Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
Sustainability of milk production in the Netherlands - A comparison between raw organic, pasteurised organic and conventional milk
Asselt, E.D. van; Capuano, E. ; Fels-Klerx, H.J. van der - \ 2015
International Dairy Journal 47 (2015). - ISSN 0958-6946 - p. 19 - 26.
life-cycle assessment - environmental impacts - production systems - dairy farms - tool - metaanalysis - agriculture - consumption - indicators - quality
Consumer preferences are changing, resulting in an increased demand for both organic milk and raw milk due to their perceived higher nutritional value and positive contribution to animal welfare. To compare the advantages and disadvantages of these products with conventional pasteurised milk, a sustainability assessment was performed incorporating social, environmental and economic factors. The assessment showed that raw organic milk gave the highest overall sustainability score. This is due to, for example, a high score for animal welfare and a high score for the environmental factors due to the omission of the pasteurisation step compared with conventional milk. The latter may pose human health risks due to the possible presence of pathogens in raw milk. As the approach followed is transparent, it allows policy makers to discuss the outcome of the sustainability assessment both with stakeholders and the general public, which will facilitate the decision making process.
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.
Detection of sunflower oil in extra virgin olive oil by fast differential scanning calorimetry
Wetten, I.A. ; Herwaarden, A.W. ; Splinter, R. ; Boerrigter-Eenling, R. ; Ruth, S.M. van - \ 2015
Thermochimica Acta 603 (2015). - ISSN 0040-6031 - p. 237 - 243.
crystallization - discrimination - adulteration - polymers - tool - dsc
Extra virgin olive oil (EVOO) is an economically valuable product, due to its high quality and premium price. Therefore it is vulnerable for adulteration by means of the addition of cheaper vegetable oils. Differential scanning calorimetry (DSC) has been suggested as a fast technique for the detection of adulteration. However, measurements still take several hours. Fast DSC measurements take several minutes. Therefore this study investigates the applicability of fast DSC for the detection of sunflower oil (SFO) in EVOO. Nine EVOOs, five SFOs and three mixtures were analysed. Cooling curves of EVOO and SFO show one major exothermic peak. Because the cooling curves of EVOO and SFO are very similar they cannot be used for the detection of adulteration. Heating curves of EVOOs show two major endothermic peaks after slow cooling (-2 °C/s), heating curves of SFOs only one. Addition of SFO to EVOO caused a rapid decrease in the coldest endothermic peak and can therefore be used in the detection of adulteration of EVOO by SFO. Depending on the type of olive oil, the presence of 2–10% SFO can already be detected.
Combining backcasting and exploratory scenarios to develop robust water strategies in face of uncertain futures
Vliet, M. van; Kok, K. - \ 2015
Mitigation and Adaptation Strategies for Global Change 20 (2015)1. - ISSN 1381-2386 - p. 43 - 74.
klimaatverandering - waterbeheer - onzekerheidsanalyse - methodologie - climatic change - water management - uncertainty analysis - methodology - stakeholder participation - sustainability - framework - management - visions - europe - world - land - tool
Water management strategies in times of global change need to be developed within a complex and uncertain environment. Scenarios are often used to deal with uncertainty. A novel backcasting methodology has been tested in which a normative objective (e.g. adaptive water management) is backcasted within the context of exploratory scenarios that sketch four different plausible futures (Economy First, Policy Rules, Fortress Europe, and Sustainability Eventually). The main advantage of combining exploratory and normative scenarios is in the identification of robust actions: actions that are effective in the different socio-environmental contexts sketched in the exploratory scenarios. This paper has three objectives: (1) to present the methodology, focussing on its novel aspects (2) to test the methodology and evaluate its perceived success by analysing organiser and stakeholder feedback and (3) to analyse and evaluate the results, in order to study the impact of the exploratory scenarios on the backcasting results and the added value of robust actions. The methodology was successfully tested in 9 local and one regional case study in a water project water scenarios for Europe and for Neighbouring States (SCENES). Results showed that the exploratory scenarios influenced the content of the backcasts, thus making the identification of robust strategies possible. The list of robust strategies includes both technological and social/organisational strategies, highlighting the need for an integrated approach. The approach shows high potential, but as the methodology is in its infancy more research is needed, particularly in methods to facilitate and monitor information flow between exploratory scenarios and backcasts.
