New insights in gill/buccal rhythm spiking activity and CO2 sensitivity in pre- and post-metamorphic tadpoles (Pelophylax ridibundus)

Central CO2chemosensitivity is crucial for all air-breathing vertebrates and raises the question of itsrole in ventilatory rhythmogenesis. In this study, neurograms of ventilatory motor outputs recorded infacial nerve of premetamorphic and postmetamorphic tadpole isolated brainstems, under normo- andhypercapnia, are investigated using Continuous Wavelet Transform spectral analysis for buccal activityand computation of number and amplitude of spikes during buccal and lung activities. Buccal burstsexhibit fast oscillations (20-30 Hz) that are prominent in premetamorphic tadpoles: they result from thepresence in periodic time windows of high amplitude spikes. Hypercapnia systematically decreases thefrequency of buccal rhythm in both pre- and postmetamorphic tadpoles, by a lengthening of the interburstduration. In postmetamorphic tadpoles, hypercapnia reduces buccal burst amplitude and unmasks smallfast oscillations. Our results suggest a common effect of the hypercapnia on the buccal part of the CentralPattern Generator in all tadpoles and a possible effect at the level of the motoneuron recruitment inpostmetamorphic tadpoles

A Bayesian method with empirically fitted priors for the evaluation of environmental radioactivity: application to low-level radioxenon measurements

International audienceThe decision that a given detection level corresponds to the effective presence of a radionuclide is still widely made on the basis of a classic hypothesis test. However, the classic framework suffers several drawbacks, such as the conceptual and practical impossibility to provide a probability of zero radioactivity, and confidence intervals for the true activity level that are likely to contain negative and hence meaningless values. The Bayesian framework being potentially able to overcome these drawbacks, several attempts have recently been made to apply it to this decision problem. Here, we present a new Bayesian method that, unlike the previous ones, presents two major advantages together. First, it provides an estimate of the probability of no radioactivity, as well as physically meaningful point and interval estimates for the true radioactivity level. Second, whereas Bayesian approaches are often controversial because of the arbitrary choice of the priors they use, the proposed method permits to estimate the parameters of the prior density of radioactivity by fitting its marginal distribution to previously recorded activity data. The new scheme is first mathematically developed. Then, it is applied to the detection of radioxenon isotopes in noble gas measurement stations of the International Monitoring System of the Comprehensive Nuclear-Test-Ban Treaty

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results: The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion: High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture

Trisomy for Synaptojanin1 in Down syndrome is functionally linked to the enlargement of early endosomes

Enlarged early endosomes have been observed in neurons and fibroblasts in Down syndrome (DS). These endosome abnormalities have been implicated in the early development of Alzheimer's disease (AD) pathology in these subjects. Here, we show the presence of enlarged endosomes in blood mononuclear cells and lymphoblastoid cell lines (LCLs) from individuals with DS using immunofluorescence and confocal microscopy. Genotype-phenotype correlations in LCLs carrying partial trisomies 21 revealed that triplication of a 2.56 Mb locus in 21q22.11 is associated with the endosomal abnormalities. This locus contains the gene encoding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1), a key regulator of the signalling phospholipid phosphatidylinositol-4,5-biphosphate that has been shown to regulate clathrin-mediated endocytosis. We found that SYNJ1 transcripts are increased in LCLs from individuals with DS and that overexpression of SYNJ1 in a neuroblastoma cell line as well as in transgenic mice leads to enlarged endosomes. Moreover, the proportion of enlarged endosomes in fibroblasts from an individual with DS was reduced after silencing SYNJ1 expression with RNA interference. In LCLs carrying amyloid precursor protein (APP) microduplications causing autosomal dominant early-onset AD, enlarged endosomes were absent, suggesting that APP overexpression alone is not involved in the modification of early endosomes in this cell type. These findings provide new insights into the contribution of SYNJ1 overexpression to the endosomal changes observed in DS and suggest an attractive new target for rescuing endocytic dysfunction and lipid metabolism in DS and in A

