Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species

<p>Abstract</p> <p>Background</p> <p>The results of transcriptome microarray analysis are usually presented as a list of differentially expressed genes. As these lists can be long, it is hard to interpret the desired experimental treatment effect on the physiology of analysed tissue, e.g. via selected metabolic or other pathways. For some organisms, gene ontologies and data visualization software have been implemented to overcome this problem, whereas for others, software adaptation is yet to be done.</p> <p>Results</p> <p>We present the classification of tentative potato contigs from the potato gene index (StGI) available from Dana-Farber Cancer Institute (DFCI) into the MapMan ontology to enable the application of the MapMan family of tools to potato microarrays. Special attention has been focused on mapping genes that could not be annotated based on similarity to Arabidopsis genes alone, thus possibly representing genes unique for potato. 97 such genes were classified into functional BINs (i.e. functional classes) after manual annotation. A new pathway, focusing on biotic stress responses, has been added and can be used for all other organisms for which mappings have been done. The BIN representation on the potato 10 k cDNA microarray, in comparison with all putative potato gene sequences, has been tested. The functionality of the prepared potato mapping was validated with experimental data on plant response to viral infection. In total 43,408 unigenes were mapped into 35 corresponding BINs.</p> <p>Conclusion</p> <p>The potato mappings can be used to visualize up-to-date, publicly available, expressed sequence tags (ESTs) and other sequences from GenBank, in combination with metabolic pathways. Further expert work on potato annotations will be needed with the ongoing EST and genome sequencing of potato. The current MapMan application for potato is directly applicable for analysis of data obtained on potato 10 k cDNA microarray by TIGR (The Institute for Genomic Research) but can also be used by researchers working on other potato gene sets. The potato mapping file and the stress mapping diagram are available from the MapMan website <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

Single-Use Plastic Bans: Exploring Stakeholder Perspectives on Best Practices for Reducing Plastic Pollution

In this study, we conducted and documented workshops and interviews in Norway and Slovenia to identify stakeholder and future generation opinions and mitigation strategies for solving one of the most prominent environmental issues: plastic pollution. As part of the EU H2020 project GoJelly, stakeholders were brought together to explore their perceptions on considering jellyfish mucus as a new resource to contribute to reducing plastic pollution from entering the marine environment. The study was conducted in the spring of 2019, in a context directly after the European Union (EU) announced its Directive to ban the most commonly used single-use plastic (SUP) items. The study applied the snowball method as a methodological choice to identify relevant stakeholders. Systems thinking was utilized as a participatory modelling approach, which allowed for the creation of conceptual mind maps from the various workshops and interviews, to understand consumers' consciousness, and to map out ideas on plastic pollution reduction. Plastic pollution takes place on a global scale and stakeholders discussed their individual perceptions of national and international solutions that could be put in place to solve it, including the opportunities around utilizing jellyfish mucus to filter and capture micro- and nanoplastic. We found that industry stakeholders in both case areas were generally more accepting of policy and increased innovation moving forward, but placed weight on the scientific community to conduct more research on the pollution issue and propose solutions. Future generation stakeholders (youth aged 14–18), however, put emphasis on consumer behavior and buying patterns of single-use products fueling the plastic crisis.publishedVersio

Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation

<p>Abstract</p> <p>Background</p> <p><it>Staphylococcus aureus </it>is a highly adaptable human pathogen and there is a constant search for effective antibiotics. Fosfomycin is a potent irreversible inhibitor of MurA, an enolpyruvyl transferase that uses phosphoenolpyruvate as substrate. The goal of this study was to identify the pathways and processes primarily affected by fosfomycin at the genome-wide transcriptome level to aid development of new drugs.</p> <p>Results</p> <p><it>S. aureus </it>ATCC 29213 cells were treated with sub-MIC concentrations of fosfomycin and harvested at 10, 20 and 40 minutes after treatment. <it>S. aureus </it>GeneChip statistical data analysis was complemented by gene set enrichment analysis. A visualization tool for mapping gene expression data into biological pathways was developed in order to identify the metabolic processes affected by fosfomycin. We have shown that the number of significantly differentially expressed genes in treated cultures increased with time and with increasing fosfomycin concentration. The target pathway - peptidoglycan biosynthesis - was upregulated following fosfomycin treatment. Modulation of transport processes, cofactor biosynthesis, energy metabolism and nucleic acid biosynthesis was also observed.</p> <p>Conclusions</p> <p>Several pathways and genes downregulated by fosfomycin have been identified, in contrast to previously described cell wall active antibiotics, and was explained by starvation response induced by phosphoenolpyruvate accumulation. Transcriptomic profiling, in combination with meta-analysis, has been shown to be a valuable tool in determining bacterial response to a specific antibiotic.</p

