Application of CAPS markers for diversity assessment in grass pea (Lathyrus sativus L.)

Abstract Genetic diversity among 20 Lathyrus sativus L. accessions from Ethiopia was investigated by using Cleaved Amplified Polymorphic Sequence (CAPS) markers. Genetic diversity statistics showed presence of a moderate level of genetic variation in the analysed accessions (P = 69.77%, Hs = 0.278). Analysis of genetic differentiation showed existence of a low level of differentiation between accessions, which accounted for only 7% of the total variation and most of the variation was due to differences among individuals within accessions (93%). Both cluster and principal coordinate analyses revealed minimal grouping of accessions based on geographical origin implying that local varieties of grass pea with different genetic backgrounds were distributed among various administrative regions in Ethiopia. The CAPS markers employed in our study demonstrated the utility of such markers for genetic diversity assessment in grass pea

Regulatory actors and alternative routes for <em>arabidopsis</em> seed germination are revealed using a pathway-based analysis of transcriptomic datasets

Regulation of seed germination by dormancy relies on a complex network of transcriptional and post-transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High-throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway-based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non-dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination

A multiscale approach reveals regulatory players of water stress responses in seeds during germination

Seed germination is regulated by environmental factors, particularly water availability. Water deficits at the time of sowing impair the establishment of crop plants. Transcriptome and proteome profiling was used to document the responses of sunflower (Helianthus annuus) seeds to moderate water stress during germination in two hybrids that are nominally classed as drought sensitive and drought tolerant. Differences in the water stress-dependent accumulation reactive oxygen species and antioxidant enzymes activities were observed between the hybrids. A pathway-based analysis of the hybrid transcriptomes demonstrated that the water stress-dependent responses of seed metabolism were similar to those of the plant, with a decreased abundance of transcripts encoding proteins associated with metabolism and cell expansion. Moreover, germination under water stress conditions was associated with increased levels of transcripts encoding heat shock proteins. Exposure of germinating seeds to water stress specifically affected the abundance of a small number of proteins, including heat shock proteins. Taken together, these data not only identify factors that are likely to play a key role in drought tolerance during seed germination, but they also demonstrate the importance of the female parent in the transmission of water stress tolerance

Re-localization of hormone effectors is associated with dormancy alleviation by temperature and after-ripening in sunflower seeds

International audienceTemperature is the primary factor that affects seed dormancy and germination. However, the molecular mechanism that underlies its effect on dormancy alleviation remained largely unknown. In this study, we investigate hormone involvement in temperature induced germination as compared to that caused by after-ripening. Dormant (D) sunflower seeds cannot germinate at 10 °C but fully germinate at 20 °C. After-ripened seeds become non-dormant (ND), i.e. able to germinate at 10 °C. Pharmacological experiments showed the importance of abscisic acid (ABA), gibberellins (GAs) and ethylene in temperature- and after-ripening-induced germination of sunflower seeds. Hormone quantification showed that after-ripening is mediated by a decline in both ABA content and sensitivity while ABA content is increased in D seeds treated at 10 or 20 °C, suggesting that ABA decrease is not a prerequisite for temperature induced dormancy alleviation. GAs and ethylene contents were in accordance with germination potential of the three conditions (GA1 was higher in D 20 °C and ND 10 °C than in D 10 °C). Transcripts analysis showed that the major change concerns ABA and GAs metabolism genes, while ABA signalling gene expression was significantly unchanged. Moreover, another level of hormonal regulation at the subcellular localization has been revealed by immunocytolocalization study. Indeed, ABA, protein Abscisic acid-Insensitive 5 (ABI5), involved in ABA-regulated gene expression and DELLA protein RGL2, a repressor of the gibberellins signalling pathway, localized mainly in the nucleus in non-germinating seeds while they localized in the cytosol in germinating seeds. Furthermore, ACC-oxidase (ACO) protein, the key ethylene biosynthesis enzyme, was detected in the meristem only in germinating seeds. Our results reveal the importance of hormone actors trafficking in the cell and their regulation in specialized tissue such as the meristem in dormancy alleviation and germination

Predicting 90-day survival of patients with COVID-19: Survival of Severely Ill COVID (SOSIC) scores.

