FlyBase 2.0: the next generation.

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research

Magnetic field and chromospheric activity evolution of HD 75332 : a rapid magnetic cycle in an F star without a hot Jupiter

ELB is supported by an Australian Government Research Training Program (RTP) Scholarship. SJ acknowledges the support of the German Science Foundation (DFG) Research Unit FOR2544 ‘Blue Planets around Red Stars’ (project JE 701/3-1) and DFG priority program SPP 1992 ‘Exploring the Diversity of Extrasolar Planets’ (JE 701/5-1). AAV acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 817540, ASTROFLOW). VS acknowledges funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No. 682393 AWESoMeStars).Studying cool star magnetic activity gives an important insight into the stellar dynamo and its relationship with stellar properties, as well as allowing us to place the Sun’s magnetism in the context of other stars. Only 61 Cyg A (K5V) and τ Boo (F8V) are currently known to have magnetic cycles like the Sun’s, where the large-scale magnetic field polarity reverses in phase with the star’s chromospheric activity cycles. τ Boo has a rapid ∼240 d magnetic cycle, and it is not yet clear whether this is related to the star’s thin convection zone or if the dynamo is accelerated by interactions between τ Boo and its hot Jupiter. To shed light on this, we studied the magnetic activity of HD 75332 (F7V) which has similar physical properties to τ Boo and does not appear to host a hot Jupiter. We characterized its long term chromospheric activity variability over 53 yrs and used Zeeman Doppler Imaging to reconstruct the large-scale surface magnetic field for 12 epochs between 2007 and 2019. Although we observe only one reversal of the large-scale magnetic dipole, our results suggest that HD 75332 has a rapid ∼1.06 yr solar-like magnetic cycle where the magnetic field evolves in phase with its chromospheric activity. If a solar-like cycle is present, reversals of the large-scale radial field polarity are expected to occur at around activity cycle maxima. This would be similar to the rapid magnetic cycle observed for τ Boo, suggesting that rapid magnetic cycles may be intrinsic to late-F stars and related to their shallow convection zones.Publisher PDFPeer reviewe

Crystal chemistry and electronic properties of the n=2 Ruddlesden-Popper manganates: unconventional CMR materials

The crystallography and electronic properties of the Ln[sub 2- x]Sr[sub 1+x]Mn[sub 2]O[sub 7] manganese oxides adopting the n=2 Ruddlesden-Popper (RP) structure are discussed, focusing on the structural phase diagrams and electronic properties in the vicinity of the Mn +3.5 oxidation state and in particular the ease of synthesis of single phases of these materials

Expansion of the Gene Ontology knowledgebase and resources

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.National Institutes of Health/National Human Genome Research Institute [HG002273] awarded to the PI group formed by (alphabetically) Judith A. Blake, J. Michael Cherry, Suzanna E. Lewis, Paul W. Sternberg and Paul D. Thomas, as well as additional funding awarded to each participating institution. For more details please visit: http://geneontology.org/page/go-consortium-contributors-list. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute [HG002273]

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations

Ageing and Long-Term Care Planning Perceptions of Hispanics in the USA: Evidence from a Case Study in New London, Connecticut

This paper explores the ageing attitudes and long-term care planning behavior of adult Hispanics in New London, Connecticut, a town with 30 thousand inhabitants that is rapidly ageing. We conducted six focus groups and had 37 participants share their ageing perceptions and long-term care needs. Our main findings suggest that informal care arrangements are vulnerable and unsustainable especially since women have historically and disproportionately provided most family eldercare even at their own personal and financial expense. Though male participants expected their female relatives to care for them when they age and need personal assistance, female participants did not necessarily expect the same from their relatives including their daughters. Also, both formal and government long-term care systems lack cultural competence and can be prohibitively costly. Therefore, Hispanics plan for ageing within their circles of family care and their resilience in a context of cultural exclusion and socio-economic disadvantage epitomizes strong intergenerational values. These support networks may help explain why may outlive whites (the Hispanic paradox ) who, on average, have higher wealth and education levels. Long-term care planning is a complex process that cannot be relayed to families only. Adequate training for family members from other relatives, and from private and government entities to appropriately convey this type of planning is vital to ensure that Hispanic families understand their options

Predictions of total and total reaction cross sections for nucleon-nucleus scattering up to 300 MeV

Total reaction cross sections are predicted for nucleons scattering from various nuclei. Projectile energies to 300 MeV are considered. So also are mass variations of those cross sections at selected energies. All predictions have been obtained from coordinate space optical potentials formed by full folding effective two-nucleon (NN) interactions with one body density matrix elements (OBDME) of the nuclear ground states. Good comparisons with data result when effective NN interactions defined by medium modification of free NN t matrices are used. Coupled with analyses of differential cross sections, these results are sensitive to details of the model ground states used to describe nuclei

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource