Skew-cyclic codes

We generalize the notion of cyclic codes by using generator polynomials in (non commutative) skew polynomial rings. Since skew polynomial rings are left and right euclidean, the obtained codes share most properties of cyclic codes. Since there are much more skew-cyclic codes, this new class of codes allows to systematically search for codes with good properties. We give many examples of codes which improve the previously best known linear codes

Construction and number of self-dual skew codes over Fp2F_{p^2}

International audienceThe aim of this text is to construct and to count self-dual θ-cyclic and θ-negacyclic codes over IF p 2 where θ is the Frobenius automorphism

Linear codes using skew polynomials with automorphisms and derivations

International audienceIn this work the de nition of codes as modules over skew polynomial rings of automorphism type is generalized to skew polynomial rings whose multiplication is de ned using an automorphism and an inner derivation. This produces a more gen- eral class of codes which, in some cases, produce better distance bounds than skew module codes constructed only with an automorphism. Extending the approach of Gabidulin codes, we introduce new notions of evaluation of skew polynomials with derivations and the corresponding evaluation codes. We propose several ap- proaches to generalize Reed Solomon and BCH codes to module skew codes and for two classes we show that the dual of such a Reed Solomon type skew code is an evaluation skew code. We generalize a decoding algorithm due to Gabidulin for the rank matrix and derive families of MDS and MRD codes

Unusual duplication of the insulin-like receptor in the crustacean Daphnia pulex

Background: The insulin signaling pathway (ISP) has a key role in major physiological events like carbohydrate metabolism and growth regulation. The ISP has been well described in vertebrates and in a few invertebrate model organisms but remains largely unexplored in non-model invertebrates. This study is the first detailed genomic study of this pathway in a crustacean species, Daphnia pulex. Results: The Daphnia pulex draft genome sequence assembly was scanned for major components of the ISP with a special attention to the insulin-like receptor. Twenty three putative genes are reported. The pathway appears to be generally well conserved as genes found in other invertebrates are present. Major findings include a lower number of insulin-like peptides in Daphnia as compared to other invertebrates and the presence of multiple insulin-like receptors (InR), with four genes as opposed to a single one in other invertebrates. Genes encoding for the Dappu_InR are likely the result of three duplication events and bear some unusual features. Dappu_InR-4 has undergone extensive evolutionary divergence and lacks the conserved site of the catalytic domain of the receptor tyrosine kinase. Dappu_InR-1 has a large insert and lacks the transmembranal domain in the b-subunit. This domain is also absent in Dappu_InR-3. Dappu_InR-2 is characterized by the absence of the cystein-rich region. Real-time q-PCR confirmed the expression of all four receptors. EST analyses of cDNA libraries revealed that the four receptors were differently expressed under various conditions. Conclusions: Duplications of the insulin receptor genes might represent an important evolutionary innovation in Daphnia as they are known to exhibit extensive phenotypic plasticity in body size and in the size of defensive structures in response to predation

Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration

International audienceNext-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

<p>Abstract</p> <p>Background</p> <p>Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.</p> <p>Results</p> <p>First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain <it>Sphingomonas paucimobilis </it>sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.</p> <p>Conclusions</p> <p>We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.</p

L'innovation, condition de la pérennité des systèmes agroalimentaires localisés

La production agroalimentaire artisanale et les produits de terroir ont bien souvent une image traditionnelle, celle de pratiques figées dans le temps, transmises de génération en génération. L'analyse montre au contraire des systèmes agroalimentaires localisés (Syal) confrontés à des besoins permanents d'innovation, pour faire face à des évolutions internes (réduction de la capacité de coordination et d'action collective) et/ ou externes (nouvelles contraintes ou opportunités techniques ou commerciales). Face à ces besoins, certains systèmes sont à même d'instaurer des interactions accrues entre acteurs locaux et acteurs extra-locaux, débouchant sur des innovations techniques ou organisationnelles. Le concept de Syal permet alors d'éclairer bien mieux ces processus d'innovation collectifs et localisés que ne le font les schémas diffusionnistes, et de mettre aussi en évidence les voies d'appui

Angiotensin inhibition enhances drug delivery and potentiates chemotherapy by decompressing tumour blood vessels

Cancer and stromal cells actively exert physical forces (solid stress) to compress tumour blood vessels, thus reducing vascular perfusion. Tumour interstitial matrix also contributes to solid stress, with hyaluronan implicated as the primary matrix molecule responsible for vessel compression because of its swelling behaviour. Here we show, unexpectedly, that hyaluronan compresses vessels only in collagen-rich tumours, suggesting that collagen and hyaluronan together are critical targets for decompressing tumour vessels. We demonstrate that the angiotensin inhibitor losartan reduces stromal collagen and hyaluronan production, associated with decreased expression of profibrotic signals TGF-β1, CCN2 and ET-1, downstream of angiotensin-II-receptor-1 inhibition. Consequently, losartan reduces solid stress in tumours resulting in increased vascular perfusion. Through this physical mechanism, losartan improves drug and oxygen delivery to tumours, thereby potentiating chemotherapy and reducing hypoxia in breast and pancreatic cancer models. Thus, angiotensin inhibitors—inexpensive drugs with decades of safe use—could be rapidly repurposed as cancer therapeutics.National Cancer Institute (U.S.) (Grant P01-CA080124)National Cancer Institute (U.S.) (Grant R01-CA126642)National Cancer Institute (U.S.) (Grant R01-CA085140)National Cancer Institute (U.S.) (Grant R01-CA115767)National Cancer Institute (U.S.) (Grant R01-CA098706)United States. Dept. of Defense. Breast Cancer Research Program (Innovator Award W81XWH-10-1-0016)Lustgarten Foundation (Dana-Farber Cancer Institute/David H. Koch Institute for Integrative Cancer Research at MIT Bridge Project Grant

Chapitre 6 - L’innovation, condition de la pérennité des systèmes agroalimentaires localisés

Résumé. La production agroalimentaire artisanale et les produits de terroir ont bien souvent une image traditionnelle, celle de pratiques figées dans le temps, transmises de génération en génération. L’analyse montre au contraire des systèmes agroalimentaires localisés (Syal) confrontés à des besoins permanents d’innovation, pour faire face à des évolutions internes (réduction de la capacité de coordination et d’action collective) et/ou externes (nouvelles contraintes ou opportunités techniques ou commerciales). Face à ces besoins, certains systèmes sont à même d’instaurer des interactions accrues entre acteurs locaux et acteurs extra-locaux, débouchant sur des innovations techniques ou organisationnelles. Le concept de Syal permet alors d’éclairer bien mieux ces processus d’innovation collectifs et localisés que ne le font les schémas diffusionnistes, et de mettre aussi en évidence les voies d’appui