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  • 1
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    The first UK measurements of nitryl chloride using a chemical ionisation mass spectrometer in central London in the summer of 2012, and an investigation of the role of Cl atom oxidation. (2015)
    Wiley
    Details
    Publication Date: 2015-04-14
    Description: The first Nitryl Chloride (ClNO 2 ) measurements in the United Kingdom were made during the summer 2012 ClearfLo campaign with a chemical ionisation mass spectrometer, utilising an I − ionisation scheme. Concentrations of ClNO 2 exceeded detectable limits (11 ppt) every night with a maximum concentration of 724 ppt. A diurnal profile of ClNO 2 peaking between 4 and 5 am, decreasing directly after sunrise was observed. Concentrations of ClNO 2 above the detection limit are generally observed between 8 pm and 11 am. Different ratios of the production of ClNO 2 : N 2 O 5 were observed throughout with both positive and negative correlations between the two species being reported. The photolysis of ClNO 2 and a box model utilising the Master Chemical Mechanism modified to include chlorine chemistry was used to calculate Cl atom concentrations. Simultaneous measurements of hydroxyl radicals (OH) using low pressure laser-induced fluorescence and ozone enabled the relative importance of the oxidation of three groups of measured VOCs (alkanes, alkenes and alkynes) by OH radicals, Cl atoms and O 3 to be compared. For the day with the maximum calculated Cl atom concentration, Cl atoms in the early morning were the dominant oxidant for alkanes, and over the entire day contributed 15%, 3% and 26% towards the oxidation of alkanes, alkenes and alkynes, respectively.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    The impact of current CH4 and N2O atmospheric loss process uncertainties on calculated ozone abundances and trends (2015)
    Wiley
    Details
    Publication Date: 2015-04-23
    Description: The atmospheric loss processes of N 2 O and CH 4 , their estimated uncertainties, lifetimes, and impacts on ozone abundance and long-term trends are examined using atmospheric model calculations and updated kinetic and photochemical parameters and uncertainty factors from SPARC [2013]. The uncertainty ranges in calculated N 2 O and CH 4 global lifetimes computed using the SPARC estimated uncertainties are reduced by nearly a factor of two compared with uncertainties from Sander et al. [2011]. Uncertainties in CH 4 loss due to reaction with OH and O( 1 D) have relatively small impacts on present day global total ozone (±0.2-0.3%). Uncertainty in the Cl + CH 4 reaction affects the amount of chlorine in radical vs. reservoir forms and has a modest impact on present day SH polar ozone (~±6%), and on the rate of past ozone decline and future recovery. Uncertainty in the total rate coefficient for the O( 1 D) + N 2 O reaction results in a substantial range in present day stratospheric odd nitrogen (±20-25%) and global total ozone (±1.5-2.5%). Uncertainty in the O( 1 D) + N 2 O reaction branching ratio for the O 2 + N 2 and 2*NO product channels results in moderate impacts on odd nitrogen (±10%) and global ozone (±1%), with uncertainty in N 2 O photolysis resulting in relatively small impacts (±5% in odd nitrogen, ±0.5% in global ozone). Uncertainties in the O( 1 D) + N 2 O reaction and its branching ratio also affect the rate of past global total ozone decline and future recovery, with a range in future ozone projections of ±1-1.5% by 2100, relative to present day.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Hydrogen oxide photochemistry in the northern Canadian spring time boundary layer (2011)
    Wiley
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    Publication Date: 2011-11-22
    Description: Measurements of OH and HO2 concentrations were made at the surface of the eastern coast of the Hudson Bay during the COBRA campaign from February 18th to March 8th 2008. Diurnally averaged OH and HO2 concentrations peaked at 1.16 (±1.02) × 106 molecule cm−3 and 1.42 (±0.64) × 108 molecule cm−3 respectively. A box-model, constrained to supporting observations, is used to access the radical budget in this cold, northerly environment. Formaldehyde (HCHO) photolysis is found to be the dominant daytime radical source, providing 74% of the observed HOx. A considerable (〉80% of the total source) surface HCHO source is required to reconcile the model and observed HCHO concentrations. Model simulations also suggest significant roles for the heterogeneous loss of HO2 and for halogen chemistry in the cycling of HO2 to OH. The formation of HO2NO2 is identified as an important radical reservoir, reducing HOx concentrations during the day and enhancing them at night. This impacts both local oxidizing capacity and reduces local ozone production by approximately 30%. The sensitivity of the local chemistry to uncertainties in these processes is explored. The majority of these processes are not currently represented in global chemistry models.