20 research outputs found
Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance
To understand the genetic basis of complex traits, it is important to be able to efficiently
phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have
been isolated from diverse populations around the globe and whole-genome sequenced. As a result,
hundreds of wild strains with known genome sequences can be used for genome-wide association studies
(GWAS). However, phenotypic analysis of these strains can be laborious, particularly for quantitative traits
requiring multiple measurements per strain. Starvation resistance is likely a fitness-proximal trait for nematodes, and it is related to metabolic disease risk in humans. However, natural variation in C. elegans
starvation resistance has not been systematically characterized, and precise measurement of the trait is
time-intensive. Here, we developed a population-selection-and-sequencing-based approach to phenotype
starvation resistance in a pool of 96 wild strains. We used restriction site-associated DNA sequencing
(RAD-seq) to infer the frequency of each strain among survivors in a mixed culture over time during
starvation. We used manual starvation survival assays to validate the trait data, confirming that strains that
increased in frequency over time are starvation-resistant relative to strains that decreased in frequency.
Further, we found that variation in starvation resistance is significantly associated with variation at a region
on chromosome III. Using a near-isogenic line (NIL), we showed the importance of this genomic interval for
starvation resistance. This study demonstrates the feasibility of using population selection and sequencing
in an animal model for phenotypic analysis of quantitative traits, documents natural variation of starvation
resistance in C. elegans, and identifies a genomic region that contributes to such variation
Production of dust by massive stars at high redshift
The large amounts of dust detected in sub-millimeter galaxies and quasars at
high redshift pose a challenge to galaxy formation models and theories of
cosmic dust formation. At z > 6 only stars of relatively high mass (> 3 Msun)
are sufficiently short-lived to be potential stellar sources of dust. This
review is devoted to identifying and quantifying the most important stellar
channels of rapid dust formation. We ascertain the dust production efficiency
of stars in the mass range 3-40 Msun using both observed and theoretical dust
yields of evolved massive stars and supernovae (SNe) and provide analytical
expressions for the dust production efficiencies in various scenarios. We also
address the strong sensitivity of the total dust productivity to the initial
mass function. From simple considerations, we find that, in the early Universe,
high-mass (> 3 Msun) asymptotic giant branch stars can only be dominant dust
producers if SNe generate <~ 3 x 10^-3 Msun of dust whereas SNe prevail if they
are more efficient. We address the challenges in inferring dust masses and
star-formation rates from observations of high-redshift galaxies. We conclude
that significant SN dust production at high redshift is likely required to
reproduce current dust mass estimates, possibly coupled with rapid dust grain
growth in the interstellar medium.Comment: 72 pages, 9 figures, 5 tables; to be published in The Astronomy and
Astrophysics Revie
WormSizer: high-throughput analysis of nematode size and shape.
The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer