MEASURING THE WAVE DISSIPATION PRODUCED BY A SWIMMING-LINE SEPARATION ROPE

Hydrodynamic drag (D) seems to be one of the major determinants of swimming performance. D is usually divided into pressure, friction and wave drag (Dw). Meanwhile, Dw can be due to two distinct phenomena: (i) wave production (Dwwp) and (ii) transfer of negative wave momentum (Dwtm). Dwwp refers to the energy dissipated from the kinetic energy of the swimmer and used to generate waves, and Dwtm refers to the drag effect (reduction of forward kinetic energy of the swimmer) attributed to the impact of waves produced by others, or produced by the swimmer itself and rebounded at a swimming pool wall. In order to define the competition lane of each swimmer, the competition swimming pools dispose of swimming-line separation ropes (S-LSR). In the meantime, the manufacturers of this S-LSR claim that they have the ability to absorb waving energy, and thus to dissipate waves avoiding Dw tm, and other perturbing wave effects. The purpose of this research was to characterize the swimmer’s wave production, and to measure the effect upon the wave energy dissipation of a common S-LSR (Fig.1)

Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools

We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1–2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties

ACOUSTIC CROSS-OVER BETWEEN THE EARS IN MICE (Mus musculus) DETERMINED USING A NOVEL ABR BASED BIO-ASSAY

ABSTRACT Closed-field stimulation of one ear, at high sound intensity, will activate both ears because of bone/soft tissue transmission of the acoustic signal across the skull. In human psychophysics and in clinical audiometry a knowledge of interaural attenuation values is important, particularly when assessing asymmetrical hearing loss or in studies of monaural hearing. Similarly, in testing monaural hearing in experimental animal studies, acoustic cross-over can result in erroneous conclusions about hearing function. The mouse has become a widely used animal model for various types of hearing loss, especially those relating to gene mutations, and also for age related deafness (presbycusis). In the present study we have measured acoustic cross-over in this species using a novel bio-assay technique based on auditory brainstem evoked responses (ABR). We report here for the mouse, an interaural attenuation of 37-45dB for click and 32kHz toneburst SOMMAIRE La stimulation de l'oreille unique à haute intensité sonore, en sphère fermée, cause l'activation des deux oreilles dù à la transmission du signal acoustique a travers les tissus mous et l'os du crâne. En psychophysique de l'homme et l'audiométrie clinique, l'atténuation interaural doit être connue dans les études d'audience mono ou de la surdité asymétrique. De même, pour tester l'audition monaurale dans les études expérimentales chez les animaux, la transmission trans-crânienne (aguillage acoustique) peut produire des conclusions erronées au sujet de la fonction auditive. La souris est devenue le modèle animal largement utilisé pour différents types de pertes auditives, en particulier celles qui ont a trait à des mutations géniques, et aussi de la surdité liée à l'âge (presbyacousie). Dans l'étude en question, nous avons mesuré la transmission trans-crânienne (aguillage acoustique) chez cette espèce en utilisant une technique de dosage biologique basée sur les potentiels évoqués auditifs (PEA). Nous rapportons ici chez la souris, une atténuation interaural de 37-45dB pour le clic et le 32kHz pip tonal

Pfam: clans, web tools and services

Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)

InterPro: the integrative protein signature database

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/

Predicting active site residue annotations in the Pfam database

<p>Abstract</p> <p>Background</p> <p>Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site annotations in the Pfam database, we have developed a strict set of rules, chosen to reduce the rate of false positives, which enable the transfer of experimentally determined active site residue data to other sequences within the same Pfam family.</p> <p>Description</p> <p>We have created a large database of predicted active site residues. On comparing our active site predictions to those found in UniProtKB, Catalytic Site Atlas, PROSITE and <it>MEROPS </it>we find that we make many novel predictions. On investigating the small subset of predictions made by these databases that are not predicted by us, we found these sequences did not meet our strict criteria for prediction. We assessed the sensitivity and specificity of our methodology and estimate that only 3% of our predicted sequences are false positives.</p> <p>Conclusion</p> <p>We have predicted 606110 active site residues, of which 94% are not found in UniProtKB, and have increased the active site annotations in Pfam by more than 200 fold. Although implemented for Pfam, the tool we have developed for transferring the data can be applied to any alignment with associated experimental active site data and is available for download. Our active site predictions are re-calculated at each Pfam release to ensure they are comprehensive and up to date. They provide one of the largest available databases of active site annotation.</p

Pfam: the protein families database

Peer reviewe

The Pfam protein families database

Peer reviewe

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences