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Find video protocols related to scientific articles indexed in Pubmed.
MicroRNA-24 regulates macrophage behavior and retards atherosclerosis.
Arterioscler. Thromb. Vasc. Biol.
PUBLISHED: 07-02-2014
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Our recent studies have highlighted membrane type-1 matrix metalloproteinase (MMP)-14 as a selective marker for an invasive subset of macrophages potentially related to atherosclerotic plaque progression. Moreover, colony stimulating factors (CSF) may exert divergent effects on macrophage MMP expression, possibly through microRNAs. We, therefore, aim to identify and test the pathophysiological role of microRNAs, which modulate macrophage MMP-14 expression in atherosclerotic plaque progression.
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Mechanisms of Integral Membrane Protein Insertion and Folding.
J. Mol. Biol.
PUBLISHED: 06-25-2014
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The biogenesis, folding, and structure of ?-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons-often referred to as protein-conducting channels-for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Type II fatty acid synthesis is essential for the replication of Chlamydia trachomatis.
J. Biol. Chem.
PUBLISHED: 06-23-2014
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The major phospholipid classes of the obligate intracellular bacterial parasite Chlamydia trachomatis are the same as its eukaryotic host except that they also contain chlamydia-made branched-chain fatty acids in the 2-position. Genomic analysis predicts that C. trachomatis is capable of type II fatty acid synthesis (FASII). AFN-1252 was deployed as a chemical tool to specifically inhibit the enoyl-acyl carrier protein reductase (FabI) of C. trachomatis to determine whether chlamydial FASII is essential for replication within the host. The C. trachomatis FabI (CtFabI) is a homotetramer and exhibited typical FabI kinetics, and its expression complemented an Escherichia coli fabI(Ts) strain. AFN-1252 inhibited CtFabI by binding to the FabI·NADH complex with an IC50 of 0.9 ?M at saturating substrate concentration. The x-ray crystal structure of the CtFabI·NADH·AFN-1252 ternary complex revealed the specific interactions between the drug, protein, and cofactor within the substrate binding site. AFN-1252 treatment of C. trachomatis-infected HeLa cells at any point in the infectious cycle caused a decrease in infectious titers that correlated with a decrease in branched-chain fatty acid biosynthesis. AFN-1252 treatment at the time of infection prevented the first cell division of C. trachomatis, although the cell morphology suggested differentiation into a metabolically active reticulate body. These results demonstrate that FASII activity is essential for C. trachomatis proliferation within its eukaryotic host and validate CtFabI as a therapeutic target against C. trachomatis.
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The sheep genome illuminates biology of the rumen and lipid metabolism.
Science
PUBLISHED: 06-07-2014
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Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
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Topology, dimerization, and stability of the single-span membrane protein CadC.
J. Mol. Biol.
PUBLISHED: 05-10-2014
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Under acid stress, Escherichia coli induce expression of CadA (lysine decarboxylase) and CadB (lysine/cadaverine antiporter) in a lysine-rich environment. The ToxR-like transcriptional activator CadC controls expression of the cadBA operon. Using a novel signal peptidase I (SPase I) cleavage assay, we show that CadC is a type II single-span membrane protein (S-SMP) with a cytoplasmic DNA-binding domain and a periplasmic sensor domain. We further show that, as long assumed, dimerization of the sensor domain is required for activating the cadBA operon. We prove this using a chimera in which the periplasmic domain of RodZ-a type II membrane protein involved in the maintenance of the rod shape of E. coli-replaces the CadC sensor domain. Because the RodZ periplasmic domain cannot dimerize, the chimera cannot activate the operon. However, replacement of the transmembrane (TM) domain of the chimera with the glycophorin A TM domain causes intramembrane dimerization and consequently operon activation. Using a low-expression protocol that eliminates extraneous TM helix dimerization signals arising from protein over-expression, we enhanced dramatically the dynamic range of the ?-galactosidase assay for cadBA activation. Consequently, the strength of the intramembrane dimerization of the glycophorin A domain could be compared quantitatively with the strength of the much stronger periplasmic dimerization of CadC. For the signal peptidase assay, we inserted an SPase I cleavage site (AAA or AQA) at the periplasmic end of the TM helix. Cleavage occurred with high efficiency for all TM and periplasmic domains tested, thus eliminating the need for the cumbersome spheroplast-proteinase K method for topology determinations.
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Conference report: AAPS and US FDA Crystal City V meeting on Quantitative Bioanalytical Method Validation and Implementation: feedback from the EBF.
Bioanalysis
PUBLISHED: 04-08-2014
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Crystal City V meeting on Quantitative Bioanalytical Method Validation and Implementation: 2013 Revised US FDA Guidance 3-5 December 2013, Hilton Baltimore, MD, USA The meeting provided an opportunity for Industry and regulators from the US FDA to discuss the recently published revised draft FDA Guidance for Industry on Bioanalytical Methods Validation during the 90 day review period. Key perspective and philosophical positions were shared leading to a healthy exchange of views and ideas on topics in the revised document. Discussions covered all aspects of bioanalytical method validation and method utilization. However, the main dialogue was focused on chromatographic methods, ligand-binding assay methods and biomarker analysis. The resulting open debate led to greater understanding of the document, but also provided clear feedback, including the request on harmonization with approved Bioanalytical Methods Validation guidance's release from other health authorities, as well as the consensus view between industry and the FDA. Members of the European Bioanalysis Forum summarized prospective discussions during the meeting in Baltimore; however, this Report is not intended to constitute the official proceedings from the meeting, which are expected to be published later this year.
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Effect of temperature and fixation on the optical properties of atherosclerotic tissue: a validation study of an ex-vivo whole heart cadaveric model.
Biomed Opt Express
PUBLISHED: 04-01-2014
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Atherosclerotic plaque composition can be imaged using the optical attenuation coefficient derived from intravascular optical coherence tomography (OCT) data. The relation between optical properties and tissue type has been established on autopsy tissues. In this study, we validate an ex-vivo model for the effect of temperature and tissue fixation on optical parameters. We studied the optical attenuation of human coronary arteries at three temperatures, before and after formalin fixation. We developed an en-face longitudinal display of attenuation data of the OCT pullbacks. Using the unfixed, body-temperature condition image as a standard, and after extensive registration with other condition images, we quantify the differences in optical attenuation and the backscattered intensity. The results suggest that tissue fixation and temperature do not introduce systematic errors in studies of arterial optical properties.
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Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase.
ACS Chem. Biol.
PUBLISHED: 03-27-2014
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The declining effectiveness of current antibiotics due to the emergence of resistant bacterial strains dictates a pressing need for novel classes of antimicrobial therapies, preferably against molecular sites other than those in which resistance mutations have developed. Dihydropteroate synthase (DHPS) catalyzes a crucial step in the bacterial pathway of folic acid synthesis, a pathway that is absent in higher vertebrates. As the target of the sulfonamide class of drugs that were highly effective until resistance mutations arose, DHPS is known to be a valuable bacterial Achilles heel that is being further exploited for antibiotic development. Here, we report the discovery of the first known allosteric inhibitor of DHPS. NMR and crystallographic studies reveal that it engages a previously unknown binding site at the dimer interface. Kinetic data show that this inhibitor does not prevent substrate binding but rather exerts its effect at a later step in the catalytic cycle. Molecular dynamics simulations and quasi-harmonic analyses suggest that the effect of inhibitor binding is transmitted from the dimer interface to the active-site loops that are known to assume an obligatory ordered substructure during catalysis. Together with the kinetics results, these structural and dynamics data suggest an inhibitory mechanism in which binding at the dimer interface impacts loop movements that are required for product release. Our results potentially provide a novel target site for the development of new antibiotics.
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A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs.
Hum. Genet.
PUBLISHED: 03-11-2014
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Familial subvalvular aortic stenosis (SAS) is one of the most common congenital heart defects in dogs and is an inherited defect of Newfoundlands, golden retrievers and human children. Although SAS is known to be inherited, specific genes involved in Newfoundlands with SAS have not been defined. We hypothesized that SAS in Newfoundlands is inherited in an autosomal dominant pattern and caused by a single genetic variant. We studied 93 prospectively recruited Newfoundland dogs, and 180 control dogs of 30 breeds. By providing cardiac screening evaluations for Newfoundlands we conducted a pedigree evaluation, genome-wide association study and RNA sequence analysis to identify a proposed pattern of inheritance and genetic loci associated with the development of SAS. We identified a three-nucleotide exonic insertion in phosphatidylinositol-binding clathrin assembly protein (PICALM) that is associated with the development of SAS in Newfoundlands. Pedigree evaluation best supported an autosomal dominant pattern of inheritance and provided evidence that equivocally affected individuals may pass on SAS in their progeny. Immunohistochemistry demonstrated the presence of PICALM in the canine myocardium and area of the subvalvular ridge. Additionally, small molecule inhibition of clathrin-mediated endocytosis resulted in developmental abnormalities within the outflow tract (OFT) of Xenopus laevis embryos. The ability to test for presence of this PICALM insertion may impact dog-breeding decisions and facilitate reduction of SAS disease prevalence in Newfoundland dogs. Understanding the role of PICALM in OFT development may aid in future molecular and genetic investigations into other congenital heart defects of various species.
