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showing 10 items of 14693 documents
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…
Photoprotection dynamics observed at leaf level from fast temporal reflectance changes
2018
Vegetation dynamically reacts to the available photosynthetically active radiation (PAR) by adjusting the photosynthetic apparatus to either a light harvesting or a photoprotective modus. When activating the photoprotection mechanism, either minor or major pigment-protein interactions may occur at the leaf level, resulting in different light absorption and consequently reflectance intensities. The reflectance changes were measured during sudden illumination transients designed to provoke fast adaptation to high irradiance. Different spectral reflectance change features were observed during different stages of photoprotection activation, extending over part of the visible spectral range (i.e…
The evolution of dwarf shrubs in alpine environments: a case study ofAlchemillain Africa
2015
BACKGROUND AND AIMS Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. METHODS Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BA…
Cannibalism facilitates gigantism in a nine-spined stickleback (Pungitius pungitius) population
2016
Cannibalism is a taxonomically widespread phenomenon that can fundamentally affect the structure and stability of aquatic communities, including the emergence of a bimodal size distribution (“dwarfs” and “giants”) in fish populations. Emergence of giants could also be driven or facilitated by parasites that divert host resources from reproduction to growth. We studied the trophic ecology of giant nine-spined sticklebacks (Pungitius pungitius) in a Finnish pond to evaluate the hypotheses that gigantism in this population would be facilitated by cannibalism and/or parasitic infections by Schistocephalus pungitii cestode. Stomach content analyses revealed an initial ontogenetic dietary shift f…
Getting there and around: Host range oscillations during colonization of the Canary Islands by the parasitic nematode Spauligodon
2016
Episodes of expansion and isolation in geographic range over space and time, during which parasites have the opportunity to expand their host range, are linked to the development of host-parasite mosaic assemblages and parasite diversification. In this study, we investigated whether island colonization events lead to host range oscillations in a taxon of host-specific parasitic nematodes of the genus Spauligodon in the Canary Islands. We further investigated whether range oscillations also resulted in shifts in host breadth (i.e., specialization), as expected for parasites on islands. Parasite phylogeny and divergence time estimates were inferred from molecular data with Bayesian methods. H…
Citrus rootstock breeding: response of four allotetraploid somatic hybrids to Citrus tristeza virus induced infections
2018
Four allotetraploid somatic hybrids of citrus, with potential for rootstock improvement, have been evaluated for their response to Citrus tristeza virus (CTV) infection. CTV is the most important viral pathogen affecting citrus production worldwide. Somatic combinations of ‘Milam’ lemon (Citrus jambhiri Lush.) + Sour orange (C. aurantium L Osb.), Calamondin (C. madurensis Lour.) + ‘Keen’ sour orange (C. aurantium L.), Calamondin + ‘Femminello‘ lemon (C. limon L. Burm. F.) and Cleopatra mandarin (C. reshni Hort. ex Tan.) + ‘Femminello’ lemon, were studied. Plants were grafted with CTV-infected “Valencia” sweet orange budwood. Two different CTV strains collected in Sicily, considered as “mild…
Characterization and purification of a bacterial chlorogenic acid esterase detected during the extraction of chlorogenic acid from arbuscular mycorrh…
2016
International audience; A Gram-negative bacterium able to grow using chlorogenic acid (5-caffeoylquinic acid) as sole carbon source has been isolated from the roots of tomato plants inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis. An intracellular esterase exhibiting very high affinity (K-m = 2 mu M) for chlorogenic acid has been extracted and purified by FPLC from the chlorogenate-grown cultures of this bacterium. The molecular mass of the purified esterase determined by SDS-PAGE was 61 kDa and its isoelectric point determined by chromatofocusing was 7.75. The esterase hydrolysed chlorogenic acid analogues (caffeoylshikimate, and the 4- and 3-caffeoylquinic acid i…
An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA mon…
2019
A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric dif…
Selection of indigenous yeast strains for the production of sparkling wines from native Apulian grape varieties.
2018
We report the first polyphasic characterization of native Saccharomyces cerevisiae in order to select candidate strains for the design of starter cultures tailored for Apulian sparkling wines obtained from local grape variety. In addition, it is the first survey in our region that propose the selection of autochthonous starter cultures for sparkling wine i) including a preliminary tailored genotypic and technological screening, and ii) monitoring analytical contribution during secondary fermentation in terms of volatile compounds (VOCs). Furthermore, we exploit the potential contribute of autochthonous cultures throughout the productive chain, including the possible improvement of base wine…
On the Occurrence of the Invasive Freshwater Limpet Ferrissia californica (Mollusca: Gastropoda: Planorbidae) in Japan.
2018
Two members of the genus Ferrissia Walker, 1903, namely Ferrissia nipponica (Kuroda, 1949) and F. japonica Habe and Burch, 1965, have been reported to occur in Japan, but due to a lack of molecular data, doubts have been expressed as to their validity. Furthermore, the possible presence of allochthonous Ferrissia taxa has been stated under a variety of names, so that even now there is no consensus on their presence and identity. Recently, freshwater limpets belonging to the planorbid genus Ferrissia were collected in an irrigation trough on the Izu island of Hachijōjima, Tokyo, Japan. Molecular identification of the collected specimens, based on a fragment of the large ribosomal subunit 16S…