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  • 1
    Publication Date: 2013-06-23
    Description: Predicting binding sites of a transcription factor in the genome is an important, but challenging, issue in studying gene regulation. In the past decade, a large number of protein–DNA co-crystallized structures available in the Protein Data Bank have facilitated the understanding of interacting mechanisms between transcription factors and their binding sites. Recent studies have shown that both physics-based and knowledge-based potential functions can be applied to protein–DNA complex structures to deliver position weight matrices (PWMs) that are consistent with the experimental data. To further use the available structural models, the proposed Web server, PiDNA, aims at first constructing reliable PWMs by applying an atomic-level knowledge-based scoring function on numerous in silico mutated complex structures, and then using the PWM constructed by the structure models with small energy changes to predict the interaction between proteins and DNA sequences. With PiDNA, the users can easily predict the relative preference of all the DNA sequences with limited mutations from the native sequence co-crystallized in the model in a single run. More predictions on sequences with unlimited mutations can be realized by additional requests or file uploading. Three types of information can be downloaded after prediction: (i) the ranked list of mutated sequences, (ii) the PWM constructed by the favourable mutated structures, and (iii) any mutated protein–DNA complex structure models specified by the user. This study first shows that the constructed PWMs are similar to the annotated PWMs collected from databases or literature. Second, the prediction accuracy of PiDNA in detecting relatively high-specificity sites is evaluated by comparing the ranked lists against in vitro experiments from protein-binding microarrays. Finally, PiDNA is shown to be able to select the experimentally validated binding sites from 10 000 random sites with high accuracy. With PiDNA, the users can design biological experiments based on the predicted sequence specificity and/or request mutated structure models for further protein design. As well, it is expected that PiDNA can be incorporated with chromatin immunoprecipitation data to refine large-scale inference of in vivo protein–DNA interactions. PiDNA is available at: http://dna.bime.ntu.edu.tw/pidna .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2013-08-02
    Description: Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ~23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ~7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 3
    Publication Date: 1993-02-05
    Description: Recoverin, a calcium ion (Ca2+)-binding protein of vertebrate photoreceptors, binds to photoreceptor membranes when the Ca2+ concentration is greater than 1 micromolar. This interaction requires a fatty acyl residue covalently linked to the recoverin amino (NH2)-terminus. Removal of the acyl residue, either by proteolytic cleavage of the NH2-terminus or by production of nonacylated recoverin, prevented recoverin from binding to membranes. The acylated recoverin NH2-terminus could be cleaved by trypsin only when Ca2+ was bound to recoverin. These results suggest that the hydrophobic NH2-terminus is constrained in Ca(2+)-free recoverin and liberated by Ca2+ binding. The hydrophobic acyl moiety of recoverin may interact with the membrane only when recoverin binds Ca2+.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dizhoor, A M -- Chen, C K -- Olshevskaya, E -- Sinelnikova, V V -- Phillipov, P -- Hurley, J B -- EYO6641/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1993 Feb 5;259(5096):829-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8430337" target="_blank"〉PubMed〈/a〉
    Keywords: 1,2-Dipalmitoylphosphatidylcholine ; Acylation ; Animals ; Antigens, Neoplasm/isolation & purification/*metabolism ; Calcium/*metabolism/pharmacology ; Calcium-Binding Proteins/isolation & purification/*metabolism ; Cattle ; Cell Membrane/metabolism ; Egtazic Acid/pharmacology ; Electrophoresis, Polyacrylamide Gel ; *Eye Proteins ; Hippocalcin ; Kinetics ; *Lipoproteins ; Liposomes ; Membrane Proteins/isolation & purification/*metabolism ; Molecular Weight ; Myristic Acid ; Myristic Acids/*metabolism ; *Nerve Tissue Proteins ; Peptide Fragments/isolation & purification ; Phosphatidylserines ; Protein Binding ; Recoverin ; Rod Cell Outer Segment/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2017-11-10
