ALBERT

Description: Two transformations are proposed that give orthogonal components with a one-to-one correspondence between the original vectors and the components. The aim is that each component should be close to the vector with which it is paired, orthogonality imposing a constraint. The transformations lead to a variety of new statistical methods, including a unified approach to the identification and diagnosis of collinearities, a method of setting prior weights for Bayesian model averaging, and a means of calculating an upper bound for a multivariate Chebychev inequality. One transformation has the property that duplicating a vector has no effect on the orthogonal components that correspond to nonduplicated vectors, and is determined using a new algorithm that also provides the decomposition of a positive-definite matrix in terms of a diagonal matrix and a correlation matrix. The algorithm is shown to converge to a global optimum.

Description: We recently presented a model for site-specific protein N-glycosylation in Trypanosoma brucei whereby the TbSTT3A oligosaccharyltransferase (OST) first selectively transfers biantennary Man 5 GlcNAc 2 from the lipid-linked oligosaccharide (LLO) donor Man 5 GlcNAc 2 -PP-Dol to N-glycosylation sequons in acidic to neutral peptide sequences and TbSTT3B selectively transfers triantennary Man 9 GlcNAc 2 to any remaining sequons. In this paper, we investigate the specificities of the two OSTs for their preferred LLO donors by glycotyping the variant surface glycoprotein (VSG) synthesized by bloodstream-form T. brucei TbALG12 null mutants. The TbALG12 gene encodes the α1-6-mannosyltransferase that converts Man 7 GlcNAc 2 -PP-Dol to Man 8 GlcNAc 2 -PP-Dol. The VSG synthesized by the TbALG12 null mutant in the presence and the absence of α-mannosidase inhibitors was characterized by electrospray mass spectrometry both intact and as pronase glycopetides. The results show that TbSTT3A is able to transfer Man 7 GlcNAc 2 as well as Man 5 GlcNAc 2 to its preferred acidic glycosylation site at Asn263 and that, in the absence of Man 9 GlcNAc 2 -PP-Dol, TbSTT3B transfers both Man 7 GlcNAc 2 and Man 5 GlcNAc 2 to the remaining site at Asn428, albeit with low efficiency. These data suggest that the preferences of TbSTT3A and TbSTT3B for their LLO donors are based on the c-branch of the Man 9 GlcNAc 2 oligosaccharide, such that the presence of the c-branch prevents recognition and/or transfer by TbSTT3A, whereas the presence of the c-branch enhances recognition and/or transfer by TbSTT3B.

Description: Motivation: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores. Results: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree. Code Availability: https://github.com/stamatak/RAxML-Light-1.0.5 Data Availability: http://www.exelixis-lab.org/onLineMaterial.tar.bz2 Contact: alexandros.stamatakis@h-its.org Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Global change challenges forest adaptability at the distributional limit of species. We studied ring-porous Quercus canariensis Willd. xylem traits to analyze how they adjust to spatio-temporal variability in climate. Trees were sampled along altitudinal transects, and annual time series of radial growth (ring width (RW)) and several earlywood vessel (EV) traits were built to analyze their relationships with climate. The trees responded to increasing water constraints with decreasing altitude and changes in climate in the short term but the analyses showed that xylem did not acclimate in response to long-term temperature increase during the past 30 years. The plants' adjustment to climate variability was expressed in a different but complementary manner by the different xylem traits. At low elevations, trees exhibited higher correlations with water stress indices and trees acclimated to more xeric conditions at low elevations by reducing radial growth and hydraulic diameter ( D H ) but increasing the density of vessels (DV). Average potential conductivity ( K H ) was similar for trees at different altitudes. However, inter-tree differences in xylem traits were higher than those between altitudes, suggesting a strong influence of individual genetic features or micro-site conditions. Trees exhibited higher RW those years with larger D H and particularly the linear density of vessels (DV l ), but partly, climatic signals expressed in RW differed from those in EVs. Trees produced larger D H after cold winters and wet years. Ring width responded positively to wet and cool weather in fall and spring, whereas the response to climate of DV and K H was generally opposite to that of RW. These relationships likely expressed the negative impact of high respiration rates in winter on the carbon pools used to produce the EVs in the next spring and the overall positive influence of water availability for trees. Our results showed that trees at different sites were able to adjust their hydraulic architecture to climatic variability and temperature increase during recent decades coordinating several complementary traits. Nonetheless, it should be monitored whether they will succeed to acclimate to future climatic scenarios of increasing water stress.

Description: We have analysed the meteor activity associated with meteoroids of fresh dust trails of Comet 209P/LINEAR, which produced an outburst of the Camelopardalid meteor shower ( IAU code #451, CAM ) in 2014 May. With this aim, we have employed an array of high-sensitivity CCD video devices and spectrographs deployed at 10 meteor observing stations in Spain in the framework of the Spanish Meteor Network. Additional meteoroid flux data were obtained by means of two forward-scatter radio systems. The observed peak zenithal hourly rate was much lower than expected, of around 20 meteors h –1 . Despite of the small meteor flux in the optical range, we have obtained precise atmospheric trajectory, radiant and orbital information for 11 meteor and fireball events associated with this stream. The ablation behaviour and low tensile strength calculated for these particles reveal that Camelopardalid meteoroids are very fragile, mostly pristine aggregates with strength similar to that of the Orionids and the Leonids. The mineral grains seem to be glued together by a volatile phase. We also present and discuss two unique emission spectra produced by two Camelopardalid bright meteors . These suggest a non-chondritic nature for these particles, which exhibit Fe depletion in their composition.

Description: Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.

Description: : New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch. Availability and implementation: PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees . Contact: Fernando.Izquierdo@h-its.org Supplementary information: Supplementary Material is available at Bioinformatics online.

Description: On 2011 October 8, the Earth crossed the dust trails left by comet 21P/Giacobini–Zinner during its 19th and 20th century perihelion approaches with the comet being close to perihelion. The geometric circumstances of that encounter were thus favourable to produce a meteor storm, but the trails were much older than in the 1933 and 1946 historical encounters. As a consequence the 2011 October Draconid display exhibited several activity peaks with Zenithal Hourly Rates of about 400 meteors h –1 . In fact, if the display had not been forecasted, it could have passed almost unnoticed as was strongly attenuated for visual observers due to the Moon. This suggests that most meteor storms of a similar nature could have passed historically unnoticed under unfavourable weather and Moon observing conditions. The possibility of obtaining information on the physical properties of cometary meteoroids penetrating the atmosphere under low geocentric velocity encounter circumstances motivated us to set up a special observing campaign. Added to the Spanish Fireball Network wide-field all-sky and CCD video monitoring, other high-sensitivity 1/2 arcsec black and white CCD video cameras were attached to the modified medium-field lenses for obtaining high-resolution orbital information. The trajectory, radiant and orbital data of October 16 Draconid meteors observed at multiple stations are presented. The results show that the meteors appeared from a geocentric radiant located at α = 263.0 ± 0 ${^{\circ}_{.}}$ 4 and  = +55.3 ± 0 ${^{\circ}_{.}}$ 3 that is in close agreement with the radiant predicted for the 1873–1894 and the 1900 dust trails. The estimated mass of material from 21P/Giacobini–Zinner delivered to Earth during the 6 h outburst was around 950 ± 150 kg.

Description: A superbolide with an estimated absolute magnitude of –20 ± 1 was seen on 2012 July 13 over the centre and south of Spain. This extraordinary event, which was witnessed by numerous casual observers, was recorded in the framework of the continuous fireball monitoring and meteor spectroscopy campaign performed by the SPanish Meteor Network (SPMN). Thus, because of optimal weather conditions, the bolide was imaged from 10 meteor observing stations. Here we present the analysis of this magnificent event, which is the brightest fireball ever recorded by our team. The atmospheric trajectory of the bolide and the orbit in the Solar system of the parent meteoroid were obtained. The emission spectrum produced during the ablation of this particle is also discussed. We found that the meteoroid, which was following a Halley Type Comet orbit, was depleted in Na and had a tensile strength one order of magnitude higher than that corresponding to typical cometary materials. By means of orbital analysis tools we have investigated the likely parent body of this particle and the results suggest that the progenitor is a damocloid. The impact area of the hypothetical remnants of the meteoroid is also given and a search for meteorites was performed, but none was found.