Genome sequence of Plesiomonas shigelloides strain 302-73 (serotype O1)

Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium associated with human diarrheal and extraintestinal disease. We present the whole-genome sequence analysis of the representative strain for the O1 serotype (strain 302-73), providing a tool for studying bacterial outbreaks, virulence factors, and accurate diagnostic methods.

Venttiili- ja toimilaitetehtaan tuotannon suunnittelu

Venttiili- ja toimilaitetehtaassa kokoonpannaan erilaisia venttiilityyppejä sekä toimi- laitteita. Koko Metso Automationin Helsingin tehtaiden tuotantotilanteen muuttuessa käynnistettiin kehitysprojekti, jonka tarkoituksena oli uudenaikaistaa venttiilien ja toimilaitteiden valmistus vastaamaan nykypäivän vaatimuksia. Laajamittaisen osa- valmistuksen ulkoistuksen ja tuotteiston muutoksen vuoksi tuotannon uudelleen- järjestäminen oli välttämätöntä. Diplomityön tarkoituksena oli suunnitella venttiili- ja toimilaitetehtaan layout sekä uutta tuotantotilannetta vastaavat toimintatavat. Haasteena oli kolmen hyvin erilailla toimivan tuotetehtaan yhdistäminen yhdeksi kokonaisuudeksi, jossa kunkin tehtaan parhaat toimintatavat yhdistyvät. Nykyinen tuotanto ja valmistusmäärät kartoitettiin ja analysoitiin, minkä jälkeen tuotannon suunnittelu uusiin tiloihin käynnistettiin. Työ jaettiin järjestelmällisesti osiin teorian ja käytännön osuuksien kesken siten, että teoria tukee työn käytännön- osuutta. Apuna käytettiin useita erilaisia materiaalivirtojen kartoitusmenetelmiä, lukuisia mittareita, selvityksiä, ennusteita ja erilaisia malleja tulevasta tuotannosta. Layout suunniteltiin käytössäolevaan tehdashalliin, mikä aiheutti runsaasti haasteita ja rajoitteita. Aikataulu tehtiin tarkasti siten, että muuttojärjestys lyötiin lukkoon, mutta kuormitustilanne ja koneiden siirrot aiheuttivat muutoksia aikataulussa. Tavoite tuotannon häiriöttömyydestä toteutui hyvin aikataulun kustannuksella. Käytännönosuudessa tarkasteltiin erityisesti kapasiteetin joustavuutta kuormituksen vaihdellessa sekä kehitettiin toimintatavat, joilla se hallitaan. Lisäksi tutkimuksen aikana käynnistettiin useita kehitysprojekteja työn tulosten pohjalta. Näitä olivat erilaiset varaston hallintaan sekä solujen itseohjautuvuuteen liittyvät asiat. Diplomityön tuloksena saatiin uusi layout sekä sitä tukeva uusi toimintatapa, solujen itseohjautuvuuden kehittäminen käynnistettiin, varastojen hallinnan osittainen ulkoistaminen aloitettiin. Lisäksi tuotannolle kehitettiin lukuisia seurantamittareita. Layoutprojekti toteutettiin loppuun diplomityön aikana

Exploring Different Types of Sharing: A Proposed Segmentation of the Market for "Sharing Businesses"

Sharing instead of buying is regaining traction among today's consumers. This study aims at identifying segments of sharing consumers to unearth potentially viable clusters of a consumer behavior that is a market of growing economic relevance. By means of a qualitative study and a survey with a roughly representative sample of 1121 Swiss-German and German consumers, a set of trait-related, motivational, and perceived socioeconomic variables is identified that can be used to group individuals into segments that differ with regard to their approach to sharing. A cluster analysis based on these variables suggests four potential clusters of sharing consumers-sharing idealists, sharing opponents, sharing pragmatists, and sharing normatives. Two sets of testable propositions are derived that can guide further research in this domain and pave the way to a more targeted approach to the growing market of "sharing" businesses.

The structure of human tRNALys3 anticodon bound to HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.

Complete genome sequence of the type strain of Bacillus toyonensis BCT-7112T, the active ingredient of the feed additive preparation Toyocerin

Strain BCT-7112, previously identified as Bacillus cereus var. toyoi, is the type strain of the species Bacillus toyonensis, a novel species of the B. cereus group. The complete genome of this strain, which is the active ingredient of the feed additive preparation Toyocerin, has been sequenced and annotated to reveal the genetic properties of this probiotic organism with a long history of safe use in animal nutrition.

Explorer les intersections entre la science forensique et la criminologie au travers de la temporalité de trois types d'actions de contrôle social

Our contribution aims to explore some intersections between forensic science and criminology through the notion of time. The two disciplines analyse the vestiges of illicit activities in order to reconstruct and understand the past, and occasionally to prevent future harms. While forensic science study the material and digital traces as signs of criminal activities and repetitions, criminology contributes to the acquisition of knowledge through its analysis of crime, its authors and victims, as well as social (re)actions to harmful behaviours. Exploratory, our contribution proposes a conceptual delimitation of the notion of time considering its importance in the study of criminality and harms. Through examples, we propose a "crimino-forensic" analysis of three types of actions of social control - prevention, investigation and intelligence - through their respective temporality (before, near or during and after the criminal activity or harm). The temporal issues of the different methodologies developed to appreciate the efficiency of these actions are also addressed to highlight the connections between forensic science and criminology. This attempt to classify the relations between different times and actions of social control are discussed through the multiple benefits and challenges carried out by the formalisation of fusing those two sciences. Notre contribution vise à explorer quelques intersections entre la science forensique (ou criminalistique) et la criminologie au travers de la notion de temps. En effet, les deux disciplines ont en commun qu'elles analysent les vestiges du phénomène criminel pour tenter de reconstruire et comprendre le passé et parfois prévenir de futurs incidents. Alors que la science forensique étudie les traces matérielles et numériques comme signe d'activités et de répétitions criminelles, la criminologie contribue à l'avancée des connaissances en ce domaine par son analyse des comportements contraires aux normes, de leurs auteurs et de leurs victimes, ainsi que des (ré)actions sociales à ces comportements. A but exploratoire, notre contribution propose une délimitation conceptuelle de la notion de temps en regard de l'importance que revêtent ses différentes manifestations dans l'étude de la criminalité. A l'appui d'exemples, nous proposons une analyse « crimino-forensique » de trois types d'action de contrôle social - la prévention, l'investigation et le renseignement - en fonction de leur temporalité respective (avant, proche voire pendant et après l'activité criminelle). Les enjeux temporels entourant les différentes stratégies méthodologiques développées pour apprécier l'efficacité de ces actions sont aussi abordés pour mettre en évidence des pistes d'intégration entre la science forensique et la criminologie. Cet essai de classification des relations entre les temps et ces trois actions de contrôle social est discuté sous l'angle des bénéfices, multiples, mais aussi des défis, que pose la formalisation des liens entre ces deux disciplines des sciences criminelles.

Types of stereoselectivity in drug metabolism: a heuristic approach.

Stereochemical factors are known to play a significant role in the metabolism of drugs and other xenobiotics. Following Prelog's lead, types of metabolic stereoselectivity can be categorized as (i) substrate stereoselectivity (the differential metabolism of two or more stereoisomeric substrates) and (ii) product stereoselectivity (the differential formation of two or more stereoisomeric metabolites from a single substrate). Combinations of the two categories exist as (iii) substrate-product stereoselectivities, meaning that product stereoselectivity itself is substrate stereoselective. Here, published examples of metabolic stereoselectivities are examined in the light of these concepts. In parallel, a graphical scheme is presented with a view to facilitate learning and help researchers to solve classification problems.

Bone structure assessed by HR-pQCT, TBS and DXL in adult patients with different types of osteogenesis imperfecta.

