Implementing a Process for Integration Research: Ecosystem Services Project, Australia

This paper reports on the design and implementation of a multi-phase interactive process among a set of scientists, policy makers, land managers, and community representatives, so as to facilitate communication, mutual understanding, and participative decision making. This was part of the Ecosystem Services Project in Australia. The project sought to broaden public understanding about the natural ecosystems in Australia. The study reported here pertains to one of the project sites--the Goulburn Broken catchment, a highly productive agricultural watershed in the south-east of Australia. The paper demonstrates how, starting from a condition of diversity of ideas and interests among the participants, systematic dialogue and mutual learning could be generated, leading to identification of options for more sustainable land management practices. The concept of "ecosystem services" was used as an integrative tool across disciplines and community perspectives. The concept of scenarios was used to encourage future-focussed thinking among the participants. The idea of "stakeholder jury" was used to promote deliberation. A process of multi-criteria evaluation was used to facilitate convergence of viewpoints, through informed trade-offs and compromises. This experience led to the development of a process for integration research, which helped in harmonising across diverse understandings and values in a transparent and structured manner

W-Curve Alignments for HIV-1 Genomic Comparisons

The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly.We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison.The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE.Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of aligning extremes of the curves to effectively phase-shift them past the HIV-1 gap problem, is presented. Besides yielding similar neighbor-joining phenogram topologies, most Mother and Infant C2-V5 sequences in the cohort pairs geometrically map closest to each other, indicating that W-curve heuristics overcame any gap problem

Solvent-Free Continuous Operations Using Small Footprint Reactors: A Key Approach for Process Intensification

A solvent-free approach to intensification of chemical processes is reported. This concept, in which reactions are carried out solvent-free, without the need for further downstream processing, was highlighted first with a full reduction of ethyl nicotinate to ethylpiperidine-3-carboxylate under continuous flow conditions. Using a small footprint reactor, a throughput of 26.4 g h–1 was achieved. Similarly, this approach was used for the telescoped two-step synthesis of 2-propyl phenol (productivity 120 g h–1) and 2-propyl cyclohexanone (productivity 30 g h–1), starting from the commercially available allyl phenol ether via Claisen rearrangement and subsequent reduction.We would like to thank Pfizer Worldwide Research & Development (CB), the EPSRC (RJM, SVL, Grant Codes EP/K009494/1, EP/M004120/1 and EP/K039520/1) and the Woolf Fisher Trust (DEF) for financial support.This is the final version of the article. It first appeared from the American Chemical Society via https://doi.org/10.1021/acssuschemeng.6b0028

Exploring Alternative Futures in the Anthropocene

Many challenges posed by the current Anthropocene epoch require fundamental transformations to humanity’s relationships with the rest of the planet. Achieving such transformations requires that humanity improve its understanding of the current situation and enhance its ability to imagine pathways toward alternative, preferable futures. We review advances in addressing these challenges that employ systematic and structured thinking about multiple possible futures (futures-thinking). Over seven decades, especially the past two, approaches to futures-thinking have helped people from diverse backgrounds reach a common understanding of important issues, underlying causes, and pathways toward optimistic futures. A recent focus has been the stimulation of imagination to produce new options. The roles of futures-thinking in breaking unhelpful social addictions and in conflict resolution are key emerging topics. We summarize cognitive, cultural, and institutional constraints on the societal uptake of futures-thinking, concluding that none are insurmountable once understood

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies

Measuring phenol oxidase and peroxidase activities with pyrogallol, l-DOPA, and ABTS: Effect of assay conditions and soil type

Microbial phenol oxidases and peroxidases mediate biogeochemical processes in soils, including microbial acquisition of carbon and nitrogen, lignin degradation, carbon mineralization and sequestration, and dissolved organic carbon export. Measuring oxidative enzyme activities in soils is more problematic than assaying hydrolytic enzyme activities because of the non-specific, free radical nature of the reactions and complex interactions between enzymes, assay substrates, and the soil matrix. We compared three substrates commonly used to assay phenol oxidase and peroxidase in soil: pyrogallol (PYGL, 1,2,3-trihydroxybenzene), l-DOPA (l-3,4-dihydroxyphenylalanine), and ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid). We measured substrate oxidation in three soils across a pH gradient from 3.0 to 10.0 to determine the pH optimum for each substrate. In addition, we compared activities across 17 soils using the three substrates. In general, activities on the substrates followed the trend PYGL>. l-DOPA>ABTS and were inversely related to substrate redox potential. PYGL and ABTS were not suitable substrates at pH>5, and ABTS oxidation often declined with addition of peroxide to the assay. Absolute and relative oxidation rates varied widely among substrates in relation to soil type and assay pH. We also tested whether autoclaved or combusted soils could be used as negative controls for the influence of abiotic factors (e.g., soil mineralogy) on oxidative activity. However, neither autoclaving nor combustion produced reliable negative controls because substrate oxidation still occurred; in some cases, these treatments enhanced substrate oxidation rates. For broad scale studies, we recommend that investigators use all three substrates to assess soil oxidation potentials. For focused studies, we recommend evaluating substrates before choosing a single option, and we recommend assays at both the soil pH and a reference pH (e.g., pH 5.0) to determine the effect of assay pH on oxidase activity. These recommendations should contribute to greater comparability of oxidase potential activities across studies. © 2013 Elsevier Ltd

