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  • 1
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    Growth of fissure ridge travertines from geothermal springs of Denizli Basin, western Turkey (2012)
    Geological Society of America (GSA)
    Details
    Publication Date: 2012-09-01
    Description: Fissure ridge travertines grown from geothermal springs of Denizli Basin, southwestern Turkey, are investigated through stratigraphic, structural, geochemical, and geochronological methods, with the aim of understanding the growth of these elongate mound-shaped structures. Two main types of travertine deposits are recognized: (1) bedded travertines, which grew as flowstone on sloping surfaces and form the bulk of fissure ridges, and (2) banded travertines, which grew as veins within the bedded travertine chiefly along its central feeding conduit. Stratigraphic and structural observations shed light on the bedded-banded travertine relationships, where the banded features grew through successive accretion phases, crosscutting the bedded travertine or forming sill-like structures. The bedded and banded travertines alternated their growth, as demonstrated by complicated crosscutting relationships and by the upward suture, in places, of banded travertine by bedded travertine that was, in turn, crosscut by younger banded travertine. The bedded travertine is often tilted away from the central axis of the fissure ridge, thus leaving more room for the central banded travertine to form. U-series ages confirm the bedded-banded travertine temporal relationships and show that the growth of the studied fissure ridges lasted up to several tens of thousands of years during Quaternary time. The banded travertine was deposited mainly during cold events, possibly in coincidence with seismic events that might have triggered the outflow of deep geothermal fluids. C and O stable isotope and rare earth element data indicate a shallow feeding circuit for the studied structures with a fluid component deriving from a deeper geothermal circuit. A crack-and-seal mechanism of fissure ridge growth is proposed, modulated by the interplay of local and regional influencing factors and mechanisms such as geothermal fluid discharge, paleoclimate, tectonics, and the progressive tilting of bedded travertine limbs over a soft substratum creating the necessary space for the central veins to grow.
    Print ISSN: 0016-7606
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 2
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    Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-02-01
    Description: Genetic and biochemical analyses of RNA interference (RNAi) and microRNA (miRNA) pathways have revealed proteins such as Argonaute and Dicer as essential cofactors that process and present small RNAs to their targets. Well-validated small RNA pathway cofactors such as these show distinctive patterns of conservation or divergence in particular animal, plant, fungal and protist species. We compared 86 divergent eukaryotic genome sequences to discern sets of proteins that show similar phylogenetic profiles with known small RNA cofactors. A large set of additional candidate small RNA cofactors have emerged from functional genomic screens for defects in miRNA- or short interfering RNA (siRNA)-mediated repression in Caenorhabditis elegans and Drosophila melanogaster, and from proteomic analyses of proteins co-purifying with validated small RNA pathway proteins. The phylogenetic profiles of many of these candidate small RNA pathway proteins are similar to those of known small RNA cofactor proteins. We used a Bayesian approach to integrate the phylogenetic profile analysis with predictions from diverse transcriptional coregulation and proteome interaction data sets to assign a probability for each protein for a role in a small RNA pathway. Testing high-confidence candidates from this analysis for defects in RNAi silencing, we found that about one-half of the predicted small RNA cofactors are required for RNAi silencing. Many of the newly identified small RNA pathway proteins are orthologues of proteins implicated in RNA splicing. In support of a deep connection between the mechanism of RNA splicing and small-RNA-mediated gene silencing, the presence of the Argonaute proteins and other small RNA components in the many species analysed strongly correlates with the number of introns in those species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762460/" 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/PMC3762460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tabach, Yuval -- Billi, Allison C -- Hayes, Gabriel D -- Newman, Martin A -- Zuk, Or -- Gabel, Harrison -- Kamath, Ravi -- Yacoby, Keren -- Chapman, Brad -- Garcia, Susana M -- Borowsky, Mark -- Kim, John K -- Ruvkun, Gary -- GM088565/GM/NIGMS NIH HHS/ -- GM098647/GM/NIGMS NIH HHS/ -- GM44619/GM/NIGMS NIH HHS/ -- R01 GM044619/GM/NIGMS NIH HHS/ -- R01 GM098647/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Jan 31;493(7434):694-8. doi: 10.1038/nature11779. Epub 2012 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23364702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/classification/*genetics ; Caenorhabditis elegans Proteins/genetics ; Eukaryota/classification/genetics ; *Genetic Variation ; Genome/genetics ; MicroRNAs/genetics ; *Phylogeny ; Proteome ; RNA Splicing ; RNA, Small Interfering/*genetics
    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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  • 3
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    MORC family ATPases required for heterochromatin condensation and gene silencing (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-05
    Description: Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, AtMORC1 and AtMORC6, which cause derepression of DNA-methylated genes and TEs but no losses of DNA or histone methylation. AtMORC1 and AtMORC6 are members of the conserved Microrchidia (MORC) adenosine triphosphatase (ATPase) family, which are predicted to catalyze alterations in chromosome superstructure. The atmorc1 and atmorc6 mutants show decondensation of pericentromeric heterochromatin, increased interaction of pericentromeric regions with the rest of the genome, and transcriptional defects that are largely restricted to loci residing in pericentromeric regions. Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing. We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376212/" 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/PMC3376212/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moissiard, Guillaume -- Cokus, Shawn J -- Cary, Joshua -- Feng, Suhua -- Billi, Allison C -- Stroud, Hume -- Husmann, Dylan -- Zhan, Ye -- Lajoie, Bryan R -- McCord, Rachel Patton -- Hale, Christopher J -- Feng, Wei -- Michaels, Scott D -- Frand, Alison R -- Pellegrini, Matteo -- Dekker, Job -- Kim, John K -- Jacobsen, Steven E -- F32 GM100617/GM/NIGMS NIH HHS/ -- F32GM100617/GM/NIGMS NIH HHS/ -- GM007185/GM/NIGMS NIH HHS/ -- GM075060/GM/NIGMS NIH HHS/ -- GM088565/GM/NIGMS NIH HHS/ -- GM60398/GM/NIGMS NIH HHS/ -- HG003143/HG/NHGRI NIH HHS/ -- R01 GM075060/GM/NIGMS NIH HHS/ -- R01 GM088565/GM/NIGMS NIH HHS/ -- R01 HG003143/HG/NHGRI NIH HHS/ -- R37 GM060398/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1448-51. doi: 10.1126/science.1221472. Epub 2012 May 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Terasaki Life Sciences Building, 610 Charles Young Drive East, Los Angeles, CA 90095-723905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22555433" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Animals ; Arabidopsis/enzymology/*genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/genetics/metabolism ; Centromere ; DNA Methylation ; DNA Transposable Elements ; *Gene Silencing ; Genes, Plant ; Heterochromatin/*metabolism/ultrastructure ; Histones/metabolism ; Methylation ; Mutation ; RNA, Small Interfering/metabolism ; Transcription, Genetic ; Transgenes ; Up-Regulation
    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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