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  • 1
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    The superluminous supernova PS1-11ap: bridging the gap between low and high redshift (2013)
    Oxford University Press
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    Publikationsdatum: 2013-12-06
    Beschreibung: We present optical photometric and spectroscopic coverage of the superluminous supernova (SLSN) PS1-11ap, discovered with the Pan-STARRS1 Medium Deep Survey at z  = 0.524. This intrinsically blue transient rose slowly to reach a peak magnitude of M u  = –21.4 mag and bolometric luminosity of 8 10 43 erg s –1 before settling on to a relatively shallow gradient of decline. The observed decline is significantly slower than those of the SLSNe-Ic which have been the focus of much recent attention. Spectroscopic similarities with the lower redshift SN2007bi and a decline rate similar to 56 Co decay time-scale initially indicated that this transient could be a candidate for a pair instability supernova (PISN) explosion. Overall the transient appears quite similar to SN2007bi and the lower redshift object PTF12dam. The extensive data set, from 30 d before peak to 230 d after, allows a detailed and quantitative comparison with published models of PISN explosions. We find that the PS1-11ap data do not match these model explosion parameters well, supporting the recent claim that these SNe are not pair instability explosions. We show that PS1-11ap has many features in common with the faster declining SLSNe-Ic, and the light-curve evolution can also be quantitatively explained by the magnetar spin-down model. At a redshift of z  = 0.524, the observer-frame optical coverage provides comprehensive rest-frame UV data and allows us to compare it with the SLSNe recently found at high redshifts between z  = 2 and 4. While these high- z explosions are still plausible PISN candidates, they match the photometric evolution of PS1-11ap and hence could be counterparts to this lower redshift transient.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
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  • 2
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    Fast and accurate imputation of summary statistics enhances evidence of functional enrichment (2014)
    Oxford University Press
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    Publikationsdatum: 2014-10-04
    Beschreibung: Motivation: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. Results: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (〉5%) and low-frequency (1–5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case–control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of $${\chi }^{2}$$ association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses. Availability and implementation: Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/ . Contact: bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu Supplementary information: Supplementary materials are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
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  • 3
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    Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum (2014)
    Springer Nature
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    Publikationsdatum: 2014-11-27
    Beschreibung: Article Novel antimalarial drugs are urgently needed to combat parasite drug resistance. Here, Vaidya et al . describe a new chemical class of potent antimalarial compounds that act by disrupting the parasite's sodium homeostasis. Nature Communications doi: 10.1038/ncomms6521 Authors: Akhil B. Vaidya, Joanne M. Morrisey, Zhongsheng Zhang, Sudipta Das, Thomas M. Daly, Thomas D. Otto, Natalie J. Spillman, Matthew Wyvratt, Peter Siegl, Jutta Marfurt, Grennady Wirjanata, Boni F. Sebayang, Ric N. Price, Arnab Chatterjee, Advait Nagle, Marcin Stasiak, Susan A. Charman, Iñigo Angulo-Barturen, Santiago Ferrer, María Belén Jiménez-Díaz, María Santos Martínez, Francisco Javier Gamo, Vicky M. Avery, Andrea Ruecker, Michael Delves, Kiaran Kirk, Matthew Berriman, Sandhya Kortagere, Jeremy Burrows, Erkang Fan, Lawrence W. Bergman
    Digitale ISSN: 2041-1723
    Thema: Biologie , Chemie und Pharmazie , Allgemeine Naturwissenschaft , Physik
    Publiziert von Springer Nature
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  • 4
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    De novo cardiomyocytes from within the activated adult heart after injury (2011)
    Nature Publishing Group (NPG)
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    Publikationsdatum: 2011-06-10
    Beschreibung: A significant bottleneck in cardiovascular regenerative medicine is the identification of a viable source of stem/progenitor cells that could contribute new muscle after ischaemic heart disease and acute myocardial infarction. A therapeutic ideal--relative to cell transplantation--would be to stimulate a resident source, thus avoiding the caveats of limited graft survival, restricted homing to the site of injury and host immune rejection. Here we demonstrate in mice that the adult heart contains a resident stem or progenitor cell population, which has the potential to contribute bona fide terminally differentiated cardiomyocytes after myocardial infarction. We reveal a novel genetic label of the activated adult progenitors via re-expression of a key embryonic epicardial gene, Wilm's tumour 1 (Wt1), through priming by thymosin