Visualization of proteomics data using R and bioconductor.

Data visualization plays a key role in high-throughput biology. It is an essential tool for data exploration allowing to shed light on data structure and patterns of interest. Visualization is also of paramount importance as a form of communicating data to a broad audience. Here, we provided a short overview of the application of the R software to the visualization of proteomics data. We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.LG was supported by the European Union 7th Framework Program (PRIME-XS project, grant agreement number 262067) and a BBSRC Strategic Longer and Larger grant (Award BB/L002817/1). LMB was supported by a BBSRC Tools and Resources Development Fund (Award BB/K00137X/1). TN was supported by a ERASMUS Placement scholarship.This is the final published version of the article. It was originally published in Proteomics (PROTEOMICS Special Issue: Proteomics Data Visualisation Volume 15, Issue 8, pages 1375–1389, April 2015. DOI: 10.1002/pmic.201400392). The final version is available at http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400392/abstract

Synthetic biology to access and expand nature's chemical diversity

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Accessing these natural products promises to reinvigorate drug discovery pipelines and provide novel routes to synthesize complex chemicals. The pathways leading to the production of these molecules often comprise dozens of genes spanning large areas of the genome and are controlled by complex regulatory networks with some of the most interesting molecules being produced by non-model organisms. In this Review, we discuss how advances in synthetic biology — including novel DNA construction technologies, the use of genetic parts for the precise control of expression and for synthetic regulatory circuits — and multiplexed genome engineering can be used to optimize the design and synthesis of pathways that produce natural products

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Vegetation and vehicle emissions around primary schools across urban Australia:associations with academic performance

BACKGROUND: Evolving evidence suggests that vegetation surrounding schools is beneficial to children's academic performance, however vehicle emissions are adversely related. Little is known about concurrent impacts of vegetation and vehicle emissions on academic performance. This study examined associations of vegetation and vehicle emissions near urban Australian primary schools with children's academic performance. METHODS: Vegetation within schoolyards and Euclidean buffers (100, 300 and 1000m) was assessed using the Normalised Difference Vegetation Index (NDVI). Weighted road density (WRD) was computed for each buffer as a vehicle emissions proxy. Cross-sectional associations and mediating pathways between vegetation and vehicle emissions and standardised average academic scores in Literacy (Reading, Writing, Language Conventions) and Mathematics for Grades 3 and 5 attending 3745 primary schools in urban areas (population ≥10,000) of Australia in 2018 were assessed using generalised linear models adjusted for school socio-educational status. RESULTS: Significant positive associations were found between vegetation and Reading in Grades 3 and 5, Mathematics in Grade 3 (all buffers), Writing in Grade 3 (100 and 300m), and Language Conventions in Grades 3 and 5 (most buffers). Increased vehicle emissions were negatively associated with Reading and Mathematics in Grades 3 and 5 (most buffers), and Language Conventions in Grade 3 (300 and 1000m) and Grade 5 (100-1000m). Within 300m, vehicle emissions partially mediated associations between vegetation with Mathematics in Grade 3 (proportion mediated, 21%), Reading and Language Conventions in Grade 5 (15%, 37% respectively). CONCLUSIONS: Our findings contribute to growing evidence that vegetation around primary schools is associated with higher achievement in Literacy and Mathematics, with partial mediation by vehicle emissions. Future studies should conduct on-site measurement of vehicle emissions and audit vegetation around schools to confirm findings and inform urban/school planners and school leaders on designing and modifying school environments to support learning