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.

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Molecular and chemical dialogues in bacteria-protozoa interactions
Song, C. ; Mazzola, M. ; Cheng, X. ; Oetjen, J. ; Alexandrov, T. ; Dorrestein, P. ; Watrous, J. ; Voort, M. van der; Raaijmakers, J.M. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 13 p.
imaging mass-spectrometry - pseudomonas-fluorescens cha0 - dictyostelium-discoideum - caenorhabditis-elegans - spatial segmentation - tetr family - aeruginosa - biosynthesis - rhizosphere - strain
Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.
The effect of developmental nutrition on life span and fecundity depends on the adult reproductive environment in Drosophila melanogaster
May, C.M. ; Doroszuk, A. ; Zwaan, B.J. - \ 2015
Ecology and Evolution 5 (2015)6. - ISSN 2045-7758 - p. 1156 - 1168.
thrifty phenotype hypothesis - ischemic-heart-disease - dietary restriction - larval nutrition - caenorhabditis-elegans - resource-allocation - prenatal exposure - history evolution - food limitation - body-size
Both developmental nutrition and adult nutrition affect life-history traits; however, little is known about whether the effect of developmental nutrition depends on the adult environment experienced. We used the fruit fly to determine whether life-history traits, particularly life span and fecundity, are affected by developmental nutrition, and whether this depends on the extent to which the adult environment allows females to realize their full reproductive potential. We raised flies on three different developmental food levels containing increasing amounts of yeast and sugar: poor, control, and rich. We found that development on poor or rich larval food resulted in several life-history phenotypes indicative of suboptimal conditions, including increased developmental time, and, for poor food, decreased adult weight. However, development on poor larval food actually increased adult virgin life span. In addition, we manipulated the reproductive potential of the adult environment by adding yeast or yeast and a male. This manipulation interacted with larval food to determine adult fecundity. Specifically, under two adult conditions, flies raised on poor larval food had higher reproduction at certain ages – when singly mated this occurred early in life and when continuously mated with yeast this occurred during midlife. We show that poor larval food is not necessarily detrimental to key adult life-history traits, but does exert an adult environment-dependent effect, especially by affecting virgin life span and altering adult patterns of reproductive investment. Our findings are relevant because (1) they may explain differences between published studies on nutritional effects on life-history traits; (2) they indicate that optimal nutritional conditions are likely to be different for larvae and adults, potentially reflecting evolutionary history; and (3) they urge for the incorporation of developmental nutritional conditions into the central life-history concept of resource acquisition and allocation
Random mutagenesis of the nucleotide-binding domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1), a downstream signalling nucleotide-binding, leucine-rich repeat (NB-LRR) protein, identifies gain-of-function mutations in the nucleotide-binding pocket
Sueldo, D.J. ; Shimels, M.Z. ; Spiridon, L.N. ; Caldararu, O. ; Petrescu, A.J. ; Joosten, M.H.A.J. ; Tameling, W.I.L. - \ 2015
New Phytologist 208 (2015)1. - ISSN 0028-646X - p. 210 - 223.
disease resistance protein - secondary structure prediction - multiple sequence alignment - tobacco-mosaic-virus - immune receptors - arc domain - caenorhabditis-elegans - artificial evolution - gene-products - coiled-coil
•Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB-LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death. •NRC1 (NB-LRR Required for HR-Associated Cell Death-1) is a tomato (Solanum lycopersicum) NB-LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae. •To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide-binding domain and screened them for the ability to induce an elicitor-independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain-of-function mutants, with 10 of them caused by a single amino acid substitution. •All substitutions are located in or very close to highly conserved motifs within the nucleotide-binding domain, suggesting modulation of the signalling activity of NRC1. Three-dimensional modelling of the nucleotide-binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain-of-function mutations in NRC1 and provides insight into how the activity of this NB-LRR is regulated.
