The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase
Koendjbiharie, Jeroen G. ; Hon, Shuen ; Pabst, Martin ; Hooftman, Robert ; Stevenson, David M. ; Cui, Jingxuan ; Amador-Noguez, Daniel ; Lynd, Lee R. ; Olson, Daniel G. ; Kranenburg, Richard van - \ 2020
Journal of Biological Chemistry 295 (2020)7. - ISSN 0021-9258 - p. 1867 - 1878.
The genomes of most cellulolytic clostridia do not contain genes annotated as transaldolase. Therefore, for assimilating pentose sugars or for generating C5 precursors (such as ribose) during growth on other (non-C5) substrates, they must possess a pathway that connects pentose metabolism with the rest of metabolism. Here we provide evidence that for this connection cellulolytic clostridia rely on the sedoheptulose 1,7-bisphosphate (SBP) pathway, using pyrophosphate-dependent phosphofructokinase (PPi-PFK) instead of transaldolase. In this reversible pathway, PFK converts sedoheptulose 7-phosphate (S7P) to SBP, after which fructose-bisphosphate aldolase cleaves SBP into dihydroxyacetone phosphate and erythrose 4-phosphate. We show that PPi-PFKs of Clostridium thermosuccinogenes and Clostridium thermocellum indeed can convert S7P to SBP, and have similar affinities for S7P and the canonical substrate fructose 6-phosphate (F6P). By contrast, (ATP-dependent) PfkA of Escherichia coli, which does rely on transaldolase, had a very poor affinity for S7P. This indicates that the PPi-PFK of cellulolytic clostridia has evolved the use of S7P. We further show that C. thermosuccinogenes contains a significant SBP pool, an unusual metabolite that is elevated during growth on xylose, demonstrating its relevance for pentose assimilation. Last, we demonstrate that a second PFK of C. thermosuccinogenes that operates with ATP and GTP exhibits unusual kinetics toward F6P, as it appears to have an extremely high degree of cooperative binding, resulting in a virtual on/off switch for substrate concentrations near its K1/2 value. In summary, our results confirm the existence of an SBP pathway for pentose assimilation in cellulolytic clostridia.
Machine learning for ecosystem services
Willcock, Simon ; Martínez-López, Javier ; Hooftman, Danny A.P. ; Bagstad, Kenneth J. ; Balbi, Stefano ; Marzo, Alessia ; Prato, Carlo ; Sciandrello, Saverio ; Signorello, Giovanni ; Voigt, Brian ; Villa, Ferdinando ; Bullock, James M. ; Athanasiadis, Ioannis N. - \ 2018
Ecosystem Services 33 (2018)B. - ISSN 2212-0416 - p. 165 - 174.
ARIES - Artificial intelligence - Big data - Data driven modelling - Data science - Machine learning - Mapping - Modelling - Uncertainty, Weka
Recent developments in machine learning have expanded data-driven modelling (DDM) capabilities, allowing artificial intelligence to infer the behaviour of a system by computing and exploiting correlations between observed variables within it. Machine learning algorithms may enable the use of increasingly available ‘big data’ and assist applying ecosystem service models across scales, analysing and predicting the flows of these services to disaggregated beneficiaries. We use the Weka and ARIES software to produce two examples of DDM: firewood use in South Africa and biodiversity value in Sicily, respectively. Our South African example demonstrates that DDM (64–91% accuracy) can identify the areas where firewood use is within the top quartile with comparable accuracy as conventional modelling techniques (54–77% accuracy). The Sicilian example highlights how DDM can be made more accessible to decision makers, who show both capacity and willingness to engage with uncertainty information. Uncertainty estimates, produced as part of the DDM process, allow decision makers to determine what level of uncertainty is acceptable to them and to use their own expertise for potentially contentious decisions. We conclude that DDM has a clear role to play when modelling ecosystem services, helping produce interdisciplinary models and holistic solutions to complex socio-ecological issues.
