A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America

Rice blast disease caused by the fungus Magnaporthe oryzae and rice sheath blight disease caused by the fungus Rhizoctonia solani are two major hurdles for stable rice production worldwide. Presently, fungicides are still needed to manage these two devastating fungal pathogens. After two decades of research efforts, a toolbox has been assembled with the following components: (1) insight into pathogen genomic identity and pathogen avirulence (AVR) genes that can be used to enhance plant breeding; (2) new mapping populations and germplasm and genetic stocks that can be used as starting materials to identify effective host resistance (R) genes; (3) user-friendly disease evaluation methods that can be used to accelerate the identification and utilization of R genes; (4) validated effective R genes that are readily available for improving genetic resistance; (5) host genetic markers that can be used to accelerate the development of new resistant germplasms/cultivars; and (6) an improved understanding of resistance mechanisms that can facilitate the engineering of resistance in commercial varieties. Appropriate employment of these tools in breeding and crop protection will reduce production costs and create an environmentally benign, sustainable rice production system

Physiological, Ecological and Genetic Interactions of Rice with Harmful Microbes

Rice is one of the most important food crops for mankind and suffers significant crop loss annually due to rice diseases. Availability of genome sequences of rice has served as a springboard to utilize its innate immunity to prevent rice diseases. Knowledge on interactions of rice and rice pathogens has rapidly accumulated. Effective resistance genes have been identified from cultivated, weedy species of rice, and wild rice relatives and their roles in plant innate immunity have been uncovered. Presently, rice diseases are being managed using host resistance genes and pesticides in diverse culture systems around the globe. This chapter presents a simple review of interactions of rice with harmful microbes causing the two major damaging diseases, rice blast and sheath blight. The review is written to target new readers in life sciences. Knowledge and critical literatures on physiological, genetic, and ecological aspects of host-pathogen interactions are presented to gain insights leading to sustainable disease management systems

De Novo Mutations Disturb Early Brain Development More Frequently Than Common Variants in Schizophrenia

Investigating functional, temporal, and cell-type expression features of mutations is important for understanding a complex disease. Here, we collected and analyzed common variants and de novo mutations (DNMs) in schizophrenia (SCZ). We collected 2,636 missense and loss-of-function (LoF) DNMs in 2,263 genes across 3,477 SCZ patients (SCZ-DNMs). We curated three gene lists: (a) SCZ-neuroGenes (159 genes), which are intolerant to LoF and missense DNMs and are neurologically important, (b) SCZ-moduleGenes (52 genes), which were derived from network analyses of SCZ-DNMs, and (c) SCZ-commonGenes (120 genes) from a recent GWAS as reference. To compare temporal gene expression, we used the BrainSpan dataset. We defined a fetal effect score (FES) to quantify the involvement of each gene in prenatal brain development. We further employed the specificity indexes (SIs) to evaluate cell-type expression specificity from single-cell expression data in cerebral cortices of humans and mice. Compared with SCZ-commonGenes, SCZ-neuroGenes and SCZ-moduleGenes were highly expressed in the prenatal stage, had higher FESs, and had higher SIs in fetal replicating cells and undifferentiated cell types. Our results suggested that gene expression patterns in specific cell types in early fetal stages might have impacts on the risk of SCZ during adulthood

deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and dynamic cellular mechanisms. However, cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation, which is cumbersome and subjective. The increasing number of scRNA-seq datasets, as well as numerous published genetic studies, has motivated us to build a comprehensive human cell type reference atlas.Here, we present decoding Cell type Specificity (deCS), an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes. We used deCS to annotate scRNA-seq data from various tissue types and systematically evaluated the annotation accuracy under different conditions, including reference panels, sequencing depth, and feature selection strategies. Our results demonstrate that expanding the references is critical for improving annotation accuracy. Compared to many existing state-of-the-art annotation tools, deCS significantly reduced computation time and increased accuracy. deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation. Finally, we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits, providing deep insights into the cellular mechanisms underlying disease pathogenesis. All documents for deCS, including source code, user manual, demo data, and tutorials, are freely available at https://github.com/bsml320/deCS

Transvaginal natural orifice transluminal endoscopic surgery-assisted versus transumbilical laparoendoscopic single-site ovarian cystectomy for ovarian mature cystic teratoma. A randomized controlled trial

Objectives: Transvaginal natural orifice transluminal endoscopic surgery (vNOTES) and transumbilical laparoendoscopic single-site surgery (LESS) have shown the prospection as minimally invasive procedures. Here we aimed to compare ovarian cystectomy assisted by vNOTES and by LESS for ovarian mature cystic teratoma (OMCT). Material and methods: A total of 81 premenopausal women with OMCT were randomized to undergo ovarian cystectomy assisted by either vNOTES (n = 41) or LESS (n = 40). The main outcome was the operative time. Secondary outcomes included the length of hospital stay, visual analog scale (VAS) pain scores, abdominal contamination by teratoma contents, and intraoperative and postoperative complications. Results: There were no intergroup differences in age, body mass index, tumor size, or bilaterality of tumor. The operative time for the vNOTES group was significantly shorter than that for the LESS group (68.41 ± 20.92 min vs 85.05 ± 32.94 min, p = 0.008). The highest VAS pain score 24 hours postoperatively was 1.21 ± 0.48 in the vNOTES group and 2.43 ± 0.57 in the LESS group (p < 0.001). Twenty-four of the 40 patients in the LESS group experienced teratoma rupture intraoperatively, leading to abdominal contamination by the teratoma content, while 5 abdominal contamination was observed in the vNOTES group （p = 0.005. No significant differences between the two groups were observed in the other outcomes. Conclusions: vNOTES assisted ovarian cystectomy has short operative time, fast recovery, no scarring, less pain, and low rate of abdominal contamination. Consequently, vNOTES might be superior to LESS for treating OMCTs