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Impacts of HOx regeneration and recycling in the oxidation of isoprene: Consequences for the composition of past, present and future atmospheres (2011)
    Wiley
    Details
    Publication Date: 2011-03-09
    Description: A global chemistry-climate model is used to assess the impact on atmospheric composition of the regeneration and recycling of HOx in the photo-oxidation of isoprene. The impact is explored subject to present-day, pre-industrial and future climate/emission scenarios. Our calculations show that, in all cases, the inclusion of uni-molecular isomerisations of the isoprene hydroxy-peroxy radicals leads to enhanced production of HOx radicals and ozone. The global burden of ozone increases by 25–36 Tg (8–18%), depending on the climate/emissions scenario, whilst the changes in OH lead to decreases in the methane lifetime of between 11% in the future and 35% in the pre-industrial. Critically the size of the change in methane lifetime depends on the VOC/NOx emission ratio. The results of the present-day calculations suggest a certain amount of parameter refinement is still needed to reconcile the updated chemistry with field observations (particularly for HO2+RO2). However, the updated chemistry could have far-reaching implications for: future-climate predictions; projections of future oxidising capacity; and our understanding of past changes in oxidising capacity.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Extensive halogen-mediated ozone destruction over the tropical Atlantic Ocean (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-06-27
    Description: Increasing tropospheric ozone levels over the past 150 years have led to a significant climate perturbation; the prediction of future trends in tropospheric ozone will require a full understanding of both its precursor emissions and its destruction processes. A large proportion of tropospheric ozone loss occurs in the tropical marine boundary layer and is thought to be driven primarily by high ozone photolysis rates in the presence of high concentrations of water vapour. A further reduction in the tropospheric ozone burden through bromine and iodine emitted from open-ocean marine sources has been postulated by numerical models, but thus far has not been verified by observations. Here we report eight months of spectroscopic measurements at the Cape Verde Observatory indicative of the ubiquitous daytime presence of bromine monoxide and iodine monoxide in the tropical marine boundary layer. A year-round data set of co-located in situ surface trace gas measurements made in conjunction with low-level aircraft observations shows that the mean daily observed ozone loss is approximately 50 per cent greater than that simulated by a global chemistry model using a classical photochemistry scheme that excludes halogen chemistry. We perform box model calculations that indicate that the observed halogen concentrations induce the extra ozone loss required for the models to match observations. Our results show that halogen chemistry has a significant and extensive influence on photochemical ozone loss in the tropical Atlantic Ocean boundary layer. The omission of halogen sources and their chemistry in atmospheric models may lead to significant errors in calculations of global ozone budgets, tropospheric oxidizing capacity and methane oxidation rates, both historically and in the future.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Read, Katie A -- Mahajan, Anoop S -- Carpenter, Lucy J -- Evans, Mathew J -- Faria, Bruno V E -- Heard, Dwayne E -- Hopkins, James R -- Lee, James D -- Moller, Sarah J -- Lewis, Alastair C -- Mendes, Luis -- McQuaid, James B -- Oetjen, Hilke -- Saiz-Lopez, Alfonso -- Pilling, Michael J -- Plane, John M C -- England -- Nature. 2008 Jun 26;453(7199):1232-5. doi: 10.1038/nature07035.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18580948" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western ; Atlantic Ocean ; Atmosphere/*chemistry ; Eukaryota/metabolism ; Geography ; Halogens/*chemistry ; Marine Biology ; Methane/chemistry ; Ozone/analysis/*chemistry/radiation effects ; Seasons ; Seawater/*chemistry/microbiology ; Temperature ; *Tropical Climate
