The BioJS article collection of open source components for biological data visualisation.

Data-driven research has gained momentum in the life sciences. Visualisation of these data is essential for quick generation of hypotheses and their translation into useful knowledge. BioJS is a new proposed standard for JavaScript-based components to visualise biological data. BioJS is an open source community project that to date provides 39 different components contributed by a global community. Here, we present the BioJS F1000Research collection series. A total of 12 components and a project status article are published in bulk. This collection does not intend to be an all-encompassing, comprehensive source of BioJS articles, but an initial set; future submissions from BioJS contributors are welcome

RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization

To survive diverse host environments, the human pathogen Streptococcus pneumoniae must prevent its self-produced, extremely high levels of peroxide from reacting with intracellular iron. However, the regulatory mechanism(s) by which the pneumococcus accomplishes this balance remains largely enigmatic, as this pathogen and other related streptococci lack all known redox-sensing transcription factors. Here we describe a two-component-derived response regulator, RitR, as the archetype for a novel family of redox sensors in a subset of streptococcal species. We show that RitR works to both repress iron transport and enable nasopharyngeal colonization through a mechanism that exploits a single cysteine (Cys128) redox switch located within its linker domain. Biochemical experiments and phylogenetics reveal that RitR has diverged from the canonical two-component virulence regulator CovR to instead dimerize and bind DNA only upon Cys128 oxidation in air-rich environments. Atomic structures show that Cys128 oxidation initiates a "helical unravelling" of the RitR linker region, suggesting a mechanism by which the DNA-binding domain is then released to interact with its cognate regulatory DNA. Expanded computational studies indicate this mechanism could be shared by many microbial species outside the streptococcus genus

Anatomy of BioJS, an open source community for the life sciences

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects

Development of ‘super-early’ pigeonpeas with good yield potential from early × early crosses

To enhance the adaptability of pigeonpea at higher latitude and altitude, a breeding program was initiated at ICRISAT involving different sources of early-maturity. A full diallel mating design involving 11 early-maturing lines were used as parents. In F2–F5 generations, selection was followed for early flowering and maturity, grain yield and 100-seed weight by pedigree method. Four brown seeded (ICPX 060064-4-6-10, ICPX 060077-6-5-14, ICPX 060064-4-6-2 and ICPX 060063-11-8-4) and one cream seeded (ICPX 060036-13-4-8) F4/F5 indeterminate super-early progenies that matured, respectively 25 and 23 days earlier than the control cultivar ICPL 88039 were recovered. ICPX 060036-13-4-8 recorded 107% and 34% grain yield advantage over the checks ICPL 86022 and ICPL 88039, respectively. These super-early lines were derived from crosses involving AL 1518-2 × ICPL 85010, AL 1621 × MN 5, AL 1518-2 × MN 8 and MN 8 × AL 1518-2. Other super-early progenies [ICPX 060016-10-8-1 (from MN 1 × AL 1518-2 cross) and ICPX 060017-12-12-20 (from MN 1 × AL 1621 cross)] with greater 100-seed weight were also recovered. Besides serving as excellent donors for earliness, these lines may be photo/thermo insensitive. These super-early pigeonpea lines may open new niches for this crop and help in intensification of farming system

The spatio-relational nature of urban innovation systems: Universities, knowledge intensive business service firms, and collaborative networks

The need to better identify the spatio-relational nature of urban innovation systems and spaces is increasingly acknowledged. The aim of this paper, therefore, is to provide an enhanced understanding of the knowledge networks existing between urban Knowledge Intensive Business Services firms (KIBS) and universities, which are often key components of such systems and spaces. Drawing on an analysis of urban KIBS firms and universities in the UK, it is found that the nature of firms, the location in which they are based, and the research intensity of their university partners are important determinants of the spatiality and localisation of the networks they form. The results show that the smallest urban KIBS firms have the highest propensity to engage in local links with universities, suggesting that they rely most significantly on their own urban innovation system for collaborative network ties. Keywords : innovation systems; urban innovation spaces; knowledge-based development; proximity; networks; KIBS; universities

Academics, Cultural Workers and Critical Labour Studies

The aim of this paper is to locate academics within the sights of critical labour studies, and, in particular, the contemporary interest in cultural workers. Despite a growing literature about - and in response to - the transformation of the University there have been few attempts to study academics as workers. This paper argues that there are a number of parallels between academic work and the much more well-documented experiences of work in the cultural and creative industries. The paper examines the increasing experience of precariousness among academics, the intensification and extensification of work, and the new modes of surveillance in the academy and their affective impacts. The aim of the article is to build on the critical lexicon of studies of cultural labour in order to think about academic work as labour and to generate new ways of thinking about power, privilege and exploitation. It argues for the need for a psychosocial perspective that can understand the new labouring subjectivities in academia

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences

CDD: a Conserved Domain Database for the functional annotation of proteins

NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml