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  • 1
    Publication Date: 2014-05-20
    Description: The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change remains elusive. Here we employed synthetic nucleotide analogues as ‘chemical mutation’ tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid enzymes in future studies.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2008-11-04
    Description: Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3' untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593745/" 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/PMC2593745/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Eric T -- Sandberg, Rickard -- Luo, Shujun -- Khrebtukova, Irina -- Zhang, Lu -- Mayr, Christine -- Kingsmore, Stephen F -- Schroth, Gary P -- Burge, Christopher B -- R01 GM085319/GM/NIGMS NIH HHS/ -- R01 GM085319-01/GM/NIGMS NIH HHS/ -- R01 HG002439/HG/NHGRI NIH HHS/ -- R01 HG002439-07/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18978772" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing/*genetics ; Base Sequence ; Cell Line ; Exons/genetics ; *Gene Expression Profiling ; Humans ; Open Reading Frames/genetics ; Organ Specificity ; Polyadenylation ; Protein Isoforms/*genetics ; RNA, Messenger/*analysis/*genetics ; RNA-Binding Proteins/metabolism ; Repressor Proteins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2007-04-21
    Description: Mekel-Bobrov et al. (Reports, 9 September 2005, p. 1720) suggested that ASPM, a gene associated with microcephaly, underwent natural selection within the last 500 to 14,100 years. Their analyses based on comparison with computer simulations indicated that ASPM had an unusual pattern of variation. However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Fuli -- Hill, R Sean -- Schaffner, Stephen F -- Sabeti, Pardis C -- Wang, Eric T -- Mignault, Andre A -- Ferland, Russell J -- Moyzis, Robert K -- Walsh, Christopher A -- Reich, David -- New York, N.Y. -- Science. 2007 Apr 20;316(5823):370.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17446375" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; African Continental Ancestry Group/genetics ; Asian Continental Ancestry Group/genetics ; Biological Evolution ; Brain/anatomy & histology ; European Continental Ancestry Group/genetics ; Gene Frequency ; Haplotypes ; Humans ; Nerve Tissue Proteins/*genetics ; *Polymorphism, Single Nucleotide ; Recombination, Genetic ; *Selection, Genetic ; Sequence Analysis, DNA ; Time
    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: 2018
    Description: 〈p〉Spinocerebellar ataxia type 8 (SCA8) is caused by a bidirectionally transcribed CTG·CAG expansion that results in the 〈i〉in vivo〈/i〉 accumulation of CUG RNA foci, an ATG-initiated polyGln and a polyAla protein expressed by repeat-associated non-ATG (RAN) translation. Although RAN proteins have been reported in a growing number of diseases, the mechanisms and role of RAN translation in disease are poorly understood. We report a novel toxic SCA8 polySer protein which accumulates in white matter (WM) regions as aggregates that increase with age and disease severity. WM regions with polySer aggregates show demyelination and axonal degeneration in SCA8 human and mouse brains. Additionally, knockdown of the eukaryotic translation initiation factor eIF3F in cells reduces steady-state levels of SCA8 polySer and other RAN proteins. Taken together, these data show polySer and WM abnormalities contribute to SCA8 and identify eIF3F as a novel modulator of RAN protein accumulation.〈/p〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
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  • 5
    Publication Date: 2014-03-01
    Description: We use ROSAT All Sky Survey broad-band X-ray images and the optical clusters identified from Sloan Digital Sky Survey Data Release 7 to estimate the X-ray luminosities around ~65 000 candidate clusters with masses 10 13 h – 1 M based on an optical to X-ray ( otx ) code we develop. We obtain a catalogue with X-ray luminosity for each cluster. This catalogue contains 817 clusters (473 at redshift z ≤ 0.12) with signal-to-noise ratio 〉3 in X-ray detection. We find about 65 per cent of these X-ray clusters have their most massive member located near the X-ray flux peak; for the rest 35 per cent, the most massive galaxy is separated from the X-ray peak, with the separation following a distribution expected from a Navarro–Frenk–White profile. We investigate a number of correlations between the optical and X-ray properties of these X-ray clusters, and find that the cluster X-ray luminosity is correlated with the stellar mass (luminosity) of the clusters, as well as with the stellar mass (luminosity) of the central galaxy and the mass of the halo, but the scatter in these correlations is large. Comparing the properties of X-ray clusters of similar halo masses but having different X-ray luminosities, we find that massive haloes with masses 10 14 h – 1 M contain a larger fraction of red satellite galaxies when they are brighter in X-ray. An opposite trend is found in central galaxies in relative low-mass haloes with masses 10 14 h – 1 M where X-ray brighter clusters have smaller fraction of red central galaxies. Clusters with masses 10 14 h – 1 M that are strong X-ray emitters contain many more low-mass satellite galaxies than weak X-ray emitters. These results are also confirmed by checking X-ray clusters of similar X-ray luminosities but having different characteristic stellar masses. A cluster catalogue containing the optical properties of member galaxies and the X-ray luminosity is available at http://gax.shao.ac.cn/data/Group.html .