Transmission of MRSA and MSSA between humans and farm animals

Human nares are the main niche of Staphylococcus aureus, but farm animals can be also infected (cows) or colonized (pigs) constituting significant reservoir of this pathogen. Previous studies indicated that human and animal strains are quite distinct but the extent of cross-species specialization and transmission remains largely unknown. However, recent reports from several European countries as well as USA and Canada have indicated that employment in farming is an emerging risk factor for MRSA carriage. Pigs were found to be frequently colonized with MRSA, usually with a strain belonging to CC398. It is not known whether animal-human transmission was specific to this particular MRSA strain. S. aureus isolates from cow mastitis and pig colonization isolates were collected in parallel to nasal swab isolates from the animals' caretakers. The isolates were genotyped by AFLP, spatyping, and when appropriate by MLST. The isolates from cow mastitis were genetically uniform in comparison with human isolates. They were quite distinct from farmers\' carriage isolates, indicating pronounced hostspecialization. However, several cases where an infected cow and a colonized farmer had the same strain were detected, including one farm where two farmers were colonized and two cows were infected with MRSA belonging to CC398. Pig isolates were genetically more diverse than cow isolates. They were different from both human and cow isolates with one notable exception. Large fraction of pigs (20%) and pig caretakers (50%) were colonized with isolates belonging to CC398, majority of which were MSSA (2 cases of MRSA). These results indicate that host specialization in S. aureus is quite pronounced. Transmission between humans and farm animals was consequently quite rare. Both MSSA and MRSA strains belonging to otherwise pig-specific CC398 had increased capacity to colonize humans. Study of the genetic factors responsible for host specialization is underway.

Buccal swabs allow efficient and reliable microsatellite genotyping in amphibians

Buccal swabs have recently been used as a minimally invasive sampling method in genetic studies of wild populations, including amphibian species. Yet it is not known to date what is the level of reliability for microsatellite genotypes obtained using such samples. Allelic dropout and false alleles may affect the genotyping derived from buccal samples. Here we quantified the success of microsatellite amplification and the rates of genotyping errors using buccal swabs in two amphibian species, the Alpine newt Triturus alpestris and the Green tree frog Hyla arborea, and we estimated two important parameters for downstream analyses, namely the number of repetitions required to achieve typing reliability and the probability of identity among genotypes. Amplification success was high, and only one locus tested required two to three repetitions to achieve reliable genotypes, showing that buccal swabbing is a very efficient approach allowing good quality DNA retrieval. This sampling method which allows avoiding the controversial toe-clipping will likely prove very useful in the context of amphibian conservation.

Osakeyhtiömuotoisen maatilan omistajan taloudellinen hyöty verotuksessa

Maatalouden perinteisen harjoittamismuodon, perheviljelmän, rinnalle on viime aikoina noussut yhtiömuotoista maataloutta. Syitä maatilan yhtiöittämiseen on useita, mutta yksi tärkeimmistä lienee osakeyhtiöön sovellettava erilainen verotus. Osakeyhtiömuotoinen maatalous asettaa uusia vaatimuksia erityisesti maatilayhtiön hallinnolle. Etukäteen on mm.selvitettävä viljelijän eläketurvaan liittyvät kysymykset, koska eläkelaki on sidoksissa tulevassa maatilaosakeyhtiössä noudatettavaan verolakiin. Tutkielman tavoitteena on selvittää osakeyhtiömuotoisen maatalouden eroja perinteiseen harjoittamismuotoon verrattuna sekä selvittää, miten tila voidaan toimintamuodon muutoksen kautta yhtiöittää ilman vero-vaikutuksia. Taulukkolaskentaohjelmaan on rakennettu verolaskentamalli ja sen tarkoituksena on toimia tilansa yhtiöittämistä pohtivan viljelijän työkaluna. Malli laskee tilan verorasituksen sekä ammatinharjoittajalle, että osakeyhtiömuotoiselle maataloudelle, ja lopuksi vertaa näitä keskenään. Tutkielmassa on rakennettu myös yksinkertainen malli osakeyhtiö-muotoisen maatalouden avaavasta taseesta, jonka tulee syntyä TVL 24 §:n tasejatkuvuutta ja identtisyyttä noudattaen. Tähän ei ole olemassa selvää ohjetta, vaan on jouduttu käyttämään perusteltuja tulkintoja ja käytäntöjä.

