Corrigendum to “Using model predictions of soil carbon in farm-scale auditing — A software tool”
Gruijter, J.J. de; Wheeler, I. ; Malone, B.P. - \ 2020
Agricultural Systems 183 (2020). - ISSN 0308-521X
The authors regret an error in Equation (2) and in Equation (5). They thank Marco Ballin of Statistics Italy for notifying us of the error in Equation (2). The authors would like to apologise for any inconvenience caused. The equations should read as below [Formula presented] [Formula presented]
Studies into B-glucan recognition in fish suggests a key role for the C-type lectin pathway
Petit, J. ; Bailey, Erin C. ; Wheeler, Robert T. ; Ferreira de Oliveira, Carlos A. ; Forlenza, M. ; Wiegertjes, G. - \ 2019
Fish and Shellfish Immunology 91 (2019). - ISSN 1050-4648 - p. 434 - 434.
Immune-modulatory effects of β-glucans are generally considered beneficial to fish health. Despite the frequent application of β-glucans in aquaculture practice, the exact receptors and downstream signalling remains to be described for fish. In mammals, Dectin-1 is a member of the C-type lectin receptor (CLR) family and the best-described receptor for β-glucans. In fish genomes, no clear homologue of Dectin-1 could be identified so far. Yet, in previous studies we could activate carp macrophages with curdlan, considered a Dectin-1-specific β-(1,3)-glucan ligand in mammals. It was therefore proposed that immune-modulatory effects of β-glucan in carp macrophages could be triggered by a member of the CLR family activating the classical CLR signalling pathway, different from Dectin-1. In the current study, we used primary macrophages of common carp to examine immune modulation by β-glucans using transcriptome analysis of RNA isolated 6 h after stimulation with two different β-glucan preparations. Pathway analysis of differentially expressed genes (DEGs) showed that both β-glucans regulate a comparable signalling pathway typical of CLR activation. Carp genome analysis identified 239 genes encoding for proteins with at least one C-type Lectin Domains (CTLD). Narrowing the search for candidate β-glucan receptors, based on the presence of a conserved glucan-binding motif, identified 13 genes encoding a WxH sugar-binding motif in their CTLD. These genes, however, were not expressed in macrophages. Instead, among the β-glucan-stimulated DEGs, a total of six CTLD-encoding genes were significantly regulated, all of which were down-regulated in carp macrophages. Several candidates had a protein architecture similar to Dectin-1, therefore potential conservation of synteny of the mammalian Dectin-1 region was investigated by mining the zebrafish genome. Partial conservation of synteny with a region on the zebrafish chromosome 16 highlighted two genes as candidate β-glucan receptor. Altogether, the regulation of a gene expression profile typical of a signalling pathway associated with CLR activation and, the identification of several candidate β-glucan receptors, suggest that immune-modulatory effects of β-glucan in carp macrophages.
Nature and mental health: An ecosystem service perspective
Bratman, Gregory N. ; Anderson, Christopher B. ; Berman, Marc G. ; Cochran, Bobby ; Vries, Sjerp De; Flanders, Jon ; Folke, Carl ; Frumkin, Howard ; Gross, James J. ; Hartig, Terry ; Kahn, Peter H. ; Kuo, Ming ; Lawler, Joshua J. ; Levin, Phillip S. ; Lindahl, Therese ; Meyer-lindenberg, Andreas ; Mitchell, Richard ; Ouyang, Zhiyun ; Roe, Jenny ; Scarlett, Lynn ; Smith, Jeffrey R. ; Bosch, Matilda Van Den; Wheeler, Benedict W. ; White, Mathew P. ; Zheng, Hua ; Daily, Gretchen C. - \ 2019
Science Advances 5 (2019)7. - ISSN 2375-2548 - 15 p.
