A decision-support tool to facilitate discussion of no-take boundaries for Marine Protected Areas during stakeholder consultation processes

Marine Protected Areas (MPAs) are proposed to help conserve marine biodiversity and ecological integrity. There is much guidance on the optimal design of MPAs but once potential MPAs are identified there is little guidance on defining the final no-take boundaries. This is especially problematic in temperate zones where ecological boundaries are “fuzzy”, which can be quite complicated during a consultation process involving the government and divergent stakeholder groups. More decision-support tools are needed to help stakeholders and government agencies objectively compare conservation and socio-economic trade-offs among proposed boundary options. To that end, we developed a method to identify which boundary minimizes spatial overlap of highly vulnerable species and a dominant stressor. We used the recently proposed boundary options of a candidate MPA in Atlantic Canada to illustrate our method. We evaluated the vulnerability of 23 key species to bottom trawling, the most prevalent stressor in the area. We then compared the spatial overlap of the most vulnerable species and the 2002–2011 footprint of bottom trawling among boundary options. The best boundary option was identified as that which minimized spatial overlap and total area. This approach identifies boundary options which provide the greatest protection of vulnerable species from their most significant stressor, at limited socio-economic cost. It is an objective decision-support tool to help stakeholders agree on final boundaries for MPAs.     

Phagosome proteomics: a powerful tool to assess bacteria-mediated immunomodulation

Bacteria-mediated immunomodulation has important implications in microbial infection and bacterial vaccines. Intraphagosomal bacteria negotiate survival niches with the intracellular environment by modulating the phagosome composition during invasion. The final phagosome composition determines the fate of the intraphagosomal bacterium or the efficacy of a bacterial vaccine. Therefore, the phagosome proteome is a valuable readout to assess the ability of a natural or genetically engineered bacterial strain to modulate the host immune response. Compared to a preparation of latex-bead-containing phagosomes, the preparation of bacterial phagosomes requires additional measures to ensure comparable purity due to their closer density to some other organelles. This bottleneck can be overcome with delicate preparation protocols, proper experimental designs to facilitate bioinformatics based discrimination against contaminating proteins, and the incorporation of stable-isotope labeled internal standards to correct for contaminating fractions of phagosomal proteins. The rapid progress in the proteomics and bioinformatics fields provides an array of techniques that promise to bring about an unprecedented coverage of both known and as yet undiscovered immunomodulation pathways within bacterial phagosome proteomes. A precise portrait of the bacteria-mediated immunomodulation pathways in phagosomes will likely aid in the intelligent design of bioengineered bacterial vaccine strains for important future biomedical applications.     

Decision-support tool for assessing biomanufacturing strategies under uncertainty: stainless steel versus disposable equipment for clinical trial material preparation

This paper presents the application of a decision-support tool, SIMBIOPHARMA, for assessing different manufacturing strategies under uncertainty for the production of biopharmaceuticals. SIMBIOPHARMA captures both the technical and business aspects of biopharmaceutical manufacture within a single tool that permits manufacturing alternatives to be evaluated in terms of cost, time, yield, project throughput, resource utilization, and risk. Its use for risk analysis is demonstrated through a hypothetical case study that uses the Monte Carlo simulation technique to imitate the randomness inherent in manufacturing subject to technical and market uncertainties. The case study addresses whether start-up companies should invest in a stainless steel pilot plant or use disposable equipment for the production of early phase clinical trial material. The effects of fluctuating product demands and titers on the performance of a biopharmaceutical company manufacturing clinical trial material are analyzed. The analysis highlights the impact of different manufacturing options on the range in possible outcomes for the project throughput and cost of goods and the likelihood that these metrics exceed a critical threshold. The simulation studies highlight the benefits of incorporating uncertainties when evaluating manufacturing strategies. Methods of presenting and analyzing information generated by the simulations are suggested. These are used to help determine the ranking of alternatives under different scenarios. The example illustrates the benefits to companies of using such a tool to improve management of their R&D portfolios so as to control the cost of goods.     

Development and application of a tool to assess laboratory hygiene in contained-use facilities

To gain information on laboratory hygiene in contained-use laboratories, a method was developed to study the presence of microorganisms on laboratory equipment. Focusing detection on genetically modified organisms (GMOs) containing the universal M13 primer binding sites enabled the detection of a broad range of GMOs using a single PCR. Swabbing surfaces in three different contained-use laboratories led to detection of M13-containing PCR products in 26 out of 34 swabs. Most sequences (up to five per sample) were detected in swabs from the centrifuge and sink, followed by swabs taken from the bin and incubator (up to four sequences per sample). The obtained sequences varied in length from 171 nucleotides (nt) to 878 nt. In most cases, sequences were only partially similar to sequences published in GenBank. The lengths of the regions with high similarity varied from 94 nt to 795 nt, and these similarities ranged from 81% to 100%. Similarities with more than one sequence were commonly found, complicating the identification of detected sequences. Nonetheless, 84% of the detected sequences were actually handled in the laboratory at the time of sampling. This demonstrates that the method may be used as a quality control tool to assess the efficacy of decontamination and cleaning of commonly used surfaces, such as laboratory benches, freezer doors, and centrifuge rotors, without prior knowledge of the identity or characteristics of the GMOs.     