Heterochromatic Genes Undergo Epigenetic Changes and Escape Silencing in Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) Syndrome

Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) syndrome is a rare autosomal recessive disorder that is characterized by a marked immunodeficiency, severe hypomethylation of the classical satellites 2 and 3 associated with disruption of constitutive heterochromatin, and facial anomalies. Sixty percent of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase

Pressure Ulcers and Dressings: A Strain Sensitivity Analysis of the Boundary Conditions of a Finite Element Model

Recently, a new bi-layer dressing was proposed by Urgo RID to reduce the healing time of pressure ulcers (PU). This dressing was numerically evaluated in previously published work. In the current work, the influence on the maximal shear strains of modelling parameters such as the dressing local geometry, the pressure applied by the gauze inside the wound, the wound deepness, and the mattress stiffness, was assessed. A sensitivity analysis was performed on these four parameters. Among all experiments, the mean maximal Green--Lagrange shear strain was 0.29. The gauze pressure explained 60% of the model response in terms of the volume of tissues under strains of 0.3, while the wound deepness explained 28%. The mattress had a significant, but low impact, whereas the dressing local geometry had no significant impact. As expected, the wound deepness was one of the most influential parameters. The gauze turned out to be more significant than expected. This may be explained by the large range of values chosen for this study. The results should be extended to more subjects, but still suggest that the gauze is a parameter that might not be neglected. Care should also be taken in clinical practice when using gauze that could have either a positive or negative impact on the soft tissues' strains. This may also depend on the wound deepness

Biplanar Low-Dose Radiograph Is Suitable for Cephalometric Analysis in Patients Requiring 3D Evaluation of the Whole Skeleton

Background: The biplanar 2D/3D X-ray technology (BPXR) is a 2D/3D imaging system allowing simultaneous stereo-corresponding posteroanterior (PA) and lateral 2D views of the whole body. The aim of our study was to assess the feasibility of cephalometric analysis based on the BPXR lateral skull view to accurately characterize facial morphology. Method: A total of 17 landmarks and 11 angles were placed and/or calculated on lateral BPXR and lateral cephalograms of 13 patients by three investigators. Five methods of angle identification were performed: the direct construction of straight lines on lateral cephalograms (LC-A) and on BPXR (BPXR-A), as well as the calculation of angles based on landmark identification on lateral cephalograms (LA-L) and on BPXR with the PA image (BPXR-LPA) or without (BPXR-L). Intra- and interoperator reliability of landmark identification and angle measurement of each method were calculated. To determine the most reliable method among the BPXR-based methods, their concordance with the reference method, LC-A, was evaluated. Results: Both imaging techniques had excellent intra- and interoperator reliability for landmark identification. On lateral BPXR, BPXR-A presented the best concordance with the reference method and a good intra- and interoperator reliability. Conclusion: BPXR provides a lateral view of the skull suitable for cephalometric analysis with good reliability

Gene expression signature of cerebellar hypoplasia in a mouse model of Down syndrome during postnatal development

Background Down syndrome is a chromosomal disorder caused by the presence of three copies of chromosome 21. The mechanisms by which this aneuploidy produces the complex and variable phenotype observed in people with Down syndrome are still under discussion. Recent studies have demonstrated an increased transcript level of the three-copy genes with some dosage compensation or amplification for a subset of them. The impact of this gene dosage effect on the whole transcriptome is still debated and longitudinal studies assessing the variability among samples, tissues and developmental stages are needed. Results We thus designed a large scale gene expression study in mice (the Ts1Cje Down syndrome mouse model) in which we could measure the effects of trisomy 21 on a large number of samples (74 in total) in a tissue that is affected in Down syndrome (the cerebellum) and where we could quantify the defect during postnatal development in order to correlate gene expression changes to the phenotype observed. Statistical analysis of microarray data revealed a major gene dosage effect: for the three-copy genes as well as for a 2 Mb segment from mouse chromosome 12 that we show for the first time as being deleted in the Ts1Cje mice. This gene dosage effect impacts moderately on the expression of euploid genes (2.4 to 7.5% differentially expressed). Only 13 genes were significantly dysregulated in Ts1Cje mice at all four postnatal development stages studied from birth to 10 days after birth, and among them are 6 three-copy genes. The decrease in granule cell proliferation demonstrated in newborn Ts1Cje cerebellum was correlated with a major gene dosage effect on the transcriptome in dissected cerebellar external granule cell layer. Conclusion High throughput gene expression analysis in the cerebellum of a large number of samples of Ts1Cje and euploid mice has revealed a prevailing gene dosage effect on triplicated genes. Moreover using an enriched cell population that is thought responsible for the cerebellar hypoplasia in Down syndrome, a global destabilization of gene expression was not detected. Altogether these results strongly suggest that the three-copy genes are directly responsible for the phenotype present in cerebellum. We provide here a short list of candidate genes

