Genetic architecture and marker-assisted breeding for salt tolerance in soybean

Salinity is one of the major abiotic stresses that inhibits plant growth and causes seed yield loss in soybean. Although a major gene for salt tolerance on chromosome (Chr.) 3 was mapped, cloned and characterized, it does not fully explain genetic variability for tolerance in soybean. Two mapping approaches, quantitative trait loci (QTL) mapping and genome-wide association study (GWAS), can complement each other to identify genomic regions and molecular markers associated with traits of interest. QTL mapping is more suitable to map traits governed by rare alleles in a designed population while GWAS is better in mapping traits underlined by few genes of large effect in the natural population. This study was performed to identify additional loci and new sources for salt tolerance by using both approaches. For bi-parental QTL mapping, salt tolerance of 132 F2 families was evaluated by accessing leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Their genotypes were obtained using the Illumina Infinium SoySNP6K BeadChip assay to map salt tolerant gene(s). A major locus significantly associated with LSS, CCR, LSC, and LCC was mapped to Chr. 3 with LOD scores of 19.1, 11.0, 7.7, and 25.6, respectively. In addition, a second locus associated with salt tolerance for LSC was also detected and mapped on Chr. 13 with a LOD score of 4.6 and an R2 of 0.115. The evaluation of salt tolerance of an F5 population derived from the same cross showed that combining salt tolerant alleles of major and minor loci significantly increased salt tolerance. On the other hand, GWAS for salt tolerance was conducted using SNPs of two datasets, SoySNP50K iSelect BeadChip and 3.7M SNP dataset (from whole-genome sequencing data), across 305 soybean accessions of a diverse panel. The known gene on Chr. 3 was confirmed by three gene-based markers (GBMs) that integrated into both datasets. Other genomic regions significantly associated with salt tolerance were identified on Chrs. 1, 2, 5, 6, 8, 14, 18, and 19 by analyzing 3.7M SNP dataset, in which the position on Chr. 8 strongly predicted a new minor locus for salt tolerance. The genotype-phenotype correlation using three GBMs discovered six new salt tolerant sources that may carry novel gene(s) for salt tolerance. By complementation tests and segregation analysis of salt tolerance among F2 plants developed from a cross of Fiskeby III and a salt tolerance accession, PI 468908, it was speculated that salt tolerance from PI 468908 was possibly controlled by a new gene instead of the known gene on Chr. 3. These significant loci in new salt tolerant sources coupled with significant SNP markers could be useful for marker-assisted selection in molecular breeding programs to improve salt tolerance in soybean.Includes bibliographical reference

Evaluation of Xpert MTB/RIF and MODS assay for the diagnosis of pediatric tuberculosis

BACKGROUND: Tuberculosis (TB) in children is rarely confirmed due to the lack of effective diagnostic tools; only 10 to 15% of pediatric TB is smear positive due to paucibacillary samples and the difficulty of obtaining high-quality specimens from children. We evaluate here the accuracy of Xpert MTB/RIF in comparison with the Micoroscopic observation drug susceptibility (MODS) assay for diagnosis of TB in children using samples stored during a previously reported evaluation of the MODS assay. METHODS: Ninety-six eligible children presenting with suspected TB were recruited consecutively at Pham Ngoc Thach Hospital in Ho Chi Minh City Viet Nam between May to December 2008 and tested by Ziehl-Neelsen smear, MODS and Mycobacterial growth Indicator (MGIT, Becton Dickinson) culture. All samples sent by the treating clinician for testing were included in the analysis. An aliquot of processed sample deposit was stored at −20°C and tested in the present study by Xpert MTB/RIF test. 183 samples from 73 children were available for analysis by Xpert. Accuracy measures of MODS and Xpert were summarized. RESULTS: The sensitivity (%) in detecting children with a clinical diagnosis of TB for smear, MODS and Xpert were 37.9 [95% CI 25.5; 51.6], 51.7 [38.2; 65.0] and 50.0 [36.6; 63.4], respectively (per patient analysis). Xpert was significantly more sensitive than smear (P=0.046). Testing of additional samples did not increase case detection for MODS while testing of a second sputum sample by Xpert detected only two additional cases. The positive and negative predictive values (%) of Xpert were 100.0 [88.0; 100.0] and 34.1 [20.5; 49.9], respectively, while those of MODS were 96.8 [83.3; 99.9] and 33.3 [19.6; 49.5]. CONCLUSION: MODS culture and Xpert MTB/RIF test have similar sensitivities for the detection of pediatric TB. Xpert MTB RIF is able to detect tuberculosis and rifampicin resistance within two hours. MODS allows isolation of cultures for further drug susceptibility testing but requires approximately one week to become positive. Testing of multiple samples by xpert detected only two additional cases and the benefits must be considered against costs in each setting. Further research is required to evaluate the optimal integration of Xpert into pediatric testing algorithms

Excess body weight and age associated with the carriage of fluoroquinolone and third-generation cephalosporin resistance genes in commensal Escherichia coli from a cohort of urban Vietnamese children.

