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  • 1
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    Genome-wide identification of zero nucleotide recursive splicing in Drosophila (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-05-15
    Description: Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points--5' splice sites recreated after splicing. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. Here we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identify four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together, these results indicate that recursive splicing is commonly used in Drosophila, occurs in humans, and provides insight into the mechanisms by which some large introns are removed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529404/" 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/PMC4529404/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duff, Michael O -- Olson, Sara -- Wei, Xintao -- Garrett, Sandra C -- Osman, Ahmad -- Bolisetty, Mohan -- Plocik, Alex -- Celniker, Susan E -- Graveley, Brenton R -- R01 GM095296/GM/NIGMS NIH HHS/ -- R01GM095296/GM/NIGMS NIH HHS/ -- U54 HG006994/HG/NHGRI NIH HHS/ -- U54HG006994/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 May 21;521(7552):376-9. doi: 10.1038/nature14475. Epub 2015 May 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA. ; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25970244" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cells, Cultured ; Drosophila melanogaster/*genetics ; Exons/genetics ; Female ; Genes, Insect/genetics ; Genome, Insect/*genetics ; Humans ; Introns/genetics ; Male ; Nuclear Proteins/deficiency/genetics/metabolism ; Nucleotides/*genetics ; RNA Splice Sites/genetics ; RNA Splicing/*genetics ; Reproducibility of Results ; Ribonucleoproteins/deficiency/genetics/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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  • 2
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    Soil science. Soil and human security in the 21st century (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-05-09
    Description: Human security has and will continue to rely on Earth's diverse soil resources. Yet we have now exploited the planet's most productive soils. Soil erosion greatly exceeds rates of production in many agricultural regions. Nitrogen produced by fossil fuel and geological reservoirs of other fertilizers are headed toward possible scarcity, increased cost, and/or geopolitical conflict. Climate change is accelerating the microbial release of greenhouse gases from soil organic matter and will likely play a large role in our near-term climate future. In this Review, we highlight challenges facing Earth's soil resources in the coming century. The direct and indirect response of soils to past and future human activities will play a major role in human prosperity and survival.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amundson, Ronald -- Berhe, Asmeret Asefaw -- Hopmans, Jan W -- Olson, Carolyn -- Sztein, A Ester -- Sparks, Donald L -- New York, N.Y. -- Science. 2015 May 8;348(6235):1261071. doi: 10.1126/science.1261071. Epub 2015 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA. earthy@berkeley.edu. ; Life and Environmental Sciences Unit, University of California, Merced, CA 95343, USA. ; Land, Air, and Water Resources, One Shields Avenue, Davis, CA 95616, USA. ; Climate Change Program Office, Office of the Chief Economist, U.S. Department of Agriculture (USDA), 14th and Independence SW, Washington, DC 20013, USA. ; Board on International Scientific Organizations, National Academy of Sciences, 500 Fifth Street NW, Washington, DC 20001, USA. ; Plant and Soil Science, Chemistry and Biochemistry, Civil and Environmental Engineering, and Marine Science and Policy, University of Delaware, Newark, DE 19716, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25954014" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/trends ; Climate Change ; *Conservation of Natural Resources ; Fertilizers ; Food Supply ; Fossil Fuels ; Humans ; Nitrogen ; *Soil ; *Survival
    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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  • 3
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    A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-01-28
    Description: Muscle contraction depends on release of Ca(2+) from the sarcoplasmic reticulum (SR) and reuptake by the Ca(2+)adenosine triphosphatase SERCA. We discovered a putative muscle-specific long noncoding RNA that encodes a peptide of 34 amino acids and that we named dwarf open reading frame (DWORF). DWORF localizes to the SR membrane, where it enhances SERCA activity by displacing the SERCA inhibitors, phospholamban, sarcolipin, and myoregulin. In mice, overexpression of DWORF in cardiomyocytes increases peak Ca(2+) transient amplitude and SR Ca(2+) load while reducing the time constant of cytosolic Ca(2+) decay during each cycle of contraction-relaxation. Conversely, slow skeletal muscle lacking DWORF exhibits delayed Ca(2+) clearance and relaxation and reduced SERCA activity. DWORF is the only endogenous peptide known to activate the SERCA pump by physical interaction and provides a means for enhancing muscle contractility.