Supercritical Fluid Chromatography of Drugs: Parallel Factor Analysis for Column Testing in a Wide Range of Operational Conditions

Retention mechanisms involved in supercritical fluid chromatography (SFC) are influenced by interdependent parameters (temperature, pressure, chemistry of the mobile phase, and nature of the stationary phase), a complexity which makes the selection of a proper stationary phase for a given separation a challenging step. For the first time in SFC studies, Parallel Factor Analysis (PARAFAC) was employed to evaluate the chromatographic behavior of eight different stationary phases in a wide range of chromatographic conditions (temperature, pressure, and gradient elution composition). Design of Experiment was used to optimize experiments involving 14 pharmaceutical compounds present in biological and/or environmental samples and with dissimilar physicochemical properties. The results showed the superiority of PARAFAC for the analysis of the three-way (column × drug × condition) data array over unfolding the multiway array to matrices and performing several classical principal component analyses. Thanks to the PARAFAC components, similarity in columns’ function, chromatographic trend of drugs, and correlation between separation conditions could be simply depicted: columns were grouped according to their H-bonding forces, while gradient composition was dominating for condition classification. Also, the number of drugs could be efficiently reduced for columns classification as some of them exhibited a similar behavior, as shown by hierarchical clustering based on PARAFAC components

Dynamic changes of DNA methylation and lung disease in cystic fibrosis: Lessons from a monogenic disease

Para avaliar se os níveis de metilação do DNA são responsáveis ​​pelas variações fenotípicas não hereditárias observadas entre pacientes com fibrose cística (FC). PACIENTES E MÉTODOS Usando o BeadChip de 450 K, nós perfilamos a metilação do DNA em células epiteliais nasais coletadas de 32 pacientes com FC e 16 controles. RESULTADOS Detectamos diferenças substanciais na metilação do DNA de até 55% (mudança β mediana de 0,13; IQR: 0,15-0,11) entre pacientes com FC e controles. Os níveis de metilação do DNA diferiram entre pacientes com FC leve e grave e se correlacionaram com a função pulmonar em 50 locais CpG. CONCLUSÃO Em amostras de FC, mudanças dinâmicas na metilação do DNA ocorreram em genes responsáveis ​​pela integridade do epitélio e pelas respostas inflamatórias e imunes, foram proeminentes em regiões genômicas transcricionalmente ativas e foram super-representadas em intensificadores ativos em tecidos pulmonares. ( Clinicaltrials.gov NCT02884622).To assess whether DNA methylation levels account for the noninherited phenotypic variations observed among cystic fibrosis (CF) patients. PATIENTS & METHODS Using the 450 K BeadChip, we profiled DNA methylation in nasal epithelial cells collected from 32 CF patients and 16 controls. RESULTS We detected substantial DNA methylation differences up to 55% (median β change 0.13; IQR: 0.15-0.11) between CF patients and controls. DNA methylation levels differed between mild and severe CF patients and correlated with lung function at 50 CpG sites. CONCLUSION In CF samples, dynamic changes of DNA methylation occurred in genes responsible for the integrity of the epithelium and the inflammatory and immune responses, were prominent in transcriptionally active genomic regions and were over-represented in enhancers active in lung tissues. ( Clinicaltrials.gov NCT02884622)