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  • 2015-2019  (6)
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  • 1
    Publication Date: 2016-07-06
    Description: The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-10-24
    Description: Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia , which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding protein ( Obp ) genes and olfactory receptor ( Or ) genes have been suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the transcriptomes of antennae, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found a higher percentage of chemosensory genes differentially expressed in the D. sechellia lineage (7.8%) than in the D. simulans lineage (5.4%); for upregulated chemosensory genes, the percentages were 8.8% in D. sechellia and 5.2% in D. simulans. Interestingly, Obp50a exhibited the highest upregulation, an approximately 100-fold increase, and Or85c —previously reported to be a larva-specific gene—showed approximately 20-fold upregulation in D. sechellia. Furthermore, Ir84a ( ionotropic receptor 84a ), which has been proposed to be associated with male courtship behavior, was significantly upregulated in D. sechellia. We also found expression divergence in most of the chemosensory gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia was associated with the enrichment of differentially expressed, particularly upregulated, chemosensory genes.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 3
    Publication Date: 2015-07-02
    Description: This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2015-10-29
    Description: Hypercubes and star graphs are widespread topologies of interconnection networks. The class of hyper-stars was introduced as a new type of interconnection network to compete with both hypercubes and star graphs, and the class of folded hyper-stars is a strengthened variation of hyper-stars with additional links to connect nodes with complemented 0/1-strings. Constructing independent spanning trees (ISTs) has numerous applications in networks such as fault-tolerant broadcasting and secure message distribution. Recently, Yang and Chang [IST on folded hyper-stars, Networks 56 (2010), 272–281] proposed an algorithm to construct $k+1$ ISTs on folded hyper-star $FHS(2k,k)$ . For $k\geqslant 4$ , their constructions include $k$ ISTs with a height $2k-2$ and the other one with a height $k+1$ . In this paper, we refine their constructed rules on $FHS(2k,k)$ for $k\geqslant 3$ and provide a set of constructions including $k$ ISTs with a height $k+2$ and the other one with a height $k+1$ . As a by-product, we obtain an improvement on the upper bound of the fault diameter (respectively, the wide diameter) of $FHS(2k,k)$ .
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 5
    Publication Date: 2015-07-29
    Description: Proteinuria is a major hallmark of glomerular nephropathy and endoplasmic reticulum (ER) stress plays an important role in glomerular nephropathy. The protein levels of integrin-β1 in podocytes are found to be negative correlation with amount of proteinuria. This study investigated whether urinary protein, particularly albumin, induced ER stress that consequently reduced integrin-β1 expression. All experiments were performed using primary cultured rat podocyte. Protein and mRNA expression were measured by western blotting and semiquantified reverse transcriptase polymerase chain reaction. Albumin uptake was found at 1 h after albumin addition. Albumin reduced precursor and mature forms of integrin-β1, but did not change mRNA levels of integrin-β1. Albumin induced reactive oxygen species (ROS) generation and ER stress. Antioxidant ( N -acetylcysteine) suppressed albumin-induced ER stress and decrements in precursor and mature forms of integrin-β1. Then, ER stress inhibitors (4-phenylbutyrate and salubrinal) also inhibited albumin-induced decrements in precursor and mature forms of integrin-β1. The potent ER stress inducers (thapsigargin and tunicamycin) directly decreased precursor and mature forms of integrin-β1 and led appearance of unglycosylated core protein of integrin-β1. Our results show that in proteinuric disease, albumin decreases precursor and mature forms of integrin-β1 through ROS-ER stress pathway in podocytes.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 6
    Publication Date: 2016-12-08
    Description: This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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