Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains
Zych, K. ; Li, Y. ; Velde, K.J. van der; Joosen, R.V.L. ; Ligterink, W. ; Jansen, R.C. ; Arends, D. - \ 2015
BMC Bioinformatics 16 (2015). - ISSN 1471-2105 - 8 p.
Background Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. Results The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. Conclusion The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl
Impacts of urban expansion on nitrogen and phosphorus flows in the food system of Beijing from 1978 to 2008
Ma, L. ; Guo, J. ; Velthof, G.L. ; Li, Y. ; Chen, Q. ; Ma, W. ; Oenema, O. ; Zhang, F. - \ 2014
Global environmental change : human and policy dimensions 28 (2014). - ISSN 0959-3780 - p. 192 - 204.
environmental implications - nutrient flows - china - cities - consumption - chain - urbanization - metabolism - ecology - balance
Rapid growth of metropolitan areas is associated with increased flows of nitrogen (N) and phosphorus (P) in the food production–consumption system. However, quantitative analyses of these flows during urban expansion and information about their controlling factors are scarce. Here, we report on N and P flows in the food system of Beijing, which experienced a remarkable growth in population number between especially 1978–2008, using a combination of statistical data bases, surveys and the NUFER model (nutrient flow in the food system, environment and resource). The N (or P) cost of food is defined as the amount of ‘new’ N (or P) used in food production for the delivery of 1 kg N (or P) in the food entering household. ‘New’ N (P) includes fertilizer N (P), biological N fixation, atmospheric N deposition, and imports of N (P) via feed and food. Recycled N (P) includes N (P) in crop residues, manures and wastes. We found that the rapid increase in temporary migrants greatly increased food imports to Beijing metropolitan areas and thereby led to an apparent decrease of the N and P cost of food. The input of ‘new’ N to the food system of Beijing metropolitan areas increased from 180 to 281 Gg, and for P from 33.5 to 50.4 Gg during 1978–2008, as a result of increases in population and changes in food consumption patterns per capita. The food and feed imports in per cent of total ‘new’ N and P inputs increased from 31 to 63% for N and from 18 to 46% for P during 1978–2008. The N and P cost of the food was relatively low compared to the mean of China, and decreased over time. About 52% of the new N input and 85% of the new P input was not recycled in 2008, it accumulated as wastes (in crop residues, animal excreta, and human excreta and household wastes). The N and P use efficiencies in crop and animal production were low, i.e., only 17% for N and 11% for P in 2008. Total losses of ammonia (NH3) and nitrous oxide (N2O) to air and of N to groundwater and surface waters increased by a factor of about 3, and losses of P to groundwater and surface waters increased by a factor of 37 in the period 1978–2008. Key measures for decreasing N and P accumulation and losses are (1) developing satellite towns, (2) expelling animal production to rural areas, and (3) effective collection of the wastes and animal manure, and the utilization of these in rural areas outside Beijing. These findings may also portend changes in other metropolitan areas in China and elsewhere in the rapidly developing world.
What are the socio-economic impacts of genetically modified crops worldwide? A systematic map protocol
Garcia-Yi, J. ; Lapikanonth, T. ; Vionita, H. ; Vu, H. ; Yang, S. ; Zhong, Y. ; Li, Y. ; Nagelschneider, V. ; Schlindwein, B. ; Wesseler, J.H.H. - \ 2014
Environmental Evidence 3 (2014). - ISSN 2047-2382 - 35 p.
Genetically modified (GM) crops have generated a great deal of controversy. Since commercially introduced to farmers in 1996, the global area cultivated with GM crops has increased 94-fold. The rapid adoption of GM technology has had substantial socio-economic impacts which a vast amount of technical and non-technical literature has addressed in the last two decades. However, contradictory results between individual studies abound. Extensive and transparent reviews concerning this contentious and complex issue could help promote evidence-based dialogue among the diverse parties involved. This protocol specifies the methodology for identifying, evaluating, and mapping evidence related to the main review question: what are the socio-economic impacts of genetically modified crops worldwide? This question has been subdivided into the following topics: (a) farm-level impacts; (b) impacts of coexistence regulations; (c) impacts along the supply chain; (d) consumer-level impacts; (e) impacts on food security; and (f) environmental economic impacts. The search strategy includes the identification of primary studies from general scientific databases; global, regional, and national specialist databases; an on-line search engine; institutional websites; journal websites; subject experts/researchers; and serendipity. Searches will be conducted in six languages (Chinese, English, French, German, Portuguese, and Spanish). Identified studies will be screened for inclusion/exclusion criteria by a group of multi-language reviewers. Finally, pre-defined data from the studies will be extracted, mapped, and presented in a report. Potential research gaps will be identified and discussed, and the review process will be documented in an open-access database (i.e. CADIMA, http://www.cadima.info/).
