Multiple introductions boosted genetic diversity in the invasive range of black cherry (Prunus serotina; Rosaceae).

BACKGROUND AND AIMS: Black cherry (Prunus serotina) is a North American tree that is rapidly invading European forests. This species was introduced first as an ornamental plant, then it was massively planted by foresters in many countries, but its origins and the process of invasion remain poorly documented. Based on a genetic survey of both native and invasive ranges, the invasion history of black cherry was investigated by identifying putative source populations and then assessing the importance of multiple introductions on the maintenance of gene diversity. METHODS: Genetic variability and structure of 23 populations from the invasive range and 22 populations from the native range were analysed using eight nuclear microsatellite loci and five chloroplast DNA regions. KEY RESULTS: Chloroplast DNA diversity suggests there were multiple introductions from a single geographic region (the north-eastern United States). A low reduction of genetic diversity was observed in the invasive range for both nuclear and plastid genomes. High propagule pressure including both the size and number of introductions shaped the genetic structure in Europe and boosted genetic diversity. Populations from Denmark, The Netherlands, Belgium and Germany showed high genetic diversity and low differentiation among populations, supporting the hypothesis that numerous introduction events, including multiple individuals and exchanges between sites, have taken place during two centuries of plantation. CONCLUSIONS: This study postulates that the invasive black cherry has originated from east of the Appalachian Mountains (mainly the Allegheny plateau) and its invasiveness in north-western Europe is mainly due to multiple introductions containing high numbers of individuals.

Biocurators and biocuration: surveying the 21st century challenges.

Curated databases are an integral part of the tool set that researchers use on a daily basis for their work. For most users, however, how databases are maintained, and by whom, is rather obscure. The International Society for Biocuration (ISB) represents biocurators, software engineers, developers and researchers with an interest in biocuration. Its goals include fostering communication between biocurators, promoting and describing their work, and highlighting the added value of biocuration to the world. The ISB recently conducted a survey of biocurators to better understand their educational and scientific backgrounds, their motivations for choosing a curatorial job and their career goals. The results are reported here. From the responses received, it is evident that biocuration is performed by highly trained scientists and perceived to be a stimulating career, offering both intellectual challenges and the satisfaction of performing work essential to the modern scientific community. It is also apparent that the ISB has at least a dual role to play to facilitate biocurators' work: (i) to promote biocuration as a career within the greater scientific community; (ii) to aid the development of resources for biomedical research through promotion of nomenclature and data-sharing standards that will allow interconnection of biological databases and better exploit the pivotal contributions that biocurators are making. DATABASE URL: http://biocurator.org.

La bérylliose chronique, une pathologie sous-diagnostiquée: état des lieux en Suisse