Agrobacterium tumefaciens-mediated transformation of Lasiodiplodia theobromae, the causal agent of gummosis in cashew nut plants
Muniz, C.R. ; Silva, C.F. da; Souza, M.T. ; Freire, F.C.O. ; Kema, G.H.J. ; Guedes, M.I.F. - \ 2014
Genetics and Molecular Research 13 (2014)2. - ISSN 1676-5680 - p. 2906 - 2913.
filamentous fungi - genetic-transformation - proteins - tool
Lasiodiplodia theobromae is a major pathogen of many different crop cultures, including cashew nut plants. This paper describes an efficient Agrobacterium tumefaciens-mediated transformation (ATMT) system for the successful delivery of T-DNA, transferring the genes of green fluorescent protein (gfp) and hygromycin B phosphotransferase (hph) to L. theobromae. When the fungal pycnidiospores were co-cultured with A. tumefaciens harboring the binary vector with hph-gfp gene, hygromycin-resistant fungus only developed with acetosyringone supplementation. The cashew plants inoculated with the fungus expressing GFP revealed characteristic pathogen colonization by epifluorescence microscopy. Intense and bright green hyphae were observed for transformants in all extensions of mycelium cultures. The penetration of parenchyma cells near to the inoculation site, beneath the epicuticle surface, was observed prior to 25 dpi. Penetration was followed by the development of hyphae within invaded host cells. These findings provide a rapid and reproducible ATMT method for L. theobromae transformation.
Fuzzy Cognitive Maps for futures studies : a methodological assessment of concepts and methods
Jetter, J.J. ; Kok, K. - \ 2014
Futures 61 (2014). - ISSN 0016-3287 - p. 45 - 57.
mapping approach - mental models - knowledge - scenarios - stakeholders - integration - management - policy - tool
Fuzzy Cognitive Map (FCM) modelling is highly suitable for the demands of future studies: it uses a mix of qualitative and quantitative approaches, it enables the inclusion of multiple and diverse sources to overcome the limitations of expert opinions, it considers multivariate interactions that lead to nonlinearities, and it aims to make implicit assumptions (or mental models) explicit. Despite these properties, the field of future studies is slow to adopt FCM and to apply the increasingly solid theoretical foundations and rigorous practices for FCM applications that are evolving in other fields. This paper therefore discusses theoretical and practical aspects of constructing and applying FCMs within the context of future studies: based on an extensive literature review and the authors’ experience with FCM projects, it provides an introduction of fundamental concepts of FCM modelling, a step-wise description and discussion of practical methods and their pitfalls, and an overview over future research directions for FCM in future studies.
Physiological and biochemical responses of Ricinus communis seedlings to different temperatures: a metabolomics approach
Ribeiro de Jesus, P.R. ; Fernandez, L.G. ; Delmondez de Castro, R. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229 - 14 p.
