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Hardware design for build a Step Width System Capture
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Different human linker histone (H1) variants are expected to have distinct binding modes to the nucleosome. The position and orientation of a number of different H1 globular domains on the nucleosome were investigated through molecular docking using MGLTools and HADDOCK. The nucleosome core and linker DNA in the GH5-chromatosome structure (PDB: 4QLC) were used as a docking template. GH5 (in PDB: 4QLC) was re-docked to this template to test the docking algorithm. Docked and re-docked GH5 compared well. The docking algorithm was further tested by docking the NMR solution structure of the globular domain of chicken H1 (GH1, PDB: 1GHC) to the nucleosome template. The position of docked GH1 on the nucleosome agreed with literature. 
The N-terminal - and globular domain H1x hybrid (NGH1x) was studied using solution NMR in both low (20 mM sodium phosphate, pH 7.0) and high (20 mM sodium phosphate, 1 M sodium perchlorate, pH 7.0) ionic strength conditions (de Wit, H., Vallet, A., Brutscher, B. et al. Biomol NMR Assign (2019) 13: 249. https://doi.org/10.1007/s12104-019-09886-x). These low and high ionic strength structures were docked to the nucleosome template. 
Homology (MODELLER) and ab initio modeling (CS-ROSETTA) were employed to model structures for other human H1 globular domains: GH1.0, GH1.4, GH1oo, and GH1t. The modeled structures were also docked to the nucleosome template.
 All the docking procedures listed above produced 100 models of different energies. In each case, the lowest energy docked model was chosen. The structures of all the H1 globular domains that were docked to the template are given as PDB files (1GHC_lowest_energy.pdb; 2LSO_lowest_energy.pdb; GH5_re-docked_position.pdb; NGH1x_high_salt_NTD.pdb; NGH1x_low_salt_NTD.pdb; modeled_GH1_0_lowest_energy.pdb; modeled_GH1_4_lowest_energy.pdb; modeled_GH1oo_lowest_energy.pdb; modelled_GH1t_lowest_energy.pdb) in the data file. The nucleosome template structure is also given in PDB file format (4QLC_nucleosome_without_GH5.pdb). Finally, the docked models are also given (GH5-chromatosome.pdb; 1GHC-chromatosome.pdb; 2LSO-chromatosome.pdb; GH1_0-chromatosome.pdb; GH1_4-chromatosome.pdb; GH1oo-chromatosome.pdb; GH1t-chromatosome.pdb; NGH1x_no_salt-chromatosome.pdb; NGH1x_salt-chromatosome.pdb). The files are compatible with most molecular graphics software. The file Dockings_modelling_test_and_results.pdf provides the modeling and docking results in figures and tables. A short description of each figure and table is given within the PDF file.
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Variant call file of DENV2 16681 passage 1 in M3 iPSC cells (open with Microsoft Excel)
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The Indeterminate Domain (IDD) proteins are a plant specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development; however the function of most of IDDs is unknown and its molecular evolution has not been explored. Here, Prochetto and Reinheimer reconstructed the evolution of IDDs during plant land conquest. They found that IDDs arose from the common ancestor of Streptophyta. Once in land, IDDs experienced a rapid radiation that accompanied key morphological, physiological and biochemical transitions required in plant terrestrialization. The authors present a solid phylogenetic framework of annotated IDD genes which links genetic and functional knowledge from model to non-model species.
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Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution. doi: 10.1002/ece3.6170 Data summarises results from the case studies and simulations presented in our paper. In addition, we provide an R script for calculation of proposed phylogenetic diversity metrics (the clade indices). Brief description of each file: 1. Grasslands_DNA_markers_info.xls - Accession numbers of all DNA markers used for phylogeny inference in grasslands 2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - DNA alignment matrix before utilisation of the GBlocks tool 3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - DNA alignment matrix after utilisation of the GBlocks tool 4. Grasslands_BEAST_file.xml - BEAST .xml file submitted to the CIPRES portal (www.phylo.org) 5. Grasslands_tree.txt - Dated MCC tree, grasslands (newick format) 6. Grasslands_tree.nex - Dated MCC tree, grasslands (nexus format) 7. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format) 8. Plot_data.slx - plot data of all case studies + species lists 9. Simulation_results.txt - Summary of R2 values (phylogeny-based metric ~ the clade index) for simulated phylogenies and community matrices (manipulated: phylogenetic scale, species pool size and species richness range) 10. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)
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Alignments for phylogenetic analyses
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Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded to be potential hot-spots of biodiversity. We assessed spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900-1,750 m) at two seasons. A fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) was used as marker for such assessments. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs, in the most diverse taxa and in MOTU richness. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, broad spatio-temporal patterns elucidated from both datasets coincided, both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high resolution method to detect ecological shifts. We also noted that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
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Supplementary files: Nutrigenomic markers identified by de novo RNAseq during the initial ontogeny of the three spot cichlid Amphilophus trimaculatus.
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Abstract:The globe was frightened with a newly isolated virus named as sars cov 2 formally called as novel corona virus 2019.This work is predicting a protein based drug for sars cov 2.A virus was outbreaks at wuhan city of china on December 2019.The RNA sequence of that virsus was published in NCBI.(NCBI Ref Sequence:NC_045512.2)We collected the serface glycoprotein sequences from NCBI and genbank and predicted the protein structure with swiss model and phyre 2 protein structure prediction tools.The predicted spike glycoprotein was have a docking function with the human ACE2 receptor.We predicted the 3D structure of ACE2- FC region of IgG1 fusion protein and docked with virus spike glycoprotein and found a good docking potential of fusion protein with Sars Cov 2.ACE2- FC region of IgG1 will be use as a protein drug against SarsCoV 2. 2020 Ijcrt / volume 8,issue 2, February 2020 / ISSN:2320-2882
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Multiple alignments of the nuclear ITS rDNA, SSU rDNA and LSU rDNA, plastid rbcL, psaA and LSU rDNA, and mitochondrial coxI loci sequences built either manually in MEGA6 or using MAFFT v6, applying the Q-INS-i strategy. In more variable loci alignments, those positions included in subsequent evolutionary analyses are indicated by mask.
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