Systemic Regulation of RAS/MAPK Signaling by the Serotonin Metabolite 5-HIAA
Schmid, T. ; Snoek, L.B. ; Fröhli, E. ; Bent, M.L. van der; Kammenga, J.E. ; Hajnal, A. - \ 2015
Plos Genetics 11 (2015)5. - ISSN 1553-7404 - 16 p.
caenorhabditis-elegans - c-elegans - natural variation - vulvar induction - complex disease - receptor - protein - gene - kinase - activation
Human cancer is caused by the interplay of mutations in oncogenes and tumor suppressor genes and inherited variations in cancer susceptibility genes. While many of the tumor initiating mutations are well characterized, the effect of genetic background variation on disease onset and progression is less understood. We have used C. elegans genetics to identify genetic modifiers of the oncogenic RAS/MAPK signaling pathway. Quantitative trait locus analysis of two highly diverged C. elegans isolates combined with allele swapping experiments identified the polymorphic monoamine oxidase A (MAOA) gene amx-2 as a negative regulator of RAS/MAPK signaling. We further show that the serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), which is a product of MAOA catalysis, systemically inhibits RAS/MAPK signaling in different organs of C. elegans. Thus, MAOA activity sets a global threshold for MAPK activation by controlling 5-HIAA levels. To our knowledge, 5-HIAA is the first endogenous small molecule that acts as a systemic inhibitor of RAS/MAPK signaling.
Target of rapamycin signalling mediates the lifespan-extending effects of dietary restriction by essential amino acid alteration
Emran, S. ; Yang, M.Y. ; He, X.L. ; Zandveld, J. ; Piper, M.D.W. - \ 2014
Aging-US 6 (2014)5. - ISSN 1945-4589 - p. 390 - 398.
caenorhabditis-elegans - drosophila-melanogaster - longevity assurance - stress resistance - food restriction - fat storage - tor - extension - growth - yeast
Dietary restriction (DR), defined as a moderate reduction in food intake short of malnutrition, has been shown to extend healthy lifespan in a diverse range of organisms, from yeast to primates. Reduced signalling through the insulin/IGF-like (IIS) and Target of Rapamycin (TOR) signalling pathways also extend lifespan. In Drosophila melanogaster the lifespan benefits of DR can be reproduced by modulating only the essential amino acids in yeast based food. Here, we show that pharmacological downregulation of TOR signalling, but not reduced IIS, modulates the lifespan response to DR by amino acid alteration. Of the physiological responses flies exhibit upon DR, only increased body fat and decreased heat stress resistance phenotypes correlated with longevity via reduced TOR signalling. These data indicate that lowered dietary amino acids promote longevity via TOR, not by enhanced resistance to molecular damage, but through modified physiological conditions that favour fat accumulation.
The ER-Associated Degradation Adaptor Protein Sel1L Regulates LPL Secretion and Lipid Metabolism
Sha, H. ; Sun, S. ; Francisco, A. ; Ehrhardt, N. ; Xue, Z.Q. ; Liu, L. ; Mattijssen, F.B.J. ; Kersten, A.H. - \ 2014
Cell Metabolism 20 (2014)3. - ISSN 1550-4131 - p. 458 - 470.
reticulum-associated-degradation - endoplasmic-reticulum - lipoprotein-lipase - caenorhabditis-elegans - membrane-protein - stress - deficiency - maturation - disease - liver
Sel1L is an essential adaptor protein for the E3 ligase Hrd1 in the endoplasmic reticulum (ER)-associated degradation (ERAD), a universal quality-control system in the cell; but its physiological role remains unclear. Here we show that mice with adipocyte-specific Sel1L deficiency are resistant to diet-induced obesity and exhibit postprandial hypertriglyceridemia. Further analyses reveal that Sel1L is indispensable for the secretion of lipoprotein lipase (LPL), independent of its role in Hrd1-mediated ERAD and ER homeostasis. Sel1L physically interacts with and stabilizes the LPL maturation complex consisting of LPL and lipase maturation factor 1 (LMF1). In the absence of Sel1L, LPL is retained in the ER and forms protein aggregates, which are degraded primarily by autophagy. The Sel1L-mediated control of LPL secretion is also seen in other LPL-expressing cell types including cardiac myocytes and macrophages. Thus, our study reports a role of Sel1L in LPL secretion and systemic lipid metabolism.
Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival
Sun, S. ; Shi, Guojun ; Han, X. ; Francisco, A. ; Ji, Y. ; Kersten, A.H. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)5. - ISSN 0027-8424 - p. E582 - E591.
unfolded-protein response - er-associated degradation - misfolded glycoproteins - stress granules - caenorhabditis-elegans - complex - cell - dislocation - substrate - retrotranslocation
Suppressor/Enhancer of Lin-12-like (Sel1L) is an adaptor protein for the E3 ligase hydroxymethylglutaryl reductase degradation protein 1 (Hrd1) involved in endoplasmic reticulum-associated degradation (ERAD). Sel1L’s physiological importance in mammalian ERAD, however, remains to be established. Here, using the inducible Sel1L knockout mouse and cell models, we show that Sel1L is indispensable for Hrd1 stability, ER homeostasis, and survival. Acute loss of Sel1L leads to premature death in adult mice within 3 wk with profound pancreatic atrophy. Contrary to current belief, our data show that mammalian Sel1L is required for Hrd1 stability and ERAD function both in vitro and in vivo. Sel1L deficiency disturbs ER homeostasis, activates ER stress, attenuates translation, and promotes cell death. Serendipitously, using a biochemical approach coupled with mass spectrometry, we found that Sel1L deficiency causes the aggregation of both small and large ribosomal subunits. Thus, Sel1L is an indispensable component of the mammalian Hrd1 ERAD complex and ER homeostasis, which is essential for protein translation, pancreatic function, and cellular and organismal survival.
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.
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.
Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension
Doroszuk, A. ; Jonker, M.J. ; Pul, N. ; Breit, T.M. ; Zwaan, B.J. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
genome-wide - starvation resistance - expression patterns - caloric restriction - dietary restriction - c-elegans - caenorhabditis-elegans - laboratory selection - oxidative stress - immune-response
Background While studying long-lived mutants has advanced our understanding of the processes involved in ageing, the mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. Here, we characterise genome-wide expression patterns of a long-lived, natural variant of Drosophila melanogaster resulting from selection for starvation resistance (SR) and compare it with normal-lived control flies (C). We do this at two time points representing middle age (90% survival) and old age (10% survival) respectively, in three adult diets (malnutrition, optimal food, and overfeeding). Results We found profound differences between Drosophila lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived Drosophila. The stress-related genes, including those involved in proteolysis and cytochrome P450, were generally higher expressed in SR flies and showed a smaller increase in expression with age compared to C flies. The genes involved in reproduction showed a lower expression in middle-aged SR than in C flies and, unlike C flies, a lack of their downregulation with age. Further, we found that malnutrition strongly affected age-associated transcript patterns overriding the differences between the lines. However, under less stressful dietary conditions, line and diet affected age-dependent expression similarly. Finally, we present lists of candidate markers of ageing and lifespan extension. Conclusions Our study unveils transcriptional changes associated with lifespan extension in SR Drosophila. The results suggest that natural genetic variation for SR and lifespan can operate through similar transcriptional mechanisms as those of dietary restriction and life-extending mutations. Keywords: Ageing; Gene expression; Microarray; Drosophila melanogaster; Natural variation; Diet
Kinesin-3 and dynein cooperate in long-range retrograde endosome motility along a nonuniform microtubule array
Schuster, M. ; Kilaru, S. ; Fink, G. ; Collemare, J.A.R. ; Roger, Y. ; Steinberg, G. - \ 2011
Molecular Biology of the Cell 22 (2011)19. - ISSN 1059-1524 - p. 3645 - 3657.
fungus ustilago-maydis - tug-of-war - lipid-droplet transport - cytoplasmic dynein - molecular motors - intracellular-transport - vesicle transport - cargo transport - caenorhabditis-elegans - polarity orientation
The polarity of microtubules (MTs) determines the motors for intracellular motility, with kinesins moving to plus ends and dynein to minus ends. In elongated cells of Ustilago maydis, dynein is thought to move early endosomes (EEs) toward the septum (retrograde), whereas kinesin-3 transports them to the growing cell tip (anterograde). Occasionally, EEs run up to 90 mu m in one direction. The underlying MT array consists of unipolar MTs at both cell ends and antipolar bundles in the middle region of the cell. Cytoplasmic MT-organizing centers, labeled with gamma-tubulin ring complex protein, are distributed along the antipolar MTs but are absent from the unipolar regions. Dynein colocalizes with EEs for 10-20 mu m after they have left the cell tip. Inactivation of temperature-sensitive dynein abolishes EE motility within the unipolar MT array, whereas long-range motility is not impaired. In contrast, kinesin-3 is continuously present, and its inactivation stops long-range EE motility. This indicates that both motors participate in EE motility, with dynein transporting the organelles through the unipolar MT array near the cell ends, and kinesin-3 taking over at the beginning of the medial antipolar MT array. The cooperation of both motors mediates EE movements over the length of the entire cell.
