Showing papers by "Wageningen University and Research Centre published in 2009"
Stockholm University1, Stockholm Environment Institute2, Australian National University3, University of Alaska Fairbanks4, Université catholique de Louvain5, University of East Anglia6, Wageningen University and Research Centre7, Royal Swedish Academy of Sciences8, University of Oxford9, Potsdam Institute for Climate Impact Research10, James Cook University11, Arizona State University12, Royal Institute of Technology13, University of Minnesota14, University of Vermont15, Stockholm International Water Institute16, California State University San Marcos17, Goddard Institute for Space Studies18, Commonwealth Scientific and Industrial Research Organisation19, University of Arizona20, Max Planck Society21
TL;DR: Identifying and quantifying planetary boundaries that must not be transgressed could help prevent human activities from causing unacceptable environmental change, argue Johan Rockstrom and colleagues.
Abstract: Identifying and quantifying planetary boundaries that must not be transgressed could help prevent human activities from causing unacceptable environmental change, argue Johan Rockstrom and colleagues.
8,837 citations
Stockholm Environment Institute1, Stockholm University2, Australian National University3, University of Alaska Fairbanks4, Université catholique de Louvain5, University of East Anglia6, Wageningen University and Research Centre7, Royal Swedish Academy of Sciences8, Potsdam Institute for Climate Impact Research9, University of Oxford10, James Cook University11, Arizona State University12, Royal Institute of Technology13, University of Minnesota14, University of Vermont15, Stockholm International Water Institute16, California State University San Marcos17, Goddard Institute for Space Studies18, Commonwealth Scientific and Industrial Research Organisation19, University of Arizona20, University of Copenhagen21, Max Planck Society22
TL;DR: In this article, the authors proposed a new approach to global sustainability in which they define planetary boundaries within which they expect that humanity can operate safely. But the proposed concept of "planetary boundaries" lays the groundwork for shifting our approach to governance and management, away from the essentially sectoral analyses of limits to growth aimed at minimizing negative externalities, toward the estimation of the safe space for human development.
Abstract: Anthropogenic pressures on the Earth System have reached a scale where abrupt global environmental change can no longer be excluded. We propose a new approach to global sustainability in which we define planetary boundaries within which we expect that humanity can operate safely. Transgressing one or more planetary boundaries may be deleterious or even catastrophic due to the risk of crossing thresholds that will trigger non-linear, abrupt environmental change within continental- to planetary-scale systems. We have identified nine planetary boundaries and, drawing upon current scientific understanding, we propose quantifications for seven of them. These seven are climate change (CO2 concentration in the atmosphere <350 ppm and/or a maximum change of +1 W m-2 in radiative forcing); ocean acidification (mean surface seawater saturation state with respect to aragonite ≥ 80% of pre-industrial levels); stratospheric ozone (<5% reduction in O3 concentration from pre-industrial level of 290 Dobson Units); biogeochemical nitrogen (N) cycle (limit industrial and agricultural fixation of N2 to 35 Tg N yr-1) and phosphorus (P) cycle (annual P inflow to oceans not to exceed 10 times the natural background weathering of P); global freshwater use (<4000 km3 yr-1 of consumptive use of runoff resources); land system change (<15% of the ice-free land surface under cropland); and the rate at which biological diversity is lost (annual rate of <10 extinctions per million species). The two additional planetary boundaries for which we have not yet been able to determine a boundary level are chemical pollution and atmospheric aerosol loading. We estimate that humanity has already transgressed three planetary boundaries: for climate change, rate of biodiversity loss, and changes to the global nitrogen cycle. Planetary boundaries are interdependent, because transgressing one may both shift the position of other boundaries or cause them to be transgressed. The social impacts of transgressing boundaries will be a function of the social-ecological resilience of the affected societies. Our proposed boundaries are rough, first estimates only, surrounded by large uncertainties and knowledge gaps. Filling these gaps will require major advancements in Earth System and resilience science. The proposed concept of "planetary boundaries" lays the groundwork for shifting our approach to governance and management, away from the essentially sectoral analyses of limits to growth aimed at minimizing negative externalities, toward the estimation of the safe space for human development. Planetary boundaries define, as it were, the boundaries of the "planetary playing field" for humanity if we want to be sure of avoiding major human-induced environmental change on a global scale.
