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  • 1
    Publication Date: 2012-06-16
    Description: Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations in addition to numerous lower frequency genetic events of uncertain significance. Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis in a mouse model of pancreatic ductal preneoplasia to identify genes that cooperate with oncogenic Kras(G12D) to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia, we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2'-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with Kras(G12D) to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376394/" 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/PMC3376394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perez-Mancera, Pedro A -- Rust, Alistair G -- van der Weyden, Louise -- Kristiansen, Glen -- Li, Allen -- Sarver, Aaron L -- Silverstein, Kevin A T -- Grutzmann, Robert -- Aust, Daniela -- Rummele, Petra -- Knosel, Thomas -- Herd, Colin -- Stemple, Derek L -- Kettleborough, Ross -- Brosnan, Jacqueline A -- Li, Ang -- Morgan, Richard -- Knight, Spencer -- Yu, Jun -- Stegeman, Shane -- Collier, Lara S -- ten Hoeve, Jelle J -- de Ridder, Jeroen -- Klein, Alison P -- Goggins, Michael -- Hruban, Ralph H -- Chang, David K -- Biankin, Andrew V -- Grimmond, Sean M -- Australian Pancreatic Cancer Genome Initiative -- Wessels, Lodewyk F A -- Wood, Stephen A -- Iacobuzio-Donahue, Christine A -- Pilarsky, Christian -- Largaespada, David A -- Adams, David J -- Tuveson, David A -- 13031/Cancer Research UK/United Kingdom -- 2P50CA101955/CA/NCI NIH HHS/ -- CA106610/CA/NCI NIH HHS/ -- CA122183/CA/NCI NIH HHS/ -- CA128920/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- K01 CA122183/CA/NCI NIH HHS/ -- K01 CA122183-05/CA/NCI NIH HHS/ -- P50 CA101955/CA/NCI NIH HHS/ -- P50CA62924/CA/NCI NIH HHS/ -- Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Apr 29;486(7402):266-70. doi: 10.1038/nature11114.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22699621" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anoikis/genetics ; Carcinoma, Pancreatic Ductal/*enzymology/genetics/pathology ; Cell Line, Tumor ; Disease Models, Animal ; Endopeptidases ; Gene Expression Regulation, Neoplastic ; Gene Knockdown Techniques ; Humans ; Mice ; Mice, Inbred C57BL ; Pancreatic Neoplasms/*enzymology/genetics/pathology ; U937 Cells ; Ubiquitin Thiolesterase/*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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  • 2
    Publication Date: 2013-04-19
    Description: Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls considerably short of the more than 22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing, and zinc finger and TAL endonucleases have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743023/" 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/PMC3743023/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kettleborough, Ross N W -- Busch-Nentwich, Elisabeth M -- Harvey, Steven A -- Dooley, Christopher M -- de Bruijn, Ewart -- van Eeden, Freek -- Sealy, Ian -- White, Richard J -- Herd, Colin -- Nijman, Isaac J -- Fenyes, Fruzsina -- Mehroke, Selina -- Scahill, Catherine -- Gibbons, Richard -- Wali, Neha -- Carruthers, Samantha -- Hall, Amanda -- Yen, Jennifer -- Cuppen, Edwin -- Stemple, Derek L -- 098051/Wellcome Trust/United Kingdom -- 5R01HG00481/HG/NHGRI NIH HHS/ -- G0777791/Medical Research Council/United Kingdom -- England -- Nature. 2013 Apr 25;496(7446):494-7. doi: 10.1038/nature11992. 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/23594742" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Exome/genetics ; Female ; Gene Knockout Techniques ; Genetic Complementation Test ; Genome/*genetics ; Genomics ; Male ; Molecular Sequence Annotation ; Mutagenesis ; Mutation/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Zebrafish/*genetics/physiology ; Zebrafish 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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  • 3
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The flowing afterglow technique, coupled with laser induced fluorescence (LIF) and vacuum ultraviolet (vuv) absorption spectroscopy, has been used to determine the fractional H-atom contributions, fH, to the product distributions for the dissociative recombination of a series of protonated ions (N2H+, HCO+, HCO+2, N2OH+, OCSH+, H2CN+, H3O+, H3S+, NH+4, and CH+5 ) with electrons. The measurements were made at 300 K in two separate ways in two laboratories by (i) directly determining the H-atom number density using vuv absorption spectroscopy at the Lα (121.6 nm) wavelength and (ii) converting the H atoms to OH radicals using the reaction H+NO2→OH+NO followed by LIF to determine the OH number density. The agreement between the two techniques is excellent and values of fH varying from ∼0.2 (for OCSH+ ) to 1.2 (for CH+5 ) have been obtained showing that in some of the cases recombination can lead to the ejection of two separate H atoms. Comparison of the oxygen/sulphur analogs, HCO+2/OCSH+ and H3O+/H3S+ showed that the fH values were very different. Possible reasons for these differences are discussed. Comparison is also made with the available theory.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Using small-angle x-ray (SAXS), neutron (SANS), x-ray diffraction and light scattering, we study the structure of colloidal silica and carbon on length scales from 4 Å 〈 q−1 〈 107 Å where q is the magnitude of the scattering vector. These materials consist of primary particles of the order of 100 Å, aggregated into micron-sized aggregates that in turn are agglomerated into 100 µ agglomerates. The diffraction data show that the primary particles in precipitated silica are composed of highly defective amorphous silica with little intermediate-range order (order on the scale of several bond distances). On the next level of morphology, primary particles arise by a complex nucleation process in which primordial nuclei briefly aggregate into rough particles that subsequently smooth out to become the seeds for the primaries. The primaries aggregate to strongly bonded clusters by a complex process involving kinetic growth, mechanical disintegration and restructuring. Finally, the small-angle scattering (SAS) data lead us to postulate that the aggregates cluster into porous, rough-surfaced, non-mass-fractal agglomerates that can be broken down to the more strongly bonded aggregates by application of shear. We find similar structure in pelletized carbon blacks. In this case we show a linear scaling relation between the primary and aggregate sizes. We attribute the scaling to mechanical processing that deforms the fractal aggregates down to the maximum size able to withstand the compaction stress. Finally, we rationalize the observed structure based on empirical optimization by filler suppliers and some recent theoretical ideas due to Witten, Rubenstein and Colby.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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