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  • American Association for the Advancement of Science  (678)
  • Oxford University Press  (81)
  • 1
    Publication Date: 1951-08-24
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    American Association for the Advancement of Science
    Publication Date: 2020-07-09
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-08-03
    Description: Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ~500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by 13 C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH , ANT , ER , AS1 , AS2 , PHB , CLV1 , ERL1–3 and TMM , were down-regulated in Ita but not in Sp2 in response to drought.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 4
    Publication Date: 2013-04-02
    Description: Zinc-finger recombinases (ZFRs) represent a potentially powerful class of tools for targeted genetic engineering. These chimeric enzymes are composed of an activated catalytic domain derived from the resolvase/invertase family of serine recombinases and a custom-designed zinc-finger DNA-binding domain. The use of ZFRs, however, has been restricted by sequence requirements imposed by the recombinase catalytic domain. Here, we combine substrate specificity analysis and directed evolution to develop a diverse collection of Gin recombinase catalytic domains capable of recognizing an estimated 3.77 x 10 7 unique DNA sequences. We show that ZFRs assembled from these engineered catalytic domains recombine user-defined DNA targets with high specificity, and that designed ZFRs integrate DNA into targeted endogenous loci in human cells. This study demonstrates the feasibility of generating customized ZFRs and the potential of ZFR technology for a diverse range of applications, including genome engineering, synthetic biology and gene therapy.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2015-04-10
    Description: Past calibrations of statistical distance scales for planetary nebulae have been problematic, especially with regard to ‘short’ versus ‘long’ scales. Reconsidering the calibration process naturally involves examining the precision and especially the systematic errors of various distance methods. Here, we present a different calibration strategy, new for planetaries, that is anchored by precise trigonometric parallaxes for 16 central stars published by Harris et al. of USNO, with four improved by Benedict et al. using the Hubble Space Telescope . We show how an internally consistent system of distances might be constructed by testing other methods against those and each other. In such a way, systematic errors can be minimized. Several of the older statistical scales have systematic errors that can account for the short–long dichotomy. In addition to scale-factor errors, all show signs of radius dependence, i.e. the distance ratio [scale/true] is some function of nebular radius. These systematic errors were introduced by choices of data sets for calibration, by the methodologies used, and by assumptions made about nebular evolution. The statistical scale of Frew and collaborators is largely free of these errors, although there may be a radius dependence for the largest objects. One set of spectroscopic parallaxes was found to be consistent with the trigonometric ones while another set underestimates distance consistently by a factor of 2, probably because of a calibration difference. ‘Gravity’ distances seem to be overestimated for nearby objects but may be underestimated for distant objects, i.e. distance dependent. Angular expansion distances appear to be suitable for calibration after correction for astrophysical effects. We find extinction distances to be often unreliable individually though sometimes approximately correct overall (total sample). Comparison of the Hipparcos parallaxes for large planetaries with our ‘best estimate’ distances confirms that those parallaxes are overestimated by a factor 2.5, as suggested by Harris et al.'s result for PHL 932. Assuming the problem arises from the presence of nebulosity, we suggest a possible connection with the much smaller overestimation recently shown for the Hipparcos Pleiades parallaxes by Melis et al.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2016-06-15
    Description: Advances in single-cell and mini-metagenome sequencing have enabled important investigations into uncultured bacteria. In this study, we applied the mini-metagenome sequencing method to assemble genome drafts of the uncultured causative agents of epitheliocystis, an emerging infectious disease in the Mediterranean aquaculture species gilthead seabream. We sequenced multiple cyst samples and constructed 11 genome drafts from a novel beta-proteobacterial lineage, Candidatus Ichthyocystis. The draft genomes demonstrate features typical of pathogenic bacteria with an obligate intracellular lifestyle: a reduced genome of up to 2.6 Mb, reduced G + C content, and reduced metabolic capacity. Reconstruction of metabolic pathways reveals that Ca . Ichthyocystis genomes lack all amino acid synthesis pathways, compelling them to scavenge from the fish host. All genomes encode type II, III, and IV secretion systems, a large repertoire of predicted effectors, and a type IV pilus. These are all considered to be virulence factors, required for adherence, invasion, and host manipulation. However, no evidence of lipopolysaccharide synthesis could be found. Beyond the core functions shared within the genus, alignments showed distinction into different species, characterized by alternative large gene families. These comprise up to a third of each genome, appear to have arisen through duplication and diversification, encode many effector proteins, and are seemingly critical for virulence. Thus, Ca . Ichthyocystis represents a novel obligatory intracellular pathogenic beta-proteobacterial lineage. The methods used: mini-metagenome analysis and manual annotation, have generated important insights into the lifestyle and evolution of the novel, uncultured pathogens, elucidating many putative virulence factors including an unprecedented array of novel gene families.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 7
