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[
International Worm Meeting,
2017]
Artificial light at night (ALAN) has many broad-scale and global implications for ecosystems and wildlife that have evolved under a 24-h circadian cycle. With increased urbanization, artificial light at night has directly altered natural photoperiods and nocturnal light intensity. Artificial light at night can disrupt behavioral patterns such as foraging activity and mating in animals. Disturbances in natural light and dark cycles also affect melatonin-regulated circadian and seasonal rhythms in Drosophila. We investigated the impact of ecologically relevant levels of light pollution on an important invertebrate model, Caenorhabditis elegans, as the impact of night lighting at these light levels is currently unknown. In this study, we exposed worms to artificial light at four intensities: 10-4 lx (control, comparable to natural nocturnal darkness), 10-2 lx (comparable to full-moon lighting and a low level of light pollution), 1 lx (comparable to dawn/dusk or intense light pollution), and 100 lx (dim daylight level comparable to extreme light pollution) on a 12L:12D photoperiod (100 lx treatments experienced constant light). We measured the impact of these light treatments on offspring production in hermaphroditic C. elegans. We grew worms for 2 generations in each light treatment, and then recorded the lifespan and counted the number of hatched offspring produced in the F3 generation. Our data show no significant differences among light levels for lifespan or offspring production suggesting that at least for these life history traits, ALAN does not affect these soil nematodes. Future directions include measuring additional life history traits and circadian gene expression for worms exposed to ALAN.
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[
International C. elegans Meeting,
1995]
The first cleavages of the C. elegans embryo are asymmetric and mark the step-wise separation of soma and germline. We have identified several differences between somatic and germline blastomeres during early cleavages (1) 1. Germline cells protect certain maternal RNAs from a rapid degradation which occurs in somatic cells. 2. Germline cells contain clusters of poly-A+ RNAs associated with the germline-specific P granules. These clusters are not seen in somatic cells. 3. As early as the four-cell stage, somatic cells transcribe certain RNAs, which are off in germline cells. So far, no transcribed gene has been identified in early germline blastomeres. An intriguing possibility is that these cells are transcriptionally inactive.
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[
Evolutionary Biology of Caenorhabditis and Other Nematodes,
2010]
We leveraged next-generation sequencing technology to obtain a genome-wide and unbiased understanding of C. elegans population structure. Through collaboration and generous donations, we obtained a set of 202 wild isolates from throughout the world. In order to reduce the 100 Mb genome to a manageable size amenable to multiplexing, we employed Restriction-Assisted DNA marker sequencing (1) where the genome of each strain was cut using EcoRI and sequenced in both directions from each restriction site. This method allowed us to sequence the same eight megabases from each strain in two runs of an Illumina Genome Analyzer. We sequenced to an average of 12.6X coverage of each region, and SNPs were identified using SAMtools after mapping to the C. elegans genome using bwa. We will present the results of our analysis of population structure, linkage disequilibrium, and indications of genome-wide selection using the roughly 20,000 identified SNPs with minor allele frequencies greater than 5%. So far, we found the average pair-wise differences between strains is roughly 1/900 base pairs, as compared to the reference N2 genome. However, there is a wide range in the pair-wise differences with some strains being much more divergent from the reference N2 than the Hawaiian strain CB4856. These data will allow us to pursue genome-wide association studies and new recombinant inbred line crosses with maximally diverse wild isolates. (1) Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. 2008 Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE 3(10):
e3376.
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[
Conf Proc IEEE Eng Med Biol Soc,
2017]
Generic and scalable data analysis procedures are highly demanded by the increasing number of multi-dimensional biomedical data. However, especially for time-lapse biological data, the high level of noise prevents for automated high-throughput analysis methods. The rapid developing of machine-learning methods and particularly deep-learning methods provide new tools and methodologies that can help in the denoising of such data. Using a convolutional encoder-decoder network, one can provide a scalable bio-image platform, called NucleiNet, to automatically segment, classify and track cell nuclei. The proposed method can achieve 0.99 F-score and 0.99 pixel-wise accuracy on C. elegans dataset, which means that over 99% of nuclei can be successfully detected with no merging nuclei found.