abiotic stress tolerance - castor-oil - phenotypic plasticity - plant-responses - arabidopsis - growth - metabolism - tool - oligosaccharides - biodiesel
Background Compared with major crops, growth and development of Ricinus communis is still poorly understood. A better understanding of the biochemical and physiological aspects of germination and seedling growth is crucial for the breeding of high yielding varieties adapted to various growing environments. In this context, we analysed the effect of temperature on growth of young R. communis seedlings and we measured primary and secondary metabolites in roots and cotyledons. Three genotypes, recommended to small family farms as cash crop, were used in this study. Results Seedling biomass was strongly affected by the temperature, with the lowest total biomass observed at 20°C. The response in terms of biomass production for the genotype MPA11 was clearly different from the other two genotypes: genotype MPA11 produced heavier seedlings at all temperatures but the root biomass of this genotype decreased with increasing temperature, reaching the lowest value at 35°C. In contrast, root biomass of genotypes MPB01 and IAC80 was not affected by temperature, suggesting that the roots of these genotypes are less sensitive to changes in temperature. In addition, an increasing temperature decreased the root to shoot ratio, which suggests that biomass allocation between below- and above ground parts of the plants was strongly affected by the temperature. Carbohydrate contents were reduced in response to increasing temperature in both roots and cotyledons, whereas amino acids accumulated to higher contents. Our results show that a specific balance between amino acids, carbohydrates and organic acids in the cotyledons and roots seems to be an important trait for faster and more efficient growth of genotype MPA11. Conclusions An increase in temperature triggers the mobilization of carbohydrates to support the preferred growth of the aerial parts, at the expense of the roots. A shift in the carbon-nitrogen metabolism towards the accumulation of nitrogen-containing compounds seems to be the main biochemical response to support growth at higher temperatures. The biochemical changes observed in response to the increasing temperature provide leads into understanding plant adaptation to harsh environmental conditions, which will be very helpful in developing strategies for R. communis crop improvement research.
An integrated catalog of reference genes in the human gut microbiome
Li, J. ; Jia, H. ; Cai, X. ; Zhong, H. ; Feng, Q. ; Sunagawa, S. ; Arumugam, M. ; Kultima, J.R. ; Prifti, E. ; Nielsen, T. ; Juncker, A.S. ; Manichanh, C. ; Chen, B. ; Zhang, W. ; Levenez, F. ; Xu, X. ; Xiao, L. ; Liang, S. ; Zhang, D. ; Zhang, Z. ; Chen, W. ; Zhao, H. ; Al-Aama, J.Y. ; Edris, S. ; Yang, H. ; Hansen, H. ; Nielsen, H.B. ; Brunak, S. ; Kristiansen, K. ; Guarner, F. ; Pedersen, O. ; Doré, J. ; Ehrlich, S.D. ; Bork, P. ; Wang, J. ; Vos, W.M. de; Tims, S. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2014
Nature Biotechnology 32 (2014)8. - ISSN 1087-0156 - p. 834 - 841.
eukaryotic diversity - fecal microbiota - population-size - metagenome - sequences - genomes - tool - alignment - impact - twins
Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nielsen, H.B. ; Almeida, M. ; Sierakowska Juncker, A. ; Rasmussen, S. ; Li, J. ; Sunagawa, S. ; Plichta, D.R. ; Gautier, L. ; Pedersen, A.G. ; Chatelier, E. Le; Pelletier, E. ; Bonde, I. ; Nielsen, T. ; Manichanh, C. ; Arumugam, M. ; Batto, J.M. ; Quintanilha dos Santos, M.B. ; Blom, N. ; Borruel, N. ; Burgdorf, K.S. ; Boumezbeur, F. ; Casellas, F. ; Doré, J. ; Dworzynski, P. ; Guarner, F. ; Hansen, T. ; Hildebrand, F. ; Kaas, R.S. ; Kennedy, S. ; Kristiansen, K. ; Kultima, J.R. ; Leonard, P. ; Levenez, F. ; Lund, O. ; Moumen, B. ; Paslier, D. Le; Pons, N. ; Pedersen, O. ; Prifti, E. ; Qin, J. ; Raes, J. ; Sørensen, S. ; Tap, J. ; Tims, S. ; Ussery, D.W. ; Yamada, T. ; Jamet, A. ; Mérieux, A. ; Cultrone, A. ; Torrejon, A. ; Quinquis, B. ; Brechot, C. ; Delorme, C. ; M'Rini, C. ; Vos, W.M. de; Maguin, E. ; Varela, E. ; Guedon, E. ; Gwen, F. ; Haimet, F. ; Artiguenave, F. ; Vandemeulebrouck, G. ; Denariaz, G. ; Khaci, G. ; Blottière, H. ; Knol, J. ; Weissenbach, J. ; Hylckama Vlieg, J.E. van; Torben, J. ; Parkhil, J. ; Turner, K. ; Guchte, M. van de; Antolin, M. ; Rescigno, M. ; Kleerebezem, M. ; Derrien, M. ; Galleron, N. ; Sanchez, N. ; Grarup, N. ; Veiga, P. ; Oozeer, R. ; Dervyn, R. ; Layec, S. ; Bruls, T. ; Winogradski, Y. ; Zoetendal, E.G. ; Renault, D. ; Sicheritz-Ponten, ; Bork, P. ; Wang, J. ; Brunak, S. ; Ehrlich, S.D. - \ 2014
Nature Biotechnology 32 (2014). - ISSN 1087-0156 - p. 822 - 828.
