Structural diversity of supercoiled DNA

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA min icircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function

On the Front Line of Community-Led Air Quality Monitoring

In this chapter, we explore the potential of community-led air quality monitoring. Community-led air quality monitoring differs from top-down monitoring in many aspects: it is focused on community needs and interests and a local problem and, therefore, has a limited geographical coverage as well as limited temporal coverage. However, localised air quality monitoring can potentially increase the spatial and temporal resolution of air quality information if there is a suitable information-sharing mechanism in place: information from multiple community-led activities can be shared at the city scale and used to augment official information. At the core of the chapter, we provide a detailed experiential description of the process of urban air quality practice, from which we draw our conclusion. We suggest that accessible and reliable community-led air quality monitoring can contribute to the understanding of local environmental issues and improve the dialogue between local authorities and communities about the impacts of air pollution on health and urban and transport planning. Document type: Part of book or chapter of boo

Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe

In the framework of a worldwide project on the phylogeny of the lichen genus Sticta, dedicated sampling was performed in four regions of Western Europe, roughly along an East-West line between N 48°02’ E 07°01’ and N 52°01’ W 09°30’, ranging from France/Vosges to Ireland/Kerry. Five clearly distinct ITS haplotypes were detected for isidia-producing species where only two were expected. Subtle anatomical and morphological characters, together with a strongly supported 4-loci molecular phylogeny, permit to distinguish, besides the easily recognized S. canariensis and S. limbata: • the two « well-known » S. fuliginosa and S. sylvatica whose type collections have been carefully reassessed; the former is widespread in both hemispheres, while the latter is correctly identified only from continental Europe and the Andes in Colombia; the barcode ITS of S. fuliginosa differs by a single substitution from S. limbata (with a single exception), and the 4-loci phylogenetic tree does not resolve them as distinct lineages, most probably highlighting a very recent divergence and incomplete lineage sorting; • three species that were formely included in S. fuliginosa: the resurrected S. ciliata Taylor, belonging to a complex group yet to be disentangled and occurring in the Neotropics, Africa, Macaronesia and Western Europe, and two species described as new for science, S. fuliginoides, found in continental Europe, the Canary Islands, eastern North America and Colombia, and S. atlantica only known from Ireland and the Azores archipelago. Molecular inferences demonstrate active divergence and dispersion within S. ciliata that may require recognition of further species. Fresh material can be identified with a morphological and anatomical preliminary key provided here. We propose that the taxonomy of all lichen species be urgently reviewed in the light of molecular data in an evolutionary context, particularly those used as bioindicators of environmental change and woodland management