The KINDRA project – towards Open Science in Hydrogeology for higher impact

Groundwater knowledge and research in the European Union is often scattered and non-standardised. Therefore, KINDRA is conducting an EU-wide assessment of existing groundwater-related practical and scientific knowledge based on a new Hydrogeological Research Classification System (HRC-SYS). The classification is supported by a web service, the European Inventory of Groundwater Research (EIGR), which acts not only as a knowledge repository but also as a tool to help identify relevant research topics, existing research trends and critical research challenges. These results will be useful for producing synergies, implementing policies and optimising water management in Europe. This article presents the work of the project during the first two years in relation to a common classification system and an activity for data collection and training delivered by the EFG’s National Associations in 20 European countries

Evaluation of the West Yorkshire Staff Mental Health and Wellbeing Hub

The West Yorkshire (WY) Staff Wellbeing Hub aims to support NHS, Social Care and Voluntary Sector staff. This evaluation has been conducted as a partnership between the WY Hub and the University of Leeds. It presents data reflecting user uptake and experiences

Peatland core domain sets: building consensus on what should be measured in research and monitoring

It is often difficult to compile and synthesise evidence across multiple studies to inform policy and practice because different outcomes have been measured in different ways or datasets and models have not been fully or consistently reported. In the case of peatlands, a critical terrestrial carbon store, this lack of consistency hampers the evidence-based decisions in policy and practice that are needed to support effective restoration and conservation. This study adapted methods pioneered in the medical community to reach consensus over peatland outcomes that could be consistently measured and reported to improve the synthesis of data and reduce research waste. Here we report on a methodological framework for identifying, evaluating and prioritising the outcomes that should be measured. We discuss the subsequent steps to standardise methods for measuring and reporting outcomes in peatland research and monitoring. The framework was used to identify and prioritise sets of key variables (known as core domain sets) for UK blanket and raised bogs, and for tropical peat swamps. Peatland experts took part in a structured elicitation and prioritisation process, comprising two workshops and questionnaires, that focused on climate (32 and 18 unique outcomes for UK and tropical peats, respectively), hydrology (26 UK and 16 tropical outcomes), biodiversity (8 UK and 22 tropical outcomes) and fire-related outcomes (13, for tropical peatlands only). Future research is needed to tackle the challenges of standardising methods for data collection, management, analysis, reporting and re-use, and to extend the approach to other types of peatland. The process reported here is a first step towards creating datasets that can be synthesised to inform evidence-based policy and practice, and contribute towards the conservation, restoration and sustainable management of this globally significant carbon store. evidence-based policy and practice, evidence synthesis, outcomes, standardisationpublishedVersio

T-REX: software for the processing and analysis of T-RFLP data

Softwar

Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called “hidden spindle hub”, proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system

Patterns of Gene Flow Define Species of Thermophilic Archaea

A genomic view of speciation in Archaea shows higher rates of gene flow within coexisting microbial species than between them

Internal Ribosomal Entry Site-Mediated Translation Is Important for Rhythmic PERIOD1 Expression

The mouse PERIOD1 (mPER1) plays an important role in the maintenance of circadian rhythm. Translation of mPer1 is directed by both a cap-dependent process and cap-independent translation mediated by an internal ribosomal entry site (IRES) in the 5′ untranslated region (UTR). Here, we compared mPer1 IRES activity with other cellular IRESs. We also found critical region in mPer1 5′UTR for heterogeneous nuclear ribonucleoprotein Q (HNRNPQ) binding. Deletion of HNRNPQ binding region markedly decreased IRES activity and disrupted rhythmicity. A mathematical model also suggests that rhythmic IRES-dependent translation is a key process in mPER1 oscillation. The IRES-mediated translation of mPer1 will help define the post-transcriptional regulation of the core clock genes