4,771 citations
TL;DR: Steam pretreatment, lime pret treatment, liquid hot water pretreatments and ammonia based Pretreatments are concluded to be pretreatment with high potentials, providing an improved accessibility of the cellulose for hydrolytic enzymes.
3,618 citations
TL;DR: Work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.
Abstract: Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.
3,450 citations
TL;DR: Responses constructed from experiments under controlled conditions showed that LMA varied strongly with light, temperature and submergence, moderately with CO2 concentration and nutrient and water stress, and marginally under most other conditions.
Abstract: Here, we analysed a wide range of literature data on the leaf dry mass per unit area (LMA). In nature, LMA varies more than 100-fold among species. Part of this variation (c. 35%) can be ascribed to differences between functional groups, with evergreen species having the highest LMA, but most of the variation is within groups or biomes. When grown in the same controlled environment, leaf succulents and woody evergreen, perennial or slow-growing species have inherently high LMA. Within most of the functional groups studied, high-LMA species show higher leaf tissue densities. However, differences between evergreen and deciduous species result from larger volumes per area (thickness). Response curves constructed from experiments under controlled conditions showed that LMA varied strongly with light, temperature and submergence, moderately with CO2 concentration and nutrient and water stress, and marginally under most other conditions. Functional groups differed in the plasticity of LMA to these gradients. The physiological regulation is still unclear, but the consequences of variation in LMA and the suite of traits interconnected with it are strong. This trait complex is an important factor determining the fitness of species in their environment and affects various ecosystem processes.
2,046 citations
TL;DR: This review focuses on the population dynamics and activity of soilborne pathogens and beneficial microorganisms, and mechanisms involved in the tripartite interactions between beneficialmicroorganisms, pathogens and the plant.
Abstract: The rhizosphere is a hot spot of microbial interactions as exudates released by plant roots are a main food source for microorganisms and a driving force of their population density and activities. The rhizosphere harbors many organisms that have a neutral effect on the plant, but also attracts organisms that exert deleterious or beneficial effects on the plant. Microorganisms that adversely affect plant growth and health are the pathogenic fungi, oomycetes, bacteria and nematodes. Most of the soilborne pathogens are adapted to grow and survive in the bulk soil, but the rhizosphere is the playground and infection court where the pathogen establishes a parasitic relationship with the plant. The rhizosphere is also a battlefield where the complex rhizosphere community, both microflora and microfauna, interact with pathogens and influence the outcome of pathogen infection. A wide range of microorganisms are beneficial to the plant and include nitrogen-fixing bacteria, endo- and ectomycorrhizal fungi, and plant growth-promoting bacteria and fungi. This review focuses on the population dynamics and activity of soilborne pathogens and beneficial microorganisms. Specific attention is given to mechanisms involved in the tripartite interactions between beneficial microorganisms, pathogens and the plant. We also discuss how agricultural practices affect pathogen and antagonist populations and how these practices can be adopted to promote plant growth and health.
1,370 citations
TL;DR: Conservation agriculture is claimed to be a panacea for the problems of poor agricultural productivity and soil degradation in sub-Saharan Africa (SSA). It is actively promoted by international research and development organisations, with such strong advocacy that critical debate is stifled as mentioned in this paper.
1,349 citations
Broad Institute1, Sainsbury Laboratory2, Ohio Agricultural Research and Development Center3, Uppsala University4, Wageningen University and Research Centre5, Virginia Bioinformatics Institute6, University of California, Riverside7, University of Aberdeen8, Scottish Crop Research Institute9, University of Warwick10, Agricultural Research Service11, Royal Institute of Technology12, Cornell University13, Oregon State University14, Lafayette College15, University of Glasgow16, Harvard University17, Delaware Biotechnology Institute18, North Carolina State University19, University of Delaware20, University of Tennessee21, University of Maryland, Baltimore22, Vanderbilt University23, College of Wooster24, Bowling Green State University25, Edinburgh Cancer Research Centre26, J. Craig Venter Institute27, Tel Aviv University28, University of Wisconsin-Madison29, University of Hohenheim30, University of Dundee31
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
1,341 citations
TL;DR: The potentials and limitations of analysis with lateral flow (immuno)assays are illustrated using a literature survey and a SWOT analysis (acronym for “strengths, weaknesses, opportunities, threats”).