peer reviewed[en] BACKGROUND: Predicting outcomes of critically ill intensive care unit (ICU) patients with coronavirus-19 disease (COVID-19) is a major challenge to avoid futile, and prolonged ICU stays. METHODS: The objective was to develop predictive survival models for patients with COVID-19 after 1-to-2 weeks in ICU. Based on the COVID-ICU cohort, which prospectively collected characteristics, management, and outcomes of critically ill patients with COVID-19. Machine learning was used to develop dynamic, clinically useful models able to predict 90-day mortality using ICU data collected on day (D) 1, D7 or D14. RESULTS: Survival of Severely Ill COVID (SOSIC)-1, SOSIC-7, and SOSIC-14 scores were constructed with 4244, 2877, and 1349 patients, respectively, randomly assigned to development or test datasets. The three models selected 15 ICU-entry variables recorded on D1, D7, or D14. Cardiovascular, renal, and pulmonary functions on prediction D7 or D14 were among the most heavily weighted inputs for both models. For the test dataset, SOSIC-7's area under the ROC curve was slightly higher (0.80 [0.74-0.86]) than those for SOSIC-1 (0.76 [0.71-0.81]) and SOSIC-14 (0.76 [0.68-0.83]). Similarly, SOSIC-1 and SOSIC-7 had excellent calibration curves, with similar Brier scores for the three models. CONCLUSION: The SOSIC scores showed that entering 15 to 27 baseline and dynamic clinical parameters into an automatable XGBoost algorithm can potentially accurately predict the likely 90-day mortality post-ICU admission (sosic.shinyapps.io/shiny). Although external SOSIC-score validation is still needed, it is an additional tool to strengthen decisions about life-sustaining treatments and informing family members of likely prognosis.Program “Alliance tous unis contre le virus

Corrigendum to "Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination" [Plant Sci. 269 (2018) 118-125]

Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination

Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination.

Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination

Purification and multi-omics characterization of human pre-beta-HDL reveals specific proteomic and lipidomic signature relevant to biological activities

International audienceAIM: Multiple biological activities of high-density lipoprotein (HDL) particles may reflect their wide diversity. While alpha-migrating spherical HDLs are well characterised in terms of composition and function, small, dense, discoid pre-beta-migrating HDLs which are thought to display potent biological activities, remain difficult to purify and thus poorly characterised. Methods: We developed an original purification protocol yielding up to 2 mg of pre-beta-HDL (d 1.21-1.25 g/ml) from 70ml plasma of healthy volunteers (n=4). Alpha-HDL (d 1.08-1.11 g/ml) were purified concomitantly. Proteomic and lipidomic analyses of pre-beta- and alpha-HDL were performed and major biological activities, including cholesterol efflux and anti-inflammatory capacities, were evaluated in human THP-1 macrophages. Results: Pre-beta-HDL proteomic analysis identified 36 scaffold proteins gathered in three GO-biological processes. Proteins enriched in pre-beta-HDL were associated with inflammatory response, (e.g. PON1, serpin A1, haptoglobin) and immune response (e.g. IGHA1, C4A/B, haptoglobin-related-protein). Most of proteins related to lipid metabolism and transport were common to alpha- and pre-beta-HDL. Importantly, several functional proteins, including LCAT, PLTP, CETP and PON3, were exclusively detected in pre-beta-HDL. Lipidomic analysis revealed that pre-beta- and alpha-HDL contained similar lipid species. Yet, pre-beta-HDL was enriched in negatively-charged biologically-active phosphatidic acid (+35%; p<0.05) and phosphatidylserine (+20%; p<0.05), as compared to alpha-HDL. Cholesterol efflux from human macrophages to pre-beta-HDL was 3.5-fold elevated relative to alpha-HDL, being similar to that to lipid-free apolipoprotein A-I. Incubation with pre-beta-HDL prior to LPS stimulation reduced mRNA levels of IL-6 (-45%, p<0.05), IL-1-beta (- 44%, p<0.05) and TNF-alpha (- 60%, p<0.01) in THP-1 macrophages, while alpha-HDL exerted no effect.Conclusion: The present study, provides the first-ever structure-function characterization of human pre-beta-HDL using multi-omics analysis allowing identification of proteins and lipids potentially accounting for the enhanced biological activities of pre-beta-HDL. Our findings may provide novel clues to understand physiological and physiopathological roles of pre-beta-HDL

Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination.

Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination