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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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  • 2
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    Factors influencing dry season ozone distributions over the tropical South Atlantic (1993)
    In:  Other Sources
    Details
    Publication Date: 2011-08-24
    Description: Airborne measurements of trace gas and aerosol species were obtained in the lower troposphere (less than 5 km) over the western Atlantic Ocean between 13 deg S and 40 deg N during the August/September 1990 NASA Chemical Instrument Test and Evaluation (CITE 3) experiment. The largest background O3 mixing ratios, averaging 35 and 70 ppbv within the mixed layer (ML) and free troposphere (FT; altitudes greater than 2.4 km), respectively, were found over the tropical South Atlantic. Several competing processes were observed to regulate O3 budgets in this region. Within the ML, rapid photochemical destruction produced a diurnal O3 variation of 8 ppbv and an O3/altitude gradient between the surface and 5 km of almost 10 ppbv (O3)/km. ML O3 concentrations were replenished by atmospheric downwelling which occurred at rates of up to and exceeding 1 cm/s. Ozone values within the subsiding FT air were enriched both by long-range transport of O3 produced photochemically within biomass combustion plumes and the downward propagation of dry, upper tropospheric air masses. Overall, the tropospheric O3 column below 3.3 km averaged 13.5 Dobson units (DU) over the South Atlantic region, which is 8-9 DU higher than observed during CITE 3 ferry flights over the northern tropical Atlantic Ocean or measured by ozonesondes over coastal Brazil during the wet season. An examination of simultaneous dew point and combustion tracer (e.g., CO) measurements suggests that the dry subsiding layers and biomass burning layers make approximately equal contributions to the observed O3 enhancement.
    Keywords: ENVIRONMENT POLLUTION
    Type: Journal of Geophysical Research (ISSN 0148-0227); 98; D12; p. 23,491-23,500
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  • 3
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    The impact of U.S. continental outflow on ozone and aerosol distributions over the western Atlantic (1993)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Aircraft measurements of selected trace gas species, aerosols, and meteorological parameters were performed in the lower troposphere off the U.S. east coast during August and September 1989 as part of the NASA Global Tropospheric Experiment (GTE) Chemical Instrumentation Test and Evaluation (CITE 3) expedition. In this paper, we examine these data to assess the impact of continental outflow on western Atlantic O3 and small aerosol budgets. Results show that mixed layer (ML) O3 concentrations and small aerosol number densities (Np) were enhanced by factors of 3 and 6, respectively, within air masses of predominantly continental origin compared with clean maritime background air. These enhancements exhibited a marked altitude dependence, declining rapidly above the ML to the point where only slight to moderate differences in O3 and Np, respectively, were notable above 2.4 km. Within continentally influenced ML's, both O3 and Np were correlated with CO, exhibiting linear regression slopes averaging 0.4 ppbv (O3)/ppbv(CO) for O3 and 7.7 (particles/cc)/ppbv(CO) for Np and indicating a primarily anthropogenic origin for the observed enhancement of these species. Comparisons between profiles in continental and background maritime air masses suggest that photochemical production below 1.4-km altitude adds over 10% to western Atlantic tropospheric column O3 abundance in continental outflow regimes. For aerosols, eastward advection of low-level continental air contributes an average net flux of 2.8 metric tons of submicron (accumulation mode) particles per kilometer of shoreline per day to the western Atlantic troposphere.
    Keywords: ENVIRONMENT POLLUTION
    Type: Journal of Geophysical Research (ISSN 0148-0227); 98; D12; p. 23,477-23,489
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  • 4
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    AASE-2 in-situ tracer correlations of methane, nitrous oxide, and ozone as observed aboard the DC-8 (1993)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: We report in situ stratospheric measurements of CH4, N2O, and O3 obtained aboard the NASA DC-8 during the January-March 1992 Airborne Arctic Stratospheric Expedition 2 field campaign. These data demonstrate a strong linear correlation between N2O and CH4 in the lower stratosphere thus indicating that both species are effective tracers of stratospheric air motion. Measurements of both species on constant geometric height surfaces indicate that significant subsidence of the arctic stratospheric air mass occurred at DC-8 altitudes over the course of the AASE-2 expedition. In addition, a widespread reduction in O3 mixing ratios (up to 20%) relative to these conserved tracers was also observed in the lower stratosphere in March as compared to January and February results.