Abstract: Lateral flow (immuno)assays are currently used for qualitative, semiquantitative and to some extent quantitative monitoring in resource-poor or non-laboratory environments. Applications include tests on pathogens, drugs, hormones and metabolites in biomedical, phytosanitary, veterinary, feed/food and environmental settings. We describe principles of current formats, applications, limitations and perspectives for quantitative monitoring. We illustrate the potentials and limitations of analysis with lateral flow (immuno)assays using a literature survey and a SWOT analysis (acronym for “strengths, weaknesses, opportunities, threats”). Articles referred to in this survey were searched for on MEDLINE, Scopus and in references of reviewed papers. Search terms included “immunochromatography”, “sol particle immunoassay”, “lateral flow immunoassay” and “dipstick assay”.
1,296 citations
University of Southern Denmark1, University of Minnesota2, Beijing Normal University3, China Agricultural University4, Boyce Thompson Institute for Plant Research5, University of Wisconsin-Madison6, Wageningen University and Research Centre7, Chinese Academy of Sciences8, Renmin University of China9, Gyeongsang National University10, Aarhus University11, University of Copenhagen12, South China University of Technology13
TL;DR: This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.
Abstract: Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.
1,289 citations
TL;DR: Analysis of literature data enabled the identification of the most important operational parameters leading to N(2)O emission in WWTPs: (i) low dissolved oxygen concentration in the nitrification and denitrification stages, (ii) increased nitrite concentrations in both nitrified stages, and (iii) low COD/N ratio in theDenitrification stage.
TL;DR: The transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities is reviewed and the process of reverse electron transfer is described, which is a key requirement in obligately syntrophic interactions.
Abstract: Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.
TL;DR: This paper provides an overview of the ecological status of agricultural systems across the European Union in the light of recent policy changes, and builds on the previous review of 2001 devoted to the impacts of agricultural intensification in Western Europe.
University of Leeds1, University of Yaoundé I2, Forestry Commission3, University of Agriculture, Faisalabad4, Smithsonian Institution5, Mbarara University of Science and Technology6, Wageningen University and Research Centre7, Salisbury University8, Wildlife Conservation Society9, University of York10, Environmental Change Institute11, University of Dar es Salaam12, University of Aberdeen13, University College Dublin14, University of Toronto15
TL;DR: Taxon-specific analyses of African inventory and other data suggest that widespread changes in resource availability, such as increasing atmospheric carbon dioxide concentrations, may be the cause of the increase in carbon stocks, as some theory and models predict.
Abstract: The response of terrestrial vegetation to a globally changing environment is central to predictions of future levels of atmospheric carbon dioxide. The role of tropical forests is critical because they are carbon-dense and highly productive. Inventory plots across Amazonia show that old-growth forests have increased in carbon storage over recent decades, but the response of one-third of the world's tropical forests in Africa is largely unknown owing to an absence of spatially extensive observation networks. Here we report data from a ten-country network of long-term monitoring plots in African tropical forests. We find that across 79 plots (163 ha) above-ground carbon storage in live trees increased by 0.63 Mg C ha(-1) yr(-1) between 1968 and 2007 (95% confidence interval (CI), 0.22-0.94; mean interval, 1987-96). Extrapolation to unmeasured forest components (live roots, small trees, necromass) and scaling to the continent implies a total increase in carbon storage in African tropical forest trees of 0.34 Pg C yr(-1) (CI, 0.15-0.43). These reported changes in carbon storage are similar to those reported for Amazonian forests per unit area, providing evidence that increasing carbon storage in old-growth forests is a pan-tropical phenomenon. Indeed, combining all standardized inventory data from this study and from tropical America and Asia together yields a comparable figure of 0.49 Mg C ha(-1) yr(-1) (n = 156; 562 ha; CI, 0.29-0.66; mean interval, 1987-97). This indicates a carbon sink of 1.3 Pg C yr(-1) (CI, 0.8-1.6) across all tropical forests during recent decades. Taxon-specific analyses of African inventory and other data suggest that widespread changes in resource availability, such as increasing atmospheric carbon dioxide concentrations, may be the cause of the increase in carbon stocks, as some theory and models predict.
