Analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta

Background: Manduca sexta is a large lepidopteran insect widely used as a model to study biochemistry of insect physiological processes. As a part of its genome project, over 50 cDNA libraries have been analyzed to profile gene expression in different tissues and life stages. While the RNA-seq data were used to study genes related to cuticle structure, chitin metabolism and immunity, a vast amount of the information has not yet been mined for understanding the basic molecular biology of this model insect. In fact, the basic features of these data, such as composition of the RNA-seq reads and lists of library-correlated genes, are unclear. From an extended view of all insects, clear-cut tempospatial expression data are rarely seen in the largest group of animals including Drosophila and mosquitoes, mainly due to their small sizes.Results: We obtained the transcriptome data, analyzed the raw reads in relation to the assembled genome, and generated heatmaps for clustered genes. Library characteristics (tissues, stages), number of mapped bases, and sequencing methods affected the observed percentages of genome transcription. While up to 40% of the reads were not mapped to the genome in the initial Cufflinks gene modeling, we identified the causes for the mapping failure and reduced the number of non-mappable reads to <8%. Similarities between libraries, measured based on library-correlated genes, clearly identified differences among tissues or life stages. We calculated gene expression levels, analyzed the most abundantly expressed genes in the libraries. Furthermore, we analyzed tissue-specific gene expression and identified 18 groups of genes with distinct expression patterns.Conclusion: We performed a thorough analysis of the 67 RNA-seq datasets to characterize new genomic features of M. sexta. Integrated knowledge of gene functions and expression features will facilitate future functional studies in this biochemical model insect.Peer reviewedBiochemistry and Molecular BiologyEntomology and Plant Patholog

Viscosity dependence of O2 escape from respiratory proteins as a function of cosolvent molecular weight.

Laser photodissociation of respiratory proteins is followed by fast geminate recombination competing with escape of the oxygen molecule into the solvent. The escape rate from myoglobin or hemerythrin has been shown previously to exhibit a reciprocal power-law dependence on viscosity. We have reinvestigated oxygen escape from hemerythrin using a number of viscous cosolvents of varying molecular weight, from glycerol to dextrans up to 500 kDa. In isoviscous solutions, the strong viscosity dependence observed with small cosolvents is progressively reduced upon increasing the cosolvent's molecular weight and disappears at molecular weights greater than about 100 kDa. Thus, viscosity is not a suitable independent parameter to describe the data. The power of the viscosity dependence of the rate coefficient is shown here to be a function of the cosolvent's molecular weight, suggesting that local protein-solvent interactions rather than bulky viscosity are affecting protein dynamics

Quelle prise en charge optimale pour un sarcome du cordon spermatique en 2018 ?

International audienceSpermatic cord sarcomas are rare tumors for which the most important is the initial diagnostic procedure. They are frequently misdiagnosed after surgery for inguinal hernia, inguinal lymphadenectomy or testicular malignancy. Any clinical suspicion has to lead to perform imaging with MRI and a core needle biopsy in order to obtain an accurate preoperative diagnosis. Liposarcoma and leiomyosarcoma are the most common histological subtypes in elderly adults, rhabdomyosarcoma in children or in young adults. A CT scan will precede the treatment in order to look for distant metastasis and abdominal involvement. The therapeutic strategy as well as the surgical planning are then adapted to the histological, morphological and prognostic factors. Surgery is the cornerstone for the treatment of spermatic cord sarcoma. The minimum requirements for the surgical procedure are a wide excision of the tumor en bloc with radical orchidectomy, excision of the ipsilateral scrotum and high spermatic cord ligation. It could be enlarged to the anterior abdominal wall and adjacent organs some required a soft tissue flap. Spermatic cord sarcoma and trunk wall sarcoma have the same prognosis for which local recurrence could significantly decrease survival. Consequently, surgeon in charge with these tumors has to be familiar with soft tissue sarcoma and the management of these patients must be carried out under the supervision of a multidisciplinary team within the Netsarc network.Le sarcome du cordon spermatique est une pathologie rare pour laquelle la prise en charge initiale est d’importance primordiale. Le diagnostic est souvent découvert a posteriori après une chirurgie pour cure de hernie inguinale, pour suspicion de cancer du testicule ou après exérèse d’une adénopathie inguinale. Toute suspicion clinique doit donc faire l’objet d’une imagerie par résonance magnétique (IRM) et d’une biopsie percutanée sous contrôle radiologique dans le but d’obtenir un diagnostic préopératoire précis. Les histologies les plus fréquentes sont le liposarcome et le léiomyosarcome chez l’adulte âgé, le rhabdomyosarcome chez l’enfant et l’adulte jeune. Un bilan d’extension intra-abdominal et à distance par scanner précédera le traitement. La stratégie thérapeutique de même que la planification chirurgicale sont ensuite adaptées aux paramètres histologiques, morphologiques et pronostiques. La chirurgie est la pierre angulaire du traitement des sarcomes du cordon spermatique. Le geste minimal requis est l’exérèse de la tumeur en bloc avec la réalisation d’une orchidectomie totale, l’exérèse du cordon spermatique et la ligature des vaisseaux spermatiques à l’orifice inguinal profond. Elle peut être élargie à la paroi abdominale et aux organes de voisinage et nécessiter si besoin une reconstruction par lambeau. Le pronostic des sarcomes du cordon spermatique est équivalent à celui des sarcomes du tronc dont l’évolutivité locale est péjorative pour la survie des patients. De fait, l’exérèse doit être réalisée par un chirurgien ayant l’expertise des problématiques liées à la chirurgie des sarcomes au sein d’un centre spécialisé du réseau Netsarc