Colonnello A et al. (2020) Neurotox Res "Correction to: Comparing the Neuroprotective Effects of Caffeic Acid in Rat Cortical Slices and Caenorhabditis elegans: Involvement of Nrf2 and SKN-1 Signaling Pathways."

Tunez I, Rubio-Lopez LC, Aguilera-Portillo G, Silva-Palacios A, Evaristo-Priego Y, Santamaria A, Galvan-Arzate S, Cortez-Nunez S, Aschner M, Rangel-Lopez E, Chen P, Colonnello A, Robles-Banuelos B, Garcia-Contreras R

[Neurotox Res, 2020]

One of the authors has incorrect family name spelling in the original article_. Michael Ashner should read as Michael Aschner.

Zhou MH et al. (1996) Worm Breeder's Gazette "Liquid Culture of the Worms with a Fermentor"

Zhou MH, Yang H, Walthall WW

[Worm Breeder's Gazette, 1996]

The yield of C. elegans and their food (E.coli) are relatively low in the large liquid cultures growth (Koelle et al.,1994) and the whole growth process is tedious. Here we report the successful growth of C.elegans with a fermentor. The following protocol is based on the protocol by Michael Koelle and Tory Herman (1994) from Internet.

Hengartner MO et al. (1992) Worm Breeder's Gazette "unc-50, a Gene Required for Acetylcholine Receptor Function, Encodes an Unfamiliar Protein"

Horvitz HR, Tsung N, Hengartner MO, Lewis JA

[Worm Breeder's Gazette, 1992]

unc-50, a gene requiired for acetylcholine receptor function, encodes an unfamiliar protein Michael Hengartner, Nancy Tsung, Jim Lewist, and Bob Horvitz HHMI, Dept. Biology, MIT, Cambridge, MA 02139, USA. t Division of Life Sciences, U. of Texas at San Antonio, San Antonio, IX 78249

Holway AH et al. (2007) J Cell Biol "Checkpoint silencing during the DNA damage response in Caenorhabditis elegans embryos"

Kim SH, Michael WM, La Volpe A, Holway AH

[J Cell Biol, 2007]

After publication of this manuscript, the authors noticed that two images (Fig. 4 B, top left and middle) had been duplicated from a previous publication (Holway, A.H., C. Hung, and W.M. Michael. 2005. Genetics. 169:14511460). Here we provide new images corresponding to these control experiments. The authors apologize for this oversight.

Meyer, Michael et al. (2009) International Worm Meeting "NUD-1 Functions in C. elegans Sperm Development."

Large, Michael, Meyer, Michael, Gratz, Scott, Miskowski, Jennifer Anne

[International Worm Meeting, 2009]

The C. elegans NUD-1 protein is the structural and functional ortholog of the fungal NudC protein. NUD-1/NudC proteins are evolutionarily conserved and have been implicated in diverse processes such as asymmetrical cell division in yeast, nuclear migration in fungi, and neuronal migration in humans; however, their exact function is unknown. When NUD-1 levels are depleted in N2 hermaphrodites by RNAi, a variety of phenotypes are found, including sterility, which supports a role for NUD-1 in C. elegans gonad development. Analysis of NUD-1(RNAi) animals revealed abnormalities in both the somatic gonad and the germ line. To ascertain whether the observed germ line defects were the result of a direct role for NUD-1 in the germ line, rather then an indirect consequence of somatic gonad defects, NUD-1 RNAi was performed in rrf-1 mutants. Treated hermaphrodites were rendered sterile, although they sometimes made sperm and/or oocytes. rrf-1 males with depleted NUD-1 levels also made sperm. To test whether these sperm were viable, the RNAi-treated males were mated to Fog females, and a significant percentage of these matings yielded no progeny compared to control matings. The expression pattern of NUD-1 further supports its function in sperm development. Observation of transgenic worms expressing a full-length NUD-1::GFP construct revealed faint staining in sperm, in addition to other tissues. Furthermore, a number of immunofluorescence experiments have been performed using two different antibodies that were generated against a phosphorylated version of mammalian NUDC and cross-react specifically in C. elegans. Consistently, NUD-1 is localized in perinuclear puncta in primary spermatocytes with more diffuse staining in secondary spermatocytes and spermatids. NUD-1 colocalizes with fibrous-body membrane organelles (FBMOs), which are sperm-specific organelles. Like FBMOs, NUD-1 is asymmetrically segregated to spermatids and away from residual bodies and this localization pattern requires functional SPE-15/Myosin VI protein. To further explore the relationship between NUD-1 and FBMOs, the localization of FBMOs in NUD-1(RNAi) mutants is being explored.

Michael WM (2017) MicroPubl Biol "Asymmetric distribution of cyb-3 in 4-cell stage embryos."

Michael WM

[MicroPubl Biol, 2017]

Early embryos were fixed and stained with Mab F2F4 (green), shown to recognize CYB-3 (Michael, 2016), and DAPI, to illuminate the DNA (blue). Either wild type or par-4 mutant embryos were examined, after 24-hour incubation at 25C (the non-permissive temperature for the it47 allele of par-4). Anterior is to the left in all images. The data presented here reveals previously not shown data that depicts CYB-3 as asymmetrically distributed at the 4-cell stage. These data further support reported findings in Michael, 2016. There is more CYB-3 in the AB cell relative to its sister P1. In 4-cell embryos there is more CYB-3 in the EMS cell relative to its sister, P2. Thus, during P-lineage divisions, CYB-3 is asymmetrically distributed such that the somatic precursor receives more than its germline precursor sister cell. This asymmetry is abolished in par-4 mutant embryos, where all blastomeres contain equivalent amounts of CYB-3.

Jing Liu et al. (2015) Conf Proc IEEE Eng Med Biol Soc "Image registration robust to sparse large errors."

Andrew CHISHOLM, Marian Chuang, Pamela Cosman, Jing Liu

[Conf Proc IEEE Eng Med Biol Soc, 2015]

Registration is difficult when images to be registered contain sparse but large-valued differences. We present a method for robust registration that ignores some fraction of large differences, while constraining the sparseness of these errors. We apply the method to stabilize microscopy videos of C. elegans tissues, in which bright moving filaments and tissue wounding appear as sparse large-valued differences. We demonstrate the advantage of the method on both synthetic and real data compared to state-of-the-art methods.

Shintoku Y et al. (2005) J Parasitol "Strongyloides ratti infection in the large intestine of wild rats, Rattus norvegicus."

Kimura E, Hasegawa H, Shintoku Y, Kondo S, Islam MZ, Kadosaka T, Itoh M

[J Parasitol, 2005]

The large intestine of a rat has been neglected almost completely as a site of Strongyloides sp. infection. We reported that adult Strongyloides ratti remained in the large intestine for more than 80 days, producing more number of infective larvae than small intestine adults, and therefore hypothesized that parasitism in this site could be a survival strategy. In wild rats, however, no study has focused on large intestine infections of Strongyloides. The present study revealed that 32.4% of 68 wild rats, Rattus norvegicus, had the infection of S. ratti in the large intestine, with an average of 4.7 worms. These worms harbored normal eggs in the uterus. In a laboratory experiment with S. ratti and Wister rats, daily output of infective larvae by 4.7 females in the large intestine was estimated to be 4,638.4, suggesting that a few parasites could play a role in the parasite transmission. Five species of nematode found in the wild rats showed seasonality in infection intensity, with highest intensities in March-May. The number of S. ratti in the large intestine was also highest in these months.

Watson A et al. (1993) Nature "The Caenorhabditis elegans genome sequencing project: first steps in automation."

Smaldon N, Watson A, Lucke R, Hawkins TL

[Nature, 1993]

Novel biochemical processes using magnetic particles have been automated to provide a robotic system to perform processes for large-scale shotgun sequencing.

Oliver JL et al. (2008) BMC Evol Biol "Phylogenetic distribution of large-scale genome patchiness."

Oliver JL, Hackenberg M, Carpena P, Bernaola-Galvan P

[BMC Evol Biol, 2008]

ABSTRACT: BACKGROUND: The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. RESULTS: The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. CONCLUSIONS: Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.