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  • 1
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    Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-08-06
    Description: Journal of Proteome Research DOI: 10.1021/acs.jproteome.6b00452
    Print ISSN: 1535-3893
    Electronic ISSN: 1535-3907
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 2
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    Proteogenomic Analysis of the Venturia pirina (Pear Scab Fungus) Secretome Reveals Potential Effectors (2014)
    American Chemical Society (ACS)
    Details
    Publication Date: 2014-07-11
    Description: Journal of Proteome Research DOI: 10.1021/pr500176c
    Print ISSN: 1535-3893
    Electronic ISSN: 1535-3907
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 3
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    Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
    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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  • 4
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    Historical overfishing and the recent collapse of coastal ecosystems (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jackson, J B -- Kirby, M X -- Berger, W H -- Bjorndal, K A -- Botsford, L W -- Bourque, B J -- Bradbury, R H -- Cooke, R -- Erlandson, J -- Estes, J A -- Hughes, T P -- Kidwell, S -- Lange, C B -- Lenihan, H S -- Pandolfi, J M -- Peterson, C H -- Steneck, R S -- Tegner, M J -- Warner, R R -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):629-37.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0244, USA. jbcj@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474098" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology ; Bacteria ; Cnidaria ; Conservation of Natural Resources ; *Ecosystem ; Eutrophication ; *Fishes ; Geologic Sediments ; Humans ; *Marine Biology ; Seaweed ; Shellfish ; Time Factors
    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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    A fidgeter's calculation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooke, R -- New York, N.Y. -- Science. 1999 May 14;284(5417):1125-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10366345" target="_blank"〉PubMed〈/a〉
    Keywords: *Energy Intake ; *Energy Metabolism ; Humans ; *Movement ; *Weight Gain
    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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    The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-25
    Description: Evenly spaced nucleosomes directly correlate with condensed chromatin and gene silencing. The ATP-dependent chromatin assembly factor (ACF) forms such structures in vitro and is required for silencing in vivo. ACF generates and maintains nucleosome spacing by constantly moving a nucleosome towards the longer flanking DNA faster than the shorter flanking DNA. How the enzyme rapidly moves back and forth between both sides of a nucleosome to accomplish bidirectional movement is unknown. Here we show that nucleosome movement depends cooperatively on two ACF molecules, indicating that ACF functions as a dimer of ATPases. Further, the nucleotide state determines whether the dimer closely engages one or both sides of the nucleosome. Three-dimensional reconstruction by single-particle electron microscopy of the ATPase-nucleosome complex in an activated ATP state reveals a dimer architecture in which the two ATPases face each other. Our results indicate a model in which the two ATPases work in a coordinated manner, taking turns to engage either side of a nucleosome, thereby allowing processive bidirectional movement. This novel dimeric motor mechanism differs from that of dimeric motors such as kinesin and dimeric helicases that processively translocate unidirectionally and reflects the unique challenges faced by motors that move nucleosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869534/" 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/PMC2869534/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Racki, Lisa R -- Yang, Janet G -- Naber, Nariman -- Partensky, Peretz D -- Acevedo, Ashley -- Purcell, Thomas J -- Cooke, Roger -- Cheng, Yifan -- Narlikar, Geeta J -- R01 GM073767/GM/NIGMS NIH HHS/ -- R01 GM073767-01/GM/NIGMS NIH HHS/ -- R01 GM073767-02/GM/NIGMS NIH HHS/ -- R01 GM073767-03/GM/NIGMS NIH HHS/ -- R01 GM073767-03S1/GM/NIGMS NIH HHS/ -- R01 GM073767-04/GM/NIGMS NIH HHS/ -- R01 GM073767-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1016-21. doi: 10.1038/nature08621.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033039" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cell Line ; Chromatin Assembly and Disassembly/*physiology ; Dimerization ; Gene Silencing/physiology ; Histones/metabolism ; Humans ; Microscopy, Electron, Transmission ; *Models, Molecular ; Multiprotein Complexes/*metabolism ; Nucleosomes/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Transcription Factors/chemistry/metabolism
    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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  • 7
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    Minerals, Vol. 8, Pages 548: Assessing Thallium Elemental Systematics and Isotope Ratio Variations in Porphyry Ore Systems: A Case Study of the Bingham Canyon District (2018)
    MDPI
    In: Minerals
    Details
    Publication Date: 2018
    Description: The Bingham Canyon porphyry deposit is one of the world’s largest Cu-Mo-Au resources. Elevated concentrations of thallium (Tl) compared to average continental crust have been found in some brecciated and igneous samples in this area, which likely result from mobilization of Tl by relatively low temperature hydrothermal fluids. The Tl-enrichment at Bingham Canyon therefore provides an opportunity to investigate if Tl isotope ratios reflect hydrothermal enrichment and whether there are systematic Tl isotope fractionations that could provide an exploration tool. We present a reconnaissance study of nineteen samples spanning a range of lithologies from the Bingham district which were analysed for their Tl content and Tl isotope ratios, reported as parts per ten thousand (ε205Tl) relative to the NIST SRM997 international standard. The range of ε205Tl reported in this study (−16.4 to +7.2) is the largest observed in a hydrothermal ore deposit to date. Unbrecciated samples collected relatively proximal to the Bingham Canyon porphyry system have ε205Tl of −4.2 to +0.9, similar to observations in a previous study of porphyry deposits. This relatively narrow range suggests that high-temperature (〉300 °C) hydrothermal alteration does not result in significant Tl isotope fractionation. However, two samples ~3–4 km away from Bingham Canyon have higher ε205Tl values (+1.3 and +7.2), and samples from more distal (~7 km) disseminated gold deposits at Melco and Barneys Canyon display an even wider range in ε205Tl (−16.4 to +6.0). The observation of large positive and negative excursions in ε205Tl relative to the mantle value (ε205Tl = −2.0 ± 1.0) contrasts with previous investigations of hydrothermal systems. Samples displaying the most extreme positive and negative ε205Tl values also contain elevated concentrations of Tl-Sb-As. Furthermore, with the exception of one sample, all of the Tl isotopic anomalies occur in hydrothermal breccia samples. This suggests that ε205Tl excursions are most extreme during the migration of low-temperature hydrothermal fluids potentially related to sediment-hosted gold mineralization. Future investigation to determine the host phase(s) for Tl in breccias displaying both chalcophile element enrichment and ε205Tl excursions can potentially provide new information about hydrothermal fluid composition and could be used to locate sites for future porphyry exploration.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
    Published by MDPI
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  • 8
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    Minerals, Vol. 8, Pages 486: Physicochemical Conditions of Formation for Bismuth Mineralization Hosted in a Magmatic-Hydrothermal Breccia Complex: An Example from the Argentine Andes (2018)
    MDPI
    In: Minerals
    Details
    Publication Date: 2018
    Description: The San Francisco de los Andes breccia-hosted deposit (Frontal Cordillera, Argentina) is characterized by complex Bi–Cu–Pb–Zn–Mo–As–Fe–Ag–Au mineralization. After magmatic-hydrothermal brecciation, tourmaline and quartz partially cemented open spaces, followed by quiescent periods where Bi–Cu–Pb–Zn ore formed. Bismuth ore precipitation is characterized by Bi-sulfides, sulfosalts, and tellurosulfide inclusions, which temporally co-exist with Ag-telluride inclusions and chalcopyrite. Three distinct Bi mineralizing stages have been defined based on the following mineral assemblages: (1) Bismuthinite (tetradymite–hessite inclusions); (2) Bismuthinite (tetradymite–hessite inclusions) + cosalite (tetradymite inclusions) + chalcopyrite; and (3) Cosalite (tetradymite inclusions) + chalcopyrite. Overall, Ag-poor bismuthinite hosts both Bi-tellurosulfide and Ag-telluride inclusions, whereas Ag-rich cosalite only hosts tetradymite inclusions.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
    Published by MDPI
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  • 9
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    Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution (2016)
    Springer Nature
    Details
    Publication Date: 2016-05-26
    Description: Article Women with germline variants in BRCA genes are predisposed to ovarian cancer. In this study, the authors demonstrate that fimbrial tissue from the ovary, the site of ovarian cancer, in BRCA mutant carriers contains marked DNA methylation changes compared with the proximal region of the ovary. Nature Communications doi: 10.1038/ncomms11620 Authors: Thomas E. Bartlett, Kantaraja Chindera, Jacqueline McDermott, Charles E. Breeze, William R. Cooke, Allison Jones, Daniel Reisel, Smita T. Karegodar, Rupali Arora, Stephan Beck, Usha Menon, Louis Dubeau, Martin Widschwendter
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 10
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    A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-03-15
    Description: A hallmark of histone H3 lysine 9 (H3K9)-methylated heterochromatin, conserved from the fission yeast Schizosaccharomyces pombe to humans, is its ability to spread to adjacent genomic regions. Central to heterochromatin spread is heterochromatin protein 1 (HP1), which recognizes H3K9-methylated chromatin, oligomerizes and forms a versatile platform that participates in diverse nuclear functions, ranging from gene silencing to chromosome segregation. How HP1 proteins assemble on methylated nucleosomal templates and how the HP1-nucleosome complex achieves functional versatility remain poorly understood. Here we show that binding of the key S. pombe HP1 protein, Swi6, to methylated nucleosomes drives a switch from an auto-inhibited state to a spreading-competent state. In the auto-inhibited state, a histone-mimic sequence in one Swi6 monomer blocks methyl-mark recognition by the chromodomain of another monomer. Auto-inhibition is relieved by recognition of two template features, the H3K9 methyl mark and nucleosomal DNA. Cryo-electron-microscopy-based reconstruction of the Swi6-nucleosome complex provides the overall architecture of the spreading-competent state in which two unbound chromodomain sticky ends appear exposed. Disruption of the switch between the auto-inhibited and spreading-competent states disrupts heterochromatin assembly and gene silencing in vivo. These findings are reminiscent of other conditionally activated polymerization processes, such as actin nucleation, and open up a new class of regulatory mechanisms that operate on chromatin in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907283/" 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/PMC3907283/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Canzio, Daniele -- Liao, Maofu -- Naber, Nariman -- Pate, Edward -- Larson, Adam -- Wu, Shenping -- Marina, Diana B -- Garcia, Jennifer F -- Madhani, Hiten D -- Cooke, Roger -- Schuck, Peter -- Cheng, Yifan -- Narlikar, Geeta J -- AR053720/AR/NIAMS NIH HHS/ -- R01 AR062279/AR/NIAMS NIH HHS/ -- R01 GM071801/GM/NIGMS NIH HHS/ -- R01GM071801/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Apr 18;496(7445):377-81. doi: 10.1038/nature12032. Epub 2013 Mar 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23485968" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/*antagonists & ; inhibitors/*chemistry/*metabolism/ultrastructure ; Cryoelectron Microscopy ; Gene Silencing ; Heterochromatin/chemistry/*metabolism/ultrastructure ; Histones/chemistry/metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Nucleosomes/chemistry/genetics/metabolism/ultrastructure ; Protein Structure, Tertiary ; Schizosaccharomyces/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/antagonists & ; inhibitors/*chemistry/*metabolism/ultrastructure ; Xenopus laevis
    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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