• Canada
• Publicationsclose
• Swiss National Science Foundation close

Abstract This study synthesizes two evaluations of a local climate change planning process in a rural town in British Columbia (Canada), which was supported through landscape visualizations. First, the impact of the visualizations, based on scientific environmental modeling and presented in three different presentation formats, verbal/visual presentation, posters and a virtual globe, was evaluated with regard to immediate impacts during the process. Second, the long-term impacts on decision-making and actual outcomes were evaluated in a retrospective evaluation 22 months after the end of the initial planning process. Two results are highlighted: according to the quantitative pre-/post-questionnaires, the visualizations contributed to increased awareness and understanding. Most importantly, the retrospective evaluation indicated that the process informed policy, operational and built changes in Kimberley, in which the landscape visualizations played a role. The post interviews with key decision-makers showed that they remembered most of the visualizations and some decision-makers were further using them, particularly the posters. The virtual globe seemed to be not a “sustainable” display format suitable for formal decision-making processes such as council meetings though. That may change with the further mainstreaming of visualization technologies or mobile devices. Until then, we recommend using display formats that can be re-used following a specific planning event such as an Open House, to ensure on-going support for effective decision-making over the longer-term.

Monthly Notices of the Royal Astronomical Society, 449 (1) ISSN:0035-8711 ISSN:1365-2966 ISSN:1365-8711

Endolysins are produced by (bacterio)phages to rapidly degrade the bacterial cell wall and release new viral particles. Despite sharing a common function, endolysins present in phages that infect a specific bacterial species can be highly diverse and vary in types, number, and organization of their catalytic and cell wall binding domains. While much is now known about the biochemistry of phage endolysins, far less is known about the implication of their diversity on phage–host adaptation and evolution. Using CRISPR-Cas9 genome editing, we could genetically exchange a subset of different endolysin genes into distinct lactococcal phage genomes. Regardless of the type and biochemical properties of these endolysins, fitness costs associated to their genetic exchange were marginal if both recipient and donor phages were infecting the same bacterial strain, but gradually increased when taking place between phage that infect different strains or bacterial species. From an evolutionary perspective, we observed that endolysins could be naturally exchanged by homologous recombination between phages coinfecting a same bacterial strain. Furthermore, phage endolysins could adapt to their new phage/host environment by acquiring adaptative mutations. These observations highlight the remarkable ability of phage lytic systems to recombine and adapt and, therefore, explain their large diversity and mosaicism. It also indicates that evolution should be considered to act on functional modules rather than on bacteriophages themselves. Furthermore, the extensive degree of evolvability observed for phage endolysins offers new perspectives for their engineering as antimicrobial agents.

© 2014 WILEY PERIODICALS INC. Methylmalonyl CoA mutase (MUT) is an essential enzyme in propionate catabolism that requires adenosylcobalamin as a cofactor. Almost 250 inherited mutations in the MUT gene are known to cause the devastating disorder methylmalonic aciduria; however the mechanism of dysfunction of these mutations more than half of which are missense changes has not been thoroughly investigated. Here we examined 23 patient missense mutations covering a spectrum of exonic/structural regions clinical phenotypes and ethnic populations in order to determine their influence on protein stability using two recombinant expression systems and a thermostability assay and enzymatic function by measuring MUT activity and affinity for its cofactor and substrate. Our data stratify MUT missense mutations into categories of biochemical defects including (1) reduced protein level due to misfolding (2) increased thermolability (3) impaired enzyme activity and (4) reduced cofactor response in substrate turnover. We further demonstrate the stabilization of wild type and thermolabile mutants by chemical chaperones in vitro and in bacterial cells. This in depth mutation study illustrates the tools available for MUT enzyme characterization guides future categorization of further missense mutations and supports the development of alternative chaperone based therapy for patients not responding to current treatment.

A major review paper part of the Tansley Review series which emerged out of the PAGES supported meeting "Climate Refugia: Joint Inference from Fossils Genetics and Models" held from the 1 3 August 2012 in Eugene Oregon USA. ABSTRACT: Climate refugia locations where taxa survive periods of regionally adverse climate are thought to be critical for maintaining biodiversity through the glacial interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia fossil records species distribution models and phylogeographic surveys in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths limitations and new advances for these three approaches. We provide case studies to illustrate their combined application and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech Qinghai spruce and Douglas fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance in particular by elucidating the fine scale processes and the particular geographic locations that buffer species against rapidly changing climate. © 2014 New Phytologist Trust.

Background When faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a small alpine mammal with limited dispersal capacity and low tolerance for thermal stress. As a result, pikas have become an important system for examining biotic responses to changing climatic conditions. Previous research using amplified fragment length polymorphisms (AFLPs) has revealed evidence for environmental-mediated selection in O. princeps populations distributed along elevation gradients, yet the anonymity of AFLP loci and lack of available genomic resources precluded the identification of associated gene regions. Here, we harnessed next-generation sequencing technology in order to characterize the American pika transcriptome and identify a large suite of single nucleotide polymorphisms (SNPs), which can be used to elucidate elevation- and site-specific patterns of sequence variation. Results We constructed pooled cDNA libraries of O. princeps from high (1400m) and low (300m) elevation sites along a previously established transect in British Columbia. Transcriptome sequencing using the Roche 454 GS FLX titanium platform generated 780 million base pairs of data, which were assembled into 7,325 high coverage contigs. These contigs were used to identify 24,261 novel SNP loci. Using high resolution melt analysis, we developed 17 of these SNPs into genotyping assays, which were validated with independent DNA samples from British Columbia Canada and Oregon State USA. In addition, we detected haplotypes in the NADH dehydrogenase subunit 5 of the mitochondrial genome that were fixed and different among elevations, suggesting that this may be an informative target gene for studying the role of cellular respiration in local adaptation. We also identified contigs that were unique to each elevation, including a high elevation-specific contig that was a positive match with the hemoglobin alpha chain from the plateau pika, a species restricted to high elevation steppes in Asia. Elevation-specific contigs may represent candidate regions subject to differential levels of gene expression along this elevation gradient. Conclusions To our knowledge, this is the first broad-scale, transcriptome-level study conducted within the Ochotonidae, providing novel genomic resources for studying pika ecology, behaviour and population history.

