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  • 1
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    Identification of a Recently Active Mammalian SINE Derived from Ribosomal RNA (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-21
    Description: Complex eukaryotic genomes are riddled with repeated sequences whose derivation does not coincide with phylogenetic history and thus is often unknown. Among such sequences, the capacity for transcriptional activity coupled with the adaptive use of reverse transcription can lead to a diverse group of genomic elements across taxa, otherwise known as selfish elements or mobile elements. Short interspersed nuclear elements (SINEs) are nonautonomous mobile elements found in eukaryotic genomes, typically derived from cellular RNAs such as tRNAs, 7SL or 5S rRNA. Here, we identify and characterize a previously unknown SINE derived from the 3'-end of the large ribosomal subunit (LSU or 28S rDNA) and transcribed via RNA polymerase III. This new element, SINE28, is represented in low-copy numbers in the human reference genome assembly, wherein we have identified 27 discrete loci. Phylogenetic analysis indicates these elements have been transpositionally active within primate lineages as recently as 6 MYA while modern humans still carry transcriptionally active copies. Moreover, we have identified SINE28s in all currently available assembled mammalian genome sequences. Phylogenetic comparisons indicate that these elements are frequently rederived from the highly conserved LSU rRNA sequences in a lineage-specific manner. We propose that this element has not been previously recognized as a SINE given its high identity to the canonical LSU, and that SINE28 likely represents one of possibly many unidentified, active transposable elements within mammalian genomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-26
    Description: X-chromosome inactivation (XCI) achieves dosage compensation between males and females through the silencing of the majority of genes on one of the female X chromosomes. Thus, the female X chromosomes provide a unique opportunity to study euchromatin and heterochromatin of allelic regions within the same nuclear environment. We examined the interplay of DNA methylation (DNAm) with CpG density, transcriptional activity and chromatin state at genes on the X chromosome using over 1800 female samples analysed with the Illumina Infinium Human Methylation450 BeadChip. DNAm was used to predict an inactivation status for 63 novel transcription start sites (TSSs) across 27 tissues. There was high concordance of inactivation status across tissues, with 62% of TSSs subject to XCI in all 27 tissues examined, whereas 9% escaped from XCI in all tissues, and the remainder showed variable escape from XCI between females in subsets of tissues. Inter-female and twin data supported a model of predominately cis -acting influences on inactivation status. The level of expression from the inactive X relative to the active X correlated with the amount of female promoter DNAm to a threshold of ~30%, beyond which genes were consistently subject to inactivation. The inactive X showed lower DNAm than the active X at intragenic and intergenic regions for genes subject to XCI, but not at genes that escape from inactivation. Our categorization of genes that escape from X inactivation provides candidates for sex-specific differences in disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Thermodynamic Model for Energy-Constrained Open-System Evolution of Crustal Magma Bodies Undergoing Simultaneous Recharge, Assimilation and Crystallization: the Magma Chamber Simulator (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-21
    Description: The Magma Chamber Simulator quantifies the impact of simultaneous recharge, assimilation and crystallization through mass and enthalpy balance in a multicomponent–multiphase (melt + solids ± fluid) composite system. As a rigorous thermodynamic model, the Magma Chamber Simulator computes phase equilibria and geochemical evolution self-consistently in resident magma, recharge magma and wallrock, all of which are connected by specified thermodynamic boundaries, to model an evolving open-system magma body. In a simulation, magma cools from its liquidus temperature, and crystals ± fluid are incrementally fractionated to a separate cumulate reservoir. Enthalpy from cooling, crystallization, and possible magma recharge heats wallrock from its initial subsolidus temperature. Assimilation begins when a critical wallrock melt volume fraction (0·04–0·12) in a range consistent with the rheology of partially molten rock systems is achieved. The mass of melt above this limit is removed from the wallrock and homogenized with the magma body melt. New equilibrium states for magma and wallrock are calculated that reflect conservation of total mass, mass of each element and enthalpy. Magma cooling and crystallization, addition of recharge magma and anatectic melt to the magma body (where appropriate), and heating and partial melting of wallrock continue until magma and wallrock reach thermal equilibrium. For each simulation step, mass and energy balance and thermodynamic assessment of phase relations provide major and trace element concentrations, isotopic characteristics, masses, and thermal constraints for all phases (melt + solids ± fluid) in the composite system. Model input includes initial compositional, thermal and mass information relevant to each subsystem, as well as solid–melt and solid–fluid partition coefficients for all phases. Magma Chamber Simulator results of an assimilation–fractional crystallization (AFC) scenario in which dioritic wallrock at 0·1 GPa contaminates high-alumina basalt are compared with results in which no assimilation occurs [fractional crystallization only (FC-only)]. Key comparisons underscore the need for multicomponent–multiphase energy-constrained thermodynamic modeling of open systems, as