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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Population complexity trumps model complexity in understanding trait variation
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Volkers, J.M. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2018
The study of expression quantitative trait loci (eQTL) through the use of recombinant inbred lines has yielded detailed information about the transcriptional regulation of complex traits. However, it has proven difficult to apply more advanced genetic models explaining genetic variation underlying gene expression differences. Here, we make use of the difference in genetic complexity of two types of inbred population in the nematode Caenorhabditis elegans to estimate the number of loci affecting gene expression.
We measured gene-expression in a recombinant inbred line (RIL) and an introgression line (IL) population constructed from crossing the strains N2 and CB4856. Both populations received a heat-shock treatment and gene-expression profiles were obtained before (48h at 20oC), directly after heat-shock (2h at 35oC), and after a recovery period (2h at 20oC). Making use of the difference in genetic make-up between the populations - few loci from one parent in the IL versus many in the RILs - allowed for the identification of transcripts regulated by multiple loci. By measuring the transcript variance within each population, for over 1,000 genes across the three conditions we found strong evidence for multiple eQTL underlying gene expression variation. Importantly, most of these multi-loci eQTL are environment-specific. Furthermore, we observed over 200 genes where the phenotypic variation in the IL panel significantly exceeded that in the RIL panel, suggesting evidence for complex genetic buffering.
In conclusion, by using two types of inbred populations the complexity of trait architectures can be investigated without reliance on models of higher complexity. The genetic complexity of a trait is directly observed, rather than estimated post-hoc. Therefore, relying on population complexity rather than model complexity can provide valuable insight in the architecture of quantitative traits.
Gene expression profiling in control, heat-shock, and recovery treatment in a RIL population of Caenorhabditis elegans L4 larvae
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, J.A.G. ; Cossins, Andrew ; Kammenga, J.E. - \ 2017
Caenorhabditis elegans - transcription profiling by array - stimulus or stress design - strain or line design - E-MTAB-5779
This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in a N2xCB4856 RIL population of Caenorhabditis elegans. The goal is to identify genetic variation linked to differences in gene expression. We exposed 48 RILs per treatment to a control, heat-stress, and recovery treatment. More specifically these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for eQTL mapping.
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, J.A.G. ; Cossins, Andrew ; Kammenga, J.E. - \ 2017
Caenorhabditis elegans - genetical genomics - eQTL - heat stress - cryptic genetic variation - trans-band - eQTL hotspot
Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. Results We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. Conclusions These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
Temporal dynamics of gene expression in heat-stressed Caenorhabditis elegans
Jovic, K. ; Sterken, M.G. ; Grilli, Jacopo ; Bevers, R.P.J. ; Rodriguez Sanchez, M. ; Riksen, J.A.G. ; Allesina, S. ; Kammenga, J.E. ; Snoek, L.B. - \ 2017
PLoS ONE 12 (2017)12. - ISSN 1932-6203 - 16 p.
There is considerable insight into pathways and genes associated with heat-stress conditions. Most genes involved in stress response have been identified using mutant screens or gene knockdowns. Yet, there is limited understanding of the temporal dynamics of global gene expression in stressful environments. Here, we studied global gene expression profiles during 12 hours of heat stress in the nematode C. elegans. Using a high-resolution time series of increasing stress exposures, we found a distinct shift in gene expression patterns between 3–4 hours into the stress response, separating an initially highly dynamic phase from a later relatively stagnant phase. This turning point in expression dynamics coincided with a phenotypic turning point, as shown by a strong decrease in movement, survival and, progeny count in the days following the stress. Both detectable at transcriptional and phenotypic level, this study pin-points a relatively small time frame during heat stress at which enough damage is accumulated, making it impossible to recover the next few days.
A point-of-no-return leading to death in C. elegans
Jovic, K. ; Sterken, M.G. ; Grilli, Jacopo ; Bevers, R.P.J. ; Rodriguez, M. ; Riksen, J.A.G. ; Allesina, S. ; Kammenga, J.E. ; Snoek, L.B. - \ 2017
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
Snoek, Basten L. ; Sterken, Mark G. ; Bevers, Roel P.J. ; Volkers, Rita J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, Joost A.G. ; Cossins, Andrew ; Kammenga, Jan E. - \ 2017
BMC Genomics 18 (2017). - ISSN 1471-2164 - 15 p.

