ISSD Version 2.0: taxonomic range extended

Two more organisms from different taxonomic groups were added to a new version of the integrated Sequence-Structure Database (ISSD). ISSD serves as an integrated source of sequence and structure information for the analysis of correlations between mRNA synonymous codon usage and threedimensional structure of the encoded proteins. ISSD now holds 88 non-homologous Escherichia coli proteins and 25 yeast Saccharomyces cerevisiae proteins in addition to the expanded set of mammalian proteins, which includes 166 proteins (107 in ISSD Version 1.0). Comparison of ISSD sequences with organism-specific codon usage data derived from CUTG database shows that it is a representative subset of the genbank coding sequences data. Preliminary results of the statistical analysis confirm that sequence-structure correlations observed by us earlier are also present in the upgraded ISSD (Version 2.0), including bacterial and yeast proteins. The ISSD version 2.0 release includes an improved web-based data search and retrieval system and is accessible via URL http://www.protein.bio.msu.su/issd/. ISSD can be also accessed at ExPASy, URL http://www.expasy.ch/swissmod/swiss-model.htm

preAssemble: a tool for automatic sequencer trace data processing

BACKGROUND: Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages – Phred and Staden are used by preAssemble to perform sequence quality processing. RESULTS: The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. CONCLUSION: preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing

An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

BACKGROUND: The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies. RESULTS: In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure. CONCLUSION: This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine

Las estrategias discursivas de Alan García y Keiko Fujimori en sus cuentas de Twitter y su uso dentro de la producción noticiosa de los medios digitales El Comercio y Expreso en el contexto de las investigaciones del caso Lava Jato

El estallido del caso Lava Jato en 2016 marca un hito en la historia de la corrupción en la política peruana. Como nunca antes, las acusaciones alcanzan a figuras como Alan García y Keiko Fujimori. Ambos actores, apoyados en el fenómeno de redes sociales como Twitter, han optado por responder los señalamientos desde estas plataformas. Lo anterior supone un reto para los periodistas, que se ven obligados a adoptar estas publicaciones digitales como fuentes válidas. El objetivo de esta investigación es determinar cómo las estrategias discursivas dentro de los tweets de ambos actores políticos se ven reflejadas en las coberturas de los diarios Expreso y El Comercio sobre el caso Lava Jato. Por ello, el marco teórico recoge teorías como la convergencia de medios, framing, mediatización de la política y propuestas sobre el rol del periodismo en este nuevo escenario como el gateekeeping. Se han analizado tweets de Alan García y Keiko Fujimori y noticias de ambos diarios peruanos que los utilizan en sus coberturas durante periodos clave de las investigaciones. La principal conclusión es que los periodistas del diario Expreso y El Comercio utilizan los tweets como elementos centrales en sus coberturas, pero las valoraciones que les dan varían según el nivel de profundidad que les dan a sus formatos periodísticos. En la mayoría de los casos se limitan a una reproducción literal de los tweets, lo que ocasiona que el discurso político se vuelva noticia por sí mismo.The outbreak of the Lava Jato case in 2016 marks a milestone in the history of corruption in peruvian politics. As never before, the accusations reached figures like Alan Garcia and Keiko Fujimori. Both actors, supported by the phenomenon of social networks such as Twitter, have chosen to respond to the accusations from these platforms. This is a challenge for journalists, who are forced to adopt these valid digital publications as sources. The objective of this research is to determine how the discursive strategies within the tweets of both political actors are reflected in the coverage about Lava Jato of newspapers like Expreso and El Comercio. For this reason, the theoretical framework includes theories such as media convergence, framing, mediatization of politics and proposals on the role of journalism in this new scenery such as gatekeeping. Tweets from Alan Garcia and Keiko Fujimori and news that use them from both peruvian newspapers coverages in key periods of the investigations have been analyzed. The main conclusion is that journalists from the newspaper Expreso and El Comercio use tweets as central elements in their coverage, but the evaluations they give vary according to the level of depth they give to their journalistic formats. In most cases they are limited to a verbatim reproduction of the tweets, which allows political discourse to become news on its own

