Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed

A compendium of genetic regulatory effects across pig tissues

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.</p

Influence of Scanning Speed on Microstructure and Properties of Laser Cladded Fe-Based Amorphous Coatings

Fe-based amorphous alloys with excellent mechanical properties are suitable for preparing wear resistant coatings by laser cladding. In this study, a novel Fe-based amorphous coating was prepared by laser cladding on 3Cr13 stainless steel substrates. The influence of scanning speeds on the microstructures and properties of the coatings was investigated. The microstructure compositions and phases were analyzed by scanning electron microscope, electron probe microanalyzer, and x-ray diffraction respectively. Results showed that the microstructures of the coatings changed significantly with the increase of scanning speeds. For a scanning speed of 6 mm/s, the cladding layer was a mixture of amorphous and crystalline regions. For a scanning speed of 8 mm/s, the cladding layer was mainly composed of block grain structures. For a scanning speed of 10 mm/s, the cladding layer was composed entirely of dendrites. Different dilution rates at the bonding zones were the main reasons for the microstructure change for different claddings. For all three scanning speeds, the coatings had higher hardness and wear resistance when compared with the substrate; as the scanning speed increased, the hardness and wear resistance of the coatings gradually decreased due to the change in microstructure

Microstructure and Wear Resistance of Fe-Cr-Mo-Co-C-B Amorphous Composite Coatings Synthesized by Laser Cladding

A novel amorphous composite coating was synthesized successfully on 3Cr13 stainless steel by laser cladding Fe-Cr-Mo-Co-C-B amorphous alloy powder. Scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and X-ray diffraction (XRD) were used to analyze the microstructure, composition, and phase structure of the coatings. Hardness and friction wear testers were used to analyze the hardness and wear resistance of the coatings. Results show that the cladding layer has an amorphous/crystalline composite structure, which is composed of a columnar grain region at the bottom and an amorphous region in the upper layer. The solute redistribution between the coating and the substrate in the bonding zone and the lower cooling rate at bottom account for the occurrence of crystallization. The highest hardness of the cladding layer is 1179 HV0.5, which is about 6 times that of the 3Cr13 stainless steel substrate (200 HV0.5). The cladding layer greatly improves the wear resistance of the substrate with a much lower coefficient of friction and wear mass loss compared with the substrate

In-Process Monitoring of Lack of Fusion in Ultra-Thin Sheets Edge Welding Using Machine Vision

Lack of fusion can often occur during ultra-thin sheets edge welding process, severely destroying joint quality and leading to seal failure. This paper presents a vision-based weld pool monitoring method for detecting a lack of fusion during micro plasma arc welding (MPAW) of ultra-thin sheets edge welds. A passive micro-vision sensor is developed to acquire clear images of the mesoscale weld pool under MPAW conditions, continuously and stably. Then, an image processing algorithm has been proposed to extract the characteristics of weld pool geometry from the acquired images in real time. The relations between the presence of a lack of fusion in edge weld and dynamic changes in weld pool characteristic parameters are investigated. The experimental results indicate that the abrupt changes of extracted weld pool centroid position along the weld length are highly correlated with the occurrences of lack of fusion. By using such weld pool characteristic information, the lack of fusion in MPAW of ultra-thin sheets edge welds can be detected in real time. The proposed in-process monitoring method makes the early warning possible. It also can provide feedback for real-time control and can serve as a basis for intelligent defect identification

Hepatotoxicity of Pyrrolizidine Alkaloid Compound Intermedine: Comparison with Other Pyrrolizidine Alkaloids and Its Toxicological Mechanism

Pyrrolizidine alkaloids (PAs) are common secondary plant compounds with hepatotoxicity. The consumption of herbal medicines and herbal teas containing PAs is one of the main causes of hepatic sinusoidal obstruction syndrome (HSOS), a potentially life-threatening condition. The present study aimed to reveal the mechanism underlying the cytotoxicity of intermedine (Im), the main PA in Comfrey. We evaluated the toxicity of the retronecine-type PAs with different structures to cell lines derived from mammalian tissues, including primary mouse hepatocytes, human hepatocytes (HepD), mouse hepatoma-22 (H22) and human hepatocellular carcinoma (HepG2) cells. The cytotoxicity of Im to hepatocyte was evaluated by using cell counting kit-8 assay, colony formation experiment, wound healing assay and dead/live fluorescence imaging. In vitro characterization showed that these PAs were cytotoxic and induced cell apoptosis in a dose-dependent manner. We also demonstrated that Im induced cell apoptosis by generating excessive reactive oxygen species (ROS), changing the mitochondrial membrane potential and releasing cytochrome c (Cyt c) before activating the caspase-3 pathway. Importantly, we directly observed the destruction of the cell mitochondrial structure after Im treatment through transmission electron microscopy (TEM). This study provided the first direct evidence of Im inducing hepatotoxicity through mitochondria-mediated apoptosis. These results supplemented the basic toxicity data of PAs and facilitated the comprehensive and systematic evaluation of the toxicity caused by PA compounds

Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing

Single-cell sequencing is a powerful tool for delineating clonal relationship and identifying key driver genes for personalized cancer management. Here we performed single-cell sequencing analysis of a case of colon cancer. Population genetics analyses identified two independent clones in tumor cell population. The major tumor clone harbored APC and TP53 mutations as early oncogenic events, whereas the minor clone contained preponderant CDC27 and PABPC1 mutations. The absence of APC and TP53 mutations in the minor clone supports that these two clones were derived from two cellular origins. Examination of somatic mutation allele frequency spectra of additional 21 whole-tissue exome-sequenced cases revealed the heterogeneity of clonal origins in colon cancer. Next, we identified a mutated gene SLC12A5 that showed a high frequency of mutation at the single-cell level but exhibited low prevalence at the population level. Functional characterization of mutant SLC12A5 revealed its potential oncogenic effect in colon cancer. Our study provides the first exome-wide evidence at single-cell level supporting that colon cancer could be of a biclonal origin, and suggests that low-prevalence mutations in a cohort may also play important protumorigenic roles at the individual level. © 2014 IBCB, SIBS, CAS All rights reserved

A compendium of genetic regulatory effects across pig tissues

Altres ajuts: Medical Research Council (MRC) MR/R025851/1 i MR/P015514/1. Biotechnology and Biological Sciences Research Council BBS/E/D/10002070 i BBS/E/D/30002275. United States Department of Agriculture 2019-67015-29321 i 2021-67015-33409. National Natural Science Foundation of China (National Science Foundation of China) 32022078.The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model. The pilot phase of PigGTEx, re-analyzing 5,457 published RNA-seq samples, presents a pan-tissue catalog of molecular quantitative trait loci. Cross-species comparisons identify traits with shared genetic regulation in humans