Background

Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population.


Results

We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL.


Conclusions

These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
Discussieavond Genetische modificatie en biologische landbouw; een valse tegenstelling?
Lotz, Bert - \ 2016
Lotz B, Lammerts van Bueren E, Bevers M (2016) Discussieavond Genetische modificatie en biologische landbouw; een valse tegenstelling?, Landelijk bureau van GroenLinks. Utrecht, 7 juli 2016
Stress tolerance and lifespan in C. elegans are modulated by natural allelic variation in CMK-1
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, A. van 't; Brenchley, R. ; Lehner, B. ; Cossins, A. ; Kammenga, J.E. - \ 2016
Genetic control of aging in C. elegans has primarily been studied using
derived mutants of the strain N2. These mutants often display extreme
lifespan accompanied by increased stress resistance. Yet, identification of
genes that underlie variation in lifespan and stress tolerance in natural
populations remains a major challenge. We investigated gene expression
architecture and longevity and found that stress tolerance and lifespan in C.
elegans are modulated by natural allelic variation in cmk-1.
Variation in gene expression levels was linked to genomic loci (eQTL)
using fully sequenced recombinant inbred populations derived from
divergent wild-type strains N2 and CB4856. In these strains regulatory loci
were identified under standard and under heat-stress conditions. After
verification, the causal regulator was identified by screening knock-out
mutants of candidate genes. Moreover, lifespan was measured under
standard conditions and in strains that received a heat shock treatment.
We identified a major stress-related regulatory locus that affects expression
variation in more than 100 genes and one of the causal genes was found to
be cmk-1. The effects of this variation include modulation of insulin-like
signaling targets supporting a model in which allelic variation in cmk-1
regulates a subset of daf-16 targets under stress conditions, leading to
increased stress resistance and prolonged lifespan.
In conclusion, genes affecting lifespan variation in nature may not be those
identified by mutagenizing a single C. elegans strain. Our data suggests that
pathways previously associated with aging are affected, but not by the usual
suspects.
Transcriptional regulation in stress recovery of Caenorhabditis elegans
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2016
C. elegans serves as an important model for integrative analysis of stress
response. Analyzing the transcriptional regulation of stress response and
subsequent recovery provides insight into the mechanisms of fitness
optimization. Although C. elegans stress responses are well studied, the
recovery from stress is poorly understood. We investigated the
transcriptional response over the course of a heat-shock experiment in fully
sequenced recombinant inbred lines (RILs). This allowed us to identify
regulatory loci for stress recovery.
The RILs, derived from a cross between N2 and CB4856, were exposed to
heat-shock after which they were allowed to recover. In both environments,
and in a control environment (no heat stress), genome-wide expression
levels were measured. We then performed expression quantitative trait loci
(eQTL) mapping across these three environments to identify regulatory loci
that contribute to the recovery response.
Across all RILs the largest difference in gene expression was found
between control and heat-shock. Recovering populations showed patterns of
gene expression that were in-between the control and heat-shock. Some
RILs had a more control-like gene expression phenotype while other RILs
were more heat-shock-like, thus allowing for mapping of loci regulating
genetic variation in recovery. We found that genetic variation in gene
expression was largely independent of the environment. More specifically,
approximately 50% of the eQTL were similar in location and effect over the
three environments; therefore did not display interaction with the
environment. Only 1% of the genes with an eQTL in all environments
displayed environment-specific interaction. The remainder of the eQTL
with an environment-specific interaction were specifically detected in one
environment.
In conclusion, the combination of natural variation and gene expression
over the course of a stress response allows for mapping loci underlying
regulation in this response. The genes with an eQTL displaying
environment interaction are specific for one environment. Incorporation of
environment interactions facilitates specifying groups of related eQTL and
thereby allows for detailed eQTL network analysis.
Stress tolerance and lifespan in C. elegans are modulated by natural allelic variation in cmk-1
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Volkers, R.J.M. ; Hof, A. van 't; Brenchley, R. ; Lehner, B. ; Cossins, A. ; Kammenga, J.E. - \ 2015
In: Proceedings of Molecular Biology of Ageing 2015. - - p. 134 - 134.
Genetic control of aging in C. elegans has primarily been studied using derived mutants of the strain N2. These mutants often display extreme lifespan accompanied by increased stress resistance. Yet, identification of genes that underlie variation in lifespan and stress tolerance in natural populations remains a major challenge. We investigated gene expression architecture and longevity and found that stress tolerance and lifespan in C. elegans are modulated by natural allelic variation in cmk-1. Variation in gene expression levels was linked to genomic loci (eQTL) using fully sequenced recombinant inbred populations derived from divergent wild-type strains N2 and CB4856. In these strains regulatory loci were identified under standard and under heat-stress conditions. After verification, the causal regulator was identified by screening knock-out mutants of candidate genes. Moreover, lifespan was measured under standard conditions and in strains that received a heat shock treatment. We identified a major stress-related regulatory locus that affects expression variation in more than 100 genes and one of the causal genes was found to be cmk-1. The effects of this variation include modulation of insulin-like signaling targets supporting a model in which allelic variation in cmk-1 regulates a subset of daf-16 targets under stress conditions, leading to increased stress resistance and prolonged lifespan. In conclusion, genes affecting lifespan variation in nature may not be those identified by mutagenizing a single C. elegans strain. Our data suggests that pathways previously associated with aging are affected, but not by the usual suspects.
Stress tolerance and lifespan in C. elegans are modulated by natural allelic variation in cmk-1
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, A. van 't; Brenchley, R. ; Lehner, B. ; Cossins, A. ; Kammenga, J.E. - \ 2015
Transcriptional regulation in stress recovery of Caenorhabditis elegans
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2015
C. elegans serves as an important model for integrative analysis of stress response. Analyzing the transcriptional regulation of stress response and subsequent recovery provides insight into the mechanisms of fitness optimization. Although C. elegans stress responses are well studied, the recovery from stress is poorly understood. We investigated the transcriptional response over the course of a heat-shock experiment in fully sequenced recombinant inbred lines (RILs). This allowed us to identify regulatory loci for stress recovery. The RILs, derived from a cross between N2 and CB4856, were exposed to heat-shock after which they were allowed to recover. In both environments, and in a control environment (no heat stress), genome-wide expression levels were measured. We then performed expression quantitative trait loci (eQTL) mapping across these three environments to identify regulatory loci that contribute to the recovery response. Across all RILs the largest difference in gene expression was found between control and heat-shock. Recovering populations showed patterns of gene expression that were in-between the control and heat-shock. Some RILs had a more control-like gene expression phenotype while other RILs were more heat-shock-like, thus allowing for mapping of loci regulating genetic variation in recovery. We found that genetic variation in gene expression was largely independent of the environment. More specifically, approximately 50% of the eQTL were similar in location and effect over the three environments; therefore did not display interaction with the environment. Only 1% of the genes with an eQTL in all environments displayed environment-specific interaction. The remainder of the eQTL with an environment-specific interaction were specifically detected in one environment. In conclusion, the combination of natural variation and gene expression over the course of a stress response allows for mapping loci underlying regulation in this response. The genes with an eQTL displaying environment interaction are specific for one environment. Incorporation of environment interactions facilitates specifying groups of related eQTL and thereby allows for detailed eQTL network analysis.
Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
Thompson, O.A. ; Snoek, L.B. ; Nijveen, H. ; Sterken, M.G. ; Volkers, R.J.M. ; Brenchley, R. ; Hof, A. van 't; Bevers, R.P.J. ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, J.E. ; Waterston, R.H. - \ 2015
Genetics 200 (2015)3. - ISSN 0016-6731 - p. 975 - 989.
natural variation data - c. elegans - arabidopsis-thaliana - gene - polymorphism - populations - diversity - nematodes - dna - evolutionary
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
Polymorphic regions and genes affecting gene transcription regulation of stress response and prolonged lifespan
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Volkers, R.J.M. ; Hof, A. van 't; Brenchley, R. ; Cleef, E. van; Bartels, R. ; Laven, Y. ; Riksen, J.A.G. ; Valba, O. ; Chavali, S. ; Lang, B. ; Francesconi, M. ; Bot, J. ; Nechaev, S. ; Vasieva, O. ; Babu, M. ; Lehner, B. ; Cossins, A. ; Kammenga, J.E. - \ 2014
In: Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. - - p. 33 - 33.
Stress and cellular stress responses underlie many age-related diseases and understanding the causal link between the two is essential for promoting healthy aging strategies. There is accumulating evidence that exposure to a mild stressor induces an adaptive response that increases eukaryotic lifespan. Insight in the biological pathways associated with lifespan has been provided by, amongst others, transcriptome analysis. But so far it is unclear how natural genetic variation affects the complex transcriptional architecture which links stress response and lifespan. Here we report the detection of polymorphic regions in the genome (eQTL) and genes that regulate stress induced gene expression levels and prolong lifespan in the nematode C. elegans. Using 106 fully sequenced recombinant inbred lines (genetic mosaics and introgression lines) we found that heat-shock profoundly affected polymorphic distant gene expression regulators (distant-eQTL). A strong distant-eQTL affecting many transcripts was detected on the top left arm of chromosome IV. This eQTL coincided with a lifespan QTL and was validated by the gene expression profiles of introgression lines. Based on gene-network assisted candidate gene selection on the distant-eQTL, gene expression analysis of mutants carrying these candidate genes (cmk-1, egl-4, daf-11, eor-1 and unc-70) confirmed the eQTL. We found egl-4, and cmk-1 to be causally affecting gene expression patterns, stress resistance and prolonged lifespan. Our results show that natural variation affects stress response and lifespan by affecting thermo sensory circuits. This is the first study which unveils the transcriptional architecture and identifies genes linking stress response and lifespan based on natural genetic variation which opens up opportunities to genetically dissect age-related diseases.
The effects of development on gene expression in L4 Caenorhabditis elegans larvae
Riksen, J.A.G. ; Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K. ; Bevers, R.P.J. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
In: Proceedings of the Berlin C. elegans Meeting. - - p. 215 - 215.
Organismal development is the most dynamic period of the life cycle yet we have only a rough understanding of the dynamics of gene expression during this period. We explore how development affects gene expression, by a detailed map of the C. elegans transcriptome. We found that over 10,000 genes display changes in expression and explored the properties of genes with different dynamics. A time series experiment was conducted on synchronized populations of C. elegans Bristol N2. The worms were grown in three batches, covering the time points from 42-64 hours post bleaching leading to a dense time series with 1 hour intervals on average. A follow up experiment was conducted using N2 and seven wild-isolates, CB4856, JU1581, JU1921, JU1930, JU1932, JU1944 and JU 1949. These were grown on two different food sources to show the applicability of the generated data as a transcriptional determinant of age. It was found that more than 10,000 genes have a dynamic expression pattern during the L4 stage. We found up- and down-regulated genes and also genes with more specific patterns. One noticeable pattern was a group of genes that is specifically up-regulated around 50 hours. Signs of purifying selection in non-coding regions of string up-regulated genes were found. This is an indication that highly up-regulated genes during development are constrained on their regulatory properties. Using the time-series we show that genotype and environment affect the development and the applicability of transcriptomics data to measure age. Our data help in understanding the transition from larvae to adult worms and can be used te eliminate experimental artefacts due to differences in developmental timing between experiments.
Genome wide mapping of stress-response and ageing pathway regulators
Sterken, M.G. ; Snoek, L.B. ; Bevers, R.P.J. ; Volkers, R.J.M. ; Hof, A. van 't; Brenchley, R. ; Cleef, E. van; Bartels, R. ; Laven, Y. ; Riksen, J.A.G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
In: Proceedings of the Berlin C. elegans Meeting. - - p. 49 - 49.