short read alignment - sequences - systems - algorithms - microbiota - protein - life - sets - tree - tool
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
Get your high-quality low-cost genome sequence
Faino, L. ; Thomma, B.P.H.J. - \ 2014
Trends in Plant Science 19 (2014)5. - ISSN 1360-1385 - p. 288 - 291.
generation - assemblies - alignments - annotation - program - tool
The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model organisms. Here, we show that a high-quality draft genome of a eukaryote can be obtained at relatively low cost by exploiting a hybrid combination of sequencing strategies.
Complementary symbiont contributions to plant decomposition in a fungus-farming termite
Poulsen, M. ; Hu, H. ; Li, C. ; Chen, Z. ; Xu, L. ; Otani, S. ; Nygaard, S. ; Nobre, T. ; Klaubauf, S. ; Schindler, P.M. ; Hauser, F. ; Pan, H. ; Yang, Z. ; Sonnenberg, A.S.M. ; Beer, W. de; Zhang, Y. ; Wingfield, M.J. ; Grimmelikhuijzen, C.J.P. ; Vries, R.P. de; Korb, J. ; Aanen, D.K. ; Wang, J. ; Boomsma, J.J. ; Zhang, G. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)40. - ISSN 0027-8424 - p. 14500 - 14505.
growing termites - bacterial community - gut microbiota - markov-models - genomes - termitomyces - evolution - tool - macrotermitinae - lignocellulose
Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis have remained enigmatic. We obtained high-quality annotated draft genomes of the termite Macrotermes natalensis, its Termitomyces symbiont, and gut metagenomes from workers, soldiers, and a queen. We show that members from 111 of the 128 known glycoside hydrolase families are represented in the symbiosis, that Termitomyces has the genomic capacity to handle complex carbohydrates, and that worker gut microbes primarily contribute enzymes for final digestion of oligosaccharides. This apparent division of labor is consistent with the Macrotermes gut microbes being most important during the second passage of comb material through the termite gut, after a first gut passage where the crude plant substrate is inoculated with Termitomyces asexual spores so that initial fungal growth and polysaccharide decomposition can proceed with high efficiency. Complex conversion of biomass in termite mounds thus appears to be mainly accomplished by complementary cooperation between a domesticated fungal monoculture and a specialized bacterial community. In sharp contrast, the gut microbiota of the queen had highly reduced plant decomposition potential, suggesting that mature reproductives digest fungal material provided by workers rather than plant substrate.
Analysis of organic contaminant desorption kinetic data for sediments and soils: Implications for the Tenax extraction time for the determination of bioavailable concentrations
Noort, P.C.M. van; Poot, A. ; Koelmans, A.A. - \ 2014
Science of the Total Environment 490 (2014). - ISSN 0048-9697 - p. 235 - 238.
polybrominated diphenyl ethers - in-field sediments - black carbon - availability - insecticides - pyrethroids - sorption - predict - tool
Solid-phase extractions with adsorbents like Tenax have been widely used to assess bioaccessible or bioavailable concentrations and non-extractable residues (NER) of organic contaminants in soils or sediments. This paper presents an analysis of literature rate constants and fractions for rapid, slow and very slow contaminant desorption from soils and sediments. Contaminant fractions desorbed from sediment to Tenax in 6 or 24. h were evaluated as to their adequacy as a proxy for rapidly desorbing fractions, which have been shown to correlate with bioavailable concentrations. Desorption rate constants appear to decrease with increasing contaminant n-octanol-water partition coefficient. The ratio of the fraction of contaminant desorbed from sediment to Tenax in 6. h and the rapidly desorbing fraction appeared to slightly decrease on increasing contaminant hydrophobicity. This was not the case for the extraction for 24. h. Rapidly desorbing fractions or bioavailable fractions can be estimated, within a factor of 1.4, by multiplying the fraction desorbed in 24. h by a factor of 0.7.
