Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.

Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses.

ADAM30 Downregulates APP-Linked Defects Through Cathepsin D Activation in Alzheimer's Disease.

Although several ADAMs (A disintegrin-like and metalloproteases) have been shown to contribute to the amyloid precursor protein (APP) metabolism, the full spectrum of metalloproteases involved in this metabolism remains to be established. Transcriptomic analyses centred on metalloprotease genes unraveled a 50% decrease in ADAM30 expression that inversely correlates with amyloid load in Alzheimer's disease brains. Accordingly, in vitro down- or up-regulation of ADAM30 expression triggered an increase/decrease in Aβ peptides levels whereas expression of a biologically inactive ADAM30 (ADAM30(mut)) did not affect Aβ secretion.

Adventitial Tertiary Lymphoid Organs as Potential Source of MicroRNA Biomarkers for Abdominal Aortic Aneurysm.

Abdominal aortic aneurysm (AAA) is an inflammatory disease associated with marked changes in the cellular composition of the aortic wall. This study aims to identify microRNA (miRNA) expression in aneurysmal inflammatory cells isolated by laser microdissection from human tissue samples. The distribution of inflammatory cells (neutrophils, B and T lymphocytes, mast cells) was evaluated in human AAA biopsies.

[High-throughput sequencing: towards a genome-based diagnosis in infectious diseases].

During a pathogen outbreak, the emergency resides in the identification and characterization of the infectious agent. In addition to the traditional phenotypic methods which are still widely used, the molecular biology is nowadays a common approach of clinical microbiology labs and the pathogen can be identified by comparing its molecular fingerprint to a data-bank. High-throughput sequencing should allow overcoming this single identification to exploit the whole information encoded in the pathogen genome.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Background: The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms.

Airway structural cells regulate TLR5-mediated mucosal adjuvant activity.

Antigen-presenting cell (APC) activation is enhanced by vaccine adjuvants. Most vaccines are based on the assumption that adjuvant activity of Toll-like receptor (TLR) agonists depends on direct, functional activation of APCs. Here, we sought to establish whether TLR stimulation in non-hematopoietic cells contributes to flagellin's mucosal adjuvant activity.

NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer.

Instability in the composition of gut bacterial communities (dysbiosis) has been linked to common human intestinal disorders, such as Crohn's disease and colorectal cancer. Here, we show that dysbiosis caused by Nod2 deficiency gives rise to a reversible, communicable risk of colitis and colitis-associated carcinogenesis in mice. Loss of either Nod2 or RIP2 resulted in a proinflammatory microenvironment that enhanced epithelial dysplasia following chemically induced injury.

Nod-like receptor pyrin domain-containing protein 6 (NLRP6) controls epithelial self-renewal and colorectal carcinogenesis upon injury.

The colonic epithelium self-renews every 3 to 5 d, but our understanding of the underlying processes preserving wound healing from carcinogenesis remains incomplete. Here, we demonstrate that Nod-like receptor pyrin domain-containing protein 6 (NLRP6) suppresses inflammation and carcinogenesis by regulating tissue repair. NLRP6 was primarily produced by myofibroblasts within the stem-cell niche in the colon.

Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element.

Background: Small bacterial RNAs (sRNAs) have been shown to participate in the regulation of gene expression and have been identified in numerous prokaryotic species. Some of them are involved in the regulation of virulence in pathogenic bacteria. So far, little is known about sRNAs in Bordetella, and only very few sRNAs have been identified in the genome of Bordetella pertussis, the causative agent of whooping cough.

Secondary ketocarotenoid astaxanthin biosynthesis in algae: a multifunctional response to stress.

Under stressful environments, many green algae such as Haematococcus pluvialis accumulate secondary ketocarotenoids such as canthaxanthin and astaxanthin. The carotenogenesis, responsible for natural phenomena such as red snows, generally accompanies larger metabolic changes as well as morphological modifications, i.e.

Identification of novel genes potentially involved in somatic embryogenesis in chicory (Cichorium intybus L.).

Background: In our laboratory we use cultured chicory (Cichorium intybus) explants as a model to investigate cell reactivation and somatic embryogenesis and have produced 2 chicory genotypes (K59, C15) sharing a similar genetic background. K59 is a responsive genotype (embryogenic) capable of undergoing complete cell reactivation i.e.

Profile of macrophages in human abdominal aortic aneurysms: a transcriptomic, proteomic, and antibody protein array study.

Abdominal aortic aneurysms (AAA) are defined by an increased aortic diameter and characterized by impairment of the extracellular matrix, macrophages infiltration and decreased density of smooth muscle cells. Our aim is to identify the key molecules involved in the pathogenesis of AAAs. This study investigated transcriptomic and proteomic profiles of macrophages from AAA patients (>50 mm aortic diameter) (n = 24) and peripheral arterial occlusion (PAO) patients without AAA detected (n = 18), who both needed a surgery.