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 4835-4847 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Our technique for mixed quantum-classical simulations has the correct limiting behavior at short and long times. Two-state systems are used to investigate coherence effects and dephasing, and to compare with results from a simpler theory of nonadiabatic dynamics. Compared to fully quantal results, our method is shown to be accurate for a wide range of models over a wide range of energies. The two-state models do not explicitly include the bath dynamics which lead to dephasing, and the models do not include tunneling. These are above barrier scattering exercises for which the dynamics is fully coherent. We apply our theory including an arbitrary dephasing time scale, and quantitatively reproduce the correct results for long dephasing times and qualitatively reproduce the results for short dephasing times. We conclude that our method is applicable to relaxation and activated processes in condensed matter where the dephasing time is unknown. We propose that our method is appropriate for simulations of electronically and vibrationally nonadiabatic processes in solids and liquids.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Calcified tissue international 7 (1971), S. 331-344 
    ISSN: 1432-0827
    Keywords: Collagen ; Dentin ; Phosphoprotein ; Covalency ; Mineralization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Description / Table of Contents: Résumé La dégradation par oxydation de matrice dentinaire décalcifiée de boeuf, à l'aide de méta-périodate alcalin de sodium, solubilise une part importante de matrice. La partie soluble comprend une fraction contenant plus de 75% de phosphore lié par covalence, qui est présent dans la dentine initiale. De l'électrophorèse préparative de la dentine solubilisée, sur gel de polyacrylamide, permet d'isoler un groupe de quatre composés fortement anioniques (I–IV). Les analyses montrent que chaque composé est une protéine caractée par un contenu élevé en groupes phosphates, en acide aspartique et sérine et, à une exception près (II), de faibles quantités de proline et d'hydroproline. Chaque composé contient un résidu d'hydroxylysine par mole. En plus de l'hydroxylysine résistant au périodate, III et IV contiennent aussi du glucose et du galactose résistant au périodate. Etant donné la présence d'hydroxyproline, en quantité variables, et celle d'hydroxylysine à un mole par mole, il semble que les composés I, II et IV sont constitués de fragments de collagène osseux liés à une fraction phospho-protéique, à contenu élevé en sérine et acide aspartique. Les hexoses, résistant au périodate, et l'hydroxylysine constituent sans doute le point d'union. Le composant II est une fraction phosphoprotéique pratiquement indemne de collagène. Ce travail met en évidence une liaison polypeptique, non collagénique, liée par covalence, et de caractère hautement acide, au niveau du collagène dentinaire.
    Abstract: Zusammenfassung Der oxydative Abbau von entkalkter boviner Dentimmatrix mit alkalischem Natriummetaperiodat bringteinen beträchtlichen Anteil der Matrix zur Lösung. Der lösliche Teil schließt eine Fraktion ein, die mehr als 75% des im nativen Dentin vorhandenen, kovalent gebundenen Phosphors enthält. Eine präparative Elektrophorese des gelösten Dentins auf Polyacrylamidgelen führte zur Isolierung einer Gruppe von 4 stark anionischen Komponenten (I–IV). Anhand weiterer Analysen wurde festgestellt, daß jede Komponente aus einem Protein besteht, welches durch einen hohen Anteil an Phosphatgruppen, Serin und Asparaginsäure und mit einer Ausnahme (II), durch kleine Prolin- und Hydroxyprolinmengen charakterisiert ist. Jede Komponente enthielt für 1 Mol einen Hydroxylysinrückstand. Zusätzlich zum periodatresistenten Hydroxylysin enthielten III und IV auch noch periodatresistente Glucose und Galaktose. Aufgrund des Vorliegens von variablen Hydroxyprolimmengen und von Hydroxylysin in einem Mol-zu-Mol Verhältnis wird vorgeschlagen, daß die Komponenten I, III und IV aus Kollagenfaserfragmenten bestehen, welche an einen Phosphoproteinteil mit hohem Serin- und Asparaginsäuregehalt gebunden sind. Die periodatresistenten Hexosen und das Hydroxylysin stellen vermutlich den Verbindungspunkt dar. Die Komponente II besteht aus einem Phosphoproteinteil, der im wesentlichen frei von Kollagenfragmenten ist. Diese Resultate beweisen, daß Dentinkollagen einen kovalent gebundenen, nicht kollagenartigen Polypeptidanteil von stark saurem Charakter enthält.
    Notes: Abstract Oxidative degradation of decalcified bovine dentin matrix with alkaline sodium metaperiodate solubilizes a substantial part of the matrix. The soluble portion includes a fraction containing more than 75% of the covalently-bound phosphorus present in the native dentin. Preparative scale electrophoresis of the solubilized dentin on polyacrylamide gels led to the isolation of a group of four strongly anionic components (I–IV). Analyses showed each component to be a protein characterized by a high content of phosphate groups, serine and aspartic acid, and, with one exception (II), small amounts of proline and hydroxyproline. Each component contained one residue of hydroxylysine per mole. In addition to the periodate resistant hydroxylysine, III and IV also contained periodate resistant glucose and galactose. On the basis of the presence of hydroxyproline in varying amount, and hydroxylysine on a mole per mole basis, it is suggested that components I, III and IV consist of collagen backbone fragments linked to a phosphoprotein moiety with a high content of serine and aspartic acid. The periodate-resistant hexoses and the hydroxylysine probably represent the linkage point. Component II is a phosphoprotein moiety essentially free of a collagen fragment. These data provide direct evidence that dentin collagen contains a covalently bound non-collagen polypeptide attachment of highly acidic character.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Calcified tissue international 2 (1968), S. 16-16 
    ISSN: 1432-0827
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Type of Medium: Electronic Resource
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  • 9
    Publication Date: 2005-12-21
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2007-12-17
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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