A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
Lees, John A. ; Ferwerda, Bart ; Kremer, Philip H.C. ; Wheeler, Nicole E. ; Valls Serón, Mercedes ; Croucher, Nicholas J. ; Gladstone, Rebecca A. ; Bootsma, Hester J. ; Rots, Nynke Y. ; Wijmega-Monsuur, Alienke J. ; Sanders, Elisabeth A.M. ; Trzciński, Krzysztof ; Wyllie, Anne L. ; Zwinderman, Aeilko H. ; Berg, Leonard H. van den; Rheenen, Wouter van; Veldink, Jan H. ; Harboe, Zitta B. ; Lundbo, Lene F. ; Groot, Lisette C.P.G.M. de; Schoor, Natasja M. van; Velde, Nathalie van der; Ängquist, Lars H. ; Sørensen, Thorkild I.A. ; Nohr, Ellen A. ; Mentzer, Alexander J. ; Mills, Tara C. ; Knight, Julian C. ; Plessis, Mignon du; Nzenze, Susan ; Weiser, Jeffrey N. ; Parkhill, Julian ; Madhi, Shabir ; Benfield, Thomas ; Gottberg, Anne von; Ende, Arie van der; Brouwer, Matthijs C. ; Barrett, Jeffrey C. ; Bentley, Stephen D. ; Beek, Diederik van de - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723 - 14 p.
Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.
Improving environmental risk assessments of chemicals: Steps towards evidence-based ecotoxicology
Martin, Olwenn V. ; Adams, Julie ; Beasley, Amy ; Belanger, Scott ; Breton, Roger L. ; Brock, Theo C.M. ; Buonsante, Vito A. ; Galay Burgos, Malyka ; Green, John ; Guiney, Patrick D. ; Hall, Tilghman ; Hanson, Mark ; Harris, Meagan J. ; Henry, Tala R. ; Huggett, Duane ; Junghans, Marion ; Laskowski, Ryszard ; Maack, Gerd ; Moermond, Caroline T.A. ; Panter, Grace ; Pease, Anita ; Poulsen, Veronique ; Roberts, Mike ; Rudén, Christina ; Schlekat, Christian E. ; Schoeters, Ilse ; Solomon, Keith R. ; Staveley, Jane ; Stubblefield, Bill ; Sumpter, John P. ; Warne, Michael S.J. ; Wentsel, Randall ; Wheeler, James R. ; Wolff, Brian A. ; Yamazaki, Kunihiko ; Zahner, Holly ; Ågerstrand, Marlene - \ 2019
Environment International 128 (2019). - ISSN 0160-4120 - p. 210 - 217.
Chemical safety - Decision-making - Ecological risk assessment - Ecotoxicology - Environmental risk assessment - Evidence-based
Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway
Petit, Jules ; Bailey, Erin C. ; Wheeler, Robert T. ; Oliveira, Carlos A.F. de; Forlenza, Maria ; Wiegertjes, Geert F. - \ 2019
Frontiers in Immunology 10 (2019). - ISSN 1664-3224 - 1 p.
C-type lectin-like domain - CTLD - Cyprinidae - primary macrophage - RNAseq analysis - teleost - transcriptome analysis - β-glucan
Immune-modulatory effects of β-glucans are generally considered beneficial to fish health. Despite the frequent application of β-glucans in aquaculture practice, the exact receptors and downstream signalling remains to be described for fish. In mammals, Dectin-1 is a member of the C-type lectin receptor (CLR) family and the best-described receptor for β-glucans. In fish genomes, no clear homologue of Dectin-1 could be identified so far. Yet, in previous studies we could activate carp macrophages with curdlan, considered a Dectin-1-specific β-(1,3)-glucan ligand in mammals. It was therefore proposed that immune-modulatory effects of β-glucan in carp macrophages could be triggered by a member of the CLR family activating the classical CLR signalling pathway, different from Dectin-1. In the current study, we used primary macrophages of common carp to examine immune modulation by β-glucans using transcriptome analysis of RNA isolated 6 h after stimulation with two different β-glucan preparations. Pathway analysis of differentially expressed genes (DEGs) showed that both β-glucans regulate a comparable signalling pathway typical of CLR activation. Carp genome analysis identified 239 genes encoding for proteins with at least one C-type Lectin Domains (CTLD). Narrowing the search for candidate β-glucan receptors, based on the presence of a conserved glucan-binding motif, identified 13 genes encoding a WxH sugar-binding motif in their CTLD. These genes, however, were not expressed in macrophages. Instead, among the β-glucan-stimulated DEGs, a total of six CTLD-encoding genes were significantly regulated, all of which were down-regulated in carp macrophages. Several candidates had a protein architecture similar to Dectin-1, therefore potential conservation of synteny of the mammalian Dectin-1 region was investigated by mining the zebrafish genome. Partial conservation of synteny with a region on the zebrafish chromosome 16 highlighted two genes as candidate β-glucan receptor. Altogether, the regulation of a gene expression profile typical of a signalling pathway associated with CLR activation and, the identification of several candidate β-glucan receptors, suggest that immune-modulatory effects of β-glucan in carp macrophages could be a result of signalling mediated by a member of the CLR family.
