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Rechavi, O.

Publications and source records attributed to Rechavi, O..

23 records · Page 2Linked to original sources

Inter-generational Consequences for Growing C. elegans in Liquid

In recent years, studies in Caenorhabditis elegans nematodes have shown that different stresses can generate multigenerational changes. Here we show that worms that grow in liquid media, and also their plate-grown progeny, are different from worms whose ancestors were grown on plates. It has been suggested that C.elegans might encounter liquid environments in nature, although actual observations in the wild are few and far between. In contrast, in the lab, growing worms in liquid is commonplace, and often used as an alternative to growing worms on agar plates, to control the composition of the worms diet, to starve (and synchronize) worms, or to grow large populations for biochemical assays. We found that plate-grown descendants of M9 liquid media-grown worms were longer than control worms, and the heritable effects were apparent already very early in development. We tested for the involvement of different known epigenetic inheritance mechanisms, but could not find a single mutant in which these intergenerational effects are canceled. While we found that growing in liquid always leads to inter-generational changes in the worms size, trans-generational effects were found to be variable, and in some cases the effects were gone after 1 -2 generations. These results demonstrate that standard cultivation conditions in early life can dramatically change the worms physiology in adulthood, and can also affect the next generations.

genetics↗

H3K9me3 is Required for Transgenerational Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

In Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via small RNAs. RNAi inheritance is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing requires a feed-forward loop between H3K9me3 and small RNAs. Here we show that in C. elegans not only is H3K9me3 unnecessary for inheritance, the modifications function depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that the SET-25-dependent heritable endo-siRNAs target newly acquired and highly H3K9me3 marked genes. Thus, \"repressive\" chromatin marks could be important specifically for heritable silencing of genes which are flagged as \"foreign\", such as gfp.

genetics↗

Asymmetric Overlap in Neuronal Sensation Constraints Rational Choice in C. elegans

Rational choice theory assumes optimality in decision-making. Violations of a basic axiom of economic rationality known as \"Independence of Irrelevant Alternatives\" (IIA), have been demonstrated in both humans and animals, and could stem from common neuronal constraints. We developed tests for IIA in the nematode Caenorhabditis elegans, an animal with only 302 neurons, using olfactory chemotaxis assays. We found that in most cases C. elegans make rational decisions. However, by probing multiple neuronal architectures using various choice sets, we show that asymmetric sensation of odor options by the AWCON neuron can lead to violations of rationality. We further show that genetic manipulations of the asymmetry between the AWC neurons can make the worm rational or irrational. Last, a normalization-based model of value coding and gain control explains how particular neuronal constraints on information coding give rise to irrationality. Thus, we demonstrate that bounded rationality could arise due to basic neuronal constraints.

neuroscience↗

WorMachine: Machine Learning-Based Phenotypic Analysis Tool for Worms

While Caenorhabditis elegans nematodes are powerful model organisms, quantification of visible phenotypes is still often labor-intensive, biased, and error-prone. We developed \"WorMachine\", a three-step MATLAB-based image analysis software that allows automated identification of C. elegans worms, extraction of morphological features, and quantification of fluorescent signals. The program offers machine learning techniques which should aid in studying a large variety of research questions. We demonstrate the power of WorMachine using five separate assays: scoring binary and continuous sexual phenotypes, quantifying the effects of different RNAi treatments, and measuring intercellular protein aggregation. Thus, WorMachine is a \"quick and easy\", high-throughput, automated, and unbiased analysis tool for measuring phenotypes.

bioinformatics↗

Small RNAs reflect grandparental environments in apomictic dandelion

Plants can show long-term effects of environmental stresses and in some cases a stress memory has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21nt and 24nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This indicates that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent and functional changes in epigenetic gene regulation.

genetics↗