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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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[
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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[
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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[
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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[
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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[
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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[
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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[
International Worm Meeting,
2013]
Postmitotic cellular identity is generally a stable feature of multicellular organisms. However, there are naturally occurring instances whereby cells can transdifferentiate into other cell types with different functions. Documented examples are rare, but intriguing, as they necessitate a highly dynamic and wide change in the gene expression program from one cell-type to another. A key question in the field is whether the complete direct conversion of one cell into a different functional cell involves epigenomic changes, especially as the state of the epigenome has been suggested to represent a barrier to induced reprogramming. Here, through the use of a forward genetic screen in C. elegans, we found that the robustness of a highly precise transdifferentiation event whereby a postmitotic hindgut epithelial cell (called Y) changes into a motoneuron (called PDA) requires the sequential and overlapping activities of a histone H3 K27 demethylase (HDM) and a H3 K4 methyltransferase (HMT). Perturbation of their catalytic activities, as well as artificial modulation of histone methylation states within the Y cell decreased the efficiency of successful transdifferentiation events. We uncovered that the different steps of the conversion process have different requirements for the HMT and HDM activities. The HMT is required early to permit the loss of hindgut epithelial identity; a role performed in association with a C. elegans Nanog and Oct4 Deacetylase complex, a known pluripotentcy complex in mammalian cells. Next, the HDM and HMT act together to promote re-differentiation into a motoneuron via induction of PDA specific genes. The exquisite timing of this step-wise epigenetic reprogramming is correlated with dynamic protein levels of the HDM during conversion. Ectopic presence of the HDM at inappropriate times negatively impacted on proper transdifferentiation, suggesting that a critical balance between H3 K4 methylation and H3 K27 demethylation activities at specific steps of conversion are required. Together, our data suggests that step-wise epigenomic reprogramming - mediated by histone H3 K27 demethylating and H3 K4 methylating enzymes - permits robust and precise conversion of postmitotic cell identity.
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[
C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany,
2010]
Left-right (LR) patterning is an intriguing but poorly understood process of bilaterian embryogenesis. We report a novel mechanism to break LR symmetry, whereby the embryo uncouples its midline from the anteroposterior (AP) axis. Specifically, the eight-cell C. elegans embryo establishes a midline that tilts 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, is based on differential regulation of cortical contractility between a pair of sister cells that are bilateral counterparts fate-wise, and is activated by non-canonical Wnt signaling. Chiral morphogenesis is timed by the division furrow of a neighbor of the sister pair, suggesting a nov el developmental clock and a novel signaling mechanism from the contractile ring to adjacent cells.