UNLABELLED: Bone microarchitecture by high-resolution peripheral quantitative computed tomography (HR-pQCT) was assessed in adult patients with mild, moderate, and severe osteogenesis imperfecta (OI). The trabecular bone score (TBS), bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA), and dual X-ray and laser (DXL) at the calcaneus were likewise assessed in patients with OI. Trabecular microstructure and BMD in particular were severely altered in patients with OI. INTRODUCTION: OI is characterized by high fracture risk but not necessarily by low BMD. The main purpose of this study was to assess bone microarchitecture and BMD at different skeletal sites in different types of OI. METHODS: HR-pQCT was performed in 30 patients with OI (mild OI-I, n = 18 (41.8 [34.7, 55.7] years) and moderate to severe OI-III-IV, n = 12 (47.6 [35.3, 58.4] years)) and 30 healthy age-matched controls. TBS, BMD by DXA at the lumbar spine and hip, as well as BMD by DXL at the calcaneus were likewise assessed in patients with OI only. RESULTS: At the radius, significantly lower trabecular parameters including BV/TV (p = 0.01 and p < 0.0001, respectively) and trabecular number (p < 0.0001 and p < 0.0001, respectively) as well as an increased inhomogeneity of the trabecular network (p < 0.0001 and p < 0.0001, respectively) were observed in OI-I and OI-III-IV in comparison to the control group. Similar results for trabecular parameters were found at the tibia. Microstructural parameters were worse in OI-III-IV than in OI-I. No significant differences were found in cortical thickness and cortical porosity between the three subgroups at the radius. The cortical thickness of the tibia was thinner in OI-I (p < 0.001), but not OI-III-IV, when compared to controls. CONCLUSIONS: Trabecular BMD and trabecular bone microstructure in particular are severely altered in patients with clinical OI-I and OI-III-IV. Low TBS and DXL and their significant associations to HR-pQCT parameters of trabecular bone support this conclusion.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite.

A new approach for the separation of spermatozoa from other cell types in forensically relevant samples.

Due to imbalance in genetic material contribution, gynecological samples collected following a sexual assault are challenging to process in order to resolve the male contributor's DNA profile. We set up a new and fast procedure for the recovery and separation of cells from cotton swabs, or other supports. Using spermatozoa specific CD52 antibody coupled to magnetic beads along with magnetic columns, this procedure was first developed and optimized by flow cytometry. It allows the recovery of two enriched cell fractions: a sperm fraction, mostly enriched with the alleged offender's spermatozoa, and a non-sperm fraction, mostly enriched with cells from the victim. Processing fresh as well as six months old mock samples, made of buccal swabs loaded with sperm dilutions, resulted in full single NGM SElect DNA profiles of the sperm donors, respectively the epithelial cells donors, for the sperm and the non-sperm fractions. Untreated duplicate samples processed in parallel only provided the autosomal DNA profiles of the epithelial cells donors. This new procedure can be rapidly tested and adopted by forensic laboratories worldwide as it uses material already commercially available. Moreover it can be easily automated with existing platform, and could therefore provide a mean to rapidly reduce existing backlogs.

High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes

Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfish is mortality due to several pathogens, especially viral diseases which are not treatable. In order to identify new genes involved in immune defense, we conducted 454-pyrosequencing of the turbot transcriptome after different immune stimulations.

Capillarity and fibre types in locomotory muscles of wild yellow-legged gulls (Larus cachinnans)

This study analyzes the capillarity and fibre-type distribution of six locomotory muscles of gulls. The morphological basis and the oxygen supply characteristics of the skeletal muscle of a species with a marked pattern of gliding flight are established, thus contributing to a better understanding of the physiology of a kind of flight with low energetic requirements. The four wing muscles studied (scapulotriceps, pectoralis, scapulohumeralis, and extensor metacarpi) exhibited higher percentages of fast oxidative glycolytic fibres (>70%) and lower percentages of slow oxidative fibres (<16%) than the muscles involved in nonflight locomotion (gastrocnemius and iliotibialis). Capillary densities ranged from 816 to 1,233 capillaries mm(-2), having the highest value in the pectoralis. In this muscle, the fast oxidative glycolytic fibres had moderate staining for succinate dehydrogenase and relatively large fibre sizes, as deduced from the low fibre densities (589-665 fibres mm(-2)). All these findings are seen as an adaptive response for gliding, when the wing is held outstretched by isometric contractions. The leg muscles studied included a considerable population of slow oxidative fibres (>14% in many regions), which suggests that they are adapted to postural activities. Regional variations in the relative distributions of fibre types in muscle gastrocnemius may reflect different functional demands placed on this muscle during terrestrial and aquatic locomotion. The predominance of oxidative fibres and capillary densities under 1,000 capillaries mm(-2) in leg muscles is probably a consequence of an adaptation for slow swimming and maintenance of the posture on land rather than for other locomotory capabilities, such as endurance or sprint activities.