Les occupations néolithiques de Persan « ZAC du Chemin Herbu » (Val d’Oise)

International audienc

Les occupations néolithiques de Persan « ZAC du Chemin Herbu » (Val d’Oise)

International audienc

A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates

Background: Construction and validation of a prognostic model for survival data in the clinical domain is still an active field of research. Nevertheless there is no consensus on how to develop routine prognostic tests based on a combination of RT-qPCR biomarkers and clinical or demographic variables. In particular, the estimation of the model performance requires to properly account for the RT-qPCR experimental design. Results: We present a strategy to build, select, and validate a prognostic model for survival data based on a combination of RT-qPCR biomarkers and clinical or demographic data and we provide an illustration on a real clinical dataset. First, we compare two cross-validation schemes: a classical outcome-stratified cross-validation scheme and an alternative one that accounts for the RT-qPCR plate design, especially when samples are processed by batches. The latter is intended to limit the performance discrepancies, also called the validation surprise, between the training and the test sets. Second, strategies for model building (covariate selection, functional relationship modeling, and statistical model) as well as performance indicators estimation are presented. Since in practice several prognostic models can exhibit similar performances, complementary criteria for model selection are discussed: the stability of the selected variables, the model optimism, and the impact of the omitted variables on the model performance. Conclusion: On the training dataset, appropriate resampling methods are expected to prevent from any upward biases due to unaccounted technical and biological variability that may arise from the experimental and intrinsic design of the RT-qPCR assay. Moreover, the stability of the selected variables, the model optimism, and the impact of the omitted variables on the model performances are pivotal indicators to select the optimal model to be validated on the test dataset

Regulation of Melanoma Progression through the TCF4/miR-125b/NEDD9 Cascade

Melanoma progression from a primary lesion to a distant metastasis is a complex process associated with genetic alterations, epigenetic modifications, and phenotypic switches. Elucidation of these phenomena may indicate how to interfere with this fatal disease. The role of microRNAs as key negative regulators of gene expression, controlling all cellular processes including cell migration and invasion, is now being recognized. Here, we used in silico analysis of microRNA expression profiles of primary and metastatic melanomas and functional experiments to show that microRNA-125b (miR-125b) is a determinant candidate of melanoma progression: (i) miR-125b is more strongly expressed in aggressive metastatic than primary melanomas, (ii) there is an inverse correlation between the amount of miR-125b and overall patient survival, (iii) invasion/migration potentials in vitro are inversely correlated with the amount of miR-125b in a series of human melanoma cell lines, and (iv) inhibition of miR-125b reduces migratory and invasive potentials without affecting cell proliferation in vitro. Furthermore, we show that neural precursor cell expressed developmentally down-regulated protein 9 (i.e., NEDD9) is a direct target of miR-125b and is involved in modulating melanoma cell migration and invasion. Also, transcription factor 4, associated with epithelial-mesenchymal transition and invasion, induces the transcription of miR-125b-1. In conclusion, the transcription factor 4/miR-125b/NEDD9 cascade promotes melanoma cell migration/invasion.publisher: Elsevier articletitle: Regulation of Melanoma Progression through the TCF4/miR-125b/NEDD9 Cascade journaltitle: Journal of Investigative Dermatology articlelink: http://dx.doi.org/10.1016/j.jid.2016.02.803 content_type: article copyright: © 2016 The Authors. Published by Elsevier, Inc. on behalf of the Society for Investigative Dermatology.status: publishe

Delayed increase of S100A9 messenger RNA predicts hospital-acquired infection after septic shock*

International audienc

Comparing the Effectiveness of Virtual and In-Person Delivery of Mindfulness-Based Skills Within Healthcare Curriculums

Purpose: To promote well-being, healthcare education programs have incorporated mindfulness-based skills and principles into existing curriculums. Pandemic-related restrictions have compelled programs to deliver content virtually. Study objectives were to determine (1) whether teaching mindfulness-based skills within physician assistant (PA) programs can promote well-being and (2) whether delivery type (virtual vs. in-person) can impact the effectiveness. Methods: During this 2-year study, a brief mindfulness-based curriculum was delivered to incoming first-year students at six PA programs, while students at two programs served as controls. The curriculum was delivered in-person in year one and virtually in year two. Validated pre- and post-test survey items assessed mindfulness (decentering ability, present moment attention and awareness, and psychological flexibility) and well-being (perceived stress and life satisfaction). Results: As expected, coping abilities and well-being were adversely impacted by educational demands. The mindfulness-based curriculum intervention was effective in increasing mindfulness and life satisfaction, while decreasing perceived stress when delivered in-person. Virtual curricular delivery was effective in decreasing perceived stress but not improving life satisfaction. Over half of the participants receiving the curriculum reported positive changes on mindfulness measures with approximately 14–38% reporting a change of greater than one standard deviation. Changes on mindfulness measures explained 30–38% of the reported changes in perceived stress and 22–26% of the changes in life satisfaction. Therefore, the mindfulness curriculum demonstrated statistically significant improvements in measures of mindfulness and mitigated declines in life satisfaction and perceived stress. Conclusion: Mindfulness-based skills effectively taught in-person or virtually within PA programs successfully promote well-being

Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates

International audienceThe initiation of mRNA degradation often requires deprotection of its 5′ end. In eukaryotes, the 5′-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5′-monophosphorylated RNA that is a substrate for 5′ exoribonucleases. In bacteria, the 5′-triphosphate group of primary transcripts is also converted to a 5′ monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5′ exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNAtargets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria

EARLY ASSESSMENT OF LEUKOCYTE ALTERATIONS AT DIAGNOSIS OF SEPTIC SHOCK

International audienceA dramatic decrease in circulating lymphocyte number is regularly described after septic shock. However, it is unknown how early this alteration develops after diagnosis of shock and if it remains stable over time. Twenty-one septic shock patients with no comorbidities were included within 2 h after the beginning of vasopressive treatment. Flow cytometry phenotyping of circulating leukocyte subpopulations and quantitative real-time polymerase chain reaction of T-bet, GATA-3, FOXP3, and ROR+ mRNA were performed in patients from the diagnosis of shock and every 6 h during thesubsequent 48 h. From their admission in the intensive care unit, patients present with major alterations of circulating leukocyte count (leukocytosis, neutrophilia, and major lymphopenia). The numbers of every lymphocyte subpopulations (T, B, and natural killer cells) were diminished. Gene expression analysis of transcription factors specific for TH1, TH2, CD4+CD25+ regulatory, and TH17 lymphocytes showed a severe decrease in comparison with healthy individuals’ values. These alterations remain stable during the first 48 h after inclusion in the protocol despite early and aggressive resuscitation and antibiotherapy administered in patients. At the time of diagnosis of shock and admission in the intensive care unit, septic patients already present with severe lymphopenia involving every lymphocyte subsets including CD4+ T-cell subpopulations. No significant variation could be detected within the first 48 h. This should be taken into account in the forthcoming clinical trials testing immunomodulating therapies in septic shock patients

The NC domain of HIV-1 Gag contributes to the interaction of Gag with TSG101

International audienceBACKGROUND:HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with RNA, and the p6 domain containing the PTAP motif that binds the cellular ESCRT factor TSG101 and ALIX. Deletion of the NC domain of Gag (GagNC) results in defective Gag assembly, a decrease in virus production and, thus probably affects recruitment of the ESCRT machinery. To investigate the role of GagNC in this recruitment, we analysed its impact on TSG101 and ALIX localisations and interactions in cells expressing Gag.METHODS:Cells expressing mCherry-Gag or derivatives, alone or together with eGFP-TSG101 or eGFP-ALIX, were analysed by confocal microscopy and FLIM-FRET. Chemical shift mapping between TSG101-UEV motif and Gag C-terminus was performed by NMR.RESULTS:We show that deletion of NC or of its two zinc fingers decreases the amount of Gag-TSG101 interacting complexes in cells. These findings are supported by NMR data showing chemical shift perturbations in the NC domain in- and outside - of the zinc finger elements upon TSG101 binding. The NMR data further identify a large stretch of amino acids within the p6 domain directly interacting with TSG101.CONCLUSION:The NC zinc fingers and p6 domain of Gag participate in the formation of the Gag-TSG101 complex and in its cellular localisation.GENERAL SIGNIFICANCE:This study illustrates that the NC and p6 domains cooperate in the interaction with TSG101 during HIV-1 budding. In addition, details on the Gag-TSG101 complex were obtained by combining two high resolution biophysical techniques

Prostate cancer biomarker annexin A3 detected in urines obtained following digital rectal examination presents antigenic variability

International audienceObjectives: Annexin A3 (ANXA3) is a potential marker for prostate cancer (PCa). We aimed to develop robust immunoassays suitable for quantifying ANXA3 in urine samples obtained following digital rectal examination (DRE) in order to facilitate the diagnostic performance evaluation of this marker. Design and methods: Anti-ANXA3 monoclonal antibodies were generated and their epitopes mapped. Two different ANXA3 assay prototypes were established on the VIDAS (R) automated immunoanalyser and analytical validation was carried out using post-DRE urine samples obtained from patients with PCa (n = 23) or benign prostate hyperplasia (n = 31). Results: The assays had the same capture antibody (TGC44) but different detection antibodies (13A12 or 5C5), recognizing novel distinct epitopes. Both had a lower limit of quantification <1 ng/mL and were highly specific for ANXA3, not cross-reacting with other annexins. Interassay imprecision was <= 11% and <= 15% for 13A12 and 5C5 assays, respectively. Surprisingly, a total lack of correlation was observed between ANXA3 levels measured by these two assays in post-DRE urines, indicating detection of distinct antigenic variants. Two freeze-thaw cycles did not affect analyte stability in either assay, whereas a lack of stability of antigenic variants was observed when samples were stored at -80 degrees C for 1 month. Conclusions: Two different antigenic variants of ANXA3 are present in post-DRE urines and their clinical significance for diagnosis of prostate cancer should be further investigated. These variants are not stable over time in samples preserved at -80 degrees C. Until this issue is resolved, ANXA3 should only be measured in freshly collected samples