Search results for "Bases"
showing 10 items of 1240 documents
Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication.
2015
Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochon…
Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study.
2017
AbstractRNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network. Our meta-analysis revealed…
X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification
2017
X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!Tandem…
EUNIS Habitat Classification: Expert system, characteristic species combinations and distribution maps of European habitats
2020
Aim The EUNIS Habitat Classification is a widely used reference framework for European habitat types (habitats), but it lacks formal definitions of individual habitats that would enable their unequivocal identification. Our goal was to develop a tool for assigning vegetation-plot records to the habitats of the EUNIS system, use it to classify a European vegetation-plot database, and compile statistically-derived characteristic species combinations and distribution maps for these habitats. Location Europe. Methods We developed the classification expert system EUNIS-ESy, which contains definitions of individual EUNIS habitats based on their species composition and geographic location. Each ha…
Assessing sampling coverage of species distribution in biodiversity databases
2019
Abstract Aim Biodiversity databases are valuable resources for understanding plant species distributions and dynamics, but they may insufficiently represent the actual geographic distribution and climatic niches of species. Here we propose and test a method to assess sampling coverage of species distribution in biodiversity databases in geographic and climatic space. Location Europe. Methods Using a test selection of 808,794 vegetation plots from the European Vegetation Archive (EVA), we assessed the sampling coverage of 564 European vascular plant species across both their geographic ranges and realized climatic niches. Range maps from the Chorological Database Halle (CDH) were used as bac…
Facebook groups as citizen science tools for plant species monitoring
2021
I social network sono canali di comunicazione utilizzati per condividere enormi quantità di dati, che possono essere utilizzati per la ricerca scientifica, anche nel campo della biodiversità. Per sapere quanto i dati ricavati dai social network possono integrare quelli raccolti per scopi scientifici, è necessario individuarne i bias. Utilizzando i dati estratti da un gruppo Facebook specializzato nella flora vascolare siciliana, abbiamo analizzato quali sono i caratteri che aumentano la probabilità che una pianta spontanea venga fotografata e postata su un social network. A tal fine, abbiamo confrontato frequenze e attributi delle specie fotografate dai membri del gruppo Facebook con quelli…
Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria
2005
International audience; Most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong AT base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. Here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. The results of this study were three-fold: (i) Stronger conservation of high expression genes at not just nonsynonymous, but also synonymous, sites. (ii) Variation in amino acid usage strongly correlates with GC content and expression level of genes. This pattern is largely explained by greater conservation of high expression genes, l…
Atlas of Finnish bats
2019
This atlas is based on information in museum collections, literature, databases and unpublished data. In the last 150 years, the number of bat species in Finland increased from six to thirteen. Of these, five are common and regularly breeding (Eptesicus nilssonii, Myotis brandtii, Myotis daubentonii, Myotis mystacinus, Plecotus auritus), and eight rare (Eptesicus serotinus, Myotis dasycneme, Myotis nattereri, Nyctalus noctula, Pipistrellus nathusii, Pipistrellus pipistrellus, Pipistrellus pygmaeus, Vespertilio murinus), of which breeding of two (M. nattereri, P. nathusii) have been confirmed. The total number of records in the study is 11 234, of which 9717 are identified to species. The re…
RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design.
2011
International audience; Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involv…
The gypsy database (GyDB) of mobile genetic elements: release 2.0
2011
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analys…