Bioactivity and structural properties of chimeric analogs of the starfish SALMFamide neuropeptides S1 and S2

The starfish SALMFamide neuropeptides S1 (GFNSALMFamide) and S2 (SGPYSFNSGLTFamide) are the prototypical members of a family of neuropeptides that act as muscle relaxants in echinoderms. Comparison of the bioactivity of S1 and S2 as muscle relaxants has revealed that S2 is ten times more potent than S1. Here we investigated a structural basis for this difference in potency by comparing the bioactivity and solution conformations (using NMR and CD spectroscopy) of S1 and S2 with three chimeric analogs of these peptides. A peptide comprising S1 with the addition of S2's N-terminal tetrapeptide (Long S1 or LS1; SGPYGFNSALMFamide) was not significantly different to S1 in its bioactivity and did not exhibit concentration-dependent structuring seen with S2. An analog of S1with its penultimate residue substituted from S2 (S1(T); GFNSALTFamide) exhibited S1-like bioactivity and structure. However, an analog of S2 with its penultimate residue substituted from S1 (S2(M); SGPYSFNSGLMFamide) exhibited loss of S2-type bioactivity and structural properties. Collectively, our data indicate that the C-terminal regions of S1 and S2 are the key determinants of their differing bioactivity. However, the N-terminal region of S2 may influence its bioactivity by conferring structural stability in solution. Thus, analysis of chimeric SALMFamides has revealed how neuropeptide bioactivity is determined by a complex interplay of sequence and conformation

Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis

© The Author(s), 2017. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Developmental Biology 424 (2017): 181-188, doi:10.1016/j.ydbio.2017.02.019We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele- specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of four crosses: inbred genomic (J)- strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains. We identify a subset of mutations specific to the B strain, which allows us to investigate the selection pressures affecting duplicated genes in this allotetraploid. From these crosses we find the ratio of non-synonymous to synonymous mutations is lower in duplicated genes, which suggests that they are under greater purifying selection. Surprisingly, we also find that function-altering ("damaging") mutations constitute a greater fraction of the non-synonymous variants in this group, which suggests a role for subfunctionalization in coding variation affecting duplicated genes.L.P. was supported by the NIH grant R01HD073104, also L.P., A.N. and V.S. were supported by R21HD81675, M.H. and E.P. by P40 OD010997.2018-03-0

VarMod: modelling the functional effects of non-synonymous variants.

Unravelling the genotype–phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein interfaces and protein–ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME†

Summary: Analysing large amounts of data generated by next-generation sequencing (NGS) technologies is difficult for researchers or clinicians without computational skills. They are often compelled to delegate this task to computer biologists working with command line utilities. The availability of easy-to-use tools will become essential with the generalization of NGS in research and diagnosis. It will enable investigators to handle much more of the analysis. Here, we describe Knime4Bio, a set of custom nodes for the KNIME (The Konstanz Information Miner) interactive graphical workbench, for the interpretation of large biological datasets. We demonstrate that this tool can be utilized to quickly retrieve previously published scientific findings

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

The resolution of genome-wide association studies (GWAS) is limited by the linkage disequilibrium (LD) structure of the population being studied. Selecting the most likely causal variants within an LD block is relatively straightforward within coding sequence, but is more difficult when all variants are intergenic. Predicting functional non-coding sequence has been recently facilitated by the availability of conservation and epigenomic information. We present HaploReg, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs. Sets of SNPs, such as those resulting from GWAS, are analyzed for an enrichment of cell type-specific enhancers. HaploReg will be useful to researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. The HaploReg database is available at http://compbio.mit.edu/HaploReg.National Institutes of Health (U.S.) (R01-HG004037)National Institutes of Health (U.S.) (RC1-HG005334)National Science Foundation (U.S.) (HG005334