The TriForC database : a comprehensive up-to-date resource of plant triterpene biosynthesis

Triterpenes constitute a large and important class of plant natural products with diverse structures and functions. Their biological roles range from membrane structural components over plant hormones to specialized plant defence compounds. Furthermore, triterpenes have great potential for a variety of commercial applications such as vaccine adjuvants, anti-cancer drugs, food supplements and agronomic agents. Their biosynthesis is carried out through complicated, branched pathways bymultiple enzyme types that include oxidosqualene cyclases, cytochrome P450s, and UDP-glycosyltransferases. Given that the number of characterized triterpene biosynthesis enzymes has been growing fast recently, the need for a database specifically focusing on triterpene enzymology became eminent. Here, we present the TriForC database (http://bioinformatics. psb. ugent. be/triforc/), encompassing a comprehensive catalogue of triterpene biosynthesis enzymes. This highly interlinked database serves as a user-friendly access point to versatile data sets of enzyme and compound features, enabling the scanning of a complete catalogue of experimentally validated triterpene enzymes, their substrates and products, as well as the pathways they constitute in various plant species. The database can be accessed by direct browsing or through convenient search tools including keyword, BLAST, plant species and substructure options. This database will facilitate gene mining and creating genetic toolboxes for triterpene synthetic biology

ConTra v3 : a tool to identify transcription factor binding sites across species, update 2017

Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes. In this updated version, with a completely re-implemented user interface using latest web technologies, users can choose from nine reference organisms ranging from human to yeast. ConTra v3 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Thousands of position weight matrices are available to choose from for detecting specific binding sites. Besides this visualization option, additional new exploration functionality is added to the tool that will automatically detect TFBSs having at the same time the highest regulatory potential, the highest conservation scores of the genomic regions covered by the predicted TFBSs and strongest co-localizations with genomic regions exhibiting regulatory activity. The ConTra v3 web server is freely available at http://bioit2.irc.ugent.be/contra/v3

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform

The Plant PTM Viewer, a central resource for exploring plant protein modifications

Posttranslational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370,000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies

AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data.

Compensating in flow cytometry is an unavoidable challenge in the data analysis of fluorescence-based flow cytometry. Even the advent of spectral cytometry cannot circumvent the spillover problem, with spectral unmixing an intrinsic part of such systems. The calculation of spillover coefficients from single-color controls has remained essentially unchanged since its inception, and is increasingly limited in its ability to deal with high-parameter flow cytometry. Here, we present AutoSpill, an alternative method for calculating spillover coefficients. The approach combines automated gating of cells, calculation of an initial spillover matrix based on robust linear regression, and iterative refinement to reduce error. Moreover, autofluorescence can be compensated out, by processing it as an endogenous dye in an unstained control. AutoSpill uses single-color controls and is compatible with common flow cytometry software. AutoSpill allows simpler and more robust workflows, while reducing the magnitude of compensation errors in high-parameter flow cytometry

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR's framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course

Community-driven ELIXIR activities in single-cell omics

Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge medical research. The rapid development of single-cell technologies has been accompanied by the active development of data analysis methods, resulting in a plethora of new analysis tools and strategies every year. Such a rapid development of SCO methods and tools poses several challenges in standardization, benchmarking, computational resources and training. These challenges are in line with the activities of ELIXIR, the European coordinated infrastructure for life science data. Here, we describe the current landscape of and the main challenges in SCO data, and propose the creation of the ELIXIR SCO Community, to coordinate the efforts in order to best serve SCO researchers in Europe and beyond. The Community will build on top of national experiences and pave the way towards integrated long-term solutions for SCO research. Keywor

