Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets

The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene expression pattern features of any large zebrafish gene set

Case of Frugivory in a Green Treefrog (Hyla cinerea) from Northeastern Arkansas

An adult green treefrog (Hyla cinerea) was collected in mid-September 2014 from Jonesboro, Craighead County, Arkansas. Contents included the remains of a beetle and two fruits. The contents were photographed, measured, and identified to the lowest achievable taxonomic level. The beetle was identified as a spotted cucumber beetle (Diabrotica undecimpuncta howardi Barber [Coleoptera: Chrysomelidae]). The fruits were identified as Persicaria sp. (likely P.punctata (Elliot) Small; Polygonaceae) and Oryza sativa L. (Poaceae). Fruits in the stomachs of frogs are rarely reported in the literature, but could represent possible mechanisms for seed dispersal in plants. It is unknown if frogs select to sometimes eat fruits or if fruits are a by-product of animal prey capture or missed predation attempts. In any case, the goal of this report is to raise awareness of a poorly documented phenomenon in an effort to direct attention to this possible method of seed dispersal

Risorse per la produzione di forme scritte di Lingua dei Segni tramite un software centrato sull'utilizzatore (SWift)

ISI CITATION INDEX - WOS 00032392773138 - IDS BGR95International audienceThe SignWriting improved fast transcriber (SWift), presented in this paper, is an advanced editor for computer-aided writing and transcribing of any Sign Language (SL) using SignWriting (SW). The application is an editor which allows composing and saving desired signs using the SW elementary components, called “glyphs”. These make up a sort of alphabet, which does not depend on the national Sign Language and which codes the basic components of any sign. The user is guided through a fully-automated procedure, making the composition process fast and intuitive. SWift pursues the goal of helping to break down the "electronic barriers" that keep deaf people away from the web, and at the same time to support linguistic research about Sign Languages features. For this reason it has been designed with a special attention to deaf user needs, and to general usability issues. The editor has been developed in a modular way, so it can be integrated everywhere the use of SW as an alternative to written “verbal” language may be advisable.Le SignWriting improved fast transcriber (SWift), présenté dans cet article, est un éditeur avancé pour l'écriture et la transcription assistées par ordinateur de toute Langue des Signes (SL) en utilisant SignWriting (SW). L'application est un éditeur qui permet de composer et de sauvegarder les signes souhaités en utilisant les unités constitutives de SW, appelés "glyphes". Ils constituent une sorte d'alphabet, qui ne dépend pas de la Langue des Signes nationale et qui codifie les éléments de base de tout Signe. L'utilisateur est guidé par un procédé entièrement automatisé, ce qui rend le processus de composition rapide et intuitif. SWift poursuit l'objectif d'aider à briser les "barrières électroniques" qui empêchent les personnes sourdes d’accéder à la Toile, et en même temps de soutenir la recherche linguistique sur les caractéristiques des Langues des Signes. Pour cette raison, il a été conçu avec une attention particulière aux besoins des utilisateurs sourds, et à des questions générales de convivialité. L'éditeur a été développé de façon modulaire, de sorte qu'il peut être intégré partout où l'utilisation de SW comme alternative à la langue écrite "verbale" peut être souhaitable.Il "SignWriting improved fast transcriber" (SWift), presentato in questo articolo, è un avanzato editor di scrittura e trascrizione "computer-aided" mediante SignWriting (SW) per qualsiasi Lingua dei Segni (SL). L'applicazione è un editor che permette di comporre e salvare i segni desiderati utilizzando le componenti elementari di SW, chiamate "glifi". Queste costituiscono una sorta di alfabeto, che non dipende dalla Lingua dei Segni nazionale, che codifica gli elementi di base di qualsiasi segno. L'utente è guidato attraverso una procedura completamente automatica, rendendo così il processo di composizione veloce ed intuitivo. SWift persegue l'obiettivo di aiutare ad abbattere le "barriere elettroniche" che tengono le persone sorde lontane dal web, e allo stesso tempo di sostenere la ricerca linguistica sulle caratteristiche delle Lingue dei Segni. Per questo motivo è stato progettato con una particolare attenzione alle esigenze degli utenti sordi, ma anche in una ottica di usabilità generale. L'editor è stato sviluppato in modo modulare, quindi può essere integrato ovunque sia consigliabile l'uso di SW in alternativa alla lingua scritta "verbale"