Stress and molecular stress responses are inextricably linked to many age-related diseases. To gain insight into the genetic regulation of the stress response machinery it is essential to uncovergene expression regulators on a genome wide scale. Here we report the uncovering of heat-shock regulators by exploring natural variation of genome wide gene transcription in C. elegansusing two fully sequenced recombinant inbred populations derived from wild types Bristol N2 and CB4856. The first population is a genetic mosaic of the two parental alleles (RILs). The second is a population of introgression lines (ILs), where each line contains only a single locus of CB4856 in an N2 background. Variation in gene expression levels waslinked to genomic loci (eQTL) inworms grown at 20oC for their entire life and worms exposed to a 2 hour 35oC heat-shock at the end of their life. This allowed us to identify novel regulatory loci affecting multiple transcriptsunder heat-stress conditions. These regulatory loci were verified using ILs. The outcomes of these experiments allowed us to identify candidate regulators by transposing our data overWormnet. Next, these candidate genes were validated by phenotyping knock-out mutants. Theregulatory locus affecting most genes upon heat-shock was found on the top left arm of chromosome IV. This locus (IV: 1.27-1.93 Mb) affects the expression of 315 genes and coincides with a QTL affecting survival after heat-shock. Subsequently we could confirm the effect of this locus on 182 genes by the IL expression profiles. Transposing the eQTL results on Wormnet identified 44 candidate genes that potentially regulate the heat-stress response, including cmk-1andegl-4. In the final experiment the transcription profiles under heat-shock were measured in44 mutants. The transcripts were investigated for differentially expressed genes compared to N2. These differentially expressed genes were investigated for overlap with eQTLs mapping (close)to the physical position of the mutant. This approach revealed four genes involved in the heatstress response of which cmk-1as a main regulator of the transcriptional response to heat-stress. This implies that heat-shock response requires cmk-1activity which is essential for normal thermo-sensory behavior. Together, our results provide a framework for using natural variation to identify stress-pathway regulators.
A rapid and massive gene expression shift marking adolescent transition in C. elegans
Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K.J. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
Scientific Reports 4 (2014). - ISSN 2045-2322
caenorhabditis-elegans - natural variation - genome - populations - robustness - diversity - profiles - genotype - project - age
Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution time series we found that in adolescent worms over 10,000 genes changed their expression. These genes were clustered according to their expression patterns. One cluster involved in chromatin remodelling showed a brief up-regulation around 50 h post-hatch. At the same time a spectacular shift in expression was observed. Sequence comparisons for this cluster across many genotypes revealed diversifying selection. Strongly up-regulated genes showed signs of purifying selection in non-coding regions, indicating that adolescence-active genes are constrained on their regulatory properties. Our findings improve our understanding of adolescent transition and help to eliminate experimental artefacts due to incorrect developmental timing.
The sudden transcriptional switch to adulthood in L4 stage C. elegans
Snoek, L.B. ; Sterken, M.G. ; Volkers, J.M. ; Klatter, M. ; Bosman, K. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2013
In: Proceedings of the 19th International C.elegans Meeting, 26-30 June 2013, Los Angeles, California, USA. - - p. 331 - 331.
De biodiversiteit van het Gelderse Hout : Verslag van de Soorten-zoekdag 2012 in Het Gelderse Hout in Lelystad.
Alebeek, F.A.N. van - \ 2013
Lelystad : KNNV afd. Lelystad - 104
flora - fauna - monitoring - natuur- en milieueducatie - veldwerk - samenwerking - organisaties - zuidelijk flevoland - nature and environmental education - field work - cooperation - organizations
Tijdens de soorten- zoekdag is er naar bevers en vleermuizen gezocht en werden nachtvlinders met felle lampen op een laken gelokt. Op zondag konden kinderen waterbeestjes zoeken en braakballen pluizen, en konden liefhebbers onder leiding van een deskundige gids op zoek naar vogels, bodembeestjes, mossen, vissen, bomen en struiken, sprinkhanen, bijen en wespen, libellen, dagvlinders, reptielen en amfibieën, plantengallen, grassen en kruiden. Daarnaast waren er diverse informatiekraampjes waar bezoekers meer konden leren over de natuur.
Groei van de beverpopulatie: lusten en lasten
Vreugdenhil, S. ; Dekker, J.J.A. ; Dijkstra, V.D. - \ 2012
Vakblad Natuur Bos Landschap 9 (2012)10. - ISSN 1572-7610 - p. 26 - 29.
castor fiber - fauna - populatiedynamica - schadelijke dieren - natuurgebieden - biesbosch - flevoland - population dynamics - noxious animals - natural areas
Het aantal bevers is in Nederland sterk gegroeid. In 1988 werden de eerste dieren losgelaten in de Biesbosch, en in 2012 wordt het aantal Nederlandse bevers al geschat op zeker 600 volwassen dieren. Bevers zijn door hun bijzondere gedrag een aanwinst voor onze natuur. Maar ditzelfde gedrag kan ook leiden tot overlast. Hoe ga je hiermee om?
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