    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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  • 6
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    Epigenetic dynamics of imprinted X inactivation during early mouse development (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-13
    Description: The initiation of X-chromosome inactivation is thought to be tightly correlated with early differentiation events during mouse development. Here, we show that although initially active, the paternal X chromosome undergoes imprinted inactivation from the cleavage stages, well before cellular differentiation. A reversal of the inactive state, with a loss of epigenetic marks such as histone modifications and polycomb proteins, subsequently occurs in cells of the inner cell mass (ICM), which give rise to the embryo-proper in which random X inactivation is known to occur. This reveals the remarkable plasticity of the X-inactivation process during preimplantation development and underlines the importance of the ICM in global reprogramming of epigenetic marks in the early embryo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okamoto, Ikuhiro -- Otte, Arie P -- Allis, C David -- Reinberg, Danny -- Heard, Edith -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):644-9. Epub 2003 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR218, Curie Institute, 26 rue d'Ulm, Paris 75005, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671313" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Blastocyst/physiology ; Blastomeres/physiology ; Chromatin/metabolism ; Chromosomes, Mammalian/physiology ; *Dosage Compensation, Genetic ; Embryo, Mammalian/*physiology ; *Embryonic and Fetal Development ; *Epigenesis, Genetic ; Female ; *Genomic Imprinting ; Histones/metabolism ; Male ; Methylation ; Mice ; Morula/physiology ; RNA, Long Noncoding ; RNA, Untranslated/metabolism ; Transcription, Genetic ; X Chromosome/*physiology
    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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  • 7
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    Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-04-08
    Description: X-chromosome inactivation (XCI) in female mammals allows dosage compensation for X-linked gene products between the sexes. The developmental regulation of this process has been extensively investigated in mice, where the X chromosome of paternal origin (Xp) is silenced during early embryogenesis owing to imprinted expression of the regulatory RNA, Xist (X-inactive specific transcript). Paternal XCI is reversed in the inner cell mass of the blastocyst and random XCI subsequently occurs in epiblast cells. Here we show that other eutherian mammals have very different strategies for initiating XCI. In rabbits and humans, the Xist homologue is not subject to imprinting and XCI begins later than in mice. Furthermore, Xist is upregulated on both X chromosomes in a high proportion of rabbit and human embryo cells, even in the inner cell mass. In rabbits, this triggers XCI on both X chromosomes in some cells. In humans, chromosome-wide XCI has not initiated even by the blastocyst stage, despite the upregulation of XIST. The choice of which X chromosome will finally become inactive thus occurs downstream of Xist upregulation in both rabbits and humans, unlike in mice. Our study demonstrates the remarkable diversity in XCI regulation and highlights differences between mammals in their requirement for dosage compensation during early embryogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okamoto, Ikuhiro -- Patrat, Catherine -- Thepot, Dominique -- Peynot, Nathalie -- Fauque, Patricia -- Daniel, Nathalie -- Diabangouaya, Patricia -- Wolf, Jean-Philippe -- Renard, Jean-Paul -- Duranthon, Veronique -- Heard, Edith -- England -- Nature. 2011 Apr 21;472(7343):370-4. doi: 10.1038/nature09872. Epub 2011 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, Paris 75248, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21471966" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Blastocyst/metabolism ; Chromosomes, Mammalian/*genetics ; Dosage Compensation, Genetic/genetics ; Embryo, Mammalian/embryology/metabolism ; Female ; Gene Expression Regulation, Developmental/*genetics ; Genes, X-Linked/genetics ; Genomic Imprinting/genetics ; Histones/metabolism ; Humans ; Hypoxanthine Phosphoribosyltransferase/genetics ; Male ; Mammals/embryology/*genetics ; Mice ; Parthenogenesis ; RNA, Long Noncoding ; RNA, Untranslated/genetics ; Rabbits ; Species Specificity ; Up-Regulation/genetics ; X Chromosome/*genetics ; X Chromosome Inactivation/*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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  • 8