Changed gene expression for candidate ageing genes in long-lived Bicyclus anynana butterflies
Pijpe, J. ; Pul, N. ; Duijn, S. van; Brakefield, P.M. ; Zwaan, B.J. - \ 2011
Experimental Gerontology 46 (2011)6. - ISSN 0531-5565 - p. 426 - 434.
quantitative trait loci - extend life-span - drosophila-melanogaster - oxidative damage - caenorhabditis-elegans - starvation resistance - adaptive evolution - stress resistance - natural variation - longevity
Candidate genes for the regulation of lifespan have emerged from studies that use mutants and genetically manipulated model organisms. However, it is rarely addressed whether these genes contribute to lifespan variation in populations of these species that capture natural standing genetic variation. Here, we explore expression variation in three candidate ageing genes, Indy, sod2, and catalase, in Bicyclus anynana, a butterfly with well understood ecology. We used lines established from natural populations and artificially selected for increased adult starvation resistance. They show a considerable increase in adult lifespan under both starvation and optimal food conditions. We measured adult butterflies of various ages, under a range of optimal and starvation diets, from two selected populations and one unselected control population. In all lines, Indy and catalase are up-regulated in response to starvation while this is not evident for sod2. Under starvation, Indy and catalase are up-regulated in, while this is not evident for sod2. Under optimal food conditions, Indy is down-regulated at a later age, with Indy expression showing relatively high inter-individual variation. We find differences between the selected lines and the unselected line. Under starvation conditions, expression is higher for catalase in one, and for sod2 in both selected lines. Importantly, sod2 expression is also higher in the selected populations under optimal food conditions. We conclude that sod2, but not Indy, is involved in the response to artificial selection for increased starvation resistance. The role of catalase is less clear because of the differences between the two selected lines. Moreover, sod2 appears to be a candidate gene that underpins the genetic correlation between starvation resistance and longevity. Our study indicates that some, but not all, genes identified through mutant screens in other organisms may underpin standing genetic variation for ageing-related traits in stocks of Bicyclus butterflies established from natural populations. Clearly, this needs to be investigated in other organisms as well, especially in the organisms to which mutants screens were applied. This information will narrow down the list of genes that underpin variation in lifespan and ageing in extant populations of organisms, and which may serve as candidate genes in humans
A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
Elvin, M. ; Snoek, L.B. ; Frejno, M. ; Klemstein, U. ; Kammenga, J.E. ; Poulin, G. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 14 p.
life-history traits - caenorhabditis-elegans - gene - interference - rde-1
Background - RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Results - Here we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which E. coli is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in ppw-1 contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important. Conclusions - In summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi.
RNA interference in Lepidoptera: An overview of successful and unsuccessful
Terenius, O. ; Papanicolaou, A. ; Garbutt, J.S. ; Eleftherianos, I. ; Huvenne, H. ; Kanginakudru, S. ; Albrechtsen, M. ; An, Chunju ; Aymeric, J.L. ; Barthel, A. ; Bebas, P. ; Bitra, K. ; Bravo, A. ; Chevalier, F. ; Collinge, D.P. ; Crava, C.M. ; Maagd, R.A. de; Duvic, B. ; Erlandson, M. ; Faye, I. ; Felfoldi, G. ; Fujiwara, H. ; Futahashi, R. ; Gandhe, A.S. ; Gatehouse, H.S. ; Gatehouse, L.N. ; Giebultowicz, J.M. ; Gomez, I. ; Grimmelikhuijzen, C.J.P. ; Groot, A.T. ; Hauser, F. ; Heckel, D.G. ; Hegedus, D.D. ; Hrycaj, S. ; Huang, L. ; Hull, J.J. ; Iatrou, K. ; Iga, M. ; Kanost, M.R. ; Kotwica, J. ; Li, Changyou ; Li, Jianghong ; Liu, Jisheng ; Lundmark, M. ; Matsumoto, S. ; Meyering-Vos, M. ; Millichap, P.J. ; Monteiro, A. ; Mrinal, N. ; Niimi, T. ; Nowara, D. ; Ohnishi, A. ; Oostra, V. ; Ozaki, K. ; Papakonstantinou, M. ; Popadic, A. ; Rajam, M.V. ; Saenko, S. ; Simpson, R.M. ; Soberon, M. ; Strand, M.R. ; Tomita, S. ; Toprak, U. ; Wang, Ping ; Wee, Choon Wei ; Whyard, S. ; Zhang, Wenqing ; Nagaraju, J. ; Ffrench-Constant, R.H. ; Herrero, S. ; Gordon, K. ; Swevers, L. ; Smagghe, G. - \ 2011
Journal of Insect Physiology 57 (2011)2. - ISSN 0022-1910 - p. 231 - 245.
double-stranded-rna - armyworm spodoptera-frugiperda - silkworm bombyx-mori - small silencing rnas - manduca-sexta - bacillus-thuringiensis - caenorhabditis-elegans - helicoverpa-armigera - immune-responses - messenger-rna
Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity. On the contrary, gene expression in epidermal tissues seems to be most difficult to silence. In addition, gene silencing by feeding dsRNA requires high concentrations for success. Possible causes for the variability of success in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as our public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments
Nematoda from the terrestrial deep subsurface of South Africa
Borgonie, G. ; García-Moyano, A. ; Litthauer, D. ; Bert, W. ; Bester, A. ; Heerden, E. van; Möller, C. ; Erasmus, M. ; Onstott, T.C. - \ 2011
Nature 474 (2011)7349. - ISSN 0028-0836 - p. 79 - 82.
caenorhabditis-elegans - witwatersrand basin - evolution - shield - water
Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere1–4. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylumNematoda that have been detected in or recovered from 0.9–3.6-kilometredeep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurfacenematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that theymay control themicrobial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.
Genome-wide gene expression regulation as a function of genotype and age in C. elegans
Viñuela Rodriguez, A. ; Snoek, L.B. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2010
Genome Research 20 (2010)7. - ISSN 1088-9051 - p. 929 - 937.
quantitative trait loci - caenorhabditis-elegans - transcriptional profile - mouse - dissection - patterns
Gene expression becomes more variable with age, and it is widely assumed that this is due to a decrease in expression regulation. But currently there is no understanding how gene expression regulatory patterns progress with age. Here we explored genome-wide gene expression variation and regulatory loci (eQTL) in a population of developing and aging C. elegans recombinant inbred worms. We found almost 900 genes with an eQTL, of which almost half were found to have a genotype-by-age effect (gxaeQTL). The total number of eQTL decreased with age, whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms, the number of genes with increased variation (1772) was nearly five times higher than the number of genes with a decreased expression variation (373). The number of cis-acting eQTL in juveniles decreased by almost 50% in old worms, whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Of the 373 genes with decreased expression level variation in aging worms, ~39% had an eQTL compared with ~14% in developing worms. gxaeQTL were found for ~21% of these genes in aging worms compared with only ~6% in developing worms. We highlight three examples of linkages: in young worms (pgp-6), in old worms (daf-16), and throughout life (lips-16). Our findings demonstrate that eQTL patterns are strongly affected by age, and suggest that gene network integrity declines with age
Tobacco rattle virus mediates gene silencing in a plant parasitic root-knot nematode
Dubreuil, G. ; Magliano, M. ; Dubrana, M.P. ; Lozano, J. ; Lecomte, P. ; Favery, B. ; Abad, P. ; Rosso, M.N. - \ 2009
Journal of Experimental Botany 60 (2009)14. - ISSN 0022-0957 - p. 4041 - 4050.
double-stranded-rna - troponin-c gene - caenorhabditis-elegans - meloidogyne-incognita - transgenic plants - expression - protein - vector - cell - interference
Root-knot nematodes (RKNs) are sedentary biotrophic parasites that induce the differentiation of root cells into feeding cells that provide the nematodes with the nutrients necessary for their development. The development of new control methods against RKNs relies greatly on the functional analysis of genes that are crucial for the development of the pathogen or the success of parasitism. In the absence of genetic transformation, RNA interference (RNAi) allows for phenotype analysis of nematode development and nematode establishment in its host after sequence-specific knock-down of the targeted genes. Strategies used to induce RNAi in RKNs are so far restricted to small-scale analyses. In the search for a new RNAi strategy amenable to large-scale screenings the possibility of using RNA viruses to produce the RNAi triggers in plants was tested. Tobacco rattle virus (TRV) was tested as a means to introduce double-stranded RNA (dsRNA) triggers into the feeding cells and to mediate RKN gene silencing. It was demonstrated that virus-inoculated plants can produce dsRNA and siRNA silencing triggers for delivery to the feeding nematodes. Interestingly, the knock-down of the targeted genes was observed in the progeny of the feeding nematodes, suggesting that continuous ingestion of dsRNA triggers could be used for the functional analysis of genes involved in early development. However, the heterogeneity in RNAi efficiency between TRV-inoculated plants appears as a limitation to the use of TRV-mediated silencing for the high-throughput functional analysis of the targeted nematode genes
Inhibition of methylation and changes in gene expression in relation to neural tube defects
Linden, I.J. van der; Heil, S.G. ; Egmont-Petersen, M. van; Straaten, H.W. ; Heijer, M. den - \ 2008
Birth defects research. Part A, Clinical and molecular teratology 82 (2008)10. - ISSN 1542-0752 - p. 676 - 683.
