Impact of wall shear stress on initial bacterial adhesion in rotating annular reactor

The objective of this study was to investigate the bacterial adhesion under different wall shear stresses in turbulent flow and using a diverse bacterial consortium. A better understanding of the mechanisms governing microbial adhesion can be useful in diverse domains such as industrial processes, medical fields or environmental biotechnologies. The impact of wall shear stress—four values ranging from 0.09 to 7.3 Pa on polypropylene (PP) and polyvinyl chloride (PVC)—was carried out in rotating annular reactors to evaluate the adhesion in terms of morphological and microbiological structures. A diverse inoculum consisting of activated sludge was used. Epifluorescence microscopy was used to quantitatively and qualitatively characterize the adhesion. Attached bacterial communities were assessed by molecular fingerprinting profiles (CE-SSCP). It has been demonstrated that wall shear stress had a strong impact on both quantitative and qualitative aspects of the bacterial adhesion. ANOVA tests also demonstrated the significant impact of wall shear stress on all three tested morphological parameters (surface coverage, number of objects and size of objects) (p-values < 2.10−16). High wall shear stresses increased the quantity of attached bacteria but also altered their spatial distribution on the substratum surface. As the shear increased, aggregates or clusters appeared and their size grew when increasing the shears. Concerning the microbiological composition, the adhered bacterial communities changed gradually with the applied shear

A Comprehensive Survey on Software as a Service (SaaS) Transformation for the Automotive Systems

Over the last few decades, automotive embedded Information and Communication Technology (ICT) systems have been used to enhance vehicle performance and enrich peopleâ’s driving experience, increasing the panel of software features within them. However, even though until now automakers have kept up with the innovation pace in terms of the functionalities that have been offered to passengers, the majority of automakers’ efforts have concentrated on bringing in these new functionalities by adding an unceasingly larger set of ECUs. All of this has been done without evolving any of the embedded software architecture consequently, due to budgetary constraints, legislative limitations, retro-compatibility problems, and a lack of awareness of the trending IT innovation. This unbalanced progress has then led to a substantial increase in in-vehicle architectural complexity, which has become a major concern for automakers nowadays as it makes the vehicle repairing process more complex, decreases software traceability and clashes with the objective of having higher business flexibility, modularity, and dynamicity within the vehicles. In this paper, we are going to go through literature, both academic and industrial, and propose a comprehensive study into automotive system transformation. We begin by giving a detailed analysis of the causes of evolution under five axes - i.e., society, business, industry, application, and technical. Then, we discuss the convergence of cars and software life cycles and propose a three-layered analysis of automotive ICT systems consisting of architecture design, software pipelines, and run-time management. Finally, we are going to propose certain detailed guidelines on the evolution perspectives for automotive systems through deriving from the convergence of advances in IT, as well as current and future automotive environmental constraints

Burner lip temperature and stabilization of a non-premixed jet flame

International audienc

Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities

International audienceAllopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA Met and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations.Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH deshydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica

DRAP: de novo RNA-Seq Assembly Pipeline

Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set

Epstein–Barr Virus-Associated T- and NK-Cell Lymphoproliferative Diseases: A Review of Clinical and Pathological Features

Epstein–Barr virus (EBV) is a ubiquitous virus detected in up to 95% of the general population. Most people are asymptomatic, while some may develop a wide range of EBV-associated lymphoproliferative disorders (LPD). Among them, EBV-positive T/NK LPD are uncommon diseases defined by the proliferation of T- or NK-cells infected by EBV. The 2017 World Health Organization (WHO) classification recognizes the following entities characterized by different outcomes: chronic active EBV infection of T- or NK-cell types (cutaneous and systemic forms), systemic EBV-positive T-cell lymphoma of childhood, EBV-positive aggressive NK-cell leukemia, extra nodal NK/T-cell lymphoma nasal type, and the new provisional entity known as primary EBV-positive nodal T/NK-cell lymphoma. In addition, EBV associated-hemophagocytic lymphohistiocytosis is part of EBV-positive T/NK LPD, but has not been included in the WHO classification due to its reactive nature. Despite novel insights from high-throughput molecular studies, EBV-positive NK/T-cell LPD diagnoses remain challenging, especially because of their rarity and overlap. Until now, an accurate EBV-positive NK/T LPD diagnosis has been based on its clinical presentation and course correlated with its histological features. This review aims to summarize clinical, pathological and molecular features of EBV-positive T/NK LPD subtypes and to provide an overview of new understandings regarding these rare disorders

NG6: Integrated next generation sequencing storage and processing environment.

Chantier qualité GAInternational audienceABSTRACT: BACKGROUND: Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. RESULTS: We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,...) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. CONCLUSIONS: NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data

Effect of reactant preheating on the stability of non-premixed methane/air flames

International audienceThis study details the influence of reactant temperature on the stability of non-premixed CH4 /air co-flow jet flames. Flame characteristics have been studied for five temperature levels (from 295 K to 600 K). The hysteresis zone formed by the limits between attached and lifted flame translates towards higher methane jet velocities with an increase of initial temperature, independently of the air velocity range. Moreover, critical velocities vary linearly with initial temperature. In addition, attachment and lift-off heights have been obtained from CH* chemiluminescence visualization. Results point out that the attachment height decreases significantly with temperature. Observations also indicate that the intrinsic process of lifting is modified. Pre-lifting anchored flame local extinctions, not observed at room-temperature, appear at higher initial temperatures; their occurrence increases with temperature. The lift-off height of turbulent lifted flames is also reduced with temperature. Overall, results show that increasing local temperature in the stabilization zone enhances flame stability

Description of the different experiments carried out.

<p>The two right-hand columns represent the number of slides per reactor that has been processed for morphological or microbiological characterization, respectively.</p

Results of the morphological characterization for Phase 2, shear stress impact test.

<p>Three morphological parameters–surface coverage (A), number of particles (B), average size of particles (C)–are reported for the different wall shear stresses tested (Shear 1 and Shear 2 experiments). Data result from microscopic observations and image analysis of acquired pictures. As mentioned in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172113#pone.0172113.t002" target="_blank">Table 2</a>, two and three slides of PP were characterized per reactor for Shear 1 and Shear 2, respectively. In order to compare on the same graph the four wall shear stresses tested, original values were scaled by the value obtained at 0.09 Pa shear. The y-axis represents this ratio, hence it is dimensionless.</p