Data for: Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: a case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)
Contributors: Keping Sun, Vu Dinh Thong, Kangkang Zhang, Jiang Feng, Hanbo Zhao, Lin Zhang, Tong Liu, YANYAN XIAO, Longru Jin, Gábor Csorba
... Raw data sets, including mitochondrial sequences, nuclear sequences, microsatellite data and GBS data used in this study.
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
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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.
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: Structural modifications of 2,3-indolobetulinic acid: design and synthesis of highly potent α-glucosidase inhibitors
Contributors: Elmira Khusnutdinova, Thi Tu Anh Le, Tra Nguyen Thanh, Anastasiya V. Petrova, Denis Babkov, Oxana Kazakova, Ha Nguyen Thi Thu, Cham Ba Thi
... A series of nineteen nitrogen-containing lupane triterpenoids was obtained by modification of C2, C3, C20 and C28 positions of betulonic acid and their α-glucosidase inhibiting activity was investigated. Being a leader compound from our previous study, 2,3-indolo-betulinic acid was used as the main template for different modifications at C-(28)-carboxyl group to obtain cyano-, methylcyanoethoxy-, propargyloxy- and carboxamide derivatives. 20-Oxo- and 29-hydroxy-20-oxo-30-nor-analogues of 2,3-indolo-betulinic acid were synthesized by ozonolysis of betulonic acid followed by Fischer indolization reaction. To compare the influence of the fused indole or the seven membered A-ring on the inhibitory activity, lupane A-azepanones with different substituents at C28 were synthesized. The structure-activity relationships revealed that the enzyme inhibition activity dramatically increased (up to 4730 times) when the carboxylic group of 2,3-indolo-betulinic acid was сonverted to the corresponding amide. Thus, the IC50 values for glycine amide and L-phenylalanine amides were 0.04 and 0.05 μM, respectively. This study also revealed that 2,3-indolo-platanic acid is 4.5 times more active than the parent triterpenoid with IC50 of 0.4 μM. Molecular modeling suggested that improved potency is due to additional polar interactions formed between C28 side chain and a sub-pocket of the α-glucosidase allosteric site.
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.
Contributors: Enade Perdana Istyastono
... A model of full human matrix metalloproteinase 9 with ligands from PDB:4H3X and PDB:1ITV from homology modeling studies using YASARA Structure.