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  • 1
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    Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations (2015)
    Oxford University Press
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    Publication Date: 2015-06-23
    Description: Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype–phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C〉T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.
    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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    The response of a helium white dwarf to an exploding Type Ia supernova (2015)
    Oxford University Press
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    Publication Date: 2015-03-22
    Description: We conduct numerical simulations of the interacting ejecta from an exploding CO white dwarf (WD) with a He WD donor in the double-detonation scenario for Type Ia supernovae (SNe Ia), and study the possibility of exploding the companion WD. We also study the long time imprint of the collision on the supernova remnant. When the donor He WD has a low mass, M WD  = 0.2 M , it is at a distance of ~0.08 R from the explosion, and helium is not ignited. The low-mass He WD casts an ‘ejecta shadow’ behind it. By evolving the ejecta for longer times, we find that the outer parts of the shadowed side are fainter and its boundary with the ambient gas is somewhat flat. More massive He WD donors, M WD ~= 0.4 M , must be closer to the CO WD to transfer mass. At a distance of a 0.045 R helium is detonated and the He WD explodes, leading to a triple detonation scenario. In the explosion of the donor WD approximately 0.15 M of unburned helium is ejected. This might be observed as a peculiar Type Ib supernova.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Constraining the double-degenerate scenario for Type Ia supernovae from merger ejected matter (2015)
    Oxford University Press
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    Publication Date: 2015-01-14
    Description: We follow the mass expelled during the WD–WD merger process in a particular case of the double-degenerate (DD) scenario for Type Ia supernovae (SNe Ia), and find that the interaction of the SN ejecta with the resulting wind affects the early (first day) light-curve in a way that may be in conflict with some SN Ia observations, if the detonation occurs shortly after the merger, i.e. (10 3 s t exp 1 d). The main source of the expelled mass is a disc-wind, or jets that are launched by the accretion disc around the more massive white dwarf (WD) during the viscous phase of the merger. This disc-originated matter will be shocked and heated by the SN ejecta from an explosion, leading to additional radiation in the early light-curve. This enhanced early radiation could then be interpreted as an explosion originating from a progenitor having an inferred radius of one solar radius or more, in conflict with observations of SN 2011fe.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Assessing the quality of restored images in optical long-baseline interferometry (2016)
    Oxford University Press
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    Publication Date: 2016-12-24
    Description: Assessing the quality of aperture synthesis maps is relevant for benchmarking image reconstruction algorithms, for the scientific exploitation of data from optical long-baseline interferometers, and for the design/upgrade of new/existing interferometric imaging facilities. Although metrics have been proposed in these contexts, no systematic study has been conducted on the selection of a robust metric for quality assessment. This article addresses the question: what is the best metric to assess the quality of a reconstructed image? It starts by considering several metrics and selecting a few based on general properties. Then, a variety of image reconstruction cases are considered. The observational scenarios are phase closure and phase referencing at the Very Large Telescope Interferometer (VLTI), for a combination of two, three, four and six telescopes. End-to-end image reconstruction is accomplished with the M i RA software, and several merit functions are put to test. It is found that convolution by an effective point spread function is required for proper image quality assessment. The effective angular resolution of the images is superior to naive expectation based on the maximum frequency sampled by the array. This is due to the prior information used in the aperture synthesis algorithm and to the nature of the objects considered. The 1 -norm is the most robust of all considered metrics, because being linear it is less sensitive to image smoothing by high regularization levels. For the cases considered, this metric allows the implementation of automatic quality assessment of reconstructed images, with a performance similar to human selection.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Diel variability in the elemental composition of the marine cyanobacterium Synechococcus (2016)
    Oxford University Press
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    Publication Date: 2016-08-20
    Description: The ratio of elements such as carbon:nitrogen:phosphorus (C:N:P) in phytoplankton is known to vary substantially within single isolates and across environmental gradients. In addition, C:N:P is known to vary throughout the day due to diel patterns in nutrient acquisition and storage. It has been hypothesized that small phytoplankton such as marine cyanobacteria have relatively invariable elemental ratios during a 24 h period, whereas larger phytoplankton have a greater capacity to store elements and thus a wider diel range of C:N:P. To test this hypothesis, we examined diel variability in cellular C:N:P, using a chemostat culturing system, for one of the most abundant marine cyanobacteria, Synechococcus (WH8102) during two 24 h periods. The cellular C quota nearly doubled during the 14 h light period and was subsequently reduced during the dark period. The cellular N quota also varied considerably, whereas the P quota remained relatively stable. These daily changes in elemental quotas led to highly variable C : N cell and C : P cell . Furthermore, the magnitude of variability in cellular elemental stoichiometry of Synechococcus was positively related to the growth rate. We constructed a model to test the extent to which variation in C : N cell and C : P cell is related to reserve carbon accumulation and depletion over each light–dark cycle. Results imply that, in addition to growth-related respiratory losses, Synechococcus also purges excess C during the dark period in order to maintain a nutritive balance within cells. Our data suggest that diel variation in C : N cell and C : P cell of Synechococcus is of the same order of magnitude as stoichiometric variation within plankton communities between major ocean environments.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Evolution of Gene Expression after Gene Amplification (2015)
    Oxford University Press
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    Publication Date: 2015-05-18
    Description: We took a rather unique approach to investigate the conservation of gene expression of prolamin storage protein genes across two different subfamilies of the Poaceae. We took advantage of oat plants carrying single maize chromosomes in different cultivars, called oat–maize addition (OMA) lines, which permitted us to determine whether regulation of gene expression was conserved between the two species. We found that -zeins are expressed in OMA7.06, which carries maize chromosome 7 even in the absence of the trans-acting maize prolamin-box-binding factor (PBF), which regulates their expression. This is likely because oat PBF can substitute for the function of maize PBF as shown in our transient expression data, using a -zein promoter fused to green fluorescent protein (GFP). Despite this conservation, the younger, recently amplified prolamin genes in maize, absent in oat, are not expressed in the corresponding OMAs. However, maize can express the oldest prolamin gene, the wheat high-molecular weight glutenin Dx5 gene, even when maize Pbf is knocked down (through PbfRNAi ), and/or another maize transcription factor, Opaque-2 (O2) is knocked out (in maize o2 mutant). Therefore, older genes are conserved in their regulation, whereas younger ones diverged during evolution and eventually acquired a new repertoire of suitable transcriptional activators.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Evolution of Gene Expression after Gene Amplification (2015)
    Oxford University Press
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    Publication Date: 2015-04-24
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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