A Caenorhabditis elegans Wild Type Defies the Temperature–Size Rule Owing to a Single Nucleotide Polymorphism in tra-3

Ectotherms rely for their body heat on surrounding temperatures. A key question in biology is why most ectotherms mature at a larger size at lower temperatures, a phenomenon known as the temperature–size rule. Since temperature affects virtually all processes in a living organism, current theories to explain this phenomenon are diverse and complex and assert often from opposing assumptions. Although widely studied, the molecular genetic control of the temperature–size rule is unknown. We found that the Caenorhabditis elegans wild-type N2 complied with the temperature–size rule, whereas wild-type CB4856 defied it. Using a candidate gene approach based on an N2 × CB4856 recombinant inbred panel in combination with mutant analysis, complementation, and transgenic studies, we show that a single nucleotide polymorphism in tra-3 leads to mutation F96L in the encoded calpain-like protease. This mutation attenuates the ability of CB4856 to grow larger at low temperature. Homology modelling predicts that F96L reduces TRA-3 activity by destabilizing the DII-A domain. The data show that size adaptation of ectotherms to temperature changes may be less complex than previously thought because a subtle wild-type polymorphism modulates the temperature responsiveness of body size. These findings provide a novel step toward the molecular understanding of the temperature–size rule, which has puzzled biologists for decades

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

Effects Induced by the Temperature and Chemical Environment on the Fluorescence of Water-Soluble Gold Nanoparticles Functionalized with a Perylene-Derivative Dye

We developed a fluorescent molecular probe based on gold nanoparticles functionalized with N,N′-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dihydrochloride, and these probes exhibit potential for applications in microscopic thermometry. The intensity of fluorescence was affected by changes in temperature. Chemical environments, such as different buffers with the same pH, also resulted in different fluorescence intensities. Due to the fluorescence intensity changes exhibited by modified gold nanoparticles, these materials are promising candidates for future technologies involving microscopic temperature measurements

Transcriptome analysis of a long-lived natural <it>Drosophila</it> variant: a prominent role of stress- and reproduction-genes in lifespan extension

<p>Abstract</p> <p>Background</p> <p>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 <it>Drosophila melanogaster</it> 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).</p> <p>Results</p> <p>We found profound differences between <it>Drosophila</it> lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived <it>Drosophila</it>. 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.</p> <p>Conclusions</p> <p>Our study unveils transcriptional changes associated with lifespan extension in SR <it>Drosophila</it>. 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.</p

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly

Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life-history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age-at-reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade-offs should be considered not only among traits within an organism, but also among adaptive responses to different—sometimes conflicting—selection pressures, including across life stages.</p

A strategy in searching for stress tolerance-correlated characteristics in nematodes while accounting for phylogenetic interdependence

Biological indicators are highly relevant for assessing the condition of a soil as they are integrative; they reflect the overall impact of physical, chemical and biological changes. Indigenous soil organisms are preferable to other test organisms because the diversity and condition of indigenous soil organisms reflect both acute and chronic effects of soil disturbances. Nematodes are ubiquitous, speciose, easily extractable and present in extremely high numbers. Given the ever increasing amount of sequence data, DNA barcode-based community analysis will soon be possible and a next step would be to define objective criteria for the ecological grouping of soil nematodes. Here, we present a framework to ascertain which traits are correlated with a tolerance to stress. For this, a field study on the effects of pH and copper on nematode communities was re-analysed. Changes in abundances of individual genera were correlated with a number of potentially stress tolerance-related characteristics. The generalised least squares (GLS) method was used to account for the phylogenetic dependence of the data. Only the relationship between the ability to enter a survival stage and tolerance to copper at pH 6.1 was found to be significant, but the quantity of missing data probably had a negative impact on the analyses. This study did, however, clearly demonstrate the importance of accounting for the effects of phylogenetic dependence in the data. When the phylogeny was taken into account, we observed an average change in P value of 0.196 (and in some cases as much as 0.6) for the correlations of possible stress-related characteristics and Cu or pH tolerance. This research constitutes a proof-of-principle for a transparent method to relate stress tolerance to (ecological) characteristics. The usefulness of this powerful method should become even clearer when substantially higher numbers of individuals are analysed (as facilitated by using DNA barcodes) and when missing data are filled i

Comparison of the “Open” Configuration of F96 and L96 Variants of the TRA-3 DIIa Domain

<p>The region between 61–114 and 149–161, containing the calcium-binding site, and the sequence stretch around position 96 is represented as a solid oval ribbon while the rest is in trace representation. Position 96 and the flexible calcium loop 66–73 with alpha carbons are shown as balls are in light blue. The side chains of N2 F96 (left) and its CB mutant L96 (right) are in space-filling representation. Mutation F96L introduces a void of ~1.5 Å that the loop containing the calcium-binding site can sample during its dynamics. As the number of configurations increases, this might reduce the ability for calcium binding. Distances shown in the figure are between the closest atom of the lateral chain of the F/L96 and the alpha carbons of F66 and G69 respectively.</p

Slope of TRB for 80 RILs and Parental Strains

<p>We calculated the slope (10⁶ μm³/degree) from a plot of body size versus temperature (12 °C and 24 °C) where: slope = (size at 24 °C − size at 12 °C)/(12 °C − 24 °C). The variance of body size calculated for all the RILs was small and differed only 7% between 12 °C and 24 °C. Most of the lines had a negative slope meaning that at low temperatures individuals grew bigger. Yet 17.5% of the RILs had a positive slope, and a few RILs were nearly nonplastic (i.e., slopes were relatively small). At 12 °C N2 was 35% larger than CB. The TRB for parental strains are designated by arrows: N2, open arrow; CB, solid arrow.</p