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[
West Coast Worm Meeting,
2000]
Chemotaxis in C. elegans involves a series of abrupt turns (pirouettes) triggered by movement down a gradient of chemical attractant (Pierce-Shimomura, J.T., et al.,J. Neurosci. 19:9557-9569, 1999). Analysis of the time series of concentration change experienced by a chemotaxing worm, together with its pirouette record, suggests a three-stage model in which instantaneous attractant concentration is differentiated, smoothed by low-pass filter, and thresholded by a sigmoidal function relating filter output to pirouette probability. This model predicts that a sudden decrease in attractant concentration will produce a sudden increase in pirouette probability. Moreover, the increase in probability should decay approximately exponentially with a time constant that reflects the worm's memory for concentration changes in the recent past. To test these predictions, we have devised an apparatus that allows us to stimulate an unteathered worm with a nearly instantaneous (step-wise) change in the concentration of soluable attractants such as NaCl. The apparatus consists of a thin (10 mm) agarose film suspended over a buffer-filled chamber, resembling trampoline placed over a swimming pool. The underside of the agarose film contacts the surface of the buffer solution, while the top side of the film contacts the air. The worm is placed on the top of the film and allowed to adapt to a buffer containing a high concentration of attractant for 5 min. The chamber is then drained and quickly refilled with buffer containing a low concentration of attractant. Preliminary results indicate that a step-wise decrease in attractant concentration causes an immediate increase in pirouette probability, as predicted by the model. We plan to use the step response to investigate the time course of the worm's memory for concentration changes, and how this memory is affected by mutations and neuronal ablations. Supported by NIMH MH51383, and NSF IBN9458102,
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[
International C. elegans Meeting,
1995]
O-glycosylation of secreted and cell surface glycoproteins proceeds in a step-wise manner, initiated by the transfer of GalNAc to specific serine or threonine acceptor sites. Unlike N- glycosylation, the recognition sequence of O- glycosylation sites does not share an easily definable consensus sequence, suggesting that discrete polypeptide GalNAc transferases [EC 2.4.1.41] may exist. Sequence comparison of a rat polypeptide GalNAc transferase with an expressed tag sequence database in the GenBank revealed the presence of six discrete C. elegans polypeptide GalNAc transferase homologs. Preliminary studies indicate that at least one of the isoforms can be functionally expressed. Our analysis suggests that the polypeptide GalNAc transferase may be an ancestral gene product and the C.elegans genome may encode for a family of at least six distinct isoforms.
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[
Worm Breeder's Gazette,
1986]
In the past, we have used the standard method for decontaminating stocks, which involves washing worms off a plate, spinning them in a centrifuge, etc The following procedure is much quicker and requires fewer worms. Also, it can be used to directly decontaminate the progeny of a mating and thus accelerate strain constructions. Using a platinum wire with a glob of bacteria on the bottom, pick up several gravid adults and/or eggs from the contaminated plate and transfer them to a seeded plate. Then put a drop of the usual sodium hypochlorite solution (2-4% NaOCl, .4M NaOH) onto the eggs. About half of the eggs will hatch. Occasionally, a very tough bacterial contaminant will survive to form a few colonies, so it is wise to transfer the survivors on the following day.
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[
International Worm Meeting,
2015]
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained in classical phenotypic screens. Sequence data from the mutant strain is aligned to the reference genome, and variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification in C. elegans have been developed, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively less attention has been invested in the underlying software components required for mutation identification. Therefore, we have benchmarked a number of commonly used tools for sequence alignment or variant calling, in all pair-wise combinations, against both synthetic and actual datasets. We compare the sensitivity and specificity of these pipelines, and recommend a workflow that is optimized for variant detection in C. elegans.
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[
Dev Cell,
2010]
Left-right (LR) patterning is an intriguing but poorly understood process of bilaterian embryogenesis. We report a mechanism for LR patterning in C. elegans in which the embryo uncouples its midline from the anteroposterior (AP) axis. Specifically, the eight-cell embryo establishes a midline that is tilted rightward from the AP axis and positions more cells on the left, allowing subsequent differential LR fate inductions. To establish the tilted midline, cells exhibit LR asymmetric protrusions and a handed collective movement. This process, termed chiral morphogenesis, involves differential regulation of cortical contractility between a pair of sister cells that are bilateral counterparts fate-wise and is activated by noncanonical Wnt signaling. Chiral morphogenesis is timed by the cytokinetic furrow of a neighbor of the sister pair, providing a developmental clock and an unexpected signaling interaction between the contractile ring and the adjacent cells.
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[
Biochem Biophys Res Commun,
2010]
Heterotrimeric kinesin-2 motors transport intraflagellar transport (IFT)-particles from the base to the tip of the axoneme to assemble and maintain cilia. These motors are distinct in containing two non-identical motor subunits together with an accessory subunit. We evaluated the significance of this organization by comparing purified wild type kinesin-2 holoenzymes that support IFT in vivo, with mutant trimers containing only one type of motor domain that do not support IFT in vivo. In motility assays, wild type kinesin-2 moved microtubules (MTs) at a rate intermediate between the rates supported by the two mutants. Interestingly, one of the mutants, but not the other mutant or the wild type protein, was observed to drive a persistent counter-clock-wise rotation of the gliding MTs. Thus one of the two motor domains of heterotrimeric kinesin-2 exerts torque as well as axial force as it moves along a MT, which may allow kinesin-2 to control its circumferential position around a MT doublet within the cilium.