Contributors: Juan_Gabriel Rueda-Bayona
... the folder contains input and setup files of the article An Alternative Method to Determine Extreme Hydrodynamic Forces with Data Limitations for Offshore Engineering
Contributors: Esteban Finol Berrueta
... raw DENV genomic data for Finol E. & Ooi EE. Iscience submision
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
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Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies. Mair et al.
Contributors: Barbara Mair, Jelena Tomic, Sanna Masud, Jason Moffat
... Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging genes that are indispensable for hPSC maintenance and proliferation. To map genetic determinants of hPSC fitness, we performed genome-scale loss-of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and feeder-free to identify essential genes. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSCs essential genes are substantially different from other cell lines, and gene essentiality in hPSCs is highly context-dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated regulators of hPSC biology to understand the genetic wiring of hPSC fitness and pluripotency.
Contributors: M. Florencia Martini
... Files of DMPC-melittin and DMPC-pentalysin interaction, and different types of data analysis
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.
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: Hongmei Li, Qilin Meng, Ting Chen, Chunhua Ren, Chaoqun Hu, Da Huo, Wen Huang, xiao jiang
... Litopenaeus vannamei Transcriptome under acid and alkline stresses. To understand the molecular mechanism of crustacean responses to low pH, we used RNA sequencing (RNA-seq) and investigated expression changes in whole gill transcriptomes of L. vannamei. We compared gill transcriptome of adult L. vannamei challenged by low pH (pH= 6.8) and a nonchallenged control group (pH= 8.0) at 1 h and 48 h, by using the Illumina HiSeq 4000 platform. This is the first study addressing the molecular response of the gills of L. vannamei to low pH stress at the whole-transcriptome level. The raw reads data can be obtained from the Short Read Archive of the National Center for Biotechnology Information under accession number SRP116151 or bioproject number PRJNA400112. The raw FASTQ file is too large for Mendeley storage limit, please refer to NCBI SRA.
Contributors: jayanthy j, Sushil Chandani, Ramakrishna Tangirala
... Datasets pertaining to our study on alanine racemases.
Contributors: Frederik Leliaert
... Alignments, trees and Biogeobears analyses related to the study "Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria". Biogeographical processes underlying Indo-Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals. Species diversity estimates were inferred using DNA-based species delimitation methods. Historical biogeographical patterns were inferred based on a six-gene time-calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographic range evolution. The importance of geographic isolation for speciation was further evaluated by population genetic analyses at the intraspecific level. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo-Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long-term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA. Our results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.