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  • 1
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    Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene (2015)
    Oxford University Press
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    Publication Date: 2015-04-04
    Description: Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease gene. By whole-exome sequencing (WES) in a consanguineous family with congenital non-syndromic deafness, we unexpectedly identified a homozygous nonsense variant, p.Arg1066*, in AHI1 , a gene associated with Joubert syndrome (JBTS), a severe recessive ciliopathy. None of four homozygotes expressed any signs of JBTS, and one of them had normal hearing, which also ruled out p.Arg1066* as the cause of deafness. Homozygosity mapping and WES in the only other reported JBTS family with a homozygous C-terminal truncation (p.Trp1088Leufs*16) confirmed AHI1 as disease gene, but based on a more N-terminal missense mutation impairing WD40-repeat formation. Morpholinos against N-terminal zebrafish Ahi1 , orthologous to where human mutations cluster, produced a ciliopathy, but targeting near human p.Arg1066 and p.Trp1088 did not. Most AHI1 mutations in JBTS patients result in truncated protein lacking WD40-repeats and the SH3 domain; disease was hitherto attributed to loss of these protein interaction modules. Our findings indicate that normal development does not require the C-terminal SH3 domain. This has far-reaching implications, considering that variants like p.Glu984* identified by preconception screening (‘Kingsmore panel’) do not necessarily indicate JBTS carriership. Genomes of individuals with consanguineous background are enriched for homozygous variants that may unmask dispensable regions of disease genes and unrecognized false positives in diagnostic large-scale sequencing and preconception carrier screening.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database ( http://genestation.org ) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Are rotating planes of satellite galaxies ubiquitous? (2015)
    Oxford University Press
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    Publication Date: 2015-09-13
    Description: We compare the dynamics of satellite galaxies in the Sloan Digital Sky Survey to simple models in order to test the hypothesis that a large fraction of satellites corotate in coherent planes. We confirm the previously reported excess of corotating satellite pairs located near diametric opposition with respect to their host, but show that this signal is unlikely to be due to rotating discs (or planes) of satellites. In particular, no overabundance of corotating satellites pairs is observed within ~20°–50° of direct opposition, as would be expected for planar distributions inclined relative to the line of sight. Instead, the excess corotation for satellite pairs within ~10° of opposition is consistent with random noise associated with undersampling of an underlying isotropic velocity distribution. Based upon the observed dynamics of the luminous satellite population, we conclude that at most 10 per cent of isolated hosts harbour corotating satellite planes (as traced by bright satellites).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Are rotating planes of satellite galaxies ubiquitous? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-27
    Description: We compare the dynamics of satellite galaxies in the Sloan Digital Sky Survey to simple models in order to test the hypothesis that a large fraction of satellites corotate in coherent planes. We confirm the previously reported excess of corotating satellite pairs located near diametric opposition with respect to their host, but show that this signal is unlikely to be due to rotating discs (or planes) of satellites. In particular, no overabundance of corotating satellites pairs is observed within ~20°–50° of direct opposition, as would be expected for planar distributions inclined relative to the line of sight. Instead, the excess corotation for satellite pairs within ~10° of opposition is consistent with random noise associated with undersampling of an underlying isotropic velocity distribution. Based upon the observed dynamics of the luminous satellite population, we conclude that at most 10 per cent of isolated hosts harbour corotating satellite planes (as traced by bright satellites).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Not so sexy in the city: urban birds adjust songs to noise but compromise vocal performance (2016)
    Oxford University Press
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    Publication Date: 2016-01-20
    Description: Anthropogenic noise affects the behavior of a variety of animal taxa around the world. In many taxa, minimum frequencies of acoustic signals increase with ambient noise levels, and males and females respond less strongly to these adjusted signals. Lower response may be due to higher minimum frequencies or to the associated decrease in frequency bandwidth. There is a performance challenge to producing notes rapidly at a wide bandwidth, and any reduction in bandwidth necessarily reduces the performance value. This measure of vocal performance is a trait under sexual selection in many taxa. We investigated the relationship between anthropogenic noise amplitude and male white-crowned sparrow vocal performance in San Francisco, CA. Males on louder territories produced songs at higher minimum frequencies but also with reduced bandwidth and lower vocal performance. These results suggest that behavioral adjustments to anthropogenic noise reduce vocal performance of songs. We conducted playback experiments to test if lower responses to urban songs are due to higher minimum frequencies or to narrower bandwidths. Males responded more strongly to normal than to reduced bandwidth songs, but equally to high- and low-pass filtered songs. Our results therefore suggest that reduced bandwidth and performance—not higher minimum frequency—could be the reason that urban birds are less responsive to songs adjusted for anthropogenic noise. Ultimately, the lower vocal performance of birds on territories with high levels of anthropogenic noise could result in fewer mating opportunities and more challenges in defending their territory.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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