Data for: Sarcocystis species identification in cattle hearts destined to human consumption in southern Brazil
Contributors: Maiara Sanitá Tafner Ferreira, Luiza Pires Portella, Pati Bräunig, 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 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.
Contributors: Adrien Cerdan, Nicolas Martin, Marco Cecchini
... The dataset presented here is supporting the article "An ion permeable state of the Glycine Receptor captured by Molecular Dynamics" (Cerdan et. al., Structure). Are available the two DCD trajectories, related to Figure 2 and Figure S2: - Trajectories/MD-open_protein_membrane_skip20.dcd - Trajectories/MD-open-replica_protein_membrane_skip20.dcd and the the corresponding topology file: - Trajectories/protein_membrane.psf leading to the MD-open structure: - MD-open.pdb that we characterized as a model for the active state of the Glycine Receptor alpha 1 (See Main Text for details). Only the protein and the membrane are available in these DCD files and a step size of 20 is applied in respect to the original trajectories. Additionally, we provide a short (10ns) all-atom DCD trajectory of the free permeation of a chloride anion ("name CLA and resid 129"), related to Movie S1 and Movie S2: - Trajectories/permeation.dcd and its corresponding topology file: - Trajectories/permeation.psf Visualization can be achieved with various software, for example VMD. See all details in our article.
Data for: Molecular phylogeny of marine mites (Acariformes: Halacaridae), the oldest radiation of extant secondarily marine animals
Contributors: Almir Pepato, Pavel Klimov, Teofânia Vidigal
... Files containing the secondary structure alignments of rRNA genes, with two secondary structure notations masks. S1 -18S; S2- 28S.
Contributors: Margo Maex, Dag Treer, Henri De Greve, Paul Proost, Ines Van Boxclaer, Franky Bossuyt
... We investigated the evolutionary trajectory of a series of 15 kDa proteins – termed persuasins – that were co-opted more recently alongside the ancient sodefrin precursor-like factor (SPF) courtship pheromone system in salamanders. Expression, genomic and molecular phylogenetic analyses show that persuasins originated from a gene that is expressed as a multi-domain protein in internal organs where it has no pheromone function, but underwent gene duplication and neofunctionalisation. The subsequent evolution combined domain-loss and the introduction of a proteolytic cleavage site in the duplicated gene to give rise to two-domain cysteine rich proteins with structural properties similar to SPF pheromones In the absence of an NCBI database for sequences assembled by third party analyses (assembly of publicly available reads, RNA sequencing), we deposited nucleotide and amino acid sequences of persuasin and DUF-persuasin transcripts assembled from publicly available short reads (NCBI: SRA) on the Mendeley Data repository. Sources of publicly available SRA datasets are cited in the main article and supplemental information (Maex et al. (2018) Exaptation as a mechanism for functional reinforcement of an animal pheromone system).