"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.

INFRAFRONTIER: mouse model resources for modelling human diseases.

Over the last decade, INFRAFRONTIER has positioned itself as a world-class Research Infrastructure for the generation, phenotyping, archiving, and distribution of mouse models in Europe. The INFRAFRONTIER network consists of 22 partners from 15 countries, and is continuously enhancing and broadening its portfolio of resources and services that are offered to the research community on a non-profit basis. By bringing together European rodent model expertise and providing valuable disease model services to the biomedical research community, INFRAFRONTIER strives to push the accessibility of cutting-edge human disease modelling technologies across the European research landscape. This article highlights the latest INFRAFRONTIER developments and informs the research community about its extensively utilised services, resources, and technical developments, specifically the intricacies of the INFRAFRONTIER database, use of Curated Disease Models, overview of the INFRAFRONTIER Cancer and Rare Disease resources, and information about its main state-of-the-art services.

INFRAFRONTIER quality principles in systemic phenotyping.

Improving reproducibility and replicability in preclinical research is a widely discussed and pertinent topic, especially regarding ethical responsibility in animal research. INFRAFRONTIER, the European Research Infrastructure for the generation, phenotyping, archiving, and distribution of model mammalian genomes, is addressing this issue by developing internal quality principles for its different service areas, that provides a quality framework for its operational activities. This article introduces the INFRAFRONTIER Quality Principles in Systemic Phenotyping of genetically altered mouse models. A total of 11 key principles are included, ranging from general requirements for compliance with guidelines on animal testing, to the need for well-trained personnel and more specific standards such as the exchange of reference lines. Recently established requirements such as the provision of FAIR (Findable, Accessible, Interoperable, Reusable) data are also addressed. For each quality principle, we have outlined the specific context, requirements, further recommendations, and key references.

INFRAFRONTIER: a European resource for studying the functional basis of human disease.

Ageing research and more generally the study of the functional basis of human diseases profit enormously from the large-scale approaches and resources in mouse functional genomics: systematic targeted mutation of the mouse genome, systemic phenotyping in mouse clinics, and the archiving and distribution of the mouse resources in public repositories. INFRAFRONTIER, the European research infrastructure for the development, systemic phenotyping, archiving and distribution of mammalian models, offers access to sustainable mouse resources for biomedical research. INFRAFRONTIER promotes the global sharing of high-quality resources and data and thus contributes to data reproducibility and animal welfare. INFRAFRONTIER puts great effort into international standardisation and quality control and into technology development to improve and expand experimental protocols, reduce the use of animals in research and increase the reproducibility of results. In concert with the research community and the International Mouse Phenotyping Consortium (IMPC), INFRAFRONTIER is currently developing new pilot platforms and services for the research on ageing and age-related diseases.

Facilitating remote and virtual access provision by European research infrastructures - requirements, issues, and recommendations.

Research Infrastructures (RIs) are strategic assets facilitating innovation and knowledge advancement across all scientific disciplines. They provide researchers with advanced tools and resources that go beyond individual or institutional capacities and promote collaboration, community-building and the application of scientific standards. Remote and virtual access to RIs enables scientists to use these essential resources without the necessity of being physically present. The COVID-19 pandemic restrictions where a catalyst for the expansion and further development of remote and virtual access models, particularly in fields where physical access had been the predominant model. The eRImote project explores pathways for digital and remote RI access through targeted surveys, stakeholder workshops, expert groups discussions, and the analysis of specific use cases. This paper provides a definition of remote and virtual access and remote training and explores their implementation across various RIs, highlighting the implications for their operational processes and the dynamics of interaction between RIs and their user communities. It presents the identified advantages, obstacles, and best-practices, alongside strategies and recommendations to navigate and mitigate challenges effectively. Key issues and recommendations are summed up separately for remote access, virtual access, and remote training, complemented by general recommendations for facilitating remote and virtual access to RIs. These relate to budgeting and funding, the balancing of RI access models, the need for regulatory frameworks for sample shipments, collaboration among RIs, impact assessment of remote and virtual access on user interactions, operational efficiency and the environment footprint of RIs, and the adaption of data sharing policies. Stakeholders are broadly invited to give their feedback on the paper's findings and conclusions, which will be integrated into improved versions of this paper.

Moving forward with forward genetics: A summary of the INFRAFRONTIER Forward Genetics Panel Discussion.

In the last few decades, forward genetics approaches have been extensively used to identify gene function. Essentially, forward genetics is the elucidation of the genetic basis of a specific phenotype by screening a population containing random genomic modifications that alter gene function. These approaches have shed light on some essential gene functions in development and disease and have expanded the realm of understanding for genetic disorders. Due to the availability of efficient mutagenesis methods, phenotyping techniques, reliable validation, comprehensive sequence information and translational potential, mouse models are favored for forward genetics approaches. However, in this post-genomic CRISPR-Cas9 era, the relevance and future of forward genetics was brought into question. With more than 7300 mouse strains archived and close interactions with several leading mouse researchers around the world, INFRAFRONTIER - the European Research Infrastructure for mouse models organised a panel discussion on forward genetics at the International Mammalian Genome Conference 2018 to discuss the future of forward genetics as well as challenges faced by researchers using this approach in the current research environment. The commentary presents an overview of this discussion.

