Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana.

Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein-coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution, genome-wide maps of both H3K9m2 and H3K27m3 in wild-type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that ectopic H3K9m2 observed in met1 can be due to defects in IBM1-mediated H3K9m2 demethylation at some sites, but most importantly targets H3K27m3-marked genes, suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whereas CG/H3K9m2 hypomethylated transposons become ectopically H3K27m3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation but ectopic hypermethylation of genes previously marked by H3K27m3

Beyond Formal Methods for Critical Interactive Systems: Dealing with Faults at Runtime

International audienceFormal methods provide support for validation and verification of interactive systems by means of complete and unambiguous description of the envisioned system. They can also be used (for instance in the requirements/needs identification phase) to define precisely what the system should do and how it should meet user needs. If the entire development process in supported by formal methods (for instance as required by DO 178C [7] and its supplement 333 [8]) then classical formal method engineers would argue that the resulting software is defect free. However, events that are beyond the envelope of the specification may occur and trigger unexpected behaviors from the formally specified system resulting in failures. Sources of such failures can be permanent or transient hardware failures, due to (when such systems are deployed in the high atmosphere e.g. aircrafts or spacecrafts) natural faults triggered by alpha-particles from radioactive contaminants in the chips or neutron from cosmic radiation. This position paper proposes a complementary view to formal approaches first by presenting an overview of causes of unexpected events on the system side as well as on the human side and then by discussing approaches that could provide support for taking into account system faults and human errors at design time

The Human Behaviour-Change Project: Harnessing the power of Artificial Intelligence and Machine Learning for evidence synthesis and interpretation

Background Behaviour change is key to addressing both the challenges facing human health and wellbeing and to promoting the uptake of research findings in health policy and practice. We need to make better use of the vast amount of accumulating evidence from behaviour change intervention (BCI) evaluations and promote the uptake of that evidence into a wide range of contexts. The scale and complexity of the task of synthesising and interpreting this evidence, and increasing evidence timeliness and accessibility, will require increased computer support. The Human Behaviour-Change Project (HBCP) will use Artificial Intelligence and Machine Learning to (i) develop and evaluate a ‘Knowledge System’ that automatically extracts, synthesises and interprets findings from BCI evaluation reports to generate new insights about behaviour change and improve prediction of intervention effectiveness and (ii) allow users, such as practitioners, policy makers and researchers, to easily and efficiently query the system to get answers to variants of the question ‘What works, compared with what, how well, with what exposure, with what behaviours (for how long), for whom, in what settings and why?’. Methods The HBCP will: a) develop an ontology of BCI evaluations and their reports linking effect sizes for given target behaviours with intervention content and delivery and mechanisms of action, as moderated by exposure, populations and settings; b) develop and train an automated feature extraction system to annotate BCI evaluation reports using this ontology; c) develop and train machine learning and reasoning algorithms to use the annotated BCI evaluation reports to predict effect sizes for particular combinations of behaviours, interventions, populations and settings; d) build user and machine interfaces for interrogating and updating the knowledge base; and e) evaluate all the above in terms of performance and utility. Discussion The HBCP aims to revolutionise our ability to synthesise, interpret and deliver evidence on behaviour change interventions that is up-to-date and tailored to user need and context. This will enhance the usefulness, and support the implementation of, that evidence.The project is funded by a Wellcome Trust collaborative award [The Human Behaviour-Change Project: Building the science of behaviour change for complex intervention development’, 201,524/Z/16/Z]. During the preparation of the manuscript RW’s salary was funded by Cancer Research UK

Temporal dominance of sensations of peanuts and peanut products in relation to Hutchings and Lillford’s “breakdown path"

Hutchings and Lillford’s (Journal of Texture Studies, 19, 103-115, 1988) proposed a “breakdown path” whereby particle size reduction occurs through mastication in conjunction with the secretion of saliva to form a swallowable bolus. The swallowing trajectory of whole peanuts, peanut meal and peanut paste were studied with the temporal dominance of sensations technique. The sensations for whole peanuts progressed from hard, to crunchy, to chewy, to soft and ended compacted on teeth. Predictably peanut meal missed out the first two sensations, progressing from chewy, to soft and ending compacted on teeth. However peanut paste, which starts as a soft suspension with relatively little structure appears to thicken and stick to the palate during oral processing. We propose that the “hard to swallow” sensation elicited by peanut paste may be due to water absorption from the saliva as they mix in the mouth

Regulation of atypical MAP kinases ERK3 and ERK4 by the phosphatase DUSP2

The atypical MAP kinases ERK3 and ERK4 are activated by phosphorylation of a serine residue lying within the activation loop signature sequence S-E-G. However, the regulation of ERK3 and ERK4 phosphorylation and activity is poorly understood. Here we report that the inducible nuclear dual-specificity MAP kinase phosphatase (MKP) DUSP2, a known regulator of the ERK and p38 MAPKs, is unique amongst the MKP family in being able to bind to both ERK3 and ERK4. This interaction is mediated by a conserved common docking (CD) domain within the carboxyl-terminal domains of ERK3 and ERK4 and the conserved kinase interaction motif (KIM) located within the non-catalytic amino terminus of DUSP2. This interaction is direct and results in the dephosphorylation of ERK3 and ERK4 and the stabilization of DUSP2. In the case of ERK4 its ability to stabilize DUSP2 requires its kinase activity. Finally, we demonstrate that expression of DUSP2 inhibits ERK3 and ERK4-mediated activation of its downstream substrate MK5. We conclude that the activity of DUSP2 is not restricted to the classical MAPK pathways and that DUSP2 can also regulate the atypical ERK3/4-MK5 signalling pathway in mammalian cells