Factores de explotación asociados a la duración del anestro postparto en vacas nodrizas de razas Parda de Montaña y Pirenaica

Para determinar los factores de explotación relacionados con la reactivación ovárica postparto en vacas nodrizas se realizó un análisis global de una serie de indicadores productivos y la duración del anestro postparto (APP) de 549 vacas explotadas en condiciones extensivas. Debido a la naturaleza multifactorial del proceso en estudio se eligió la metodología estadística multivariante (Análisis Factorial de Correspondencias Múltiples y Análisis Cluster). La duración del APP estuvo asociada a cuatro factores que explicaron el 59% de la heterogeneidad inicial de la muestra y que se definieron como: «Alimentación preparto» (19% de la inercia), «Alimentación postparto-Edad» (16.4%), «Manejo del ternero» (13%) y «Dificultad al parto» (10.5%). Estos factores se introdujeron en un Análisis Cluster que identificó cinco grupos de vacas con características productivas y reproductivas diferentes, y que denominamos como: «Primíparas», «Acceso restringido», «Acceso Libre-Parda de Montaña», «Parto de otoño» y «Parto de primavera». La raza no estuvo relacionada con la duración del APP, aunque el análisis Cluster asoció los largos APP inducidos por la crianza libre con la raza Parda de Montaña. En la raza Parda de Montaña, la duración del APP fue mayor en primavera que en otoño debido a diferencias nutricionales más que a un efecto estacional en sí. El parto de otoño se adaptó mejor a las condiciones de montaña seca.

Las condiciones de reproducción de la unidad familiar campesina en la Catalunya Nova: las "Terres de Lleida"

El trabajo intenta evaluar la dimensión mínima de la tierra que debiera poseer la unidad familiar campesina para garantizar su reproducción en el marco histórico de la etapa final de la Edad Moderna. Geográficamente, el trabajo se refiere a las tierras del interior llano catalán, que experimentaron durante el siglo XVIII un notable proceso de colonización agraria para atender los déficits cerealísticos del litoral catalán. Dado que la mayor parte del campesinado no disfruta de explotaciones viables económicamente, se analizan las estrategias campesinas encaminadas a la obtención de ingresos complementarios. Estas, lejos de situarse en actividades no agrarias, tienen una estrecha relación con la agricultura y con el aprovechamiento de los recursos naturales.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Sostenibilidad de la producción porcina en Cataluña (España). Aplicación del análisis multicriterio

La evaluación de la sostenibilidad en modelos de producción porcina en Cataluña (España), mediante el análisis multicriterio, se estructura en dos partes. Una primera de establecimiento del marco de análisis donde, de forma participativa, se fijan los criterios de evaluación, sus indicadores y las escalas de evaluación. En la segunda se implementa la metología expuesta para evaluar la sostenibilidad de tres modelos productivos y detectar posibles conflictos entre los diferentes grupos de interés. Los resultados obtenidos demuestran que desde el punto de vista de la sostenbilidad, en base a los criterios considerados y bajo distintas opciones de robustez, el modelo productivo más sostenible es el ecológico, seguido del familiar y, en último puesto, el del modelo denominado de integración. En cuanto a la formación de coaliciones se observa que hay un importante grupo de actores que apuestan, en primer lugar, por el modelo de integración. Los anteriores resultados avalan la necesidad de potenciar modelos intermedios entre el ecológico y el de integración. Una opción conciliadora, entre las existentes, podría ser el tipo familiar, aplicando algunas mejoras en el manejo si se quieren satisfacer plenamente los requerimientos de sostenibilidad.

L'aprofitament ramader a la vall del Madriu-Perafita-Claror (Principat d'Andorra)

The farming exploitation in the Madriu-Perafita-Claror Valley (Principality of Andorra). The Madriu-Perafita-Claror Valley, a natural space located in the Principality of Andorra, has kept a high ecological and landscape value through time. At present, the Valley is considered in the cultural landscape category of the UNESCO World-wide Heritage. A study of the spatial variability of pastures in the Valley conducted from 1994 to 2003 concluded that there was an optimistic future for livestock. This future was mainly explained by new policies in the country, as well as by the new hopes of the tockbreeders. The study also stated that cattle and horse movements within the Valley did not varied over the study period, although entrance and exit points changed. Sheep only fed in the Madriu-Perafita-Claror Valley, but it wouldbe convenient its introduction in other areas where horses and cattle did not pasture. The study concluded that the use of the Valley by the stockbreeders contributed to the development of the vegetation and the landscape, and that the livestock is very important to keep natural and landscape values of the Valley.