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Structural polymorphism in the N-terminal oligomerization domain of NPM1.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 03-10-2014
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Nucleophosmin (NPM1) is a multifunctional phospho-protein with critical roles in ribosome biogenesis, tumor suppression, and nucleolar stress response. Here we show that the N-terminal oligomerization domain of NPM1 (Npm-N) exhibits structural polymorphism by populating conformational states ranging from a highly ordered, folded pentamer to a highly disordered monomer. The monomer-pentamer equilibrium is modulated by posttranslational modification and protein binding. Phosphorylation drives the equilibrium in favor of monomeric forms, and this effect can be reversed by Npm-N binding to its interaction partners. We have identified a short, arginine-rich linear motif in NPM1 binding partners that mediates Npm-N oligomerization. We propose that the diverse functional repertoire associated with NPM1 is controlled through a regulated unfolding mechanism signaled through posttranslational modifications and intermolecular interactions.
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Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members.
Acta Crystallogr. D Biol. Crystallogr.
PUBLISHED: 02-28-2014
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Peptidoglycan O-acetylesterase (Ape1), which is required for host survival in Neisseria sp., belongs to the diverse SGNH hydrolase superfamily, which includes important viral and bacterial virulence factors. Here, multi-domain crystal structures of Ape1 with an SGNH catalytic domain and a newly identified putative peptidoglycan-detection module are reported. Enzyme catalysis was performed in Ape1 crystals and key catalytic intermediates along the SGNH esterase hydrolysis reaction pathway were visualized, revealing a substrate-induced productive conformation of the catalytic triad, a mechanistic detail that has not previously been observed. This substrate-induced productive conformation of the catalytic triad shifts the established dogma on these enzymes, generating valuable insight into the structure-based design of drugs targeting the SGNH esterase superfamily.
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Galactoside-binding site in LacY.
Biochemistry
PUBLISHED: 02-26-2014
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Although an X-ray crystal structure of lactose permease (LacY) has been presented with bound galactopyranoside, neither the sugar nor the residues ligating the sugar can be identified with precision at ~3.5 Å. Therefore, additional evidence is important for identifying side chains likely to be involved in binding. On the basis of a clue from site-directed alkylation suggesting that Asn272, Gly268, and Val264 on one face of helix VIII might participate in galactoside binding, molecular dynamics simulations were conducted initially. The simulations indicate that Asn272 (helix VIII) is sufficiently close to the galactopyranosyl ring of a docked lactose analogue to play an important role in binding, the backbone at Gly268 may be involved, and Val264 does not interact with the bound sugar. When the three side chains are subjected to site-directed mutagenesis, with the sole exception of mutant Asn272 ? Gln, various other replacements for Asn272 either markedly decrease affinity for the substrate (i.e., high KD) or abolish binding altogether. However, mutant Gly268 ? Ala exhibits a moderate 8-fold decrease in affinity, and binding by mutant Val264 ? Ala is affected only minimally. Thus, Asn272 and possibly Gly268 may comprise additional components of the galactoside-binding site in LacY.
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The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Bioorg. Med. Chem.
PUBLISHED: 02-04-2014
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6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is an essential enzyme in the microbial folate biosynthetic pathway. This pathway has proven to be an excellent target for antimicrobial development, but widespread resistance to common therapeutics including the sulfa drugs has stimulated interest in HPPK as an alternative target in the pathway. A screen of a pterin-biased compound set identified several HPPK inhibitors that contain an aryl substituted 8-thioguanine scaffold, and structural analyses showed that these compounds engage the HPPK pterin-binding pocket and an induced cryptic pocket. A preliminary structure activity relationship profile was developed from biophysical and biochemical characterizations of derivative molecules. Also, a similarity search identified additional scaffolds that bind more tightly within the HPPK pterin pocket. These inhibitory scaffolds have the potential for rapid elaboration into novel lead antimicrobial agents.
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Small molecule specific run acceptance, specific assay operation, and chromatographic run quality assessment: recommendation for best practices and harmonization from the global bioanalysis consortium harmonization teams.
AAPS J
PUBLISHED: 01-30-2014
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Consensus practices and regulatory guidance for liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) assays of small molecules are more aligned globally than for any of the other bioanalytical techniques addressed by the Global Bioanalysis Consortium. The three Global Bioanalysis Consortium Harmonization Teams provide recommendations and best practices for areas not yet addressed fully by guidances and consensus for small molecule bioanalysis. Recommendations from all three teams are combined in this report for chromatographic run quality, validation, and sample analysis run acceptance.
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Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion.
Nat Commun
PUBLISHED: 01-28-2014
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The favourable transfer free energy for a transmembrane (TM) ?-helix between the aqueous phase and lipid bilayer underlies the stability of membrane proteins. However, the connection between the energetics and process of membrane protein assembly by the Sec61/SecY translocon complex in vivo is not clear. Here, we directly determine the partitioning free energies of a family of designed peptides using three independent approaches: an experimental microsomal Sec61 translocon assay, a biophysical (spectroscopic) characterization of peptide insertion into hydrated planar lipid bilayer arrays, and an unbiased atomic-detail equilibrium folding-partitioning molecular dynamics simulation. Remarkably, the measured free energies of insertion are quantitatively similar for all three approaches. The molecular dynamics simulations show that TM helix insertion involves equilibrium with the membrane interface, suggesting that the interface may play a role in translocon-guided insertion.
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SecA Drives Transmembrane Insertion of RodZ, an Unusual Single-Span Membrane Protein.
J. Mol. Biol.
PUBLISHED: 01-24-2014
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The transmembrane (TM) helices of most type II single-span membrane proteins (S-SMPs) of Escherichia coli occur near the N-terminus, where the cell's targeting mechanisms can readily identify it as it emerges from the ribosome. However, the TM helices of a few S-SMPs, such as RodZ, occur a hundred or more residues downstream from the N-terminus, which raises fundamental questions about targeting and assembly. Because of RodZ's novelty and potential usefulness for understanding TM helix insertion in vivo, we examined its membrane targeting and assembly. We used RodZ constructs containing immunotags before the TM domain to assess membrane insertion using proteinase K digestion. We confirmed the Nin-Cout (type II) topology of RodZ and established the absence of a targeting signal other than the TM domain. RodZ was not inserted into the membrane under SecA depletion conditions or in the presence of sodium azide, which is known to inhibit SecA. Insertion failed when the TM proton gradient was abolished with Carbonyl cyanide m-chlorophenyl hydrazone. Insertion also failed when RodZ was expressed in SecE-depleted E. coli, indicating that the SecYEG translocon is required for RodZ assembly. Protease accessibility assays of RodZ in other E. coli depletion strains revealed that insertion is independent of SecB, YidC, and SecD/F. Insertion was found to be only weakly dependent on the signal recognition particle pathway: insertion was weakly dependent on the Ffh but independent of FtsY. We conclude that membrane insertion of RodZ requires only the SecYEG translocon, the SecA ATPase motor, and the TM proton motive force.
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Recent advances in computer-aided drug design as applied to anti-influenza drug discovery.
Curr Top Med Chem
PUBLISHED: 01-01-2014
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Influenza is a seasonal and serious health threat, and the recent outbreak of H7N9 following the pandemic spread of H1N1 in 2009 has served to emphasize the importance of anti-influenza drug discovery. Zanamivir (Relenza™) and oseltamivir (Tamiflu(®)) are two antiviral drugs currently recommended by the CDC for treating influenza. Both are examples of the successful application of structure-based drug design strategies. These strategies have combined computer- based approaches, such as docking- and pharmacophore-based virtual screening with X-ray crystallographic structural analyses. Docking is a routinely used computational method to identify potential hits from large compound libraries. This method has evolved from simple rigid docking approaches to flexible docking methods to handle receptor flexibility and to enhance hit rates in virtual screening. Virtual screening approaches can employ both ligand-based and structurebased pharmacophore models depending on the available information. The exponential growth in computing power has increasingly facilitated the application of computer-aided methods in drug discovery, and they now play significant roles in the search for novel therapeutics. An overview of these computational tools is presented in this review, and recent advances and challenges will be discussed. The focus of the review will be anti-influenza drug discovery and how advances in our understanding of viral biology have led to the discovery of novel influenza protein targets. Also discussed will be strategies to circumvent the problem of resistance emerging from rapid mutations that has seriously compromised the efficacy of current anti-influenza therapies.
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Knockdown of the Rhipicephalus microplus cytochrome c oxidase subunit III gene is associated with a failure of Anaplasma marginale transmission.
PLoS ONE
PUBLISHED: 01-01-2014
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Rhipicephalus microplus is an obligate hematophagous ectoparasite of cattle and an important biological vector of Anaplasma marginale in tropical and subtropical regions. The primary determinants for A. marginale transmission are infection of the tick gut, followed by infection of salivary glands. Transmission of A. marginale to cattle occurs via infected saliva delivered during tick feeding. Interference in colonization of either the tick gut or salivary glands can affect transmission of A. marginale to naïve animals. In this study, we used the tick embryonic cell line BME26 to identify genes that are modulated in response to A. marginale infection. Suppression-subtractive hybridization libraries (SSH) were constructed, and five up-regulated genes {glutathione S-transferase (GST), cytochrome c oxidase sub III (COXIII), dynein (DYN), synaptobrevin (SYN) and phosphatidylinositol-3,4,5-triphosphate 3-phosphatase (PHOS)} were selected as targets for functional in vivo genomic analysis. RNA interference (RNAi) was used to determine the effect of tick gene knockdown on A. marginale acquisition and transmission. Although RNAi consistently knocked down all individually examined tick genes in infected tick guts and salivary glands, only the group of ticks injected with dsCOXIII failed to transmit A. marginale to naïve calves. To our knowledge, this is the first report demonstrating that RNAi of a tick gene is associated with a failure of A. marginale transmission.
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Skin diseases in pet rabbits: a retrospective study of 334 cases seen at the University of California at Davis, USA (1984-2004).
Vet. Dermatol.
PUBLISHED: 09-13-2013
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Rabbits are growing in popularity as companion animals, and dermatology problems are often the presenting complaint when seeing a veterinarian.
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Donkey dermatology.
Vet. Clin. North Am. Equine Pract.
PUBLISHED: 09-12-2013
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Donkeys (Equus asinus) are a species used throughout the world primarily as beasts of burden, but occasionally for other functions, as a meat source or as pets. Although closely related to other equids, they have some unique features of their own with regard to dermatologic disease. This article highlights some of the various dermatoses seen or reported in donkeys, as well as some comparisons with horses when prevalence, presentation, or treatment may differ.
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Identification of a treatment-resistant, ketamine-sensitive genetic line in the chick anxiety-depression model.
Pharmacol. Biochem. Behav.
PUBLISHED: 08-12-2013
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The introduction of pharmacotherapies for treatment-resistant depression is hindered by translational challenges with existing preclinical screening models that fail to adequately model the clinical features of this syndrome. This research sought to screen antidepressants in two selected genetic lines previously identified as stress-vulnerable and -resilient in the chick anxiety-depression model. Separate groups of socially-raised 5-6 day-old Black Australorps (stress-vulnerable) and Production Reds (stress-resilient) were administered imipramine (0-20 mg/kg), fluoxetine (0-10 mg/kg), maprotiline (0-10 mg/kg) or ketamine 0-15 mg/kg) IP (1 ml/kg) and placed into isolation for 90 min. Distress vocalizations (DVoc) were recorded. Onset of behavioral despair and Dvoc rates during the depression-like phase (30-90 min) were calculated. Black Australorps entered behavioral despair approximately 25% faster than Productions Reds highlighting stress-vulnerability in this Black Australorp line. In the depression-like phase, Black Australorps were insensitive to imipramine and fluoxetine but sensitive to ketamine, a finding that parallels stress-vulnerable, treatment resistant depressive disorder. The chick anxiety-depression model using the Black Australorp line may prove useful in pre-clinical screening of novel antidepressant targets for use in treatment-resistant depression.
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Architecture of the bacteriophage T4 activator MotA/promoter DNA interaction during sigma appropriation.
J. Biol. Chem.
PUBLISHED: 07-31-2013
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Gene expression can be regulated through factors that direct RNA polymerase to the correct promoter sequence at the correct time. Bacteriophage T4 controls its development in this way using phage proteins that interact with host RNA polymerase. Using a process called ? appropriation, the T4 co-activator AsiA structurally remodels the ?(70) subunit of host RNA polymerase, while a T4 activator, MotA, engages the C terminus of ?(70) and binds to a DNA promoter element, the MotA box. Structures for the N-terminal (NTD) and C-terminal (CTD) domains of MotA are available, but no structure exists for MotA with or without DNA. We report the first molecular map of the MotA/DNA interaction within the ?-appropriated complex, which we obtained by using the cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). We conjugated surface-exposed, single cysteines in MotA with FeBABE and performed cleavage reactions in the context of stable transcription complexes. The DNA cleavage sites were analyzed using ICM Molsoft software and three-dimensional physical models of MotA(NTD), MotA(CTD), and the DNA to investigate shape complementarity between the protein and the DNA and to position MotA on the DNA. We found that the unusual "double wing" motif present within MotA(CTD) resides in the major groove of the MotA box. In addition, we have used surface plasmon resonance to show that MotA alone is in a very dynamic equilibrium with the MotA element. Our results demonstrate the utility of fine resolution FeBABE mapping to determine the architecture of protein-DNA complexes that have been recalcitrant to traditional structure analyses.
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Workplace assessment of targeted violence risk: the development and reliability of the WAVR-21.
J. Forensic Sci.
PUBLISHED: 07-18-2013
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This study describes the development of the WAVR-21, a structured professional judgment guide for the assessment of workplace targeted violence, and presents initial interrater reliability results. The 21-item instrument codes both static and dynamic risk factors and change, if any, over time. Five critical items or red flag indicators assess violent motives, ideation, intent, weapons skill, and pre-attack planning. Additional items assess the contribution of mental disorder, negative personality factors, situational factors, and a protective factor. Eleven raters each rated 12 randomly assigned cases from actual files of workplace threat scenarios. Summary interrater reliability correlation coefficients (ICCs) for overall presence of risk factors, risk of violence, and seriousness of the violent act were in the fair to good range, similar to other structured professional judgment instruments. A subgroup of psychologists who were coders produced an ICC of 0.76 for overall presence of risk factors. Some of the individual items had poor reliability for both clinical and statistical reasons. The WAVR-21 appears to improve the structuring and organizing of empirically based risk-relevant data and may enhance communication and decision making.
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Replacing sulfa drugs with novel DHPS inhibitors.
Future Med Chem
PUBLISHED: 07-18-2013
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More research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. The enzyme DHPS has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. The use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. Despite the large amount of structural information available for DHPS, few recent publications address the possibility of using this knowledge for novel drug design. This article reviews the relevant papers and patents that report promising new small-molecule inhibitors of DHPS, and discuss these data in light of new insights into the DHPS catalytic mechanism and recently determined crystal structures of DHPS bound to potent small-molecule inhibitors. This new functional understanding confirms that DHPS deserves further consideration as an antimicrobial drug target.
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In vitro structure-activity relationships of aplysinopsin analogs and their in vivo evaluation in the chick anxiety-depression model.
Bioorg. Med. Chem.
PUBLISHED: 07-02-2013
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Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms and have been shown to possess a range of biological activities. In vitro receptor binding assays showed that of the 12 serotonin receptor subtypes, analogues showed a high affinity for the 5-HT2B and 5-HT2C receptor subtypes, with selectivity for 5-HT2B over 5-HT2C. While no conclusions could be drawn about the number and position of N-methylations, bromination at C-4 and C-5 of the indole ring resulted in greater binding affinities, with Kis as low as 35 nM. This data, combined with previous knowledge of the CNS activity of aplysinopsin analogs, suggested that these compounds may have potential as leads for antidepressant drugs. Compounds 3c, 3u, and 3x were evaluated in the chick anxiety-depression model to assess their in vivo efficacy. Compound 3c showed a modest antidepressant effect at a dose of 30 nM/kg in the animal model.
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Copper-transporting P-type ATPases use a unique ion-release pathway.
Nat. Struct. Mol. Biol.
PUBLISHED: 05-23-2013
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Heavy metals in cells are typically regulated by PIB-type ATPases. The first structure of the class, a Cu(+)-ATPase from Legionella pneumophila (LpCopA), outlined a copper transport pathway across the membrane, which was inferred to be occluded. Here we show by molecular dynamics simulations that extracellular water solvated the transmembrane (TM) domain, results indicative of a Cu(+)-release pathway. Furthermore, a new LpCopA crystal structure determined at 2.8-Å resolution, trapped in the preceding E2P state, delineated the same passage, and site-directed-mutagenesis activity assays support a functional role for the conduit. The structural similarities between the TM domains of the two conformations suggest that Cu(+)-ATPases couple dephosphorylation and ion extrusion differently than do the well-characterized PII-type ATPases. The ion pathway explains why certain Menkes and Wilsons disease mutations impair protein function and points to a site for inhibitors targeting pathogens.
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Extent of linkage disequilibrium in large-breed dogs: chromosomal and breed variation.