    Description: Protein concentration process using filter membrane has a significant advantage on energy saving compared to the traditional drying processes. However, fouling on large membrane area and frequent membrane cleaning will increase the energy consumption and operation cost for the protein concentration process with filter membrane. In this study, the membrane filtration for protein concentration will be conducted and compared with the recent protein concentration technology. The analysis of operating factors for protein concentration process using filter membrane was discussed. The separation mechanism of membrane filtration was developed according to the size difference between the pore of membrane and the particle of filter material. The Darcy’s Law was applied to discuss the interaction on flux, TMP (transmembrane pressure) and resistance in this study. The effect of membrane pore size, pH value and TMP on the steady-state flux (J st ) and protein rejection (R) were stud...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
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  • 5
    Publication Date: 2011-11-24
    Description: There are various ways to measure the shape difference between two n -node rooted binary trees (binary trees for short). A rotation on a binary tree is a local restructuring that changes the tree into another one preserving the in-order sequence. The rotation distance between two binary trees is the minimum number of rotations needed to transform one into another. Till now, no polynomial–time algorithm exists for computing the rotation distance between any two binary trees. Recently, Lucas ( Comput. J. , 47, 259–269, 2004) presented an O ( n 2 )–time algorithm for finding the rotation distance between two binary trees, where the source tree is a degenerate tree and the destination tree is an angle tree. This paper improves the time-complexity to O ( n ) under this constraint.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 6
    Publication Date: 2012-12-12
    Description: Half the world's population is chronically infected with Helicobacter pylori, causing gastritis, gastric ulcers and an increased incidence of gastric adenocarcinoma. Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach. The channel is closed at neutral pH and opens at acidic pH to allow the rapid access of urea to cytoplasmic urease. Urease produces NH(3) and CO(2), neutralizing entering protons and thus buffering the periplasm to a pH of roughly 6.1 even in gastric juice at a pH below 2.0. Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids. Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices. The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian-type urea transporters. Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting the preservation of channel architecture and oligomeric state in this superfamily. Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel. Mutation of Trp 153 in the cytoplasmic constriction site to Ala or Phe decreases the selectivity for urea in comparison with thiourea, suggesting that solute interaction with Trp 153 contributes specificity. The previously unobserved hexameric channel structure described here provides a new model for the permeation of urea and other small amide solutes in prokaryotes and archaea.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974264/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974264/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strugatsky, David -- McNulty, Reginald -- Munson, Keith -- Chen, Chiung-Kuang -- Soltis, S Michael -- Sachs, George -- Luecke, Hartmut -- 5T32CA9054-34/CA/NCI NIH HHS/ -- P30CA062203/CA/NCI NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI078000/AI/NIAID NIH HHS/ -- R01AI78000/AI/NIAID NIH HHS/ -- R01DK53462/DK/NIDDK NIH HHS/ -- R01DK58333/DK/NIDDK NIH HHS/ -- T32 CA009054/CA/NCI NIH HHS/ -- England -- Nature. 2013 Jan 10;493(7431):255-8. doi: 10.1038/nature11684. Epub 2012 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉David Geffen School of Medicine, University of California Los Angeles, Greater West Los Angeles Health Care System, Los Angeles, California 90073, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23222544" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Helicobacter pylori/*chemistry ; Hydrogen-Ion Concentration ; Models, Molecular ; Protein Multimerization ; Protein Structure, Secondary ; *Protons ; Structural Homology, Protein ; Urea/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2015-04-29
    Description: Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional silencing, we still do not know any proteins required for this role. The main challenge is that there are currently no methods to comprehensively define the proteins that directly interact with a lncRNA in the cell. Here we develop a method to purify a lncRNA from cells and identify proteins interacting with it directly using quantitative mass spectrometry. We identify ten proteins that specifically associate with Xist, three of these proteins--SHARP, SAF-A and LBR--are required for Xist-mediated transcriptional silencing. We show that SHARP, which interacts with the SMRT co-repressor that activates HDAC3, is not only essential for silencing, but is also required for the exclusion of RNA polymerase II (Pol II) from the inactive X. Both SMRT and HDAC3 are also required for silencing and Pol II exclusion. In addition to silencing transcription, SHARP and HDAC3 are required for