The evolution of alternative splicing patterns and regulatory mechanisms

Alternative splicing produces multiple isoforms from the same gene, thus increasing the number of transcripts of the species. Alternative splicing is a virtually ubiquitous mechanism in eukaryotes, for example more than 90% of protein-coding genes in human are alternatively spliced. Recent evolutionary studies showed that alternative splicing is a fast evolving and highly species- specific mechanism. The rapid evolution of alternative splicing was considered as a contribution to the phenotypic diversity between species. However, the function of many isoforms produced by alternative splicing remains unclear and they might be the result of noisy splicing. Thus, the functional relevance of alternative splicing and the evolutionary mechanisms of its rapid divergence among species are still poorly understood. During my thesis, I performed a large-scale analysis of the regulatory mechanisms that drive the rapid evolution of alternative splicing. To study the evolution of alternative splicing regulatory mechanisms, I used an extensive RNA-sequencing dataset comprising 12 tetrapod species (human, chimpanzee and bonobo, gorilla, orangutan, macaque, marmoset, mouse, opossum, platypus, chicken and frog) and 8 tissues (cerebellum, brain, heart, kidney, liver, testis, placenta and ovary). To identify the catalogue of alternative splicing eis-acting regulatory elements in the different tetrapod species, I used a previously defined computational approach. This approach is a statistical analysis of exons/introns and splice sites composition and relies on a principle of compensation between splice sites strength and the presence of additional regulators. With an evolutionary comparative analysis of the exonic eis-acting regulators, I showed that these regulatory elements are generally shared among primates and more conserved than non-regulatory elements. In addition, I showed that the usage of these regulatory elements is also more conserved than expected by chance. In addition to the identification of species- specific eis-acting regulators, these results may explain the rapid evolution of alternative splicing. I also developed a new approach based on evolutionary sequence changes and corresponding alternative splicing changes to identify potential splicing eis-acting regulators in primates. The identification of lineage-specific substitutions and corresponding lineage-specific alternative splicing changes, allowed me to annotate the genomic sequences that might have played a role in the alternative splicing pattern differences among primates. Finally, I showed that the identified splicing eis-acting regulator datasets are enriched in human disease-causing mutations, thus confirming their biological relevance.

Els assentaments de les edats del bronze, ibèrica i romana d"Els Llirians del Mas i Les Torres (Salàs de Pallars, Pallars Jussà)

[cat] En els anys 2003 i 2004 una intervenció arqueològica preventiva en el terme de Salàs de Pallars va permetre documentar seixanta estructures excavades al subsòl. La majoria de les estructures foren identificades com a sitges, però també es documentaren cubetes i fosses de diversa funció, algunes utilitzades com a sepultures. L"estudi dels materials recuperats, complementats per datacions radiocarbòniques, indiquen dos períodes cronològics: el bronze inicial i l"etapa ibèrica plena, als quals s"ha d"afegir una única estructura que pertany a començaments de l"Imperi romà. Les dades obtingudes informen sobre les pràctiques de les comunitats agrícoles assentades en el sector meridional de la comarca del Pallars Jussà en tres moments històrics diferents. [eng]In 2003 and 2004 a Preventive Archaeological Excavation was done in the locality of Salàs de Pallars. This allowed to catalogue the sixty structures found in the subsoil. Most of the structures were identified as silos, but we also documented basins and pits with different functions, some used as graves. The study of the recovered materials, supported by a radiocarbon analysis technique, ages this around two chronological periods: the Early Bronze Age and Iberian Period. We must add a third period to classify a single structure that belongs to the Early Roman Empire. The obtained results provide us information about the farming methods used by the communities placed in the southern Region of the Pallars Jussà during the three different historical moments.

Propuesta metodológica para la valoración de la producción en empresas ganaderas. Una aplicación práctica al sector ganadero porcino

El objetivo de este trabajo es proponer cuáles son los portadores de coste de las explotaciones ganaderas porcinas intensivas y su valoración. Para ello en primer lugar hemos descrito el proceso productivo para poder determinar los portadores de coste y finalmente la valoración de los mismos así como la producción en curso. Al tratarse de seres biológicos una de las problemáticas que se plantea para la valoración es la existencia de animales fallecidos durante el proceso productivo. A partir de este aspecto proponemos un sistema de valoración de los portadores de coste. Para comprobar que este modelo es factible, desarrollamos en el último apartado una aplicación práctica a los datos de una explotación ganadera porcina. En la elaboración del producto, en cada una de sus fases de transformación, se obtendrán los portadores de coste del proceso de producción y, eslabón a eslabón, se irá completando de forma minuciosa todo el proceso de valoración.

Estudi de la producció i de la qualitat farratgera de les pastures de la finca dels Cingles de l'Avenc (Tavertet). 2011