Stress indicators in steers at slaughtering

This work aimed to assess the blood modifications of some slaughtering-linked stress hormones in cattle subject to butcher standardized procedures. The blood samples of 20 Limousine 12-13 months old steers have been collected before slaughtering, during lairage, and after stunning by captive bolt gun, during exsanguination. The plasma level of epinephrine, norepinephrine, cortisol and beta-endorphin have been assayed by EIA. The data indicate that catecholamines, cortisol and beta-endorphin did not significantly increase after stunning in these animals

Pig, F1 (wild boar x pig) and wild boar meat quality

Sixteen carcasses of wild boars, pigs, hybrids F1 (wild boar x pig) and reared wild boar have been examined to study the meat quality and the fatty acid composition. Four carcasses came from hunted wild boars and twelve from animals reared in outdoor pens till nine months of age. The meat produced by the hunted wild animals, although not marketable, offers the best quality and nutritional characteristics. The use of hybrids reared in outdoor pens can approximate or equalize the hunted wild boars meat traits. Reared wild boar meat has, in the complex, better compositional characters than hybrids and domestic groups, but acidic quality of fat is not particularly useful for human feeding

Synthetic/ECM-inspired hybrid platform for hollow microcarriers with ROS-triggered nanoporation hallmarks

Reactive oxygen species (ROS) are key pathological signals expressed in inflammatory diseases such as cancer, ischemic conditions and atherosclerosis. An ideal drug delivery system should not only be responsive to these signals but also should not elicit an unfavourable host response. This study presents an innovative platform for drug delivery where a natural/synthetic composite system composed of collagen type I and a synthesized polythioether, ensures a dual stimuli-responsive behaviour. Collagen type I is an extracellular matrix constituent protein, responsive to matrix metalloproteinases (MMP) cleavage per se. Polythioethers are stable synthetic polymers characterized by the presence of sulphur, which undergoes a ROS-responsive swelling switch. A polythioether was synthesised, functionalized and tested for cytotoxicity. Optimal conditions to fabricate a composite natural/synthetic hollow sphere construct were optimised by a template-based method. Collagen-polythioether hollow spheres were fabricated, revealing uniform size and ROS-triggered nanoporation features. Cellular metabolic activity of H9C2 cardiomyoblasts remained unaffected upon exposure to the spheres. Our natural/synthetic hollow microspheres exhibit the potential for use as a pathological stimuli-responsive reservoir system for applications in inflammatory diseases

Effects of legume seeds and processing treatment on growth, carcass traits and blood constituents of fattening lambs

This study aimed to evaluate the effects of faba bean, white lupin and pea seed when fed as protein supplements on growth performance, carcass characteristics and haematological characteristics of growing lambs. Forty-eight Gentile di Puglia male lambs, weaned at 38 ± 2 days old with an average initial bodyweight of 12.8 ± 0.5 kg, were divided into six homogenous groups. The six dietary treatments were RFB (diet containing raw faba bean seeds); EFB (diet containing extruded faba bean seeds); RL (diet containing raw lupin seeds); EL (diet containing extruded lupin seeds); RP (diet containing raw pea seeds); and EP (diet containing extruded pea seeds). Feeding lupin seeds reduced average daily feed intake compared with the other protein sources. Carcass conformation, loin weight as a percentage of half-carcass weight, and fat weight as a percentage of loin weight improved in the lambs that consumed both EP and RP diets. Extrusion reduced hide weight as a percentage of empty bodyweight and fat weight as a percentage of leg weight. The protein source had a significant effect on glucose and total cholesterol concentrations, albumin, α1-globulin, β-globulin, and γ-globulin percentages and albumin-globulin ratios. The processing treatment decreased total cholesterol concentrations. Thus, feeding the various legumes did not affect growth performance, but only carcass characteristics; changes which may be due to the differences in feed intake. Extrusion also had minor effects, and further work is required to investigate the use of these protein sources, both raw and extruded.Keywords: extrusion, faba bean, haematology, lupin, pea, protein source, slaughter dat