Worm variation made accessible: Take your shopping cart to store, link, and investigate!
Snoek, L.B. ; Velde, K.J. van der; Li, Y. ; Jansen, R.C. ; Swertz, M.A. ; Kammenga, J.E. - \ 2014
Worm 3 (2014)1. - ISSN 2162-4054 - 7 p.
In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus
Lin, K. ; Limpens, E.H.M. ; Zhang, Z. ; Ivanov, S. ; Saunders, D.G.O. ; Mu, D. ; Pang, E. ; Cao, H. ; Cha, H. ; Lin, T. ; Zhou, Q. ; Shang, Y. ; Li, Y. ; Sharma, T.C. ; Velzen, R. van; Ruijter, N.C.A. de; Aanen, D.K. ; Win, J. ; Kamoun, S. ; Bisseling, T. ; Geurts, R. ; Huang, S.W. - \ 2014
Plos Genetics 10 (2014)1. - ISSN 1553-7404 - 13 p.
arbuscular mycorrhizal fungi - pathogen phytophthora-infestans - glomus-intraradices - sexual reproduction - protein families - cdna sequences - kingdom fungi - gene - identification - efficient
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
WormQTL HD—a web database for linking human disease to natural variation data in C. elegans
Velde, K.J. van der; Haan, M. de; Zych, K. ; Arends, D. ; Snoek, L.B. ; Kammenga, J.E. ; Jansen, R.C. ; Swertz, M.A. ; Li, Y. - \ 2014
Nucleic acids research 42 (2014)D1. - ISSN 0305-1048 - p. D794 - D801.
life-history traits - caenorhabditis-elegans - systems biology - stress-response - genotype - genome - qtl - environment - identification - polymorphism
Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism— Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.
Dietary patterns as compared with physical activity in relation to metabolic syndrome among Chinese adults
He, Y. ; Li, Y. ; Lai, J. ; Wang, D. ; Zhang, J. ; Fu, P. ; Yang, X. ; Qi, L. - \ 2013
Nutrition, Metabolism & Cardiovascular Diseases 23 (2013)10. - ISSN 0939-4753 - p. 920 - 928.
blood-pressure - population - prevalence - women - management - shanghai - health - risk
Aims: To examine the nationally-representative dietary patterns and their joint effects with physical activity on the likelihood of metabolic syndrome (MS) among 20,827 Chinese adults. Methods and results: CNNHS was a nationally representative cross-sectional observational study. Metabolic syndrome was defined according to the Joint Interim Statement definition. The "Green Water" dietary pattern, characterized by high intakes of rice and vegetables and moderate intakes in animal foods was related to the lowest prevalence of MS (15.9%). Compared to the "GreenWater" dietary pattern, the "Yellow Earth" dietary pattern, characterized by high intakes of refined cereal products, tubers, cooking salt and salted vegetable was associated with a significantly elevated odds of MS (odds ratio 1.66, 95% CI: 1.40e1.96), after adjustment of age, sex, socioeconomic status and lifestyle factors. The "Western/new affluence" dietary pattern characterized by higher consumption of beef/lamb, fruit, eggs, poultry and seafood also significantly associated with MS (odds ratio: 1.37, 95% CI: 1.13e1.67). Physical activity showed significant interactions with the dietary patterns in relation to MS risk (P for interaction = 0.008). In the joint analysis, participants with the combination of sedentary activity with the "Yellow Earth" dietary pattern or the "Western/new affluence" dietary pattern both had more than three times (95% CI: 2.8-6.1) higher odds of MS than those with active activity and the "Green Water" dietary pattern. Conclusions: Our findings from the large Chinese national representative data indicate that dietary patterns affect the likelihood of MS. Combining healthy dietary pattern with active lifestyle may benefit more in prevention of MS. (C) 2012 Elsevier B.V. All rights reserved.