TL;DR: Pectin or pectic substances are collective names for a group of closely associated polysaccharides present in plant cell walls where they contribute to complex physiological processes like cell growth and cell differentiation and so determine the integrity and rigidity of plant tissue as mentioned in this paper.
Abstract: Pectin or pectic substances are collective names for a group of closely associated polysaccharides present in plant cell walls where they contribute to complex physiological processes like cell growth and cell differentiation and so determine the integrity and rigidity of plant tissue. They also play an important role in the defence mechanisms against plant pathogens and wounding. As constituents of plant cell walls and due to their anionic nature, pectic polysaccharides are considered to be involved in the regulation of ion transport, the porosity of the walls and in this way in the control of the permeability of the walls for enzymes. They also determine the water holding capacity. The amount and composition of pectic molecules in fruits and vegetables and other plant produce strongly determine quality parameters of fresh and processed food products. Pectin is also extracted from suitable agro-by-products like citrus peel and apple pomace and used in the food industry as natural ingredients for their gelling, thickening, and stabilizing properties. Some pectins gain more and more interest for their health modulating activities. Endogenous as well as exogenous enzymes play an important role in determining the pectic structures present in plant tissue, food products, or ingredients at a given time. In this paper functional and structural characteristics of pectin are described with special emphasis on the structural elements making up the pectin molecule, their interconnections and present models which envisage the accommodation of all structural elements in a macromolecule. Attention is also given to analytical methods to study the pectin structure including the use of enzymes as analytical tools.
TL;DR: Even though glucosinolates are constitutive defenses, their levels are influenced by abiotic and biotic factors including insect damage.
Abstract: Glucosinolates present classical examples of plant compounds affecting insect-plant interactions. They are found mainly in the family Brassicaceae, which includes several important crops. More than 120 different glucosinolates are known. The enzyme myrosinase, which is stored in specialized plant cells, converts glucosinolates to the toxic isothiocyanates. Insect herbivores may reduce the toxicity of glucosinolates and their products by excretion, detoxification, or behavioral adaptations. Glucosinolates also affect higher trophic levels, via reduced host or prey quality or because specialist herbivores may sequester glucosinolates for their own defense. There is substantial quantitative and qualitative variation between plant genotypes, tissues, and ontogenetic stages, which poses specific challenges to insect herbivores. Even though glucosinolates are constitutive defenses, their levels are influenced by abiotic and biotic factors including insect damage. Plant breeders may use knowledge on glucosinolates to increase insect resistance in Brassica crops. State-of-the-art techniques, such as mutant analysis and metabolomics, are necessary to identify the exact role of glucosinolates.
TL;DR: Variation observed among fungal effectors shows two types of selection that appear to relate to whether they interact directly or indirectly with their cognate resistance proteins, which seem to favor point mutations in effector genes and amino acid substitutions.
Abstract: It is accepted that most fungal avirulence genes encode virulence factors that are called effectors. Most fungal effectors are secreted, cysteine-rich proteins, and a role in virulence has been shown for a few of them, including Avr2 and Avr4 of Cladosporium fulvum, which inhibit plant cysteine proteases and protect chitin in fungal cell walls against plant chitinases, respectively. In resistant plants, effectors are directly or indirectly recognized by cognate resistance proteins that reside either inside the plant cell or on plasma membranes. Several secreted effectors function inside the host cell, but the uptake mechanism is not yet known. Variation observed among fungal effectors shows two types of selection that appear to relate to whether they interact directly or indirectly with their cognate resistance proteins. Direct interactions seem to favor point mutations in effector genes, leading to amino acid substitutions, whereas indirect interactions seem to favor jettison of effector genes.
TL;DR: This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out, and correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings.
Abstract: Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. Highthroughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genuslevel with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult.
TL;DR: The results indicate that conservation benefits are disproportionally more costly on high-intensity than on low-intensity farmland, and conservation initiatives are most (cost-)effective if they are preferentially implemented in extensively farmed areas that still support high levels of biodiversity.
