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  • 1
    Publication Date: 2016-07-14
    Description: Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus , which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus , a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae . We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus . The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 2
    Publication Date: 2016-04-07
    Description: The new release AIUB-RL02 of monthly gravity models from GRACE GPS and K-Band range-rate data is based on reprocessed satellite orbits referring to the reference frame IGb08. The release is consistent with the IERS2010 conventions. Improvements with respect to its predecessor AIUB-RL01 include the use of reprocessed (RL02) GRACE observations, new atmosphere and ocean dealiasing products (RL05), an upgraded ocean tide model (EOT11A), and the interpolation of shallow ocean tides (admittances). The stochastic parametrization of AIUB-RL02 was adapted to include daily accelerometer scale factors, which drastically reduces spurious signal at the 161 d period in C 20 and at other low degree and order gravity field coefficients. Moreover, the correlation between the noise in the monthly gravity models and solar activity is considerably reduced in the new release. The signal and the noise content of the new AIUB-RL02 monthly gravity fields are studied and calibrated errors are derived from their non-secular and non-seasonal variability. The short-period time-variable signal over the oceans, mostly representing noise, is reduced by 50 per cent with respect to AIUB-RL01. Compared to the official GFZ-RL05a and CSR-RL05 monthly models, the AIUB-RL02 stands out by its low noise at high degrees, a fact emerging from the estimation of seasonal variations for selected river basins and of mass trends in polar regions. Two versions of the monthly AIUB-RL02 gravity models, with spherical harmonics resolution of degree and order 60 and 90, respectively, are available for the time period from March 2003 to March 2014 at the International Center for Global Earth Models or from ftp://ftp.unibe.ch/aiub/GRAVITY/GRACE (last accessed 22 March 2016).
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
    Publication Date: 2016-01-07
    Description: MG-RAST ( http://metagenomics.anl.gov ) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200 000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. To show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2016-06-15
    Description: In the yearly Internationally Genetically Engineered Machines (iGEM) competition, teams of Bachelor's and Master's students design and build an engineered biological system using DNA technologies. Advising an iGEM team poses unique challenges due to the inherent difficulties of mounting and completing a new biological project from scratch over the course of a single academic year; the challenges in obtaining financial and structural resources for a project that will likely not be fully realized; and conflicts between educational and competition-based goals. This article shares tips and best practices for iGEM team advisors, from two team advisors with very different experiences with the iGEM competition.
    Keywords: Professional Development
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 5
    Publication Date: 2016-06-05
    Description: Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage ( Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3'-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3'-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 6
    Publication Date: 2016-06-01
    Description: This paper continues a series in which we intend to show how all observables of galaxy clusters can be combined to recover the two-dimensional, projected gravitational potential of individual clusters. Our goal is to develop a non-parametric algorithm for joint cluster reconstruction taking all cluster observables into account. For this reason we focus on the line-of-sight projected gravitational potential, proportional to the lensing potential, in order to extend existing reconstruction algorithms. In this paper, we begin with the relation between the Compton- y parameter and the Newtonian gravitational potential, assuming hydrostatic equilibrium and a polytropic stratification of the intracluster gas. Extending our first publication we now consider a spheroidal rather than a spherical cluster symmetry. We show how a Richardson–Lucy deconvolution can be used to convert the intensity change of the CMB due to the thermal Sunyaev–Zel'dovich effect into an estimate for the two-dimensional gravitational potential. We apply our reconstruction method to a cluster based on an N -body/hydrodynamical simulation processed with the characteristics (resolution and noise) of the ALMA interferometer for which we achieve a relative error of 20 per cent for a large fraction of the virial radius. We further apply our method to an observation of the galaxy cluster RXJ1347 for which we can reconstruct the potential with a relative error of 20 per cent for the observable cluster range.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2016-09-13
    Description: We study the spherical collapse model in the presence of external gravitational tidal shear fields for different dark energy scenarios and investigate the impact on the mass function and cluster number counts. While previous studies of the influence of shear and rotation on c have been performed with heuristically motivated models, we try to avoid this model dependence and sample the external tidal shear values directly from the statistics of the underlying linearly evolved density field based on first-order Lagrangian perturbation theory. Within this self-consistent approach, in the sense that we restrict our treatment to scales where linear theory is still applicable, only fluctuations larger than the scale of the considered objects are included into the sampling process which naturally introduces a mass dependence of c . We find that shear effects are predominant for smaller objects and at lower redshifts, i. e. the effect on c is at or below the percent level for the CDM model. For dark energy models we also find small but noticeable differences, similar to CDM. The virial overdensity V is nearly unaffected by the external shear. The now mass dependent c is used to evaluate the mass function for different dark energy scenarios and afterwards to predict cluster number counts, which indicate that ignoring the shear contribution can lead to biases of the order of 1 in the estimation of cosmological parameters like m , 8 or w .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2016-09-03
    Description: Heating by short-lived radioisotopes (SLRs) such as 26 Al and 60 Fe fundamentally shaped the thermal history and interior structure of Solar system planetesimals during the early stages of planetary formation. The subsequent thermo-mechanical evolution, such as internal differentiation or rapid volatile degassing, yields important implications for the final structure, composition and evolution of terrestrial planets. SLR-driven heating in the Solar system is sensitive to the absolute abundance and homogeneity of SLRs within the protoplanetary disc present during the condensation of the first solids. In order to explain the diverse compositions found for extrasolar planets, it is important to understand the distribution of SLRs in active planet formation regions (star clusters) during their first few Myr of evolution. By constraining the range of possible effects, we show how the imprint of SLRs can be extrapolated to exoplanetary systems and derive statistical predictions for the distribution of 26 Al and 60 Fe based on N -body simulations of typical to large clusters (10 3 –10 4 stars) with a range of initial conditions. We quantify the pollution of protoplanetary discs by supernova ejecta and show that the likelihood of enrichment levels similar to or higher than the Solar system can vary considerably, depending on the cluster morphology. Furthermore, many enriched systems show an excess in radiogenic heating compared to Solar system levels, which implies that the formation and evolution of planetesimals could vary significantly depending on the birth environment of their host stars.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2016-05-27
    Description: In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012–2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia , 10% of Olea , Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus , four Ceratonia , two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.
    Print ISSN: 1567-1356
    Electronic ISSN: 1567-1364
    Topics: Biology
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  • 10
    Publication Date: 2016-02-20
    Description: Culture medium from an isolate of the fungus Aspergillus candidus was extracted, fractionated and examined to discover compounds antagonistic to plant-parasitic nematodes that are important pathogens of agricultural crops. Column, thin layer and preparative chromatographies and spectral and elemental analyses, were used to isolate and identify two major constituents of an active fraction (Fraction F) obtained from the medium. Compound 1 was identified as 2-hydroxypropane-1, 2, 3-tricarboxylic acid (citric acid). Compound 2 was identified as 3-hydroxy-5-methoxy-3-(methoxycarbonyl)-5-oxopentanoic acid, an isomer of 1, 2-dimethyl citrate. Compound 1 and a citric acid standard, each tested at 50 mg mL –1 in water, decreased hatch from eggs of the plant-parasitic nematode Meloidogyne incognita by more than 94%, and completely immobilized second-stage juveniles after 4–6 days exposure. Fraction F and Compounds 1 and 2 decreased the mobility of adults of the plant-parasitic nematode Ditylenchus destructor in vitro . Fraction F (25 mg mL –1 ) inhibited mobility 〉99% at 72 hrs. Compounds 1 and 2 (50 mg mL –1 ) each inhibited mobility more than 25% at 24 hr and more than 50% at 72 hr. This is the first assignment of nematode-antagonistic properties to specifically identified A. candidus metabolites.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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