Introduction.- La bérylliose chronique est une granulomatose pulmonaire pour laquelle le diagnostic est rarement posé en raison d'une méconnaissance du risque d'exposition professionnelle au béryllium.En outre, le tableau clinique, les signes radiologiques et les symptômes ressemblent a` une sarcoïdose. Ainsi, la fréquence de la maladie est probablement sous-estimée malgré l'utilisation de béryllium dans la fabrication de nombreux produits industriels et techniques en Suisse, tels que ressorts, prothèses dentaires, micro-électronique... Comme aide au diagnostic, un test de prolifération lymphocytaire au béryllium (BeLPT) a été développé pour évaluer la réponse immunocellulaire spécifique au béryllium. Mais celui-ci présente des inconvénients : utilisation de produits radioactifs, variabilité interlaboratoire importante, valeur prédictive contesteé. L'utilisation de l'Elispot, évaluant également la réponse lymphocytaire pourrait être une alternative au BeLPT. Objectifs.- Les objectifs de l'étude sont, d'une part, de déceler parmi les cas de sarcoïdose du registre SIOLD (Swiss Group for Interstitial and Orphan Lung Diseases) des cas de bérylliose sous-diagnostiqués et, d'autre part, d'améliorer les tests de de´pistage (questionnaire et test immunologique) de sensibilisation et de diagnostic. Méthode.- Cent soixante autoquestionnaires évaluant l'exposition professionnelle au béryllium ont été adressés à des patients référencés dans le registre SIOLD, souffrant de sarcoïdose. Les patients relatant dans l'autoquestionnaire un contact professionnel avec le béryllium ont bénéficié d'une visite médicale à l'Institut universitaire romand de santé au travail (IST) comportant une anamnèse professionnelle, un questionnaire spécifique à l'exposition au béryllium (questionnaire de Cherry) et une prise de sang. Par la suite, le sang a été analysé par Elispot pour évaluer la possibilité d'une sensibilisation au béryllium. En parallèle, des patients déjà diagnostiqués pour une bérylliose par un BeLPT ont servi de cas contrôle positifs pour la mise en place du test. Résultats.- Cinquante pour cents des autoquestionnaires adressés aux patients du registre SIOLD ont été renvoyés. Parmi ceux-ci, 33 %(26 personnes) rapportaient une exposition professionnelle possible au béryllium et ont été reçus a` l'IST pour compléter l'anamnèse professionnelle et répondre au questionnaire adapté de Cherry. Il ressort de ce questionnaire que 3 personnes ont effectivement travaillé avec du béryllium au cours de leur carrière professionnelle et que 4 ont potentiellement été exposées dans le contexte de leur environnement professionnel. Tous les patients ont été testés par Elispot, mais aucun n'a montré de prolifération évoquant une sensibilisation au béryllium. Des résultats supplémentaires devraient être disponibles dès février. Conclusion.- Au vu de ces résultats où seules 7 personnes sur les 80 ayant répondu au questionnaire (8 %) sont suspectées d'avoir été exposées directement ou indirectement au béryllium au cours de leur activité professionnelle, il est possible que le risque d'exposition au béryllium soit anecdotique, malgré une utilisation importante de ce métal dans certaines régions de Suisse. Une hypothèse envisageable est que la population de l'étude ne soit pas représentative de la population exposée. En outre, le fait que les tests lymphocytaires effectués sur les 7 personnes ayant rapporté une exposition au béryllium soient revenus négatifs peut être expliqué de 2 manières : soit que chez ces personnes, la maladie pulmonaire n'est pas due au béryllium, même si l'anamnèse professionnelle est positive et qu'il s'agit bien d'une sarcoïdose, soit que la prise de corticoïdes modifie la réponse immunitaire, soit que le test n'est pas suffisamment sensible.

Middle and Late Jurassic carbon stable-isotope stratigraphy and radiolarite sedimentation of the Umbria-Marche basin (Central Italy)

A continuous carbon isotope curve from Middle-Upper Jurassic pelagic carbonate rocks was acquired from two sections in the southern part of the Umbria-Marche Apennines in central Italy. At the Colle Bertone section (Terni) and the Terminilletto section (Rieti), the Upper Toarcian to Bajocian Calcari e Marne a Posidonia Formation and the Aalenian to Kimmeridgian Calcari e Marne a Posidonia and Calcari Diasprigni formations were sampled, respectively. Biostratigraphy in both sections is based on rich assemblages of calcareous nannofossils and radiolarians, as well as some ammonites found in the upper Toarcian-Bajocian interval. Both sections revealed a relative minimum of delta(13)C(PDB) close to + 2 parts per thousand in the Aalenian and a maximum around 3.5 parts per thousand in early Bajocian, associated with an increase in visible chert. In basinal sections in Umbria-Marche, this interval includes the very cherry base of the Calcari Diasprigni Formation (e.g. at Valdorbia) or the chert-rich uppermost portion of the Calcari a Posidonia (e.g at Bosso). In the Terminilletto section, the Bajocian-early Barthonian interval shows a gradual decrease in delta(13)C(PDB) values and a low around 2.3 parts per thousand. This part of the section is characterised by more than 40 m of almost chart-free limestones and correlates with a recurrence of limestone-rich facies in basinal sections at Valdorbia. A double peak with values of delta(13)C(PDB) around + 3 parts per thousand was observed in the Callovian and Oxfordian, constrained by well preserved radiolarian faunas. The maxima lie in the Callovian and the middle Oxfordian, and the minimum between the two peaks should be near the Callovian/Oxfordian boundary. In the Terminilletto section, visible chert increases together with delta(13)C(PDB) values from the middle Bathonian and reaches peak values in the Callovian-Oxfordian. In basinal sections in Umbria-Marche, a sharp increase in visible chert is observed at this level within the Calcari Diasprigni. A drop of delta(13)C values towards + 2 parts per thousand occurs in the Kimmeridgian and coincides with a decrease of visible chert in outcrop. The observed delta(13)C positive anomalies during the early Bajocian and the Callovian-Oxfordian may record changes in global climate towards warmer, more humid periods characterised by increased nutrient mobilisation and increased carbon burial. High biosiliceous (radiolarians, siliceous sponges) productivity and preservation appear to coincide with the delta(13)C positive anomalies, when the production of platform carbonates was subdued and ceased in many areas, with a drastic reduction of periplatform ooze input in many Tethyan basins. The carbon and silica cycles appear to be linked through global warming and increased continental weathering. Hydrothermal events related to extensive rifting and/or accelerated oceanic spreading may be the endogenic driving force that created a perturbation of the exogenic system (excess CO2 into the atmosphere and greenhouse conditions) reflected by the positive delta(13)C shifts and biosiliceous episodes.

