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  • 1
    Publication Date: 2012-03-15
    Description: The aim of this work is to explore the effectiveness of theoretical information approaches for the reduction of data complexity in multimodel ensemble systems. We first exploit a weak form of independence, i.e. uncorrelation, as a mechanism for detecting linear relationships. Then, stronger and more general forms of independence measure, such as mutual information, are used to investigate dependence structures for model selection. A distance matrix, measuring the interdependence between data, is derived for the investigated measures, with the scope of clustering correlated/dependent models together. Redundant information is discarded by selecting a few representative models from each cluster. We apply the clustering analysis in the context of atmospheric dispersion modeling, by using the ETEX-1 data set. We show how the selection of a small subset of models, according to uncorrelation or mutual information distance criteria, usually suffices to achieve a statistical performance comparable to, or even better than, that achieved from the whole ensemble data set, thus providing a simpler description of ensemble results without sacrificing accuracy.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2013-02-20
    Description: Paternal duplications of chromosome 6q24, a region that contains the imprinted PLAGL1 and HYMAI transcripts, are associated with transient neonatal diabetes mellitus. A common feature of imprinted genes is that they tend to cluster together, presumably as a result of sharing common cis -acting regulatory elements. To determine the extent of this imprinted cluster in human and mouse, we have undertaken a systematic analysis of allelic expression and DNA methylation of the genes mapping within an ~1.4-Mb region flanking PLAGL1/Plagl1 . We confirm that all nine neighbouring genes are biallelically expressed in both species. In human we identify two novel paternally expressed PLAGL1 coding transcripts that originate from unique promoter regions. Chromatin immunoprecipitation for CTCF and the cohesin subunits RAD21 and SMC3 reveals evolutionarily conserved binding sites within unmethylated regions ~5 kb downstream of the PLAGL1 differentially methylated region and within the PLAGL1 3' untranslated region (UTR). Higher-order chromatin looping occurs between these regions in both expressing and non-expressing tissues, forming a non-allelic chromatin loop around the PLAGL1/Plagl1 gene. In placenta and brain tissues, we identify an additional interaction between the PLAGL1 P3/P4 promoters and the unmethylated element downstream of the PLAGL1 differentially methylated region that we propose facilitates imprinted expression of these alternative isoforms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2011-12-28
    Description: Analytical Chemistry DOI: 10.1021/ac2031805
    Print ISSN: 0003-2700
    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 4
    Publication Date: 2014-07-04
    Description: CXCR4 and CXCR7 transduce through mTOR in human renal cancer cells Cell Death and Disease 5, e1310 (July 2014). doi:10.1038/cddis.2014.269 Authors: C Ieranò, S Santagata, M Napolitano, F Guardia, A Grimaldi, E Antignani, G Botti, C Consales, A Riccio, M Nanayakkara, M V Barone, M Caraglia & S Scala
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 5
    Publication Date: 1999-12-22
    Description: Nerve growth factor (NGF) and other neurotrophins support survival of neurons through processes that are incompletely understood. The transcription factor CREB is a critical mediator of NGF-dependent gene expression, but whether CREB family transcription factors regulate expression of genes that contribute to NGF-dependent survival of sympathetic neurons is unknown. CREB-mediated gene expression was both necessary for NGF-dependent survival and sufficient on its own to promote survival of sympathetic neurons. Moreover, expression of Bcl-2 was activated by NGF and other neurotrophins by a CREB-dependent transcriptional mechanism. Overexpression of Bcl-2 reduced the death-promoting effects of CREB inhibition. Together, these data support a model in which neurotrophins promote survival of neurons, in part through a mechanism involving CREB family transcription factor-dependent expression of genes encoding prosurvival factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riccio, A -- Ahn, S -- Davenport, C M -- Blendy, J A -- Ginty, D D -- NS34814-04/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2358-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600750" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Axons/drug effects/metabolism ; Brain-Derived Neurotrophic Factor/pharmacology ; Cell Nucleus/metabolism ; Cell Survival ; Cells, Cultured ; Cyclic AMP Response Element-Binding Protein/antagonists & inhibitors/*metabolism ; *Gene Expression Regulation ; Genes, bcl-2 ; Genetic Vectors ; Nerve Growth Factor/*pharmacology ; Neurons/*cytology/drug effects/metabolism ; PC12 Cells ; Promoter Regions, Genetic ; Proto-Oncogene Proteins c-bcl-2/genetics/metabolism ; Rats ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Sympathetic Nervous System/*cytology/drug effects/metabolism ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2008-08-30
    Description: Brain-derived neurotrophic factor (BDNF) and other neurotrophins have a vital role in the development of the rat and mouse nervous system by influencing the expression of many specific genes that promote differentiation, cell survival, synapse formation and, later, synaptic plasticity. Although nitric oxide (NO) is known to be an important mediator of BDNF signalling in neurons, the mechanisms by which neurotrophins influence gene expression during development and plasticity remain largely unknown. Here we show that BDNF triggers NO synthesis and S-nitrosylation of histone deacetylase 2 (HDAC2) in neurons, resulting in changes to histone modifications and gene activation. S-nitrosylation of HDAC2 occurs at Cys 262 and Cys 274 and does not affect deacetylase activity. In contrast, nitrosylation of HDAC2 induces its release from chromatin, which increases acetylation of histones surrounding neurotrophin-dependent gene promoters and promotes transcription. Notably, nitrosylation of HDAC2 in embryonic cortical neurons regulates dendritic growth and branching, possibly by the activation of CREB (cyclic-AMP-responsive-element-binding protein)-dependent genes. Thus, by stimulating NO production and S-nitrosylation of HDAC2, neurotrophic factors promote chromatin remodelling and the activation of genes that are associated with neuronal development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nott, Alexi -- Watson, P Marc -- Robinson, James D -- Crepaldi, Luca -- Riccio, Antonella -- G0500792/Medical Research Council/United Kingdom -- G117/533/Medical Research Council/United Kingdom -- G120/934/Medical Research Council/United Kingdom -- MC_U122663296/Medical Research Council/United Kingdom -- England -- Nature. 2008 Sep 18;455(7211):411-5. doi: 10.1038/nature07238. Epub 2008 Aug 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory for Molecular and Cell Biology, and Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18754010" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain-Derived Neurotrophic Factor/pharmacology ; Chromatin/*metabolism ; *Chromatin Assembly and Disassembly ; Cysteine/metabolism ; Cytoplasm/metabolism ; Dendrites/metabolism ; Female ; Histone Deacetylase 2 ; Histone Deacetylases/genetics/*metabolism ; Male ; Mice ; Nerve Growth Factors/metabolism ; Neurons/cytology/enzymology/*metabolism ; Nitric Oxide/biosynthesis/metabolism ; Nuclear Proteins/metabolism ; Rats ; Repressor Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 1997-08-22
    Description: Nerve growth factor (NGF) is a neurotrophic factor secreted by cells that are the targets of innervation of sympathetic and some sensory neurons. However, the mechanism by which the NGF signal is propagated from the axon terminal to the cell body, which can be more than 1 meter away, to influence biochemical events critical for growth and survival of neurons has remained unclear. An NGF-mediated signal transmitted from the terminals and distal axons of cultured rat sympathetic neurons to their nuclei regulated phosphorylation of the transcription factor CREB (cyclic adenosine monophosphate response element-binding protein). Internalization of NGF and its receptor tyrosine kinase TrkA, and their transport to the cell body, were required for transmission of this signal. The tyrosine kinase activity of TrkA was required to maintain it in an autophosphorylated state upon its arrival in the cell body and for propagation of the signal to CREB within neuronal nuclei. Thus, an NGF-TrkA complex is a messenger that delivers the NGF signal from axon terminals to cell bodies of sympathetic neurons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riccio, A -- Pierchala, B A -- Ciarallo, C L -- Ginty, D D -- New York, N.Y. -- Science. 1997 Aug 22;277(5329):1097-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9262478" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; *Axonal Transport ; Axons/*metabolism ; Carbazoles/pharmacology ; Cell Membrane/metabolism ; Cells, Cultured ; Cyclic AMP Response Element-Binding Protein/*metabolism ; Indole Alkaloids ; Microspheres ; Nerve Growth Factors/*metabolism/pharmacology ; Neurons/*metabolism ; Phosphorylation ; Proto-Oncogene Proteins/antagonists & inhibitors/*metabolism ; Rats ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors/*metabolism ; Receptor, trkA ; Receptors, Nerve Growth Factor/antagonists & inhibitors/*metabolism ; Signal Transduction ; Superior Cervical Ganglion/cytology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2011-11-05
