Flexible mapping of homology onto structure with Homolmapper

<p>Abstract</p> <p>Background</p> <p>Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine.</p> <p>Results</p> <p>We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs.</p> <p>Conclusion</p> <p>Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at <url>http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm</url>.</p

Estradiol, testosterone, 11-ketotestosterone, 17, 20b-dihydroxy-4-pregnen-3-one and vitellogenin plasma levels in females of captive European sturgeon, Acipenser sturio

International audienceThe changes for plasma level of sex steroid hormones and vitellogenin (VTG) during oogenesis and at ovulation are studied in the aim of being potentially used as predictive markers of breeding performance in sturgeon species. In the present work we describe the development of plasma steroid hormones and vitellogenin (VTG) profiles in three females which were followed over 5 years and approaching the spawning, and we focus on the months preceding the spawning induction. Plasma estradiol (E2), testosterone (T), 11-ketotestosterone (11KT), 17, 20b dihydroxy-4-pregnen-3-one (17, 20bP) and vitellogenin (VTG) are measured by Enzyme Linked Immuno Sorbant Assay (ELISA). During the 5-year period study, hormonal profile varies differently from one female to the other, linked to stage of development of the ovary. High levels of E2 and VTG are found, although restricted to the years when oocytes develop. There is some seasonal variation, with a peak of E2 at the end of winter, and a dramatic decrease in May. During months before the spawning induction, E2 levels are decreasing, while VTG remains at high level, 11KT sharply increases while 17, 20bP increases 20 to hundred fold during the same time. Only one female achieves GVBD that triggered ovulation and gives fertile eggs. The comparison of the three females is a first step aiming at correlating some of the plasma parameters to the success of hormone-induced ovulation in this highly endangered species

Hormonal profile in adult European sturgeon, Acipenser sturio, adapted to hatchery conditions in France

International audiencePlasma levels of estradiol (E2) testosterone (T), 11-etotestosterone, 17,20bP and vitellogenin (VTG ) are reported for the first time in mature male and female sturgeon, Acipenser sturio. T (40 ng/ml) correlates each year with spermiation. High E2 (33 ng/ml) correlates with VTG (90 mg/ml) and maturation

Plasma sex steroids and vitellogenin levels in stellate sturgeon (Acipenser stellatus Pallas) during spawning migration in the Danube River

International audienceData are presented on the levels of vitellogenin (VTG) and sex steroids plasma [testosterone (T), estradiol (E2), 11-keto-testosterone (11KT), and 17 [alpha] ,20 [beta] -dihydroxy-4-pregnen-3-one (DP)] in stellate sturgeon spawners during their spawning migration in the Danube River. Most sampled fish were 7 years old. Vitellogenesis was still ongoing during the spawning migration. All measured biochemical parameters suggest that spawning will occur by the end of May or later. The VTG values, as well as the ratios E2/T (discriminating value of 0.002) and E2/11KT (discriminating value of 0.02), permit differentiation between sexes; the use of these parameters might be applied as a sex identification method for spawners during their spawning migration. The presence of VTG in male plasma indicated a possible exposure to xenobiotic substances in the Black Sea. As a result of high levels of T and 11KT in the females and males during their upstream migration, it is suggested that both of these steroids are involved in stimulating migratory behaviour

Installation d'un élevage d'esturgeon menacés de façon critique, l'Acipenser sturio, avec une attention particulière sur les gros poissons

Over-exploitation, damming, dredging and most probably deterioration in hydrological characteristics led to a dramatic decrease of the European Atlantic sturgeon, Acipenser sturio, population in the 1960s. Maintaining a farmed broodstock is a way for regular provision of fingerlings. Due to uncertainty of long-term maintenance of the wild population, a conservation objective was recently added. All possibilities were investigated to increase the rate of success.The first two are based on the acclimation of small and large wild fish to farm conditions. The third concerns the rearing of artificially-produced fingerlings.The present paper deals mainly with the large wild fish beginning in late 1993.Cette initiative est prise dans un but de conservation. La première étape a consisté en l'acclimatation des petites et gros poissons aux condition d'élevage et la troisième à la production artificielle de lingues. Cet article porte essentiellement sur les gros poissons

Stage-dependent expression and alternative splicing of sGnRH messengers in gonads during rainbow trout gametogenesis

International audienc

Stage-dependent expression and alternative splicing of sGnRH messengers in gonads during rainbow trout gametogenesis

International audienc

Création d'un stock de géniteurs d'Acipenser sturio, une espèce d'esturgeons en danger critique de disparition : problèmes et observations associés à l'adaptation d'individus sauvages aux conditions d'élevage