From water as curative agent to enabling waterscapes : Diverse experiences of the ‘therapeutic
Doughty, Karolina - \ 2019
In: Blue Space, Health and Wellbeing / Foley, Ronan, Kearns, Robin, Kistemann, Thomas, Wheeler, Ben, Routledge - ISBN 9780815359142 - p. 79 - 94.
Recent years have seen an increase in scholarly attention applied to the experiential relationship between humans and water. Significant insights have been gained into the human-water relationship more broadly, for instance in regard to the rich and evolving meanings of seascapes (Brown and Humberstone, 2015), as well as the growing literature on the health-enabling potential of being in or near water (Foley, 2010, 2011, 2014; Foley and Kistemann, 2015). In relation to questions about water and health, the literature within and beyond health geography exploring ‘therapeutic blue space’ has emerged strongly, contributing to the already large body of work which has applied the concept of therapeutic landscape (Gesler, 1992) to a wide range of contexts, to investigate how environmental, societal and individual factors interact in the creation of health-enabling places (for a scoping review, see Bell et al., 2018). In Gesler’s (1992) original conceptualisation, a therapeutic landscape is a place (a) where a material setting has been created to support the pursuit of health and wellbeing, (b) which is culturally associated with health and (c) where social practices related to ‘healing’ take place. Through these three elements the ‘healing process’ is situated geographically in places. As such, the therapeutic landscape concept has been applied to a wide range of environments from the perspective of exploring the attribution of health-related meaning to places and landscapes by individuals, groups and more broadly societies.
Using model predictions of soil carbon in farm-scale auditing - A software tool
Gruijter, J.J. de; Wheeler, I. ; Malone, B.P. - \ 2019
Agricultural Systems 169 (2019). - ISSN 0308-521X - p. 24 - 30.
Julia - Map uncertainty - Prediction error - Soil carbon auditing - Stratified random sampling - Value of information
We introduce a software tool for optimal sampling design in the context of farm-scale soil carbon auditing, where the amount of sequestered soil carbon will be estimated from a random sample. Existing tools do not use available ancillary information, or do not have the functionality needed for farm-scale soil carbon auditing. Using a grid of predicted carbon content with associated uncertainty, the software optimises a stratified random sampling design, such that the profit is maximised on the basis of sequestered carbon price, sampling costs, and a trading parameter that balances farmer's and buyer's risks due to uncertainty of the estimated amount of sequestered carbon. As the algorithm is computationally intensive, the package is written in Julia for speed. From a case study we conclude that our software is an effective tool for farm-scale soil carbon auditing, and that it outperforms the existing tools in terms of efficiency and functionality.
Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements
Pfeifer, Marion ; Gonsamo, Alemu ; Woodgate, William ; Cayuela, Luis ; Marshall, Andrew R. ; Ledo, Alicia ; Paine, Timothy C.E. ; Marchant, Rob ; Burt, Andrew ; Calders, Kim ; Courtney-mustaphi, Colin ; Cuni-sanchez, Aida ; Deere, Nicolas J. ; Denu, Dereje ; Gonzalez De Tanago Meñaca, J. ; Hayward, Robin ; Lau Sarmiento, A.I. ; Macía, Manuel J. ; Olivier, Pieter I. ; Pellikka, Petri ; Seki, Hamidu ; Shirima, Deo ; Trevithick, Rebecca ; Wedeux, Beatrice ; Wheeler, Charlotte ; Munishi, Pantaleo K.T. ; Martin, Thomas ; Mustari, Abdul ; Platts, Philip J. - \ 2018
Forest Ecosystems 5 (2018). - ISSN 2095-6355 - 14 p.
Background: Canopy structure, defined by leaf area index (LAI), fractional vegetation cover (FCover) and fraction of absorbed photosynthetically active radiation (fAPAR), regulates a wide range of forest functions and ecosystem services. Spatially consistent field-measurements of canopy structure are however lacking, particularly for the tropics. Methods: Here, we introduce the Global LAI database: a global dataset of field-based canopy structure measurements spanning tropical forests in four continents (Africa, Asia, Australia and the Americas). We use these measurements to test for climate dependencies within and across continents, and to test for the potential of anthropogenic disturbance and forest protection to modulate those dependences. Results: Using data collected from 887 tropical forest plots, we show that maximum water deficit, defined across the most arid months of the year, is an important predictor of canopy structure, with all three canopy attributes declining significantly with increasing water deficit. Canopy attributes also increase with minimum temperature, and with the protection of forests according to both active (within protected areas) and passive measures (through topography). Once protection and continent effects are accounted for, other anthropogenic measures (e.g. human population) do not improve the model. Conclusions: We conclude that canopy structure in the tropics is primarily a consequence of forest adaptation to the maximum water deficits historically experienced within a given region. Climate change, and in particular changes in drought regimes may thus affect forest structure and function, but forest protection may offer some resilience against this effect.
Toward a new generation of agricultural system data, models, and knowledge products: State of agricultural systems science
Jones, James W. ; Antle, John M. ; Basso, Bruno ; Boote, Kenneth J. ; Conant, Richard T. ; Foster, Ian ; Godfray, H.C.J. ; Herrero, Mario ; Howitt, Richard E. ; Janssen, Sander ; Keating, Brian A. ; Munoz-Carpena, Rafael ; Porter, Cheryl H. ; Rosenzweig, Cynthia ; Wheeler, Tim R. - \ 2017
Agricultural Systems 155 (2017). - ISSN 0308-521X - p. 269 - 288.
Agricultural data - Crop models - Economic models - Integrated agricultural systems models - Livestock models - Use cases
We review the current state of agricultural systems science, focusing in particular on the capabilities and limitations of agricultural systems models. We discuss the state of models relative to five different Use Cases spanning field, farm, landscape, regional, and global spatial scales and engaging questions in past, current, and future time periods. Contributions from multiple disciplines have made major advances relevant to a wide range of agricultural system model applications at various spatial and temporal scales. Although current agricultural systems models have features that are needed for the Use Cases, we found that all of them have limitations and need to be improved. We identified common limitations across all Use Cases, namely 1) a scarcity of data for developing, evaluating, and applying agricultural system models and 2) inadequate knowledge systems that effectively communicate model results to society. We argue that these limitations are greater obstacles to progress than gaps in conceptual theory or available methods for using system models. New initiatives on open data show promise for addressing the data problem, but there also needs to be a cultural change among agricultural researchers to ensure that data for addressing the range of Use Cases are available for future model improvements and applications. We conclude that multiple platforms and multiple models are needed for model applications for different purposes. The Use Cases provide a useful framework for considering capabilities and limitations of existing models and data.