    Keywords: ENVIRONMENT POLLUTION
    Type: Geophysical Research Letters (ISSN 0094-8276); 20; 22; p. 2543-2546
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  • 5
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    Influence of plumes from biomass burning on atmospheric chemistry over the equatorial and tropical South Atlantic during CITE 3 (1994)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: During all eight flights conducted over the equatorial and tropical South Atlantic in the course of the Chemical Instrumentation Test and Evaluation (CITE 3) experiment, we observed haze layers with elevated concentrations of aerosols, O3, CO, and other trace gases related to biomass burning emissions. They occurred at altitudes between 1000 and 5200 m and were usually only some 100-300 m thick. These layers extended horizontally over several 100 km and were marked by the presence of visible brownish haze. Air mass trajectories indicate that these layers originate in the biomass burning regions of Africa and South America and typically have aged at least 10 days since the time of emission. In the haze layers, O3 and CO concentrations up to 90 and 210 ppb were observed, respectively. The two species were highly correlated. The ratio concentrations in plume minus background concentrations of O3/CO is typically in the range 0.2-0.7, much higher than the ratios in the less aged plumes investigated previously in Amazonia. In most cases, aerosol (0.12-3 micrometer diameter) number concentrations were also elevated by up to 400/cu cm in the layers; aerosol enrichments were also strongly correlated with elevated CO levels. Clear correlations between CO and NO(x) enrichments were not apparent due to the age of the plumes, in which most NO(x) would have already reacted away within 1-2 days. Only in some of the plumes could clear correlations between NO(y) and CO be identified; the absence of a general correlation between NO(y) and CO may be due to instrumental limitations and to variable sinks for NO(y). The average enrichment of the ratio concentrations in plume minus background concentrations of NO(y)/CO was quite high, consistent with the efficient production of ozone observed in the plumes. The chemical characteristics of the haze layers, together with remote sensing information and trajectory calculations, suggest that fire emissions (in Africa and/or South America) are the primary source of the haze layer components.
    Keywords: ENVIRONMENT POLLUTION
    Type: Journal of Geophysical Research (ISSN 0148-0227); 99; D6; p. 12,793-12,808
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  • 6
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    Stratospheric NO(y) measurements on the NASA DC-8 during AASE 2 (1993)
    In:  Other Sources
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    Publication Date: 2019-08-27
    Description: We survey measurements of stratospheric NO(y) on the NASA DC-8 during AASE 2 in early 1992. Emphasis is on correlations with other long-lived species: O3, N2O, and CH4. No cases of extremely high NO(y)/O3 ratios were seen in 1992. This suggests that denitrification at higher altitudes was less pervasive than in 1989. Values of NO(y)/O3 in 1992 are comparable to, though perhaps lower than, those measured in 1989. The correlation of NO(y) with N2O changes over the course of the mission. Relative to the correlation for the whole season, low values of NO(y) occur in February, most notably on the 22nd. The reason for the low NO(y) is unknown. It is generally too warm at DC-8 altitudes for the presence of Polar Stratospheric Cloud (PSC) particles, but denitrification at higher altitudes, followed by descent, might account for the low values seen on 22 February. However, this may be unlikely since the NASA ER-2, flying during the same period, saw no evidence of denitrification at higher altitudes (Loewenstein et al., 1993).
    Keywords: ENVIRONMENT POLLUTION
    Type: Geophysical Research Letters (ISSN 0094-8276); 20; 22; p. 2563-2566
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