MODIS VCF should not be used to detect discontinuities in tree cover due to binning bias. A comment on Hanan et al. (2014) and Staver and Hansen (2015)
Gerard, France ; Hooftman, Danny ; Langevelde, Frank van; Veenendaal, Elmar ; White, Steven M. ; Lloyd, Jon - \ 2017
Global Ecology and Biogeography 26 (2017)7. - ISSN 1466-822X - p. 854 - 859.
alternative stable states - forest - frequency distribution - MODIS VCF - remote sensing - savanna - tree cover
In their recent paper, Staver and Hansen (Global Ecology and Biogeography, 2015, 24, 985–987) refute the case made by Hanan et al. (Global Ecology and Biogeography, 2014, 23, 259–263) that the use of classification and regression trees (CARTs) to predict tree cover from remotely sensed imagery (MODIS VCF) inherently introduces biases, thus making the resulting tree cover unsuitable for showing alternative stable states through tree cover frequency distribution analyses. Here we provide a new and equally fundamental argument for why the published frequency distributions should not be used for such purposes. We show that the practice of pre-average binning of tree cover values used to derive cover values to train the CART model will also introduce errors in the frequency distributions of the final product. We demonstrate that the frequency minima found at tree covers of 8–18%, 33–45% and 55–75% can be attributed to numerical biases introduced when training samples are derived from landscapes containing asymmetric tree cover distributions and/or a tree cover gradient. So it is highly likely that the CART, used to produce MODIS VCF, delivers tree cover frequency distributions that do not reflect the real world situation.
|Ringspots in Phalaenopsis, is there a role for a putative new virus?
Meekes, E. ; Dullemans, A.M. ; Hooftman, R. ; Gawehns, Fleur ; Ebskamp, M. ; Verbeek, M. ; Vlugt, R.A.A. van der; Lee, T.A.J. van der - \ 2016
Abiotic stress QTLs in lettuce crop–wild hybrids: comparing greenhouse and field experiments
Hartman, Y. ; Hooftman, D.A.P. ; Uwimana, B. ; Schranz, M.E. ; Wiel, C.C.M. van de; Smulders, M.J.M. ; Visser, R.G.F. ; Michelmore, R.W. ; Tienderen, P.H. van - \ 2014
Ecology and Evolution 4 (2014)12. - ISSN 2045-7758 - p. 2395 - 2409.
quantitative trait loci - genetically-modified crops - lactuca-sativa l. - domestication traits - root architecture - weedy populations - linkage maps - selection - introgression - tolerance
The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives.
Genomic and environmental selection patterns in two distinct lettuce crop-wild hybrid crosses
Hartman, Y. ; Uwimana, B. ; Hooftman, D.A.P. ; Schranz, M.E. ; Wiel, C.C.M. van de; Smulders, M.J.M. ; Visser, R.G.F. ; Tienderen, P.H. van - \ 2013
Evolutionary Applications 6 (2013)4. - ISSN 1752-4563 - p. 569 - 584.
quantitative trait loci - rape brassica-napus - lactuca-sativa l. - avena-barbata - transgressive segregation - field conditions - domestication traits - hybridization - fitness - introgression
Genomic selection patterns and hybrid performance influence the chance that crop (trans)genes can spread to wild relatives. We measured fitness(-related) traits in two different field environments employing two different crop–wild crosses of lettuce. We performed quantitative trait loci (QTL) analyses and estimated the fitness distribution of early- and late-generation hybrids. We detected consistent results across field sites and crosses for a fitness QTL at linkage group 7, where a selective advantage was conferred by the wild allele. Two fitness QTL were detected on linkage group 5 and 6, which were unique to one of the crop–wild crosses. Average hybrid fitness was lower than the fitness of the wild parent, but several hybrid lineages outperformed the wild parent, especially in a novel habitat for the wild type. In early-generation hybrids, this may partly be due to heterosis effects, whereas in late-generation hybrids transgressive segregation played a major role. The study of genomic selection patterns can identify crop genomic regions under negative selection across multiple environments and cultivar–wild crosses that might be applicable in transgene mitigation strategies. At the same time, results were cultivar-specific, so that a case-by-case environmental risk assessment is still necessary, decreasing its general applicability.
QTL analysis reveals the genetic architecture of domestication traits in Crisphead lettuce
Hartman, Y. ; Hooftman, D.A.P. ; Schranz, M.E. ; Tienderen, P.H. van - \ 2013
Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1487 - 1500.
lactuca-serriola asteraceae - marker-assisted selection - arabidopsis-thaliana - plant domestication - crop domestication - sativa l. - wild - loci - sunflower - evolution
The genetic architecture of crop domestication is generally characterized by three trends: relatively few genomic regions with major QTL effects are involved, QTL are often clustered, and alleles derived from the crop do not always contribute to the crop phenotype. We have investigated the genetic architecture of lettuce using a recombinant inbred line population from a cross between a crop Lactuca sativa (‘Salinas’) and its wild relative L. serriola. Few genomic regions with major QTL, plus various intermediate QTL, largely control the transition from wild to cultivated Crisphead lettuce. Allelic effects of all major QTL were in the expected direction, but there were intermediate QTL where the crop contributed to the wild phenotype and vice versa. We found two main regions with clusters of QTL, one on linkage group 3, where the crop allele induced lower seed output, another on linkage group 7, where the crop allele caused a delay in flowering time. Potentially, knowledge of genetic changes due to the domestication could be relevant for the chance that a transgene inserted in a crop genome will spread to wild relatives due to hitchhiking effects. If a transgene would be inserted in one of these regions, background selection on the crop alleles may lead to a reduced fitness of hybrids with the transgene. QTL research on the effects of domestication genes can thus indicate regions in the crop genome that are less likely to introgress, although these still need to be verified under field conditions.
Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions
Uwimana, B. ; Smulders, M.J.M. ; Hooftman, D.A.P. ; Hartman, Y. ; Tienderen, P.H. van; Jansen, J. ; McHale, L.K. ; Michelmore, R.W. ; Wiel, C.C.M. van de; Visser, R.G.F. - \ 2012
Theoretical and Applied Genetics 125 (2012)6. - ISSN 0040-5752 - p. 1097 - 1111.
quantitative trait loci - genetically-engineered organisms - lactuca-sativa l. - gene flow - helianthus-paradoxus - sunflower hybrids - vegetative growth - transgenic plants - field conditions - brassica-napus
With the development of transgenic crop varieties, crop–wild hybridization has received considerable consideration with regard to the potential of transgenes to be transferred to wild species. Although many studies have shown that crops can hybridize with their wild relatives and that the resulting hybrids may show improved fitness over the wild parents, little is still known on the genetic contribution of the crop parent to the performance of the hybrids. In this study, we investigated the vigour of lettuce hybrids using 98 F2:3 families from a cross between cultivated lettuce and its wild relative Lactuca serriola under non-stress conditions and under drought, salinity and nutrient deficiency. Using single nucleotide polymorphism markers, we mapped quantitative trait loci associated with plant vigour in the F2:3 families and determined the allelic contribution of the two parents. Seventeen QTLs (quantitative trait loci) associated with vigour and six QTLs associated with the accumulation of ions (Na+, Cl- and K+) were mapped on the nine linkage groups of lettuce. Seven of the vigour QTLs had a positive effect from the crop allele and six had a positive effect from the wild allele across treatments, and four QTLs had a positive effect from the crop allele in one treatment and from the wild allele in another treatment. Based on the allelic effect of the QTLs and their location on the genetic map, we could suggest genomic locations where transgene integration should be avoided when aiming at the mitigation of its persistence once crop–wild hybridization takes place
Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations
Uwimana, B. ; Smulders, M.J.M. ; Hooftman, D.A.P. ; Hartman, Y. ; Tienderen, P.H. van; Jansen, J. ; McHale, L.K. ; Michelmore, R. ; Visser, R.G.F. ; Wiel, C.C.M. van de - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
quantitative trait loci - genetically-engineered organisms - gene flow - qtl analysis - lycopersicon-esculentum - domestication traits - helianthus-paradoxus - sunflower hybrids - field conditions - mixed models
After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.
Genomic regions in crop-wild hybrids of Lettuce are affected differrently in different environments: implications for crop breeding
Hartman, Y. ; Hooftman, D.A.P. ; Uwimana, B. ; Wiel, C.C.M. van de; Smulders, M.J.M. ; Visser, R.G.F. ; Tienderen, P.H. van - \ 2012
Evolutionary Applications 5 (2012)6. - ISSN 1752-4563 - p. 629 - 640.
quantitative trait loci - lactuca-serriola asteraceae - genetically-modified crops - avena-barbata - arabidopsis-thaliana - field conditions - natural environments - domestication traits - population-genetics - tandem constructs
Many crops contain domestication genes that are generally considered to lower fitness of crop–wild hybrids in the wild environment. Transgenes placed in close linkage with such genes would be less likely to spread into a wild population. Therefore, for environmental risk assessment of GM crops, it is important to know whether genomic regions with such genes exist, and how they affect fitness. We performed quantitative trait loci (QTL) analyses on fitness(-related) traits in two different field environments employing recombinant inbred lines from a cross between cultivated Lactuca sativa and its wild relative Lactuca serriola. We identified a region on linkage group 5 where the crop allele consistently conferred a selective advantage (increasing fitness to 212% and 214%), whereas on linkage group 7, a region conferred a selective disadvantage (reducing fitness to 26% and 5%), mainly through delaying flowering. The probability for a putative transgene spreading would therefore depend strongly on the insertion location. Comparison of these field results with greenhouse data from a previous study using the same lines showed considerable differences in QTL patterns. This indicates that care should be taken when extrapolating experiments from the greenhouse, and that the impact of domestication genes has to be assessed under field conditions.
A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe
Uwimana, B. ; Andrea, L. D'; Felber, F. ; Hooftman, D.A.P. ; Nijs, H.C.M. den; Smulders, M.J.M. ; Visser, R.G.F. ; Wiel, C.C.M. van de - \ 2012
Molecular Ecology 21 (2012)11. - ISSN 0962-1083 - p. 2640 - 2654.
genetically-modified crops - multilocus genotype data - populus-nigra l. - population-structure - sect lactuca - situ conservation - hybridization - asteraceae - hybrids - spp.
Interspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop-specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.
Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development
Hooftman, D.A.P. ; Flavell, A.J. ; Jansen, J. ; Nijs, J.C.M. den; Syed, N.H. ; Sorensen, A.P. ; Wengel, P.O. ter; Wiel, C.C.M. van de - \ 2011
Evolutionary Applications 4 (2011)5. - ISSN 1752-4563 - p. 648 - 659.
sunflower helianthus-annuus - genetically-modified crops - linkage disequilibrium - gene flow - cultivated sunflower - artificial selection - disease resistance - lactuca-serriola - risk-assessment - transgene flow
Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter’s ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent’s habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.
|Characterization of nepoviruses by an intergrated approach.
Botermans, M. ; Meekes, E.T.M. ; Jansen, C.C.C. ; Hooftman, M. ; Schadewijk, T. van; Miglino, R. ; Pham, K.T.K. ; Kock, M.J.D. de; Roenhorst, J.W. - \ 2010
A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers
Syed, N. ; Sorensen, A.P. ; Antonise, R. ; Wiel, C.C.M. van de; Linden, C.G. van der; Westende, W.P.C. van 't; Hooftman, D.A.P. ; Nijs, H.C.M. den; Flavell, A. - \ 2006
Theoretical and Applied Genetics 112 (2006)3. - ISSN 0040-5752 - p. 517 - 527.
ty1-copia group retrotransposons - transpositional activity - disease resistance - assisted selection - diversity analysis - molecular markers - genetic diversity - s-sap - barley - polymorphisms
Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187 retrotransposon-specific SSAP markers, 29 NBS-LRR markers and 242 AFLP markers were mapped in an F2 population, derived from an interspecific cross between a Lactuca sativa cultivar commonly used in Europe and a wild Lactuca serriola isolate from Northern Europe. The cross has been designed to aid efforts to assess gene flow from cultivated lettuce into the wild in the perspective of genetic modification biosafety. The markers were mapped in nine major and one minor linkage groups spanning 1,266.1 cM, with an average distance of 2.8 cM between adjacent mapped markers. The markers are well distributed throughout the lettuce genome, with limited clustering of different marker types. Seventy-seven of the AFLP markers have been mapped previously and cross-comparison shows that the map from this study corresponds well with the previous linkage map
Copper toxicity in relation to surface water-dissolved organic matter: biological effects to Daphnia magna
Kramer, K.J.M. ; Jak, R.G. ; Hattum, B. van; Hooftman, R.N. ; Zwolsman, J.J.G. - \ 2004
Environmental Toxicology and Chemistry 23 (2004)12. - ISSN 0730-7268 - p. 2971 - 2980.
koper - toxiciteit - organische stof - waterverontreiniging - daphnia magna - biologische beschikbaarheid - nederland - waterbodems - copper - toxicity - organic matter - water pollution - daphnia magna - bioavailability - netherlands - water bottoms - biotic ligand model - humic-acid - ceriodaphnia-dubia - ion activity - metals - hardness - bioaccumulation - complexation - cadmium - speciation
Water quality standards for copper are usually stated in total element concentrations. It is known, however, that a major part of the copper can be bound in complexes that are biologically not available. Natural organic matter, such as humic and fulvic acids, are strong complexing agents that may affect the bioavailable copper (Cu2+) concentration. The aim of this study was to quantify the relation between the concentration of dissolved natural organic matter and free Cu2+ in surface waters, and the biological effect, as measured in a standardized ecotoxicological test (48 h¿median effective concentration [EC50] Daphnia magna, mobility). Six typical Dutch surface waters and an artificial water, ranging from 0.1 to 22 mg/L dissolved organic carbon (DOC), were collected and analyzed quarterly. Chemical speciation modeling was used as supporting evidence to assess bioavailability. The results show clear evidence of a linear relation between the concentration of dissolved organic carbon (in milligrams DOC/L) and the ecotoxicological effect (as effect concentration, EC50, expressed as micrograms Cu/L): 48-h EC50 (Daphnia, mobility) = 17.2 × DOC + 30.2 (r2 = 0.80, n = 22). Except for a brook with atypical water quality characteristics, no differences were observed among water type or season. When ultraviolet (UV)-absorption (380 nm) was used to characterize the dissolved organic carbon, a linear correlation was found as well. The importance of the free copper concentration was demonstrated by speciation calculations: In humic-rich waters the free Cu2+ concentration was estimated at ¿10¿11 M, whereas in medium to low dissolved organic carbon waters the [Cu2+] was ¿10¿10 M. Speciation calculations performed for copper concentrations at the effective concentration level (where the biological effect is considered the same) resulted in very similar free copper concentrations (¿10¿8 M Cu) in these surface waters with different characteristics. These observations consistently show that the presence of organic matter decreases the bioavailability, uptake, and ecotoxicity of copper in the aquatic environment. It demonstrates that the DOC content must be included in site-specific environmental risk assessment for trace metals (at least for copper). It is the quantification of the effects described that allows policy makers to review the criteria for copper in surface waters.
A combination of baiting and different PCR formats, including measurement of real-time quantitative fluorescence, for the detection of Phytophthora fragariae in strawberry plants
Bonants, P.J.M. ; Gent-Pelzer, M.P.E. van; Hooftman, R. ; Cooke, D.E.L. ; Guy, D.C. ; Duncan, J.M. - \ 2004
European Journal of Plant Pathology 110 (2004)7. - ISSN 0929-1873 - p. 689 - 702.
polymerase-chain-reaction - molecular beacons - dna - hybridization - infestans - identification - amplification - rna - quantification - organization
Phytophthora fragariae, the cause of strawberry red stele disease, is a quarantine pathogen in Europe. Detecting low levels of infection requires sensitive and specific methods. In the past, Dutch and English inspection services have used bait plants to test strawberry propagation stocks destined for export. Increasingly though, PCR is being incorporated into these testing procedures in an effort to increase sensitivity and speed. Various combinations of baiting and PCR assays were compared with existing testing procedures. Water and root samples from the bait test were screened by nested PCR and the PCR amplicon was detected by several methods, including fluorescent labelled probes (TaqMan and Molecular Beacon). PCR amplification was monitored in real-time and semi-quantitative detection was possible. Because PCR reactions are sensitive to inhibitors present in extracted DNA samples, an internal control containing the primer sequences specific for P. fragariae was developed to avoid false negatives
Bronnenonderzoek agrobacterium in aster
Wubben, J.P. ; Hazendonk, D.A. ; Lanser, C.J. ; Hooftman, R. - \ 2003
Aalsmeer : Praktijkonderzoek Plant & Omgeving, Sector Glastuinbouw - 25
aster - snijbloemen - bacteriën - teelt onder bescherming - plantentumoren - infectiebestrijding - inventarisaties - aster - cut flowers - bacteria - protected cultivation - tumours - infection control - inventories
Determinants of Non-Home-Prepared Food Consumption in Two Low-Income Areas in Nairobi
Riet, H. van 't; Hartog, A.P. den; Hooftman, D.A.P. ; Foeken, D.W.J. ; Mwangi, A.M. ; Staveren, W.A. van - \ 2003
Nutrition 19 (2003). - ISSN 0899-9007 - p. 1006 - 1012.
street foods - dietary-intake - policy
OBJECTIVE: Street foods are an important source of nutrients for poor urban residents. This study aimed to identify determinants of the proportion of daily energy provided by non-home-prepared foods. METHODS: A survey was conducted in a slum and a low- to middle-income area of Nairobi. The survey included 241 men and 254 women. Through a structured questionnaire, data on demographic and socioeconomic factors were collected and food intake was assessed with three standardized 24-hour recalls. A measure of socioeconomic status was constructed with principal component analysis. RESULTS: For women in the slum area, the presence of school-age children and distance to work were determinants of non-home-prepared food consumption, whereas employment status and distance to work were determinants for men in the slum area (P <0.05). Having their own income and, for those employed, employment status were determinants for women in the low- to middle-income area, whereas socioeconomic status was the determinant for the men (P <0.05). In the Slum area, most non-home-prepared foods were derived from street foods, whereas in the low- to middle-income area, both kiosks and street foods were important sources of non-home-prepared foods. CONCLUSION: In the determinants of non-home-prepared energy consumption, we discerned a pattern from rather basic determinants to determinants of a more complicated nature with increasing socioeconomic level of the groups. Furthemore, a shift from street foods to kiosks as the main source of non-home-prepared foods consumed appeared with increasing socioeconomic levels. (C) Elsevier Inc. 2003.
|New developments in detection of plant pathogenic bacteria by combining methods based on microbial enrichment, serology and PCR-amplification
Wolf, J.M. van der; Beckhoven, J.R.C.M. van; Hooftman, M. ; Kastelein, P. ; Vries, Ph.M. de; Vuurde, J.W.L. van - \ 1999
Petria 9 (1999). - p. 67 - 72.
The resource balance hypothesis of plant species diversity in grassland
Braakhekke, W.G. ; Hooftman, D.A.P. - \ 1999
Journal of Vegetation Science 10 (1999). - ISSN 1100-9233 - p. 187 - 200.