Influence of soil humic and fulvic acid on the activity and stability of lysozyme and urease
Li, Y. ; Tan, W. ; Koopal, L.K. ; Wang, M. ; Liu, Fan ; Norde, W. - \ 2013
Environmental Science and Technology 47 (2013). - ISSN 0013-936X - p. 5050 - 5056.
isothermal titration calorimetry - insecticidal cry1ab protein - ionic-strength - prion protein - ph - adsorption - complexes - binding - substances - fractions
Humic substances (HS), including humic acids (HA) and fulvic acids (FA), are important components of soil systems. HS form strong complexes with oppositely charged proteins, which will lead to changes in the enzyme activity. The effect of soil HS on the activity and stability of two enzymes was investigated as a function of pH, ionic strength, and mass ratio HS/enzyme. Humic acid (JGHA) and fulvic acid (JGFA) are negatively charged, lysozyme is net positive at pH values below 10.4, and urease is net positive below pH 5.2 or net negative above pH 5.2. The enzyme activities in the HS-enzyme complexes were suppressed when the enzymes were oppositely charged to the HS. The largest activity suppression was observed around the mass ratio HS/enzyme where the HS-protein complex was at its isoelectric point (IEP). At the IEP strong aggregation of the complexes led to encapsulation of the enzyme. The ionic strength was important; an increase decreased complex formation, but increased aggregation. Due to the larger hydrophobicity of JGHA than JGFA, the reduction in enzyme activity was stronger for JGHA. The enzyme stability also decreased maximally at mass ratio around the IEP of the complex when HS and protein were oppositely charged. When urease and HS were both negatively charged no complexes were formed, but the presence of JGHA or JGFA improved the activity and stability of the enzyme.
Proton binding to soil humic and fulvic acids: Experiments and NICA-Donnan modelling
Tan, W. ; Xiong, J. ; Li, Y. ; Wang, M. ; Weng, L. ; Koopal, L.K. - \ 2013
Colloids and Surfaces. A: Physicochemical and Engineering Aspects 436 (2013). - ISSN 0927-7757 - p. 1152 - 1158.
natural organic-matter - metal-ion binding - potentiometric titrations - affinity distributions - base properties - substances - heterogeneity - parameters - adsorption
Proton binding to one soil fulvic acid (JGFA), two soil humic acids (JGHA, JLHA) and a lignite-based humic acid (PAHA) was investigated. The results were fitted to NICA-Donnan model and compared directly with the predictions using the generic parameters. NICA-Donnan model can describe proton binding satisfactorily when parameter fitting is allowed for humic substance (HS). However, predictions based on the generic parameter sets deviate for soil samples in a non-systematic way from the measured results. Replacing Qmax,H1 in generic parameter sets with material-specific values improves the predictions for soil HA significantly. For JGFA, the agreement between the model prediction and data is still not satisfactory after substitution. This is due to a very different pattern of site distribution of JGFA from that of generic FA. For two other soil FAs (FH-14, FH-22 of Milne's database) the generic predictions can be improved significantly with material-specific Qmax,H1. Adjusting also Qmax,H2 to HS material-specific value improves the prediction only slightly further. In practice, Qmax,H1 and Qmax,H2 of HS can be obtained in a relatively simple way by performing one acid–base titration at a given ionic strength and applying the procedure of Lenoir et al. to fit data to NICA equation. Introduction of thus obtained Qmax,H1 and Qmax,H2 into generic parameter sets improves the generic predictions significantly. The functional group contents as obtained by SG-method are not adequate for this purpose.
