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  • 1
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    The zebrafish reference genome sequence and its relationship to the human genome (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-04-19
    Description: Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927/" 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/PMC3703927/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howe, Kerstin -- Clark, Matthew D -- Torroja, Carlos F -- Torrance, James -- Berthelot, Camille -- Muffato, Matthieu -- Collins, John E -- Humphray, Sean -- McLaren, Karen -- Matthews, Lucy -- McLaren, Stuart -- Sealy, Ian -- Caccamo, Mario -- Churcher, Carol -- Scott, Carol -- Barrett, Jeffrey C -- Koch, Romke -- Rauch, Gerd-Jorg -- White, Simon -- Chow, William -- Kilian, Britt -- Quintais, Leonor T -- Guerra-Assuncao, Jose A -- Zhou, Yi -- Gu, Yong -- Yen, Jennifer -- Vogel, Jan-Hinnerk -- Eyre, Tina -- Redmond, Seth -- Banerjee, Ruby -- Chi, Jianxiang -- Fu, Beiyuan -- Langley, Elizabeth -- Maguire, Sean F -- Laird, Gavin K -- Lloyd, David -- Kenyon, Emma -- Donaldson, Sarah -- Sehra, Harminder -- Almeida-King, Jeff -- Loveland, Jane -- Trevanion, Stephen -- Jones, Matt -- Quail, Mike -- Willey, Dave -- Hunt, Adrienne -- Burton, John -- Sims, Sarah -- McLay, Kirsten -- Plumb, Bob -- Davis, Joy -- Clee, Chris -- Oliver, Karen -- Clark, Richard -- Riddle, Clare -- Elliot, David -- Threadgold, Glen -- Harden, Glenn -- Ware, Darren -- Begum, Sharmin -- Mortimore, Beverley -- Kerry, Giselle -- Heath, Paul -- Phillimore, Benjamin -- Tracey, Alan -- Corby, Nicole -- Dunn, Matthew -- Johnson, Christopher -- Wood, Jonathan -- Clark, Susan -- Pelan, Sarah -- Griffiths, Guy -- Smith, Michelle -- Glithero, Rebecca -- Howden, Philip -- Barker, Nicholas -- Lloyd, Christine -- Stevens, Christopher -- Harley, Joanna -- Holt, Karen -- Panagiotidis, Georgios -- Lovell, Jamieson -- Beasley, Helen -- Henderson, Carl -- Gordon, Daria -- Auger, Katherine -- Wright, Deborah -- Collins, Joanna -- Raisen, Claire -- Dyer, Lauren -- Leung, Kenric -- Robertson, Lauren -- Ambridge, Kirsty -- Leongamornlert, Daniel -- McGuire, Sarah -- Gilderthorp, Ruth -- Griffiths, Coline -- Manthravadi, Deepa -- Nichol, Sarah -- Barker, Gary -- Whitehead, Siobhan -- Kay, Michael -- Brown, Jacqueline -- Murnane, Clare -- Gray, Emma -- Humphries, Matthew -- Sycamore, Neil -- Barker, Darren -- Saunders, David -- Wallis, Justene -- Babbage, Anne -- Hammond, Sian -- Mashreghi-Mohammadi, Maryam -- Barr, Lucy -- Martin, Sancha -- Wray, Paul -- Ellington, Andrew -- Matthews, Nicholas -- Ellwood, Matthew -- Woodmansey, Rebecca -- Clark, Graham -- Cooper, James D -- Tromans, Anthony -- Grafham, Darren -- Skuce, Carl -- Pandian, Richard -- Andrews, Robert -- Harrison, Elliot -- Kimberley, Andrew -- Garnett, Jane -- Fosker, Nigel -- Hall, Rebekah -- Garner, Patrick -- Kelly, Daniel -- Bird, Christine -- Palmer, Sophie -- Gehring, Ines -- Berger, Andrea -- Dooley, Christopher M -- Ersan-Urun, Zubeyde -- Eser, Cigdem -- Geiger, Horst -- Geisler, Maria -- Karotki, Lena -- Kirn, Anette -- Konantz, Judith -- Konantz, Martina -- Oberlander, Martina -- Rudolph-Geiger, Silke -- Teucke, Mathias -- Lanz, Christa -- Raddatz, Gunter -- Osoegawa, Kazutoyo -- Zhu, Baoli -- Rapp, Amanda -- Widaa, Sara -- Langford, Cordelia -- Yang, Fengtang -- Schuster, Stephan C -- Carter, Nigel P -- Harrow, Jennifer -- Ning, Zemin -- Herrero, Javier -- Searle, Steve M J -- Enright, Anton -- Geisler, Robert -- Plasterk, Ronald H A -- Lee, Charles -- Westerfield, Monte -- de Jong, Pieter J -- Zon, Leonard I -- Postlethwait, John H -- Nusslein-Volhard, Christiane -- Hubbard, Tim J P -- Roest Crollius, Hugues -- Rogers, Jane -- Stemple, Derek L -- 095908/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 1 R01 DK55377-01A1/DK/NIDDK NIH HHS/ -- P01 HD022486/HD/NICHD NIH HHS/ -- P01 HD22486/HD/NICHD NIH HHS/ -- R01 GM085318/GM/NIGMS NIH HHS/ -- R01 OD011116/OD/NIH HHS/ -- R01 RR010715/RR/NCRR NIH HHS/ -- R01 RR020833/RR/NCRR NIH HHS/ -- England -- Nature. 2013 Apr 25;496(7446):498-503. doi: 10.1038/nature12111. Epub 2013 Apr 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23594743" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosomes/genetics ; Conserved Sequence/*genetics ; Evolution, Molecular ; Female ; Genes/genetics ; Genome/*genetics ; Genome, Human/genetics ; Genomics ; Humans ; Male ; Meiosis/genetics ; Molecular Sequence Annotation ; Pseudogenes/genetics ; Reference Standards ; Sex Determination Processes/genetics ; Zebrafish/*genetics ; Zebrafish Proteins/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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    PAPER CURRENT
  • 2
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    AASE-2 observations of trace carbon species distributions in the mid to upper troposphere (1993)
    In:  Other Sources
    Details
    Publication Date: 2011-08-24
    Description: We report tropospheric (altitudes greater than 5 km) observations of CO2, CO, CH4, and light hydrocarbons (C2-C4) over the latitude range from 90 deg N to 23 deg S recorded onboard the NASA DC-8 aircraft during the winter 1992 Second Airborne Arctic Stratospheric Expedition (AASE-2). Mixing ratios for these species exhibited significant north-south gradients with maximum values in subpolar and arctic regions and minima over the southern tropics. At latitudes greater than 40 deg N, the mixing ratios of most species increased significantly over the course of the 3-month measurement period. Also at high northern latitudes, the variations of all relatively long-lived reactive carbon species were linearly correlated with fluctuations of CO2 with CO, CH4, C2H6, C2H2, C3H8, and n-C4H10 exhibiting average enhancement ratios in terms of ppbv(X)/ppmb(CO2) of 13.8, 8.4, 0.21, 0.075, 0.085, and 0.037, respectively.
    Keywords: GEOPHYSICS
    Type: Geophysical Research Letters (ISSN 0094-8276); 20; 22; p. 2539-2542
    Format: text
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    NASA TECHNICAL REPORTS
  • 3
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    Reevaluation of the NOAA/CMDL carbon monoxide reference scale and comparisons with CO reference gases at NASA-Langley and the Fraunhofer Institut (1994)
    In:  Other Sources
    Details
    Publication Date: 2011-08-24
    Description: The carbon monoxide (CO) reference scale created by the National Oceanic and Atmospheric Administration/Climate Monitoring and Diagnostics Laboratory (NOAA/CMDL) is used to quantify measurements of CO in the atmosphere, calibrate standards of other laboratories and to otherwise provide reference gases to the community measuring atmospheric CO. This reference scale was created based upon a set of primary standards prepared by gravimetric methods at CMDL and has been propagated to a set of working standards. In this paper we compare CO mixing ratios assigned to the working standards by three approaches: (1) calibration against the original gravimetric standards, (2) calibration using only working standards as the reference gas, and (3) calibration against three new gravimetric standards prepared to CMDL. The agreement between these values was typically better than 1%. The calibration histories of CMDL working standards are reviewed with respect to expected rates of CO change in the atmosphere. Using a Monte Carlo approach to simulate the effect of drifting standards on calculated mixing ratios, we conclude that the error solely associated with the maintenance of standards will limit the ability to detect small CO changes in the atmosphere. We also report results of intercalibration experiments conducted between CMDL and the Diode Laser Sensor Group (DACOM) at the NASA Langley Research Center (Hampton, Virginia), and CMDL and the Fraunhofer-Institut (Garmisch-Partenkirchen, Germany). Each laboratory calibrated several working standards for CO using their reference gases, and these results were compared to calibrations conducted by CMDL. The intercomparison of eight standards (CO concentrations between approximately 100 and approximately 165 ppb) by CMDL and NASA agreed to better than +/- 2%. The calibration of six standards (CO concentrations between approximately 50 and approximately 210 ppb) by CMDL and the Fraunhofer-Institut agreed to within +/- 2% for four standards, and to within +/- 5% for all six standards.
