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  • 1
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    PAF1 regulation of promoter-proximal pause release via enhancer activation (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-09-22
    Description: Gene expression in metazoans is regulated by RNA polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we showed that Pol II–associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we found that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of PAF1 loss releases Pol II from paused promoters of nearby PAF1 target genes. Knockout of PAF1-regulated enhancers attenuates the release of paused Pol II on PAF1 target genes without major interference in the establishment of pausing at their cognate promoters. Thus, a subset of enhancers can primarily modulate gene expression by controlling the release of paused Pol II in a PAF1-dependent manner.
    Keywords: Biochemistry, Development
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Geochemical constraints on the origins of calcite cements and their impacts on reservoir heterogeneities: A case study on tight oil sandstones of the Upper Triassic Yanchang Formation, southwestern Ordos Basin, China (2019)
    American Association of Petroleum Geologists (AAPG)
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉ABSTRACT〈/div〉Calcite cementation has been identified as an active process in the Upper Triassic Yanchang Formation throughout its burial history and as a major diagenetic factor causing strong reservoir heterogeneities. The origins of calcite cements and their relevance to reservoir heterogeneities were investigated using a suite of petrographic and geochemical methods, including optical microscopy with fluorescence and cathodoluminescence, scanning and backscattered electron microscopy with energy-dispersive spectrometry, x-ray diffraction, x-ray fluorescence, electron probe microanalysis, quantitative evaluation of minerals by scanning electron microscopy, fluid inclusion analysis, and carbon and oxygen stable isotope analyses. The sandstones are compositionally immature with relatively high amounts of volcanic rock fragments. The two generations of calcite cements are Ca-I and Ca-II. The Ca-I calcites are distributed along the interface of sandstone and mudstone units and were formed during the Late Triassic to Early Jurassic at formation temperatures of approximately 90°C. The Ca-II calcite mainly developed in the lower part of the fining-upward sandstone units and was formed in the Late Jurassic at higher temperatures of approximately 110°C. The origins of calcite cements were constrained by geochemical and isotope measurements, fluid inclusion homogenization temperature, and in situ element analysis. The Ca-I calcite cement originated from dissolution of the lacustrine depositional carbonates in the interbedded mudstones and reprecipitation in the adjacent sandstones. The Ca-II calcite was mainly related to organic matter decarboxylation, with Ca〈sup〉2+〈/sup〉 having been provided internally by volcanic fragment alteration and plagioclase dissolution. Calcite cementation had caused strong reservoir heterogeneities in the Yanchang Formation tight sandstones. The Ca-I calcite cementation destroyed reservoir properties along the interface of sandstones and mudstones. The lower parts of the fining-upward sandstone units were tightly cemented by Ca-II calcite, although they originally had high porosity and permeability. The middle–upper parts of the fining-upward sandstone units contain less calcite cements and thus have better preserved reservoir pores because of oil emplacement inhibiting the calcite cementation processes.〈/span〉
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by American Association of Petroleum Geologists (AAPG)
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  • 3
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    Grx2 regulates vascular development [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-12-11
    Description: Embryonic development depends on complex and precisely orchestrated signaling pathways including specific reduction/oxidation cascades. Oxidoreductases of the thioredoxin family are key players conveying redox signals through reversible posttranslational modifications of protein thiols. The importance of this protein family during embryogenesis has recently been exemplified for glutaredoxin 2, a vertebrate-specific glutathione–disulfide...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Saturns magnetic field revealed by the Cassini Grand Finale (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-10-05
    Description: During 2017, the Cassini fluxgate magnetometer made in situ measurements of Saturn’s magnetic field at distances ~2550 ± 1290 kilometers above the 1-bar surface during 22 highly inclined Grand Finale orbits. These observations refine the extreme axisymmetry of Saturn’s internal magnetic field and show displacement of the magnetic equator northward from the planet’s physical equator. Persistent small-scale magnetic structures, corresponding to high-degree (〉3) axisymmetric magnetic moments, were observed. This suggests secondary shallow dynamo action in the semiconducting region of Saturn’s interior. Some high-degree magnetic moments could arise from strong high-latitude concentrations of magnetic flux within the planet’s deep dynamo. A strong field-aligned current (FAC) system is located between Saturn and the inner edge of its D-ring, with strength comparable to the high-latitude auroral FACs.
    Keywords: Geochemistry, Geophysics, Online Only, Planetary Science
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Chromosome alignment and segregation regulated by ubiquitination of survivin (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: Proper chromosome segregation requires the attachment of sister kinetochores to microtubules from opposite spindle poles to form bi-oriented chromosomes on the metaphase spindle. The chromosome passenger complex containing Survivin and the kinase Aurora B regulates this process from the centromeres. We report that a de-ubiquitinating enzyme, hFAM, regulates chromosome alignment and segregation by controlling both the dynamic association of Survivin with centromeres and the proper targeting of Survivin and Aurora B to centromeres. Survivin is ubiquitinated in mitosis through both Lys(48) and Lys(63) ubiquitin linkages. Lys(63) de-ubiquitination mediated by hFAM is required for the dissociation of Survivin from centromeres, whereas Lys(63) ubiquitination mediated by the ubiquitin binding protein Ufd1 is required for the association of Survivin with centromeres. Thus, ubiquitinaton regulates dynamic protein-protein interactions and chromosome segregation independently of protein degradation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vong, Queenie P -- Cao, Kan -- Li, Hoi Y -- Iglesias, Pablo A -- Zheng, Yixian -- GM56312/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1499-504.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Embryology, Carnegie Institution of Washington and Howard Hughes Medical Institute, 3520 San Martin Drive, Baltimore, MD 21218, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322459" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aurora Kinase B ; Aurora Kinases ; Centromere/*metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Segregation/*physiology ; Egg Proteins/metabolism ; Endopeptidases/metabolism ; HeLa Cells ; Humans ; Inhibitor of Apoptosis Proteins ; Lysine/metabolism ; Microtubule-Associated Proteins/metabolism ; Molecular Sequence Data ; Neoplasm Proteins/metabolism ; Protein Binding ; Protein-Serine-Threonine Kinases/metabolism ; Ubiquitin/*metabolism ; Ubiquitin Thiolesterase ; Xenopus ; Xenopus Proteins/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Nature of exciton transitions in hexagonal boron nitride (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-03-23
    Description: In contrast to other III-nitride semiconductors GaN and AlN, the intrinsic (or free) exciton transition in hexagonal boron nitride ( h- BN) consists of rather complex fine spectral features (resolved into six sharp emission peaks) and the origin of which is still unclear. Here, the free exciton transition (FX) in h- BN bulk crystals synthesized by a solution method at atmospheric pressure has been probed by deep UV time-resolved photoluminescence (PL) spectroscopy. Based on the separations between the energy peak positions of the FX emission lines, the identical PL decay kinetics among different FX emission lines, and the known phonon modes in h- BN, we suggest that there is only one principal emission line corresponding to the direct intrinsic FX transition in h- BN, whereas all other fine features are a result of phonon-assisted transitions. The identified phonon modes are all associated with the center of the Brillouin zone. Our results offer a simple picture for the understanding of the fundamental exciton transitions in h -BN.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-02-22
    Description: Human neurodegenerative diseases have the temporal hallmark of afflicting the elderly population. Ageing is one of the most prominent factors to influence disease onset and progression, yet little is known about the molecular pathways that connect these processes. To understand this connection it is necessary to identify the pathways that functionally integrate ageing, chronic maintenance of the brain and modulation of neurodegenerative disease. MicroRNAs (miRNA) are emerging as critical factors in gene regulation during development; however, their role in adult-onset, age-associated processes is only beginning to be revealed. Here we report that the conserved miRNA miR-34 regulates age-associated events and long-term brain integrity in Drosophila, providing a molecular link between ageing and neurodegeneration. Fly mir-34 expression exhibits adult-onset, brain-enriched and age-modulated characteristics. Whereas mir-34 loss triggers a gene profile of accelerated brain ageing, late-onset brain degeneration and a catastrophic decline in survival, mir-34 upregulation extends median lifespan and mitigates neurodegeneration induced by human pathogenic polyglutamine disease protein. Some of the age-associated effects of miR-34 require adult-onset translational repression of Eip74EF, an essential ETS domain transcription factor involved in steroid hormone pathways. Our studies indicate that miRNA-dependent pathways may have an impact on adult-onset, age-associated events by silencing developmental genes that later have a deleterious influence on adult life cycle and disease, and highlight fly miR-34 as a key miRNA with a role in this process.