Mamm. Genome
PUBLISHED: 05-15-2013
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The aim of this study was to better define the extent of linkage disequilibrium (LD) in populations of large-breed dogs and its variation by breed and chromosomal region. Understanding the extent of LD is a crucial component for successful utilization of genome-wide association studies and allows researchers to better define regions of interest and target candidate genes. Twenty-four Golden Retriever dogs, 28 Rottweiler dogs, and 24 Newfoundland dogs were genotyped for single-nucleotide polymorphism (SNP) data using a high-density SNP array. LD was calculated for all autosomes using Haploview. Decay of the squared correlation coefficient (r (2)) was plotted on a per-breed and per-chromosome basis as well as in a genome-wide fashion. The point of 50 % decay of r (2) was used to estimate the difference in extent of LD between breeds. Extent of LD was significantly shorter for Newfoundland dogs based upon 50 % decay of r (2) data at a mean of 344 kb compared to Golden Retriever and Rottweiler dogs at 715 and 834 kb, respectively (P < 0.0001). Notable differences in LD by chromosome were present within each breed and not strictly related to the length of the corresponding chromosome. Extent of LD is breed and chromosome dependent. To our knowledge, this is the first report of SNP-based LD for Newfoundland dogs, the first report based on genome-wide SNPs for Rottweilers, and an almost tenfold improvement in marker density over previous genome-wide studies of LD in Golden Retrievers.
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Crystal structure of the avian astrovirus capsid spike.
J. Virol.
PUBLISHED: 05-08-2013
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Astroviruses are small, nonenveloped, single-stranded RNA viruses that cause diarrhea in a wide variety of mammals and birds. On the surface of the viral capsid are globular spikes that are thought to be involved in attachment to host cells. To understand the basis of species specificity, we investigated the structure of an avian astrovirus capsid spike and compared it to a previously reported human astrovirus capsid spike structure. Here we report the crystal structure of the turkey astrovirus 2 (TAstV-2) capsid surface spike domain, determined to 1.5-Å resolution, and identify three conserved patches on the surface of the spike that are candidate avian receptor-binding sites. Surprisingly, the overall TAstV-2 capsid spike structure is unique, with only distant structural similarities to the human astrovirus capsid spike and other viral capsid spikes. There is an absence of conserved putative receptor-binding sites between the human and avian spikes. However, there is evidence for carbohydrate-binding sites in both human and avian spikes, and studies with human astrovirus 1 (HAstV-1) suggest a minor role in infection for chondroitin sulfate but not heparin. Overall, our structural and functional studies provide new insights into astrovirus host cell entry, species specificity, and evolution.
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Expanding possibilities for intervention against small ruminant lentiviruses through genetic marker-assisted selective breeding.
Viruses
PUBLISHED: 03-11-2013
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Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.
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Calcinosis cutis in dogs: histopathological and clinical analysis of 46 cases.
Vet. Dermatol.
PUBLISHED: 02-24-2013
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Calcinosis cutis is well recognized in dogs with endogenous hyperglucocorticism and iatrogenic hyperglucocorticism, but the pathogenesis is still unclear.
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Equine alopecia areata: a retrospective clinical descriptive study at the University of California, Davis (1980-2011).
Vet. Dermatol.
PUBLISHED: 02-22-2013
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Alopecia areata (AA) causes hair loss due to inflammatory changes within and around hair bulbs and lower portions of the hair follicles. Documentation of AA in horses is limited to a few case reports.
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Charge composition features of model single-span membrane proteins that determine selection of YidC and SecYEG translocase pathways in Escherichia coli.
J. Biol. Chem.
PUBLISHED: 01-25-2013
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We have investigated the features of single-span model membrane proteins based upon leader peptidase that determines whether the proteins insert by a YidC/Sec-independent, YidC-only, or YidC/Sec mechanism. We find that a protein with a highly hydrophobic transmembrane segment that inserts into the membrane by a YidC/Sec-independent mechanism becomes YidC-dependent if negatively charged residues are inserted into the translocated periplasmic domain or if the hydrophobicity of the transmembrane segment is reduced by substituting polar residues for nonpolar ones. This suggests that charged residues in the translocated domain and the hydrophobicity within the transmembrane segment are important determinants of the insertion pathway. Strikingly, the addition of a positively charged residue to either the translocated region or the transmembrane region can switch the insertion requirements such that insertion requires both YidC and SecYEG. To test conclusions from the model protein studies, we confirmed that a positively charged residue is a SecYEG determinant for the endogenous proteins ATP synthase subunits a and b and the TatC subunit of the Tat translocase. These findings provide deeper insights into how pathways are selected for the insertion of proteins into the Escherichia coli inner membrane.
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Pemphigus vulgaris in a Welsh pony stallion: case report and demonstration of antidesmoglein autoantibodies.
Vet. Dermatol.
PUBLISHED: 01-25-2013
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To describe the clinical, histological and immunological findings of an equine case of pemphigus vulgaris, including the demonstration of antidesmoglein (anti-Dsg) autoantibodies.
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Conformational states of melittin at a bilayer interface.
Biophys. J.
PUBLISHED: 01-24-2013
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The distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics. Here, we describe melittin partitioning into dioleoylphosphatidylcholine lipids using CHARMM and OPLS force fields. Although the OPLS simulation failed to reproduce experimental results, the CHARMM simulation reported was consistent with experiments. The CHARMM simulation showed melittin to be represented by a narrow distribution of folding states in the membrane interface.
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Brain-derived neurotrophic factor response in vulnerable and resilient genetic lines in the chick anxiety-depression model.
Behav. Brain Res.
PUBLISHED: 01-24-2013
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Altered BDNF-mediated synaptogenesis is a major contributor to stress-vulnerability and depression. This study sought to determine patterns of hippocampal BDNF expression in stress-vulnerable and -resilient strains in the chick anxiety-depression model. Socially raised Black Australorp and Production Red strains were tested at 5-6 days post hatch under either 30, 60, 90, or 120 min of social separation stress; chicks tested with 2 social companions for 120 min served as controls. Distress vocalizations were recorded throughout the test session and latency to behavioral despair calculated. Following tests, bilateral hippocampal sections were harvested and analyzed via ELISA for BDNF levels. Black Australorps had shorter latencies to behavioral despair than Production Reds reflecting greater stress vulnerability. No differences were detected in BDNF levels between a No-Test and Social group within or between strains. The stress resilient Production Reds showed stable BDNF levels across the isolation test period whereas the vulnerable Black Australorps showed an increase in hippocampal BDNF levels that peaked at 90 min and declined thereafter. These findings fit well with the notion that strain-dependent stress-vulnerability reflects, in part, poor homeostatic mechanisms controlling synaptogenesis.
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Prevalence of and risk factors for isolation of meticillin-resistant Staphylococcus spp. from dogs with pyoderma in northern California, USA.
Vet. Dermatol.
PUBLISHED: 01-22-2013
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Canine pyodermas associated with meticillin-resistant Staphylococcus spp. (MRS) have increased in prevalence over the past decade.
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PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis.
Nat. Chem. Biol.
PUBLISHED: 01-20-2013
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Following DNA damage, nuclear p53 induces the expression of PUMA, a BH3-only protein that binds and inhibits the antiapoptotic BCL-2 repertoire, including BCL-xL. PUMA, unique among BH3-only proteins, disrupts the interaction between cytosolic p53 and BCL-xL, allowing p53 to promote apoptosis via direct activation of the BCL-2 effector molecules BAX and BAK. Structural investigations using NMR spectroscopy and X-ray crystallography revealed that PUMA binding induced partial unfolding of two ?-helices within BCL-xL. Wild-type PUMA or a PUMA mutant incapable of causing binding-induced unfolding of BCL-xL equivalently inhibited the antiapoptotic BCL-2 repertoire to sensitize for death receptor-activated apoptosis, but only wild-type PUMA promoted p53-dependent, DNA damage-induced apoptosis. Our data suggest that PUMA-induced partial unfolding of BCL-xL disrupts interactions between cytosolic p53 and BCL-xL, releasing the bound p53 to initiate apoptosis. We propose that regulated unfolding of BCL-xL provides a mechanism to promote PUMA-dependent signaling within the apoptotic pathways.
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Strain vulnerability and resiliency in the chick anxiety-depression model.
Physiol. Behav.
PUBLISHED: 01-16-2013
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Increasing research is focused on genetic contributions to variability in stress-related endophenotypes in humans and animal model simulations. The current study sought to identify strain vulnerabilities and resiliencies to an isolation-stressor in the chick anxiety-depression model. Nine different strains of socially raised chicks were tested in isolated or non-isolated conditions for 90 min in which distress vocalization (DVoc) rates were collected and then transformed to depression-like phase threshold (@ 25, 50, 75 and 95%) latencies. In general, chicks in the non-isolated condition displayed relatively low DVoc rates throughout the test session, despite some variability in initial rates. Chicks in the isolated condition displayed relatively high DVoc rates in the first 3 min, indicative of an anxiety-like state, which declined by approximately 50% within 10-25 min in all strains and remained stable thereafter, indicative of a depression-like state. Contrast effects revealed that, relative to all other strains, the Black Australorp strain displayed shorter and the Producrain displayed longer depression threshold latencies, respectively. Of the remaining strains, the Silver Laced Wyandotte displayed depression thresholds that best represent an intermediate stress response. These findings identify vulnerable and resilient strains for examining depression-related endophenotypes in the chick anxiety-depression model.
