Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Dutch forest reserves database and network
Bijlsma, R.J. ; Clerkx, A.P.P.M. - \ 2019
forest reserve - monitoring - database - nin-intervention dynamics - ecology
The Dutch forest reserves network encompasses about 60 forest reserves representing all major forest types in the Netherlands. The reserves were designated between 1983 and 2000. The present Access-database presents all measurements (mostly between 1982 and 2005) on trees and regeneration in circular sample plots throughout the reserves and in a one ha rectangular core area in each reserve. The data set also includes map data at the reserve level (such as reserve boundaries, samples plots and core areas) and of GIS files derived from tree measurements in the core area.
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Koehorst, J.J. ; Dam, J.C.J. van; Heck, R.G.A. van; Saccenti, E. ; Martins dos Santos, V.A.P. ; Suarez Diez, M. ; Schaap, P.J. - \ 2018
database - genome annotation - protein domains - Pseudomonas - semantic web
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
PLATFORM DB - Bioeconomy P2P Partnerships Database - An online web resource on bioeconomy Public-to-Public Parternships, joint calls and research projects
Kuzniar-van der Zee, B. ; Bunthof, C.J. ; Boheemen, P.J.C. van; Leon, C.D. - \ 2016
H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM)
PLATFORM - ERA-NET - P2P - p2p partnerships - public-to-public partnerships - Bioeconomy - Database - joint calls - research projects - database
Poster PLATFORM DB - Bioeconomy P2P partnerships database - An online web resource on bioeconomy Public-to-Public Partnerships, joint calls and research projects
Kuzniar-van der Zee, B. - \ 2016
H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 1 p.
platform - database - p2p partnerships - public-to-public partnerships - bioeconomy - joint calls - research projects - PLATFORM - P2P - Bioeconomy - Database - Platform db
Plant functional type classification for earth system models: results from the European Space Agency's Land Cover Climate Change Initiative
Poulter, B. ; MacBean, N. ; Hartley, A. ; Khlystova, I. ; Arino, O. ; Betts, R. ; Bontemps, S. ; Boettcher, M. ; Brockmann, C. ; Defourny, P. ; Hagemann, S. ; Herold, M. ; Kirches, C. ; Lamarche, C. ; Lederer, D. ; Ottlé, C. ; Peters, M. ; Peylin, P. - \ 2015
Geoscientific Model Development 8 (2015). - ISSN 1991-959X - p. 2315 - 2328.
global vegetation model - world map - ecosystems - forests - cycle - uncertainties - resolution - feedbacks - phenology - database
Global land cover is a key variable in the earth system with feedbacks on climate, biodiversity and natural resources. However, global land cover data sets presently fall short of user needs in providing detailed spatial and thematic information that is consistently mapped over time and easily transferable to the requirements of earth system models. In 2009, the European Space Agency launched the Climate Change Initiative (CCI), with land cover (LC_CCI) as 1 of 13 essential climate variables targeted for research development. The LC_CCI was implemented in three phases: first responding to a survey of user needs; developing a global, moderate-resolution land cover data set for three time periods, or epochs (2000, 2005, and 2010); and the last phase resulting in a user tool for converting land cover to plant functional type equivalents. Here we present the results of the LC_CCI project with a focus on the mapping approach used to convert the United Nations Land Cover Classification System to plant functional types (PFTs). The translation was performed as part of consultative process among map producers and users, and resulted in an open-source conversion tool. A comparison with existing PFT maps used by three earth system modeling teams shows significant differences between the LC_CCI PFT data set and those currently used in earth system models with likely consequences for modeling terrestrial biogeochemistry and land–atmosphere interactions. The main difference between the new LC_CCI product and PFT data sets used currently by three different dynamic global vegetation modeling teams is a reduction in high-latitude grassland cover, a reduction in tropical tree cover and an expansion in temperate forest cover in Europe. The LC_CCI tool is flexible for users to modify land cover to PFT conversions and will evolve as phase 2 of the European Space Agency CCI program continues.
Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC
Oosterkamp, M.J. ; Boeren, S. ; Atashgahi, S. ; Plugge, C.M. ; Schaap, P.J. ; Stams, A.J.M. - \ 2015
FEMS Microbiology Letters 362 (2015)11. - ISSN 0378-1097 - 7 p.
desulfococcus-biacutus - rhodobacter-capsulatus - anaerobic degradation - denitrifying bacteria - microbial-metabolism - gen-nov - carboxylase - database - proteins - fixation
Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a ß-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to ß-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-ß-hydroxybutyrate. Accordingly, we confirmed the formation of poly-ß-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor
Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests
Addisalem, A.B. ; Esselink, G. ; Bongers, F. ; Smulders, M.J.M. - \ 2015
AoB Plants 7 (2015). - ISSN 2041-2851 - 11 p.
populus-nigra l. - conservation genetics - frankincense - populations - ethiopia - database - plants - reads - tool - dna
Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin.
Financial fragility and natural disasters: An empirical analysis
Klomp, J.G. - \ 2014
Journal of Financial Stability 13 (2014). - ISSN 1572-3089 - p. 180 - 192.
basel core principles - economic-growth - bank soundness - panel-data - risk - crises - database - deposit - models - sector
Using data for more than 160 countries in the period 1997-2010, we explore the impact of large-scale natural disasters on the distance-to-default of commercial banks. The financial consequences of natural catastrophes may stress and threaten the existence of a bank by adversely affecting their solvency. After extensive testing for the sensitivity of the results, our main findings suggest that natural disasters increase the likelihood of a banks' default. More precisely, we conclude that geophysical and meteorological disasters reduce the distance-to-default the most due to their widespread damage caused. In addition, the impact of a natural disaster depends on the size and scope of the catastrophe, the rigorousness of financial regulation and supervision, and the level of financial and economic development of a particular country. (C) 2014 Elsevier B.V. All rights reserved.
HyMeX, a 10-year multidisciplinary program on the Mediterranean water cycle
Drobinski, P. ; Ducrocq, V.P. ; Alpert, P. ; Anagnostou, A. ; Béranger, K. ; Borga, M. ; Braud, I. ; Chanzy, A. ; Davolio, S. ; Delrieu, G. ; Estournel, C. ; Filali Boubrahmi, N. ; Uijlenhoet, R. ; Font, J. ; Grubisic, V. ; Gualdi, S. ; Homar, V. ; Ivancan-Picek, B. ; Kottmeier, C. ; Kotroni, V. ; Lagouvardos, K. ; Lionello, P. ; Llasat, M.C. ; Ludwig, W. ; Lutoff, C. ; Mariotti, A. ; Richard, E. ; Romero, R. ; Rotunno, R. ; Roussot, O. ; Ruin, I. ; Somot, S. ; Taupier-Letage, L. ; Tintore, J. ; Wernli, H. - \ 2014
Bulletin of the American Meteorological Society 95 (2014)7. - ISSN 0003-0007 - p. 1063 - 1082.
regional climate model - flash-flood - synoptic climatology - deep convection - september 2002 - north-western - precipitation - events - sea - database
The Mediterranean countries are experiencing important challenges related to the water cycle, including water shortages and floods, extreme winds, and ice/snow storms, that impact critically the socioeconomic vitality in the area (causing damage to property, threatening lives, affecting the energy and transportation sectors, etc.). There are gaps in our understanding of the Mediterranean water cycle and its dynamics that include the variability of the Mediterranean Sea water budget and its feedback on the variability of the continental precipitation through air–sea interactions, the impact of precipitation variability on aquifer recharge, river discharge, and soil water content and vegetation characteristics specific to the Mediterranean basin and the mechanisms that control the location and intensity of heavy precipitating systems that often produce floods. The Hydrological Cycle in Mediterranean Experiment (HyMeX) program is a 10-yr concerted experimental effort at the international level that aims to advance the scientific knowledge of the water cycle variability in all compartments (land, sea, and atmosphere) and at various time and spatial scales. It also aims to improve the processes-based models needed for forecasting hydrometeorological extremes and the models of the regional climate system for predicting regional climate variability and evolution. Finally, it aims to assess the social and economic vulnerability to hydrometeorological natural hazards in the Mediterranean and the adaptation capacity of the territories and populations therein to provide support to policy makers to cope with water-related problems under the influence of climate change, by linking scientific outcomes with related policy requirements.