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    The pluripotent genome in three dimensions is shaped around pluripotency factors (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-07-26
    Description: It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells such as embryonic stem cells were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here we combine chromatin conformation capture technologies with chromatin factor binding data to demonstrate that inactive chromatin is unusually disorganized in pluripotent stem-cell nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner, whereas enhancers have a more tissue-restricted interaction profile. Notably, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly pluripotent-stem-cell-specific, dependent on the presence of Oct4 and Nanog protein and inducible after artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Wit, Elzo -- Bouwman, Britta A M -- Zhu, Yun -- Klous, Petra -- Splinter, Erik -- Verstegen, Marjon J A M -- Krijger, Peter H L -- Festuccia, Nicola -- Nora, Elphege P -- Welling, Maaike -- Heard, Edith -- Geijsen, Niels -- Poot, Raymond A -- Chambers, Ian -- de Laat, Wouter -- G0901533/Medical Research Council/United Kingdom -- England -- Nature. 2013 Sep 12;501(7466):227-31. doi: 10.1038/nature12420. Epub 2013 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23883933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Chromatin/*chemistry/genetics/*metabolism ; Chromatin Immunoprecipitation ; *Chromosome Positioning ; Embryonic Stem Cells/cytology/metabolism ; Enhancer Elements, Genetic ; Genome/*genetics ; Homeodomain Proteins/metabolism ; *Imaging, Three-Dimensional ; Induced Pluripotent Stem Cells/cytology/metabolism ; Mice ; Molecular Imaging ; Octamer Transcription Factor-3/metabolism ; Organ Specificity ; Pluripotent Stem Cells/*cytology/*metabolism ; Promoter Regions, Genetic ; SOXB1 Transcription Factors/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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  • 9
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    Spatial partitioning of the regulatory landscape of the X-inactivation centre (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-04-13
    Description: In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555144/" 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/PMC3555144/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nora, Elphege P -- Lajoie, Bryan R -- Schulz, Edda G -- Giorgetti, Luca -- Okamoto, Ikuhiro -- Servant, Nicolas -- Piolot, Tristan -- van Berkum, Nynke L -- Meisig, Johannes -- Sedat, John -- Gribnau, Joost -- Barillot, Emmanuel -- Bluthgen, Nils -- Dekker, Job -- Heard, Edith -- R01 HG003143/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Apr 11;485(7398):381-5. doi: 10.1038/nature11049.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Curie, 26 rue d'Ulm, Paris F-75248, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; DNA, Intergenic/genetics ; Embryonic Stem Cells/cytology/metabolism ; Epigenesis, Genetic ; Epigenomics ; Female ; Fibroblasts ; Gene Expression Regulation ; Histones/metabolism ; In Situ Hybridization, Fluorescence ; Male ; Methylation ; Mice ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; RNA, Long Noncoding ; RNA, Untranslated/*genetics ; Transcriptome ; X Chromosome/chemistry/*genetics ; X Chromosome Inactivation/*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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  • 10
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    [ASAP] Rapid Acceleration of Hydrogen Atom Abstraction Reactions of OH at Very Low Temperatures through Weakly Bound Complexes and Tunneling (2018)
    American Chemical Society (ACS)
    Details
    Publication Date: 2018-10-26
    Description: Accounts of Chemical Research DOI: 10.1021/acs.accounts.8b00304
    Print ISSN: 0001-4842
    Electronic ISSN: 1520-4898
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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