Efficient strategies to assess yield stability in winter wheat

Key message

Selecting contrasting environments allows decreasing phenotyping intensity but still maintaining high accuracy to assess yield stability.

Abstract

Improving yield stability of wheat varieties is important to cope with enhanced abiotic stresses caused by climate change. The objective of our study was to (1) develop and implement an improved heritability estimate to examine the required scale of phenotyping for assessing yield stability in wheat, (2) compare yield performance and yield stability of wheat hybrids and inbred lines, (3) investigate the association of agronomic traits with yield stability, and (4) explore the possibility of selecting subsets of environments allowing to portray large proportion of the variation of yield stability. Our study is based on phenotypic data from five series of official winter wheat registration trials in Germany each including 119–132 genotypes evaluated in up to 50 environments. Our findings suggested that phenotyping in at least 40 environments is required to reliably estimate yield stability to guarantee heritability estimates above 0.7. Contrasting the yield stability of hybrids versus lines revealed no significant differences. Absence of stable associations between yield stability and further agronomic traits suggested low potential of indirect selection to improve yield stability. Selecting posteriori contrasting environments based on the genotype-by-environment interaction effects allowed decreasing phenotyping intensity, but still maintaining high accuracy to assess yield stability. The huge potential of the developed strategy to select contrasting and informative environments has to be validated as a next step in an a priori scenario based on genotype-by-location interaction effects.

     

External validation of a measurement tool to assess systematic reviews (AMSTAR)

Background

Thousands of systematic reviews have been conducted in all areas of health care. However, the methodological quality of these reviews is variable and should routinely be appraised. AMSTAR is a measurement tool to assess systematic reviews.

Methodology

AMSTAR was used to appraise 42 reviews focusing on therapies to treat gastro-esophageal reflux disease, peptic ulcer disease, and other acid-related diseases. Two assessors applied the AMSTAR to each review. Two other assessors, plus a clinician and/or methodologist applied a global assessment to each review independently.

Conclusions

The sample of 42 reviews covered a wide range of methodological quality. The overall scores on AMSTAR ranged from 0 to 10 (out of a maximum of 11) with a mean of 4.6 (95% CI: 3.7 to 5.6) and median 4.0 (range 2.0 to 6.0). The inter-observer agreement of the individual items ranged from moderate to almost perfect agreement. Nine items scored a kappa of >0.75 (95% CI: 0.55 to 0.96). The reliability of the total AMSTAR score was excellent: kappa 0.84 (95% CI: 0.67 to 1.00) and Pearson''s R 0.96 (95% CI: 0.92 to 0.98). The overall scores for the global assessment ranged from 2 to 7 (out of a maximum score of 7) with a mean of 4.43 (95% CI: 3.6 to 5.3) and median 4.0 (range 2.25 to 5.75). The agreement was lower with a kappa of 0.63 (95% CI: 0.40 to 0.88). Construct validity was shown by AMSTAR convergence with the results of the global assessment: Pearson''s R 0.72 (95% CI: 0.53 to 0.84). For the AMSTAR total score, the limits of agreement were −0.19±1.38. This translates to a minimum detectable difference between reviews of 0.64 ‘AMSTAR points’. Further validation of AMSTAR is needed to assess its validity, reliability and perceived utility by appraisers and end users of reviews across a broader range of systematic reviews.     

Sorting and pooling strategy: a novel tool to map a virus proteome for CD8 T-cell epitopes

Human cytomegalovirus (CMV) is a major cause of morbidity in immunocompromised individuals. However, no efficient vaccine has been developed to date. Identification of T-cell target proteins and epitopes is crucial not only for developing a successful immunization strategy, but also for new approaches using adoptive transfer of antigen-specific T-cells. The CMV genome has more than 200 open reading frames potentially coding for as many proteins. Here, we describe a robust, fast, and simple SPOT synthesis strategy, which allowed us to micro-synthesize every possible CD8 T-cell epitope in the entire potential CMV proteome. So far, 9069 of these peptides have been tested in an ex vivo T-cell stimulation assay. As well as confirming a number of previously known epitopes, we identified several new ones.     

Leaf manganese concentrations as a tool to assess belowground plant functioning in phosphorus-impoverished environments

Plant and Soil - Root-released carboxylates enhance the availability of manganese (Mn), which enters roots through transporters with low substrate specificity. Leaf Mn concentration ([Mn]) has been...     

