6 Papers found (0.008 seconds)

Sterken MG et al. (2021) Sci Rep "Transcriptional analysis of the response of C. elegans to ethanol exposure."

Carnell L, Sterken MG, Kammenga JE, Mathies LD, Davies AG, Bettinger JC, van Wijk MH, Quamme EC, Riksen JAG

[

Sci Rep,

2021]

Ethanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved in the physiological response to ethanol, including direct ethanol targets, were regulated at 8 h of exposure. This longer exposure to ethanol also resulted in the regulation of genes involved in cilia function, which is consistent with an important role for the effects of ethanol on cilia in the deleterious effects of chronic ethanol consumption in humans. Finally, we found that food deprivation for an 8-h period induced gene expression changes that were somewhat ameliorated by the presence of ethanol, supporting previous observations that worms can use ethanol as a calorie source.

Sterken MG et al. (2017) G3 (Bethesda) "Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans."

Kammenga JE, Riksen JA, Rodriguez M, Hajnal A, van Bemmelen van der Plaat L, Schmid T, Snoek BL, Sterken MG

[

G3 (Bethesda),

2017]

The oncogenic Ras/MAPK pathway is evolutionarily conserved across metazoans. Yet, almost all our knowledge on this pathway comes from studies using single genetic backgrounds, whereas mutational effects can be highly background dependent. Therefore, we lack insight in the interplay between genetic backgrounds and the Ras/MAPK-signaling pathway. Here, we used a Caenorhabditis elegans RIL population containing a gain-of-function mutation in the Ras/MAPK pathway gene let-60 and measured how gene expression regulation is affected by this mutation. We mapped eQTL and found that the majority (~73%) of the 1516 detected cis-eQTL were not specific for the let-60 mutation, whereas most (~76%) of the 898 detected trans-eQTL were associated with the let-60 mutation. We detected 6 eQTL trans-bands specific for the interaction between the genetic background and the mutation, one of which co-localized with the polymorphic Ras/MAPK modifier amx-2 Comparison between transgenic lines expressing allelic variants of amx-2 showed the involvement of amx-2 in 79% of the trans-eQTL for genes mapping to this trans-band. Together, our results have revealed loci hidden loci affecting Ras/MAPK signaling using sensitized backgrounds in C. elegans These loci harbor putative polymorphic modifier genes that would not have been detected using mutant screens in single genetic backgrounds.

Sterken MG et al. (2020) Front Genet "Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans."

Riksen JAG, Volkers RJM, Bevers RPJ, Kammenga JE, Snoek BL, Sterken MG

[

Front Genet,

2020]

The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.

Sterken MG et al. (2014) PLoS One "A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2."

Kammenga JE, Bosman KJ, Bakker J, Pijlman GP, Daamen J, Snoek LB, Sterken MG, Riksen JA

[

PLoS One,

2014]

Orsay virus (OrV) is the first virus known to be able to complete a full infection cycle in the model nematode species Caenorhabditis elegans. OrV is transmitted horizontally and its infection is limited by antiviral RNA interference (RNAi). However, we have no insight into the kinetics of OrV replication in C. elegans. We developed an assay that infects worms in liquid, allowing precise monitoring of the infection. The assay revealed a dual role for the RNAi response in limiting Orsay virus infection in C. elegans. Firstly, it limits the progression of the initial infection at the step of recognition of dsRNA. Secondly, it provides an inherited protection against infection in the offspring. This establishes the heritable RNAi response as anti-viral mechanism during OrV infections in C. elegans. Our results further illustrate that the inheritance of the anti-viral response is important in controlling the infection in the canonical wild type Bristol N2. The OrV replication kinetics were established throughout the worm life-cycle, setting a standard for further quantitative assays with the OrV-C. elegans infection model.

Sterken MG et al. (2021) J Virol "Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility of Caenorhabditis elegans strains Bristol N2 and Hawaiian CB4856."

Sterken MG, Riksen JAG, Ritmahan W, Volkers RJM, Wang YA, van Sluijs L, Snoek LB, Kammenga JE, Gultom ML, Pijlman GP

[

J Virol,

2021]

Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinct Caenorhabditis elegans strains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility and we found that a single nucleotide polymorphism in cul-6 may contribute to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became as susceptible as the N2 strain by having an N2 cul-6 allele, although having the CB4856 cul-6 allele did not increase resistance in N2. Additionally, we found that multiple strains with non-overlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility in C. elegans and suggest that viral susceptibility is governed by multiple genes.ImportanceGenetic variation determines the viral susceptibility of hosts. Yet, pinpointing which genetic variants determine viral susceptibility remains challenging. Here, we have exploited the genetic tractability of the model organism C. elegans to dissect the genetic architecture of Orsay virus infection. Our results provide novel insight into natural determinants of Orsay virus infection.

