Some statistical questions raised by a particular RNAseq study

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Acidose lactique et interférence analytique lors du dosage de l'éthylène glycol selon une méthode colorimétrique : à propos d'un cas

Cas clinique : Un homme de 44 ans a été admis aux urgences suite à une perte de connaissance avec arrêt cardio-respiratoire récupéré sous adrénaline. Devant le tableau clinico-biologique (défaillance cardiovasculaire, œdème cérébral, acidose lactique avec lactates à 17,54 mmol/L) et les antécédents du patient (diabète traité par metformine, antécédents psychiatriques), l'origine toxicologique a été explorée : dosage de l'éthylène glycol et de la metformine. Matériel et méthodes : Deux techniques ont été mises à profit pour doser l'éthylène glycol : la première, par colorimétrie, réservée à l'urgence et la deuxième, technique de confirmation, par chromatographie gazeuse couplée à la spectrométrie de masse (GC-MS) qui permet le dosage de 6 autres glycols. La metformine a été dosée par chromatographie liquide haute performance. Résultats : La concentration plasmatique de l'éthylène glycol mesurée par colorimétrie a été de 84 mg/L sur le premier prélèvement (réalisé à l'arrivée aux urgences) pour un seuil de quantification à 50 mg/L. Sur un deuxième prélèvement (2$^{\textrm{\`{e}me}}$ jour d'hospitalisation), la concentration est passée en dessous du seuil de quantification. Le dosage par GC-MS sur ces mêmes prélèvements n'a pas retrouvé de traces d'éthylène glycol. Les concentrations plasmatiques de metformine mesurées aux 1er et 2$^{\textrm{\`{e}me}}$ jours d'hospitalisation ont été respectivement de 14,46 mg/L et 0,70 mg/L (concentration thérapeutique < 1,34 mg/L). Conclusion : Les résultats discordants entre la technique GC-MS et la technique colorimétrique (peu spécifique) ont permis de révéler une interférence analytique entre l'éthylène glycol et les lactates plasmatiques pour une lactatémie > 6,25 mmol/L. Pour tout dosage colorimétrique de l'éthylène glycol, un dosage des lactates doit être réalisé pour évaluer le risque d'interférence analytique

MiR-497 suppresses cycle progression through an axis involving CDK6 in ALK-positive cells.

International audienceAnaplastic large-cell lymphoma, a T cell neoplasm, is primarily a pediatric disease. 75% of pediatric anaplastic large-cell lymphoma cases harbor the chromosomal translocation t(2;5)(p23;q35) leading to the ectopic expression of NPM-ALK, a chimeric tyrosine kinase. NPM-ALK consists of an N-terminal nucleophosmin (NPM) domain fused to an anaplastic lymphoma kinase (ALK) cytoplasmic domain. Pediatric NPM-ALK(+) anaplastic large-cell lymphoma is often a disseminated disease and young patients are prone to chemoresistance or relapse shortly after chemotherapeutic treatment. Furthermore, there is no gold standard protocol for the treatment of relapses. To the best of our knowledge, this is the first study on the potential role of the microRNA, miR-497, in NPM-ALK(+) anaplastic large-cell lymphoma tumorigenesis. Our results show that miR-497 expression is repressed in NPM-ALK(+) cell lines and patient samples through the hypermethylation of its promoter and the activity of NPM-ALK is responsible for this epigenetic repression. We demonstrate that overexpression of miR-497 in human NPM-ALK(+) anaplastic large-cell lymphoma cells inhibits cellular growth and causes cell cycle arrest by targeting CDK6, E2F3 and CCNE1 - the three regulators of the G1 phase of the cell cycle. Interestingly, we show that a scoring system based on CDK6, E2F3 and CCNE1 expression could help identify relapsing pediatric patients. In addition, we demonstrate the sensitivity of NPM-ALK(+) cells to CDK4/6 inhibition using for the first time a selective inhibitor, Palbociclib. Together, our findings suggest that CDK6 could be a therapeutic target for the development of future treatments for NPM-ALK(+) anaplastic large-cell lymphoma

Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae

97 ref.International audiencePerturbations of the yeast cell wall trigger a repair mechanism that reconfigures its molecular structure to preserve cell integrity. To investigate this mechanism, we compared the global gene expression in five mutant strains, each bearing a mutation (i.e. fks1, kre6, mnn9, gas1, and knr4 mutants) that affects in a different manner the cell wall construction. Altogether, 300 responsive genes were kept based on high stringency criteria during data processing. Functional classification of these differentially expressed genes showed a substantial subset of induced genes involved in cell wall construction and an enrichment of metabolic, energy generation, and cell defense categories, whereas families of genes belonging to transcription, protein synthesis, and cellular growth were underrepresented. Clustering methods isolated a single group of ∼80 up-regulated genes that could be considered as the stereotypical transcriptional response of the cell wall compensatory mechanism. The in silico analysis of the DNA upstream region of these co-regulated genes revealed pairwise combinations of DNA-binding sites for transcriptional factors implicated in stress and heat shock responses (Msn2/4p and Hsf1p) with Rlm1p and Swi4p, two PKC1-regulated transcription factors involved in the activation genes related to cell wall biogenesis and G1/S transition. Moreover, this computational analysis also uncovered the 6-bp 5′-AGCCTC-3′ CDRE (calcineurin-dependent response element) motif in 40% of the co-regulated genes. This motif was recently shown to be the DNA binding site for Crz1p, the major effector of calcineurin-regulated gene expression in yeast. Taken altogether, the data presented here lead to the conclusion that the cell wall compensatory mechanism, as triggered by cell wall mutations, integrates three major regulatory systems: namely the PKC1-SLT2 mitogen-activated protein kinase-signaling module, the “global stress” response mediated by Msn2/4p, and the Ca2+/calcineurin-dependent pathway. The relative importance of these regulatory systems in the cell wall compensatory mechanism is discussed

Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application

International audienceWe investigated the scalability of a previously developed growth switch based on external control of RNA polymerase expression. Our results indicate that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multiomics quantification of the physiology of the cells shows that, apart from acetate production, few metabolic side effects occur. However, a number of specific responses to growth slow-down and growth arrest are launched at the transcriptional level. These notably include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation. Interestingly, the transcriptional responses are buffered at the proteome level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. Growth arrest thus reduces the opportunities for dynamically adjusting the proteome composition, which poses constraints on the design of biotechnological production processes but may also avoid the initiation of deleterious stress responses

The role of budget and tax regulation instruments in improvement of territory’s environmental quality

В статье рассматривается подход к определению эффективности инструментов бюджетно-налогового регулирования, направленных на стимулирование процессов улучшения качества окружающей среды. Авторами предлагается разделить виды антропогенного воздействия на первичное и вторичное с соответствующим выделением ущербов и затрат, обусловленных этими ущербами. Обосновывается применение инструментов к части вторичного воздействия. Рассматриваются показатели, которые позволяют оценить результативность, применяемых налоговых льгот, преференций и выделения минимальных объемов финансирования на поддержание приемлемого качества окружающей среды.The paper presents an approach to the determination of the effectiveness of budget and tax regulation instruments, aimed at stimulating the processes of improving the quality of the environment. Authors propose to divide the types of human impact on the primary and secondary, with the appropriate pointing out of damages and costs, arising from these damages. Proved the use of tools to secondary type of human impact. In paper considered indicators that evaluate the effectiveness of applicable tax benefits, preferences and budget funding to maintain an acceptable quality of the environment.Исследование проводилось при финансовой поддержке Российского гуманитарного научного фонда и Правительства Свердловской области (проект РГНФ-Урал № 13-12-66011)

Dynamic transcriptomic analysis of ischemic injury in a porcine pre-clinical model mimicking donors deceased after circulatory death

Due to organ shortage, clinicians are prone to consider alternative type of organ donors among them donors deceased after circulatory death (DCD). However, especially using these organs which are more prone to graft dysfunction, there is a need to better understand mechanistic events ocuring during ischemia phase and leading to ischemia/reperfusion injuries (IRI). The aim of this study is to provide a dynamic transcriptomic analysis of preclinical porcine model kidneys subjected to ischemic stress mimicking DCD donor. We compared cortex and corticomedullary junction (CMJ) tissues from porcine kidneys submitted to 60 min warm ischemia (WI) followed by 0, 6 or 24 hours of cold storage in University of Wisconsin solution versus control non-ischemic kidneys (n=5 per group). 29 cortex genes and 113 CMJ genes were significantly up or down-regulated after WI versus healthy kidneys, and up to 400 genes were regulated after WI followed by 6 or 24 hours of cold storage (p < 0.05). Functionnal enrichment analysis (home selected gene kinetic classification, Gene-ontology-biological processes and Gene-ontology-molecular-function) revealed relevant genes implication during WI and cold storage. We uncovered targets which we will further validate as biomarkers and new therapeutic targets to optimize graft kidney quality before transplantation and improve whole transplantation outcome

How to Design a good RNA-Seq experiment in an interdisciplinary context?

How to Design a good RNA-Seq experiment in an interdisciplinary context?. European conference on Computational Biolog