Guidelines for the use and interpretation of assays for monitoring autophagy.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Downregulation of cannabinoid receptor 1 from neuropeptide Y interneurons in the basal ganglia of patients with Huntington's disease and mouse models.

Cannabinoid receptor 1 (CB(1) receptor) controls several neuronal functions, including neurotransmitter release, synaptic plasticity, gene expression and neuronal viability. Downregulation of CB(1) expression in the basal ganglia of patients with Huntington's disease (HD) and animal models represents one of the earliest molecular events induced by mutant huntingtin (mHtt). This early disruption of neuronal CB(1) signaling is thought to contribute to HD symptoms and neurodegeneration. Here we determined whether CB(1) downregulation measured in patients with HD and mouse models was ubiquitous or restricted to specific striatal neuronal subpopulations. Using unbiased semi-quantitative immunohistochemistry, we confirmed previous studies showing that CB(1) expression is downregulated in medium spiny neurons of the indirect pathway, and found that CB(1) is also downregulated in neuropeptide Y (NPY)/neuronal nitric oxide synthase (nNOS)-expressing interneurons while remaining unchanged in parvalbumin- and calretinin-expressing interneurons. CB(1) downregulation in striatal NPY/nNOS-expressing interneurons occurs in R6/2 mice, Hdh(Q150/Q150) mice and the caudate nucleus of patients with HD. In R6/2 mice, CB(1) downregulation in NPY/nNOS-expressing interneurons correlates with diffuse expression of mHtt in the soma. This downregulation also occludes the ability of cannabinoid agonists to activate the pro-survival signaling molecule cAMP response element-binding protein in NPY/nNOS-expressing interneurons. Loss of CB(1) signaling in NPY/nNOS-expressing interneurons could contribute to the impairment of basal ganglia functions linked to HD.

Recent advances in biocuration: meeting report from the fifth International Biocuration Conference.

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration's (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB's goal to support exchanges among members of the biocuration community. Next year's conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society's activities (http://biocurator.org), as well as related events of interest.

Plastid DNA variation in Prunus serotina var. serotina (Rosaceae), a North American tree invading Europe

Black cherry (Prunus serotina) is a tree from North America, where it is often used for economical purposes, whereas it is widespread and invasive in Europe. Plastid DNA variation was Wrst investigated in both its native and invasive ranges using microsatellite loci and sequences of three intergenic spacers (trnT-trnL, trnD-trnT and trnS-trnG). This analysis was focused on P. serotina var. serotina, with the inclusion of samples of closely related taxa. Length variation at a microsatellite locus (ccmp5) and a few sequence polymorphisms were identi- Wed among P. serotina samples. Four new primer pairs were then designed to speciWcally amplify variable regions and a combination of Wve markers was Wnally proposed for phylogeographic studies in P. serotina. These loci allow identiWcation of six chlorotypes in P. serotina var. serotina, which may be particularly useful to depict the maternal origins of European invasive populations