Distinct Effects of p19 RNA Silencing Suppressor on Small RNA Mediated Pathways in Plants

RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection. We showed that ectopically expressed p19 sequesters endogenous small RNAs (sRNAs) in the absence, but not in the presence of virus infection. Our presented data question the generalized model in which the sequestration of endogenous sRNAs by the viral suppressor contributes to the viral symptom development. We further showed that p19 preferentially binds the perfectly paired ds-viral small interfering RNAs (vsiRNAs) but does not select based on their sequence or the type of the 5’ nucleotide. Finally, co-immunoprecipitation of sRNAs with AGO1 or AGO2 from virus-infected plants revealed that p19 specifically impairs vsiRNA loading into AGO1 but not AGO2. Our findings, coupled with the fact that p19-expressing wild type Cymbidium ringspot virus (CymRSV) overcomes the Nicotiana benthamiana silencing based defense killing the host, suggest that AGO1 is the main effector of antiviral silencing in this host-virus combination

Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense

[EN] The mechanisms underlying induction and suppression of RNA silencing in the ongoing plant-virus arms race are poorly understood. We show here that virus-derived small RNAs produced by Arabidopsis Dicer-like 4 (DCL4) program an effector complex conferring antiviral immunity. Inhibition of DCL4 by a viral-encoded suppressor revealed the subordinate antiviral activity of DCL2. Accordingly, inactivating both DCL2 and DCL4 was necessary and sufficient to restore systemic infection of a suppressor-deficient virus. The effects of DCL2 were overcome by increasing viral dosage in inoculated leaves, but this could not surmount additional, non - cell autonomous effects of DCL4 specifically preventing viral unloading from the vasculature. These findings define a molecular framework for studying antiviral silencing and defense in plants.We thank members of the Voinnet laboratory for discussions and Z. Xie for dcl seeds. Funded by CNRS grant to A.D.; NSF grant MCB-0209836, NIH grant AI43288, and U.S. Department of Agriculture grant NRI 2005-35319-15280 to J.C.; and Pao Schloarship (Zhejiang University, China) to J.B. This work is dedicated to the memory of M. and G. Voinnet.Deleris, A.; Gallego Bartolomé, J.; Bao, J.; Kasschau, KD.; Carrinton, JC.; Voinnet, O. (2006). Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science. 313(5783):68-71. https://doi.org/10.1126/science.11282146871313578

Beyond Formal Methods for Critical Interactive Systems: Dealing with Faults at Runtime

Formal methods provide support for validation and verification of interactive systems by means of complete and unambiguous description of the envisioned system. They can also be used (for instance in the requirements/needs identification phase) to define precisely what the system should do and how it should meet user needs. If the entire development process in supported by formal methods (for instance as required by DO 178C [7] and its supplement 333 [8]) then classical formal method engineers would argue that the resulting software is defect free. However, events that are beyond the envelope of the specification may occur and trigger unexpected behaviors from the formally specified system resulting in failures. Sources of such failures can be permanent or transient hardware failures, due to (when such systems are deployed in the high atmosphere e.g. aircrafts or spacecrafts) natural faults triggered by alpha-particles from radioactive contaminants in the chips or neutron from cosmic radiation. This position paper proposes a complementary view to formal approaches first by presenting an overview of causes of unexpected events on the system side as well as on the human side and then by discussing approaches that could provide support for taking into account system faults and human errors at design time

A reassessment of the infra-species diversity patterns in the wine-associated Oenococcus oeni

Oenococcus oeni is the predominant species of lactic acid bacteria in wine, where it carries out malolactic fermentation (MLF), which helps to ensure and preserve the quality of the wine. Today, existing combinations of grape varieties, soil composition, fluctuating climatic parameters, and specific technical processes implemented by wineries lead to incredibly varied wine compositions that pose challenges for spontaneous MLF. Commercial starter cultures have been developed for use as inoculants. However, their effectiveness in ensuring consistent and reliable MLF is also limited in modern wines. The selection process must therefore adapt to these new challenges, which means expanding current portfolios by selecting more robust bacteria from wines that are more varied in terms of grape varieties and chemical constraints. We have assembled a set of 21 wines produced in Europe from different grape varieties, with varying and, in some cases, extreme ethanol contents, total polyphenolic indices, and pH levels. The isolation and MLVA typing of 385 dominant colonies were combined with whole-genome sequencing of 48 representative strains, and we observed several strains with unique accessory genomic content. Different selective pressures led to the formation of groups of genetically related individuals, particularly in white and rosé wines with moderate ethanol content. However, cohabiting strains with contrasting genetic profiles were also observed in some red wines. Our data highlight the complexity of the factors involved in population heterogeneity and raise the possibility that this phenomenon may increase fitness through diversification of strategies or division of labor in specific production environments