follows. (1) Partial melting of dioritic wallrock yields cooler silicic melt that contaminates hotter magma. Magma responds by cooling, but a pulse of crystallization, possibly expected based on thermal arguments, does not occur because assimilation suppresses crystallization by modifying the topology of multicomponent phase saturation surfaces. As a consequence, contaminated magma composition and crystallizing solids are distinct compared with the FC-only case. (2) At similar stages of evolution, contaminated melt is more voluminous (~3·5 x ) than melt formed by FC-only. (3) In AFC, some trace element concentrations are lower than their FC-only counterparts at the same stage of evolution. Elements that typically behave incompatibly in mafic and intermediate magmas (e.g. La, Nd, Ba) may not be ‘enriched’ by crustal contamination, and the most ‘crustal’ isotope signatures may not correlate with the highest concentrations of such elements. (4) The proportion of an element contributed by anatectic melt to resident magma is typically different for each element, and thus the extent of mass exchange between crust and magma should be quantified using total mass rather than the mass of a single element. Based on these sometimes unexpected results, it can be argued that progress in quantifying the origin and evolution of open magmatic systems and documenting how mantle-derived magmas and the crust interact rely not only on improvements in instrumentation and generation of larger datasets, but also on continued development of computational tools that couple thermodynamic assessment of phase equilibria in multicomponent systems with energy and mass conservation.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 4
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    Crystal structure of invasin: a bacterial integrin-binding protein (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: The Yersinia pseudotuberculosis invasin protein promotes bacterial entry by binding to host cell integrins with higher affinity than natural substrates such as fibronectin. The 2.3 angstrom crystal structure of the invasin extracellular region reveals five domains that form a 180 angstrom rod with structural similarities to tandem fibronectin type III domains. The integrin-binding surfaces of invasin and fibronectin include similarly located key residues, but in the context of different folds and surface shapes. The structures of invasin and fibronectin provide an example of convergent evolution, in which invasin presents an optimized surface for integrin binding, in comparison with host substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamburger, Z A -- Brown, M S -- Isberg, R R -- Bjorkman, P J -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):291-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 156-29, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514372" target="_blank"〉PubMed〈/a〉
    Keywords: *Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Fibronectins/chemistry/metabolism ; Hydrogen Bonding ; Integrins/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Yersinia pseudotuberculosis/*chemistry/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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  • 5
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    Science over politics (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lanza, R P -- Arrow, K J -- Axelrod, J -- Baltimore, D -- Benacerraf, B -- Bloch, K E -- Bloembergen, N -- Brown, H C -- Brown, M S -- Cibelli, J B -- Cohen, S -- Cooper, L N -- Corey, E J -- Dulbecco, R -- Fischer, E H -- Fitch, V L -- Friedmen, M -- Friedman, M -- Furchgott, R F -- Gell-Mann, M -- Glaser, D A -- Glashow, S L -- Gilbert, W -- Goldstein, J L -- Wilson, R W -- New York, N.Y. -- Science. 1999 Mar 19;283(5409):1849-50.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10206888" target="_blank"〉PubMed〈/a〉
    Keywords: *Bioethics ; Biomedical Research ; *Embryo Research ; Embryo, Mammalian/*cytology ; Federal Government ; Government Regulation ; Humans ; Politics ; Research/*legislation & jurisprudence ; Research Support as Topic/legislation & jurisprudence ; *Risk Assessment ; *Stem Cells ; United States ; United States Dept. of Health and Human Services
    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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    Molecular medicine. The cholesterol quartet (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldstein, J L -- Brown, M S -- New York, N.Y. -- Science. 2001 May 18;292(5520):1310-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA. jgolds@mednet.swmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11360986" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Carrier Proteins/chemistry/*genetics/metabolism ; Cholesterol/blood/*metabolism ; Chromosome Mapping ; Humans ; Hypercholesterolemia/blood/*genetics/*metabolism ; Hyperlipoproteinemia Type II/blood/genetics/metabolism ; Lipoproteins, LDL/blood/metabolism ; Mutation/*genetics ; Protein Binding ; Receptors, LDL/genetics/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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  • 7
