GFF3sort: a novel tool to sort GFF3 files for tabix indexing

Abstract Background The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. Results We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results with acceptable efficiency compared with currently available tools. Conclusions GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization

CottonFGD: an integrated functional genomics database for cotton

Abstract Background Cotton (Gossypium spp.) is the most important fiber and oil crop in the world. With the emergence of huge -omics data sets, it is essential to have an integrated functional genomics database that allows worldwide users to quickly and easily fetch and visualize genomic information. Currently available cotton-related databases have some weakness in integrating multiple kinds of -omics data from multiple Gossypium species. Therefore, it is necessary to establish an integrated functional genomics database for cotton. Description We developed CottonFGD (Cotton Functional Genomic Database, https://cottonfgd.org ), an integrated database that includes genomic sequences, gene structural and functional annotations, genetic marker data, transcriptome data, and population genome resequencing data for all four of the sequenced Gossypium species. It consists of three interconnected modules: search, profile, and analysis. These modules make CottonFGD enable both single gene review and batch analysis with multiple kinds of -omics data and multiple species. CottonFGD also includes additional pages for data statistics, bulk data download, and a detailed user manual. Conclusion Equipped with specialized functional modules and modernized visualization tools, and populated with multiple kinds of -omics data, CottonFGD provides a quick and easy-to-use data analysis platform for cotton researchers worldwide

Different Sources of Copper Effect on Intestinal Epithelial Cell: Toxicity, Oxidative Stress, and Metabolism

Copper (Cu) is widely used in the swine industry to improve the growth performance of pigs. However, high doses of copper will induce cell damage and toxicity. The aim of this study was to evaluate toxicity, bioavailability, and effects on metabolic processes of varying copper sources using porcine intestinal epithelial cells (IPEC-J2) as a model. The IPEC-J2 were treated with two doses (30 and 120 μM) of CuSO4, Cu Glycine (Cu-Gly), and Cu proteinate (Cu-Pro) for 10 h, respectively. Cell damage and cellular copper metabolism were measured by the changes in cell viability, copper uptake, oxidative stress biomarkers, and gene/protein expression levels. The results showed that cell viability and ratio of reduced and oxidized glutathione (GSH/GSSG) decreased significantly in all treatment groups; intracellular copper content increased significantly in all treatment groups; total superoxide dismutase (SOD) activity increased significantly in the 120 μM exposed groups; SOD1 protein expression levels were significantly upregulated in 30 μM Cu-Pro, 120 μM Cu-Gly, and 120 μM Cu-Pro treatment groups; intracellular reactive oxygen species (ROS) generation and malondialdehyde (MDA) content increased significantly in 30 μM treatment groups and 120 μM CuSO4 treatment group. CTR1 and ATP7A gene expression were significantly downregulated in the 120 μM exposed groups. While upregulation of ATOX1 expression was observed in the presence of 120 μM Cu-Gly and Cu-Pro. ASCT2 gene expression was significantly upregulated after 120 μM Cu-Glycine and CuSO4 exposure, and PepT1 gene expression was significantly upregulated after Cu-Pro exposure. In addition, CTR1 protein expression level decreased after 120 μM CuSO4 and Cu-Gly exposure. PepT1 protein expression level was only upregulated after 120 μM Cu-Pro exposure. These findings indicated that extra copper supplementation can induce intestinal epithelial cell injury, and different forms of copper may have differing effects on cell metabolism

Preparation and Magnetic Properties of Nd/FM (FM=Fe, Co, Ni)/PA66 Three-Layer Coaxial Nanocables

Abstract A new preparation method of three-layer coaxial nanocables has been developed in this work. Nd/FM (FM=Fe, Co, Ni)/PA66 three-layer coaxial nanocables were assembled successfully from outer to inner layer by layer. PA66 nanotubes which served as the outer shell were prepared by polymer solution wetting AAO template. Ferromagnetic metals and Nd were deposited into pre-prepared PA66 nanotubes to be served as the middle layer and inner core, respectively. The results show that the structure has effects on the magnetic properties, and the nanocable preparation allows each layer, length, and thickness of the nanocables to be tuned

Additional file 1: of GFF3sort: a novel tool to sort GFF3 files for tabix indexing

Benchmark data. This file displays: 1) the detailed running time of GFF3-to-JSON conversion and the bgzip-tabix process on our test datasets; 2) the detailed running time and 3) memory usage of GFF3sort, GNU sort (v8.4 and v8.28), and GenomeTools on our test datasets. (PDF 720 kb

Additional file 1: of CottonFGD: an integrated functional genomics database for cotton

List of all used cotton genome assemblies. Including seven cotton assemblies from four Gossypium species. (DOCX 23 kb

Additional file 2: of GFF3sort: a novel tool to sort GFF3 files for tabix indexing

The full GFF3 annotation lines used in Fig. 1a and c. It is the gene AT1G01110 extracted from the Arabidopsis thaliana (Araport11) annotation files. It includes three plain-text files: raw.gff3, GNUsort.gff3 (Fig. 1a), and GFF3sort.gff3 (Fig. 1c). (ZIP 2 kb

Additional file 5: of CottonFGD: an integrated functional genomics database for cotton

Snapshots of the profile module. Several snapshots for the gene and transcript profile page are provided. (PDF 1306 kb