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Can J Biochem Cell Biol,
1985]
In this paper we describe the coexistence of two forms of the transposable element Tc1 in the genome of the nematode Caenorhabditis elegans. A copy of the variant form has been isolated from the Bergerac genome and characterized. Restriction mapping and DNA sequencing have shown that a G to T transversion generated a HindIII restriction site to form the variant Tc1(Hin). The presence of this new restriction site makes this variant easily detectable on genomic blot hybridizations. There are approximately 20 copies of Tc1(Hin) amongst the Tc1's present in the Bergerac genome. Bergerac has approximately 250 copies of Tc1 per genome, whereas Bristol has about 30. In the Bristol strain we detected at least one copy Tc1(Hin). The ratio of Tc1(Hin) to total Tc1's is similar in the genomes of Bristol and Bergerac, even though they have markedly different total numbers of Tc1. Our results suggest that a trans-acting change in either the elements or the host genome was responsible for the expansion of Tc1 copy number in the Bergerac genome.
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IEEE Access,
2019]
Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the <i>Caenorhabditis elegans</i> embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Our experiments showed that with 10-15 well-labeled rosette images and 30-40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.
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Mol Cell Biol,
1986]
We investigated the ability of the transposable element Tc1 to excise from the genome of the nematode Caenorhabditis elegans var. Bristol N2. Our results show that in the standard lab strain (Bristol), Tc1 excision occurred at a high frequency, comparable to that seen in the closely related Bergerac strain BO. We examined excision in the following way. We used a unique sequence flanking probe (pCeh29) to investigate the excision of Tc1s situated in the same location in both strains. Evidence of high-frequency excision from the genomes of both strains was observed. The Tc1s used in the first approach, although present in the same location in both genomes, were not known to be identical. Thus, a second approach was taken, which involved the genetic manipulation of a BO variant, Tc1(Hin). The ability of this BO Tc1(Hin) to excise was retained after its introduction into the N2 genome. Thus, we conclude that excision of Tc1 from the Bristol genome occurs at a high frequency and is comparable to that of Tc1 excision from the Bergerac genome. We showed that many Tc1 elements in N2 were apparently functionally intact and were capable of somatic excision. Even so, N2 Tc1s were prevented from exhibiting the high level of heritable transposition displayed by BO elements. We suggest that Bristol Tc1 elements have the ability to transpose but that transposition is heavily repressed in the gonadal tissue.
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Nature,
1984]
The mobilization of Tc1, a transposable element in the genome of the roundworm Caenorhabditis elegans, has been investigated. Genomic blot hybridization has shown that Tc1 exists in very different numbers in the genomes of two closely related strains of C. elegans: there are -30 copies of Tc1 in the Bristol, whereas in the Bergerac strain there are 200-300. Most of these Tc1 elements are structurally highly conserved although there exists a second form which contains a HindIII restriction site (Tc1 (Hin) form) and comprises -10% of the population. Excision of Tc1 from its chromosomal location in the Bergerac strain is indicated by the presence, on genomic blots, of a minor bind corresponding to the size of the uninserted restriction fragment. Here we describe the recovery of extrachromosomal linear and closed circular copies of Tc1 from the Bergerac strain, presumably a result of Tc1
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Journal of Pesticide Science,
2000]
Great losses to crop productivity are annually induced by plant-parasitic nematodes. However, nematicides available for the last few decades have been imperfect with respect to environmental safety or healthy life. The need to develop new generation nematicides, less hazardous for Mammalia, is urgent. The free-living soil-inhabiting nematode, Caenorhabditis elegans, is an excellent laboratory animal in terms of being easily cultured, its short life cycle and normally hermaphroditic mode of reproduction. Therefore, it has been long popular as a useful screen for nematicides, anthelmintics, neurotoxins and environmental pollutants. Using C. elegans as a test animal, thus far screening of nematicidal compounds from methanol extracts of 230 wild plant species covering 190 genera among 77 families in Kagawa, Japan, has been performed in our laboratory for two years. The ellagitannin-rich fruit of Cornaceae Cornus officinalis has been used as one of the ingredients in the Kanpo medicine, Hachimi-gan. A macrocyclic ellagitannin dimer isolated from Woodfordia fruticosa exhibits antitumor activity. This paper deals with ellagitannin toxicity in the soil-inhabiting nematode, C. elegans.
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Parasitology,
1989]
The DNA from a number of free-living and parasitic nematode species was examined to determine the genomic number and distribution of DNA sequences encoding two evolutionarily conserved proteins; the major sperm protein (MSP) and nematode actin. Ascaris and Caenorhabditis MSP cDNA sequences and Ascaris genomic actin sequences were used to probe Southern blots of Eco RI and Hin d III digested nematode DNA. The number of MSP genes varied widely between the 1 MSP gene in Ascaris and the 60 MSP genes in Caenorhabditis. Filarial nematodes appeared to have 1-4 MSP genes while the plant and insect parasitic species showed from 5-12 MSP-hybridizing restriction fragments. Mammalian intestinal parasites showed between 1 and 13 bands hybridizing with the MSP probes. Blots probed to estimate the number of actin genes showed that, with the exception of Ascaris which contains more than 20 germ line sequences that encode actin, all of the nematodes tested had between 3 and 9 bands that hybridized to the Ascaris genomic actin probe. The possible use of highly conserved sequences such as MSP and actin to differentiate between nematode species in diagnostic and taxonomic studies is discussed.