Nematicidal activity of plant extracts against the root-knot nematode, Meloidogyne incognita

Nematicidal activity of extracts from plants was assayed against Meloidogyne incognita. In laboratory assays extracts from tobacco (Nicotiana tabacum L), clove (Syzygium aromaticum L), betelvine (Piper betle L), and sweet flag (Acorus calamus L) were most effective in killing the nematode, with an EC50 that was 5-10 times lower than the EC50 of the synthetic pesticides chlorpyrifos, carbosulfan and deltamethrin. The shapes of the dead nematodes differed in a characteristic way, and groups of pesticides and plant extracts could clearly be distinguished based on this phenomenon, which may be an indicator for the modes of action of the tested pesticides. In a greenhouse bioassay clove bud and betelvine were tested as mulch. Experiments revealed that the total number of live nematodes on roots of pepper plants treated with mulch of the clove bud was 7% of that of the controls and did not differ significantly from that of plants treated with the recommended synthetic pesticide carbofuran. The application of clove buds as a botanical pesticide for future use against nematodes is highly promising since clove is the 6th major plant grown on Bangka Island, and the market value of clove has decreased sharply over the last year

Aging Uncouples Heritability and Expression-QTL in Caenorhabditis elegans

The number and distribution of gene expression QTL (eQTL) represent the genetic architecture of many complex traits, including common human diseases. We previously reported that the heritable eQTL patterns are highly dynamic with age in an N2 × CB4856 recombinant inbred population of the nematode Caenorhabditis elegans. In particular, we showed that the number of eQTL decreased with age. Here, we investigated the reason for this decrease by combining gene expression profiles at three ages in the wild types N2 and CB4856 with the reported expression profiles of the RIL population. We determined heritability and transgression (when gene expression levels in the RILs are more extreme than the parents) and investigated their relation with eQTL changes with age. Transgressive segregation was widespread but depended on physiological age. The percentage of genes with an eQTL increased with a higher heritability in young worms. However, for old worms this percentage hardly increased. Using a single marker approach, we found that almost 20% of genes with heritability >0.9 had an eQTL in developing worms. Surprisingly, only 10% was found in old worms. Using a multimarker approach, this percentage increased to almost 30% for both age groups. Comparison of the single marker to a multiple marker eQTL mapping indicated that heritable regulation of gene expression becomes more polygenic in aging worms due to multiple loci and possible epistatic interactions. We conclude that linkage studies should account for the relation between increased polygenic regulation and diminished effects at older ages

A Second Look at String-Inspired Models for Proton-Proton Scattering via Pomeron Exchange

We re-examine a string dual model for elastic proton-proton scattering via Pomeron exchange. We argue that the method of "Reggeizing" a propagator to take into account an entire trajectory of exchanged particles can be generalized, in particular by modifying the value of the mass-shell parameter in the model. We then fit the generalized model to scattering data at large s and small t. The fitting results are inconclusive, but suggest that a better fit might be obtained by allowing the mass-shell to vary. The model fits the data equally well (roughly) for a wide range of values of the mass-shell parameter, but the other fitting parameters (the slope and intercept of the Regge trajectory, and the coupling constant and dipole mass from the proton-proton-glueball coupling) are then inconsistent with what we expect. On the other hand, using the traditional method of Reggeization generates a weaker fit, but the other parameters obtain more physically reasonable values. In analyzing the fitting results, we also found that our model is more consistent with the sqrt(s) = 1800 GeV coming from the E710 experiment than that coming from the CDF experiment, and that our model has the greatest discrepancy with the data in the range 0.5 GeV^2 < |t| < 0.6 GeV^2, suggesting that the transition from soft Pomeron to hard Pomeron may occur closer to t = -0.5 GeV^2 rather than t = -0.6 GeV^2 as previously thought.Comment: 16 pages, 7 figures, 2 table

