Staff Publications

Staff Publications

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

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

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

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

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    We will mail you new results for this query: keywords==nematode caenorhabditis-elegans
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Worms under stress: C. elegans stress response and its relevance to complex human disease and aging
Rodriguez Sanchez, M. ; Snoek, L.B. ; Bono, M. de; Kammenga, J.E. - \ 2013
Trends in Genetics 29 (2013)6. - ISSN 0168-9525 - p. 367 - 374.
heat-shock factor - nematode caenorhabditis-elegans - widespread protein damage - age-related disease - life-span - molecular chaperones - parkinsons-disease - human longevity - natural variation - oxidative stress
Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery
Practical considerations for conducting ecotoxicity test methods with manufactured nanomaterials: what have we learnt so far?
Handy, R.D. ; Brink, N.W. van den; Chappell, M. ; Muhling, M. ; Behra, R. ; Dusinska, M. ; Simpson, P. ; Ahtiainen, J. ; Jha, A.N. ; Seiter, J. ; Bednar, A. ; Kennedy, A. ; Fernandes, T.F. ; Riediker, M. - \ 2012
Ecotoxicology 21 (2012)4. - ISSN 0963-9292 - p. 933 - 972.
walled carbon-nanotubes - nematode caenorhabditis-elegans - titanium-dioxide nanoparticles - environmental risk-assessment - fullerene water suspensions - soil microbial community - dna strand breaks - in-vitro - silver nanoparticles - rainbow-trout
This review paper reports the consensus of a technical workshop hosted by the European network, NanoImpactNet (NIN). The workshop aimed to review the collective experience of working at the bench with manufactured nanomaterials (MNMs), and to recommend modifications to existing experimental methods and OECD protocols. Current procedures for cleaning glassware are appropriate for most MNMs, although interference with electrodes may occur. Maintaining exposure is more difficult with MNMs compared to conventional chemicals. A metal salt control is recommended for experiments with metallic MNMs that may release free metal ions. Dispersing agents should be avoided, but if they must be used, then natural or synthetic dispersing agents are possible, and dispersion controls essential. Time constraints and technology gaps indicate that full characterisation of test media during ecotoxicity tests is currently not practical. Details of electron microscopy, dark-field microscopy, a range of spectroscopic methods (EDX, XRD, XANES, EXAFS), light scattering techniques (DLS, SLS) and chromatography are discussed. The development of user-friendly software to predict particle behaviour in test media according to DLVO theory is in progress, and simple optical methods are available to estimate the settling behaviour of suspensions during experiments. However, for soil matrices such simple approaches may not be applicable. Alternatively, a Critical Body Residue approach may be taken in which body concentrations in organisms are related to effects, and toxicity thresholds derived. For microbial assays, the cell wall is a formidable barrier to MNMs and end points that rely on the test substance penetrating the cell may be insensitive. Instead assays based on the cell envelope should be developed for MNMs. In algal growth tests, the abiotic factors that promote particle aggregation in the media (e.g. ionic strength) are also important in providing nutrients, and manipulation of the media to control the dispersion may also inhibit growth. Controls to quantify shading effects, and precise details of lighting regimes, shaking or mixing should be reported in algal tests. Photosynthesis may be more sensitive than traditional growth end points for algae and plants. Tests with invertebrates should consider non-chemical toxicity from particle adherence to the organisms. The use of semi-static exposure methods with fish can reduce the logistical issues of waste water disposal and facilitate aspects of animal husbandry relevant to MMNs. There are concerns that the existing bioaccumulation tests are conceptually flawed for MNMs and that new test(s) are required. In vitro testing strategies, as exemplified by genotoxicity assays, can be modified for MNMs, but the risk of false negatives in some assays is highlighted. In conclusion, most protocols will require some modifications and recommendations are made to aid the researcher at the bench.
Genetic variation for stress-response hormesis in C. elegans lifespan
Rodriguez Sanchez, M. ; Snoek, L.B. ; Riksen, J.A.G. ; Bevers, R.P.J. ; Kammenga, J.E. - \ 2012
Experimental Gerontology 47 (2012)8. - ISSN 0531-5565 - p. 581 - 587.
quantitative trait loci - genotype-environment interactions - nematode caenorhabditis-elegans - long-lived mutant - drosophila-melanogaster - heat-shock - history traits - natural variation - longevity - resistance
Increased lifespan can be associated with greater resistance to many different stressors, most notably thermal stress. Such hormetic effects have also been found in C. elegans where short-term exposure to heat lengthens the lifespan. Genetic investigations have been carried out using mutation perturbations in a single genotype, the wild type Bristol N2. Yet, induced mutations do not yield insight regarding the natural genetic variation of thermal tolerance and lifespan. We investigated the genetic variation of heat-shock recovery, i.e. hormetic effects on lifespan and associated quantitative trait loci (QTL) in C. elegans. Heat-shock resulted in an 18% lifespan increase in wild type CB4856 whereas N2 did not show a lifespan elongation. Using recombinant inbred lines (RILs) derived from a cross between wild types N2 and CB4856 we found natural variation in stress-response hormesis in lifespan. Approx. 28% of the RILs displayed a hormesis effect in lifespan. We did not find any hormesis effects for total offspring. Across the RILs there was no relation between lifespan and offspring. The ability to recover from heat-shock mapped to a significant QTL on chromosome II which overlapped with a QTL for offspring under heat-shock conditions. The QTL was confirmed by introgressing relatively small CB4856 regions into chromosome II of N2. Our observations show that there is natural variation in hormetic effects on C. elegans lifespan for heat-shock and that this variation is genetically determined.
Ecotoxicity test methods for engineered nanomaterials: practical experiences and recommendations from the bench
Handy, R. ; Cornelis, G. ; Fernandes, T. ; Tsyusko, O. ; Decho, A. ; Sabo-Attwood, T. ; Metcalfe, C. ; Steevens, J.A. ; Klaine, S.J. ; Koelmans, A.A. ; Horne, N. - \ 2012
Environmental Toxicology and Chemistry 31 (2012)1. - ISSN 0730-7268 - p. 15 - 31.
nematode caenorhabditis-elegans - titanium-dioxide nanoparticles - walled carbon nanotubes - zinc-oxide nanoparticles - silver nanoparticles - rainbow-trout - in-vitro - manufactured nanoparticles - oncorhynchus-mykiss - daphnia-magna
Ecotoxicology research is using many methods for engineered nanomaterials (ENMs), but the collective experience from researchers has not been documented. This paper reports the practical issues for working with ENMs and suggests nano-specific modifications to protocols. The review considers generic practical issues, as well as specific issues for aquatic tests, marine grazers, soil organisms, and bioaccumulation studies. Current procedures for cleaning glassware are adequate, but electrodes are problematic. The maintenance of exposure concentration is challenging, but can be achieved with some ENMs. The need to characterize the media during experiments is identified, but rapid analytical methods are not available to do this. The use of sonication and natural/synthetic dispersants are discussed. Nano-specific biological endpoints may be developed for a tiered monitoring scheme to diagnose ENM exposure or effect. A case study of the algal growth test highlights many small deviations in current regulatory test protocols that are allowed (shaking, lighting, mixing methods), but these should be standardized for ENMs. Invertebrate (Daphnia) tests should account for mechanical toxicity of ENMs. Fish tests should consider semistatic exposure to minimize wastewater and animal husbandry. The inclusion of a benthic test is recommended for the base set of ecotoxicity tests with ENMs. The sensitivity of soil tests needs to be increased for ENMs and shortened for logistics reasons; improvements include using Caenorhabditis elegans, aquatic media, and metabolism endpoints in the plant growth tests. The existing bioaccumulation tests are conceptually flawed and require considerable modification, or a new test, to work for ENMs. Overall, most methodologies need some amendments, and recommendations are made to assist researchers.
Genome-Wide Gene Expression Analysis in Response to Organophosphorus Pesticide Chlorpyrifos and Diazion in C.Elegans
Viñuela Rodriguez, A. ; Snoek, L.B. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2010
PLoS ONE 5 (2010)8. - ISSN 1932-6203 - 8 p.
nematode caenorhabditis-elegans - binary-mixture - microarray data - in-vitro - toxicity - model - mechanism - rat - neurotoxicity - bioconductor
pesticides (OPs) were originally designed to affect the nervous system by inhibiting the enzyme acetylcholinesterase, an important regulator of the neurotransmitter acetylcholine. Over the past years evidence is mounting that these compounds affect many other processes. Little is known, however, about gene expression responses against OPs in the nematode Caenorhabditis elegans. This is surprising because C. elegans is extensively used as a model species in toxicity studies. To address this question we performed a microarray study in C. elegans which was exposed for 72 hrs to two widely used Ops, chlorpyrifos and diazinon, and a low dose mixture of these two compounds. Our analysis revealed transcriptional responses related to detoxification, stress, innate immunity, and transport and metabolism of lipids in all treatments. We found that for both compounds as well as in the mixture, these processes were regulated by different gene transcripts. Our results illustrate intense, and unexpected crosstalk between gene pathways in response to chlorpyrifos and diazinon in C. elegans
Beyond induced mutants: using worms to study natural variation in genetic pathways
Kammenga, J.E. ; Philips, P.C. ; Bono, M. de; Doroszuk, A. - \ 2008
Trends in Genetics 24 (2008)4. - ISSN 0168-9525 - p. 178 - 185.
quantitative trait loci - life-history traits - genotype-environment interactions - single-nucleotide polymorphisms - nematode caenorhabditis-elegans - c-elegans - linkage disequilibrium - genus caenorhabditis - wild populations - expression