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326599/" 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/PMC3326599/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Nan -- Landreh, Michael -- Cao, Kajia -- Abe, Masashi -- Hendriks, Gert-Jan -- Kennerdell, Jason R -- Zhu, Yongqing -- Wang, Li-San -- Bonini, Nancy M -- AG010124/AG/NIA NIH HHS/ -- R01 NS043578/NS/NINDS NIH HHS/ -- R01 NS043578-05/NS/NINDS NIH HHS/ -- R01-NS043578/NS/NINDS NIH HHS/ -- RC2 AG036528/AG/NIA NIH HHS/ -- RC2 AG036528-01/AG/NIA NIH HHS/ -- RC2-AG036528-01/AG/NIA NIH HHS/ -- T32 AG000255/AG/NIA NIH HHS/ -- T32 AG000255-02/AG/NIA NIH HHS/ -- T32 AG00255/AG/NIA NIH HHS/ -- U01 AG032984/AG/NIA NIH HHS/ -- U01 AG032984-02/AG/NIA NIH HHS/ -- U01-AG-032984-02/AG/NIA NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 15;482(7386):519-23. doi: 10.1038/nature10810.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22343898" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/*genetics ; Animals ; Brain/metabolism/pathology ; *Disease Models, Animal ; Down-Regulation ; Drosophila Proteins/biosynthesis/genetics ; Drosophila melanogaster/*genetics/*physiology ; Female ; Gene Expression Regulation/*genetics ; Hot Temperature ; Humans ; Longevity/genetics ; Male ; MicroRNAs/*genetics ; Mutation ; Neurodegenerative Diseases/*genetics/pathology ; Protein Biosynthesis ; RNA, Messenger/analysis/genetics ; Survival Analysis ; Time Factors ; Transcription Factors/biosynthesis/genetics ; Up-Regulation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    H2S as a physiologic vasorelaxant: hypertension in mice with deletion of cystathionine gamma-lyase (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-25
    Description: Studies of nitric oxide over the past two decades have highlighted the fundamental importance of gaseous signaling molecules in biology and medicine. The physiological role of other gases such as carbon monoxide and hydrogen sulfide (H2S) is now receiving increasing attention. Here we show that H2S is physiologically generated by cystathionine gamma-lyase (CSE) and that genetic deletion of this enzyme in mice markedly reduces H2S levels in the serum, heart, aorta, and other tissues. Mutant mice lacking CSE display pronounced hypertension and diminished endothelium-dependent vasorelaxation. CSE is physiologically activated by calcium-calmodulin, which is a mechanism for H2S formation in response to vascular activation. These findings provide direct evidence that H2S is a physiologic vasodilator and regulator of blood pressure.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749494/" 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/PMC2749494/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Guangdong -- Wu, Lingyun -- Jiang, Bo -- Yang, Wei -- Qi, Jiansong -- Cao, Kun -- Meng, Qinghe -- Mustafa, Asif K -- Mu, Weitong -- Zhang, Shengming -- Snyder, Solomon H -- Wang, Rui -- DA00074/DA/NIDA NIH HHS/ -- K05 DA000074/DA/NIDA NIH HHS/ -- K05 DA000074-29/DA/NIDA NIH HHS/ -- MH18501/MH/NIMH NIH HHS/ -- R37 MH018501/MH/NIMH NIH HHS/ -- R37 MH018501-40/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):587-90. doi: 10.1126/science.1162667.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948540" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aorta/metabolism ; *Blood Pressure ; Calcium/metabolism ; Calmodulin/metabolism ; Cystathionine gamma-Lyase/deficiency/genetics/*metabolism ; Cysteine/blood ; Endothelium, Vascular/metabolism ; Homocysteine/blood ; Hydrogen Sulfide/blood/*metabolism ; Hypertension/*physiopathology ; Mesenteric Arteries/physiology ; Methacholine Chloride/pharmacology ; Mice ; Mice, Knockout ; Myocardium/metabolism ; Oxidation-Reduction ; Sulfides/pharmacology ; *Vasodilation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Genetic Evidence of Paleolithic Colonization and Neolithic Expansion of Modern Humans on the Tibetan Plateau (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-12
    Description: Tibetans live on the highest plateau in the world, their current population size is approximately 5 million, and most of them live at an altitude exceeding 3,500 m. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population history. However, the chronological profile of the Tibetan Plateau’s colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal ( n = 2,354) and maternal ( n = 6,109) lineages as well as genome-wide single nucleotide polymorphism markers ( n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to approximately 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7–10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the last glacial maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    MnSb_{2}O_{6}: A Polar Magnet with a Chiral Crystal Structure (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-07-04
    Description: Author(s): R. D. Johnson, K. Cao, L. C. Chapon, F. Fabrizi, N. Perks, P. Manuel, J. J. Yang, Y. S. Oh, S.-W. Cheong, and P. G. Radaelli Structural and magnetic chiralities are found to coexist in a small group of materials in which they produce intriguing phenomenologies such as the recently discovered Skyrmion phases. Here, we describe a previously unknown manifestation of this interplay in MnSb 2 O 6 , a trigonal oxide with a chiral c... [Phys. Rev. Lett. 111, 017202] Published Wed Jul 03, 2013
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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