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Huang, Y. ; Li, Y. ; Burt, D.W. ; Chen, H. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Kraus, R.H.S. - \ 2013
Nature Genetics 45 (2013). - ISSN 1061-4036 - p. 776 - 783.
gene family evolution - positive selection - a virus - maximum-likelihood - phylogenetic trees - protein - transmission - duplication - expression - defensins
The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
Identifying genotype-by-environment interactions in the metabolism of germinating Arabidopsis seeds using Generalized Genetical Genomics
Joosen, R.V.L. ; Arends, D. ; Li, Y. ; Willems, L.A.J. ; Keurentjes, J.J.B. ; Ligterink, W. ; Jansen, R.C. ; Hilhorst, H.W.M. - \ 2013
Plant Physiology 162 (2013)2. - ISSN 0032-0889 - p. 553 - 566.
quantitative trait loci - chromatography-mass spectrometry - heterogeneous inbred family - natural allelic variation - controlling root-growth - plant development - line population - complex traits - potato-tuber - thaliana
A complex phenotype such as seed germination is the resultant of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with omics analysis can help to disentangle the genetic basis of such quantitative traits. This so called genetical genomics approach can effectively capture both genetic (G) and epistatic interactions (G:G). However, to understand how the environment interacts with genomic encoded information (G:E) a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated QTL mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. Additionally, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis seeds. Many changes were observed in the metabolome which are both under environmental and genetic control and their interactions. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics which requires a broad understanding of both plasticity and dynamic regulation.
Population structure of Phytophthora infestans in China – geographic clusters and presence of the EU genotype Blue_13
Li, Y. ; Lee, T.A.J. van der; Zhu, J.H. ; Jin, G.H. ; Lan, C.Z. ; Zhu, S.X. ; Zhang, R.F. ; Liu, B.W. ; Zhao, Z.J. ; Kessel, G.J.T. ; Huang, S.W. ; Jacobsen, E. - \ 2013
Plant Pathology 62 (2013)4. - ISSN 0032-0862 - p. 932 - 942.
potato - diversity - haplotypes - virulence - markers - tomato - dna
The population structure of Phytophthora infestans in China was studied and three mitochondrial haplotypes (Ia, IIa, IIb) were observed. Genetic analysis with 10 highly informative SSR markers identified 68 different genotypes, including three dominant clonal lineages. In the Chinese P. infestans population, the genotypes were strongly clustered according to their geographic origin. One of dominant clonal lineages was genetically similar to Blue_13, a dominant clonal lineage found in Europe since 2004. This is the first report of Blue_13 outside Europe. Only one mating type (A1) was found in the northern and southeastern provinces, but in southern and northwestern China both mating types were observed. The mating type ratio and SSR allele frequencies indicate that in China the sexual cycle of P. infestans is rare. These results emphasize that the migration of asexual propagules and the generation of subclonal variation are the dominant driving factors of the population structure of P. infestans in China. They may also have implications for the role of monitoring P. infestans populations in potato late blight management strategies in China
Generic Top-Functionalization of Patterned Antifouling Zwitterionic Polymers on Indium Tin Oxide
Li, Y. ; Giesbers, M. ; Zuilhof, H. - \ 2012
Langmuir 28 (2012)34. - ISSN 0743-7463 - p. 12509 - 12517.
transfer radical polymerization - click chemistry - poly(ethylene glycol) - protein adsorption - thin-film - surfaces - monolayers - coatings - biofunctionalization - nanoparticles
This paper presents a novel surface engineering approach that combines photochemical grafting and surface-initiated atom transfer radical polymerization (SI-ATRP) to attach zwitterionic polymer brushes onto indium tin oxide (ITO) substrates. The photochemically grafted hydroxyl-terminated organic layer serves as an excellent platform for initiator attachment, and the zwitterionic polymer generated via subsequent SI-ATRP exhibits very good antifouling properties. Patterned polymer coatings can be obtained when the surface with covalently attached initiator was subjected to photomasked UV-irradiation, in which the C–Br bond that is present in the initiator was broken upon exposure to UV light. A further, highly versatile top-functionalization of the zwitterionic polymer brush was achieved by a strain-promoted alkyne–azide cycloaddition, without compromising its antifouling property. The attached bioligand (here: biotin) enables the specific immobilization of target proteins in a spatially confined fashion, pointing to future applications of this approach in the design of micropatterned sensing platforms on ITO substrates
Hybrids of Organic Molecules and Flat, Oxide-Free Silicon: High-Density Monolayers, Electronic Properties, and Functionalization
Li, Y. ; Calder, S.A. ; Yaffe, O. ; Cahen, D. ; Haick, H. ; Kronik, L. ; Zuilhof, H. - \ 2012
Langmuir 28 (2012)26. - ISSN 0743-7463 - p. 9920 - 9929.
hydrogen-terminated si(111) - mixed methyl/allyl monolayers - alkyl monolayers - porous silicon - si surfaces - carrier lifetime - label-free - interfaces - hydrosilylation - passivation
Since the first report of Si–C bound organic monolayers on oxide-free Si almost two decades ago, a substantial amount of research has focused on studying the fundamental mechanical and electronic properties of these Si/molecule surfaces and interfaces. This feature article covers three closely related topics, including recent advances in achieving high-density organic monolayers (i.e., atomic coverage >55%) on oxide-free Si(111) substrates, an overview of progress in the fundamental understanding of the energetics and electronic properties of hybrid Si/molecule systems, and a brief summary of recent examples of subsequent functionalization on these high-density monolayers, which can significantly expand the range of applicability. Taken together, these topics provide an overview of the present status of this active area of research.
Photochemical Grafting and Patterning of Organic Monolayers on Indium Tin Oxide Substrates
Li, Y. ; Zuilhof, H. - \ 2012
Langmuir 28 (2012)12. - ISSN 0743-7463 - p. 5350 - 5359.
self-assembled monolayers - click chemistry - terminated monolayers - surface modification - biomolecular interfaces - aqueous-solutions - molecular layers - silicon - functionalization - attachment
Covalently attached organic layers on indium tin oxide (ITO) surfaces were prepared by the photochemical grafting with 1-alkenes. The surface modification was monitored with static water contact angle, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM) measurements. Hydrophobic methyl-terminated ITO surfaces can be obtained via the grafting of tetradec-1-ene, whereas the attachment of ¿-functionalized 1-alkenes leads to functionalized ITO surfaces. The use of a C=C—Ge(CH3)3 terminus allows for facile tagging of the surface with an azido group via a one-pot deprotection/click reaction, resulting in bio/electronically active interfaces. The combination of nonaggressive chemicals (alkenes), mild reaction conditions (room temperature), and a light-induced grafting that facilitates the direct patterning of organic layers makes this simple approach highly promising for the development of ITO-based (bio)electronic devices.
Testing two models for the estimation of leaf stomatal conductance in four greenhouse crops cucumber, chrysanthemum, tulip and lilium
Li, G. ; Lin, L. ; Dong, Y. ; An, D. ; Li, Y. ; Luo, W. ; Yin, X. ; Li, W. ; Shao, J. ; Zhou, Y. ; Dai, J. ; Chen, W. ; Zhao, C. - \ 2012
Agricultural and Forest Meteorology 165 (2012). - ISSN 0168-1923 - p. 92 - 103.
dioxide response curves - soil-water stress - gas-exchange - mesophyll conductance - temperature response - photosynthesis model - carbon-dioxide - net photosynthesis - critical-appraisal - elevated co2
Estimating leaf stomatal conductance for CO2 diffusion (gsc) is pivotal for further estimation of crop transpiration as well as energy and mass balances between air and plant in greenhouses. In this study, we tested two models, i.e. the Jarvis model and a new version of BWB–Leuning model (BWB–Leuning–Yin model), for estimating gsc in four greenhouse crops (cucumber, chrysanthemum, tulip and lilium), using data from extensive experiments conducted under a wide range of environmental conditions from 2003 to 2010. The models were parameterized from a subset of the experimental data. The remaining data sets for model validation were classified into two groups: group one was from experiments conducted during the similar seasons at the same sites as those for model parameterization, whereas group two was from experiments in different seasons and sites. When using data of group one, both models gave satisfactory estimations of gsc under both ample water supply and water stress conditions. When using data of group two, the BWB–Leuning–Yin model gave better estimations of gsc than the Jarvis model did. Functions or parameters of the Jarvis model, if applied to independent environmental conditions, have to be re-derived. Compared to its earlier versions, the BWB–Leuning–Yin model gave better estimated gsc under low light intensities and low CO2 concentrations, suggesting that the new version is especially suitable for estimation of gsc for crops grown in low-investment greenhouses where levels of light and CO2 are lower than ambient levels. In addition, analytical algorithms for the coupled FvCB model and diffusional conductance as adopted in the BWB–Leuning–Yin model make parameterization and simultaneous estimation of net photosynthetic rate and gsc an easy task, using readily obtained information
Application of satellite remote sensing for mapping wind erosion risk and dusk emission-deposition in Inner Mongolia grassland, China
Reiche, M. ; Funk, R. ; Zhang, Z. ; Hoffmann, C. ; Reiche, J. ; Wehrhan, M. ; Li, Y. ; Sommer, M. - \ 2012
Grassland Science 58 (2012)1. - ISSN 1744-6961 - p. 8 - 19.
