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

Cold Adaptation of Proteins. Purification, Characterization, and Sequence of the Heat-Labile Subtilisin from the Antarctic Psychrophile Bacillus Ta41

The gene of subtilisin S41, an alkaline protease secreted by the psychrophile Bacillus TA41, encodes for a preproenzyme of 419 amino acids residues. The nucleotide sequence and NH2- and COOH-terminal amino acid sequencing of the purified enzyme indicate that the mature subtilisin S41 is composed of 309 residues with a predicted M(r) = 31,224. Subtilisin S41 shares most of its properties with mesophilic subtilisins (structure of the precursor, 52% amino acid sequence identity, alkaline pH optimum, broad specificity, Ca2+ binding) but is characterized by a higher specific activity on macromolecular substrate, by a shift of the optimum of activity toward low temperatures, and by a low thermal stability. The enzyme also differs by an acidic pI (5.3) and the presence of one disulfide bond. It is proposed that the psychrophilic enzyme possesses a more flexible molecular structure when compared to mesophilic and thermophilic subtilases in order to compensate for the reduction of reaction rates at low temperatures. The model of subtilisin S41 indeed reveals several features able to induce a more flexible, heat-labile conformation: the occurrence of four extended surface loops, a very hydrophilic surface through 11 extra Asp residues, and the lack of several salt bridges and aromatic-aromatic interactions. The low affinity of the Ca1 calcium binding site (Kd(app) = 10(-6) M), resulting possibly from one chelating side chain substitution and the stacking of Gly residues, also reflect a less compact conformation. The difference of free energy of stabilization between subtilisin S41 and a mesophilic subtilisin suggests that the balance of exo- and endothermically formed weak bonds is critical for the enzyme flexibility

Transversalité entre sciences vétérinaires et odontologiques : revue systématique de la prévalence des pathologies parodontales chez le chat

Purpose: with this work, we aim to show that there is a high prevalence of periodontal diseases in cats and thus highlight the need and the opportunity of collaboration between dental surgeons and veterinarians for the management of oral care in cats.Moreover, a comparison between cat’s and human’s oral cavity anatomy has been realised and also aa reminder of periodontal diseases’ aetiology and treatment.In this study, gingivostomatitis were incorporated into periodontal diseases. Material and method: a systematic review, according to PRISMA recommendations and using the PubMed and Embase databases, was performed until June 2022. The aim was to establish the prevalence of periodontal disease in cats. The data have been selected on a primary reading of the titles and the abstracts, which then led to a full reading of the publications. Two reviewers selected and extracted data. Results: 14 articles have been included in the revue. The heterogeneity of the studies made it impossible to compare their results.However, periodontal diseases were the most common pathology in cats, especially in older cats or brachycephalic species.Among the 5 articles about gingivostomatitis, there was a strong correlation with the age or with the retroviral status, but none with gender or racial status. Conclusion: the results of this systematic review highlights the high prevalence of periodontal diseases in cats. It also underlines the similarity between the periodontal disease aetiology and treatment in Cats and Humans.In this way, the high prevalence of these pathologies, and the lack of time, equipment or background, revealed us that a collaboration between dental surgeons and veterinarians could be benefic.Objectif : par ce travail, nous souhaitons montrer qu'il existe une forte prévalence des pathologies parodontales chez le chat et ainsi mettre en évidence la nécessité et la possibilité d'une collaboration entre chirurgiens- dentistes et vétérinaires pour la prise en charge de certains soins bucco-dentaires chez le chat. De plus, une comparaison entre l’anatomie de la cavité buccale du Chat et de l’Homme ainsi qu’un rappel de l’étiologie et du traitement des pathologies parodontales ont été réalisés. Dans cette étude, les lésions de gingivostomatites ont été prises en compte dans les pathologies affectant le parodonte. Matériel et méthode : une revue systématique de la littérature a été réalisée jusqu’en juin 2022, selon les critères PRISMA et en utilisant les bases de données Pubmed et Embase. Le but était d’établir la prévalence des pathologies parodontales chez le chat. Une sélection s’est faite d’abord par la lecture des titres et des résumés, puis par la lecture complète des publications. Deux examinateurs ont sélectionné et extrait les données. Résultats : un total de 14 articles a été retenu. L’hétérogénéité des articles n’a pas permis de comparer les résultats entre eux. Cependant, les maladies parodontales sont revenues comme étant une des pathologies les plus fréquentes chez les chats, notamment les chats âgés et brachycéphales. Parmi les 5 articles qui abordaient la gingivostomatite, une corrélation a été faite avec l’âge et le statut rétroviral des chats atteints, mais aucune avec le sexe ou la race. Conclusions : les résultats de cette revue de la littérature montrent l’importance de la prévalence des pathologies parodontales chez le Chat. Notre travail met aussi en évidence la similitude entre l’étiologie et la prise en charge des pathologies parodontales chez le Chat et l’Homme. Ainsi, devant l’ampleur de la prévalence de ces pathologies, ainsi que le manque de temps, de formation et de matériels spécialisés, nous pensons qu’une transversalité entre chirurgien-dentistes et vétérinaires pourrait être bénéfique

Description de méningoradiculites présumées infectieuses à Borrelia burgdorferi (maladie de Lyme) dans un service de médecine interne du Centre hospitalier de Blois (à propos de 22 observations)

TOURS-BU Médecine (372612103) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

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

Opportunities and challenges for connecting environmental assessment and CAD software tools : example of implementation by Legrand

International audienc

Sequence of the Subtilisin-Encoding Gene from an Antarctic Psychrotroph Bacillus Ta41

peer reviewedThe nucleotide sequence of the subtilisin-encoding gene from the antarctic psychrotroph, Bacillus TA41, was determined. The primary structure of the subtilisin precursor corresponds to a preproenzyme of 419 amino acids. Asp144, His181 and Ser359 are the proposed catalytic residues of the protease active site