SoilGrids250m: Global gridded soil information based on machine learning
Hengl, T. ; Mendes de Jesus, J.S. ; Heuvelink, G.B.M. ; Ruiperez Gonzalez, M. ; Kilibarda, Milan ; Blagotic, Aleksandar ; Wei, Shangguan ; Wright, Marvin N. ; Geng, Xiaoyuan ; Bauer-Marschallinger, Bernhard ; Guevara, Mario Antonio ; Vargas, Rodrigo ; MacMillan, Robert A. ; Batjes, N.H. ; Leenaars, J.G.B. ; Carvalho Ribeiro, E.D. ; Wheeler, Ichsani ; Mantel, S. ; Kempen, B. - \ 2017
PLoS ONE 12 (2017)2. - ISSN 1932-6203 - 40 p.
This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total).
Soil nutrient maps of Sub-Saharan Africa : assessment of soil nutrient content at 250 m spatial resolution using machine learning
Hengl, Tomislav ; Leenaars, Johan G.B. ; Shepherd, Keith D. ; Walsh, Markus G. ; Heuvelink, Gerard B.M. ; Mamo, Tekalign ; Tilahun, Helina ; Berkhout, Ezra ; Cooper, Matthew ; Fegraus, Eric ; Wheeler, Ichsani ; Kwabena, Nketia A. - \ 2017
Nutrient Cycling in Agroecosystems 109 (2017)1. - ISSN 1385-1314 - p. 77 - 102.
Africa - Machine learning - Macro-nutrients - Micro-nutrients - Random forest - Soil nutrient map - Spatial prediction
Spatial predictions of soil macro and micro-nutrient content across Sub-Saharan Africa at 250 m spatial resolution and for 0–30 cm depth interval are presented. Predictions were produced for 15 target nutrients: organic carbon (C) and total (organic) nitrogen (N), total phosphorus (P), and extractable—phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), sodium (Na), iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), aluminum (Al) and boron (B). Model training was performed using soil samples from ca. 59,000 locations (a compilation of soil samples from the AfSIS, EthioSIS, One Acre Fund, VitalSigns and legacy soil data) and an extensive stack of remote sensing covariates in addition to landform, lithologic and land cover maps. An ensemble model was then created for each nutrient from two machine learning algorithms—random forest and gradient boosting, as implemented in R packages ranger and xgboost—and then used to generate predictions in a fully-optimized computing system. Cross-validation revealed that apart from S, P and B, significant models can be produced for most targeted nutrients (R-square between 40–85%). Further comparison with OFRA field trial database shows that soil nutrients are indeed critical for agricultural development, with Mn, Zn, Al, B and Na, appearing as the most important nutrients for predicting crop yield. A limiting factor for mapping nutrients using the existing point data in Africa appears to be (1) the high spatial clustering of sampling locations, and (2) missing more detailed parent material/geological maps. Logical steps towards improving prediction accuracies include: further collection of input (training) point samples, further harmonization of measurement methods, addition of more detailed covariates specific to Africa, and implementation of a full spatio-temporal statistical modeling framework.
Assessing the relevance of ecotoxicological studies for regulatory decision making
Rudén, Christina ; Adams, Julie ; Ågerstrand, Marlene ; Brock, Theo C.M. ; Poulsen, Veronique ; Schlekat, Christian E. ; Wheeler, James R. ; Henry, Tala R. - \ 2017
Integrated Environmental Assessment and Management 13 (2017)4. - ISSN 1551-3793 - p. 652 - 663.