The use of bootstrap resampling to assess the uncertainty of cooper statistics

The predictive abilities of two-group classification models (CMs) are often expressed in terms of their Cooper statistics. These statistics are often reported without any indication of their uncertainty, making it impossible to judge whether the predicted classifications are significantly better than the predictions made by a different CM, or whether the predictive performance of the CM exceeds predefined performance criteria in a statistically significant way. Bootstrap resampling routines are reported that provide a means of expressing the uncertainty associated with Cooper statistics. The usefulness of the bootstrapping routines is illustrated by constructing 95% confidence intervals for the Cooper statistics of four alternative skin-corrosivity tests (the rat skin transcutaneous electrical resistance assay, EPISKIN, Skin(2) and CORROSITEX), and four two-step sequences in which each in vitro test is used in combination with a physicochemical test for skin corrosion based on pH measurements.     

Testate amoebae community analysis as a tool to assess biological impacts of peatland use

As most ecosystems, peatlands have been heavily exploited for different human purposes. For example, in Finland the majority is under forestry, agriculture or peat mining use. Peatlands play an important role in carbon storage, water cycle, and are a unique habitat for rare organisms. Such properties highlight their environmental importance and the need for their restoration. To monitor the success of peatland restoration sensitive indicators are needed. Here we test whether testate amoebae can be used as a reliable bioindicator for assessing peatland condition. To qualify as reliable indicators, responses in testate amoebae community structure to ecological changes must be stronger than random spatial and temporal variation. In this study, we simultaneously assessed differences between the effects of seasonality, intermediate scale spatial variation and land uses on living testate amoebae assemblages in natural, forested and restored peatlands. We expected the effects of seasonality on testate amoebae communities to be less pronounced than those of land use and within site variation. On average, natural sites harboured the highest richness and density, while the lowest numbers were found at forestry sites. Despite small changes observed in taxa dominance and differences in TA community structure between seasons and years at some sites, spatial heterogeneity, temperature, pH, nor water table depth seemed to significantly affect testate amoebae communities. Instead, observed differences were related to type of land use, which explained 75% of the community variation. Our results showed that testate amoebae community monitoring is a useful tool to evaluate impacts of human land use on boreal peatlands.     

Fish early life stage tests as a tool to assess embryotoxic potentials in small streams

Early life stage (ELS) studies with brown trout(Salmo trutta f. fario L.) andstone loach (Barbatula barbatula L.)were performed between 1995 and 2000 toevaluate embryotoxic potentials in twodifferently polluted streams in southwestGermany. With both species, semistatic exposureexperiments with water samples and sedimenteluates were conducted in the laboratory.Additionally, brown trout ELS tests wereperformed in flow-through systems in thesemi-field and in the field. Thus, differentlevels of complexity of environmentalconditions were addressed which allowed thestudy of effects of xenobiotic contamination,temperature, and sediments on the success ofembryonic development. Additionally, effects ofwater from the polluted stream on fertilizationof brown trout eggs were determined. In themore polluted stream, xenobiotics caused anembryotoxic potential for both brown trout andstone loach, and viability of exposed browntrout eggs was drastically reduced by suspendedsolids in the water which covered the eggs.Additionally, fertilization rates of browntrout eggs were significantly decreased inwater of the more polluted stream. In the lesspolluted stream, low water temperature andinfestations by protozoic ectoparasites causedmortality of embryos. In this stream, pollutionand sediment effects were not observed. Resultsmade evident that in the more polluted streamrecruitment of brown trout was drasticallyimpaired.     

Characteristics of Poaceae pollen grains as a tool to assess palaeoecological grassland dynamics in South America

Despite the dominance of grasslands during the last glacial period, especially in South America, the highly uniform morphology of Poaceae pollen grains has so far allowed only very few palynological studies based on Poaceae pollen. In our study we compare two methods of distinguishing between South American grassland ecosystems based on quantitative morphology of Poaceae pollen grains. We investigated data sets from Páramo in southern Ecuador, Campos de Altitude and Campos in south-eastern and southern Brazil as well as data sets from the Pampa in Argentina by measuring the pollen grain length, grain width, pore diameter and annulus width. Firstly we investigated the potential influence of chemical treatment of pollen grains on pollen grain size as well as the measurement setting for defining the boundary conditions for using Poaceae pollen grains in a palaeoecological investigation. Finally the measured pollen grain parameters were analyzed by comparison of average grain length using statistical tests. This approach reveals highly significant differences in average grain size between all grassland ecosystems. Assuming that a certain grain size range can be assigned to a certain Poaceae taxon, conclusions about differences and similarities in taxa composition can be derived. We used two methods of multivariate data analysis. One uses the pollen grain parameters directly for a Principle Component Analysis (PCA). The other is an already established method in grassland ecology which defines parameter based pollen grain types to investigate similarities between grassland ecosystems. Both approaches confirm the results of the grain length analysis. In this work we demonstrate that the method we developed has the potential to provide acquisition of so far inaccessible information on spatial and temporal patterns and dynamics of South American grasslands.     