A Catalunya, la protecció i gestió de zones d’especial interès natural ha estat majoritàriament realitzada pel conjunt de les administracions públiques. Tot i així, en els últims anys han sorgit un conjunt d’iniciatives privades que a través d’acords de custòdia han passat a tenir un paper actiu en la protecció i gestió d’algunes finques amb un alt valor natural. És el cas de la finca els Cingles de l’Avenc, on s’ha dut a terme aquest treball, en la qual es pretén desenvolupar una activitat ramadera compatible amb la conservació dels valors naturals de la finca. L’objectiu principal d’aquest treball és conèixer la producció i qualitat farratgera dels diferents tipus de pastures que hi ha a la finca, i establir la càrrega ramadera que poden admetre. Aquest estudi ha tingut una durada de 3 anys i en aquest treball es presenten els resultats del 2011 i es fa l’anàlisi dels resultats dels 3 anys (2009, 2010, i 2011). L’estudi s’ha portat a terme en els 4 tipus principals de pastures que hi ha a la finca: joncedes, pastures mesòfiles, prats de dall i pastures sembrades. S’han utilitzat 11 parcel·les permanents excloses de la pastura, establertes l’any 2009, que inclouen la diversitat de tipus i zones de pastura. S’ha realitzat un mostreig de la biomassa mensual, d’abril a novembre, que ha consistit en dallar 4 quadrats de 50 x 50 cm, i s’ha calculat la producció anual. S’ha determinat la qualitat farratgera de l’herba de 4 moments de l’any: maig, juny, juliol i octubre. Després dels tres anys d’estudi hem obtingut que les pastures sembrades i els prats de dall són els més productius (1.067 g/m2.any i 1.005 g/m2.any, respectivament). La producció de les pastures mesòfiles i de les joncedes són més baixes (554 g/m2.any i 291 g/m2.any, respectivament). La qualitat farratgera de les pastures és bona a totes les comunitats, amb valors mitjans de proteïna digerible de 6,63%, de fibra bruta de 29,13%, de lignina de 7,29% i de 0,69 (ENL/1,700) unitats farratgeres. La producció anual global obtinguda a la finca durant aquests tres anys permet suportar una càrrega ramadera admissible d’unes 208 UBG (Unitats de Bestiar Gros. 1 U.B.G equival a 1 vaca a partir de 2 anys).

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Khat (Catha edulis Forsk., Celastraceae) is a flowering perennial shrub with a long history of use and cultivation in East Africa and the Arabian Peninsula. Young khat leaves are traditionally chewed in social gatherings to attain special states of mind, aimed especially at awakeness and enhanced mind focus. Since khat chewing contains amphetamine-like molecules and reponedly causes addiction among users it is banned in most countries, but it is part of social life and legal in some countries. The main phannacoactive compounds present in khat leaves are the phenylpropylamino alkaloids (S) cathinone and (S)-cathine. L-Phenylalan:ine serves as a key biosynthetic precursor of phenylpropylalkaloids. Phenylalanine is converted by a series of not yet fully characterized reactions involving chain-shortening to benzaldehyde, then ligation to decarboxylated pyruvate, oxidation and incorporation of an amino group to yield (S)-cath inone, the most active compound accumulating in young leaves. (S)-Cathinone is subsequently reduced to (S)-cathine, the main compound accumulated in mature leaves, but pharmacologically less active than (S)-cathinone. The pharmacological prospects of khat uses and some personal experiences of one of the authors in khat chewing are described here.

Introgressive hybridization of threatened European tree frogs (Hyla arborea) by introduced H. intermedia in Western Switzerland

Hybridization by introduced taxa is a major threat to native species. Characterizing human introductions is thus one of the missions of conservation geneticists. Here we survey a declining population of the regionally endangered European tree frog (Hyla arborea) in the Grangettes natural reserve (Rhone valley, Western Switzerland), where previous evidence indicated human introduction of the Italian taxon H. intermedia. We combined fast-evolving mitochondrial and nuclear markers and an extended sampling to conduct population genetic analyses of the Grangettes and putative source areas. We show that the Grangettes population is a hybrid swarm, with all individuals featuring recent nuclear admixture and mitochondrial DNA of introduced H. intermedia, most likely of proximate south Alpine origin. In contrast, H. arborea and H. intermedia hardly introgress in their natural parapatric ranges, consistent with an advanced reproductive isolation. Thus, potential hybrid incompatibilities may account for the strong decline of this population, despite important conservation efforts. Although their hybrid nature makes them a priori unworthy of any protection, we propose specific measures to recover local H. arborea gene pool and preserve tree frogs in the Grangettes, the last population remaining from this heavily impacted part of the Alps.

A inovação por sustração : contribução para a sociología do distanciamento

To develop the understanding of innovation processes conceptualized in terms of association through the "sociology of translation" (cf. actor-network theory) studies, this article analyses innovation processes in terms of dissociation and detachment mechanisms, examining innovation through "withdrawal"; that is, innovation based on reducing or withdrawing use of a practice - "subtracting", "detaching" - a given artefact. Specifically, it focuses on the shift to farming techniques that have eliminated ploughing, bringing to light four major mechanisms constitutive of dissociation : centrifugal association ; making entities and associations visible ; making other entities and associations invisible; bringing together or " associating " new entities. The study helps refine our understanding of the detachment processes at work in innovation.