vegetation indexes - northern china - landsat tm - degradation - variability - topography - forest - cover - hills - aster
Intensive grazing leads to land degradation and desertification of grassland ecosystems followed by serious environmental and social problems. The Xilingol steppe grassland in Inner Mongolia, China, which has been a sink area for dust for centuries, is strongly affected by the negative effects of overgrazing and wind erosion. The aim of this study is the provision of a wind erosion risk map with a spatial high resolution of 25 m to identify actual source and sink areas. In an integrative approach, field measurements of vegetation features and surface roughness length z0 were combined with Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) image data for a land use classification. To determine the characteristics of the different land use classes, a field observation (ground truth) was performed in April 2009. The correlation of vegetation height and z0 (R2 = 0.8, n = 55) provided the basis for a separation of three main classes, “grassland”, “non-vegetation” and “other”. The integration of the soil-adjusted vegetation index (SAVI) and the spectral information from the atmospheric corrected ASTER bands 1, 2 and 3 (visible to near-infrared) led to a classification of the overall accuracy (OA) of 0.79 with a kappa () statistic of 0.74, respectively. Additionally, a digital elevation model (DEM) was used to identify topographical effects in relation to the main wind direction, which enabled a qualitative estimation of potential dust deposition areas. The generated maps result in a significantly higher description of the spatial variability in the Xilingol steppe grassland reflecting the different land use intensities on the current state of the grassland – less, moderately and highly degraded. The wind erosion risk map enables the identification of characteristic mineral dust sources, sinks and transition zones.
Production of oat-based synbiotic beverage by two-stage fermentation with Rhizopus oryzae and Lactobacillus acidophilus
Gao, F. ; Cai, S. ; Nout, M.J.R. ; Wang, Y. ; Xia, Y. ; Li, Y. ; Ji, B. - \ 2012
Journal of Food, Agriculture & Environment 10 (2012)2. - ISSN 1459-0255 - p. 175 - 179.
lactic-acid bacteria - beta-glucan - dietary fiber - in-vitro - survival - bifidobacterium - temperature - strains - health - model
Many studies have reported that oats could effectively reduce the serum cholesterol levels in humans, and the ß-glucan in oat is believed to be responsible for this physiologic effect. Probiotics are live microorganisms that can confer a healthy benefit on the host when administered in adequate amounts. There is an increasing use of these microorganisms in food, aiming to balance intestinal microflora and alleviate dysfunction of the human gastrointestinal tract. However, a number of studies have shown that only 10-30% of these probiotic bacteria could survive after passing through the gastrointestinal (GI) tract. Lactobacillus acidophilus is used as a probiotic bacterium in many probiotic foods. However, L. acidophilus shows poor growth in cereal products due to its poor hydrolytic ability of protein and macromolecule carbohydrates. The aim of the present study was to combine Rhizopus oryzae-fermented oat mash and Lactobacillus acidophilus in an oat-based synbiotic beverage. Several factors, including starter culture concentration, R. oryzae-fermented oat mash and skim milk powder, were investigated. The nutritional contents in R. oryzae-fermented oat flour were just sufficient for survival but not growth of L. acidophilus. Adding sucrose (1% or 2%, w/v) did not improve the proliferation of L. acidophilus; however, L. acidophilus grew quickly when skim milk powder (1% or 2%, w/v) was added. When 5.5% R. oryzae-fermented oat mash with 2% added skim milk powder was used, the viable cell counts reached about 9.0 log cfu/ml at the end of 10 h fermentation. The concentration of ß-glucans (about 781 mg/l) was not significantly lowered during fermentation.
|WormQTL – Public archive and analysis web portal for C. elegans natural variation data
Snoek, L.B. ; Li, Y. ; Velde, J.K. van der; Arends, D. ; Beyer, A. ; Elvin, M. ; Fisher, J. ; Hajnal, A. ; Hengartner, M. ; Poulin, G. ; Rodriguez Sanchez, M. ; Schmid, T. ; Schrimpf, S. ; Xue, F. ; Zheng, X. ; Jansen, R.C. ; Kammenga, J.E. ; Swertz, M.A. - \ 2012
In: Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. - - p. 48 - 48.