Anther culture as a breeding tool in rape

Summary Progeny analysis of androgenetic plants from inbred rape-seed (Brassica napus) shows that selective growth of microspores can occur in cultured anthers. The property of privileged growth in culture seems to be linked to such characters as flowering time and seed glucosinolate content which can be analyzed in regenerated plants. This type of selection and the fact that more variability is visible in regenerants from different microspores than in the progeny of the highly inbred anther donor line, demonstrates the higher degree of homozygosity in the doubled amphihaploids of B. napus. Furthermore, it is shown that haploid genomes of rape may be mutable. Thus it is possible to obtain several different homozygous lines from a single microspore. A system of haploid embryoids arising from single cells of the primary microspore regenerant has also been used to produce experimentally induced mutants. It is demonstrated that recessive mutations can be obtained in a homozygous state in doubled haploid regenerants from mutagenized haploid single cells.Part of the material analyzed in this work was produced under the guidance of Emrys Thomas when he was one of the project leaders of the Projektgruppen Haploide in der Pflanzenzüchtung at the Max-Planck-Institut für Pflanzengenetik in Ladenburg. His untimely death at the age of 36 (May 23, 1981), which overtook him at his new place of work at Harpenden, prevented him seeing the completion of this paper. It is dedicated to the memory of this distinguished and restless researcher and highly-valued colleague     

Use of lactate dehydrogenase release to assess changes in culture viability

This study reports the use of lactate dehydrogenase release to monitor changes in culture viability in flask culture and fixed bed, porosphere bioreactor systems. Lactate dehydrogenase release shows good agreement with increase in non-viable cell numbers and decline in glucose utilisation in flask cultures. Studies with the immobilised system show that lactate dehydrogenase release can detect loss of viability which is not always indicated by a decrease in glucose utilisation. The data show that culture viability in a repeated-feed-and-harvest system is influenced markedly by both a) the medium change regime itself and b) the use of an immobilised bioreactor compared to a flask system for the same medium change regime.     

A decision-support tool to predict spray deposition of insecticides in commercial potato fields and its implications for their performance

Approximately US $1.3 billion is spent each year on insecticide applications in major row crops. Despite this significant economic importance, there are currently no widely established decision-support tools available to assess suitability of spray application conditions or of the predicted quality or performance of a given commercial insecticide applications. We conducted a field study, involving 14 commercial spray applications with either fixed wing airplane (N=8) or ground rig (N=6), and we used environmental variables as regression fits to obtained spray deposition (coverage in percentage). We showed that (1) ground rig applications provided higher spray deposition than aerial applications, (2) spray deposition was lowest in the bottom portion of the canopy, (3) increase in plant height reduced spray deposition, (4) wind speed increased spray deposition, and (5) higher ambient temperatures and dew point increased spray deposition. Potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae), mortality increased asymptotically to approximately 60% in response to abamectin spray depositions exceeding around 20%, whereas mortality of psyllid adults reached an asymptotic response approximately 40% when lambda-cyhalothrin/thiamethoxam spray deposition exceeded 30%. A spray deposition support tool was developed (http://pilcc.tamu.edu/) that may be used to make decisions regarding (1) when is the best time of day to conduct spray applications and (2) selecting which insecticide to spray based on expected spray deposition. The main conclusion from this analysis is that optimization of insecticide spray deposition should be considered a fundamental pillar of successful integrated pest management programs to increase efficiency of sprays (and therefore reduce production costs) and to reduce risk of resistance development in target pest populations.     

Ecological indicators based on trophic spectrum as a tool to assess ecosystems fishing impacts

Trophic indicators were used to compare two Malian freshwater reservoirs whose main differences are based on their different fishing pressures. Data were collected from a scientific survey of small-scale fishery landings conducted in 2002/2003. The trophic levels of fish species caught by artisanal fisheries are estimated from observations of scientific fishing or from the metabase Fishbase. Important differences exist in the trophic structure of both reservoirs. In Selingue (with high fishing pressure), very few top predators are found in the catches while the low trophic level fishes increase in total catches. In Manantali (with low fishing pressure), the top predators contribute twice as much to catches compared to Selingue. Hence, the mean trophic level of catches in Selingue (2.80) is lower than in Manantali (2.97). When comparing these results with those of study made in 1994/1995, it clearly appears that the effects of the fishing pressure in Selingue are obvious through a decrease of 0.12 in the mean trophic level while in Manantali this mean level has increased by 0.33 due to a recent strategic targeting of top predators. Trophic spectra seem to be relevant tools to characterize exploited fish communities from multi-specific and multi-gear small-scale fisheries catch data.