Data evaluation - Environmental risk assessment - Peer-reviewed literature - Regulatory decision making - Relevance evaluation
Regulatory policies in many parts of the world recognize either the utility of or the mandate that all available studies be considered in environmental or ecological hazard and risk assessment (ERA) of chemicals, including studies from the peer-reviewed literature. Consequently, a vast array of different studies and data types need to be considered. The first steps in the evaluation process involve determining whether the study is relevant to the ERA and sufficiently reliable. Relevance evaluation is typically performed using existing guidance but involves application of "expert judgment" by risk assessors. In the present paper, we review published guidance for relevance evaluation and, on the basis of the practical experience within the group of authors, we identify additional aspects and further develop already proposed aspects that should be considered when conducting a relevance assessment for ecotoxicological studies. From a regulatory point of view, the overarching key aspect of relevance concerns the ability to directly or indirectly use the study in ERA with the purpose of addressing specific protection goals and ultimately regulatory decision making. Because ERA schemes are based on the appropriate linking of exposure and effect estimates, important features of ecotoxicological studies relate to exposure relevance and biological relevance. Exposure relevance addresses the representativeness of the test substance, environmental exposure media, and exposure regime. Biological relevance deals with the environmental significance of the test organism and the endpoints selected, the ecological realism of the test conditions simulated in the study, as well as a mechanistic link of treatment-related effects for endpoints to the protection goal identified in the ERA. In addition, uncertainties associated with relevance should be considered in the assessment. A systematic and transparent assessment of relevance is needed for regulatory decision making. The relevance aspects also need to be considered by scientists when designing, performing, and reporting ecotoxicological studies to facilitate their use in ERA.
Proteomics data in support of the quantification of the changes of bovine milk proteins during mammary gland involution
Boggs, Irina ; Hine, Brad ; Smolenksi, Grant ; Hettinga, Kasper ; Zhang, Lina ; Wheeler, Thomas T. - \ 2016
Data in Brief 8 (2016). - ISSN 2352-3409 - p. 52 - 55.
Dairy - Drying off - Host defence - Proteomics
Here we provide data from three proteomics techniques; two-dimensional electrophoresis (2-DE) followed by identification of selected spots using PSD MALDI-TOF MS/MS, one-dimensional gel electrophoresis followed by LC-MS/MS analysis of gel slices (GeLC) and dimethyl isotopic labelling of tryptic peptides followed by Orbitrap MS/MS (DML), to quantify the changes in the repertoire of bovine milk proteins that occurs after drying off. We analysed skim milk and whey sampled at day 0 and either day 3 or day 8 after drying off. These analyses identified 45 spots by MALDI-TOF, 51 proteins by GeLC and 161 proteins by DML, for which the detailed data work-up is presented as three Excel files. The data supplied in this article supports the accompanying publication "Changes in the repertoire of bovine milk proteins during mammary involution" (Boggs et al., 2015) . Data are available via ProteomeXchange with identifiers ProteomeXchange: PXD003110 and ProteomeXchange: PXD003011.
Changes in the repertoire of bovine milk proteins during mammary involution.
Boggs, I. ; Hine, B. ; Smolenski, G. ; Hettinga, K.A. ; Zhang, L. ; Wheeler, T. - \ 2015
EuPA Open Proteomics 9 (2015). - ISSN 2212-9685 - p. 65 - 75.
Changes of abundance that occur in the repertoire of low abundance milk proteins after cessation of milk removal have not been characterised. Skimmed milk and whey from cows sampled at day 0 and either day 3 or day 8 after drying off were subjected to three untargeted proteomics techniques; 2-D gel electrophoresis, GeLC-MS, and dimethyl isotopic labelling of tryptic peptides. The changes observed included 45 fragments of abundant milk proteins and 36 host-defence proteins, suggesting activation of proteolysis and inflammation. The findings form a basis for adding value to dairy production.
|Characterisation of Ave1 orthologs in Venturia scab pathogens
Wheeler, J. ; Kastner, P. ; Taranto, A. ; Shiller, J. ; Boshoven, J.C. ; Mesarich, C.H. ; Thomma, B.P.H.J. ; Deng, C. ; Bowen, J. ; Plummer, K.M. - \ 2015
In: Book of Abstracts 28th Fungal Genetics Conference. - - p. 211 - 211.