Structure-based design of hyaluronidase inhibitors

Hyaluronan and hyaluronidases have been used in several medical fields for many years and some hyaluronidases play a role in, e.g., meningitis, septicaemia, arthroses and cancer. To further investigate the function of hyaluronan and hyaluronidases in (patho)physiological processes, selective and potent hyaluronidase inhibitors are required. Originated by the lack of such compounds, the main goal of this thesis was the prediction of lead-like structures by de novo ligand design. For de novo ligand design with the programme LUDI, a homology model of S. agalactiae strain 4755 hyaluronidase (hylB4755) was constructed starting from two bacterial hyaluronidases. Screening of the LeadQuest®, Accelrys and the adapted ChemACX (ChemACXF) databases resulted in 1275 hits. 13 out of 19 selected compounds were active on hylB4755 in the milli- and submillimolar range. 1,3-Diacetylbenzimidazole-2-thione was identified to be one of the most potent inhibitors of bacterial hyaluronidases (IC50 values of 5 µM and 160 µM at physiological pH and optimum pH, respectively). To validate the usage of the aforementioned databases in virtual screening, the distribution of six (physico)chemical properties (molecular weight, log P, numbers of H-bond donors and acceptors, numbers of rotatable bonds and of rings) within these databases were analysed with respect to drug-likeness. The analysis revealed that the LeadQuest® databases Vol. 1&2 and Vol. 1-3 are suitable compound selections for virtual screening with drug-like molecules. Furthermore, the raw pre-filtering of the ChemACX database by elimination of reactive compounds and of entities outside a certain molecular weight range resulted in a database with significantly different property distributions, though covering the essential pharmacological space. For de novo design of inhibitors of bovine testicular hyaluronidase (BTH) a homology model of the enzyme based on crystal structures of bee venom hyaluronidase was constructed using MODELLER. Filtering of the Lead-Quest® and the ChemACXF databases resulted in ca. 5500 hits. 5 compounds were selected for testing hyaluronidase inhibition; none of the compounds inhibited BTH. Additionally, a ligand-based approach was performed. The superposition of the active sites of the BTH model, the crystal structures of bee venom hyaluronidase and the bacterial chitinases A and B in complex with inhibitors revealed a very good overlap of the amino acids involved in catalysis and of the co-crystallised ligands. By considering essential substructures mimicking the proposed intermediate of hyaluronic acid hydrolysis and by introducing suitable substituents suggested to interact with amino acids of the active site of the bovine enzyme, two compounds were proposed as potential inhibitors of BTH. Due to the weak inhibition of S. pneumoniae hyaluronidase by vitamin C, the more hydrophobic derivative L-ascorbic acid-6-hexadecanoate was investigated and proved to be a potent inhibitor of hylB4755, S. pneumoniae hyaluronidase and BTH (IC50 values of 4 µM, 100 µM and 56 µM, respectively). The binding mode of L-ascorbic acid-6-hexadecanoate at S. pneumoniae hyaluronidase was determined by X-ray analysis, supporting the hypothesis that additional hydrophobic interactions in the active site contribute to the higher affinity. The potential binding mode of L-ascorbic acid-6-hexadecanoate at BTH was predicted by flexible docking with FlexX suggesting two alternative binding modes. That binding mode seems to be clearly favoured where the long alkyl chain of L-ascorbic acid-6-hexadecanoate favourably interacts with an extended, strongly hydrophobic channel. The analysis of two hyaluronate lyase-inhibitor complexes revealed that the the indole moiety of the inhibitor sulfamic acid 1-decyl-2-(4-sulfamoyloxy-phenyl)-1H-indol-6-yl ester and the vitamin C portion of L-ascorbic acid-6-hexadecanoate bind in exactly the same region of the catalytic site. Additionally, the long aliphatic substituents of both compounds dunk in the same surface crevice. Using the programmes LUDI and GRID, regions where H-bond donor, H-bond acceptor and hydrophobic moieties of inhibitors may interact most favourably were identified and transferred into a 3D pharmacophore model. The analysis of known SAR of 2-phenylindole derivatives with respect to the observed binding mode of sulfamic acid 1-decyl-2-(4-sulfamoyloxy-phenyl)-1H-indol-6-yl ester and to the 3D pharmacophore model led to suggestions about the binding mode of benzoxazole-2-thione derivatives. Based on the superposition of the crystal structure of this bacterial lyase in complex with the co-crystallised indole derivative and a substrate-based hexasaccharide, novel benzoxazole-2-thiones with 3-substituted N-propanoyl groups were predicted as putative hyaluronate lyase inhibitors. This design strategy was confirmed by the activity of the 3-phenylpropanoyl derivative which potently inhibits hylB4755 with an IC50 value of 15 µM

PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Motivation: Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. Results: Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. Availability and implementation: More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/. Supplementary information: Supplementary data are available at Bioinformatics online

Protein Homeostasis Database: protein quality control in E.coli

MOTIVATION: In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these. RESULTS: We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets. AVAILABILITY AND IMPLEMENTATION: The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.status: publishe