Shortest Paths and Probabilities on Time-Dependent Graphs - Applications to Transport Networks

International audienceIn this paper, we focus on time-dependent graphs which seem to be a good way to model transport Networks. In the first part, we remind some notations and techniques related to time-dependent graphs. In the second one, we introduce new algorithms to take into account the notion of probability related to paths in order to guarantee travelling times with a certain accuracy. We also discuss different probabilistic models and show the links between them

Shortest Paths and Probabilities on Time-Dependent Graphs - Applications to Transport Networks

International audienceIn this paper, we focus on time-dependent graphs which seem to be a good way to model transport Networks. In the first part, we remind some notations and techniques related to time-dependent graphs. In the second one, we introduce new algorithms to take into account the notion of probability related to paths in order to guarantee travelling times with a certain accuracy. We also discuss different probabilistic models and show the links between them

Silencing mutated β-catenin inhibits cell proliferation and stimulates apoptosis in the adrenocortical cancer cell line H295R

Adrenocortical carcinoma (ACC) is a rare and highly aggressive endocrine neoplasm, with limited therapeutic options. Activating β-catenin somatic mutations are found in ACC and have been associated with a poor clinical outcome. In fact, activation of the Wnt/β-catenin signaling pathway seems to play a major role in ACC aggressiveness, and might, thus, represent a promising therapeutic target. Similar to patient tumor specimen the H295 cell line derived from an ACC harbors a natural activating β-catenin mutation. We herein assess the in vitro and in vivo effect of β-catenin inactivation using a doxycyclin (dox) inducible shRNA plasmid in H295R adrenocortical cancer cells line (clone named shβ). Following dox treatment a profound reduction in β-catenin expression was detectable in shβ clones in comparison to control clones (Ctr). Accordingly, we observed a decrease in Wnt/βcatenin-dependent luciferase reporter activity as well as a decreased expression of AXIN2 representing an endogenous β-catenin target gene. Concomitantly, β-catenin silencing resulted in a decreased cell proliferation, cell cycle alterations with cell accumulation in the G1 phase and increased apoptosis in vitro. In vivo, on established tumor xenografts in athymic nude mice, 9 days of β-catenin silencing resulted in a significant reduction of CTNNB1 and AXIN2 expression. Moreover, continous β-catenin silencing, starting 3 days after tumor cell inoculation, was associated with a complete absence of tumor growth in the shβ group while tumors were present in all animals of the control group. In summary, these experiments provide evidences that Wnt/β-catenin pathway inhibition in ACC is a promising therapeutic target

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely used to sequence eukaryotic and viral RNAs. However, experimental approaches implementing this technique for prokaryotic transcriptomes remain scarce. Here, we present an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, which can be applied to any microorganism. Our study highlights critical steps of library preparation and computational analysis and compares the results to gold standards in the field. Furthermore, we comprehensively evaluate the applicability and advantages of different ONT-based RNA sequencing protocols, including direct RNA, direct cDNA, and PCR-cDNA. We find that (PCR)-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing. Notably, (PCR)-cDNA-seq is suitable for quantitative measurements and can be readily used for simultaneous and accurate detection of transcript 5′ and 3′ boundaries, analysis of transcriptional units, and transcriptional heterogeneity. In summary, based on our comprehensive study, we show nanopore RNA-seq to be a ready-to-use tool allowing rapid, cost-effective, and accurate annotation of multiple transcriptomic features. Thereby nanopore RNA-seq holds the potential to become a valuable alternative method for RNA analysis in prokaryotes

Template-growth of periodically domain-structured KTiOPO4

International audienceWe performed the first growth, from a high temperature solution, of a 38.86 μm-periodicity PPKTP crystal of good optical quality over a thickness of more than 800 μm onto each of the two faces perpendicular to the c direction of a PPKTP substrate previously obtained by electric field poling. The quasi-phase matched second harmonic generation properties in the grown layer and substrate are similar and in accordance with calculation

Comparative evaluation of approaches in T.4.1-4.3 and working definition of adaptive module

The goal of this deliverable is two-fold: (1) to present and compare different approaches towards learning and encoding movements us- ing dynamical systems that have been developed by the AMARSi partners (in the past during the first 6 months of the project), and (2) to analyze their suitability to be used as adaptive modules, i.e. as building blocks for the complete architecture that will be devel- oped in the project. The document presents a total of eight approaches, in two groups: modules for discrete movements (i.e. with a clear goal where the movement stops) and for rhythmic movements (i.e. which exhibit periodicity). The basic formulation of each approach is presented together with some illustrative simulation results. Key character- istics such as the type of dynamical behavior, learning algorithm, generalization properties, stability analysis are then discussed for each approach. We then make a comparative analysis of the different approaches by comparing these characteristics and discussing their suitability for the AMARSi project

Evolution of Microphase Separation with Variations of Segments of Sequence-Controlled Multiblock Copolymers