Induced mutants in the nematode Caenorhabditis elegans are used to study genetic pathways of processes ranging from aging to behavior. The effects of such mutations are usually analyzed in a single wildtype background: N2. However, studies in other species demonstrate that the phenotype(s) of induced mutations can vary widely depending on the genetic background. Moreover, induced mutations in one genetic background do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Because other wildtype Caenorhabditis spp., including C. elegans, are now available, we review how current mapping resources and methodologies within and between species support the use of Caenorhabditis spp. for studying genetic variation, with a focus on pathways associated with human disease.
Type of disturbance and ecological history determine structural stability
Wurff, A.W.G. van der; Kools, S.A.E. ; Boivin, M.E.Y. ; Brink, P.J. van den; Megen, H.H.B. van; Riksen, J.A.G. ; Doroszuk, A. ; Kammenga, J.E. - \ 2007
Ecological Applications 17 (2007)1. - ISSN 1051-0761 - p. 190 - 202.
induced community tolerance - nematode caenorhabditis-elegans - microbial communities - ecosystem function - soil - biodiversity - diversity - toxicity - copper - responses
This study aims to reveal whether complexity, namely, community and trophic structure, of chronically stressed soil systems is at increased risk or remains stable when confronted with a subsequent disturbance. Therefore, we focused on a grassland with a history of four centuries of patchy contamination. Nematodes were used as model organisms because they are an abundant and trophically diverse group and representative of the soil food web and ecosystem complexity. In a field survey, a relationship between contaminants and community structures was established. Following, two groups of soil mesocosms from the field that differed in contamination level were exposed to different disturbance regimes, namely, to the contaminant zinc and a heat shock. The zinc treatment revealed that community structure is stable, irrespective of soil contamination levels. This implies that centuries of exposure to contamination led to adaptation of the soil nematode community irrespective of the patchy distribution of contaminants. In contrast, the heat shock had adverse effects on species richness in the highly contaminated soils only. The total nematode biomass was lower in the highly contaminated field samples; however, the biomass was not affected by zinc and heat treatments of the mesocosms. This means that density compensation occurred rapidly, i.e., tolerant species quickly replaced sensitive species. Our results support the hypothesis that the history of contamination and the type of disturbance determine the response of communities. Despite that ecosystems may be exposed for centuries to contamination and communities show adaptation, biodiversity in highly contaminated sites is at increased risk when exposed to a different disturbance regime. We discuss how the loss of higher trophic levels from the entire system, such as represented by carnivorous nematodes after the heat shock, accompanied by local biodiversity loss at highly contaminated sites, may result in detrimental effects on ecosystem functions.
Temporal Dynamics of Effect Concentrations
Alda Alvarez, O. ; Jager, T. ; Nuñez Colao, B. ; Kammenga, J.E. - \ 2006
Environmental Science and Technology 40 (2006)7. - ISSN 0013-936X - p. 2478 - 2484.
nematode caenorhabditis-elegans - toxicity tests - bioconcentration kinetics - risk-assessment - model - ecotoxicology - consequences - populations - chemicals - bioassays
In effect assessment the comparability and applicability of LCx and ECx values, which are calculated at single points in time during exposure, relies on the ability to perform a valid extrapolation to other time points of interest. The behavior of LCx in time has been extensively studied, and the behavior of ECx in time is expected to follow similar dynamics, as it is considered that the LCx is just a specific case of ECxs. However, most models have focused on validating the dynamics of LCx, and hardly anything is known about the time dependence of ECx for other endpoints or whether it is comparable to that of LCxs. We have created four scenarios where we study the dynamics of the ECx for different endpoints and how it is affected by the characteristics of two different compounds (carbendazim and pentachlorobenzene) and of two different life history strategies (hermaphroditic and sexually reproducing strains of Caenorhabditis elegans). The observed patterns of behavior in time of the ECx for body size and for reproduction showed unexpected dynamics that deviate considerably from that of the LCx. It was demonstrated that the temporal dynamics of ECx were very different for each particular endpoint. The shape of the ECx-time curves depends on the intrinsic characteristics of the endpoint of study, as well as on the characteristics of the compound and life history strategy of the organism. This makes extrapolation in time or between endpoints difficult and hampers the comparability of results based on this summary statistic. The interpretation of the results from toxicity tests can be improved through process-based modeling, as demonstrated on the current data set
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