SoilGrids1km— global soil information based on automated mapping
Hengl, T. ; Mendes de Jesus, J.S. ; Macmillan, R.A. ; Batjes, N.H. ; Heuvelink, G.B.M. ; Carvalho Ribeiro, E.D. ; Samuel Rosa, A. ; Kempen, B. ; Leenaars, J.G.B. ; Walsh, M.G. ; Ruiperez Gonzalez, M. - \ 2014
PLoS ONE 9 (2014)8. - ISSN 1932-6203
global land areas - organic-carbon - resolution - climate - world - maps - interpolation - database - models
Background Soils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited spatial detail. Methodology/Principal Findings We present SoilGrids1km — a global 3D soil information system at 1 km resolution — containing spatial predictions for a selection of soil properties (at six standard depths): soil organic carbon (g kg-1), soil pH, sand, silt and clay fractions (%), bulk density (kg m-3), cation-exchange capacity (cmol+/kg), coarse fragments (%), soil organic carbon stock (t ha-1), depth to bedrock (cm), World Reference Base soil groups, and USDA Soil Taxonomy suborders. Our predictions are based on global spatial prediction models which we fitted, per soil variable, using a compilation of major international soil profile databases (ca. 110,000 soil profiles), and a selection of ca. 75 global environmental covariates representing soil forming factors. Results of regression modeling indicate that the most useful covariates for modeling soils at the global scale are climatic and biomass indices (based on MODIS images), lithology, and taxonomic mapping units derived from conventional soil survey (Harmonized World Soil Database). Prediction accuracies assessed using 5–fold cross-validation were between 23–51%. Conclusions/Significance SoilGrids1km provide an initial set of examples of soil spatial data for input into global models at a resolution and consistency not previously available. Some of the main limitations of the current version of SoilGrids1km are: (1) weak relationships between soil properties/classes and explanatory variables due to scale mismatches, (2) difficulty to obtain covariates that capture soil forming factors, (3) low sampling density and spatial clustering of soil profile locations. However, as the SoilGrids system is highly automated and flexible, increasingly accurate predictions can be generated as new input data become available. SoilGrids1km are available for download via http://soilgrids.org under a Creative Commons Non Commercial license.
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
Dam, J.C.J. van; Schaap, P.J. ; Martins dos Santos, V.A.P. ; Suarez Diez, M. - \ 2014
BMC Systems Biology 8 (2014). - ISSN 1752-0509 - 21 p.
data sets - expression profiles - microarray data - global analysis - biological data - promoter motif - inference - database - dormancy - regulon
Background: Different methods have been developed to infer regulatory networks from heterogeneous omics datasets and to construct co-expression networks. Each algorithm produces different networks and efforts have been devoted to automatically integrate them into consensus sets. However each separate set has an intrinsic value that is diluted and partly lost when building a consensus network. Here we present a methodology to generate co-expression networks and, instead of a consensus network, we propose an integration framework where the different networks are kept and analysed with additional tools to efficiently combine the information extracted from each network. Results: We developed a workflow to efficiently analyse information generated by different inference and prediction methods. Our methodology relies on providing the user the means to simultaneously visualise and analyse the coexisting networks generated by different algorithms, heterogeneous datasets, and a suite of analysis tools. As a show case, we have analysed the gene co-expression networks of Mycobacterium tuberculosis generated using over 600 expression experiments. Regarding DNA damage repair, we identified SigC as a key control element, 12 new targets for LexA, an updated LexA binding motif, and a potential mismatch repair system. We expanded the DevR regulon with 27 genes while identifying 9 targets wrongly assigned to this regulon. We discovered 10 new genes linked to zinc uptake and a new regulatory mechanism for ZuR. The use of co-expression networks to perform system level analysis allows the development of custom made methodologies. As show cases we implemented a pipeline to integrate ChIP-seq data and another method to uncover multiple regulatory layers. Conclusions: Our workflow is based on representing the multiple types of information as network representations and presenting these networks in a synchronous framework that allows their simultaneous visualization while keeping specific associations from the different networks. By simultaneously exploring these networks and metadata, we gained insights into regulatory mechanisms in M. tuberculosis that could not be obtained through the separate analysis of each data type.