Xist-mediated recruitment of the polycomb repressive complex 2 (PRC2) across the X chromosome. Our results suggest that Xist silences transcription by directly interacting with SHARP, recruiting SMRT, activating HDAC3, and deacetylating histones to exclude Pol II across the X chromosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516396/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516396/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McHugh, Colleen A -- Chen, Chun-Kan -- Chow, Amy -- Surka, Christine F -- Tran, Christina -- McDonel, Patrick -- Pandya-Jones, Amy -- Blanco, Mario -- Burghard, Christina -- Moradian, Annie -- Sweredoski, Michael J -- Shishkin, Alexander A -- Su, Julia -- Lander, Eric S -- Hess, Sonja -- Plath, Kathrin -- Guttman, Mitchell -- 1S10RR029591-01A1/RR/NCRR NIH HHS/ -- DP2 OD001686/OD/NIH HHS/ -- DP5 OD012190/OD/NIH HHS/ -- DP5OD012190/OD/NIH HHS/ -- T32GM07616/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 May 14;521(7551):232-6. doi: 10.1038/nature14443. Epub 2015 Apr 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA. ; 1] Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA. ; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25915022" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Line ; Embryonic Stem Cells/enzymology/metabolism ; Female ; *Gene Silencing ; Heterogeneous-Nuclear Ribonucleoprotein U/metabolism ; Histone Deacetylases/*metabolism ; Histones/metabolism ; Male ; Mass Spectrometry/*methods ; Mice ; Nuclear Proteins/*metabolism ; Nuclear Receptor Co-Repressor 2/metabolism ; Polycomb Repressive Complex 2/metabolism ; Protein Binding ; RNA Polymerase II/metabolism ; RNA, Long Noncoding/genetics/*metabolism ; RNA-Binding Proteins/analysis/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Transcription, Genetic/*genetics ; X Chromosome/*genetics/metabolism ; X Chromosome Inactivation/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    ISSN: 1619-6937
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Summary This study presents the numerical calculations of the fluid flow and turbulent heat transfer characteristics of hot flow over a sudden-expansion with cold air base mass injection. The turbulent governing equations are solved by a control-volume-based finite-difference method with power-law scheme, the well knownk-ε model, and its associate wall function to describe the turbulent behavior. The velocity and pressure terms of momentum equations are solved by the SIMPLE (Semi-Implicid Method for Pressure-Linked Equation) method. In this study non uniform staggered grids are used. The parameters interested include the inlet Reynolds number (Re), inlet temperature (T0), and the injection flow rate (Q). The numerical results show that the reattachment lengths are reasonably predicted with a maximum discrepancy within 9.1%. It also shows that the base mass injection suppresses the horizontal velocity and turbulence intensity. In these high temperature heat transfer characteristics, the heat transfer coefficient increased with increasing inlet temperature and inlet Reynolds number, but decreased with increasing injection flow rate of the cooling air.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1572-9613
    Keywords: solidification of alloys ; phase field models ; interfaces ; nonlocal effects ; solidus curves ; solute trappings ; partition coefficient ; asymptotics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract A discussion is given of recent advances in phase-field modeling of materials which change phase. On one hand, general models incorporating elasticity properties of the material, nonconserved and conserved order parameters, and nonlocal effects are now available. On the other hand, gradient theories for binary alloys have been developed which reflect such effects as the dependence of capillarity on the concentration of impurities, solute trapping in its dependence on velocity of solidification fronts, and other nonequilibrium phenomena.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 57 (1990), S. 1111-1113 
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Schottky barrier PtSi-Si diodes formed by ultrahigh vacuum deposition and annealing of 1-nm-thick Pt films on n- and p-type (100) Si substrates were characterized by current-voltage measurements at liquid-nitrogen temperature. The diodes exhibited nearly ideal characteristics, with barrier heights of 0.914 and 0.197 eV, respectively, for typical n- and p-type devices. Subsequent annealing in hydrogen increased the barrier height by 0.013 eV for the n-type devices and decreased it by the same amount for the p-type devices. Vacuum annealing of H2-annealed devices restored the barrier heights to approximately their initial values. These results can be attributed to the presence of Si interface defects that are passivated by hydrogen incorporation and subsequently reactivated by vacuum annealing to remove the hydrogen.
    Type of Medium: Electronic Resource
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