    Keywords: GEOPHYSICS
    Type: Journal of Geophysical Research (ISSN 0148-0227); 99; D6; p. 12,833-12,839
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    NASA TECHNICAL REPORTS
  • 4
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    Meridional distributions of NO(X), NO(Y), and other species in the lower statosphere and upper troposphere during AASE 2 (1994)
    In:  Other Sources
    Details
    Publication Date: 2011-08-24
    Description: The meridional distribution of NO(x) in the lower stratosphere and upper troposphere is inferred form 10 flights of the NASA DC-8 in the northern winter of 1992 along with like distributions of NO(y), NO(x)/NO(y), CO, and C2Cl4. In the lowest few km of the stratosphere there is little vertical gradient in NO(x) over the range of latitiudes measured (40 deg-90 deg N). There is a substantial latitudinal gradient, with 50 pptv above the pole and 120 pptv near 40 deg N. In the uppermost few km of the troposphere, background values range from 30 pptv over the pole to 90 pptv near 40 deg N. On two occasions higher values, up to 140 pptv in the mean, were seen 2-3 km below the tropopause in association with frontal systems. The meridional distributions of CO and C2Cl4 show the same feature, suggesting that the source of the elevated NO(x) is near the earth's system.
    Keywords: GEOPHYSICS
    Type: Geophysical Research Letters (ISSN 0094-8276); 21; 23; p. 2583-2586
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    NASA TECHNICAL REPORTS
  • 5
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    The role of airborne eddy correlation measurements in global change studies (1994)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: We have obtained measurements of the mean and turbulent quantities of heat, moisture, momentum, O3, CO, and CH4 from an airborne platform. Species flux measurements obtained from these data provide unique regional-scale information which can be used to evaluate 'scaled-up' flux estimates based on smaller scale observations. Airborne flux data also provide a basis for assessing the uncertainties associated with large-scale ground level flux extrapolations. Airborne constituent budget analyses are possible with this suite of measurements. The local change in the mean value of a parameter can be explained in terms of horizontal advection, vertical turbulent transport, and, in the case of chemically reactive species (i.e., O3), in situ production or destruction. This technique is used to indicate a direct relationship between O3 precursors and the measured in situ production rate.
    Keywords: GEOPHYSICS
    Type: Advances in Space Research (ISSN 0273-1177); 14; 1; p. (1)183-(1)186
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    NASA TECHNICAL REPORTS
  • 6
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    An analysis of aircraft exhaust plumes form accidental encounters (1994)
    In:  Other Sources
    Details
    Publication Date: 2019-08-28
    Description: An analysis of data obtained during the second Airborne Arctic Stratospheric Expedition (AASE-II) was made with emphasis on aircraft exhaust plumes accidentally encountered during the mission. Twenty spikes were found with peak NO(y) increments greater than or equal to 1 ppbv. The examination of CO and CO2 indicated that there was only one NO(y) spike having clearly corresponding spikes of both CO and CO2 and another four with unambigious CO2 spikes. No significant increases were found for CH4 and N2O for these 5 spikes. The ratio of the excess CO2 and NO(y) compares well with the ratio of published subsonic aircraft emission indices. The study of the selected spikes from the DC-8 and another two spikes observed during other missions shows that the odd nitrogen other than NO(x) accounts for a very small percentage of the NO(y) increase associated with the observed spikes.
    Keywords: GEOPHYSICS
    Type: Geophysical Research Letters (ISSN 0094-8276); 21; 23; p. 2579-2582
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    NASA TECHNICAL REPORTS
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