PURPOSE: Antimicrobial-resistant bacterial infections in low- and middle-income countries (LMICs) are a well-established global health issue. We aimed to assess the prevalence of and epidemiological factors associated with the carriage of ciprofloxacin- and ceftriaxone-resistant Escherichia coli and associated resistance genes in a cohort of 498 healthy children residing in urban Vietnam. METHODOLOGY: We cultured rectal swabs onto MacConkey agar supplemented with resistant concentrations of ciprofloxacin and ceftriaxone. Additionally, we screened meta-E. coli populations by conventional PCR to detect plasmid-mediated quinolone resistance (PMQR)- and extended-spectrum β-lactamase (ESBL)-encoding genes. We measured the associations between phenotypic/genotypic resistance and demographic characteristics using logistic regression.Results/Key findings. Ciprofloxacin- and ceftriaxone-resistant E. coli were cultured from the faecal samples of 67.7 % (337/498) and 80.3 % (400/498) of children, respectively. The prevalence of any associated resistance marker in the individual samples was 86.7 % (432/498) for PMQR genes and 90.6 % (451/498) for β-lactamase genes. Overweight children were significantly more likely to carry qnr genes than children with lower weight-for-height z-scores [odds ratios (OR): 1.24; 95 % confidence interval (CI): 10.5-1.48 for each unit increase in weight for height; P=0.01]. Additionally, younger children were significantly more likely to carry ESBL CTX-M genes than older children (OR: 0.97, 95 % CI: 0.94-0.99 for each additional year, P=0.01). CONCLUSION: The carriage of genotypic and phenotypic antimicrobial resistance is highly prevalent among E. coli in healthy children in the community in Vietnam. Future investigations on the carriage of antimicrobial resistant organisms in LMICs should focus on the progression of carriage from birth and structure of the microbiome in obesity

Safety and efficacy of fluoxetine on functional outcome after acute stroke (AFFINITY): a randomised, double-blind, placebo-controlled trial

Background Trials of fluoxetine for recovery after stroke report conflicting results. The Assessment oF FluoxetINe In sTroke recoverY (AFFINITY) trial aimed to show if daily oral fluoxetine for 6 months after stroke improves functional outcome in an ethnically diverse population. Methods AFFINITY was a randomised, parallel-group, double-blind, placebo-controlled trial done in 43 hospital stroke units in Australia (n=29), New Zealand (four), and Vietnam (ten). Eligible patients were adults (aged ≥18 years) with a clinical diagnosis of acute stroke in the previous 2–15 days, brain imaging consistent with ischaemic or haemorrhagic stroke, and a persisting neurological deficit that produced a modified Rankin Scale (mRS) score of 1 or more. Patients were randomly assigned 1:1 via a web-based system using a minimisation algorithm to once daily, oral fluoxetine 20 mg capsules or matching placebo for 6 months. Patients, carers, investigators, and outcome assessors were masked to the treatment allocation. The primary outcome was functional status, measured by the mRS, at 6 months. The primary analysis was an ordinal logistic regression of the mRS at 6 months, adjusted for minimisation variables. Primary and safety analyses were done according to the patient's treatment allocation. The trial is registered with the Australian New Zealand Clinical Trials Registry, ACTRN12611000774921. Findings Between Jan 11, 2013, and June 30, 2019, 1280 patients were recruited in Australia (n=532), New Zealand (n=42), and Vietnam (n=706), of whom 642 were randomly assigned to fluoxetine and 638 were randomly assigned to placebo. Mean duration of trial treatment was 167 days (SD 48·1). At 6 months, mRS data were available in 624 (97%) patients in the fluoxetine group and 632 (99%) in the placebo group. The distribution of mRS categories was similar in the fluoxetine and placebo groups (adjusted common odds ratio 0·94, 95% CI 0·76–1·15; p=0·53). Compared with patients in the placebo group, patients in the fluoxetine group had more falls (20 [3%] vs seven [1%]; p=0·018), bone fractures (19 [3%] vs six [1%]; p=0·014), and epileptic seizures (ten [2%] vs two [<1%]; p=0·038) at 6 months. Interpretation Oral fluoxetine 20 mg daily for 6 months after acute stroke did not improve functional outcome and increased the risk of falls, bone fractures, and epileptic seizures. These results do not support the use of fluoxetine to improve functional outcome after stroke

Time dependent reliability analysis of lined tunnel within the linear viscoelastic Burger rocks using the Response Surface Method

International audienc

Closed-Form Solution and Reliability Analysis of Deep Tunnel Supported by a Concrete Liner and a Covered Compressible Layer Within the Viscoelastic Burger Rock

International audienc

Kriging-based reliability analysis of the long-term stability of a deep drift constructed in the Callovo-Oxfordian claystone

International audienc

Effect of spatial variability of creep rock on the stability of a deep double-lined drift

International audienceThis work aims at investigating the effect of aleatoric uncertainty of creep rock properties on the stability of an underground structure. This uncertainty relates to the spatial variability of the mechanical parameters representing the time-dependent behavior of geological rock formation due to the change in its mineralogy. The chosen methodology consists of representing the aleatoric uncertainty of rock properties by random fields, written as correlation functions with respect to the spatial correlation length. The adaptation of the well-known Expansion Optimal Linear Estimationmethod (EOLE) is performed to account for the cross-correlation of the random fields of the viscoplastic parameters of the host rock. Then, the Kriging-based reliability analysis is undertaken with respect to the discretized random fields, which allows elucidating the effect of spatial variability. As an application, the proposed approach is chosen to study the stability in the long-term of a deep double-lined drift within the geological disposal facilities (Cigeo project) conducted by the French National Radioactive Waste Management Agency (Andra). The drift will be excavated in Callovo-Oxfordian (COx) claystone (if the Cigeo project is licensed), considered as a potential host rock for the deep geological nuclear waste disposal in France. The results show that the chosen Kriging metamodel for the reliability analysis can be appropriate for the case of high correlation length represented by a moderate number of random variables (up to about 50) after the discretization of random fields. Further, the consideration of aleatoric uncertainty exhibits a lower probability of exceedance in comparison with the case where spatial variability is ignored. Still, more investigations need to be conducted in the future to conclude this observation