Ultrafast PubChem Searching Combined with Improved Filtering Rules for Elemental Composition Analysis
Lommen, A. - \ 2014
Analytical Chemistry 86 (2014)11. - ISSN 0003-2700 - p. 5463 - 5469.
mass-spectrometry - identification - metabolomics - database
A new and improved software tool for elemental composition annotation of molecular ions detected in mass spectrometry, based on improved filtering rules followed by ultrafast querying in publicly available compound databases, is provided. Pubchem is used as a general source of 1.3 million unique chemical formulas. A plant metabolomics database containing ca. 100¿000 formulas is used as a source of naturally occurring compounds. Four modes with different sets of rules for heuristic filtering of candidate formulas coming from elemental composition analysis are incorporated and tested on both databases. The elemental composition analysis is then coupled to ultrafast PubChem searching based on a mass-indexed intermediate system. The performance of the filters is compared and discussed. When reactive compounds are assumed not to be present, 99.95% of the 1.3 million PubChem formulas is correctly found, while ca. 30% less formulas per mass are given compared to previously published rules. For the ca. 100¿000 plant metabolomics based formulas, 100% fit the improved rules.
Constructing a mass measurement error surface to improve automatic annotations in liquid chromatography/mass spectrometry based metabolomics
Shahaf, N. ; Franceschi, P. ; Arapitsas, P. ; Rogachev, I. ; Vrhovsek, U. ; Wehrens, H.R.M.J. - \ 2013
Rapid Communications in Mass Spectrometry 27 (2013)21. - ISSN 0951-4198 - p. 2425 - 2431.
accuracy - database - recalibration - precision - molecules - sample
RATIONALE Estimation of mass measurement accuracy is an elementary step in the application of mass spectroscopy (MS) data towards metabolite annotations and has been addressed several times in the past. However, the reproducibility of mass measurements over a diverse set of analytes and in variable operating conditions, which are common in high-throughput metabolomics studies, has, to the best of our knowledge, not been addressed so far. METHODS A method to automatically extract mass measurement errors from a large data set of measurements made on a quadrupole time-of-flight (QTOF) MS instrument has been developed. The size of the data processed in this study has enabled us to use a statistical data driven approach to build a model which reliably predicts the confidence interval of the absolute mass measurement error based on individual ion peak conditions in a fast, high-throughput manner. RESULTS We show that our model predictions are reproducible in external datasets generated in similar, but not identical conditions, and have demonstrated the advantage of our approach over the common practice of fixed mass measurement error limits. CONCLUSIONS Outlined is an approach which can promote a more rational use of MS technology by automatically evaluating the absolute mass measurement error based on the individual peak conditions. The immediate application of our method is integration in high-throughput peak annotation pipelines for database searches.
Political regime and human capital: A cross-country analysis
Klomp, J.G. ; Haan, J. de - \ 2013
Social Indicators Research 111 (2013)1. - ISSN 0303-8300 - p. 45 - 73.
economic-growth - democracy - education - institutions - database
We examine the relationship between different dimensions of the political regime in place and human capital using a two-step structural equation model. In the first step, we employ factor analysis on 16 human capital indicators to construct two new human capital measures (basic and advanced human capital). In the second step, we estimate the impact of our political variables on human capital, using a cross-sectional structural model for some 100 countries. We conclude that democracy is positively related to basic human capital, while regime instability has a negative link with basic human capital. Governance has a positive relationship with advanced human capital, while government instability has a negative link with advanced human capital. Finally, we also find an indirect positive effect of governance and democracy on both types of human capital through their effect on income.
A novel bacterial enzyme with D-glucuronyl C5-epimerase activity
Raedts, J.G.J. ; Lundgren, M. ; Kengen, S.W.M. ; Li, J.P. ; Oost, J. van der - \ 2013
Journal of Biological Chemistry 288 (2013)34. - ISSN 0021-9258 - p. 24332 - 24339.
l-iduronic acid - heparan-sulfate - heparin/heparan sulfate - escherichia-coli - biosynthesis - polysaccharide - glycosaminoglycans - oligosaccharides - purification - database
Glycosaminoglycans are biologically active polysaccharides that are found ubiquitously in the animal kingdom. The biosynthesis of these complex polysaccharides involves complicated reactions that turn the simple glycosaminoglycan backbone into highly heterogeneous structures. One of the modification reactions is the epimerization of D-glucuronic acid to its C5-epimer L-iduronic acid, which is essential for the function of heparan sulfate. Although L-iduronic acid residues have been shown to exist in polysaccharides of some prokaryotes, there has been no experimental evidence for the existence of a prokaryotic D-glucuronyl C5-epimerase. This work for the first time reports on the identification of a bacterial enzyme with D-glucuronyl C5-epimerase activity. A gene of the marine bacterium Bermanella marisrubri sp. RED65 encodes a protein (RED65_08024) of 448 amino acids that has an overall 37% homology to the human D-glucuronic acid C5-epimerase. Alignment of this peptide with the human and mouse sequences revealed a 60% similarity at the carboxyl terminus. The recombinant protein expressed in Escherichia coli showed epimerization activity toward substrates generated from heparin and the E. coli K5 capsular polysaccharide, thereby providing the first evidence for bacterial D-glucuronyl C5-epimerase activity. These findings may eventually be used for modification of mammalian glycosaminoglycans
Mining minimal motif pair sets maximally covering interactions in a protein-protein interaction network
Boyen, P. ; Neven, F. ; Valentim, F.L. ; Dijk, A.D.J. van - \ 2013
IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (2013)1. - ISSN 1545-5963 - p. 73 - 86.
interaction sites - high-throughput - binding-sites - prediction - database - hardness
Correlated motif covering (CMC) is the problem of finding a set of motif pairs, i.e., pairs of patterns, in the sequences of proteins from a protein-protein interaction network (PPI-network) that describe the interactions in the network as concisely as possible. In other words, a perfect solution for CMC would be a minimal set of motif pairs that describes the interaction behavior perfectly in the sense that two proteins from the network interact if and only if their sequences match a motif pair in the minimal set. In this paper, we introduce and formally define CMC and show that it is closely related to the red-blue set cover (RBSC) problem and its weighted version (WRBSC)--both well-known NP-hard problems for that there exist several algorithms with known approximation factor guarantees. We prove the hardness of approximation of CMC by providing an approximation factor preserving reduction from RBSC to CMC. We show the existence of a theoretical approximation algorithm for CMC by providing an approximation factor preserving reduction from CMC to WRBSC. We adapt the latter algorithm into a functional heuristic for CMC, called CMC-approx, and experimentally assess its performance and biological relevance. The implementation in Java can be found at >http://bioinformatics.uhasselt.be
Translating land cover/land use classifications to habitat taxonomies for landscape monitoring: a Mediterranean assessment
Tomaselli, V. ; Dimopoulos, P. ; Marangi, C. ; Kallimanis, A. ; Adamo, M. ; Tarantino, C. ; Panitsa, M. ; Terzi, M. ; Veronico, G. ; Lovergine, F. ; Nagendra, H. ; Lucas, R. ; Mairota, P. ; Mücher, C.A. ; Blonda, P. - \ 2013
Landscape Ecology 28 (2013)5. - ISSN 0921-2973 - p. 905 - 930.
biodiversity - database - europe
Periodic monitoring of biodiversity changes at a landscape scale constitutes a key issue for conservation managers. Earth observation (EO) data offer a potential solution, through direct or indirect mapping of species or habitats. Most national and international programs rely on the use of land cover (LC) and/or land use (LU) classification systems. Yet, these are not as clearly relatable to biodiversity in comparison to habitat classifications, and provide less scope for monitoring. While a conversion from LC/LU classification to habitat classification can be of great utility, differences in definitions and criteria have so far limited the establishment of a unified approach for such translation between these two classification systems. Focusing on five Mediterranean NATURA 2000 sites, this paper considers the scope for three of the most commonly used global LC/LU taxonomies—CORINE Land Cover, the Food and Agricultural Organisation (FAO) land cover classification system (LCCS) and the International Geosphere-Biosphere Programme to be translated to habitat taxonomies. Through both quantitative and expert knowledge based qualitative analysis of selected taxonomies, FAO-LCCS turns out to be the best candidate to cope with the complexity of habitat description and provides a framework for EO and in situ data integration for habitat mapping, reducing uncertainties and class overlaps and bridging the gap between LC/LU and habitats domains for landscape monitoring—a major issue for conservation. This study also highlights the need to modify the FAO-LCCS hierarchical class description process to permit the addition of attributes based on class-specific expert knowledge to select multi-temporal (seasonal) EO data and improve classification. An application of LC/LU to habitat mapping is provided for a coastal Natura 2000 site with high classification accuracy as a result.
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org
Eijssen, L.M. ; Jaillard, M. ; Adriaens, M.E. ; Gaj, S. ; Groot, P.J. de; Müller, M.R. ; Evelo, C.T. - \ 2013
Nucleic acids research 41 (2013)W1. - ISSN 0305-1048 - p. W71 - W76.
affymetrix-genechip data - expression analysis - probe level - bioconductor - interface - database - package - biology - biomart - update
Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.
Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome
Bargsten, J.W. ; Folta, A. ; Mlynárová, L. ; Nap, J.P.H. - \ 2013
PLoS ONE 8 (2013)11. - ISSN 1932-6203 - 11 p.
directed dna methylation - pol-ivb - sequence - chromatin - database - arabidopsis - proteins - transcripts - subfamilies - generation
As part of large protein complexes, Snf2 family ATPases are responsible for energy supply during chromatin remodeling, but the precise mechanism of action of many of these proteins is largely unknown. They influence many processes in plants, such as the response to environmental stress. This analysis is the first comprehensive study of Snf2 family ATPases in plants. We here present a comparative analysis of 1159 candidate plant Snf2 genes in 33 complete and annotated plant genomes, including two green algae. The number of Snf2 ATPases shows considerable variation across plant genomes (17-63 genes). The DRD1, Rad5/16 and Snf2 subfamily members occur most often. Detailed analysis of the plant-specific DRD1 subfamily in related plant genomes shows the occurrence of a complex series of evolutionary events. Notably tomato carries unexpected gene expansions of DRD1 gene members. Most of these genes are expressed in tomato, although at low levels and with distinct tissue or organ specificity. In contrast, the Snf2 subfamily genes tend to be expressed constitutively in tomato. The results underpin and extend the Snf2 subfamily classification, which could help to determine the various functional roles of Snf2 ATPases and to target environmental stress tolerance and yield in future breeding
Assess ecosystem resilience: Linking response and effect traits to environmental variability
Sterk, M. ; Gort, G. ; Klimkowska, A. ; Ruijven, J. van; Teeffelen, A.J.A. van; Wamelink, G.W.W. - \ 2013
Ecological Indicators 30 (2013). - ISSN 1470-160X - p. 21 - 27.
plant functional traits - european flora - species traits - climate-change - biodiversity - diversity - database - conservation - landscape - services
Disturbances, nature as well as human, are putting constant pressure on ecosystems. These include small scale disturbances like a falling tree, but also large scale disturbances like eutrophication and climate change. Resilience is a useful indicator to assess whether an ecosystem has the capacity to maintain functioning with environmental variability. In this study we tested whether plant functional traits can be distinguished to develop a response-and-effect framework for general predictions concerning resilience. We defined response traits to assess the system's resistance to disturbance, and effect traits to assess its recovery after disturbance. We used a dataset with 932 vegetation plots containing 104 species from a selected wetland area in The Netherlands. The environmental variability was related to response traits and the response traits to effect traits with RLQ analysis, fourth-corner analysis and Spearman's rank correlation. As a result, combinations of traits that specify effects of environmental change on ecosystem resilience were found. A strong resistance to environmental variability was shown, and consequently, a positive effect on resilience. Due to correlations between response and effect traits, combinations of traits were identified having a variable effect on the resilience of the system. In this way this study argues to further develop a response-and-effect framework to understand and assess ecosystem resilience. The selection of traits is system-specific, and therefore, one should only select those response and effect traits that differentiate between response to environmental variability and effects on ecosystem functioning.
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