Multiblock copolymers (MBCPs) are an emerging class of materials that are becoming more accessible in recent years. However, to date there is still a lack of fundamental understanding of their physical properties. In particular, the glass transition temperature (Tg) which is known to be affected by the phase separation has not been well characterized experimentally. To this end, we report the first experimental study on the evolution of the Tgs and the corresponding phase separation of linear MBCPs with increasing number of blocks while keeping the overall degree of polymerization (DP) constant (DP = 200). Ethylene glycol methyl ether acrylate (EGMEA) and tert-butyl acrylate (tBA) were chosen as monomers for reversible addition-fragmentation chain transfer polymerization to synthesize MBCPs. We found the Tgs (as measured by differential scanning calorimetry) of EGMEA and tBA segments within the MCBPs to converge with increasing number of blocks and decreasing block length, correlating with the loss of the heterogeneity as observed from small-angle X-ray scattering (SAXS) analysis. The Tgs of the multiblock copolymers were also compared to the Tgs of the polymer blends of the corresponding homopolymers, and we found that Tgs of the polymer blends were similar to those of the respective homopolymers, as expected. SAXS experiments further demonstrated microphase separation of multiblock copolymers. This work demonstrates the enormous potential of multiblock architectures to tune the physical properties of synthetic polymers, by changing their glass transition temperature and their morphologies obtained from microphase separation, with domain sizes reaching under 10 nm

Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis.

Inflammatory bowel disease (IBD) arises by unknown environmental triggers in genetically susceptible individuals. Epigenetic regulation of gene expression may integrate internal and external influences and may thereby modulate disease susceptibility. Epigenetic modification may also affect the germ-line and in certain contexts can be inherited to offspring. This study investigates epigenetic alterations consequent to experimental murine colitis induced by dextran sodium sulphate (DSS), and their paternal transmission to offspring. Genome-wide methylome- and transcriptome-profiling of intestinal epithelial cells (IECs) and sperm cells of males of the F0 generation, which received either DSS and consequently developed colitis (F0(DSS)), or non-supplemented tap water (F0(Ctrl)) and hence remained healthy, and of their F1 offspring was performed using reduced representation bisulfite sequencing (RRBS) and RNA-sequencing (RNA-Seq), respectively. Offspring of F0(DSS) males exhibited aberrant methylation and expression patterns of multiple genes, including Igf1r and Nr4a2, which are involved in energy metabolism. Importantly, DSS colitis in F0(DSS) mice was associated with decreased body weight at baseline of their F1 offspring, and these F1 mice exhibited increased susceptibility to DSS-induced colitis compared to offspring from F0(Ctrl) males. This study hence demonstrates epigenetic transmissibility of metabolic and inflammatory traits resulting from experimental colitis.This study was carried out as part of the Research Training Group “Genes, Environment and Inflammation”, supported by the Deutsche Forschungsgemeinschaft (RTG 1743/1) of which A.F. is the spokesperson, the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007–2013)/ERC Grant agreement no. 260961 (A.K.), the Austrian Science Fund and Ministry of Science P21530-B18 and START Y446-B18 (A.K.), the Wellcome Trust (investigator award 106260/Z/14/Z) to A.K., the Cambridge Biomedical Research Centre (A.K.), a fellowship from the European Crohn’s and Colitis Organisation (M.T. and T.E.A.) and a DOC fellowship from the Austrian Academy of Sciences (J.K.).This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/srep3164

Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea

Ribosomal RNA (rRNA) maturation in archaea is a complex multistep process that requires well-defined endo- and exoribonuclease activities to generate fully mature linear rRNAs. However, technical challenges prevented detailed mapping of rRNA processing steps and a systematic analysis of rRNA maturation pathways across the tree of life. In this study, we used long-read (PCR)-cDNA and direct RNA nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the Euryarchaea Haloferax volcanii and Pyrococcus furiosus and the Crenarchaeon Sulfolobus acidocaldarius. Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5′- and 3′-positions, which is required for the classification of rRNA processing intermediates. More specifically, we (i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon (ii) explore the stage-dependent installation of the KsgA-mediated dimethylations in H. volcanii using base-calling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence, revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby significantly expanding our understanding of rRNA maturation pathways in archaea

Using carbon-14 and carbon-13 measurements for source attribution of atmospheric methane in the Athabasca oil sands region

The rapidly expanding and energy-intensive production from the Canadian oil sands, one of the largest oil reserves globally, accounts for almost 12&thinsp;% of Canada's greenhouse gas emissions according to inventories. Developing approaches for evaluating reported methane (CH4) emission is crucial for developing effective mitigation policies, but only one study has characterized CH4 sources in the Athabasca oil sands region (AOSR). We tested the use of 14C and 13C carbon isotope measurements in ambient CH4 from the AOSR to estimate source contributions from key regional CH4 sources: (1)&nbsp;tailings ponds, (2)&nbsp;surface mines and processing facilities, and (3)&nbsp;wetlands. The isotopic signatures of ambient CH4 indicate that the CH4 enrichments measured at the site were mainly influenced by fossil CH4 emissions from surface mining and processing facilities (56&thinsp;&plusmn;&thinsp;18&thinsp;%), followed by fossil CH4 emissions from tailings ponds (34&thinsp;&plusmn;&thinsp;18&thinsp;%) and to a lesser extent modern CH4 emissions from wetlands (10&thinsp;&plusmn;&thinsp;&lt;1&thinsp;%). Our results confirm the importance of tailings ponds in regional CH4 emissions and show that this method can successfully distinguish wetland CH4 emissions. In the future, the isotopic characterization of CH4 sources and measurements from different seasons and wind directions are needed to provide a better source attribution in the AOSR. &nbsp;</p