International audienceThis study deals with the establishment of a confined broodstock of the critically endangered sturgeon Acipenser sturio L., with special emphasis on two groups of wild captive fish. One is composed of 40 juveniles hatched in the wild in 1994 and caught in the Gironde estuary in 1995. The other is made up of older juveniles (n = 8) and adults (n = 6) caught at different times. The fish were fed frozen shrimps and reared in recirculated water systems. The main aims of the study were i) to determine optimal rearing conditions, ii) to improve our knowledge of the species (sex ratio, genetics), and iii) to determine how to manage adults in captivity to produce gametes. Short trawling, rapid transportation with water from the fish habitat and maintaining them in the hatchery in water of similar salinity reduced the initial weight loss which was measured at up to 30%. Growth of juvenile fish 1994-95 was similar in fresh and brackish water till mid 2001. Weight range increased with age. Analysis of 11-ketotestosterone (11 KT) levels shows that one third of these 1994-95-fish are probably males. Of the large juveniles kept in brackish water, some required several months to resume feeding but two 10-kg fish exhibited no weight loss, suggesting a great potential for adaptation. Some breeders did not recover their initial weight for several years, with growth best described as irregularly cyclic. The large fish (10 out of 12) exhibited better growth in a 2 m deep tank compared with a 1 m tank. Out of the 14 large fish, 6 died after one to three years holding for no known reason. The 8 remaining fish are sires, 5 of which matured in 2000 and 2001. Four of the five matured in the two consecutive years. Vernalisation (11°C in winter), natural daylight, one week in fresh water in late spring to mimic upstream migration, and hormonal stimulation with either carp pituitary homogenate or GnRH analogue provided high quality semen. The genetic variability of the Gironde population, assessed from the present experimental fish, is low and all specimens share the same mitochondrial haplotype. Characterisation of mitochondrial DNA fragments suggests that the juveniles born in the wild in 1994 were produced by the same dam and sire.Ce travail a pour but de contribuer à la création d'un stock confiné de géniteurs d'Acipenser sturio L., en particulier à partir de l'adaptation à l'élevage de 2 groupes de poissons sauvages. L'un est composé de 40 jeunes juvéniles nés dans la nature en 1994 et capturés dans l'estuaire de la Gironde en 1995. L'autre groupe est composé de 8 grands juvéniles et de 6 adultes capturés à divers moments. Les poissons élevés en circuits fermés sont nourris avec des crevettes congelées. Les principaux objectifs de travail sont :i) déterminer les conditions optimales d'élevage, ii) améliorer nos connaissances sur l'espèce (sexe ratio, génétique, ), et iii) déterminer comment on doit gérer les adultes en captivité pour obtenir des gamètes. Des traits de chalut courts, un transport rapide dans le même type d'eau dans laquelle ils ont été capturés, et le maintien dans l'écloserie dans une salinité identique à celle de l'eau où ils ont été capturés réduisent la perte de poids initial qui a pu atteindre jusqu'à 30%. La croissance des jeunes juvéniles de 1994-95 est similaire en eau douce et en eau saumâtre jusqu'au milieu 2001. L'écart des poids a augmenté avec l'âge. L'analyse des taux de 11-kétotestostérone montre qu'un tiers des animaux de 1994-95 sont probablement des mâles. Parmi les grands juvéniles maintenus en eau saumâtre, plusieurs mois ont été nécessaires à certains pour retrouver l'appétit sauf pour 2 animaux de 10 kg suggérant ainsi un grand potentiel d'adaptation à ce poids. Quelques géniteurs n'ont retrouvé leur poids initial qu'après plusieurs années, leur croissance a été irrégulièrement cyclique. Les gros animaux (10 parmi 12) ont montré une meilleure croissance dans un bassin plus profond (2 m contre 1 m). Parmi les 14 grands individus, 6 sont morts pour des raisons inconnues après un à 3 ans de stockage. Les 8 animaux restants sont des mâles, 5 d'entre eux sont parvenus à maturité en 2000 et 2001. Quatre parmi ces 5 poissons ont fourni du sperme deux années consécutives. Une vernalisation (11°C en hiver), une photopériode normale, une semaine en eau douce tard au printemps pour mimer la migration de ponte, et une stimulation hormonale avec un extrait hypophysaire de carpe ou un analogue du GnRH ont permis d'obtenir du sperme de qualité. La variabilité génétique de la population de la Gironde, estimée par les animaux objet de la présente étude, est très faible et tous les individus partagent le même haplotype mitochondrial. Une caractérisation de fragments de d'ADN mitochondrial suggère que les jeunes juvéniles de 1994 ont été produit par un seul couple de géniteurs