Contributors: Gabriel Fiorin, Andrea Sanchez-Vallet, Daniela Thomazella, Paula Prado, Leandro Nascimento, Antonio Figueira, Bart Thomma, Goncalo Pereira, Paulo Jose 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: 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).
Contributors: oliver purcell
... This is a genbank file containing the 16 plasmids used in the publication: "Encryption and Steganography of Synthetic Gene Circuits".
Data for: Performance Metrics for Targeted Next Generation Sequencing Panels Using Reference Materials
Contributors: Megan Cleveland, Justin Zook
... This is NGS data (VCF files) for targeted sequencing panels (Illumina Inherited Disease Panel and Ion Torrent AmpliSeq Inherited Disease Panel) performed on NIST RMs 8398, 8392 and 8393 (NA12878, GM24149, GM24143, GM24385, GM24631).
Contributors: Patricia Ramey-Balci, Fiege Dieter, Torsten Struck
... These files are fasta-files used for the tree reconstructions from the COI data set, the 16S data set, which is not masked, the concatenated masked 16S and COI data set as well as the three different data sets for ITS.
Methanomethylophilus alvus Mx1201 provides basis for mutual orthogonal pyrrolysyl tRNA/aminoacyl-tRNA synthetase pairs in mammalian cells.
Contributors: Simon Elsässer, Birthe Meineke
... Genetic code expansion via stop codon suppression is a versatile tool for engineering proteins in mammalian cells with site-specifically encoded non-canonical amino acids (ncAAs). Current methods rely on very few available tRNA/aminoacyl-tRNA synthetase pairs orthogonal in mammalian cells, the pyrrolysyl tRNA/aminoacyl-tRNA synthetase pair from Methanosarcina mazei (Mma PylRS/PylT) being the most active and versatile to date. We found a previously uncharacterized pyrrolysyl tRNA/aminoacyl-tRNA synthetase pair from the human gut archaeon Methanomethylophilus alvus Mx1201 (Mx1201 PylRS/PylT) to be active and orthogonal in mammalian cells. We show that the new PylRS enzyme can be engineered to expand its ncAA substrate spectrum. We find that due to the large evolutionary distance of the two pairs, Mx1201 PylRS/PylT is partially orthogonal to Mma PylRS/PylT. Through rational mutation of Mx1201 PylT, we abolish its non-cognate interaction with Mma PylRS, creating two mutually orthogonal PylRS/PylT pairs. Combined in the same cell, we show that the two pairs can site-selectively introduce two different ncAAs in response to two distinct stop codons. Our work expands the repertoire of mutually orthogonal tools for genetic code expansion in mammalian cells and provides the basis for advanced in vivo protein engineering applications for cell biology and protein production.
Contributors: Muhammad Arslan
... Transcriptome of Juncus effusus. Plant tissues (roots and shoots) were harvested from individuals at the vegetative developmental stage representing in total 18 genotypes that were raised from seeds collected in the field.
Data for: The impact of spatial isolation and local habitat conditions on colonization of recent forest stands by ectomycorrhizal fungi
Contributors: Margaux Boeraeve, Nele Mullens, Kris Vandekerkhove, Olivier Honnay, Arno Thomaes, Hans Jacquemyn, Luc De Keersmaeker
... In this study, we selected 17 recently established (between 18 and 45 years old) forest stands and nine ancient forest stands (continuous forest land use since at least 1775) across Flanders (Northern Belgium). Nine of the recent forest stands were adjacent to ancient forest, and 8 were isolated from ancient forests (minimum, median and maximum distance from ancient forest: respectively 219, 1901 and 7605 m). The recent forest stands were all homogeneous stands of Quercus robur planted on former agricultural land, while the tree layer of the ancient forest stands was dominated by Q. robur, with admixtures of other tree species (Acer pseudoplatanus, Betula pendula, Castanea sativa, Fagus sylvatica, Tilia sp. and Q. rubra). In each stand, a 10x10m plot was established in such a way that only Q. robur was present in and around the plot. In each plot, 10 soil cores were randomly taken with a narrow-bladed gouge auger (diameter 3 cm). The F, H and A horizon, depth 0-15 cm were collected. The samples were pooled in two composite soil samples (five soil cores pooled in one sample, resulting in two samples per plot). Roots from oak (Quercus robur) were isolated from all samples, brushed to remove remaining soil particles and 0.25 g of root per sample was used to extract DNA using the Power Soil DNA Isolation Kit. After DNA extraction, the ITS1 region of the nuclear ribosomal RNA genes was amplified using modified versions of the primer set ITS1F and ITS2. After PCR, gel electrophoresis and purification from gel, samples were pooled and sent for 250bp paired-end sequencing on an Illumina Miseq. Raw sequence data was submitted to NCBI SRA (Bioproject PRJNA477418). The demultiplexed reads provided by Genomics Core UZ Leuven were quality filtered, clustered into OTUs and assigned a taxonomy through the PIPITS pipeline. Representative sequences that could not be assigned a taxonomy at genus-level were subjected to a BLAST-search against the NCBI nucleotide database. Sequences from environmental or uncultured samples were excluded from the results and the ten best matches with maximum e-value e-100 and minimum sequence similarity of 90% (genus level) and 97% (species level) were used to assign a taxonomy. In an additional quality filtering step, OTUs represented by less than 0.01% of the reads in a sample were considered absent from that sample. Finally, the results were put in an OTU table, which was run through FUNGuild, in order to select the ectomycorrhizal OTUs from the dataset. Rarefaction curves were fitted in order to check whether they were sufficiently deep sequenced. Samples of which the rarefaction curve did not reach an asymptote were removed. If the two samples from the same plot still remained after the removal, their results were merged by averaging their read numbers. Nitrate, ammonium, plant available phosphorus, pH, gravimetric water content and organic carbon content were analyzed for each of the two composite soil samples.
Contributors: Mark Perlin
... NIST prepared 40 two person DNA mixtures at 10, 30, 50, 70 and 90% weights in 1, 0.5, 0.25 and 0.125 ng amounts from 2 pairs of contributors. Cybergenetics amplified the DNA templates using a Promega PowerPlex 16 STR kit, and read out the EPG data on an ABI 310 genetic analyzer. File “design.TIF” gives the .fsa file naming from Table 1 of Perlin & Sinelnikov, PLoS ONE, 2009. Funded by NIJ grant 2001-IJ-CX-K003.