Metabolomics reveals organ-specific metabolic rearrangements during early tomato seedling development
Gomez-Roldan, M.V. ; Engel, B. ; Vos, R.C.H. de; Vereijken, P.F.G. ; Astola, L. ; Groenenboom, M.A.C. ; Geest, H.C. van de; Bovy, A.G. ; Molenaar, J. ; Eeuwijk, F.A. van; Hall, R.D. - \ 2014
Metabolomics 10 (2014)5. - ISSN 1573-3882 - p. 958 - 974.
transcriptome coexpression analysis - mass-spectrometry - fruit-development - integrated analysis - network analysis - systems biology - arabidopsis - pathway - expression - tool
Tomato seedlings (Solanum lycopersicum cv.MoneyMaker), grown under strictly controlled conditions, have been used to study alterations occurring in secondary metabolite biosynthetic pathways following developmental and environmental perturbations. Robustness and reproducibility of the system were confirmed using detailed statistical analyses of the metabolome. LCMS profiling was applied using whole germinated seeds as well as cotyledons, hypocotyls and roots from 3 to 9 days old seedlings to generate relative levels of 433 metabolites, of which 62 were annotated. Initial focus was given to the polyphenol pathway and several additional mass signals have been putatively annotated using high mass resolution fragmentation. Clear organ and developmental stage—specific differences were observed. Seeds accumulated saponin-like compounds; roots accumulated mainly alkaloids; cotyledons contained mainly glycosylated flavonols and; hypocotyls contained mainly anthocyanins. For each organ, the developmental changes in metabolite profiles were described by using linear mixed models. Across three independent experiments, 85 % of the metabolites showed similar developmental trends. This tomato seedling system has given us valuable additional insights into the complexity of seedling secondary metabolism. How metabolic profiles reflect an interplay between depletion of stored molecules and de novo synthesis and how the overall picture for this important crop plant contrasts to e.g. Arabidopsis are emphasised.
A protocol for evaluating the sustainability of agri-food production systems - case study on potato production in peri-urban agriculture in The Netherlands.
Asselt, E.D. van; Bussel, L.G.J. van; Voet, H. van der; Heijden, G.W.A.M. van der; Tromp, S.O. ; Rijgersberg, H. ; Evert, F.K. van; Wagenberg, C.P.A. van; Fels, H.J. van der - \ 2014
Ecological Indicators 43 (2014). - ISSN 1470-160X - p. 315 - 321.
indicators - tool
Frameworks describing the overall assessment of sustainability are limited and usually not well described. This study proposes a protocol for the selection and quantification of indicators that can be used to discuss and communicate the sustainability of agri-food production systems. A gross list of indicators was established covering the social, environmental and economic dimensions. Core indicators were selected from this gross list using predefined criteria. Then, sustainability limits were set for these core indicators to evaluate their sustainability impact. Policy makers can determine the effects of different weights and the extent to which indicators can compensate each other (compensability) either at the level of the individual indicator or on the overall sustainability. The protocol was tested in a case study comparing potato production in peri-urban agriculture to conventional and to organic agriculture. Data were based on literature, expert opinion and additional calculations. Application in the case study showed that the protocol can be a valuable tool in assessing the sustainability of agri-food production systems. It enables more transparent policy decisions and facilitates communication with stakeholders about these decisions.