beta4, a peptide previously shown to restore vascular potential to adult epicardium-derived progenitor cells with injury. Cumulative evidence indicates an epicardial origin of the progenitor population, and embryonic reprogramming results in the mobilization of this population and concomitant differentiation to give rise to de novo cardiomyocytes. Cell transplantation confirmed a progenitor source and chromosome painting of labelled donor cells revealed transdifferentiation to a myocyte fate in the absence of cell fusion. Derived cardiomyocytes are shown here to structurally and functionally integrate with resident muscle; as such, stimulation of this adult progenitor pool represents a significant step towards resident-cell-based therapy in human ischaemic heart disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696525/" 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/PMC3696525/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smart, Nicola -- Bollini, Sveva -- Dube, Karina N -- Vieira, Joaquim M -- Zhou, Bin -- Davidson, Sean -- Yellon, Derek -- Riegler, Johannes -- Price, Anthony N -- Lythgoe, Mark F -- Pu, William T -- Riley, Paul R -- FS/08/004/23625/British Heart Foundation/United Kingdom -- G0700933/Medical Research Council/United Kingdom -- PG/10/005/28175/British Heart Foundation/United Kingdom -- RG/08/003/25264/British Heart Foundation/United Kingdom -- U01 HL100401/HL/NHLBI NIH HHS/ -- British Heart Foundation/United Kingdom -- England -- Nature. 2011 Jun 8;474(7353):640-4. doi: 10.1038/nature10188.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Medicine Unit, UCL Institute of Child Health, London WC1N 1EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21654746" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adult Stem Cells/*cytology ; Animals ; *Cell Differentiation ; Cellular Reprogramming ; Gene Expression Regulation ; *Heart Injuries ; Mice ; Myocardial Infarction/pathology ; Myocytes, Cardiac/*cytology/metabolism ; Thymosin/metabolism ; WT1 Proteins/genetics/metabolism
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von Nature Publishing Group (NPG)
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  • 5
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    Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc (2013)
    Oxford University Press
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    Publikationsdatum: 2013-07-12
    Beschreibung: The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea . The "stolen" plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.
    Print ISSN: 0737-4038
    Digitale ISSN: 1537-1719
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 6
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    X-ray selected galaxy clusters in the Pan-STARRS Medium Deep Survey (2013)
    Oxford University Press
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    Publikationsdatum: 2013-05-21
    Beschreibung: We present the results of a pilot study for the extended Massive Cluster Survey (eMACS), a comprehensive search for distant, X-ray luminous galaxy clusters at z 〉 0.5. Our pilot study applies the eMACS concept to the 71 deg 2 area extended by the 10 fields of the Pan-STARRS1 (PS1) Medium Deep Survey (MDS). Candidate clusters are identified by visual inspection of PS1 images in the g , r , i and z bands in a 5  x 5 arcmin 2 region around X-ray sources detected in the ROSAT All-Sky Survey (RASS). To test and optimize the eMACS X-ray selection criteria, our pilot study uses the largest possible RASS data base, i.e. all RASS sources listed in the Bright and Faint Source Catalogues (BSC and FSC) that fall within the MDS footprint. We apply no additional constraints regarding X-ray flux, spectral hardness ratio or photon statistics and lower the redshift threshold to z 〉 0.3 to extend the probed luminosity range to poorer systems. Scrutiny of PS1/MDS images for 41 BSC and 200 FSC sources combined with dedicated spectroscopic follow-up observations results in a sample of 11 clusters with estimated or spectroscopic redshifts of z 〉 0.3. In order to assess and quantify the degree of point source contamination of the observed RASS fluxes, we examine archival Chandra data obtained in targeted and serendipitous observations of six of the 11 clusters found. As expected, the diffuse emission from all six systems is contaminated by point sources to some degree, and for half of them active galactic nucleus emission dominates. X-ray follow-up observations will thus be crucial in order to establish robust cluster luminosities for eMACS clusters. Although the small number of distant X-ray luminous clusters in the MDS does not allow us to make firm predictions for the over 20 000 deg 2 of extragalactic sky covered by eMACS, the identification of two extremely promising eMACS cluster candidates at z 0.6 (both yet to be observed with Chandra ) in such a small solid angle is encouraging. Representing a tremendous gain over the presently known two dozen such systems from X-ray, optical and Sunyaev–Zel’dovich cluster surveys combined, the sample of over 100 extremely massive clusters at z 〉 0.5 expected from eMACS would be invaluable for the identification of the most powerful gravitational lenses in the Universe, as well as for in-depth and statistical studies of the physical properties of the most massive galaxy clusters out to z  ~ 1.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
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  • 7
