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[
Bioinformatics,
2003]
SUMMARY: GoFish is a Java application that allows users to search for gene products with particular gene ontology (GO) attributes, or combinations of attributes. GoFish ranks gene products by the degree to which they satisfy a Boolean query. Four organisms are currently supported: Saccaromyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and M.musculus.
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[
Worm Breeder's Gazette,
1993]
THE C. ELEGANS CLEAVAGE AND POLYADENYLATION SlGNAL Tom Blumenthal, Department of Biology, Indiana University. Bloomington, IN 47405; Owen White and Chris Fields, Institute For Genomic Research, Gaithersburg, MD, 20878
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[
Nematologica,
1976]
The growth promoting activity of protein-haemin co-precipitates from ferritin, apoferritin, transferrin, bovine serum albumin, conalbumin and egg white on maturation and reproduction of C. briggsae has been evaluated. Ferritin, apoferritin and transferrin were found to be biologically highly active in the presence of haemin. Bovine serum albumin, conalbumin and egg white were slightly active. Maturation and reproduction of C. briggsae on the coagulates from bovine serum albumin and egg white were nearly independent of the dose administered, probably because the limited availability of haemin from these coagulates permits but slow growth, even in the presence of abundant proteinaceous material. Bovine serum albumin, egg white and conalbumin failed to support continuous growth of C. briggsae. It is supposed that the limited availability of haemin from these coagulates inhibits normal maturation and reproduction of the F1 progeny. These experiments clearly demonstrate the requirement for particulate haem. The requirement for
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[
Worm Breeder's Gazette,
1999]
For everyone who deals with the characterization of expression patterns in the nervous system, the truly impressive paper of White et al., 1986 ("Mind of the Worm") serves as the ultimate source of knowledge. While the largely invariant neural cell body positions described by Sulston et al. are an essential tool in the identification of neurons, the axon morphologies described by White et al. greatly facilitate the identification of a given neuron.
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[
Microsc Microanal,
2014]
A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.
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[
J Environ Sci Health A Tox Hazard Subst Environ Eng,
2017]
This study aimed to investigate the biological impact of exposure on domestic light emitting diodes (LED) lighting using the free-living nematode Caenorhabditis elegans as a model. Nematodes were separately exposed to white LED light covering the range of 380-750nm, blue light at 450nm and black light at 380-420nm for one life cycle (egg to adult) with dark exposure as the control. Each light range induced stress to the nematode C. elegans such as reducing the number of the hatched eggs and/or delayed the maturation of the hatched eggs to the adult stage. In addition, it lowered or prevented the ability of adults to lay eggs and impaired the locomotion in the exposed worms. The observed type of biological stress was also associated with the production of reactive oxygen species (ROS) as compared to nematodes grown in the dark. It is concluded that the blue light component of white LED light may cause health problems, and further investigation is required to test commercial brands of white LEDs that emit different amounts of blue light.
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[
Nat Neurosci,
2013]
In the version of this article initially published, the average durations for N2,
cha-1(
n2411) and
cha-1(
p503) shown in Figure 2b (white bars) were incorrect because the n-values used to calculate them included cases in which no nictation was observed:The error has been corrected in the HTML and PDF versions of the article.
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[
Neuron,
2002]
Drosophila melanogaster has been a premier genetic model system for nearly 100 years, yet lacks a simple method to disrupt gene expression. Here, we show genomic cDNA fusions predicted to form double-stranded RNA (dsRNA) following splicing, effectively silencing expression of target genes in adult transgenic animals. We targeted three Drosophila genes: lush, white, and dGqalpha. In each case, target gene expression is dramatically reduced, and the white RNAi phenotype is indistinguishable from a deletion mutant. This technique efficiently targets genes expressed in neurons, a tissue refractory to RNAi in C. elegans. These results demonstrate a simple strategy to knock out gene function in specific cells in living adult Drosophila that can be applied to define the biological function of hundreds of orphan genes and open reading frames.
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[
Worm Breeder's Gazette,
1980]
In our laboratory, we routinely use dauer larvae to obtain large, synchronous cultures of L4's and adults for biochemical purposes. We have found that large numbers of dauer larvae can be obtained using eggwhite plates (a modification of the method of D. Baillie and R. Rosenbluth, WBG 2 (1)). Egg-white plates are prepared by stirring the white of one chicken egg with 50 ml of boiling distilled water for several seconds, homogenizing the mixture for one minute in a Waring blender, and layering 3-4 ml of the resultant liquid slurry onto a standard 100mm NGM plate containing a lawn of E . coli . After drying overnight, egg-white plates are seeded with about 1500 dauer larvae and incubated at 20 C . These dauer larvae develop into adults, but for some unknown reason a large proportion of their progeny develop into dauer larvae and become arrested at this stage . Approximately 1x10+E5 dauer larvae are usually recovered per plate after 5-7 days incubation time . Yields as high as 2x10+E5 per plate have been obtained in some instances. For purification of dauer larvae, animals washed from individual egg- white plates are incubated with 5-10 ml of 1% SDS for 30-60 minutes, collected by low speed centrifugation, resuspended in 0.5 -1 ml of buffer, and centrifuged through a 2 ml cusion of ice-cold 15% ficoll for 10 minutes at 300 xg. Intact dauer larvae pellet through the ficoll, while egg matter and worm carcasses remain at the interface . Because a small number of non-dauer animals sometimes escape this first SDS treatment, the entire procedure is usually repeated . Purified dauer larvae can be stored in Mg buffer at 16 C until use and retain good viability for 30-60 days . It has been our experience that dauer larvae obtained from egg-white plates recover much more synchronously than do dauer larvae isolated from starved E . coli plates, especially if they are used within 2 weeks of isolation. Also we have noted that the synchrony of recovering populations tends to decrease as dauer larvae are stored for longer periods of time.
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[
Nucleic Acids Res,
2020]
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.