A metabolomics approach to identify factors influencing glucosinolate thermal degradation rates in Brassica vegetables
Hennig, K. ; Vos, R.C.H. de; Maliepaard, C.A. ; Dekker, M. ; Verkerk, R. ; Bonnema, G. - \ 2014
Food Chemistry 155 (2014). - ISSN 0308-8146 - p. 287 - 297.
quantitative trait loci - mass-spectrometry - red cabbage - oleracea - flavonols - health - leaves - tool
Thermal processing of Brassica vegetables can lead to substantial loss of potential health-promoting glucosinolates (GLs). The extent of thermal degradation of a specific GL varies in different vegetables, possibly due to differences in the composition of other metabolites within the plant matrices. An untargeted metabolomics approach followed by random forest regression was applied to identify metabolites associated to thermal GL degradation in a segregating Brassica oleracea population. Out of 413 metabolites, 15 were associated with the degradation of glucobrassicin, six with that of glucoraphanin and two with both GLs. Among these 23 metabolites three were identified as flavonols (one kaempferol- and two quercetinderivatives) and two as other GLs (4-methoxyglucobrassicin, gluconasturtiin). Twenty quantitative trait loci (QTLs) for these metabolites, which were associated with glucoraphanin and glucobrassicin degradation, were identified on linkage groups C01, C07 and C09. Two flavonols mapped on linkage groups C07 and C09 and co-localise with the QTL for GL degradation determined previously.
The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution
Bolton, M.D. ; Jonge, R. de; Inderbitzin, P. ; Liu, Z. ; Birla, K. ; Peer, Y. Van de; Subbarao, K. ; Thomma, B.P.H.J. ; Secor, G. - \ 2014
Fungal Genetics and Biology 62 (2014). - ISSN 1087-1845 - p. 43 - 54.
de-novo identification - sexual reproduction - neurospora-tetrasperma - molecular-organization - fungal pathogens - loci - systems - recombination - resistance - tool
Dothideomycetes is one of the most ecologically diverse and economically important classes of fungi. Sexual reproduction in this group is governed by mating type (MAT) genes at the MAT1 locus. Self-sterile (heterothallic) species contain one of two genes at MAT1 (MAT1-1-1 or MAT1-2-1) and only isolates of opposite mating type are sexually compatible. In contrast, self-fertile (homothallic) species contain both MAT genes at MAT1. Knowledge of the reproductive capacities of plant pathogens are of particular interest because recombining populations tend to be more difficult to manage in agricultural settings. In this study, we sequenced MAT1 in the heterothallic Dothideomycete fungus Cercospora beticola to gain insight into the reproductive capabilities of this important plant pathogen. In addition to the expected MAT gene at MAT1, each isolate contained fragments of both MAT1-1-1 and MAT1-2-1 at ostensibly random loci across the genome. When MAT fragments from each locus were manually assembled, they reconstituted MAT1-1-1 and MAT1-2-1 exons with high identity, suggesting a retroposition event occurred in a homothallic ancestor in which both MAT genes were fused. The genome sequences of related taxa revealed that MAT gene fragment pattern of Cercospora zeae-maydis was analogous to C. beticola. In contrast, the genome of more distantly related Mycosphaerella graminicola did not contain MAT fragments. Although fragments occurred in syntenic regions of the C. beticola and C. zeae-maydis genomes, each MAT fragment was more closely related to the intact MAT gene of the same species. Taken together, these data suggest MAT genes fragmented after divergence of M. graminicola from the remaining taxa, and concerted evolution functioned to homogenize MAT fragments and MAT genes in each species.
Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data
Hettne, K.M. ; Boorsma, A. ; Dartel, D.A.M. van; Goeman, J.J. ; Jong, E. de; Piersma, A.H. ; Stierum, R.H. ; Kleinjans, J.C. ; Kors, J.A. - \ 2013
BMC Medical Genomics 6 (2013). - ISSN 1755-8794 - 17 p.