STREAM PERIPHYTON PHOTOACCLIMATION RESPONSE IN FIELD CONDITIONS: EFFECT OF COMMUNITY DEVELOPMENT AND SEASONAL CHANGES(1).

The photochemical behavior of intact stream periphyton communities in France was evaluated in response to the time course of natural light. Intact biofilms grown on glass substrata were collected at three development stages in July and November, and structural parameters of the biofilms were investigated (diatom density and taxonomy). At each season, physiological parameters based on pigment analysis (HPLC) and pulse-amplitude-modulated (PAM) chl fluorescence technique were estimated periodically during a day from dawn to zenith.

Genomic island excisions in Bordetella petrii.

Background: Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B.

Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease.

The only recognized genetic determinant of the common forms of Alzheimer's disease (AD) is the epsilon 4 allele of the apolipoprotein E gene (APOE). To identify new candidate genes, we recently performed transcriptomic analysis of 2741 genes in chromosomal regions of interest using brain tissue of AD cases and controls. From 82 differentially expressed genes, 1156 polymorphisms were genotyped in two independent discovery subsamples (n=945).

Genetic stability of the live attenuated Bordetella pertussis vaccine candidate BPZE1.

Despite the extensive use of efficacious pertussis vaccines, Bordetella pertussis infections are still among the main causes for childhood morbidity and mortality. Severe pertussis occurs mostly in very young children, often too young to be sufficiently protected by current vaccines, which require several administrations in regimens that vary between countries. Since natural infection with B.

The Dijon Physical Activity Score: reproducibility and correlations with physical fitness in patients with coronary artery disease.

Objectives: To study the clinimetric properties of the Dijon Physical Activity Score (PAS) in patients with coronary artery disease (CAD).

Patients: Two populations of patients with CAD: one group of stabilized patients from the RICO county-wide monitoring program and one group in the initial phase of a cardiovascular rehabilitation program (CVR group).

Methods: The patients carried out a maximal effort test on a cycle ergometer, plus two walking tests (a six-minute walk test and a 200 m fast walk test).

Preparation of alpha-Oxo semicarbazone oligonucleotide microarrays.

This unit describes the preparation of alpha-oxo aldehyde functionalized oligodeoxynucleotides, the preparation and characterization of semicarbazide glass slides, and the fabrication of alpha-oxo semicarbazone microarrays by site-specific ligation of alpha-oxo-aldehyde oligodeoxynucleotides to the semicarbazide glass slides. The alpha-oxo aldehyde group COCHO is extensively used in ligation chemistry for the preparation of large molecular constructs. It is stable toward air oxidation and mainly present in aqueous solution in the hydrated form COC(OH)(2).

Evidence for induction of the ornithine transcarbamylase expression in Alzheimer's disease.

To more rapidly identify candidate genes located within chromosomal regions of interest defined by genome scan studies in Alzheimer's disease (AD), we have developed a customized microarray containing all the ORFs (n=2741) located within nine of these regions. Levels of gene expression were assessed in total RNA from brain tissue of 12 controls and 12 AD patients. Of all genes showing differential expression, we focused on the ornithine transcarbamylase (OTC) gene on Xp21.

Temporal analysis of French Bordetella pertussis isolates by comparative whole-genome hybridization.

Bordetella pertussis, a gram-negative beta-proteobacterium, is the agent of whooping cough in humans. Whooping cough remains a public health problem worldwide, despite well-implemented infant/child vaccination programs. It continues to be endemic and is observed cyclically in vaccinated populations.

Assembly of the photosynthetic apparatus in embryos from Fucus serratus L.

The assembly of the photosynthetic apparatus was studied during the first six days of development of Fucus serratus L. embryos. HPLC analysis revealed that oospheres and zygotes contain the same photosynthetic pigments (i.

Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium Synechococcus sp. strain WH8102.

The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II).

Bordetella pertussis from functional genomics to intranasal vaccination.

Whooping cough still represents a major health problem, despite the use of effective vaccines for several decades. Being classically a typical childhood disease, whooping cough in young adults is now more common than it used to be, suggesting that protection after vaccination wanes during adolescence. As an alternative to the current vaccines, we wish to develop live attenuated vaccines to be delivered by the nasal route, such as to mimic the natural route of infection and to induce long lasting immunity.

Transcriptomic analysis in the leech Theromyzon tessulatum: involvement of cystatin B in innate immunity.

At the present time, there is little information on mechanisms of innate immunity in invertebrate groups other than insects, especially annelids. In the present study, we have performed a transcriptomic study of the immune response in the leech Theromyzon tessulatum after bacterial challenge, by a combination of differential display RT (reverse transcriptase)-PCR and cDNA microarrays. The results show relevant modulations concerning several known and unknown genes.