'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine

<p>Abstract</p> <p>Background</p> <p>Phytoplasmas are bacteria without cell walls from the class <it>Mollicutes</it>. They are obligate intracellular plant pathogens which cause diseases in hundreds of economically important plants including the grapevine (<it>Vitis vinifera</it>). Knowledge of their biology and the mechanisms of their interactions with hosts is largely unknown because they are uncultivable and experimentally inaccessible in their hosts. We detail here the global transcriptional profiling in grapevine responses to phytoplasmas. The gene expression patterns were followed in leaf midribs of grapevine cv. 'Chardonnay' naturally infected with a phytoplasma from the stolbur group 16SrXII-A, which is associated with the grapevine yellows disease 'Bois noir'.</p> <p>Results</p> <p>We established an on field experimental system in a productive vineyard that allowed application of molecular tools in a plant natural environment. Global transcription profiles of infected samples were compared with the healthy ones using microarray datasets and metabolic pathway analysis software (MapMan). The two-year-long experiment revealed that plant genes involved in primary and secondary metabolic pathways were changed in response to infection and that these changes might support phytoplasma nutrition. A hypothesis that phytoplasmas interact with the plant carbohydrate metabolism was proven and some possibilities how the products of this pathway might be utilized by phytoplasmas are discussed. In addition, several photosynthetic genes were largely down-regulated in infected plants, whereas defense genes from the metabolic pathway leading to formation of flavonoids and some PR proteins were significantly induced. Few other genes involved in defense-signaling were differentially expressed in healthy and infected plants. A set of 17 selected genes from several differentially expressed pathways was additionally analyzed with quantitative real-time PCR and confirmed to be suitable for a reliable classification of infected plants and for the characterization of susceptibility features in the field conditions.</p> <p>Conclusion</p> <p>This study revealed some fundamental aspects of grapevine interactions with the stolbur 'Bois noir' phytoplasma in particular and some plant interactions with phytoplasmas in general. In addition, the results of the study will likely have an impact on grape improvement by yielding marker genes that can be used in new diagnostic assays for phytoplasmas or by identifying candidate genes that contribute to the improved properties of grape.</p

Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine

<p>Abstract</p> <p>Background</p> <p>Whole genome transcriptomics analysis is a very powerful approach because it gives an overview of the activity of genes in certain cells or tissue types. However, biological interpretation of such results can be rather tedious. MapMan is a software tool that displays large datasets (e.g. gene expression data) onto diagrams of metabolic pathways or other processes and thus enables easier interpretation of results. The grapevine (<it>Vitis vinifera</it>) genome sequence has recently become available bringing a new dimension into associated research. Two microarray platforms were designed based on the TIGR Gene Index database and used in several physiological studies.</p> <p>Results</p> <p>To enable easy and effective visualization of those and further experiments, annotation of <it>Vitis vinifera </it>Gene Index (VvGI version 5) to MapMan ontology was set up. Due to specificities of grape physiology, we have created new pictorial representations focusing on three selected pathways: carotenoid pathway, terpenoid pathway and phenylpropanoid pathway, the products of these pathways being important for wine aroma, flavour and colour, as well as plant defence against pathogens. This new tool was validated on Affymetrix microarrays data obtained during berry ripening and it allowed the discovery of new aspects in process regulation. We here also present results on transcriptional profiling of grape plantlets after exposal to the fungal pathogen <it>Eutypa lata </it>using Operon microarrays including visualization of results with MapMan. The data show that the genes induced in infected plants, encode pathogenesis related proteins and enzymes of the flavonoid metabolism, which are well known as being responsive to fungal infection.</p> <p>Conclusion</p> <p>The extension of MapMan ontology to grapevine together with the newly constructed pictorial representations for carotenoid, terpenoid and phenylpropanoid metabolism provide an alternative approach to the analysis of grapevine gene expression experiments performed with Affymetrix or Operon microarrays. MapMan was first validated on an already published dataset and later used to obtain an overview of transcriptional changes in a susceptible grapevine – <it>Eutypa lata </it>interaction at the time of symptoms development, where we showed that the responsive genes belong to families known to be involved in the plant defence towards fungal infection (PR-proteins, enzymes of the phenylpropanoid pathway).</p

A new tool for faster construction of marine biotechnology collaborative networks.