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    Regulation of SREBP processing and membrane lipid production by phospholipids in Drosophila (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: Animal cells exert exquisite control over the physical and chemical properties of their membranes, but the mechanisms are obscure. We show that phosphatidylethanolamine, the major phospholipid in Drosophila, controls the release of sterol regulatory element-binding protein (SREBP) from Drosophila cell membranes, exerting feedback control on the synthesis of fatty acids and phospholipids. The finding that SREBP processing is controlled by different lipids in mammals and flies (sterols and phosphatidylethanolamine, respectively) suggests that an essential function of SREBP is to monitor cell membrane composition and to adjust lipid synthesis accordingly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobrosotskaya, I Y -- Seegmiller, A C -- Brown, M S -- Goldstein, J L -- Rawson, R B -- GM 08014/GM/NIGMS NIH HHS/ -- HL-20948/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2002 May 3;296(5569):879-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9046, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988566" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CCAAT-Enhancer-Binding Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Cell Nucleus/metabolism ; Ceramides/metabolism/pharmacology ; Cholesterol/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Drosophila/genetics/*metabolism ; Drosophila Proteins/genetics/metabolism ; Enzyme Inhibitors/pharmacology ; Fatty Acids/biosynthesis ; Fatty Acids, Monounsaturated/pharmacology ; Feedback, Physiological ; Gene Silencing ; Intracellular Signaling Peptides and Proteins ; Membrane Lipids/*biosynthesis ; Membrane Proteins/metabolism ; Palmitates/*metabolism/pharmacology ; Phosphatidylcholines/biosynthesis ; Phosphatidylethanolamines/biosynthesis/*metabolism ; Phospholipids/biosynthesis ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering ; RNA, Untranslated/pharmacology ; Sterol Regulatory Element Binding Protein 1 ; Transcription Factors/*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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  • 8
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    Diet-induced hypercholesterolemia in mice: prevention by overexpression of LDL receptors (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-30
    Description: The current studies were designed to determine whether chronic overexpression of low density lipoprotein (LDL) receptors in the liver would protect mice from the increase in plasma LDL-cholesterol that is induced by high-fat diets. A line of transgenic mice was studied that express the human LDL receptor gene in the liver under control of the transferrin promoter. When fed a diet containing cholesterol, saturated fat, and bile acids for 3 weeks, the transgenic mice, in contrast to normal mice, did not develop a detectable increase in plasma LDL. The current data indicate that unregulated overexpression of LDL receptors can protect against diet-induced hypercholesterolemia in mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yokode, M -- Hammer, R E -- Ishibashi, S -- Brown, M S -- Goldstein, J L -- HL 20948/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 30;250(4985):1273-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Texas, Southwestern Medical Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2244210" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cholesterol, Dietary/adverse effects ; Cholesterol, LDL/*blood ; Dietary Fats/*adverse effects ; Exons ; *Gene Expression ; Humans ; Hypercholesterolemia/etiology/*prevention & control ; Introns ; Lipoproteins/blood ; Lipoproteins, HDL/blood ; Lipoproteins, IDL ; Lipoproteins, VLDL/blood ; Liver/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Nucleic Acid Hybridization ; Promoter Regions, Genetic/genetics ; RNA, Messenger/genetics ; Receptors, LDL/*genetics ; Transferrin/genetics
    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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    History of science. A golden era of Nobel laureates (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldstein, Joseph L -- Brown, Michael S -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1033-4. doi: 10.1126/science.1231699.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA. joe.goldstein@utsouthwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180848" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/*history/trends ; Education, Medical/history/trends ; History, 20th Century ; History, 21st Century ; National Institutes of Health (U.S.)/*history ; *Nobel Prize ; Translational Medical Research/history/trends ; United States
    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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  • 10
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    Structure of the LDL receptor extracellular domain at endosomal pH (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-03
    Description: The low-density lipoprotein receptor mediates cholesterol homeostasis through endocytosis of lipoproteins. It discharges its ligand in the endosome at pH 〈 6. In the crystal structure at pH = 5.3, the ligand-binding domain (modules R2 to R7) folds back as an arc over the epidermal growth factor precursor homology domain (the modules A, B, beta propeller, and C). The modules R4 and R5, which are critical for lipoprotein binding, associate with the beta propeller via their calcium-binding loop. We propose a mechanism for lipoprotein release in the endosome whereby the beta propeller functions as an alternate substrate for the ligand-binding domain, binding in a calcium-dependent way and promoting lipoprotein release.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rudenko, Gabby -- Henry, Lisa -- Henderson, Keith -- Ichtchenko, Konstantin -- Brown, Michael S -- Goldstein, Joseph L -- Deisenhofer, Johann -- HL20948/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 20;298(5602):2353-8. Epub 2002 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard Y4-206, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12459547" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Endosomes/*metabolism ; Epidermal Growth Factor/chemistry ; Humans ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lipoproteins, LDL/*metabolism ; Models, Biological ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Precursors/chemistry ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Receptors, LDL/*chemistry/genetics/*metabolism ; Repetitive Sequences, Amino Acid
    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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