Search results for "POSAS"
showing 10 items of 17 documents
Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data
2020
The European Union's Natura 2000 (N2000) is among the largest international networks of protected areas. One of its aims is to secure the status of a predetermined set of (targeted) bird and butterfly species. However, nontarget species may also benefit from N2000. We evaluated how the terrestrial component of this network affects the abundance of nontargeted, more common bird and butterfly species based on data from long-term volunteer-based monitoring programs in 9602 sites for birds and 2001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased (slope estimates ranged from 0.101 [SD 0.042] to 3.51 [SD 1.30…
Ecological and genomic features of two widespread freshwater picocyanobacteria
2018
We present two genomes of widespread freshwater picocyanobacteria isolated by extinction dilution from a Spanish oligotrophic reservoir. Based on microscopy and genomic properties, both picocyanobacteria were tentatively designated Synechococcus lacustris Tous, formerly described as a metagenome assembled genome (MAG) from the same habitat, and Cyanobium usitatum Tous, described here for the first time. Both strains were purified in unicyanobacterial cultures, and their genomes were sequenced. They are broadly distributed in freshwater systems; the first seems to be a specialist on temperate reservoirs (Tous, Amadorio, Dexter, Lake Lanier, Sparkling), and the second appears to also be abund…
New Genes Involved in Mild Stress Response Identified by Transposon Mutagenesis in Lactobacillus paracasei
2018
International audience; Lactic acid bacteria (LAB) are associated with various plant, animal, and human niches and are also present in many fermented foods and beverages. Thus, they are subjected to several stress conditions and have developed advanced response mechanisms to resist, adapt, and grow. This work aimed to identify the genes involved in some stress adaptation mechanisms in LAB. For this purpose, global reverse genetics was applied by screening a library of 1287 Lactobacillus paracasei transposon mutants for mild monofactorial stresses. This library was submitted independently to heat (52 degrees C, 30 min), ethanol (170 g.L-1, 30 min), salt (NaCl 0.8 M, 24 h), acid (pH 4.5, 24 h…
The Patient and Observer Scar Assessment Scale to Evaluate the Cosmetic Outcomes of the Robotic Single-Site Hysterectomy in Endometrial Cancer
2017
ObjectiveThe objective of this study was to evaluate the cosmetic outcome of robotic single-site hysterectomy (RSSH) in early-stage endometrial cancer.MethodsWe prospectively collected patient demographics, operative times, complications, pathologic results, and length of stay on all patients who underwent RSSH for early-stage endometrial cancer. The Patient and Observer Scar Assessment Scale (POSAS) was used for the evaluation of the cosmetic outcome.ResultsForty-five patients were included in our study from January 2012 to October 2015. The median age of patients was 63 years (range, 35–84 years), and the median body mass index was 26.5 kg/m2 (range, 18–39 kg/m2). No laparoscopic/laparoto…
Assessment of computational methods for the analysis of single-cell ATAC-seq data
2019
Abstract Background Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges. scATAC-seq experiments sample DNA, which, due to low copy numbers (diploid in humans), lead to inherent data sparsity (1–10% of peaks detected per cell) compared to transcriptomic (scRNA-seq) data (10–45% of expressed genes detected per cell). Such challenges in data generation emphasize the need for informative features to assess cell heterogeneity at the chromatin level. Results We present a benchmarking framework that …
Photobacterium damselae subsp. damselae Major Virulence Factors Dly, Plasmid-Encoded HlyA, and Chromosome-Encoded HlyA Are Secreted via the Type II S…
2015
ABSTRACT Photobacterium damselae subsp. damselae is a marine bacterium that causes septicemia in marine animals and in humans. Previously, we had determined a major role of pPHDD1 plasmid-encoded Dly (damselysin) and HlyA (HlyA pl ) and the chromosome-encoded HlyA (HlyA ch ) hemolysins in virulence. However, the mechanisms by which these toxins are secreted remain unknown. In this study, we found that a mini-Tn 10 transposon mutant in a plasmidless strain showing an impaired hemolytic phenotype contained an insertion in epsL , a component of a type II secretion system (T2SS). Reconstruction of the mutant by allelic exchange confirmed the specific involvement of epsL in HlyA ch secretion. In…
Clostridium difficile IStron CdISt1: Discovery of a Variant Encoding Two Complete Transposase-Like Proteins
2004
ABSTRACT Screening a Clostridium difficile strain collection for the chimeric element Cd ISt1 , we identified two additional variants, designated Cd ISt1 -0 and Cd ISt1 -III. In in vitro assays, we could prove the self-splicing ribozyme activity of these variants. Structural comparison of all known Cd ISt1 variants led us to define four types of IStrons that we designated Cd ISt1 -0 through Cd ISt1 -III. Since Cd ISt1 -0 encodes two complete transposase-like proteins (TlpA and TlpB), we suggest that it represents the original genetic element, hypothesized before to have originated by fusion of a group I intron and an insertion sequence element.
Impact of Insertion Sequences and RNAs on Genomic Inversions in Pseudomonas aeruginosa
2022
Abstract In this article, a bioinformatics pipeline is proposed that focuses on two types of elements, namely the mobile genetic elements (MGE) and Ribonucleic acids (RNAs). The MGEs are called insertion sequences (ISs) in the prokaryotic domain. The objective of this research work is to study the behaviour of RNAs and MGEs genes, and the effects of their presence around inversions in genome sequences. The proposed pipeline finds the relation between the transposase gene types (e.g., DDE and DEDD) located within insertion sequences according to their IS family and sub-family, and RNAs (tRNA and rRNA) on the one hand, and genomic inversion on the other hand. More precisely, we wonder whether…
Sleeping Beauty transposon system – future trend in T-cell-based gene therapies?
2006
Evaluation of: Huang X, Wilber AC, Bao L et al.: Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system. Blood 107, 483–491 (2006). The Sleeping Beauty (SB) transposon system can mediate stable gene transfer and expression in primary human T cells. Optimal in vitro conditions for maximum gene transfer efficiencies have been developed with regard to further application of the SB transposon system in T cell based gene therapies. This raises the question of whether or not the SB transposon system is a convincing alternative for virus-mediated gene transfer based on the currently available data. Here, we will discuss controversial safety and effic…
On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain
2012
SCAND3 and KRBA2 are two mammalian proteins originally described as “cellular-integrases” due to sharing of a similar DDE-type integrase domain whose origin and relationship with other recombinases remain unclear. Here we perform phylogenetic analyses of 341 integrase/transposase sequences to reveal that the integrase domain of SCAND3 and KRBA2 derives from the same clade of GINGER2, a superfamily of cut-and-paste transposons widely distributed in insects and other protostomes, but seemingly absent or extinct in vertebrates. Finally, we integrate the results of phylogenetic analyses to the taxonomic distribution of SCAND3 and KRBA2 and their transposon relatives to discuss some of the proce…