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  • 1
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    Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-16
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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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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  • 3
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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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  • 4
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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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  • 5
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    Are rotating planes of satellite galaxies ubiquitous? (2015)
    Oxford University Press
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    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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  • 6
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    Small rare recurrent deletions and reciprocal duplications in 2q21.1, including brain-specific ARHGEF4 and GPR148 (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-10
    Description: We have identified a rare small (~450 kb unique sequence) recurrent deletion in a previously linked attention-deficit hyperactivity disorder (ADHD) locus at 2q21.1 in five unrelated families with developmental delay (DD)/intellectual disability (ID), ADHD, epilepsy and other neurobehavioral abnormalities from 17 035 samples referred for clinical chromosomal microarray analysis. Additionally, a DECIPHER ( http://decipher.sanger.ac.uk ) patient 2311 was found to have the same deletion and presented with aggressive behavior. The deletion was not found in either six control groups consisting of 13 999 healthy individuals or in the DGV database. We have also identified reciprocal duplications in five unrelated families with autism, developmental delay (DD), seizures and ADHD. This genomic region is flanked by large, complex low-copy repeats (LCRs) with directly oriented subunits of ~109 kb in size that have 97.7% DNA sequence identity. We sequenced the deletion breakpoints within the directly oriented paralogous subunits of the flanking LCR clusters, demonstrating non-allelic homologous recombination as a mechanism of formation. The rearranged segment harbors five genes: GPR148, FAM123C, ARHGEF4 , FAM168B and PLEKHB2 . Expression of ARHGEF4 (Rho guanine nucleotide exchange factor 4) is restricted to the brain and may regulate the actin cytoskeletal network, cell morphology and migration, and neuronal function. GPR148 encodes a G-protein-coupled receptor protein expressed in the brain and testes. We suggest that small rare recurrent deletion of 2q21.1 is pathogenic for DD/ID, ADHD, epilepsy and other neurobehavioral abnormalities and, because of its small size, low frequency and more severe phenotype might have been missed in other previous genome-wide screening studies using single-nucleotide polymorphism analyses.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: Pyrrole–imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by autophosphorylation of ATR, the S-phase checkpoint kinase, and by recruitment of ATR and the ATR activators RPA, 9-1-1, and Rad17 to chromatin. Surprisingly, ATR activation was accompanied by only a slight increase in single-stranded DNA, and the ATR targets RPA2 and Chk1, a cell cycle checkpoint kinase, were not phosphorylated. However, ATR activation resulted in phosphorylation of the replicative helicase subunit MCM2, an ATR effector. Polyamide treatment also induced accumulation of monoubiquitinated FANCD2, which is recruited to stalled replication forks and interacts transiently with phospho-MCM2. This suggests that polyamides induce replication stress that ATR can counteract independently of Chk1 and that the FA/BRCA pathway may also be involved in the response to polyamides. In biochemical assays, polyamides inhibit DNA helicases, providing a plausible mechanism for S-phase inhibition.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The mass dependence of satellite quenching in Milky Way-like haloes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-20
    Description: Using the Sloan Digital Sky Survey, we examine the quenching of satellite galaxies around isolated Milky Way-like hosts in the local Universe. We find that the efficiency of satellite quenching around isolated galaxies is low and roughly constant over two orders of magnitude in satellite stellar mass ( M *  = 10 8.5 –10 10.5 M ), with only ~20 per cent of systems quenched as a result of environmental processes. While largely independent of satellite stellar mass, satellite quenching does exhibit clear dependence on the properties of the host. We show that satellites of passive hosts are substantially more likely to be quenched than those of star-forming hosts, and we present evidence that more massive haloes quench their satellites more efficiently. These results extend trends seen previously in more massive host haloes and for higher satellite masses. Taken together, it appears that galaxies with stellar masses larger than about 10 8 M are uniformly resistant to environmental quenching, with the relative harshness of the host environment likely serving as the primary driver of satellite quenching. At lower stellar masses (〈10 8 M ), however, observations of the Local Group suggest that the vast majority of satellite galaxies are quenched, potentially pointing towards a characteristic satellite mass scale below which quenching efficiency increases dramatically.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Spectral decompositions and nonnormality of boundary integral operators in acoustic scattering (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-09
    Description: Understanding the spectral properties of boundary integral operators in acoustic scattering has important practical implications, such as for the analysis of the stability of boundary element discretizations or the convergence of iterative solvers as the wave number k grows. Yet, little is known about spectral decompositions of the standard boundary integral operators in acoustic scattering. Theoretical results are mainly available on the unit circle, where these operators diagonalize in a simple Fourier basis. In this paper we investigate spectral decompositions for more general smooth domains. Based on the decomposition of the acoustic Green's function in elliptic coordinates, we give spectral decompositions on ellipses. For general smooth domains we show that approximate spectral decompositions can be given in terms of circle Fourier modes transplanted onto the boundary of the domain. An important underlying question is whether the operators are normal. Based on previous numerical investigations it appears that the standard boundary integral operators are normal only when the domain is a ball and here we prove that this is indeed the case for the acoustic single layer potential. We show that the acoustic single, double and conjugate double layer potential are normal in a scaled inner product on the ellipse. On more general smooth domains the operators can be split into a normal component plus a smooth perturbation. Numerical computations of pseudospectra are presented to demonstrate the nonnormal behaviour on general domains.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press
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  • 10
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    The mass dependence of satellite quenching in Milky Way-like haloes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-29
    Description: Using the Sloan Digital Sky Survey, we examine the quenching of satellite galaxies around isolated Milky Way-like hosts in the local Universe. We find that the efficiency of satellite quenching around isolated galaxies is low and roughly constant over two orders of magnitude in satellite stellar mass ( M *  = 10 8.5 –10 10.5 M ), with only ~20 per cent of systems quenched as a result of environmental processes. While largely independent of satellite stellar mass, satellite quenching does exhibit clear dependence on the properties of the host. We show that satellites of passive hosts are substantially more likely to be quenched than those of star-forming hosts, and we present evidence that more massive haloes quench their satellites more efficiently. These results extend trends seen previously in more massive host haloes and for higher satellite masses. Taken together, it appears that galaxies with stellar masses larger than about 10 8 M are uniformly resistant to environmental quenching, with the relative harshness of the host environment likely serving as the primary driver of satellite quenching. At lower stellar masses (〈10 8 M ), however, observations of the Local Group suggest that the vast majority of satellite galaxies are quenched, potentially pointing towards a characteristic satellite mass scale below which quenching efficiency increases dramatically.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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