A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area
Contributors: Timothy Jenkins, Fabio Formenti, Cecilia Castro, Chiara Piubelli, Francesca Peradin, Dora Buonfrate, Domenico Otranto, Jules Griffin, Lutz Krause, Zeno Bisoffi
... In this study, we explore the impact of sole, natural infections by the human parasite Strongyloides stercoralis on the faecal gut microbiota and metabolic profiles of a cohort of human volunteers from northern Italy (S+), pre- and post-anthelmintic treatment, and compare the findings with data obtained from a cohort of uninfected controls from the same geographical area (S-). The collected data was obtained through high-throughput sequencing of bacterial 16S rRNA using an Illumina Miseq and nuclear magnetic resonance (NMR) and gas chromatography - mass spectrometry analyses of raw faecal samples. The data set includes four types of files: Raw joined read files - 1 per sample (demultiplexed): e.g. S+pre-treatment1.fasta OTU table created using Qiime including all of the taxonomic information: OTU_table.biom A table containing the metabolite quantification from the NMR and GC-MS analyses. These tables have been normalised to total area: Metabolomic_data_NMR_GC-MS_nomalised_to_total_area.xlsx Metadata file containing the relevant contextual information for each sample: Supplementary table S1.xlsx
Contributors: Ervin Fodor
... See Serna Martin et al Mol Cell 70, 1101-1110, 2018 for the description of data.
Contributors: Dr. Chitra Mandal, Devawati Dutta, Chhabinath Mandal
... We have conducted molecular dynamics simulations to obtain information about the structural aspects of sialylated glycans incorporated into the OprD protein. Four N-glycosylation sites on Asn196 (NLS), Asn218 (NYT), Asn251 (NTT) and Asn288 (NGS). Out of the four sites, Asn288 site is present in the extracellular loop region having high solvent accessibility, for its proper glycosylation. Molecular dynamic studies revealed that the core glycan moiety can properly fit into Asn288 with no spatial overlap for its proper glycosylation. Simulation of sialylated-glycan in free and conjugated states depicted that the population distribution of different conformers were in good agreement with the experimental structures. The permeability of the docked antibiotic into the OprD channel revealed its binding in loop2 region and interaction with a ladder of basic amino acids helps in traversing the channel. Furthermore, we demonstrated that sialylated-glycan core structure at Asn288 blocks the channel and hinders the antibiotic binding to loop2.
Data for: Sarcocystis species identification in cattle hearts destined to human consumption in southern Brazil
Contributors: Maiara Sanitá Tafner Ferreira, Luiza Pires Portella, Patricia Braunig, Giovana Camillo, Sonia Botton, Alfredo Cezar, Luis Antonio Sangioni, fernanda vogel
... Electropherogram. Electropherogram corresponding to research article "Sarcocystis species identification in cattle hearts destined to human consumption in southern Brazil" Nucleotides sequence. Nucleotides sequence corresponding to research article "Sarcocystis species identification in cattle hearts destined to human consumption in southern Brazil"
Contributors: Adam Hill
... Presented is the source code for the CrystalGrower Visualiser: a visualisation package for use with the CrystalGrower simulation tool. The visualiser software is open source for users to modify. Source code is formatted for use with Visual Studio 2015 or later. This program allows users to visualise and study simulations performed with the CrystalGrower program. Images and movies can be captured using this tool and presented for use in publications or presentations. Visualisation methods include: natural tiling, spheres and atoms + bonds, dependent on the structures selected. The CrystalGrower Visualiser can display zeolite, MOF, molecular, ionic and atomic crystals. File manuals are included for both the CG and CGV, with examples provided for all file types
Contributors: Eric Edsinger
... Supporting data for the Current Biology publication - A conserved role for serotonergic neurotransmission in mediating social behavior in octopus - by Edsinger and Dölen.
Contributors: Martin Schnittler
... Alignment data for three marker genes in the clubmoss genus Diphasiastrum.
Alterations in structural and functional responses of bacterial community in response to different levels of compost application in long term fertilized paddy ecosystems
Contributors: Sandipan Samaddar, Gwang Hyun Han, Puneet Singh Chauhan, Poulami Chatterjee, Sunyoung Jeon, Tongmin Sa
... In this study, we used pyro-sequencing tags between V1-V3 regions of the 16S rRNA gene to analyse and compare the effect of long term application of different compost levels on the composition of paddy soil bacterial communities. The treatments were (i) inorganic nitrogen (N), phosphorus (P) and potassium (K) fertilizers (NPK) (ii) NPK and organic compost (C) (NPKC750) (iii) NPKC1500 (iv) NPKC2250 (v) NPKC3000. Inorganic chemical fertilizer was applied as N–P2O5–K2O at a rate of 75-75-75 kg ha-1 from 1954-1970, 100-75-75 kg ha-1 from 1971-1978, 150-86-86 kg ha-1 from 1978-1985 and 110-70-80 kg ha-1 from 1986 onwards. Organic compost was prepared by fermenting rice straws for 5 months and then applied at 7.5, 15.0, 22.5 and 30.0 Mg ha-1 in the NPKC750, NPKC1500, NPKC2250 and NPKC3000 soils, respectively.
Contributors: Gabriel Fiorin, Andrea Sanchez-Vallet, Daniela Thomazella, Paula Prado, Leandro Nascimento, Antonio Figueira, Bart Thomma, Goncalo Pereira, Paulo Jose Teixeira
... Source data of the paper "Suppression of plant immunity by fungal chitinase-like effectors".
Dataset for: Structural analysis of a novel N-carbamoyl-D-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling, docking and molecular dynamics.
Contributors: Reinaldo Bellini, Monika Coronado, Alexandre Paschoal, Marisa Nicolás, Ana Vasconselos
... 3D structures of D-NCAase after 50 ns of molecular dynamics simulations and ligands for virtual screening experiment.