Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.

ABSTRACT: Identification of small polymorphisms from next generation sequencing short read data is relatively easy, but detection of larger deletions is less straightforward. Here, we analyzed four divergent Arabidopsis accessions and found that intersection of absent short read coverage with weak tiling array hybridization signal reliably flags deletions. Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partly reflects a common history of deletion events.

Testing the use of two types of nest box by the common dormouse Muscardinus avellanarius

British mammalogists have used two different systems for surveying the common dormouse Muscardinus avellanarius: a modified bird nest box with the entrance facing the tree trunk, and a smaller, cheaper model called a "nest tube". However, only few data comparing different nest box systems are currently available. To determine which system is more efficient, we compared the use of the large (GB-type) and small nest boxes (DE-type, a commercial wooden mouse trap without a door) in three Swiss forest. The presence of Muscardinus, potential competitors, and any evidence of occupation were examined in 60 pairs of nest boxes based on 2,280 nest box checks conducted over 5 years. Mean annual occupation and cumulative numbers of Muscardinus present were both significantly higher for the DE than for the GB boxes (64.6% versus 32.1%, and 149 versus 67 dormice, respectively). In contrast, the annual occupation by competitors including Glis glis, Apodemus spp. and hole-nesting birds was significantly higher in the GB than in the DE boxes in all forest (19-68% versus 0-16%, depending on the species and forest). These results suggest that smaller nest boxes are preferred by the common dormouse and are rarely occupied by competitors. These boxes hence appear to be preferable for studying Muscardinus populations.

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

BACKGROUND: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. RESULTS: We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. CONCLUSIONS: The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.

Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

1-11-19, stade Bergeyre, football association, équipe de Londres [disputant un match contre Paris] : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 56757

1-11-19, stade Bergeyre, football association, équipe de Londres [disputant un match contre Paris] : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 56758

Urban mobilities: the anglo-catalan production of the Barcelona model

The aim of the project was to gauge the extent to which the so-called ‘Barcelona Model’ of urban transformation has been ‘exported’ to Britain and whether Barcelona has learned from British cities. We engage with the literature on successive British governments’ strategies for cities, focused on collecting data on contemporary policy initiatives and debates in the UK, did interviews in Manchester, London Barcelona and participated in the official visit of Leeds to Barcelona in March. Our research findings to date suggest that there is a good deal of mobility and interaction between Barcelona and the UK. However, it is by no means certain that this has resulted in definite instances of policy transfer. While the ‘Barcelona model’ has indeed featured in oficial discourse on urban regeneration in the UK, it does not appear to be the preferred best practice ‘model’ – other North American and European cities figure discursively as much, if not more. Where Barcelona does feature in official discourse, it is usually as an example of good design and an appealing urban aesthetic, rather than in terms of economic or social policy best practice. Our research suggests that the Barcelona model is seen as non-transferable to the UK due to the relatively more centralised governance structure therein.In contrast, evidence collected suggests that the Barcelona model is not influenced by UK British cities experiences but there is small evidence of being influenced by UK-based professionals.

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi.

ABSTRACT: BACKGROUND: Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. RESULTS: 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. CONCLUSIONS: Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.

Roux-en-Y gastric bypass vs gastric banding for morbid obesity: a case-matched study of 442 patients.

HYPOTHESIS: Gastric banding (GB) and Roux-en-Y gastric bypass (RYGBP) are used in the treatment of morbidly obese patients. We hypothesized that RYGBP provides superior results. DESIGN: Matched-pair study in patients with a body mass index (BMI) less than 50. SETTING: University hospital and regional community hospital with a common bariatric surgeon. PATIENTS: Four hundred forty-two patients were matched according to sex, age, and BMI. INTERVENTIONS: Laparoscopic GB or RYGBP. MAIN OUTCOME MEASURES: Operative morbidity, weight loss, residual BMI, quality of life, food tolerance, lipid profile, and long-term morbidity. RESULTS: Follow-up was 92.3% at the end of the study period (6 years postoperatively). Early morbidity was higher after RYGBP than after GB (17.2% vs 5.4%; P<.001), but major morbidity was similar. Weight loss was quicker, maximal weight loss was greater, and weight loss remained significantly better after RYGBP until the sixth postoperative year. At 6 years, there were more failures (BMI>35 or reversal of the procedure/conversion) after GB (48.3% vs 12.3%; P<.001). There were more long-term complications (41.6% vs 19%; P.001) and more reoperations (26.7% vs 12.7%; P<.001) after GB. Comorbidities improved more after RYGBP. CONCLUSIONS: Roux-en-Y gastric bypass is associated with better weight loss, resulting in a better correction of some comorbidities than GB, at the price of a higher early complication rate. This difference, however, is largely compensated by the much higher long-term complication and reoperation rates seen after GB.

Parc des Princes, rugby, 1/1/20, match France-Écosse : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 57449

Parc des Princes, rugby, 1/1/20, match France-Écosse : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 57453

Parc des Princes, 1/1/20, match France-Écosse [rugby] : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 57454

31-1-20, rugby, match France-Angleterre [à Twickenham] : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 57852

31-1-20, rugby, match France-Angleterre [à Twickenham] : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 57853