Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool

<p>Abstract</p> <p>Background</p> <p>Roche 454 pyrosequencing platform is often considered the most versatile of the Next Generation Sequencing technology platforms, permitting the sequencing of large genomes, the analysis of variations or the study of transcriptomes. A recent reported bias leads to the production of multiple reads for a unique DNA fragment in a random manner within a run. This bias has a direct impact on the quality of the measurement of the representation of the fragments using the reads. Other cleaning steps are usually performed on the reads before assembly or alignment.</p> <p>Findings</p> <p>PyroCleaner is a software module intended to clean 454 pyrosequencing reads in order to ease the assembly process. This program is a free software and is distributed under the terms of the GNU General Public License as published by the Free Software Foundation. It implements several filters using criteria such as read duplication, length, complexity, base-pair quality and number of undetermined bases. It also permits to clean flowgram files (.sff) of paired-end sequences generating on one hand validated paired-ends file and the other hand single read file.</p> <p>Conclusions</p> <p>Read cleaning has always been an important step in sequence analysis. The pyrocleaner python module is a Swiss knife dedicated to 454 reads cleaning. It includes commonly used filters as well as specialised ones such as duplicated read removal and paired-end read verification.</p

Primal-dual interior point optimization for a regularized reconstruction of NMR relaxation time distributions

International audienceThis paper deals with the reconstruction of relaxation time distributions in Nuclear Magnetic Resonance (NMR) spectroscopy. This large scale and ill-posed inverse problem is solved by the iterative minimization of a regularized objective function allowing to encode some prior assumptions on the sought distribution. The numerical optimization of the criterion is performed using a primal-dual interior point algorithm allowing to handle the non-negativity constraint. The performances of the proposed approach are illustrated through the processing of real data from a two-dimensional NMR experiment

Reconstruction d'un spectre RMN 2D par maximum d'entropie

International audienceLa résonance magnétique nucléaire (RMN) est une méthode moderne de spectroscopie utilisée pour l'analyse de la composition de produits biologiques. Nous nous intéressons dans cet article à l'estimation d'un spectre corrélation T1-T2 à partir de mesures RMN. Les difficultés de l'estimation sont liées au caractère mal-posé de ce problème inverse et à la taille importante des données à traiter. La méthode d'estimation est fondée sur le Maximum d'Entropie et nous proposons deux algorithmes de reconstruction itérative ; le premier est fondé sur l'algorithme de Bryan et Skilling et le second utilise le gradient conjugué non-linéaire. Par ailleurs, la structure du modèle d'observation est avantageusement exploitée pour alléger le coût de calcul sans employer les approximations proposées récemment par Vankataramanan et al. De plus, nous proposons le rajout d'une étape de recherche de pas adaptée à la fonction entropique afin d'assurer une décroissance du critère. Les algorithmes sont évalués sur un exemple synthétique et leur applicabilité est illustrée sur des données réelle

From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploration

From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploratio

The ruminal level of trans-10 fatty acids of dairy cows is linked to the composition of bacterial community

The ruminal level of trans-10 fatty acids of dairy cows is linked to the composition of bacterial communit

Classification non supervisée d'un graphe de co-expression avec des méta-données pour la détection de micro-ARNs

National audienceNous présentons dans cet article une méthode de classification non supervisée de sommets d'un graphe qui est utilisée dans un contexte biologique particulier. La problématique est de détecter de manière non supervisée des micro-ARNs probables. Pour ce faire, nous utilisons une approche multi-noyaux permettant d'intégrer des informations sur le graphe de co-expression et des informations supplémentaires sur les sommets de ce graphe. Cette approche est rendue robuste par une technique de bagging de classifications. Les résultats obtenus donnent des groupes de miRNAs potentiels dont certains permettent de discriminer avec une bonne confiance les vrais miRNAs des faux positifs

Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells.

We studied the sub-population level evolution of a duck influenza A virus isolate during passage in swine tracheal cells. The complete genomes of the A/mallard/Netherlands/10-Nmkt/1999 strain and its swine cell-passaged descendent were analysed by 454 pyrosequencing with coverage depth ranging from several hundred to several thousand reads at any point. This allowed characterization of defined minority sub-populations of gene segments 2, 3, 4, 5, 7, and 8 present in the original isolate. These minority sub-populations ranged between 9.5% (for segment 2) and 46% (for segment 4) of their respective gene segments in the parental stock. They were likely contributed by one or more viruses circulating within the same area, at the same period and in the same or a sympatric host species. The minority sub-populations of segments 3, 4, and 5 became extinct upon viral passage in swine cells, whereas the minority sub-populations of segments 2, 7 and 8 completely replaced their majority counterparts. The swine cell-passaged virus was therefore a three-segment reassortant and also harboured point mutations in segments 3 and 4. The passaged virus was more homogenous than the parental stock, with only 17 minority single nucleotide polymorphisms present above 5% frequency across the whole genome. Though limited here to one sample, this deep sequencing approach highlights the evolutionary versatility of influenza viruses whereby they exploit their genetic diversity, predilection for mixed infection and reassortment to adapt to a new host environmental niche.This work was supported by a grant from DEFRA and HEFCE under the Veterinary Training and Research Initiative to the Cambridge Infectious Diseases Consortium (VB, LT), BBSRC grants BB/H014306/1 and BB/G00479X/1 (LT), and the French Ministry of Agriculture, INRA and the French Région Midi-Pyrénées (GC, J-LG, VB).This is the accepted version of the original version available at: http://dx.doi.org/10.1016/j.meegid.2013.04.03

Personal hygiene in schools: retrospective survey in the northern part of Côte d'Ivoire

Introduction Students’ personal hygiene helps maintain good health and promote good academic results. When the sanitary infrastructure is insufficient, maintaining this hygiene can be difficult to achieve. We wanted to analyse the determinants of personal hygiene among pupils in schools in the northern region of Côte D'Ivoire. Methods This cross-sectional retrospective study gathers data on 2,035 schoolchildren recruited from thirty schools in the northern part &nbsp;of Côte D'Ivoire. The personal hygiene index is established and analysed in comparison to the socio-demographic characteristics of students, homes and schools. They are analyzed using &nbsp;R Software version 1.1.463, the χ2 test and a logistic regression model. &nbsp; Results Overall, the majority of students had good personal hygiene (82.75%) with an average personal hygiene score of 4.74 ± 1.36. The predictors of good personal hygiene among schoolchildren are female (OR=1,5&nbsp;; CI95%= 4,31-16,37), father's level of education, primary school (OR=1,55&nbsp;; CI95%= 1,07-2,29), father's monthly income higher than 60000FCFA (90 Euros) and modern housing (OR= 1,45&nbsp;; CI95%=1,05-2,03). However, poor sanitation at home caused poor personal hygiene among pupils (OR=0,34&nbsp;; CI95%= 0,23-0,5). Conclusion Measures to raise the standard of living of families and the provision of sanitory facilities in homes becomes necessary in order to improve students personal hygiene. Keywords: Personal Hygiene, Primary school pupils, Northern Côte d'Ivoire. &nbsp

Using metabarcoding to reveal and quantify plant-pollinator interactions.

12 pagesInternational audienceGiven the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.Peer reviewe