Making land available for woodland creation

In order to support the Forestry Commission in achieving woodland planting targets, the overall aim of this research was to better understand the availability of land in England for afforestation, reflecting the interests and motivation of land owners and occupiers. In particular the research has attempted to identify where (either in a geographical sense and/or in terms of owner 'type') the Forestry Commission might focus its efforts in terms of accessing land for woodland creation

The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.

BACKGROUND: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown. METHODS: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163. RESULTS: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway. CONCLUSIONS: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization

Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships

Disordered domains are long regions of intrinsic disorder that ideally have conserved sequences, conserved disorder, and conserved functions. These domains were first noticed in protein–protein interactions that are distinct from the interactions between two structured domains and the interactions between structured domains and linear motifs or molecular recognition features (MoRFs). So far, disordered domains have not been systematically characterized. Here, we present a bioinformatics investigation of the sequence–disorder–function relationships for a set of probable disordered domains (PDDs) identified from the Pfam database. All the Pfam seed proteins from those domains with at least one PDD sequence were collected. Most often, if a set contains one PDD sequence, then all members of the set are PDDs or nearly so. However, many seed sets have sequence collections that exhibit diverse proportions of predicted disorder and structure, thus giving the completely unexpected result that conserved sequences can vary substantially in predicted disorder and structure. In addition to the induction of structure by binding to protein partners, disordered domains are also induced to form structure by disulfide bond formation, by ion binding, and by complex formation with RNA or DNA. The two new findings, (a) that conserved sequences can vary substantially in their predicted disorder content and (b) that homologues from a single domain can evolve from structure to disorder (or vice versa), enrich our understanding of the sequence ➔ disorder ensemble ➔ function paradigm

Is there a future for the small family farm? A report to The Prince’s Countryside Fund

Final published report. Also available from the publisher via: www.princescountrysidefund.org.uk/researchForeword Over the last two or three decades, the farms which populate the landscape of the United Kingdom and have shaped its topography through centuries, have experienced profound change, and whatever the consequences of the European referendum decision will continue to do so. Their resilience has been continually tested. Notwithstanding the challenges of policy and paperwork, they have also had to deal with the day-to-day demands of farming: price volatility, disease and climate change, and a public increasingly unfamiliar with an agrarian lifestyle. Not surprisingly, many are struggling. A recent report for The Prince’s Countryside Fund demonstrated that half of all farms no longer make a living from farming itself and a fifth are losing money before even accounting for family labour. Does this matter? The Prince's Countryside Fund believes it does and that is why we commissioned this wide-ranging and in-depth report from Professors Michael Winter and Matt Lobley of the University of Exeter and their team, to whom I offer my thanks for their hard work and dedication. The Fund has a track record of providing practical help to farming businesses and the rural community through its grant giving, direct action projects and advocacy, supported by a strong network of business supporters and committed individuals. This report will focus our efforts and, we hope, those of our agricultural institutions and policy makers. The report concludes with a series of recommendations which The Fund believes will be vital for farm businesses, and a catalyst for action for the agricultural sector and policy makers in order to retain the wonderful mosaic of farm types we have in the UK. In the uncertain times ahead we fervently hope that it will allow this particular “endangered species” to be given the best possible opportunity to survive and to thrive for many generations to come. Lord Curry of Kirkharle - Chairman, The Prince’s Countryside Fun