Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars‐like conditions outside the space station

Despite the increasing interest in using microbial‐based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non‐Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars‐like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE‐R2 facility installed outside the International Space Station. Genomic alterations were determined in a space‐derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space‐exposed cells. Comparative analysis of whole‐genome sequences showed no increased variant numbers in the space‐derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria‐based technologies to support human space exploration

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins

Elevated soluble Flt1 mediates an anti-angiogenic state in patients with ANCA-associated vasculitis

International audiencen.

Deterministic polarization chaos from a laser diode

Fifty years after the invention of the laser diode and fourty years after the report of the butterfly effect - i.e. the unpredictability of deterministic chaos, it is said that a laser diode behaves like a damped nonlinear oscillator. Hence no chaos can be generated unless with additional forcing or parameter modulation. Here we report the first counter-example of a free-running laser diode generating chaos. The underlying physics is a nonlinear coupling between two elliptically polarized modes in a vertical-cavity surface-emitting laser. We identify chaos in experimental time-series and show theoretically the bifurcations leading to single- and double-scroll attractors with characteristics similar to Lorenz chaos. The reported polarization chaos resembles at first sight a noise-driven mode hopping but shows opposite statistical properties. Our findings open up new research areas that combine the high speed performances of microcavity lasers with controllable and integrated sources of optical chaos.Comment: 13 pages, 5 figure

Notes on Dynamics of an External Cavity Semiconductor Lasers

Dynamics of external cavity semiconductor lasers is known to be a complex and uncontrollable phenomenon. Due to the lack of experimental studies on the nature of the external cavity semiconductor lasers, there is a need to theoretically clarify laser dynamics. The stability of laser dynamics in the present paper, is analyzed through plotting the Lyapunov exponent spectra, bifurcation diagrams, phase portrait and electric field intensity time series. The analysis is preformed with respect to applied feedback phase $C_p$, feedback strength $\eta$ and the pump current of the laser. The main argument of the paper is to show that the laser dynamics can not be accounted for through simply a bifurcation diagram and single-control parameter. The comparison of the obtained results provides a very detailed picture of the qualitative changes in laser dynamics.Comment: 7 pages, 34 figure

Visualizing the Template of a Chaotic Attractor

Chaotic attractors are solutions of deterministic processes, of which the topology can be described by templates. We consider templates of chaotic attractors bounded by a genus-1 torus described by a linking matrix. This article introduces a novel and unique tool to validate a linking matrix, to optimize the compactness of the corresponding template and to draw this template. The article provides a detailed description of the different validation steps and the extraction of an order of crossings from the linking matrix leading to a template of minimal height. Finally, the drawing process of the template corresponding to the matrix is saved in a Scalable Vector Graphics (SVG) file.Comment: Appears in the Proceedings of the 26th International Symposium on Graph Drawing and Network Visualization (GD 2018

Quantifying the extent to which index event biases influence large genetic association studies

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.As genetic association studies increase in size to 100,000s of individuals, subtle biases may influence conclusions. One possible bias is "index event bias" (IEB) that appears due to the stratification by, or enrichment for, disease status when testing associations between genetic variants and a disease-associated trait. We aimed to test the extent to which IEB influences some known trait associations in a range of study designs and provide a statistical framework for assessing future associations. Analysing data from 113,203 non-diabetic UK Biobank participants, we observed three (near TCF7L2, CDKN2AB and CDKAL1) overestimated (BMI-decreasing) and one (near MTNR1B) underestimated (BMI-increasing) associations among 11 type 2 diabetes risk alleles (at P  500,000 if the prevalence of those diseases differs by > 10% from the background population. In conclusion, IEB may result in false positive or negative genetic associations in very large studies stratified or strongly enriched for/against disease cases.H.Y., A.R.W. and T.M.F. are supported by the European Research Council grant: 323195; SZ-245 50371-GLUCOSEGENES-FP7-IDEAS-ERC. S.E.J. is funded by the Medical Research Council (grant: MR/M005070/1). M.A.T., M.N.W. and A.M. are supported by the Wellcome Trust Institutional Strategic Support Award (WT097835MF). R.M.F. is a Sir Henry Dale Fellow (Wellcome Trust and Royal Society grant: 104150/Z/14/Z). R.B. is funded by the Wellcome Trust and Royal Society grant: 104150/Z/14/Z. J.T. is funded by a Diabetes Research and Wellness Foundation Fellowship. Z.K. received financial support from the Leenaards Foundation, the Swiss Institute of Bioinformatics and the Swiss National Science Foundation (31003A-143914) and SystemsX.ch (39). The work of M.P.B was supported by the National Heart, Lung, And Blood Institute of the National Institutes of Health under Award no. T32HL007779. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. E.R.P. holds a WT New investigator award 102820/Z/13/Z