BOOSting excellence in environmental EPIgenetics
In boosting, a random sample of data is selected, fitted with a model and then trained sequentially
The EPIBOOST project was funded under the HE programme for Widening participation and spreading excellence as a Twinning Action. It joins the Widening coordinator UAVR (PT) with UGent (BE) and CSIC (SP), two internationally-leading partners for boosting research excellence in the field of environmental epigenetics. This is a new research arena in general, even at its infancy regarding application in environmental assessment, which allows a win-win scenario within the Consortium. Critically, epigenetics regulates gene expression and therefore the responses of organisms to their environment, primarily defining how a species will be affected by a given stressor, hence the relevance of epigenetic modifications in Ecological Risk Assessment (ERA).
Although the UAVR team is internationally recognized for excellent research in ERA, their reputation and attractiveness in omics fields, epigenomics in particular, is limited. This is where CSIC and UGent are additionally stronger and willing to support the leveraging of the expertise level of the Widening Coordinator. As per their advanced position, CSIC and UGent will also support the tailoring of existing facilities at UAVR, namely for next generation sequencing and animal experimentation, as well as the improvement of Science management practices towards an efficient tacking the demands of the HE funding atmosphere.
epiboost at a glance
This workpackage provides the practical challenges for the capacitation and expertise leveraging of UAVR researchers in the field of environmental epigenetics. Scientifically, it aims at generating knowledge on the epigenetic effects and their translation into phenotypic changes of environmental stressors in marine and freshwater species playing a key role in Ecological Risk Assessment – phytoplankton, zooplankton and fish. Related specific objectives are:
• To optimize and apply experiments and techniques for assessing differential patterns of DNA methylation and gene expression in selected species responding to model environmental stressors – one metal, one antibiotic and one toxin.
• To link DNA methylation to stress with transcriptional and phenotypic effects.
The overarching aim of this workpackage is the hands-on capacitation of the UAVR research team for skills leverage in the field of environmental epigenetics/epigenomics, under an improving-by-doing philosophy. The work plan is strictly parallel to the course of the preparatory project, and close supervision and collaboration of the advanced partners will be implemented through:
• Online training sessions for experimental planning dedicating to each grouped species models.
• Exchanges with UAVR visiting advanced partners and vice-versa for direct supervision and training on experimental protocols.
• Exchanges with UAVR visiting the advanced partners for training regarding next generation sequencing technologies and targeted analysis of DNA methylation and gene expression.
• Exchanges with UAVR visiting the advanced partners for training on the bioinformatic and data analysis pipelines applicable to the epigenomic/transcriptomic datasets generated by the research project.
This workpackage is focused on the training of early-career researchers, providing them with the baseline knowledge, tools and network contacts for a future investment in the field of environmental epigenetics. This supports the sustainability of the field growth within the European Research Area. Three different types of activities will be implemented:
• Advanced post-graduation courses covering key concepts and driving aspects of experimental approaches in the field of environmental epigenetics.
• Summer Schools offering training on critical fields for the leveraging of environmental epigenetics research to the best standards and impact levels.
• Short-courses embedded in international conferences in advanced aspects of the analysis and interpretation of epigenetic data.
Herein, EPIBOOST will promote the growing of research excellence in the field of environmental epigenetics by focusing on the capacitation of key infrastructures and project/funding management. Specific objectives and main activities implemented through this workpackage are as follows.
• To develop the management skills of UAVR regarding critical infrastructures supporting research in environmental epigenetics, namely ethically-compliant animal housing and next-generation sequencing facility infrastructure, via workshops, visits and the production of work-flow and administration guidelines.
• To train UAVR Science managers on best practice day-to-day support to EU projects, efficient support to fundraising and DE&C development, via exchanges where UAVR visits the advanced partners for on-site training.
• To leverage the Consortium capacity to successfully build and coordinate excellent HE-funded projects, following on training workshops delivered by professionals on key new aspects of the Programme and on the immersive collaborative writing of a new R&I proposal stepping up from the EPIBOOST research.
This workpackage ensures the widest visibility of EPIBOOST by specific aiming to: set up and implement the Dissemination and Exploitation, including Communication (DE&C) strategy, ensuring project activities and results advertisement, distribution and/or use of outputs as broadly as possible; develop and engage the Consortium network; draft and implement the project’s data management strategy. Tasks to tackle these aims include the set-up of the project website, stakeholder mapping and engagement, network development and engagement, the elaboration and implementation of the dissemination strategy through an efficient communication framework, and exploitation steering and data management.
Structured according to the size and specific needs of EPIBOOST, this workpackage aims to administratively and financially steer the project according to Consortium and Grant Agreements; establish and maintain effective internal and external communication flows, solving any arising conflicts and address contingencies as necessary; monitor the successful implementation of all activities, as well as promote the timely achievement of deliverables. Structure wise, tasks comprise the overall coordination and financial management, management of the preparatory research project, management of capacitation activities, ethics and gender dimension management, organization of plenary meetings. Although the Coordinator is the main responsible for WP6 and its tasks, the advanced partners are deeply involved, which is also a way of sharing their higher experience and exercised practice with UAVR.