Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

<p>Abstract</p> <p>Background</p> <p>Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited.</p> <p>Results</p> <p>We analyzed 3 monoclonal TCR from TCR transgenic, Rag^-/-mice using Illumina^®sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR) 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters.</p> <p>Conclusions</p> <p>Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.</p

Out-of-school girls’ lives in Zimbabwe: what can we learn from a storytelling research approach?

This paper focuses on the experiences of out-of-school girls in Zimbabwe. It draws on a research strand of SAGE (Supporting Adolescent Girls’ Education), a UKAid programme funded through the Foreign, Commonwealth and Development Office’s (FCDO) Girls’ Education Challenge (GEC) initiative. Using a digital storytelling approach the research highlights critical events that have changed girls’ lives and impacted on how they see their futures. The paper explores insights made possible by this alternative methodology. Crucially, it challenges the often-static representation of ‘marginalised’ and ‘out-of-school’ girls in Sub-Saharan Africa by illustrating the unpredictability of individual circumstances and girls’ perceptions of these, within broader contexts of persistent vulnerability factors. Drawing on the capability approach the paper also offers new insights into the perceived value and purpose of school for out-of-school girls. The findings have implications for conceptualising more creative, contextually appropriate policies and practices for young people who miss out on formal school

Influenza in Migratory Birds and Evidence of Limited Intercontinental Virus Exchange

Migratory waterfowl of the world are the natural reservoirs of influenza viruses of all known subtypes. However, it is unknown whether these waterfowl perpetuate highly pathogenic (HP) H5 and H7 avian influenza viruses. Here we report influenza virus surveillance from 2001 to 2006 in wild ducks in Alberta, Canada, and in shorebirds and gulls at Delaware Bay (New Jersey), United States, and examine the frequency of exchange of influenza viruses between the Eurasian and American virus clades, or superfamilies. Influenza viruses belonging to each of the subtypes H1 through H13 and N1 through N9 were detected in these waterfowl, but H14 and H15 were not found. Viruses of the HP Asian H5N1 subtypes were not detected, and serologic studies in adult mallard ducks provided no evidence of their circulation. The recently described H16 subtype of influenza viruses was detected in American shorebirds and gulls but not in ducks. We also found an unusual cluster of H7N3 influenza viruses in shorebirds and gulls that was able to replicate well in chickens and kill chicken embryos. Genetic analysis of 6,767 avian influenza gene segments and 248 complete avian influenza viruses supported the notion that the exchange of entire influenza viruses between the Eurasian and American clades does not occur frequently. Overall, the available evidence does not support the perpetuation of HP H5N1 influenza in migratory birds and suggests that the introduction of HP Asian H5N1 to the Americas by migratory birds is likely to be a rare event

Cephalosporin-resistant Pneumococci and Sickle Cell Disease

Increasingly resistant bacteria in sickle cell disease patients indicate need to evaluate extendedspectrum cephalosporin therapy

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

<p>Abstract</p> <p>Background</p> <p>Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited.</p> <p>Results</p> <p>We analyzed 3 monoclonal TCR from TCR transgenic, Rag^-/-mice using Illumina^®sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR) 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters.</p> <p>Conclusions</p> <p>Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.</p

Benoît XII et les collèges cisterciens du Languedoc

Obert Caroline. Benoît XII et les collèges cisterciens du Languedoc. In: Les cisterciens de Languedoc. Toulouse : Éditions Privat, 1986. pp. 139-150. (Cahiers de Fanjeaux, 21

La guerre d’Algérie au travers des archives du SHAT

Obert Caroline. La guerre d’Algérie au travers des archives du SHAT. In: Bulletin de l'Institut d'Histoire du Temps Présent, n°56, juin 1994. pp. 31-39

Transparence et secret : l'accès aux archives contemporaines

Obert Caroline. Transparence et secret : l'accès aux archives contemporaines. In: Vingtième Siècle, revue d'histoire, n°52, octobre-décembre 1996. Les crises économiques du 20e siècle. pp. 126-128

Quinupristin-Dalfopristin Nonsusceptibility in Pneumococci from Sickle Cell Disease Patients

Sickle cell disease (SCD) is a risk factor for fatal pneumococcal infection. Nonsusceptibilty to quinupristin-dalfopristin (Q-D) was absent from 105 non-SCD-associated pneumococcal isolates but was present in 33/148 (22%) SCD-associated isolates. One-third of the isolates harbored a known resistance mechanism. Q-D is not optimal for use for the treatment of pneumococcal infection in SCD patients

Étude des pratiques enseignantes déclarées concernant le programme de sciences citoyennes Vigie-Nature École

International audienceThis research focuses on teaching practices related to the French citizen science program, Vigie-Nature École (VNE), initiated by the National Museum of Natural History, which studies ordinary biodiversity through standardized protocols. Our study aims to characterize the self-reported practices in order to understand how teachers appropriate this program, at the interface between a biological fieldwork and its dimension of citizen science. An a priori analysis of VNE allows us to define its epistemological stance and to identify its didactical and educational potentialities. A questionnaire collected 254 responses from primary and secondary teachers. The results indicate that the participants assign VNE many objectives, such as raising students' awareness of biodiversity outdoor, working on the scientific inquiry, changing the image of the Nature of Science, engaging in interdisciplinary projects and contributing to scientific research. While the latter objective is strongly emphasized, there is a significant discrepancy in the actual contribution to research. Only half of the participants send data to researchers. This contrast with the intentions of the Museum researchers reflects a misuse by some teachers. A categorization of practices shows contrasting profiles, revealing very different ways of implementing VNE.Cette recherche porte sur les pratiques enseignantes relatives au programme français de sciences citoyennes, Vigie-Nature École (VNE), initié par le Muséum national d’Histoire naturelle étudiant la biodiversité ordinaire par des protocoles standardisés. Notre étude vise à caractériser les pratiques déclarées afin de comprendre comment les enseignants s'approprient ce dispositif, à l’interface entre une étude de terrain et sa dimension de sciences citoyennes. Une analyse a priori de VNE permet de cerner son positionnement épistémologique et de dégager ses potentialités didactiques et éducatives. Un questionnaire a recueilli 254 réponses de professeurs des écoles et de collège-lycée. Les résultats indiquent que les participants assignent à VNE de nombreux objectifs, tels que sensibiliser les élèves à la biodiversité par le terrain, travailler la démarche scientifique, modifier l’image de la nature de la science, engager des projets interdisciplinaires et contribuer à la recherche scientifique. Si ce dernier objectif est fortement mis en avant, un écart important est constaté quant à la contribution effective à la recherche. Seule la moitié des participants envoie les données aux chercheurs. Ce décalage par rapport aux intentions des concepteurs de VNE traduit un détournement d’usage par certains enseignants. Une catégorisation des pratiques permet de dégager des profils contrastés, révélant des façons très différentes de mettre en œuvre VNE