Microbial enzymatic responses to drought and to nitrogen addition in a southern California grassland

Microbial enzymes play a fundamental role in ecosystem processes and nutrient mineralization. Therefore understanding enzyme responses to anthropogenic environmental change is important for predicting ecosystem function in the future. In a previous study, we used a reciprocal transplant design to examine the direct and indirect effects of drought and nitrogen (N) fertilization on litter decomposition in a southern California grassland. This work showed direct and indirect negative effects of drought on decomposition, and faster decomposition by N-adapted microbial communities in N-fertilized plots than in non-fertilized plots. Here we measured microbial biomass and the activities of nine extracellular enzymes to examine the microbial and enzymatic mechanisms underlying litter decomposition responses to drought and N. We hypothesized that changes in fungal biomass and potential extracellular enzyme activity (EEA) would relate directly to litter decomposition responses. We also predicted that fungal biomass would dominate the microbial community in our semi-arid study site. However, we found that the microbial community was dominated by bacterial biomass, and that bacteria responded negatively to drought treatment. In contrast to patterns in decomposition, fungal biomass and most potential EEA increased in direct response to drought treatment. Potential EEA was also decoupled from the decomposition response to N treatment. These results suggest that drought and N alter the efficiencies of EEA, defined as the mass of target substrate lost per unit potential EEA. Enzyme efficiencies declined with drought treatment, possibly because reduced water availability increased enzyme immobilization and reduced diffusion rates. In the N experiment, the efficiencies of β-glucosidase, β-xylosidase, and polyphenol oxidase were greater when microbes were transplanted into environments from which they originated. This increase in enzymatic efficiency suggests that microbial enzymes may adapt to their local environment. Overall, our results indicate that drought and N addition may have predictable impacts on the efficiencies of extracellular enzymes, providing a means of linking enzyme potentials with in-situ activities

One health, une seule santé

One Health, « Une seule santé », est une stratégie mondiale visant à développer les collaborations interdisciplinaires pour la santé humaine, animale et environnementale. Elle promeut une approche intégrée, systémique et unifiée de la santé aux échelles locale, nationale et mondiale, afin de mieux affronter les maladies émergentes à risque pandémique, mais aussi s'adapter aux impacts environnementaux présents et futurs. Bien que ce mouvement s’étende, la littérature en français reste rare. Traduit de l’anglais, coordonné par d’éminents épidémiologistes et s'appuyant sur un large panel d' approches scientifiques rarement réunies autour de la santé, cet ouvrage retrace les origines du concept et présente un contenu pratique sur les outils méthodologiques, la collecte de données, les techniques de surveillance et les plans d’étude. Il combine recherche et pratique en un seul volume et constitue un ouvrage de référence unique pour la santé mondiale

Improving Habitat Models and their Utility in Koala Conservation

Models of what makes good koala habitat are a key to developing effective conservation policy and practices. Koala habitat models are based on (1) ecological studies of high-density koala populations in limited areas, (2) physiological studies of koala nutrition and characteristics of food plants, and (3) surveys of koala geographic distribution and biophysical features of forests and woodlands. The role of models in koala conservation varies because legislators, decisionmakers, land managers, and citizens have different expectations and uses for models. Although current habitat models address many of these needs, overall they lack sufficient certainty and authority to resolve disputes and develop policy. Unpublished and inadequately peer-reviewed data and models add to misinterpretation and argument. Improvements are needed in the decision-making process to increase the constructive involvement of all interest groups and to focus on the koala conservation problem, thereby reducing use of the popular media and courts of law to achieve objectives

Coping with chemical complexity in mammal-plant interactions: near-infrared spectroscopy as a predictor of Eucalyptus foliar nutrients and of the feeding rates of folivorous marsupials

We investigated the utility of near-infrared reflectance spectroscopy (NIRS) as a means of rapidly assaying chemical constituents of Eucalyptus leaves and of directly predicting the intake of foliage from individual trees by greater gliders (Petauroides volans) and common ringtail possums (Pseudocheirus peregrinus). The concentrations of total nitrogen, neutral detergent fiber, condensed tannins and total phenolics could be predicted accurately by partial least squares regression models relating the near-infrared reflectance spectra of foliage samples to analyses performed using standard laboratory procedures. Coefficients of determination (r2) for all four constituents ranged between 0.88 and 0.98, and standard errors of prediction between 0.80 mg g-1 dry matter (DM) for total nitrogen and 5.14 quebracho equivalents g-1 DM for condensed tannins. Near-infrared spectral-based models of food intake had r2 values of 0.90 and 0.95 with a standard error of prediction of 3.4 and 8.3 g DM kg-0.75 day-1 for greater gliders and common ringtail possums respectively. We used the predictive model of food intake for greater gliders to examine the relationship between leaf palatability and documented food preferences of animals in the wild. Ranked differences in leaf palatability across four Eucalyptus species were consistent with documented food preferences of greater gliders in the wild. We conclude that NIRS provides a powerful tool to predict foraging behaviour of herbivores where forage choices are determined by compositional attributes of food