Contributors: Bram Lories
... A differential fluorescence induction screening was performed in order to identify genes of Salmonella Typhimurium SL1344 that respond to conditions of high bacterial competition. This dataset contains the sequences of all positives hits after two rounds of positive and one round of negative selection. Description of the methods and experimental details of the DFI screening can be found at: Lories et al. (2020). Biofilm bacteria use stress responses to detect and respond to competitors. Current Biology.
Contributors: Martin Bitomský, Pavla Mládková, Robin Pakeman, Martin Duchoslav
... Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (accepted pending minor revision 12.11.2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution 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. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format) 7. Plot_data.slx - plot data of all case studies + species lists 8. 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) 9. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)
Contributors: Michiel de Kock
... The dataset contains demagnetization data and least squares analyses data for samples of the Klipriviersberg Group (as .sam and .lsq format).
Contributors: Johannes Bischof
... NGS data for primary WT as wells as primary and immortalized RDEB keratinocytes treated with frameshift CRISPR gRNAs. gRNA with precise and predictable repair outcome (+1 nucleotide insertion).
Characterisation of the complete plastid genome of Astelia australiana (J.H.Willis) L.B.Moore (Asteliaceae, Asparagales).
Contributors: Michael Amor
... This project produced the complete chloroplast genome for Astelia australiana. It contains the circular annotated cpDNA sequence and the CDS-based alignment used to generate the phylogeny.
Stronger effect of management legacies than recent management treatments on soil fungal communities in a Mediterranean scrubland
Contributors: Carles Castaño
... Dataset contains four files and one folder. ·Folder sequencing: contains all the raw sequencing data, already demultiplexed. ·file community4: contains all the fungal community in each soil sample. Numbers represent read numbers ·env: contains the environmental data ·guilds2: contains the fungal community according to their guilds. Numbers represent percentages ·identifications_guilds_and__calculations: contains all the fungal identifications and the functional assignments to each OTU.
Utilizing Indicator Kriging to Identify Suitable Zones for Manual Drilling in Weathered Crystalline Basement Aquifers
Contributors: Philip Deal
... Manual drilling offers a practical and affordable method of increasing access to groundwater supply in regions struggling with economic water scarcity. However, manual techniques are limited to specific hydrogeological contexts and must be sited appropriately. Indicator kriging is proposed as an interpolation method that builds upon previous efforts to identify suitable zones for manual drilling, particularly in weathered crystalline basement aquifers. This approach allows for heterogeneity within weathering profiles and provides probability mapping of success for regional planning. Modeling was conducted in the Upper East Region of Ghana using available borehole-log data, including: transmissivity, static water depth, laterite thickness, depth to hard rock, water quality parameters, and the degree of weathering. Indicator kriging interpolations predicted binary variables with over 90% accuracy. The model predicts that drilling into highly weathered layers will be common, and percussion techniques will be necessary to reach sufficient depths. The results suggest that suitable zones occur near Bolgatanga, Bawku, and Zebila, which coincide with historical drilling efforts in the central and eastern portions of the region. The original dataset was derived from the Hydrogeological Assessment of the Northern Regions of Ghana Project (HAP) implemented by SNC-Lavalin, Institut national de Recherche Scientifique (INRS) and the Water Resources Comission (WRC) of Ghana, and was supported by the Canadian International Development Agency. Hydrogeological data was collected and aggregated for the Voltaian Sedimentary Basin and Precambrian Basement complexes in Ghana from numerous sources. The data was compiled into a GIS databased for further study and analysis of the groundwater resources in Ghana. For this study, the dataset was obtained from the University of Ghana upon request with a focus on manual drilling feasibility. Borehole records were manipulated with various interpolation methods within the Upper East Region in ArcGIS, as described within the journal article.
OTUs and assignments for bacteria associated to the shell of Cancer pagurus according to ENA PRJEB27139.
Contributors: Philipp Kraemer
... Bacterial OTUs found associated to the shell of Cancer pagurus. OTUs were calculated based on samples from the accession PRJEB27139 in ENA. Provided is the OTUs.fasta for sequence information and the associated assignments in Assignments.txt.
Effects of enzyme additives and Lactobacillus plantarum on the bacterial community as determined of Medicago sativa silageby Illumina sequencing
Contributors: Zong Fu HU
... more and more research are used new technique to investigate bacterial community of silage, such as next generation sequencing. This study aimed to evaluate the effects of enzymes (cellulase combined with alpha-galactosidase), Lactobacillus plantarum (LP), and combinations of these enzymes with LP on the bacterial diversity and fermentation quality of alfalfa silage. Three repetitions for each treated were evaluated by ensiling for 56 days: (1) control with no additives; (2) treated with enzyme (a mix of cellulase and alpha-galactosidase) (EN), 2.5g/kg forgae of each enzyme; (3) 1 ×1 ×107 CFU/g LP; (4) 2.5g/kg forgae of EN combined with 1 ×107 CFU/g LP (CENLP). Illumina sequencing was used to reveal the bacterial community of these silage. As revealed by data, treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. At the class level, Bacilli and Clostridia were predominant in the untreated silage, with abundances of 51.21% and 37.08%, respectively, while only Bacilli dominated the bacterial communities of all the treated silages, with an abundance of 94.98% in the EN silage, 98.61% in the LP silage, 98.57% in the ENLP silage. Gammaproteobacteria were present in all the silages. At the genus level, Garciella, Enterococcus, Lactobacillus and Pediococcus were predominant in the control silage, while Lactobacillus and Pediococcus were predominant in the EN silage, and Lactobacillus was predominant in the LP, ENLP silages. As showed below, 1_1 to 1_3 represent three samples of each treated silage. 1_1 to 1_3 represent control silage, 2_1 to 2_3 represent EN silage, 3_1 to 3_3 represent LP silage, 4_1 to 4_3 represent ENLP silage.
Contributors: Qinglin Kang
... MCDS is an autosomal dominant disorder caused by COL10A1 mutations, which is characterized by short stature, waddling gait, coxa vara and bowing of the long bones. However, descriptions of the expressivity of MCDS are rare. Two probands and available family members affected with MCDS were subjected to clinical and radiological examination. Genomic DNA was subjected to whole-exome sequencing and Sanger sequencing in all available family members. A spatial model of the type X collagen (α1) C-terminal noncollagenous (NC1) domain was further constructed. Based on these, we found that the phenotype of affected family members exhibited incomplete dominance. Mutation analysis indicated that there were two novel heterozygous missense mutations, [c.1765T>A (p.Phe589Ile)] and [c.1846A>G (p.Lys616Glu)] in the COL10A1 gene in family 1 and 2, respectively. The two novel substitution sites were highly conserved and the mutations were predicted to be deleterious by in silico analysis. Furthermore, protein modeling revealed that the two substitutions were located in the NC1 domain of collagen X (α1), which potentially impacted the trimerization of collagen X (α1) and combination with molecules in the pericellular matrix. We draw the conclusion that two novel mutations were identified in the present work, which will further expand the spectrum of the COL10A1 mutations associated with MCDS patients. In addition, our research revealed the phenomenon of incomplete dominance in MCDS.