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A divergent Artiodactyl MYADM-like repeat is associated with erythrocyte traits and weight of lamb weaned in domestic sheep.
PLoS ONE
PUBLISHED: 01-01-2013
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A genome-wide association study (GWAS) was performed to investigate seven red blood cell (RBC) phenotypes in over 500 domestic sheep (Ovis aries) from three breeds (Columbia, Polypay, and Rambouillet). A single nucleotide polymorphism (SNP) showed genome-wide significant association with increased mean corpuscular hemoglobin concentration (MCHC, P?=?6.2×10(-14)) and genome-wide suggestive association with decreased mean corpuscular volume (MCV, P?=?2.5×10(-6)). The ovine HapMap project found the same genomic region and the same peak SNP has been under extreme historical selective pressure, demonstrating the importance of this region for survival, reproduction, and/or artificially selected traits. We observed a large (>50 kb) variant haplotype sequence containing a full-length divergent artiodactyl MYADM-like repeat in strong linkage disequilibrium with the associated SNP. MYADM gene family members play roles in membrane organization and formation in myeloid cells. However, to our knowledge, no member of the MYADM gene family has been identified in development of morphologically variant RBCs. The specific RBC differences may be indicative of alterations in morphology. Additionally, erythrocytes with altered morphological structure often exhibit increased structural fragility, leading to increased RBC turnover and energy expenditure. The divergent artiodactyl MYADM-like repeat was also associated with increased ewe lifetime kilograms of lamb weaned (P?=?2×10(-4)). This suggests selection for normal RBCs might increase lamb weights, although further validation is required before implementation in marker-assisted selection. These results provide clues to explain the strong selection on the artiodactyl MYADM-like repeat locus in sheep, and suggest MYADM family members may be important for RBC morphology in other mammals.
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Hyperadrenocorticism in 10 dogs with skin lesions as the only presenting clinical signs.
J Am Anim Hosp Assoc
PUBLISHED: 11-08-2011
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Ten dogs that had skin lesions as the only presenting signs of hyperadrenocorticism (HAC) and as the owners primary complaint are described. Dogs were included if the initial examination was for skin disease, there were no signs of systemic illness on initial presentation and there was a confirmed diagnosis of HAC by specific screening tests. Dogs were excluded if they had a severe disease that might interfere with screening tests for HAC or if the screening tests were not diagnostic. There were five males and five females; six dogs were intact. Nine dogs were diagnosed at ?7 years. Eight dogs weighed ?10 kg. Alopecia was present in nine dogs. Eight dogs had bacterial pyoderma, five had hyperpigmentation, and four had thin skin. One dog had unresolved dermatophytosis. Skin lesions resolved after treatment in eight dogs. One dog was not treated and one was lost to follow-up. This study showed that skin lesions may be the only clinical signs of HAC. The presence of the more common clinical signs of HAC, such as a non-pruritic, truncal alopecia and/or thin skin, without any systemic signs of HAC and/or the presence of poorly responsive skin infections warrant screening for this disease.
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Development of a pterin-based fluorescent probe for screening dihydropteroate synthase.
Bioconjug. Chem.
PUBLISHED: 09-30-2011
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Dihydropteroate synthase (DHPS) is the classical target of the sulfonamide class of antimicrobial agents, whose use has been limited by widespread resistance and pharmacological side effects. We have initiated a structure-based drug design approach for the development of novel DHPS inhibitors that bind to the highly conserved and structured pterin subsite rather than to the adjacent p-aminobenzoic acid binding pocket that is targeted by the sulfonamide class of antibiotics. To facilitate these studies, a robust pterin site-specific fluorescence polarization (FP) assay has been developed and is discussed herein. These studies include the design, synthesis, and characterization of two fluorescent probes, and the development and validation of a rapid DHPS FP assay. This assay has excellent DMSO tolerance and is highly reproducible as evidenced by a high Z factor. This assay offers significant advantages over traditional radiometric or phosphate release assays against this target, and is suitable for site-specific high-throughput and fragment-based screening studies.
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Hydrogen bond dynamics in membrane protein function.
Biochim. Biophys. Acta
PUBLISHED: 09-21-2011
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Changes in inter-helical hydrogen bonding are associated with the conformational dynamics of membrane proteins. The function of the protein depends on the surrounding lipid membrane. Here we review through specific examples how dynamical hydrogen bonds can ensure an elegant and efficient mechanism of long-distance intra-protein and protein-lipid coupling, contributing to the stability of discrete protein conformational substates and to rapid propagation of structural perturbations. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions.
J. Am. Chem. Soc.
PUBLISHED: 09-14-2011
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Nascent transmembrane (TM) polypeptide segments are recognized and inserted into the lipid bilayer by the cellular translocon machinery. The recognition rules, described by a biological hydrophobicity scale, correlate strongly with physical hydrophobicity scales that describe the free energy of insertion of TM helices from water. However, the exact relationship between the physical and biological scales is unknown, because solubility problems limit our ability to measure experimentally the direct partitioning of hydrophobic peptides across lipid membranes. Here we use microsecond molecular dynamics (MD) simulations in which monomeric polyleucine segments of different lengths are allowed to partition spontaneously into and out of lipid bilayers. This approach directly reveals all states populated at equilibrium. For the hydrophobic peptides studied here, only surface-bound and transmembrane-inserted helices are found. The free energy of insertion is directly obtained from the relative occupancy of these states. A water-soluble state was not observed, consistent with the general insolubility of hydrophobic peptides. The approach further allows determination of the partitioning pathways and kinetics. Surprisingly, the transfer free energy appears to be independent of temperature, which implies that surface-to-bilayer peptide insertion is a zero-entropy process. We find that the partitioning free energy of the polyleucine segments correlates strongly with values from translocon experiments but reveals a systematic shift favoring shorter peptides, suggesting that translocon-to-bilayer partitioning is not equivalent but related to spontaneous surface-to-bilayer partitioning.
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Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.
J. Mol. Biol.
PUBLISHED: 08-16-2011
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Tyrosyl-DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily that hydrolyzes 3-phospho-DNA adducts via two conserved catalytic histidines-one acting as the lead nucleophile and the second acting as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease spinocerebellar ataxia with axonal neuropathy (SCAN1). We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics, and theoretical chemistry. The structures of wild-type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observed in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts the access of nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitutions with Asn, Gln, Leu, Ala, Ser, and Thr all result in severely compromised enzymes and DNA topoisomerase I-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate that suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pK(a) of this histidine is crucially dependent on the second histidine and on the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily.
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Equine atopic skin disease and response to allergen-specific immunotherapy: a retrospective study at the University of California-Davis (1991-2008).
Vet. Dermatol.
PUBLISHED: 07-21-2011
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This retrospective study reports on the clinical presentation of equine atopic skin disease and evaluates response to treatment with allergen-specific immunotherapy (ASIT) based on intradermal testing and/or serum testing. Computerized medical records from January 1991 to December 2008 yielded 54 horses included in the study. Presenting clinical signs (CS) included urticaria (n=28), pruritus (n=8) or both (n=18). Forty-one of 54 horses received ASIT, and response to ASIT (n=32) was evaluated via telephone survey. Eighty-four per cent (n=27) of owners reported that ASIT reduced their horses CS; 59% (n=19) were able to manage CS by ASIT alone. Three horses (9%) were managed with ASIT in combination with doxepin and discontinued use of corticosteroids. There was no statistical significance between type of test performed and reported success of ASIT (?(2) analysis, P=0.53). Ninety-three per cent (n=30) of owners reported use of antipruritic medications prior to starting ASIT; 57% (n=17) of these owners reported discontinuing those medications due to success of ASIT. Adverse effects were limited to swelling at the injection site, seen in 16% (n=5). Seventy-five per cent (n=24) of owners elected to discontinue ASIT after 6 months to 8 years (mean 2.2 years): 15 due to resolution of CS, six due to persistent CS, two because the horse was sold, and one due to cost. Ten owners reported no recurrence of CS after discontinuing ASIT; five had recurrence within a median of 2 years of discontinuing ASIT (range 1-12 years). Allergen-specific immunotherapy is a safe and effective way to manage equine atopic skin disease.
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Acid stability of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity.
PLoS Pathog.
PUBLISHED: 07-07-2011
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Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 Å resolution and two structures of HP HA at 2.95 and 3.10 Å resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.
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In vitro activity of ponazuril against Theileria equi.