    Description: Non-mammalian vertebrates have an intrinsically photosensitive iris and thus a local pupillary light reflex (PLR). In contrast, it is thought that the PLR in mammals generally requires neuronal circuitry connecting the eye and the brain. Here we report that an intrinsic component of the PLR is in fact widespread in nocturnal and crepuscular mammals. In mouse, this intrinsic PLR requires the visual pigment melanopsin; it also requires PLCbeta4, a vertebrate homologue of the Drosophila NorpA phospholipase C which mediates rhabdomeric phototransduction. The Plcb4(-/-) genotype, in addition to removing the intrinsic PLR, also essentially eliminates the intrinsic light response of the M1 subtype of melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (M1-ipRGCs), which are by far the most photosensitive ipRGC subtype and also have the largest response to light. Ablating in mouse the expression of both TRPC6 and TRPC7, members of the TRP channel superfamily, also essentially eliminated the M1-ipRGC light response but the intrinsic PLR was not affected. Thus, melanopsin signalling exists in both iris and retina, involving a PLCbeta4-mediated pathway that nonetheless diverges in the two locations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270891/" 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/PMC3270891/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xue, T -- Do, M T H -- Riccio, A -- Jiang, Z -- Hsieh, J -- Wang, H C -- Merbs, S L -- Welsbie, D S -- Yoshioka, T -- Weissgerber, P -- Stolz, S -- Flockerzi, V -- Freichel, M -- Simon, M I -- Clapham, D E -- Yau, K-W -- EY14596/EY/NEI NIH HHS/ -- R01 DC006904/DC/NIDCD NIH HHS/ -- R01 DC006904-07/DC/NIDCD NIH HHS/ -- R01 DC006904-08/DC/NIDCD NIH HHS/ -- R01 DC006904-09/DC/NIDCD NIH HHS/ -- R01 EY006837/EY/NEI NIH HHS/ -- R01 EY006837-22/EY/NEI NIH HHS/ -- R01 EY006837-23/EY/NEI NIH HHS/ -- R01 EY006837-24/EY/NEI NIH HHS/ -- R37 EY006837/EY/NEI NIH HHS/ -- R37 EY006837-13/EY/NEI NIH HHS/ -- R37 EY006837-14/EY/NEI NIH HHS/ -- R37 EY006837-15/EY/NEI NIH HHS/ -- R37 EY006837-15S1/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Nov 2;479(7371):67-73. doi: 10.1038/nature10567.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. txue77@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22051675" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Iris/anatomy & histology/cytology/*metabolism/*radiation effects ; Light Signal Transduction/physiology/*radiation effects ; Mammals/*physiology ; Mice ; Phospholipase C beta/metabolism ; Photic Stimulation ; Primates/physiology ; Reflex, Pupillary/physiology/radiation effects ; Retina/cytology/*metabolism/*radiation effects ; Retinal Ganglion Cells/metabolism/radiation effects ; Rod Opsins/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2019
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 10
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of fish biology 57 (2000), S. 0 
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Pagothenia borchgrevinki, has a higher haemoglobin concentration than other Antarctic notothenioids and the high oxygen capacity may correlate with the relatively active mode of life of this fish. The fish has five haemoglobins (Hb C, Hb 0, Hb 1, Hb 2 and Hb 3) with Hb 1 accounting for 70–80% of the total, and Hb C being present in trace amounts. Hb 1 and Hb 2 are functionally similar in terms of Bohr and Root effects. Hb 3 has a weaker Bohr effect than Hb 1 and Hb 2, and the Root effect is similar to that of Hb 1. Hb 0 has a strong Bohr effect and the Root effect is enhanced to a larger extent by the physiological effectors chlorides and phosphates than that of the other components with the exception of Hb C. The heats of oxygenation are lower than those of temperate fish haemoglobins. Temperature variations may have a different effect on the functional properties of each haemoglobin, and chloride and phosphates may play an important role in the conformational change between the oxy and deoxy structures. The complete amino acid sequences of Hb 1 and Hb 0, as well as partial N-terminal or internal sequences of the other haemoglobins, have been established. The high multiplicity of functionally distinct haemoglobins indicates that P. borchgrevinki, has a specialized haemoglobin system.
    Type of Medium: Electronic Resource
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