The increasing and rapid development in technologies, infrastructures, computational power, data availability and information flow has enabled rapid scientific advances. These entail transdisciplinary collaborations that maximize sharing of data and knowledge and, consequently, results, and possible technology transfer. However, in emerging scientific fields it is sometimes difficult to provide all necessary expertise within existing collaborative circles. This is especially true for marine biotechnology that directly addresses global societal challenges. This article describes the creation of a platform dedicated to facilitating the formation of short or mid-term collaborative networks in marine biotechnology. This online platform (https://www.ocean4biotech.eu/map/) enables experts (researchers and members of the marine biotechnology community in general) to have the possibility to showcase their expertise with the aim of being integrated into new collaborations/consortia on the one hand, or to use it as a search tool to complement the expertise in planned/running collaborations, on the other. The platform was created within the Ocean4Biotech (European transdisciplinary networking platform for marine biotechnology) Action, funded under the framework of the European Cooperation in Science and Technology (COST). To build the platform, an inquiry was developed to identify experts in marine biotechnology and its adjunct fields, to define their expertise, to highlight their infrastructures and facilities and to pinpoint the main bottlenecks in this field. The inquiry was open to all experts in the broad field of marine biotechnology, including non-members of the consortium. The inquiry (https://ee.kobotoolbox.org/single/UKVsBNtD) remains open for insertion of additional expertise and the resulting interactive map can be used as a display and search tool for establishing new collaborations

Marine anticancer agents: An overview with a particular focus on their chemical classes

UID/Multi/04378/2019 IF/00700/2014 grant number 216Z167 grant RTA 2015-00010-C03-02 No. PBA/MB/16/01 PDOC/19/02/01The marine environment is a rich source of biologically active molecules for the treatment of human diseases, especially cancer. The adaptation to unique environmental conditions led marine organisms to evolve different pathways than their terrestrial counterparts, thus producing unique chemicals with a broad diversity and complexity. So far, more than 36,000 compounds have been isolated from marine micro- and macro-organisms including but not limited to fungi, bacteria, microalgae, macroalgae, sponges, corals, mollusks and tunicates, with hundreds of new marine natural products (MNPs) being discovered every year. Marine-based pharmaceuticals have started to impact modern pharmacology and different anti-cancer drugs derived from marine compounds have been approved for clinical use, such as: cytarabine, vidarabine, nelarabine (prodrug of ara-G), fludarabine phosphate (pro-drug of ara-A), trabectedin, eribulin mesylate, brentuximab vedotin, polatuzumab vedotin, enfortumab vedotin, belantamab mafodotin, plitidepsin, and lurbinectedin. This review focuses on the bioactive molecules derived from the marine environment with anticancer activity, discussing their families, origin, structural features and therapeutic use.publishersversionpublishe

Why we need sustainable networks bridging countries, disciplines, cultures and generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on matching the composition of assemblages of organisms identified using morphological criteria present in aquatic ecosystems to those expected in the absence of anthropogenic pressures. Through decade-long and difficult intercalibration exercises among networks of regulators and scientists in European countries, a pragmatic biomonitoring approach was developed and adopted, which now produces invaluable information. Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, data acquisition is often slow due to a lack of taxonomic experts for many taxa and regions and time-consuming morphological identification of organisms. High-throughput genetic screening methods such as (e)DNA metabarcoding have been proposed as a possible solution to these shortcomings. Such "next-generation biomonitoring", also termed "biomonitoring 2.0", has many advantages over the traditional approach in terms of speed, comparability and costs. It also creates the potential to include new bioindicators and thereby further improves the assessment of aquatic ecosystem health. However, several major conceptual and technological challenges still hinder its implementation into legal and regulatory frameworks. Academic scientists sometimes tend to overlook legal or socioeconomic constraints, which regulators have to consider on a regular basis. Moreover, quantification of species abundance or biomass remains a significant bottleneck to releasing the full potential of these approaches. Here, we highlight the main challenges for next-generation aquatic biomonitoring and outline principles and good practicCOST - European Cooperation in Science and Technology(CA15219). COST Action DNAqua-Net (CA15219), supported by the COST (European Cooperation in Science and Technology) programm