Software: An automated approach to quantify chemotaxis index in C. elegans

A command-line interface to measure chemotaxis index (CI) from chemotaxis assay imagesRelated Publication

Image: An automated approach to quantify chemotaxis index in C. elegans

Plans for the custom, acrylic plate holder that fits securely on the COPAS BIOSORT stage and accommodates six 6 cm chemotaxis platesRelated Publication

The effect of temperature adaptation on the ubiquitin-proteasome pathway in notothenioid fishes.

There is an accumulating body of evidence suggesting that the sub-zero Antarctic marine environment places physiological constraints on protein homeostasis. Levels of ubiquitin (Ub)-conjugated proteins, 20S proteasome activity and mRNA expression of many proteins involved in both the Ub tagging of damaged proteins as well as the different complexes of the 26S proteasome were measured to examine whether there is thermal compensation of the Ub-proteasome pathway in Antarctic fishes to better understand the efficiency of the protein degradation machinery in polar species. Both Antarctic (Trematomus bernacchii, Pagothenia borchgrevinki) and non-Antarctic (Notothenia angustata, Bovichtus variegatus) notothenioids were included in this study to investigate the mechanisms of cold adaptation of this pathway in polar species. Overall, there were significant differences in the levels of Ub-conjugated proteins between the Antarctic notothenioids and B. variegatus, with N. angustata possessing levels very similar to those of the Antarctic fishes. Proteasome activity in the gills of Antarctic fishes demonstrated a high degree of temperature compensation such that activity levels were similar to activities measured in their temperate relatives at ecologically relevant temperatures. A similar level of thermal compensation of proteasome activity was not present in the liver of two Antarctic fishes. Higher gill proteasome activity is likely due in part to higher cellular levels of proteins involved in the Ub-proteasome pathway, as evidenced by high mRNA expression of relevant genes. Reduced activity of the Ub-proteasome pathway does not appear to be the mechanism responsible for elevated levels of denatured proteins in Antarctic fishes, at least in the gills

Data from: Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans

Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness in multicellular organisms, the most pervasive of which is simply the time it takes to count many individuals of different types from many replicate populations. Methods by which counting can be automated in high throughput are desirable, but for automated methods to be useful, the bias and technical variance associated with the method must be (a) known, and (b) sufficiently small relative to other sources of bias and variance to make the effort worthwhile. The nematode Caenorhabditis elegans is an important model organism, and the fitness effects of genotype and environmental conditions are often of interest. We report a comparison of three experimental methods of quantifying competitive fitness, in which wild-type strains are competed against GFP-marked competitors under standard laboratory conditions. Population samples were split into three replicates and counted (1) "by eye" from a saved image, (2) from the same image using CellProfiler image analysis software, and (3) with a large particle flow cytometer (a "worm sorter"). From 720 replicate samples, neither the frequency of wild-type worms nor the among-sample variance differed significantly between the three methods. CellProfiler and the worm sorter provide at least a tenfold increase in sample handling speed with little (if any) bias or increase in variance

Data from: The mutational decay of male-male and hermaphrodite-hermaphrodite competitive fitness in the androdioecious nematode C. elegans

Androdioecious Caenorhabditis have a high frequency of self-compatible hermaphrodites and a low frequency of males. The effects of mutations on male fitness are of interest for two reasons. First, when males are rare, selection on male-specific mutations is less efficient than in hermaphrodites. Second, males may present a larger mutational target than hermaphrodites because of the different ways in which fitness accrues in the two sexes. We report the first estimates of male-specific mutational effects in an androdioecious organism. The rate of male-specific inviable or sterile mutations is ≤ 5 x 10-4/generation, below the rate at which males would be lost solely due to those kinds of mutations. The rate of mutational decay of male competitive fitness is ~0.17%/generation; that of hermaphrodite competitive fitness is ~0.11%/generation. The point estimate of ~1.5X faster rate of mutational decay of male fitness is nearly identical to the same ratio in Drosophila. Estimates of mutational variance (VM) for male mating success and competitive fitness are not significantly different from zero, whereas VM for hermaphrodite competitive fitness is similar to that of non-competitive fitness. Two independent estimates of the average selection coefficient against mutations affecting hermaphrodite competitive fitness agree to within two-fold, 0.33%-0.5%

competitive fitness data

Excel workbook with four worksheets. Sheet 1, "malefitness" contains male fitness data; sheet two, "malefit_readme" contains descriptions of column headings. Sheet 3, "hermfitness" contains hermaphrodite fitness data; sheet 4, "hermfit_readme" contains descriptions of column headings

Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans

Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing decreases the effective population size, effective recombination rate and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times, and all three species, including the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example of how species can avoid the evolutionary dead end associated with selfing.</p

OSIRIS-APEX: An OSIRIS-REx Extended Mission to Asteroid Apophis

The Origins, Spectral Interpretation, Resource Identification, and Security–Regolith Explorer (OSIRIS-REx) spacecraft mission characterized and collected a sample from asteroid (101955) Bennu. After the OSIRIS-REx Sample Return Capsule released to Earth’s surface in 2023 September, the spacecraft diverted into a new orbit that encounters asteroid (99942) Apophis in 2029, enabling a second mission with the same unique capabilities: OSIRIS–Apophis Explorer (APEX). On 2029 April 13, the 340 m diameter Apophis will draw within ∼32,000 km of Earth’s surface, less than 1/10 the lunar distance. Apophis will be the largest object to approach Earth this closely in recorded history. This rare planetary encounter will alter Apophis’s orbit, will subject it to tidal forces that change its spin state, and may seismically disturb its surface. APEX will distantly observe Apophis during the Earth encounter and capture its evolution in real time, revealing the consequences of an asteroid undergoing tidal disturbance by a major planet. Beginning in 2029 July, the spacecraft’s instrument suite will begin providing high-resolution data of this “stony” asteroid—advancing knowledge of these objects and their connection to meteorites. Near the mission’s end, APEX will use its thrusters to excavate regolith, a technique demonstrated at Bennu. Observations before, during, and after excavation will provide insight into the subsurface and material properties of stony asteroids. Furthermore, Apophis’s material and structure have critical implications for planetary defense