suk Song, David W. Rodgers, Louis B. Hersh 2010 University of Kentucky

A Monomeric Variant Of Insulin Degrading Enzyme (Ide) Loses Its Regulatory Properties, Eun Suk Song, David W. Rodgers, Louis B. Hersh

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Insulin degrading enzyme (IDE) is a key enzyme in the metabolism of both insulin and amyloid beta peptides. IDE is unique in that it is subject to allosteric activation which is hypothesized to occur through an oligomeric structure.

METHODOLOGY/PRINCIPAL FINDINGS: IDE is known to exist as an equilibrium mixture of monomers, dimers, and higher oligomers, with the dimer being the predominant form. Based on the crystal structure of IDE we deleted the putative dimer interface in the C-terminal region, which resulted in a monomeric variant. Monomeric IDE retained enzymatic activity, however instead of the allosteric behavior seen with ...


Functional Interaction Between Telomere Protein Tpp1 And Telomerase, Arthur J. Zaug, Elaine R. Podell, Jayakrishnan Nandakumar, Thomas R. Cech 2010 University of Colorado Boulder

Functional Interaction Between Telomere Protein Tpp1 And Telomerase, Arthur J. Zaug, Elaine R. Podell, Jayakrishnan Nandakumar, Thomas R. Cech

Chemistry & Biochemistry Faculty Contributions (1986-2018)

Human chromosome end-capping and telomerase regulation require POT1 (Protection of Telomeres 1) and TPP1 proteins, which bind to the 3′ ssDNA extension of human telomeres. POT1–TPP1 binding to telomeric DNA activates telomerase repeat addition processivity. We now provide evidence that this POT1–TPP1 activation requires specific interactions with telomerase, rather than it being a DNA substrate-specific effect. First, telomerase from the fish medaka, which extends the same telomeric DNA primer as human telomerase, was not activated by human POT1–TPP1. Second, mutation of a conserved glycine, Gly100 in the TEN (telomerase essential N-terminal) domain of TERT, abolished the enhancement ...


In The Tradition Of Science: An Interview With Victor Ambros, Victor R. Ambros 2010 University of Massachusetts Medical School

In The Tradition Of Science: An Interview With Victor Ambros, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

No abstract provided.


Role Of Members Of The Phosducin Gene Family In Protein Translation And Folding, Nana Sono-Koree 2010 Brigham Young University - Provo

Role Of Members Of The Phosducin Gene Family In Protein Translation And Folding, Nana Sono-Koree

Theses and Dissertations

G proteins regulate various physiological processes by way of transducing a wide variety of signals ranging from hormonal to sensory stimuli. Malfunctions in G protein signaling lead to numerous diseases. G protein signaling begins with binding of a ligand to a G protein-coupled receptor resulting in a conformational change that leads to the exchange of a GDP for a GTP on G α. The GTP bound α subunit dissociates for its stable Gβγ dimer partner. G α-GTP and Gβγ control the activity of effector enzymes and ion channels that ultimately orchestrate the cellular response to stimulus. Current reports have shown ...


Putting Metal In The Middle, David Bollivar 2010 Illinois Wesleyan University

Putting Metal In The Middle, David Bollivar

Scholarship

Placing metal ions into the center of a porphyrin ring is a significant cellular challenge. Lundqvist et ai. (2010) provide snapshots of the AAA + motor unit of magnesium chelatase, an enzyme that insert magnesium ion into the porphyrin ring accompanied by ATP expenditure, in different states of binding to adenosyl nucleotides.


The Asymmetric Phase-Transfer Catalyzed Alkylation Of Imidazolyl Ketones And Aryl Acetates And Their Applications To Total Synthesis, Michael Andrew Christiansen 2010 Brigham Young University - Provo

The Asymmetric Phase-Transfer Catalyzed Alkylation Of Imidazolyl Ketones And Aryl Acetates And Their Applications To Total Synthesis, Michael Andrew Christiansen

Theses and Dissertations

Phase-transfer catalysts derived from the cinchona alkaloids cinchonine and cinchonidine are widely used in the asymmetric alkylation of substrates bearing moieties that resonance stabilize their enolates. The investigation of α-oxygenated esters revealed decreased α-proton acidity, indicating the oxygen's overall destabilizing effect on enolates by electron-pair repulsion. Alkylation of α-oxygenated aryl ketones with various alkyl halides proved successful with a cinchonidine catalyst, giving products with high yield and enantioselectivity. The resulting compounds were converted to esters through modified Baeyer-Villiger oxidation. Alkylation with indolyl electrophiles gave products that underwent decomposition under Baeyer-Villiger conditions. Alternative N-methylimidazolyl ketones were explored. Alkylated imidazolyl ketones ...


Putting Metal In The Middle, David Bollivar 2010 Illinois Wesleyan University

Putting Metal In The Middle, David Bollivar

David Bollivar

Placing metal ions into the center of a porphyrin ring is a significant cellular challenge. Lundqvist et ai. (2010) provide snapshots of the AAA + motor unit of magnesium chelatase, an enzyme that insert magnesium ion into the porphyrin ring accompanied by ATP expenditure, in different states of binding to adenosyl nucleotides.


Time-Resolved Infrared Spectroscopy And Density Functional Theory Study Of Weak Interactions Of Metal Carbonyls And Organic Solvents, Carolyn Evans Sheffield 2010 Brigham Young University - Provo

Time-Resolved Infrared Spectroscopy And Density Functional Theory Study Of Weak Interactions Of Metal Carbonyls And Organic Solvents, Carolyn Evans Sheffield

Theses and Dissertations

Pulsed laser flash photolysis of M(CO)6 (M = Cr, W) in cyclohexane with a small amount of benzene results in three sequential reactions. The first is the photodissociation of the parent to yield a M(CO)5:C6H12 complex, which takes place faster than the time resolution of our experiments. The second reaction is the replacement of the cyclohexane ligand with benzene to form a M(CO)5:C6H6 complex, in which benzene is coordinated to the metal via one side of the ring. This complex then falls apart in solution as M(CO)5 coordinates with a trace ...


Digital Commons powered by bepress