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    Thymosin β4-sulfoxide attenuates inflammatory cell infiltration and promotes cardiac wound healing (2013)
    Springer Nature
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    Publikationsdatum: 2013-07-04
    Beschreibung: Article Hydrogen peroxide attracts immune cells and induces wound inflammation. Evans et al . show that hydrogen peroxide also leads to the production of thymosin β4–sulfoxide in zebrafish wounds and in mouse hearts after myocardial infarction, where it acts as an anti-inflammatory factor that promotes wound healing. Nature Communications doi: 10.1038/ncomms3081 Authors: Mark A. Evans, Nicola Smart, Karina N. Dubé, Sveva Bollini, James E. Clark, Hayley G. Evans, Leonie S. Taams, Rebecca Richardson, Mathieu Lévesque, Paul Martin, Kevin Mills, Johannes Riegler, Anthony N. Price, Mark F. Lythgoe, Paul R. Riley
    Digitale ISSN: 2041-1723
    Thema: Biologie , Chemie und Pharmazie , Allgemeine Naturwissenschaft , Physik
    Publiziert von Springer Nature
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  • 8
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    Functional and phylogenetic community assembly linked to changes in species diversity in a long-term resource manipulation experiment (2013)
    Wiley
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    Publikationsdatum: 2013-09-01
    Beschreibung: Question There are contrasting opinions about how communities assemble along a productivity gradient, particularly in relation to competitive interactions. One view is that functionally similar, and closely related species, are less likely to co-exist (limiting similarity). Alternatively, competitive exclusion may act on dissimilar species because species bearing traits associated with low competitive ability are excluded (weaker competitor exclusion). We ask if patterns of functional and phylogenetic diversity are related to changes in species diversity in response to fertility manipulations. Location Species-rich mesophytic grassland in Estonia. Methods The grassland has been manipulated from 2002 to 2011 to increase (fertilizer addition) and decrease productivity (sucrose addition) in small-scale (50 cm × 50 cm) plots. We linked annual increases and decreases in species diversity to changes in functional and phylogenetic diversity. We used abundance-weighted mean pair-wise functional or phylogenetic distance of all possible species pairs. Results We found convergence in four traits (plant height, leaf distribution, lateral spread, type of reproduction) and a decrease in mean functional and phylogenetic diversity, in support of weaker competitor exclusion or habitat filtering. There was less support for limiting similarity, with divergence found for two traits associated with decreasing species diversity (leaf distribution in the sucrose treatment and lateral spread in the fertilizer treatment). Conclusions Our results support the view that competition can lead to the exclusion of weaker competitors, rather than increasing functional and phylogenetic diversity, as expected from the principle of limiting similarity. However, multiple assembly processes, which are generally seen as mutually exclusive, are operating simultaneously, albeit on different traits and at different stages of community assembly. We used a long-term resource manipulation experiment to determine patterns of trait diversity and phylogenetic relatedness in relation to changes in species diversity to test the idea that competitive exclusion acts on the most similar coexisting species. We found mostly a reduction in functional and phylogenetic diversity associated with species loss indicating that species more dissimilar are excluded particularly following fertilization.
    Print ISSN: 1100-9233
    Digitale ISSN: 1654-1103
    Thema: Biologie
    Publiziert von Wiley im Namen von The International Association for Vegetation Science (IAVS).
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  • 9
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    Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates (2013)
    Springer Nature
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    Publikationsdatum: 2013-06-19
    Beschreibung: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.30 Authors: Jeffrey M Skerker, Dacia Leon, Morgan N Price, Jordan S Mar, Daniel R Tarjan, Kelly M Wetmore, Adam M Deutschbauer, Jason K Baumohl, Stefan Bauer, Ana B Ibáñez, Valerie D Mitchell, Cindy H Wu, Ping Hu, Terry Hazen & Adam P Arkin
    Digitale ISSN: 1744-4292
    Thema: Biologie
    Publiziert von Springer Nature im Namen von The European Molecular Biology Organization (EMBO).
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  • 10
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    Indirect and suboptimal control of gene expression is widespread in bacteria (2013)
    Springer Nature
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    Publikationsdatum: 2013-04-17
    Beschreibung: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.16 Authors: Morgan N Price, Adam M Deutschbauer, Jeffrey M Skerker, Kelly M Wetmore, Troy Ruths, Jordan S Mar, Jennifer V Kuehl, Wenjun Shao & Adam P Arkin
    Schlagwort(e): bacterial evolutiongene regulationoptimal regulation
    Digitale ISSN: 1744-4292
    Thema: Biologie
    Publiziert von Springer Nature im Namen von The European Molecular Biology Organization (EMBO).
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