Common genetic variations associated with the persistence of immunity following childhood immunisation
Contributors: Daniel O'Connor
... Genotyping data of common genetic variations associated with the persistence of immunity following childhood immunisation
Contributors: Esteban Finol
... raw DENV genomic data for Finol E. & Ooi EE. Iscience submision
Contributors: Gil Sharon
... Raw data (excluding raw sequencing and metabolomic data) used to construct figures for manuscript. Data is predominantly in csv or tsv format. qza and qzv files are QIIME2 outputs and can be viewed at https://view.qiime2.org/ . mat files are mat lab datasets. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Gil Sharon1,*, Nikki Jamie Cruz1, Dae-Wook Kang2,3,21, Michael J. Gandal4,5,6,7, Bo Wang1, Young-Mo Kim8, Erika M. Zink8, Cameron P. Casey8, Bryn C. Taylor9, Christianne J. Lane10, Lisa M. Bramer11, Nancy G. Isern8, David W. Hoyt8, Cecilia Noecker12, Michael J. Sweredoski1, Annie Moradian1, Elhanan Borenstein12,13,14,15,16, Janet K. Jansson8, Rob Knight17,18,19, Thomas O. Metz8, Carlos Lois1, Daniel H. Geschwind4,5,6, Rosa Krajmalnik-Brown2,3, and Sarkis K. Mazmanian1,20,* Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically-developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD and TD controls into germ-free mice, and reveal that colonization with ASD microbiota was sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and affects neuronal excitability in the brain. We propose that the gut microbiome modulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
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Contributors: UnaElsLive Natra, mdgmatest5 live
... RDM - File Type Support 21May2019 ElsCustomer Apart from .u3d all files preview [ .obj / .ply / .vtk / .stl / .ent / .brk / .pdb / .pse / .mol / .mol2 / .cif / .u3d / .dcm / .nii] - .pse is not supported
Contributors: Yevgen Yurenko, Martin Lepšík, Juraj Dobiaš
... The dataset contains molecular dynamics trajectories of 300ns simulation of three complexes of Helidye1, a novel cationic helicene-like probe for DNA detection, with double-stranded DNA. In addition to trajectories, we add parameter files (mol2 and frc) for HeliDye1 containing atomic charges and parameter for dihedral and improper torsion angles.
Induction of Rare Conformation of Oligosaccharide by Binding to Calcium-dependent Bacterial Lectin: X-ray Crystallography and Modelling Study
Contributors: Martin Lepsik, Anne Imberty
... Parameters, inputs and trajectories for 600 ns molecular dynamics of Pseudomonas aeruginosa lectin LecB in complex with Lewis x tetrasaccharide using the most promising Setup4 (see the publication).
Data for: Multi-gene global phylogeography of the Gypsy Moth, reveals misaligned subspecies concepts and a cryptic lineage
Contributors: Reza Zahiri, B. Christian Schmidt, Michal Rindos, Alexander Schintlmeister, Roman V. Yakovlev
... Various datasets used in this study are uploaded here.
Contributors: luz america chi uluac, M. Cristina Vargas González
... In silico design of peptides to target resistin algorithm Binding free energy (peptide-protein) script We have been able to design a great set of peptides with high scoring binding energy to resistin. Further, two peptides were chosen, to perform a more rigorous calculation of binding free energy based on the Alchemical Absolute Binding Free Energy method. We were able to establish a methodological route for the development of strong candidates for the design of ligands to resistin.
Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli. Fedorec et. al.
Contributors: Chris Barnes, Alex J H Fedorec
... Data from publication "Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli." Fedorec et. al. iScience 2019
Data for: DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in central Brazil
Contributors: Justin Bagley
... Data accession in support of the manuscript by Bagley et al. (in revision) on DNA barcoding headwater stream freshwater fishes of the Brazilian Distrito Federal (DF) and surrounding areas of the Brazilian Shield in central Brazil. This accession contains several folders of files, including data and code that will allow the user to recreate the analyses in the corresponding paper. Directories include Alignments/, PartitionFinder/, SpeciesIdentifier/, MrBayes/, and R/ subfolders. Contents are as follows: - Alignments/ contains a small set of aligned, edited DNA sequences in different alignment formats (NEXUS, PHYLIP). Alignments with "n149" in the name contain the full 'final' dataset analyzed in our study, with n = 149 DNA barcodes corresponding to specimens listed in Data S1 of the Supporting Information for the paper. The PHYLIP alignment with "n103" in the name contains the reduced "No-Characidium" dataset analyzed for the paper, from which Characidium individuals have been removed. - The PartitionFinder/ subfolder contains folders with files for conducting two separate runs of our dataset in PartitionFinder v2.1.1 (Lanfear et al. 2014), as described in the paper. - The SpeciesIdentifier/ subfolder contains input files formatted for SpeciesIdentifier v1.8 (Meier et al. 2006), which were used during SpeciesIdentifier analyses described in the paper. - MrBayes/ directory contains a run folder for one run of MrBayes conducted for the paper. A NEXUS file formatted for MrBayes v3.2+ and a batch submission file for queueing the run on a supercomputing cluster are provided. The file named "Mrbayes_sumtp_log.txt" provides the output of running parameter and tree summaries, to summarize the posterior results of the run, using the 'sumt' and 'sump' functions in MrBayes. - The R/ subfolder contains several DNA sequence input files and an R script named "CerradoFish_cox1_n149_DNA_Barcoding_R_Analysis.R" that runs a variety of DNA barcoding-related analyses in R while drawing on the sequence files. The "seqs2" / "fishSpp2" objects are the main objects used when analyzing the full dataset (n = 149 barcodes). The "seqs3" / "fishSpp3" objects are the main objects used when analyzing the No-Characidium dataset (n = 103 barcodes). Running the R script produces many outputs and figures used or modified for the manuscript. REFERENCES Bagley, J. C., De Podestà Uchôa de Aquino, P., Breitman, M. F., Langeani, F., & Colli, G. R. (in revision) DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in central Brazil. Journal of Fish Biology. Lanfear, R., Calcott, B., Kainer, D., Mayer, C., & Stamatakis, A. (2014) Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14, 82. Meier, R., Shiyang, K., Vaidya, G., & Ng, P. K. L. (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55, 715–728.