Abstract: Worldwide agriculture is one of the main drivers of biodiversity decline. Effective conservation strategies depend on the type of relationship between biodiversity and land-use intensity, but to date the shape of this relationship is unknown. We linked plant species richness with nitrogen (N) input as an indicator of land-use intensity on 130 grasslands and 141 arable fields in six European countries. Using Poisson regression, we found that plant species richness was significantly negatively related to N input on both field types after the effects of confounding environmental factors had been accounted for. Subsequent analyses showed that exponentially declining relationships provided a better fit than linear or unimodal relationships and that this was largely the result of the response of rare species (relative cover less than 1%). Our results indicate that conservation benefits are disproportionally more costly on high-intensity than on low-intensity farmland. For example, reducing N inputs from 75 to 0 and 400 to 60 kg ha−1 yr−1 resulted in about the same estimated species gain for arable plants. Conservation initiatives are most (cost-)effective if they are preferentially implemented in extensively farmed areas that still support high levels of biodiversity.
TL;DR: A large number of pathogens that are directly or indirectly transmitted by rodents are described and a simplified rodent disease model is discussed.
Abstract: Rodents are the most abundant and diversified order of living mammals in the world. Already since the Middle Ages we know that they can contribute to human disease, as black rats were associated with distribution of plague. However, also in modern times rodents form a threat for public health. In this review article a large number of pathogens that are directly or indirectly transmitted by rodents are described. Moreover, a simplified rodent disease model is discussed.
Wageningen University and Research Centre1, University of Cambridge2, University of Edinburgh3, University of Illinois at Urbana–Champaign4, Aarhus University5, Wellcome Trust Sanger Institute6, Institut national de la recherche agronomique7, Illumina8, Iowa State University9, Agricultural Research Service10, University of Missouri11, United States Department of Agriculture12
TL;DR: The results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs and demonstrate that the PorcineSNP60 Beadchip is an excellent tool that will likely be used in a variety of future studies in pigs.
Abstract: Background: The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings: A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina’s Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
TL;DR: In this paper, it was shown that past behaviour, habit and hedonic appreciation are usually better predictors of actual food choice behavior than psychological constructs like attitudes and intentions, which should lead to a rethinking of the methods used in sensory and consumer research.
TL;DR: In this paper, the authors explored the potential impact of dietary changes on achieving ambitious climate stabilization levels and found that a global food transition to less meat, or even a complete switch to plant-based protein food, can have a dramatic effect on land use.
Abstract: Climate change mitigation policies tend to focus on the energy sector, while the livestock sector receives surprisingly little attention, despite the fact that it accounts for 18% of the greenhouse gas emissions and for 80% of total anthropogenic land use. From a dietary perspective, new insights in the adverse health effects of beef and pork have lead to a revision of meat consumption recommendations. Here, we explored the potential impact of dietary changes on achieving ambitious climate stabilization levels. By using an integrated assessment model, we found a global food transition to less meat, or even a complete switch to plant-based protein food to have a dramatic effect on land use. Up to 2,700 Mha of pasture and 100 Mha of cropland could be abandoned, resulting in a large carbon uptake from regrowing vegetation. Additionally, methane and nitrous oxide emission would be reduced substantially. A global transition to a low meat-diet as recommended for health reasons would reduce the mitigation costs to achieve a 450 ppm CO2-eq. stabilisation target by about 50% in 2050 compared to the reference case. Dietary changes could therefore not only create substantial benefits for human health and global land use, but can also play an important role in future climate change mitigation policies.
TL;DR: An overview of scientific issues that need to be addressed with priority in order to improve the risk assessment of nanotechnologies and nanoparticles in food products is given.
TL;DR: In this paper, the authors introduce a modeling approach that integrates demand-driven changes in land area with locally determined conversion processes to simulate the evolution of natural vegetation on abandoned farmland in Europe.
Abstract: Land use change is the result of interactions between processes operating at different scales. Simulation models at regional to global scales are often incapable of including locally determined processes of land use change. This paper introduces a modeling approach that integrates demand-driven changes in land area with locally determined conversion processes. The model is illustrated with an application for European land use. Interactions between changing demands for agricultural land and vegetation processes leading to the re-growth of (semi-) natural vegetation on abandoned farmland are explicitly addressed. Succession of natural vegetation is simulated based on the spatial variation in biophysical and management related conditions, while the dynamics of the agricultural area are determined by a global multi-sector model. The results allow an exploration of the future dynamics of European land use and landscapes. The model approach is similarly suitable for other regions and processes where large scale processes interact with local dynamics.