Vet. Parasitol.
PUBLISHED: 06-29-2011
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The equid hemoprotozoan parasite Theileria equi is endemic in most regions worldwide. Infection of horses is a cause of significant economic loss due to costs associated with disease and restriction of trade with non-endemic nations. The ability of certain drugs such as imidocarb dipropionate to eliminate persistent T. equi infection and transmission risk is controversial. The anti-protozoal agent ponazuril has been used successfully to treat equine Sarcosystis neurona and Toxoplasma gondii. The hypothesis that ponazuril inhibits replication of T. equi in vitro was tested. T. equi infected equine erythrocyte cultures were treated with ponazuril at multiple concentrations. Cessation of parasite replication was observed over a 5-day period and the degree of inhibition was variable between drug concentrations. Ponazuril inhibited T. equi in erythrocyte culture at all concentrations tested but parasite elimination required at least 500 ?g/mL. The high dose of ponazuril required for in vitro inhibition likely limits its ability to control or clear T. equi infection in vivo, however additional research to evaluate related drugs is warranted.
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Structural dynamics of the S4 voltage-sensor helix in lipid bilayers lacking phosphate groups.
J Phys Chem B
PUBLISHED: 06-22-2011
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Voltage-dependent K(+) (Kv) channels require lipid phosphates for functioning. The S4 helix, which carries the gating charges in the voltage-sensing domain (VSD), inserts into membranes while being stabilized by a protein-lipid interface in which lipid phosphates play an essential role. To examine the physical basis of the protein-lipid interface in the absence of lipid phosphates, we performed molecular dynamics (MD) simulations of a KvAP S4 variant (S4mut) in bilayers with and without lipid phosphates. We find that, in dioleoyltrimethylammoniumpropane (DOTAP) bilayers lacking lipid phosphates, the gating charges are solvated by anionic counterions and, hence, lack the bilayer support provided by phosphate-containing palmitoyloleoylglycerophosphocholine (POPC) bilayers. The result is a water-permeable bilayer with significantly smaller deformations around the peptide. Together, these results provide an explanation for the nonfunctionality of VSDs in terms of a destabilizing protein-lipid interface.
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Water wires in atomistic models of the Hv1 proton channel.
Biochim. Biophys. Acta
PUBLISHED: 06-03-2011
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The voltage-gated proton channel (Hv1) is homologous to the voltage-sensing domain (VSD) of voltage-gated potassium (Kv) channels but lacks a separate pore domain. The Hv1 monomer has dual functions: it gates the proton current and also serves as the proton conduction pathway. To gain insight into the structure and dynamics of the yet unresolved proton permeation pathway, we performed all-atom molecular dynamics simulations of two different Hv1 homology models in a lipid bilayer in excess water. The structure of the Kv1.2-Kv2.1 paddle-chimera VSD was used as template to generate both models, but they differ in the sequence alignment of the S4 segment. In both models, we observe a water wire that extends through the membrane, whereas the corresponding region is dry in simulations of the Kv1.2-Kv2.1 paddle-chimera. We find that the kinetic stability of the water wire is dependent upon the identity and location of the residues lining the permeation pathway, in particular, the S4 arginines. A measurement of water transport kinetics indicates that the water wire is a relatively static feature of the permeation pathway. Taken together, our results suggest that proton conduction in Hv1 may occur via Grotthuss hopping along a robust water wire, with exchange of water molecules between inner and outer ends of the permeation pathway minimized by specific water-protein interactions. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Hydrogen-bond energetics drive helix formation in membrane interfaces.
Biochim. Biophys. Acta
PUBLISHED: 06-03-2011
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The free energy cost ?G of partitioning many unfolded peptides into membrane interfaces is unfavorable due to the cost of partitioning backbone peptide bonds. The partitioning cost is dramatically reduced if the peptide bonds participate in hydrogen bonds. The reduced cost underlies secondary structure formation by amphiphilic peptides partitioned into membrane interfaces through a process referred to as partitioning-folding coupling. This coupling is characterized by the free energy reduction per residue, ?G(res) that drives folding. There is some debate about the correct value of ?G(res) and its dependence on the hydrophobic moment (?(H)) of amphiphilic ?-helical peptides. We show how to compute ?G(res) correctly. Using published data for two families of peptides with different hydrophobic moments and charges, we find that ?G(res) does not depend upon ?(H). The best estimate of ?G(res) is -0.37 ± 0.02 kcal mol(-1). This article is part of a Special Issue entitled: Membrane protein structure and function.
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Apolar surface area determines the efficiency of translocon-mediated membrane-protein integration into the endoplasmic reticulum.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-23-2011
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Integral membrane proteins are integrated cotranslationally into the membrane of the endoplasmic reticulum in a process mediated by the Sec61 translocon. Transmembrane ?-helices in a translocating polypeptide chain gain access to the surrounding membrane through a lateral gate in the wall of the translocon channel [van den Berg B, et al. (2004) Nature 427:36-44; Zimmer J, et al. (2008) Nature 455:936-943; Egea PF, Stroud RM (2010) Proc Natl Acad Sci USA 107:17182-17187]. To clarify the nature of the membrane-integration process, we have measured the insertion efficiency into the endoplasmic reticulum membrane of model hydrophobic segments containing nonproteinogenic aliphatic and aromatic amino acids. We find that an amino acids contribution to the apparent free energy of membrane-insertion is directly proportional to the nonpolar accessible surface area of its side chain, as expected for thermodynamic partitioning between aqueous and nonpolar phases. But unlike bulk-phase partitioning, characterized by a nonpolar solvation parameter of 23 cal/(mol · ?(2)), the solvation parameter for transfer from translocon to bilayer is 6-10 cal/(mol · ?(2)), pointing to important differences between translocon-guided partitioning and simple water-to-membrane partitioning. Our results provide compelling evidence for a thermodynamic partitioning model and insights into the physical properties of the translocon.
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Oral vitamin A as an adjunct treatment for canine sebaceous adenitis.
Vet. Dermatol.
PUBLISHED: 05-20-2011
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Medical records of dogs with sebaceous adenitis diagnosed by histopathology over an 18-year period were reviewed. From a total of 40 cases, 24 were treated with oral vitamin A. Dogs ranged from 9 months to 12 years of age at the time of disease onset. Purebred as well as mixed-breed dogs were affected. Akitas represented approximately one-third of the affected population. No sex predilections were observed. Vitamin A was administered for a minimum of 1 month. Doses varied from 380 to 2667 IU/kg/day, with a mean of 1037 IU/kg/day. Two dogs received oral vitamin A exclusively. Concurrent treatments included systemic antibiotics, systemic antifungal medications, fatty acid supplementation and various topical treatments. Of 24 dogs treated with vitamin A, three were lost to follow-up. Twelve owners were satisfied with the overall appearance of their dogs, reporting ?25% improvement in clinical signs, including level of pruritus, amount of scale, alopecia and overall coat quality, compared with pretreatment appearance. Three owners observed adequate initial improvement, with regression to pretreatment state within 6 months of starting treatment. Two owners reported 25-50% improvement in clinical signs while on oral vitamin A supplementation; however, changes were attributed to concurrent topical treatment. Six owners reported no improvement and discontinued oral administration of vitamin A within 7 months. No correlations could be made between vitamin A dosage and response to treatment; prognoses could not be made based on clinical and histopathological findings.
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Characterization of the differential response of endothelial cells exposed to normal and elevated laminar shear stress.
J. Cell. Physiol.
PUBLISHED: 02-09-2011
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Most acute coronary events occur in the upstream region of stenotic atherosclerotic plaques that experience laminar shear stress (LSS) elevated above normal physiological levels. Many studies have described the atheroprotective effect on endothelial behavior of normal physiological LSS (approximately 15?dynes/cm(2)) compared to static or oscillatory shear stress (OSS), but it is unknown whether the levels of elevated shear stress imposed by a stenotic plaque would preserve, enhance or reverse this effect. Therefore we used transcriptomics and related functional analyses to compare human endothelial cells exposed to laminar shear stress of 15 (LSS15-normal) or 75?dynes/cm(2) (LSS75-elevated). LSS75 upregulated expression of 145 and downregulated expression of 158 genes more than twofold relative to LSS15. Modulation of the metallothioneins (MT1-G, -M, -X) and NADPH oxidase subunits (NOX2, NOX4, NOX5, and p67phox) accompanied suppression of reactive oxygen species production at LSS75. Shear induced changes in dual specificity phosphatases (DUSPs 1, 5, 8, and 16 increasing and DUSPs 6 and 23 decreasing) were observed as well as reduced ERK1/2 but increased p38 MAP kinase phosphorylation. Amongst vasoactive substances, endothelin-1 expression decreased whereas vasoactive intestinal peptide (VIP) and prostacyclin expression increased, despite which intracellular cAMP levels were reduced. Promoter analysis by rVISTA identified a significant over representation of ATF and Nrf2 transcription factor binding sites in genes upregulated by LSS75 compared to LSS15. In summary, LSS75 induced a specific change in behavior, modifying gene expression, reducing ROS levels, altering MAP kinase signaling and reducing cAMP levels, opening multiple avenues for future study.