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, Benjamin R -- Makarewich, Catherine A -- Anderson, Douglas M -- Winders, Benjamin R -- Troupes, Constantine D -- Wu, Fenfen -- Reese, Austin L -- McAnally, John R -- Chen, Xiongwen -- Kavalali, Ege T -- Cannon, Stephen C -- Houser, Steven R -- Bassel-Duby, Rhonda -- Olson, Eric N -- AR-063182/AR/NIAMS NIH HHS/ -- DK-099653/DK/NIDDK NIH HHS/ -- F30AR 067094/AR/NIAMS NIH HHS/ -- HL-077439,/HL/NHLBI NIH HHS/ -- HL-093039/HL/NHLBI NIH HHS/ -- HL-111665/HL/NHLBI NIH HHS/ -- R01 AR063182/AR/NIAMS NIH HHS/ -- U01-HL-100401/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2016 Jan 15;351(6270):271-5. doi: 10.1126/science.aad4076.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. ; Department of Physiology, Temple University School of Medicine, Philadelphia, PA 19140, USA. Department of Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA. ; Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. ; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. ; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. eric.olson@utsouthwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26816378" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium-Binding Proteins/metabolism ; Humans ; Mice ; Mice, Knockout ; *Muscle Contraction ; Muscle Proteins/metabolism ; Muscle, Skeletal/*metabolism ; Myocardial Contraction ; Myocytes, Cardiac/*metabolism ; Peptides/genetics/*metabolism ; Proteolipids/metabolism ; RNA, Long Noncoding/genetics/metabolism ; Sarcoplasmic Reticulum/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/*metabolism ; Transcription, Genetic
    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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    Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life (2018)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: In the coming years and decades, advanced space- and ground-based observatories will allow an unprecedented opportunity to probe the atmospheres and surfaces of potentially habitable exoplanets for signatures of life. Life on Earth, through its gaseous products and reflectance and scattering properties, has left its fingerprint on the spectrum of our planet. Aided by the universality of the laws of physics and chemistry, we turn to Earth's biosphere, both in the present and through geologic time, for analog signatures that will aid in the search for life elsewhere. Considering the insights gained from modern and ancient Earth, and the broader array of hypothetical exoplanet possibilities, we have compiled a comprehensive overview of our current understanding of potential exoplanet biosignatures, including gaseous, surface, and temporal biosignatures. We additionally survey biogenic spectral features that are well known in the specialist literature but have not yet been robustly vetted in the context of exoplanet biosignatures. We briefly review advances in assessing biosignature plausibility, including novel methods for determining chemical disequilibrium from remotely obtainable data and assessment tools for determining the minimum biomass required to maintain short-lived biogenic gases as atmospheric signatures. We focus particularly on advances made since the seminal review by Des Marais et al. The purpose of this work is not to propose new biosignature strategies, a goal left to companion articles in this series, but to review the current literature, draw meaningful connections between seemingly disparate areas, and clear the way for a path forward.
    Keywords: Astrophysics
    Type: GSFC-E-DAA-TN56547 , Astrobiology (ISSN 1531-1074) (e-ISSN 1557-8070); 18; 6; 663-708
    Format: text
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    NASA TECHNICAL REPORTS
  • 5
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    PE-46 The Design of the Lynx X-Ray Microcalorimeter (2017)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: Lynx is an x-ray telescope, one of four large satellite mission concepts currently being studied by NASA to be the next astrophysics flagship mission after WFIRST. One of Lynx's three instruments is an imaging spectrometer consisting of an x-ray microcalorimeter behind an X-ray optic with an angular resolution of 0.5 arc-seconds and approximately 3 sq m of area at 1 keV. This instrument will provide unparalleled diagnostics of distant extended structures and in particular will allow the detailed study of the role of cosmic feedback in the evolution of the Universe. We discuss the design and read-out of the of the array configuration including a number of sub-array options for increasing the capabilities to maximize the scientific return of the Lynx observatory.
    Keywords: Astrophysics
    Type: GSFC-E-DAA-TN45004 , International Workshop on Low Temperature Detectors; Jul 17, 2017 - Jul 21, 2017; Kurume; Japan
    Format: application/pdf
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    NASA TECHNICAL REPORTS
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