TL;DR: It is concluded that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial.
Abstract: To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated the colinearity. A significant number of strain-specific genes were predicted in these islands (80 in GG and 72 in LC705). The GG-specific islands included genes coding for bacteriophage components, sugar metabolism and transport, and exopolysaccharide biosynthesis. One island only found in L. rhamnosus GG contained genes for 3 secreted LPXTG-like pilins (spaCBA) and a pilin-dedicated sortase. Using anti-SpaC antibodies, the physical presence of cell wall-bound pili was confirmed by immunoblotting. Immunogold electron microscopy showed that the SpaC pilin is located at the pilus tip but also sporadically throughout the structure. Moreover, the adherence of strain GG to human intestinal mucus was blocked by SpaC antiserum and abolished in a mutant carrying an inactivated spaC gene. Similarly, binding to mucus was demonstrated for the purified SpaC protein. We conclude that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial. The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues.
TL;DR: MetAlign software is capable of automatic format conversions, accurate mass calculations, baseline corrections, peak-picking, saturation and mass-peak artifact filtering, as well as alignment of up to 1000 data sets, and is compatible with most multivariate statistics programs.
Abstract: Hyphenated full-scan MS technology creates large amounts of data. A versatile easy to handle automation tool aiding in the data analysis is very important in handling such a data stream. MetAlign software—as described in this manuscript—handles a broad range of accurate mass and nominal mass GC/MS and LC/MS data. It is capable of automatic format conversions, accurate mass calculations, baseline corrections, peak-picking, saturation and mass-peak artifact filtering, as well as alignment of up to 1000 data sets. A 100 to 1000-fold data reduction is achieved. MetAlign software output is compatible with most multivariate statistics programs.
TL;DR: New research strategies, as well as access to the draft of the rice genome, will not only advance the understanding of the molecular mechanisms that lead to quality rice but will also pave the way for efficient and targeted grain improvement.
TL;DR: Available evidence suggests climate-related changes in recruitment success to be the key process, stemming from either higher production or survival in the pelagic egg or larval stage, or owing to changes in the quality/quantity of nursery habitats.
Abstract: This paper develops a framework for the study of climate on fish populations based on first principles of physiology, ecology, and available observations. Environmental variables and oceanographic features that are relevant to fish and that are likely to be affected by climate change are reviewed. Working hypotheses are derived from the differences in the expected response of different species groups. A review of published data on Northeast Atlantic fish species representing different biogeographic affinities, habitats, and body size lends support to the hypothesis that global warming results in a shift in abundance and distribution (in patterns of occurrence with latitude and depth) of fish species. Pelagic species exhibit clear changes in seasonal migration patterns related to climateinduced changes in zooplankton productivity. Lusitanian species have increased in recent decades (sprat, anchovy, and horse mackerel), especially at the northern limit of their distribution areas, while Boreal species decreased at the southern limit of their distribution range (cod and plaice), but increased at the northern limit (cod). Although the underlying mechanisms remain uncertain, available evidence suggests climate-related changes in recruitment success to be the key process, stemming from either higher production or survival in the pelagic egg or larval stage, or owing to changes in the quality/quantity of nursery habitats.
Technical University of Denmark1, University of Helsinki2, Chalmers University of Technology3, Norwegian Meteorological Institute4, Earth System Research Laboratory5, Centre national de la recherche scientifique6, Cooperative Institute for Research in Environmental Sciences7, University of Oslo8, Blaise Pascal University9, University of Grenoble10, University of Urbino11, University of Leicester12, University of Bonn13, Research Institute for Nature and Forest14, Institut national de la recherche agronomique15, Wageningen University and Research Centre16, Finnish Meteorological Institute17, Catholic University of the Sacred Heart18, University of Giessen19, University of Copenhagen20, Estonian University of Life Sciences21, University of Edinburgh22, Stockholm University23, Indiana University24, University of Manchester25, Max Planck Society26, National University of Ireland, Galway27, Energy Research Centre of the Netherlands28
TL;DR: A review of the state of the art in understanding the processes involved in the exchange of trace gases and aerosols between the earth's surface and the atmosphere can be found in this article.