Ow, Maria C. et al. (2020) MicroPubl Biol

Ow, Maria C., Hall, Sarah E.

[

MicroPubl Biol,

2020]

During its first larval stage (L1), the nematode C. elegans makes a critical decision regarding its developmental trajectory based on environmental conditions. Poor conditions such food scarcity, crowding, or high temperatures promote the entry into a stress-resistant, non-aging, diapause stage named dauer where they can survive for months. Upon improved conditions, dauer larvae resume development as postdauer (PD) L4 larvae and continue to reproductive adulthood as PD adults (Cassada and Russell, 1975). If conditions are favorable, L1 larvae proceed through additional larval stages (L2-L4) until reaching reproductive adulthood (control adults or CON) (Sulston and Horvitz, 1977). We have previously shown that PD adults retain a cellular memory of their early life experience that results in stress-specific transcriptome changes that promote alterations in their life history traits (Hall et al. 2010, 2013; Ow et al. 2018). For instance, wild-type CON adults and PD adults that experienced early-life starvation exhibit reproductive differences that are manifested as decreased brood size in PD animals relative to CON adults. Reproduction in self-fertilizing hermaphrodites is sperm-limited; thus, brood size differences can result from varying numbers of sperm produced by individual animals. We showed previously that postdauers animals that experienced early-life starvation exhibit a significant delay in germline proliferation during the period when sperm are produced compared to control animals of comparable developmental stage. This observation suggests that the decrease in postdauers adult brood size is consistent with a reduction in sperm number, which we have referred to as reproductive plasticity (Ow et al. 2018). The standard wild-type N2 strain was first cultivated in the laboratory over five decades ago, resulting in the fixation of random mutations over thousands of generations in laboratory conditions atypical to what are experienced by natural populations (Sterken et al. 2015). We wondered whether the reproductive plasticity observed in the canonical laboratory wild-type N2 strain is an adaptive trait acquired over time as a result of laboratory conditions, or represents a conserved mechanistic response to starvation stress. We assessed CON and PD brood sizes of six natural isolates representing various branches of the C. elegans phylogenetic tree (Andersen et al. 2012). CON L4 larvae were obtained from a continuously growing mixed population of worms cultured on NGM plates at 20oC. To obtain PD L4 larvae, well-fed worms were first starved on NGM plates at 20oC for about one week until dauers were visible, then worms were collected and incubated for 30 minutes in 1% SDS (sodium dodecyl sulfate) at room temperature with gentle rotation. Because dauers have suspended pharyngeal pumping (Cassada and Russell, 1975), they survive the 1% SDS treatment that would otherwise be lethal if the detergent were ingested. Dauers were then washed with M9 buffer to rinse away the SDS and placed onto seeded NGM plates at 20oC to promote dauer exit. Once the dauers had developed into postdauer L4s, brood size assays were performed in parallel with their CON counterparts by randomly singling out L4 larvae onto seeded 35 mm NGM plates at 20oC, transferring daily them to fresh plates until egg laying ceased, and counting the number of surviving progeny. These surviving progenies were counted as young adults (four days after the mothers were transferred to fresh NGM plates). We found that certain wild isolates, (e.g. AF16 in Figure 1), had the proclivity to crawl to the side of an NGM plate assay plate and desiccate. We thus censored the data for any animal that died before the end of the egg-laying period. We found that four out of six natural isolates (AB1, CB4856, ED3040, and TR403) displayed a significant reduction in brood size in PD adults relative to CON adults similar to N2. The strains, JU440 and KR314, did not exhibit reproductive plasticity and had a similar number of progeny between CON and PD adults (Figure 1). Interestingly, when we measured the brood size in CON and PD adults of another nematode species closely related to C. elegans, C. briggsae AF16, it displayed a modest but statistically insignificant decrease in PD brood size compared to CON adults (Figure 1). Is the reproductive plasticity between CON and PD a reflection of different mating strategies among Caenorhabditis strains? The spontaneous male frequency in the N2 strain is a low ~0.1%, and reproduction is usually achieved through hermaphrodite self-fertilization (Chasnov and Chow, 2002). However, we found that one natural isolate, CB4856, which harbors a higher frequency of males in their population than the laboratory N2 strain (Wegewitz et al. 2008), also exhibits reproductive plasticity between CON and PD. This observation suggests that reproductive plasticity between CON and PD adults may not be simply due to changes in male frequency and levels of mating. The distinction between strains exhibiting adult reproductive plasticity and those that do not is not immediately obvious when comparing phylogenetic proximity or strain isolation date (Andersen et al. 2012). Thus, additional experiments would be necessary to determine the genetic loci in N2 Bristol and the wild isolates that modulate this reproductive trait. Taken together, these results suggest that reproductive plasticity observed in C. elegans is a naturally occurring developmental trait rather than an adaptive trait stemming from decades of cultivation in a laboratory.