Behavioural and hormonal effects of social isolation and neophobia in a gregarious bird species, the European starling (Sturnus vulgaris).

Separating gregarious individuals from their group members often results in behavioural and physiological changes, like increased levels of corticosterone. Testosterone and corticosterone, in particular, have been implicated in the response of mammals to novelty. Data in birds are, however, rare. The presence or absence of group members may also influence an individual's response to novel stimuli. We assessed the behaviour and hormonal response of European starlings (Sturnus vulgaris) to a novel object in two different situations and seasons: each starling was tested when separated and when in contact with its group members in May/June (breeding season) and again in September/October (non-breeding season). Starlings are gregarious throughout the year, but as foraging flocks are small during the breeding season and large during the non-breeding season, we assumed that non-breeding starlings would be more affected by social isolation. Overall, starlings had higher levels of corticosterone, lost more body mass, and were more active when they were separated from their group. Isolated individuals, however, did not show a greater neophobic response than individuals in the presence of their group members in either season. Circulating levels of testosterone and corticosterone were higher after a test with novel object than after a test with only the familiar feeding dish in both sexes and seasons. However, control tests for handling effects confirmed only the increase in testosterone. Our study shows that social isolation is stressful for unrelated and unpaired members of a wild flocking bird species and demonstrates that novelty can lead to a rise in testosterone in birds.

Hormonal responses to male-male social challenge in the blue tit Cyanistes caeruleus: single-broodedness as an explanatory variable.

The "challenge hypothesis" posits that when established social orders are challenged, plasma testosterone (T) in socially monogamous breeding male birds will temporarily increase to facilitate aggressive responses. However, not all birds conform to predictions. To expand upon past findings, we examined effects of direct territorial challenge on T levels in the blue tit (Cyanistes caeruleus). We found that simulated territorial intrusions caused a decline in plasma T during both territory establishment and laying/incubation. Conversely, corticosterone (CORT) levels dramatically increased. We also examined challenged blue tit males for levels of corticosterone-binding globulin (CBG), a carrier molecule that displays affinity for both CORT and T in birds. Although the CBG showed increased occupation by CORT during challenge, effects were not accompanied by a significant increase in the unbound T fraction. Thus, competitive hormone interactions on the CBG do not seem sufficient to explain changes in circulating T levels. To place our results within the context of past findings, we compared all socially monogamous birds tested to date for plasma levels of T during situational territorial intrusion experiments. We found that birds raising only one brood per season (e.g., the blue tit) consistently show no increase in plasma T but instead show elevations in circulating CORT. Thus, we suggest that single-broodedness plays an important role in determining patterns of hormone change and should be considered in future discussions of hormone-behavior interactions.

Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening.

Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on the origins of developmental disease and congenital abnormalities. Current international efforts to examine gene function in the mouse provide a unique opportunity to pinpoint genes that are involved in embryogenesis, owing to the emergence of embryonic lethal knockout mutants. Through internationally coordinated efforts, the International Knockout Mouse Consortium (IKMC) has generated a public resource of mouse knockout strains and, in April 2012, the International Mouse Phenotyping Consortium (IMPC), supported by the EU InfraCoMP programme, convened a workshop to discuss developing a phenotyping pipeline for the investigation of embryonic lethal knockout lines. This workshop brought together over 100 scientists, from 13 countries, who are working in the academic and commercial research sectors, including experts and opinion leaders in the fields of embryology, animal imaging, data capture, quality control and annotation, high-throughput mouse production, phenotyping, and reporter gene analysis. This article summarises the outcome of the workshop, including (1) the vital scientific importance of phenotyping embryonic lethal mouse strains for basic and translational research; (2) a common framework to harmonise international efforts within this context; (3) the types of phenotyping that are likely to be most appropriate for systematic use, with a focus on 3D embryo imaging; (4) the importance of centralising data in a standardised form to facilitate data mining; and (5) the development of online tools to allow open access to and dissemination of the phenotyping data.

Molecular and phenotypic divergence in the bluethroat (Luscinia svecica) subspecies complex.

Subspecies complexes may provide valuable insights into the early stages of the speciation process. The bluethroat (Luscinia svecica) consists of many morphologically distinct subspecies that differ most strikingly in the ornamental colour pattern of the male throat. We investigated the genetic and phenotypic differentiation in this subspecies complex, using (i) microsatellite genotyping (11 loci) of a sample of 364 individuals from bluethroat populations in Europe and Asia, and (ii) spectrometric and morphological measurements of a sample of 131 museum skin specimens. Population genetic analyses, based on microsatellite allele frequency variation, revealed a slight but significant overall population differentiation (F(ST) = 0.042). There was a well-differentiated southern group of subspecies with white or no throat spots and a less-differentiated northern group of chestnut-spotted populations. Phylogenetic analyses indicated that the southern all-blue and white-spotted forms are ancestral to the chestnut-spotted subspecies. In addition to the qualitative variation in throat plumage pattern already described in the literature, we found significant quantitative variation among subspecies in hue, chroma and brightness of the ultraviolet (UV)/blue throat coloration, and this variation seemed to be unrelated to the phylogenetic distance between subspecies.