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A female mass murder.
J. Forensic Sci.
PUBLISHED: 02-03-2011
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A case study of a 44-year-old woman who committed a mass murder is presented. Following a chronic course of psychotic deterioration, and a likely diagnosis of paranoid schizophrenia that remained untreated, she returned to her workplace after 3 years from her termination and killed seven people and herself. Her history is reconstructed through investigation of primary and secondary source materials. Although there are very few female mass murderers in recorded criminal history, this case is quite similar to the known research on mass murderers in general. Such individuals often have a psychotic disorder evident in violent and paranoid delusions, show a deteriorating life course before the mass murder, intentionally plan and prepare for their assault, and methodically kill as many individuals as possible before taking their own lives. They typically do not directly threaten the target beforehand, but do leak their intent to third parties--however, in this case, leakage and other obvious warning behaviors did not occur. Such acts are impossible to predict but depend on threat management and target security for risk mitigation.
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Characterization of ovine herpesvirus 2-induced malignant catarrhal fever in rabbits.
Vet. Microbiol.
PUBLISHED: 01-26-2011
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Malignant catarrhal fever (MCF) is a frequently fatal lymphoproliferative disease syndrome primarily of ruminant species, caused by gammaherpesviruses in the genus Macavirus. Ovine herpesvirus 2 (OvHV-2), carried by sheep, causes sheep-associated MCF worldwide, while Alcelaphine herpesvirus 1 (AlHV-1), carried by wildebeest, causes wildebeest-associated MCF, mainly in Africa. Diseases in rabbits can be induced by both viruses, which are clinically and pathologically similar; however, recent studies revealed different expression of viral genes associated with latency or lytic replication during clinical disease between the two viruses. In this study, we further characterized experimentally induced MCF in rabbits by nebulization with OvHV-2 from sheep nasal secretions to elucidate the course of viral replication, along with in vivo incorporation of 5-Bromo-2-Deoxyuridine (BrdU), to evaluate lymphoproliferation. All six rabbits nebulized with OvHV-2 developed MCF between 24 and 29 days post infection. OvHV-2 DNA levels in peripheral blood leukocytes (PBL) remained undetectable during the incubation period and increased dramatically a few days before onset of clinical signs. During the clinical stage, we found that predominantly lytic gene expression was detected in PBL and tissues, and both T and B cells were proliferating. The data showed that the viral gene expression profile and lymphoproliferation in rabbits with OvHV-2 induced MCF were different from that in rabbits with AlHV-1 induced MCF, suggesting that OvHV-2 and AlHV-1 may play a different role in MCF pathogenesis.
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Acyl-chain methyl distributions of liquid-ordered and -disordered membranes.
Biophys. J.
PUBLISHED: 01-19-2011
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A central feature of the lipid raft concept is the formation of cholesterol-rich lipid domains. The introduction of relatively rigid cholesterol molecules into fluid liquid-disordered (L(d)) phospholipid bilayers can produce liquid-ordered (L(o)) mixtures in which the rigidity of cholesterol causes partial ordering of the flexible hydrocarbon acyl chains of the phospholipids. Several lines of evidence support this concept, but direct structural information about L(o) membranes is lacking. Here we present the structure of L(o) membranes formed from cholesterol and dioleoylphosphatidylcholine (DOPC). Specific deuteration of the DOPC acyl-chain methyl groups and neutron diffraction measurements reveal an extraordinary disorder of the acyl chains of neat L(d) DOPC bilayers. The disorder is so great that >20% of the methyl groups are in intimate contact with water in the bilayer interface. The ordering of the DOPC acyl chains by cholesterol leads to retraction of the methyl groups away from the interface. Molecular dynamics simulations based on experimental systems reveal asymmetric transbilayer distributions of the methyl groups associated with each bilayer leaflet.
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The Twin Peg Oxford partial knee replacement: the first 100 cases.
Knee
PUBLISHED: 01-19-2011
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We present the clinical results of the first 100 patients who received the Twin Peg Oxford partial knee replacement which has a 15° extra femoral surface for contact in deep flexion, and has two pegs for more secure fixation. We measured the clinical outcome 2 years after the medial unicompartmental arthroplasty using patient and surgeon derived outcome measures. The results showed a mean Oxford Knee Score of 41, a mean American Knee Society Objective Score of 93 and a Functional Score of 84, a mean range of motion of 130° and a high satisfaction rate. Results were significantly better in male patients. There were no deaths, infections, dislocations, fractures or revisions. There were no pathological radiolucencies suggestive of early loosening. We conclude that the Twin Peg Oxford partial knee replacement shows excellent clinical and radiological results at 2 years. For surgeons who have concern over the risk of femoral loosening with the single peg Oxford knee, or seek an improved surface area of contact in full flexion, this implant offers an excellent alternative.
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Prevalence of the mutation in cyclophilin B (PPIB), a causal candidate gene for HERDA, among Quarter Horses in France.
Vet. Dermatol.
PUBLISHED: 11-30-2010
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Hereditary equine regional dermal asthenia (HERDA) in Quarter Horses is an inherited degenerative skin disease. Initially reported as hyperelastosis cutis, HERDA has a phenotype of hyperextensible, fragile skin, with secondary seromas, haematomas, ulcers and scarring. It primarily affects the dorsal aspect of the body. An autosomal recessive mode of inheritance is considered likely, with affected horses more at risk to produce affected offspring. A mutation in cyclophilin B (PPIB) as a novel, causal candidate gene for HERDA has been described, and verified as segregating with carriers and affected horses. Screening of control Quarter Horses in the USA has indicated a 3.5% carrier frequency. The prevalence of this mutation among Quarter Horses in France was determined to be 1.6%.
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The receptor-binding domain of influenza virus hemagglutinin produced in Escherichia coli folds into its native, immunogenic structure.
J. Virol.
PUBLISHED: 11-10-2010
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The hemagglutinin (HA) surface glycoprotein promotes influenza virus entry and is the key protective antigen in natural immunity and vaccines. The HA protein is a trimeric envelope glycoprotein consisting of a globular receptor-binding domain (HA-RBD) that is inserted into a membrane fusion-mediating stalk domain. Similar to other class I viral fusion proteins, the fusogenic stalk domain spontaneously refolds into its postfusion conformation when expressed in isolation, consistent with this domain being trapped in a metastable conformation. Using X-ray crystallography, we show that the influenza virus HA-RBD refolds spontaneously into its native, immunogenic structure even when expressed in an unglycosylated form in Escherichia coli. In the 2.10-Å structure of the HA-RBD, the receptor-binding pocket is intact and its conformational epitopes are preserved. Recombinant HA-RBD is immunogenic and protective in ferrets, and the protein also binds with specificity to sera from influenza virus-infected humans. Overall, the data provide a structural basis for the rapid production of influenza vaccines in E. coli. From an evolutionary standpoint, the ability of the HA-RBD to refold spontaneously into its native conformation suggests that influenza virus acquired this domain as an insertion into an ancestral membrane-fusion domain. The insertion of independently folding domains into fusogenic stalk domains may be a common feature of class I viral fusion proteins.
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Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments.
J. Membr. Biol.
PUBLISHED: 10-21-2010
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Several laboratories have carried out molecular dynamics (MD) simulations of arginine interactions with lipid bilayers and found that the energetic cost of placing arginine in lipid bilayers is an order of magnitude greater than observed in molecular biology experiments in which Arg-containing transmembrane helices are inserted across the endoplasmic reticulum membrane by the Sec61 translocon. We attempt here to reconcile the results of the two approaches. We first present MD simulations of guanidinium groups alone in lipid bilayers, and then, to mimic the molecular biology experiments, we present simulations of hydrophobic helices containing single Arg residues at different positions along the helix. We discuss the simulation results in the context of molecular biology results and show that the energetic discrepancy is reduced, but not eliminated, by considering free energy differences between Arg at the interface and at the center of the model helices. The reduction occurs because Arg snorkeling to the interface prevents Arg from residing in the bilayer center where the energetic cost of desolvation is highest. We then show that the problem with MD simulations is that they measure water-to-bilayer free energies, whereas the molecular biology experiments measure the energetics of partitioning from translocon to bilayer, which raises the fundamental question of the relationship between water-to-bilayer and water-to-translocon partitioning. We present two thermodynamic scenarios as a foundation for reconciliation of the simulation and molecular biology results. The simplest scenario is that translocon-to-bilayer partitioning is independent of water-to-bilayer partitioning; there is no thermodynamic cycle connecting the two paths.
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A ten-year audit of perforated sigmoid diverticulitis: highlighting the outcomes of laparoscopic lavage.