WormQTL – Public archive and analysis web portal for C. elegans natural variation data Basten L Snoek¹, Yang Li², Joeri K van der Velde², Danny Arends², Antje Beyer³, Mark Elvin 4, Jasmin Fisher³, Alex Hajnal5, Michael Hengartner5, Gino B Poulin4, Miriam Rodriguez¹,Tobias Schmid5, Sabine Schrimpf5, Feng Xue4, Xue Zheng5 , Ritsert C Jansen², Jan E Kammenga¹, Morris A Swertz2,6 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Groningen, Bioinformatics Centre, Groningen, 9747AG, Netherlands, ³Microsoft Research, Programming Principles and Tools, Cambridge, CB3 0FB, United Kingdom, 4 University of Manchester, Life Sciences, Manchester, M13 9PT, United Kingdom, 5University of Zurich, Molecular Life Sciences, Zurich, CH-8057, Switzerland, 6University Medical Centre, Genomics Coordination, Groningen, 9700RB, Netherlands Over the past decade increased efforts have been made to explore the model species C. elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a huge amount of phenotypic and genotypic data across developmental worm stages and environments. To facilitate the accessibility, comparative analysis and meta-analysis of all these data we present WormQTL, a public web portal for the management of all these new data and for integrated development of suitable analysis tools. The web server provides a rich set of data and analysis tools available for direct use, based on R/qtl software. But users can also upload and share new scripts as ‘plugin’ for colleagues in the community. Furthermore, new data can be uploaded and downloaded using XGAP, which is an extensible text format for genotypes and phenotypes (Swertz et al. 2010a). All data and tools can be accessed via web user interfaces and programming interfaces. Large consortia as well as individual researchers can make use of a private area that is under embargo for publication. All software is free for download as MOLGENIS ‘app’ (Swertz et al. 2010b). WormQTL is freely accessible without registration and is hosted on a large computational cluster enabling high throughput analyses. We present WormQTL as an online scalable system for QTL exploration to service the worm community. WormQTL provides many publicly available datasets and welcomes submissions from other worm researchers. Funding: The Centre for BioSystems Genomics (CBSG) and the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.
Functional stacking of three resistance genes against Phytophthora infestans in potato
Suxian Zhu, Suxian ; Li, Y. ; Vossen, J.H. ; Visser, R.G.F. ; Jacobsen, E. - \ 2012
Transgenic Research 21 (2012)1. - ISSN 0962-8819 - p. 89 - 99.
late blight resistance - broad-spectrum resistance - solanum-bulbocastanum - disease resistance - plant-resistance - transformation - expression - protein - bombardment - effector
Functional stacking of broad spectrum resistance (R) genes could potentially be an effective strategy for more durable disease resistance, for example, to potato late blight caused by Phytophthora infestans (Pi). For this reason, three broad spectrum potato R genes (Rpi), Rpi-sto1 (Solanum stoloniferum), Rpi-vnt1.1 (S. venturii) and Rpi-blb3 (S. bulbocastanum) were selected, combined into a single binary vector pBINPLUS and transformed into the susceptible cultivar Desiree. Among the 550 kanamycin resistant regenerants, 28 were further investigated by gene specific PCRs. All regenerants were positive for the nptII gene and 23 of them contained the three Rpi genes, referred to as triple Rpi gene transformants. Detached leaf assay and agro-infiltration of avirulence (Avr) genes showed that the 23 triple Rpi gene transformants were resistant to the selected isolates and showed HR with the three Avr effectors indicating functional stacking of all the three Rpi genes. It is concluded that Avr genes, corresponding to the R genes to be stacked, must be available in order to assay for functionality of each stack component. No indications were found for silencing or any other negative effects affecting the function of the inserted Rpi genes. The resistance spectrum of these 23 triple Rpi gene transformants was, as expected, a sum of the spectra from the three individual Rpi genes. This is the first example of a one-step approach for the simultaneous domestication of three natural R genes against a single disease by genetic transformation.