Most fungal effectors are genus, species or race-specific, however a few are more broadly conserved (e.g. ECP6), and some are discontinuously distributed within the Fungi (Ave1 & AvrLm6). Single orthologs of Ave1 from Verticillium dahliae, a virulence effector that activates Ve1-mediated resistance in tomato, have been identified in unrelated fungi (Colletotrichum higginsianum, Cercospora beticola, Fusarium oxysporum f. sp. lycopersici). A subset of these activate Ve1-mediated resistance in tomato (de Jonge et al. 2012). Ave1 also shares similarity to an ortholog in the phytopathogenic bacterium Xanthomonas axonopodis pv. citri, as well as to a common family of plant natriuretic peptides and expansins, involved in plant homeostasis and plant cell wall modifications (de Jonge et al. 2012). We have identified highly expanded Ave1-like gene families (with conserved predicted cysteine patterns & 37-57% overall aa identity) in the biotrophic scab fungi, Venturia inaequalis (5 genomes) & V. pirina. The orthologs are closely associated with repeats in Venturia genomes, however only a few appear to be impacted by RIP. Like VdAve1, Venturia orthologs have a conserved intron in the 5’UTR, which causes problems for automated gene calling, especially those packages informed by transcriptome data. Several of the Venturia orthologs are up-regulated during leaf infection (RNAseq data), and some are also highly expressed during in vitro growth on cellophane (RNAseq and proteomic data, Cook et al. 2014). Synthetic peptides (36 & 39 amino acids) from two V. inaequalis Ave1 orthologs, based on conserved homeostasis-regulating domains of plant proteins, affected Arabidopsis thaliana protoplasts (swelling) and guard cells (collapse) of Tradescantia leaves in epidermal peels exposed to the peptides (0.1µM) in solution. We hypothesize that Venturia Ave1 proteins may play a role during biotrophic infection in disturbing plant homeostasis and promoting nutrient release from plant cells.
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Aflitos, S.A. ; Schijlen, E.G.W.M. ; Jong, J.H.S.G.M. de; Ridder, D. de; Smit, S. ; Finkers, H.J. ; Bakker, F.T. ; Geest, H.C. van de; Lintel Hekkert, B. te; Haarst, J.C. van; Smits, L.W.M. ; Koops, A.J. ; Sanchez-Perez, M.J. ; Heusden, A.W. van; Visser, R.G.F. ; Schranz, M.E. ; Peters, S.A. - \ 2014
The Plant Journal 80 (2014)1. - ISSN 0960-7412 - p. 136 - 148.
single-nucleotide polymorphisms - burrows-wheeler transform - wild tomatoes - genus lycopersicon - read alignment - fruit size - evolution - domestication - solanaceae - plant
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment reveals group-, species-, and accession-specific polymorphisms, which explains characteristic fruit traits and growth habits in the different cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, pointing to positive selection and to differences in selection pressure between crop accessions and wild species. In wild species SNPs are found in excess of 10 million, i.e. 20 fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, highest levels of heterozygosity were found for allogamous SI wild species, while facultative and autogamous SC species display a lower heterozygosity level. Using whole genome SNP information for Maximum Likelihood analysis we achieved complete tree resolution, whereas ML trees based on SNPs from 10 fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat pointing at the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
A European perspective on alternatives to animal testing for environmental hazard identification and risk assessment
Scholz, S. ; Sela, E. ; Blaha, L. ; Braunbeck, T. ; Galay-Burgos, M. ; Garcia-Franco, M. ; Guinea, J. ; Kluver, N. ; Schirmer, K. ; Tanneberger, K. ; Tobor-Kaplon, M. ; Witters, H. ; Belanger, S. ; Benfenati, E. ; Creton, S. ; Cronin, M.T.D. ; Eggen, R.I.L. ; Embry, M. ; Ekman, D. ; Gourmelon, A. ; Halder, M. ; Hardy, B. ; Hartung, T. ; Hubesch, B. ; Jungmann, D. ; Lampi, M.A. ; Lee, L. van; Leonard, M. ; Kuster, E. ; Lillicrap, A. ; Luckenbach, T. ; Murk, A.J. ; Navas, J.M. ; Peijnenburg, W. ; Repetto, G. ; Salinas, E. ; Schuurmann, G. ; Spielmann, H. ; Tollefsen, K.E. ; Walter-Rohde, S. ; Whale, G. ; Wheeler, J.R. ; Winter, M.J. - \ 2013
Regulatory Toxicology and Pharmacology 67 (2013). - ISSN 0273-2300 - p. 506 - 530.