factor-i - methylenetetrahydrofolate reductase - serine/threonine kinase - caenorhabditis-elegans - mammalian development - common mutation - risk-factor - dna - serine - folate
BACKGROUND: An impaired DNA methylation has been suggested to underlie the complex etiology of neural tube defects (NTDs). Previously, we have demonstrated that inhibition of methylation by periodate oxidized adenosine (Adox) results in a widening of the anterior neuropore (ANP) in our in vitro chick embryo model. Since DNA methylation is the chief regulator of gene expression, we hypothesize that inhibition of methylation by Adox in our in vitro chick embryo model will affect the expression of genes that may be involved in neurulation. In the present study, we therefore examined differential gene expression between Adox-treated and control chick embryos, using the Affymetrix Genechip Chicken Genome Array. METHODS: Chick embryos of 4/5 somites were cultured in vitro with saline (control) or Adox and cranial parts were excised. Gene expression profiling was determined using the Affymetrix Genechip Chicken Genome Array on RNA isolated from two pools of Adox-treated cranial parts (n = 12) and two pools of saline-treated cranial parts (n = 12). Microarray data were validated by QPCR analysis. RESULTS: In the Adox-treated chick embryos, 45 probesets were up-regulated (fold 2.0, p <0.05) and 32 probesets were down-regulated (fold 0.5, p <0.05). Of the 15 genes selected for QPCR analysis, the up-regulation of phosphoserine phosphatase (PSPH), unc-51-like kinase 1 (ULK1), and chemokine (C-X-C motif) ligand 12/stromal cell-derived factor 1 (CXCL12/SDF-1) was confirmed. CONCLUSIONS: Inhibition of methylation by Adox affects gene expression in our in vitro chick embryo model. Further research will focus on the gene-specific methylation patterns of PSPH, ULK1, and CXCL12/SDF-1 and the role of the products of these genes in neurulation.
Efficient cloning system for construction of gene silencing vectors in Aspergillus niger
Oliveira, J.M. ; Veen, D. van der; Graaff, L.H. de; Qin Ling, - \ 2008
Applied Microbiology and Biotechnology 80 (2008)5. - ISSN 0175-7598 - p. 917 - 924.
transcriptional activator xlnr - double-stranded-rna - neurospora-crassa - caenorhabditis-elegans - functional-analysis - expression - interference - transformation - fungus - inactivation
An approach based on Gateway recombination technology to efficiently construct silencing vectors was developed for use in the biotechnologically important fungus Aspergillus niger. The transcription activator of xylanolytic and cellulolytic genes XlnR of A. niger was chosen as target for gene silencing. Silencing was based on the expression vector pXLNRir that was constructed and used in co-transformation. From all the strains isolated (N = 77), nine showed poor xylan-degrading activities in two semi-quantitative plate assays testing different activities for xylan degradation. Upon induction on D-xylose, transcript levels of xlnR were decreased in the xlnR-silenced strains, compared to a wild-type background. Under these conditions, the transcript levels of xyrA and xynB (two genes regulated by XlnR) were also decreased for these xlnR-silenced strains. These results indicate that the newly developed system for rapid generation of silencing vectors is an effective tool for A. niger, and this can be used to generate strains with a tailored spectrum of enzyme activities or product formation by silencing specific genes encoding, e.g., regulators such as XlnR
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
Abad, P. ; Gouzy, J. ; Aury, J.M. ; Tytgat, T.O.G. ; Smant, G. - \ 2008
Nature Biotechnology 26 (2008)8. - ISSN 1087-0156 - p. 909 - 915.
root-knot nematodes - caenorhabditis-elegans - phytopathogenic bacteria - bdelloid rotifers - genes - protein - cloning - identification - expression - prediction
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall¿degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies
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