Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome

Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive web-based survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features

Synthesis of polyethersulfone (PES)/GO-SiO2 mixed matrix membranes for oily wastewater treatment

Abstract The treatment of oily wastewater continues to pose a challenge in industries worldwide. Membranes have been investigated recently for their use in oily wastewater treatment due to their efficiency and relatively facile operational process. Graphene oxide (GO) and silica (SiO2) nanoparticles have been found to improve membrane properties. In this study, a polyethersulfone (PES) based GO-SiO2 mixed matrix membrane (MMM) was fabricated, using the phase inversion technique, for the treatment of oil refinery wastewater. The PES/GO-SiO2 membrane exhibited the highest water flux (2,561 LMH) and a 38% increase in oil removal efficiency by comparison to a PES membrane. Compared to PES/GO and PES/SiO2 membranes, the PES/GO-SiO2 MMM also displayed the best overall properties in terms of tensile strength, water permeability, and hydrophilicity

Relation between Insertion Sequences and Genome Rearrangements in Pseudomonas aeruginosa

International audienc

On the Ability to Reconstruct Ancestral Genomes from Mycobacterium Genus

International audienceTechnical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and essential questions in Evolution. However, reconstructing evolution of DNA sequences requires models, algorithms, statistical and computational methods of ever increasing complexity. Since most dramatic genomic changes are caused by genome rearrangements (gene duplications, gain/loss events), it becomes crucial to understand their mechanisms and reconstruct ancestors of the given genomes. This problem is known to be NP-complete even in the ``simplest'' case of three genomes. Heuristic algorithms are usually executed to provide approximations of the exact solution. We state that, even if the ancestral reconstruction problem is NP-hard in theory, its exact resolution is feasible in various situations, encompassing organelles and some bacteria. Such accurate reconstruction, which identifies too some highly homoplasic mutations whose ancestral status is undecidable, will be initiated in this work-in-progress, to reconstruct ancestral genomes of two Mycobacterium pathogenetic bacterias. By mixing automatic reconstruction of obvious situations with human interventions on signaled problematic cases, we will indicate that it should be possible to achieve a concrete, complete, and really accurate reconstruction of lineages of the Mycobacterium tuberculosis complex. Thus, it is possible to investigate how these genomes have evolved from their last common ancestors

Mutations in TMEM216 perturb ciliogenesis and cause Joubert, Meckel and related syndromes

Joubert syndrome (JBTS), related disorders (JSRDs) and Meckel syndrome (MKS) are ciliopathies. We now report that MKS2 and CORS2 (JBTS2) loci are allelic and caused by mutations in TMEM216, which encodes an uncharacterized tetraspan transmembrane protein. Individuals with CORS2 frequently had nephronophthisis and polydactyly, and two affected individuals conformed to the oro-facio-digital type VI phenotype, whereas skeletal dysplasia was common in fetuses affected by MKS. A single G218T mutation (R73L in the protein) was identified in all cases of Ashkenazi Jewish descent (n = 10). TMEM216 localized to the base of primary cilia, and loss of TMEM216 in mutant fibroblasts or after knockdown caused defective ciliogenesis and centrosomal docking, with concomitant hyperactivation of RhoA and Dishevelled. TMEM216 formed a complex with Meckelin, which is encoded by a gene also mutated in JSRDs and MKS. Disruption of tmem216 expression in zebrafish caused gastrulation defects similar to those in other ciliary morphants. These data implicate a new family of proteins in the ciliopathies and further support allelism between ciliopathy disorders