zebrafish danio-rerio - plant-protection products - messenger-rna expression - adverse outcome pathways - acute fish toxicity - in-vitro - toxicological concern - disrupting chemicals - aquatic toxicity - aromatic-hydrocarbons
Tests with vertebrates are an integral part of environmental hazard identification and risk assessment of chemicals, plant protection products, pharmaceuticals, biocides, feed additives and effluents. These tests raise ethical and economic concerns and are considered as inappropriate for assessing all of the substances and effluents that require regulatory testing. Hence, there is a strong demand for replacement, reduction and refinement strategies and methods. However, until now alternative approaches have only rarely been used in regulatory settings. This review provides an overview on current regulations of chemicals and the requirements for animal tests in environmental hazard and risk assessment. It aims to highlight the potential areas for alternative approaches in environmental hazard identification and risk assessment. Perspectives and limitations of alternative approaches to animal tests using vertebrates in environmental toxicology, i.e. mainly fish and amphibians, are discussed. Free access to existing (proprietary) animal test data, availability of validated alternative methods and a practical implementation of conceptual approaches such as the Adverse Outcome Pathways and Integrated Testing Strategies were identified as major requirements towards the successful development and implementation of alternative approaches. Although this article focusses on European regulations, its considerations and conclusions are of global relevance
|Use of cold plasma in food processing
Mastwijk, H.C. ; Nierop Groot, M.N. - \ 2010
In: Encyclopedia of biotechnology in agriculture and food / Heldman, D.R., Hoover, D.G., Wheeler, M.B., [s.l.] : Taylor & Francis - ISBN 9780849350276 - p. 174 - 177.
Application of cold plasma has been reported in agriculture, food, and bioscience literature as an effective, non-chemical, gas-phase disinfection agent that can be applied at moderate temperatures. The unusual thermodynamic properties of these gases are discussed with focus on nitrogen-based atmospheric plasma. Typical concepts, such as electron temperature and charge-exchange processes with surfaces are explained in more detail. Finally, some general phenomena related to microbial inactivation are presented, including a survey on outstanding issues concerning research and development efforts aimed at utilization of cold plasma disinfection.
Impacts of the Madden-Julian oscillation on Australian rainfall and circulation
Wheeler, M.C. ; Hendon, H.H. ; Cleland, S. ; Meinke, H.B. ; Donald, A. - \ 2009
Journal of Climate 22 (2009)6. - ISSN 0894-8755 - p. 1482 - 1498.
outgoing longwave radiation - tropical-extratropical interaction - northern winter - climate variability - prediction - monsoon - precipitation - temperature - reanalysis - atmosphere
Impacts of the Madden¿Julian oscillation (MJO) on Australian rainfall and circulation are examined during all four seasons. The authors examine circulation anomalies and a number of different rainfall metrics, each composited contemporaneously for eight MJO phases derived from the real-time multivariate MJO index. Multiple rainfall metrics are examined to allow for greater relevance of the information for applications. The greatest rainfall impact of the MJO occurs in northern Australia in (austral) summer, although in every season rainfall impacts of various magnitude are found in most locations, associated with corresponding circulation anomalies. In northern Australia in all seasons except winter, the rainfall impact is explained by the direct influence of the MJO's tropical convective anomalies, while in winter a weaker and more localized signal in northern Australia appears to result from the modulation of the trade winds as they impinge upon the eastern coasts, especially in the northeast. In extratropical Australia, on the other hand, the occurrence of enhanced (suppressed) rainfall appears to result from induced upward (downward) motion within remotely forced extratropical lows (highs), and from anomalous low-level northerly (southerly) winds that transport moisture from the tropics. Induction of extratropical rainfall anomalies by remotely forced lows and highs appears to operate mostly in winter, whereas anomalous meridional moisture transport appears to operate mainly in the summer, autumn, and to some extent in the spring