    Publication Date: 2015-10-02
    Description: We present Spitzer /Infrared Spectrograph (IRS) 5–21 μm spectroscopic maps towards 12 regions in the Andromeda galaxy (M31). These regions include the nucleus, bulge, an active region in the star-forming ring and nine other regions chosen to cover a range of mid-to-far-infrared colours. In line with previous results, polycyclic aromatic hydrocarbon (PAH) feature ratios (6.2 and 7.7 μm features compared to the 11.2 μm feature) measured from our extracted M31 spectra, except the nucleus, strongly correlate. The equivalent widths of the main PAH features, as a function of metallicity and radiation hardness, are consistent with those observed for other nearby spiral and starburst galaxies. Reprocessed data from the ISOCAM instrument on the Infrared Space Observatory agree with the IRS data; early reports of suppressed 6–8 μm features and enhanced 11.3 μm feature intensity and full width at half-maximum apparently resulted from background-subtraction problems. The nucleus does not show any PAH emission but does show strong silicate emission at 9.7 μm. Furthermore, different spectral features (11.3 μm PAH emission, silicate emission and [Ne  iii ] 15.5 μm line emission) have distinct spatial distributions in the nuclear region: the silicate emission is strongest towards the stellar nucleus, while the PAH emission peaks 15 arcsec north of the nucleus. The PAH feature ratios at this position are atypical with strong emission at 11.2 and 15–20 μm but weak emission at 6–8 μm. The nucleus itself is dominated by stellar light giving rise to a strong blue continuum and silicate emission.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2013-12-07
    Description: Changes in cell-surface glycan patterns are markers of the presence of many different disease and cancer types, offering a relatively untapped niche for glycan-targeting reagents and therapeutics in diagnosis and treatment. Of paramount importance for the success of any glycan-targeting reagent is the ability to specifically recognize the target among the plethora of different glycans that exist in the human body. The preeminent technique for defining specificity is glycan array screening, in which a glycan-binding protein (GBP) can be simultaneously screened against multiple glycans. Glycan array screening has provided unparalleled insight into GBP specificity, but data interpretation suffers from difficulties in identifying false-negative binding arising from altered glycan presentation, associated with the linker used to conjugate the glycan to the surface. In this work, we model the structure and dynamics of the linkers employed in the glycan arrays developed by the Consortium for Functional Glycomics. The modeling takes into account the physical presence and surface polarity of the array, and provides a structure-based rationalization of false-negative results arising from the so-called "linker effect." The results also serve as a guide for interpreting glycan array screening data in a biological context; in particular, we show that attempts to employ natural amino acids as linkers may be prone to unexpected artifacts compromising glycan recognition.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 9
    Publication Date: 2014-10-16
    Description: The total infrared (IR) luminosity is very useful for estimating the star formation rate (SFR) of galaxies, but converting the IR luminosity into an SFR relies on assumptions that do not hold for all galaxies. We test the effectiveness of the IR luminosity as an SFR indicator by applying it to synthetic spectral energy distributions generated from three-dimensional hydrodynamical simulations of isolated disc galaxies and galaxy mergers. In general, the SFR inferred from the IR luminosity agrees well with the true instantaneous SFR of the simulated galaxies. However, for the major mergers in which a strong starburst is induced, the SFR inferred from the IR luminosity can overestimate the instantaneous SFR during the post-starburst phase by greater than two orders of magnitude. Even though the instantaneous SFR decreases rapidly after the starburst, the stars that were formed in the starburst can remain dust-obscured and thus produce significant IR luminosity. Consequently, use of the IR luminosity as an SFR indicator may cause one to conclude that post-starburst galaxies are still star forming, whereas in reality, star formation was recently quenched.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 10
    Publication Date: 2012-05-23
    Description: Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To clarify these issues we established genome-wide STAT5 binding upon growth hormone (GH) stimulation of wild-type (WT) mouse embryonic fibroblasts (MEFs) and MEFs overexpressing STAT5A more than 20-fold. Upon GH stimulation, 23 827 and 111 939 STAT5A binding sites were detected in WT and STAT5A overexpressing MEFs, respectively. 13 278 and 71 561 peaks contained at least one GAS motif. 1586 and 8613 binding sites were located within 2.5 kb of promoter sequences, respectively. Stringent filtering revealed 78 genes in which the promoter/upstream region (–10 kb to +0.5 kb) was recognized by STAT5 both in WT and STAT5 overexpressing MEFs and 347 genes that bound STAT5 only in overexpressing cells. Genome-wide expression analyses identified that the majority of STAT5-bound genes was not under GH control. Up to 40% of STAT5-bound genes were not expressed. For the first time we demonstrate the magnitude of opportunistic genomic STAT5 binding that does not translate into transcriptional activation of neighboring genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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