On the role of dauer in the adaptation of nematodes to a parasitic lifestyle

Abstract Nematodes are presumably the most abundant Metazoa on Earth, and can even be found in some of the most hostile environments of our planet. Various types of hypobiosis evolved to adapt their life cycles to such harsh environmental conditions. The five most distal major clades of the phylum Nematoda (Clades 8–12), formerly referred to as the Secernentea, contain many economically relevant parasitic nematodes. In this group, a special type of hypobiosis, dauer, has evolved. The dauer signalling pathway, which culminates in the biosynthesis of dafachronic acid (DA), is intensively studied in the free-living nematode Caenorhabditis elegans, and it has been hypothesized that the dauer stage may have been a prerequisite for the evolution of a wide range of parasitic lifestyles among other nematode species. Biosynthesis of DA is not specific for hypobiosis, but if it results in exit of the hypobiotic state, it is one of the main criteria to define certain behaviour as dauer. Within Clades 9 and 10, the involvement of DA has been validated experimentally, and dauer is therefore generally accepted to occur in those clades. However, for other clades, such as Clade 12, this has hardly been explored. In this review, we provide clarity on the nomenclature associated with hypobiosis and dauer across different nematological subfields. We discuss evidence for dauer-like stages in Clades 8 to 12 and support this with a meta-analysis of available genomic data. Furthermore, we discuss indications for a simplified dauer signalling pathway in parasitic nematodes. Finally, we zoom in on the host cues that induce exit from the hypobiotic stage and introduce two hypotheses on how these signals might feed into the dauer signalling pathway for plant-parasitic nematodes. With this work, we contribute to the deeper understanding of the molecular mechanisms underlying hypobiosis in parasitic nematodes. Based on this, novel strategies for the control of parasitic nematodes can be developed

Genetic Variation in Complex Traits in Transgenic α-Synuclein Strains of Caenorhabditis elegans.

Different genetic backgrounds can modify the effect of mutated genes. Human α-synuclein (SNCA) gene encodes α-synuclein, and its oligomeric complexes accumulate with age and mediate the disruption of cellular homeostasis, resulting in the neuronal death that is characteristic of Parkinson's Disease. Polymorphic variants modulate this complex pathologic mechanism. Previously, we constructed five transgenic introgression lines of a Caenorhabditis elegans model of α-synuclein using genetic backgrounds that are genetically diverse from the canonical wild-type Bristol N2. A gene expression analysis revealed that the α-synuclein transgene differentially affects genome-wide transcription due to background modifiers. To further investigate how complex traits are affected in these transgenic lines, we measured the α-synuclein transgene expression, the overall accumulation of the fusion protein of α-synuclein and yellow fluorescent protein (YFP), the lysosome-related organelles, and the body size. By using quantitative PCR (qPCR), we demonstrated stable and similar expression levels of the α-synuclein transgene in different genetic backgrounds. Strikingly, we observed that the levels of the a-synuclein:YFP fusion protein vary in different genetic backgrounds by using the COPAS™ biosorter. The quantification of the Nile Red staining assay demonstrates that α-synuclein also affects lysosome-related organelles and body size. Our results show that the same α-synuclein introgression in different C. elegans backgrounds can produces differing effects on complex traits due to background modifiers

A fitness assay for comparing RNAi effects across multiple C. elegans genotypes

<p>Abstract</p> <p>Background</p> <p>RNAi technology by feeding of <it>E. coli </it>containing dsRNA in <it>C. elegans </it>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.</p> <p>Results</p> <p>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 <it>E. coli </it>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 <it>ppw-1 </it>contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important.</p> <p>Conclusions</p> <p>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.</p

A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans

Recombinant inbred lines (RILs) derived from Caenorhabditis elegans wild-type N2 and CB4856 are increasingly being used for mapping genes underlying complex traits. To speed up mapping and gene discovery, introgression lines (ILs) offer a powerful tool for more efficient QTL identification. We constructed a library of 90 ILs, each carrying a single homozygous CB4856 genomic segment introgressed into the genetic background of N2. The ILs were genotyped by 123 single-nucleotide polymorphism (SNP) markers. The proportion of the CB4856 segments in most lines does not exceed 3%, and together the introgressions cover 96% of the CB4856 genome. The value of the IL library was demonstrated by identifying novel loci underlying natural variation in two ageing-related traits, i.e. lifespan and pharyngeal pumping rate. Bin mapping of lifespan resulted in six QTLs, which all have a lifespan-shortening effect on the CB4856 allele. We found five QTLs for the decrease in pumping rate, of which four colocated with QTLs found for average lifespan. This suggests pleiotropic or closely linked QTL associated with lifespan and pumping rate. Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans

A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

Background The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. Results To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. Conclusion Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs

Transcriptional analysis of the response of \u3ci\u3eC. elegans\u3c/i\u3e to ethanol exposure

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