Dis. Colon Rectum
PUBLISHED: 10-14-2010
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This study was designed to review the results of laparoscopic lavage for the management of perforated sigmoid diverticulitis.
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Reptiles with dermatological lesions: a retrospective study of 301 cases at two university veterinary teaching hospitals (1992-2008).
Vet. Dermatol.
PUBLISHED: 10-01-2010
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This retrospective study reviews the medical records of 301 reptiles with dermatological lesions that were examined at the Veterinary Medical Teaching Hospital, University of California at Davis (VMTH-UCD) and the Unité de Dermatologie-Parasitologie-Mycologie, Ecole Nationale Vétérinaire de Nantes (UDPM-ENVN) from 1 January 1992 to 1 July 2008. The most common reptile groups differed between the two hospitals, with lizards being the most common at the VMTH-UCD and chelonians at the UDPM-ENVN. At the VMTH-UCD, boa constrictors (Boa constrictor), ball pythons (Python regius) and other Python species were over-represented, and box turtles (Terrapene carolina) were under-represented in the dermatological lesion caseload. When institutional data were combined, 47% of all reptiles at both institutions with confirmed or suspected cases of sepsis had petechiae, with the highest association seen in chelonians at 82%. Dependent on institution and reptile group, from 29% to 64% of the cases had underlying husbandry issues. Sixty-two per cent of all cases were alive at final status. Veterinarians treating reptiles with skin disease should be aware of the following: (i) that boa constrictors and Python species may be predisposed to dermatological lesions; (ii) that client education is important for proper husbandry; and (iii) that there is a possible association between petechiae and sepsis, especially in chelonians. The conjectural association between certain skin lesions and sepsis remains to be confirmed by systematically derived data that demonstrate a causal relationship between the two.
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Synthesis of bi-substrate state mimics of dihydropteroate synthase as potential inhibitors and molecular probes.
Bioorg. Med. Chem.
PUBLISHED: 09-21-2010
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The increasing emergence of resistant bacteria drives us to design and develop new antimicrobial agents. Pursuant to that goal, a new targeting approach of the dihydropteroate synthase enzyme, which serves as the site of action for the sulfonamide class of antimicrobial agents, is being explored. Using structural information, a new class of transition state mimics has been designed and synthesized that have the capacity to bind to the pterin, phosphate and para-amino binding sites. The design, synthesis and evaluation of these compounds as inhibitors of Bacillusanthracis dihydropteroate synthase is described herein. Outcomes from this work have identified the first trivalent inhibitors of dihydropteroate synthase whose activity displayed slow binding inhibition. The most active compounds in this series contained an oxidized pterin ring. The binding of these inhibitors was modeled into the dihydropteroate synthase active site and demonstrated a good correlation with the observed bioassay data, as well as provided important insight for the future design of higher affinity transition state mimics.
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Structure and dynamics of cholesterol-containing polyunsaturated lipid membranes studied by neutron diffraction and NMR.
J. Membr. Biol.
PUBLISHED: 09-20-2010
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A direct and quantitative analysis of the internal structure and dynamics of a polyunsaturated lipid bilayer composed of 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0-22:6n3-PC) containing 29 mol% cholesterol was carried out by neutron diffraction, (2)H-NMR and (13)C-MAS NMR. Scattering length distribution functions of cholesterol segments as well as of the sn-1 and sn-2 hydrocarbon chains of 18:0-22:6n3-PC were obtained by conducting experiments with specifically deuterated cholesterol and lipids. Cholesterol orients parallel to the phospholipids, with the A-ring near the lipid glycerol and the terminal methyl groups 3 Å away from the bilayer center. Previously, we reported that the density of polyunsaturated docosahexaenoic acid (DHA, 22:6n3) chains was higher near the lipid-water interface. Addition of cholesterol partially redistributes DHA density from near the lipid-water interface to the center of the hydrocarbon region. Cholesterol raises chain-order parameters of both stearic acid and DHA chains. The fractional order increase for stearic acid methylene carbons C(8)-C(18) is larger, reflecting the redistribution of DHA chain density toward the bilayer center. The correlation times of DHA chain isomerization are short and mostly unperturbed by the presence of cholesterol. The uneven distribution of saturated and polyunsaturated chain densities and the cholesterol-induced balancing of chain distributions may have important implications for the function and integrity of membrane receptors, such as rhodopsin.
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Management of malignant left-sided large bowel obstruction: a comparison between colonic stents and surgery.
ANZ J Surg
PUBLISHED: 09-16-2010
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Management of distal malignant large bowel obstruction (LBO) remains challenging. Acute surgical intervention is often associated with poorer clinical outcome compared to an elective procedure. Self-expandable metallic stents (SEMS) as a bridge to surgery (BTS) or palliation remain controversial and are not yet widely available.
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Evaluation of the clinical efficacy of pradofloxacin tablets for the treatment of canine pyoderma.
J Am Anim Hosp Assoc
PUBLISHED: 09-03-2010
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A third-generation fluoroquinolone, pradofloxacin (PRA), is currently being developed to treat bacterial infections in dogs. The purpose of this study was to assess the clinical efficacy in 20 dogs affected with superficial and deep pyoderma. An initial aerobic skin culture was performed in dogs with superficial pyoderma; aerobic/anaerobic tissue culture was performed in dogs with deep pyoderma; and skin cytology and biopsies were obtained from all dogs. Pradofloxacin (approximately 3 mg/kg per os [PO]) was administered daily to all dogs. Clinical efficacy was recorded at 4 weeks for dogs with superficial pyoderma and at 3 and 6 weeks for dogs with deep pyoderma. At a mean dosage of 3.7 mg/kg PO once daily, PRA treatment resulted in an excellent to good clinical response within 3 to 6 weeks for all 20 dogs with superficial and deep pyoderma.
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Membrane partitioning: "classical" and "nonclassical" hydrophobic effects.
J. Membr. Biol.
PUBLISHED: 08-15-2010
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The free energy of transfer of nonpolar solutes from water to lipid bilayers is often dominated by a large negative enthalpy rather than the large positive entropy expected from the hydrophobic effect. This common observation has led to the idea that membrane partitioning is driven by the "nonclassical" hydrophobic effect. We examined this phenomenon by characterizing the partitioning of the well-studied peptide melittin using isothermal titration calorimetry (ITC) and circular dichroism (CD). We studied the temperature dependence of the entropic (-T?S) and enthalpic (?H) components of free energy (?G) of partitioning of melittin into lipid membranes made of various mixtures of zwitterionic and anionic lipids. We found significant variations of the entropic and enthalpic components with temperature, lipid composition and vesicle size but only small changes in ?G (entropy-enthalpy compensation). The heat capacity associated with partitioning had a large negative value of about -0.5 kcal mol(-1) K(-1). This hallmark of the hydrophobic effect was found to be independent of lipid composition. The measured heat capacity values were used to calculate the hydrophobic-effect free energy ?G (h?), which we found to dominate melittin partitioning regardless of lipid composition. In the case of anionic membranes, additional free energy comes from coulombic attraction, which is characterized by a small effective peptide charge due to the lack of additivity of hydrophobic and electrostatic interactions in membrane interfaces [Ladokhin and White J Mol Biol 309:543-552, 2001]. Our results suggest that there is no need for a special effect-the nonclassical hydrophobic effect-to describe partitioning into lipid bilayers.
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Overexpression of scavenger receptor LOX-1 in endothelial cells promotes atherogenesis in the ApoE(-/-) mouse model.
Cardiovasc. Pathol.
PUBLISHED: 08-04-2010
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The oxidized low-density lipoprotein receptor LOX-1 is up-regulated on activated endothelial cells, for example, the endothelium of atherosclerosis-prone sites, in both human and animal models. We examined whether endothelial LOX-1 overexpression may contribute to atherogenesis.
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Crystal structure of the phage T4 recombinase UvsX and its functional interaction with the T4 SF2 helicase UvsW.
J. Mol. Biol.
PUBLISHED: 07-23-2010
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Bacteriophage T4 provides an important model system for studying the mechanism of homologous recombination. We have determined the crystal structure of the T4 UvsX recombinase, and the overall architecture and fold closely resemble those of RecA, including a highly conserved ATP binding site. Based on this new structure, we reanalyzed electron microscopy reconstructions of UvsX-DNA filaments and docked the UvsX crystal structure into two different filament forms: a compressed filament generated in the presence of ADP and an elongated filament generated in the presence of ATP and aluminum fluoride. In these reconstructions, the ATP binding site sits at the protomer interface, as in the RecA filament crystal structure. However, the environment of the ATP binding site is altered in the two filament reconstructions, suggesting that nucleotide cannot be as easily accommodated at the protomer interface of the compressed filament. Finally, we show that the phage helicase UvsW completes the UvsX-promoted strand-exchange reaction, allowing the generation of a simple nicked circular product rather than complex networks of partially exchanged substrates.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.