Contributors:Anna Fernández, Fouad El Baidouri, Christophe Ravel, Montserrat Gallego, Carmen Munoz
This dataset supplements the Material and Methods section of the paper "The Leishmania donovani species complex: a new insight into taxonomy". It includes the codes and data used to perform the SH test on PAUP* v 4.0a165, as well as the codes, raw data and matrices used to perform the Mantel test on the package ade4 of R software.
The original data of this study include the geographic data, the NetLogo model (the code and user interface), videos of the model running processes recorded by a built-in recorder, and the output index data analyzed on Excel.
Glyphosate (GLYPH) is an herbicide that is commonly used in agriculture and is the active ingredient in Roundup. Studies have shown that ingestion of GLYPH by honeybees increases the susceptibility of the insects to natural infection, a phenomenon attributed to perturbation of the resident gut microbiome. One of the aims of this study was to determine if GLYPH has similar effects on the microbiome of Anopheles gambiae mosquitoes. Mosquitoes were drugged with varying doses of GLYPH, and their gut microbiota were analyzed by 16S rRNA amplicon sequencing. Results indicate that while GLYPH does not alter the bacterial load of the A. gambiae gut microbiome, the makeup of the community is altered in a dose-independent manner.
This dataset consists of raw sequencing data (fasta) and analysed relative abundance data (histograms of the dominant 10 species in respective taxonomic ranks ). This project shows the first bacterial diversity profiling of high-microbial-abundance wild tropical marine sponges of southern South China Sea, which are Aaptos aaptos and Xestospongia muta from Bidong and Redang islands, Malaysia. Marine sponges are acknowledged as a bacterial hotspot and resource of novel natural products or genetic material. However, sponge-associated bacteria are difficult to be cultivated and the production of their desirable metabolites are inadequate in terms of rate and quantity, yet bioinformatics and metagenomics tools are progressing. Therefore, the diversity profiling of bacterial communities in marine sponges reveals the approximate gene pool for the gene mining or isolation of bacteria that are potentially and commercially beneficial in manufacturing industry, medicine, or agriculture. The bacterial community data exploited from this project is useful for critical comparison through additional or integrated bioinformatics processing with other marine sponge-associated bacterial community profile data. The community data of this project also unveils some general physiological function of the sponge-associated bacterial assemblage in its local environment. In the data provided, the sponge-associated bacterial communities in A. aaptos of Pulau Bidong, A. aaptos of Pulau Redang, and X. muta of Pulau Bidong have been denoted by A, B, and M, respectively.
Contributors:MYEONG-HO YEO, Van-Thanh-Van Nguyen, Alfred Kpodonu
Historical at-site annual maximum precipitation series at the two stations (Dorval (Canada) and Seoul (South Korea)) for the 1961-1990 period. In addition, the user can install an integrated extreme rainfall modeling tool (SDExtreme) using the setup.exe file.
Contributors:Elia-Aguado Fraile, Evangelia Chavdoula, Georgios I. Laliotis, Vollter Anastas, Oksana Serebrennikova, Maria D. Paraskevopoulou, Philip N. Tsichlis
KDM2B is a JmjC domain H3K36me2/H3K36me1 demethylase, which immortalizes cells in culture and contributes to the biology of both embryonic and adult stem and progenitor cells. It also functions as an oncogene that contributes to the self-renewal of breast cancer stem cells by regulating polycomb complexes. Here we show that the silencing of KDM2B results in the downregulation of SNAI2 (SLUG), SNAI1 (SNAIL) and SOX9, which also contribute to the biology of mammary stem and progenitor cells. The downregulation of these molecules is posttranscriptional and in the case of the SNAI2-encoded SLUG, it is due to calpain-dependent proteolytic degradation. Mechanistically, the latter depends on the activation of calpastatin-sensitive classical calpain(s) and on the phosphorylation-dependent inhibition of GSK3 via paracrine mechanisms. GSK3 inhibition sensitizes its target SLUG to classical calpains, which are activated by Ca2+ influx and calpastatin down regulation. The degradation of SLUG, induced by the KDM2B knockdown, promotes the differentiation of breast cancer stem cells in culture and reveals an unexpected mechanism of stem cell regulation by a histone demethylase.
Raw 16S rRNA sequence data (Illumina fastq and .biom file created in Qiime), volatile organic compound metabolome data from the colon contents of horses with and without Anoplocephala perfoliata (tapeworm). The meta table containing sample labels and groups is also included.
Contributors:Raquel de M. Barbosa, Marcelo A. C. Fernandes
The dataset provides five types of k-mers genome representation characterized as k-mers count 1D, k-mers probability 1D, k-mers count 2D, k-mers probability 2D, and k-mers image. The dataset is composed of 1557 virus instances of SARS-CoV-2. Besides, the dataset also provides a data stream of 11540 viruses from the Virus-Host DB dataset and the other three Riboviria viruses from NCBI (Betacoronavirus RaTG13, bat-SL-CoVZC45, and bat-SL-CoVZXC21).