stem-cell test - developmental toxicity - global test - disease - tool
Background: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles. Methods: We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values <0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data sets of five chemicals (from experimental models). We tested for SDE of gene sets for six fibrates in a peroxisome proliferator-activated receptor alpha (PPARA) knock-out GE dataset and compared to results from the Connectivity Map. We tested for SDE of 319 next-gen TM-derived gene sets for environmental toxicants in three GE data sets of triazoles, and tested for SDE of 442 gene sets associated with embryonic structures. We compared the gene sets to triazole effects seen in the Whole Embryo Culture (WEC), and used principal component analysis (PCA) to discriminate triazoles from other chemicals. Results: Next-gen TM-derived gene sets matching the chemical treatment were significantly altered in three GE data sets, and the corresponding CTD-derived gene sets were significantly altered in five GE data sets. Six next-gen TM-derived and four CTD-derived fibrate gene sets were significantly altered in the PPARA knock-out GE dataset. None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants had a similar toxicity pattern as the triazoles. We confirmed embryotoxic effects, and discriminated triazoles from other chemicals. Conclusions: Gene set analysis with next-gen TM-derived chemical response-specific gene sets is a scalable method for identifying similarities in gene responses to other chemicals, from which one may infer potential mode of action and/or toxic effect.
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Katayama, T. ; Wilkinson, D.W. ; Micklem, G. ; Kawashima, S. ; Yamaguchi, A. ; Nakao, M. ; Yamamoto, T. ; Okamoto, S. ; Oouchida, K. ; Chung, H. ; Aerts, J. ; Afzal, H. ; Antezana, E. ; Arakawa, K. ; Aranda, B. ; Belleau, F. ; Bolleman, J. ; Bonnal, R.J.P. ; Chapman, B. ; Cock, P.J.A. ; Eriksson, T. ; Gordon, P.M.K. ; Goto, N. ; Hayashida, K. ; Horn, H. ; Ishiwata, R. ; Kaminuma, E. ; Kasprzyk, A. ; Kawaji, H. ; Kido, N. ; Kim, Y. ; Kinjo, A.R. ; Konishi, F. ; Kwon, K.H. ; Labarga, A. ; Lamprecht, A. ; Lin, Y. ; Lindenbaum, P. ; McCarthy, L. ; Morita, H. ; Murakami, K. ; Nagao, K. ; Nishida, K. ; Nishimura, K. ; Nishizawa, T. ; Ogishima, S. ; Ono, K. ; Oshita, K. ; Park, K. ; Prins, J.C.P. ; Saito, T. ; Samwald, M. ; Satagopam, V.P. ; Shigemoto, Y. ; Smith, R. ; Splendiani, A. ; Sugawara, H. ; Taylor, J. ; Vos, R.A. ; Withers, D. ; Yamasaki, C. ; Zmasek, C.M. ; Kawamoto, S. ; Okubo, K. ; Asai, K. ; Takagi, T. - \ 2013
Journal of Biomedical Semantics 4 (2013). - ISSN 2041-1480
protein-interaction database - systems biology - ontology - bioinformatics - tool - representation - services - language - framework - networks
Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. source provider, through middleware, to the end-consumer.
Profiling the environmental risk management of Chinese local environmental agencies
He, G. ; Zhang, L. ; Mol, A.P.J. ; Lu, Y. - \ 2013
Journal of Risk Research 16 (2013)10. - ISSN 1366-9877 - p. 1259 - 1275.
governance - tool
The increasing frequency and impact of environmental accidents have pushed the issue of environmental risk management (ERM) to the top of the Chinese governments’ agendas and popularized the term ‘emergency response.’ Although the boundary between environmental accidents and other types of accidents is blurred and effective ERM requires an integrated and coordinated management system, environmental risks have not been given due weight in the overall risk management framework in China. The Ministry of Environmental Protection and Environmental Protection Bureaus at various governmental levels are responsible for the management of environmental risks. In recent years, major developments have taken place within these environmental agencies, but the upward trend in number of environmental accidents has remained unchanged. This raises questions on how these organizations respond to and prevent environmental risks, which shortcomings can be indicated, and what improvements can be made in ERM. This study addresses these questions through a survey among environmental bureaus at provincial and municipal levels. The results indicate that environmental emergency response and ERM have become a major concern of local environmental officials. However, the attitudes, available resources, and organizational capacities vary among environmental agencies, which results in considerable differences in the adopted strategies and management tools. This survey is the first attempt to profile the ERM of the Chinese environmental agencies, which serves as a basis for further analysis of ERM in China.