Search

SUMMARY: Bacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole‐genome deep sequencing of pools of the most resistant and most susceptible individuals of a large (n = 7484) biparental F2 population segregating for resistance to Xtg. Using chromosome‐level genome assemblies as references, we were able to define a ~300 kb region highly associated with resistance on pseudo‐chromosome 4. Further investigation of this region revealed multiple genes with a known role in disease resistance, including genes encoding for Pik2‐like disease resistance proteins, cysteine‐rich kinases, and RGA4‐ and RGA5‐like disease resistance proteins. Investigation of allele frequencies in the pools and comparative genome analysis in the grandparents of the F2 population revealed that some of these genes contain variants with allele frequencies that correspond to the expected heterozygosity in the resistant grandparent. This study emphasizes the efficacy of combining BSA studies in very large populations with whole genome deep sequencing and high‐quality genome assemblies to pinpoint regions associated with a binary trait of interest and accurately define a small set of candidate genes. Furthermore, markers identified in this region hold significant potential for marker‐assisted breeding strategies to breed resistance to Xtg in Italian ryegrass cultivars more efficiently. Significance Statement: Elucidating the genetic control of phenotypic traits in highly heterozygous, outbreeding plant species is laborious as it requires phenotyping and genotyping of a large number of individuals. Using 7484 individuals of an Italian ryegrass population, bulked segregant analysis, and whole genome deep sequencing of pools, we identified a 300 kb genomic region harboring promising candidate genes for resistance to bacterial wilt, an important target trait in forage grass breeding. [ABSTRACT FROM AUTHOR]

The empirical expressions for predicting the small-strain shear modulus (G0) of granular soils in current engineering practice are established mainly on experimental data under isotropic stress conditions. In most geotechnical applications, however, soils are subjected to anisotropic stress conditions. The impact of stress anisotropy on G0 is a critical concern but is not yet fully understood. In this paper, we present a specifically designed experimental study to address the question. Various principal stress ratios were applied to isotropically consolidated sand specimens in a triaxial apparatus, and the elastic shear waves were generated by the bender elements installed in the apparatus such that the variations of G0 from isotropic stress states to anisotropic stress states were determined. Three quartz sands with different particle shapes were tested under a range of states in terms of void ratio, axial stress, and radial stress. The study shows that the impact of stress anisotropy is much more complicated than commonly thought. It depends on the magnitude of the stress ratio and the loading mode. A simple model that accounts for two primary mechanisms associated with the impact of stress anisotropy is proposed, and its performance is evaluated using various sources of data in the literature. [ABSTRACT FROM AUTHOR]

Establishing the influence of sample preparation method on shear wave velocity or associated small-strain shear modulus (G0) of silty sands is a subject of considerable interest. This paper presents an attempt to address this topic through a comprehensive experimental programme covering four sample preparation methods. The experiments were conducted on clean Toyoura sand and its mixtures with two types of fines of different sizes. For each sample preparation method, a range of void ratio and confining stress was investigated to obtain a comprehensive view of the influence of sample preparation and its interplay with other factors. One of the notable findings is that, compared with clean sand, the difference of G0 induced by different sample reconstitution methods can be much enlarged for silty sand, and the influence is coupled with the size disparity ratio of the mixtures. The reduction of G0 due to the presence of fines also depends on sample preparation method and for smaller fines the reduction is more significant. A careful examination of the X-ray images of the specimens made by different methods suggests that the observed effects are mainly associated with the different contact conditions of coarse and fine grains. [ABSTRACT FROM AUTHOR]

Subarachnoid hemorrhage (SAH) is a hemorrhagic cerebrovascular disease with an extremely poor prognosis. The molecular mechanism and biomarkers involved in neurological outcome after SAH still need to be explored. This study assessed the microRNA expression characteristics of SAH patients with different neurological outcomes by meta-analysis. Public databases were searched from database inception until December 2022. The study reported that microRNA expression data in SAH patients with different neurological outcomes were included in the analysis. The differential expression of miRNAs was evaluated by meta-analysis. Overrepresentation analysis was performed for the targeted genes of significant miRNAs. The XGBoost algorithm was used to assess the predictive ability for neurological outcomes with clinical characteristics and significantly expressed miRNAs. Seven studies were finally included in the meta-analysis. The results showed that the levels of miR-152-3p (SMD: − 0.230; 95% CI − 0.389, − 0.070; padj = 0.041), miR-221-3p (SMD: − 0.286; 95% CI − 0.446, − 0.127; padj = 0.007), and miR-34a-5p (SMD: − 0.227; 95% CI − 0.386, − 0.067; padj = 0.041) were significantly lower in SAH patients with good neurological outcomes than in those with poor neurological outcomes. The PI3K-AKT signaling pathway may have an important role in neurological recovery after SAH. Based on the XGBoost algorithm, the neurological outcome could be accurately predicted with clinical characteristics plus the three miRNAs. The expression levels of miR-152-3p, miR-221-3p, and miR-34a-5p were significantly lower in patients with good neurological outcomes than in those with poor outcomes. These miRNAs can serve as potential predictive biomarkers for neurological outcomes. The molecular mechanism and biomarkers involved in neurological outcome after SAH still need to be explored. Our study analyzed microRNA expression characteristics of SAH patients with different neurological outcomes by meta-analysis. After analyze studies reporting the microRNA expression data in SAH patients with different neurological outcomes, results show that the levels of miR-152-3p, miR-221-3p, and miR-34a-5p were significantly lower in SAH patients with good neurological outcomes than in those with poor neurological outcomes. The PI3K-AKT signaling pathway may have an important role in neurological recovery after SAH. Based on the XGBoost algorithm, the neurological outcome could be accurately predicted with clinical characteristics plus the three miRNAs. [ABSTRACT FROM AUTHOR]

Background. Accurate and effective biomarkers for the prognosis of patients with hepatocellular carcinoma (HCC) are poorly identified. A network-based gene signature may serve as a valuable biomarker to improve the accuracy of risk discrimination in patients. Methods. The expression levels of cancer hallmarks were determined by Cox regression analysis. Various bioinformatic methods, such as GSEA, WGCNA, and LASSO, and statistical approaches were applied to generate an MTORC1 signaling-related gene signature (MSRS). Moreover, a decision tree and nomogram were constructed to aid in the quantification of risk levels for each HCC patient. Results. Active MTORC1 signaling was found to be the most vital predictor of overall survival in HCC patients in the training cohort. MSRS was established and proved to hold the capacity to stratify HCC patients with poor outcomes in two validated datasets. Analysis of the patient MSRS levels and patient survival data suggested that the MSRS can be a valuable risk factor in two validated datasets and the integrated cohort. Finally, we constructed a decision tree which allowed to distinguish subclasses of patients at high risk and a nomogram which could accurately predict the survival of individuals. Conclusions. The present study may contribute to the improvement of current prognostic systems for patients with HCC. [ABSTRACT FROM AUTHOR]