This work was supported by the U.S. Department of Energy and National Science Foundation; the Italian Istituto Nazionale di Fisica Nucleare; the Ministry of Education, Culture, Sports, Science and Technology of Japan; the Natural Sciences and Engineering Research Council of Canada; the National Science Council of the Republic of China; the Swiss National Science Foundation; the A. P. Sloan Foundation; the Bundesministerium für Bildung und Forschung, Germany; the Korean World Class University Program, the National Research Foundation of Korea; the Science and Technology Facilities Council and the Royal Society, United Kingdom; the Russian Foundation for Basic Research; the Ministerio de Ciencia e Innovación, and Programa Consolider-Ingenio 2010, Spain; the Slovak R&D Agency; the Academy of Finland; the Australian Research Council (ARC); and the EU community Marie Curie Fellowship Contract No. 302103. This work was also supported by the Shrum Foundation, the Weizman Institute of Science and the Israel Science Foundation. Results of a study of the substructure of the highest transverse momentum (pT) jets observed by the CDF Collaboration are presented. Events containing at least one jet with pT>400 GeV/c in a sample corresponding to an integrated luminosity of 5.95 fb−1, collected in 1.96 TeV proton-antiproton collisions at the Fermilab Tevatron collider, are selected. A study of the jet mass, angularity, and planar-flow distributions is presented, and the measurements are compared with predictions of perturbative quantum chromodynamics. A search for boosted top-quark production is also described, leading to a 95% confidence level upper limit of 38 fb on the production cross section of top quarks with pT>400 GeV/c. Peer Reviewed et al.

We have derived values of the Ultraviolet Index (UVI) at solar noon using the Tropospheric Ultraviolet Model (TUV) driven by ozone, temperature and aerosol fields from climate simulations of the first phase of the Chemistry-Climate Model Initiative (CCMI-1). Since clouds remain one of the largest uncertainties in climate projections, we simulated only the clear-sky UVI. We compared the modelled UVI climatologies against present-day climatological values of UVI derived from both satellite data (the OMI-Aura OMUVBd product) and ground-based measurements (from the NDACC network). Depending on the region, relative differences between the UVI obtained from CCMI/TUV calculations and the ground-based measurements ranged between −5.9% and 10.6%. We then calculated the UVI evolution throughout the 21st century for the four Representative Concentration Pathways (RCPs 2.6, 4.5, 6.0 and 8.5). Compared to 1960s values, we found an average increase in the UVI in 2100 (of 2–4%) in the tropical belt (30°N-30°S). For the mid-latitudes, we observed a 1.8 to 3.4 % increase in the Southern Hemisphere for RCP 2.6, 4.5 and 6.0, and found a 2.3% decrease in RCP 8.5. Higher increases in UVI are projected in the Northern Hemisphere except for RCP 8.5. At high latitudes, ozone recovery is well identified and induces a complete return of mean UVI levels to 1960 values for RCP 8.5 in the Southern Hemisphere. In the Northern Hemisphere, UVI levels in 2100 are higher by 0.5 to 5.5% for RCP 2.6, 4.5 and 6.0 and they are lower by 7.9% for RCP 8.5. We analysed the impacts of greenhouse gases (GHGs) and ozone-depleting substances (ODSs) on UVI from 1960 by comparing CCMI sensitivity simulations (1960–2100) with fixed GHGs or ODSs at their respective 1960 levels. As expected with ODS fixed at their 1960 levels, there is no large decrease in ozone levels and consequently no sudden increase in UVI levels. With fixed GHG, we observed a delayed return of ozone to 1960 values, with a corresponding pattern of change observed on UVI, and looking at the UVI difference between 2090s values and 1960s values, we found an 8 % increase in the tropical belt during the summer of each hemisphere. Finally we show that, while in the Southern Hemisphere the UVI is mainly driven by total ozone column, in the Northern Hemisphere both total ozone column and aerosol optical depth drive UVI levels, with aerosol optical depth having twice as much influence on the UVI as total ozone column does.

SummaryOpioid receptors (ORs) precisely modulate behavior when activated by native peptide ligands but distort behaviors to produce pathology when activated by non-peptide drugs. A fundamental question is how drugs differ from peptides in their actions on target neurons. One way that drugs can differ is by imposing selective effects on the conformational equilibrium of individual ORs. We wondered if drugs can also impose selective effects on the location of OR activation in individual OR-expressing neurons. Here we develop a genetically encoded biosensor that directly localizes ligand-induced activation and deactivation of ORs in living cells, and use it to generate the first real-time map of the spatiotemporal organization of μ‐ and δ-OR activation in neurons. Peptide agonists produce a characteristic activation pattern initiated in the plasma membrane and propagating to endosomes after receptor internalization. Drugs produce a different activation pattern by uniquely driving OR activation in the somatic Golgi apparatus and extending throughout the dendritic arbor in Golgi outposts. These results demonstrate a new approach to probe the cellular basis of neuromodulation and reveal that drugs profoundly distort the spatiotemporal landscape of neuronal OR activation.

Additional file 1. STable 1: Online follow-up survey questions.