Chang SY et al. (2017) J Microbiol Biotechnol "Erratum to: Genome Characteristics of Lactobacillus fermentum Strain JDFM216 for Application as Probiotic Bacteria."

Lee HK, Heo J, Chang SY, Jeong DY, Oh S, Jo SH, Kim Y, Park MR, Song MH, Kim JN

[J Microbiol Biotechnol, 2017]

This erratum is being published to correct the 1st author's name of above manuscript by Jang et al. that was published in Journal of Microbiology and Biotechnology (2017, 27: 1266-1271). The 1st author name(Sung Yong Jang) should appear as 'Sung Yong Chang'.

Sung Min Han et al. (2003) International Worm Meeting "The Caenorhabditis elegans DICE-1 homologue is required for germ-line development and embryogenesis in Caenorhabditis elegans"

Sung Min Han, Hyeon-Sook Koo, Sung-Shin Ryu

[International Worm Meeting, 2003]

The protein encoded by the open reading frame F08B4.1 was found to interact with a RecQ family DNA helicase (RecQ5) encoded by E03A3.2 in yeast two-hybrid assay. The gene product of F08b4.1 is homologous to human DICE-1 protein, which was first identified in a human lung carcinoma cell as a candidate tumor suppressor. Although human DICE-1 (deleted in cancer 1) is presumed to be a tumor suppressor, its detailed molecular function is unknown. We have examined the functions and expression pattern of Ce-Dice-1 by RNA interference and GFP reporter expression. When the Ce-dice-1 was inhibited by double-stranded RNA microinjection, complete embryonic lethality was observed. In order to examine the functions of Ce-Dice-1 at postembryonic stage, Ce-dice-1 gene expression was inhibited by feeding Caenorhabditis elegans worms with the double-stranded RNA from the L1 stage. Protruding vulva, growth arrest at the L4 stage, and pleiotropic phenotypes in the germ-line such as undersized gonads, abnormal gonad migration, defective oocyte development, endomitotic oocytes, and increased apoptosis appeared. GFP reporter gene expression induced by the promoter sequence was observed in hypodermal cells after the L4 stage. The gene expression in hypodermal cells probably is associated with the phenotypes of protruding vulva and growth arrest at the L4 stage. Ce-dice-1 is probably also expressed in the germ-line and early embryos, as deduced from the RNAi phenotypes. Although, Ce-Dice-1 interacts with RecQ5 protein in yeast two-hybrid assay, no genetic interaction has been detected in double RNAi of the two genes.

Palikaras K et al. (2016) Bio Protoc "Measuring Oxygen Consumption Rate in Caenorhabditis elegans."

Palikaras K, Tavernarakis N

[Bio Protoc, 2016]

The rate of oxygen consumption is a vital marker indicating cellular function during lifetime under normal or metabolically challenged conditions. It is used broadly to study mitochondrial function (Artal-Sanz and Tavernarakis, 2009; Palikaras et al., 2015; Ryu et al., 2016) or investigate factors mediating the switch from oxidative phosphorylation to aerobic glycolysis (Chen et al., 2015; Vander Heiden et al., 2009). In this protocol, we describe a method for the determination of oxygen consumption rates in the nematode Caenorhabditis elegans.

Rocco V et al. (1996) Worm Breeder's Gazette "Cloning of the Rad51 gene in C. elegans"

Ederle S, La Volpe A, Valenzi M, Rocco V, De Martino A

[Worm Breeder's Gazette, 1996]

We are interested in the mechanisms of homologous recombination in the nematode C. elegans. In prokaryotes, the RecA protein has a pivotal role in homologous recombination, and in vitro it has been demonstrated to catalyse the transfer of a DNA strand on a homologous molecule. In different eukaryotes (as yeast, mouse, man, and others) structural homologues of the bacterial RecA protein have been found, suggesting a certain level of conservation in some recombination pathways among living organisms (Shinohara et al. 1993 Cell 4: 239). In yeast an ATP- dependent DNA binding activity and, more recently, a strand transfer activity of the Rad51 gene product have been shown, whereas for the other Rad51 homologues the strand transfer activity has not yet been demonstrated (Sung and Robberson 1995 Cell 82). Experimental evidences in yeast (Milne and Weaver 1993 Genes Dev. 7:1755) suggest that the Rad51 product acts in a multiprotein complex in eukaryotes.

Ashraf S et al. (1997) International C. elegans Meeting "DOMINANT MATERNAL EFFECT STERILE MUTANTS"

Shin T-H, Ashraf S, Mello CC

[International C. elegans Meeting, 1997]

The PIE-1 protein is localized to cells of the germ lineage in the early C. elegans embryo where it functions to suppress somatic cell fates. We have found that mutant strains in which PIE-1 protein is mislocalized to somatic cells exhibit a sterile phenotype, but in most cases undergo fairly normal somatic differentiation. These observations suggest that while the threshold for PIE-1 function in suppressing somatic development is set high, slight reductions in PIE-1 levels may be sufficient to prevent germline protection leading to sterility. This may explain why certain PIE-1 genetic backgrounds as well as strains defective in functions required for PIE-1 localization appear to exhibit haplo-insufficient dominant sterile phenotypes (See Shin, et al). These observations led us to initiate screens for Dominant Maternal Effect Sterile mutations (DMES). Steriles are a very common phenotypic class. In standard genetic screens dominant maternal effect steriles will arise in the F2 among a huge background of recessive zygotic steriles. To avoid this difficulty we decided to ask if the diploid oocytes within the proximal arms of a mutagenized animal might be considered as independent mothers. If so then this would permit us to screen for dominant maternal effects among the F1 progeny of a mutagenized animal. We know from our previous dealings with pie-1 associated sterility that affected animals can often produce a few fertile viable offspring so we screened in an egg-laying defective background for F1 animals with only a few embryos developing inside. We first did a pilot screen of 30,000 F1 mutagenized animals. From this screen we obtained two mutations that behave like bona fide DMES loci, and a few that appear to be zygotic effect Dominants. One of the DMES mutants (ne146) , exhibits mislocalization of both the PIE-1 protein and of the P-granules. This mutation fails to complement previously identified maternal effect lethal alleles of the par-2 locus. The second DMES mutation mapped genetically to the location of a gene, alp-1 that encodes a PIE-1 binding protein, and indeed our mutant allele appears to contain a point mutation in this gene (See Shin et al.). This initial success has encouraged more screens which are presently underway.

Park, Y. et al. (2019) International Worm Meeting "Identify genes to mediate ascr#3 avoidance in C. elegansIdentify genes to mediate ascr#3 avoidance in C. elegans."

Ryu, L., Cheon, Y., Kim, K., Park, Y.

[International Worm Meeting, 2019]

Insulin-like signaling pathway plays diverse roles in metabolism, growth, longevity, development, and behaviors in the animal kingdom. C. elegans genome encodes 40 insulin-like genes (Duret et al., 1998; Pierce et al., 2001; Li et al., 2003; Li and Kim, 2008), which regulate development and behaviors. Also, C. elegans releases small molecules ascarosides, which control dauer formation, sex-specific and social behaviors. We and others previously showed that C. elegans hermaphrodite exhibits acute avoidance behavior to ascr#3 (asc-?C9, C9) exposure via the ascr#3-sensing ADL neurons (Jang et al., 2012). Moreover, we also showed that feeding state affects ascr#3 avoidance through DAF-2 insulin-like receptor (Ryu et al., 2018). To further investigate role of ILPs in ascr#3 avoidance, we examined contribution of INS-1 to ascr#3 avoidance. We first found that ins-1 mutant animals decrease ascr#3 avoidance behaviors in well-fed condition. We are currently identifying where and how INS-1 acts to mediate ascr#3 avoidance. Additionally, we are testing whether energy-sensing AMPK signaling affects ascr#3 avoidance. Key words: ILPs, Pheromone Avoidance, Starvation. AMPK signaling

Reboul J et al. (2001) Nat Genet "Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans."

Doucette-Stamm L, Lamesch PE, Reboul J, Temple GF, Hartley JL, Brasch MA, Hill DE, Vaglio P, Thierry-Mieg N, Shin-i T, Lee H, Moore T, Vandenhaute J, Kohara Y, Vidal M, Jackson C, Thierry-Mieg J, Tzellas N, Thierry-Mieg D, Hitti J

[Nat Genet, 2001]

The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.AD - Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.FAU - Reboul, JAU - Reboul JFAU - Vaglio, PAU - Vaglio PFAU - Tzellas, NAU - Tzellas NFAU - Thierry-Mieg, NAU - Thierry-Mieg NFAU - Moore, TAU - Moore TFAU - Jackson, CAU - Jackson CFAU - Shin-i, TAU - Shin-i TFAU - Kohara, YAU - Kohara YFAU - Thierry-Mieg, DAU - Thierry-Mieg DFAU - Thierry-Mieg, JAU - Thierry-Mieg JFAU - Lee, HAU - Lee HFAU - Hitti, JAU - Hitti JFAU - Doucette-Stamm, LAU - Doucette-Stamm LFAU - Hartley, J LAU - Hartley JLFAU - Temple, G FAU - Temple GFFAU - Brasch, M AAU - Brasch MAFAU - Vandenhaute, JAU - Vandenhaute JFAU - Lamesch, P EAU - Lamesch PEFAU - Hill, D EAU - Hill DEFAU - Vidal, MAU - Vidal MLA - engID - R21 CA81658 A 01/CA/NCIID - RO1 HG01715-01/HG/NHGRIPT - Journal ArticleCY - United StatesTA - Nat GenetJID - 9216904SB - IM

Shin, Heaji J. et al. (2013) International Worm Meeting "Characterization of SYGL-1, a novel regulator of germline stem cells."

Haupt, Kimberly, Kershner, Aaron M., Shin, Heaji J., Kimble, Judith

[International Worm Meeting, 2013]

C. elegans germline stem cells (GSCs) are maintained by GLP-1/Notch signaling from the stem cell niche. Two GLP-1/Notch target genes, lst-1 (lateral signaling target) and sygl-1 (synthetic germline proliferation defective), act redundantly to maintain GSCs throughout development and in both sexes (Kershner, Shin, and Kimble, manuscript in preparation). Here we focus on our characterization of the sygl-1 gene, which had not been analyzed previously. The sygl-1 locus encodes a single transcript (T27F6.4) that is predicted to generate a novel protein with no folded domains or motifs. To begin to investigate sygl-1 function, we have characterized a strong loss of function sygl-1(tm5040) mutant and generated a rescuing epitope-tagged SYGL-1 transgene. The sygl-1(tm5040) homozygote is viable, but it possesses a smaller than normal mitotic zone. The sygl-1 mRNA is restricted to the distal mitotic zone and is dependent on GLP-1/Notch signaling. The SYGL-1 protein is similarly restricted to the distal mitotic zone and is cytoplasmic. Our characterization so far is therefore consistent with a role for SYGL-1 in GSC maintenance, but we still know very little about this enigmatic locus. Experiments to explore sygl-1 regulation and function are in progress, and results will be reported.

I Maeda et al. (1999) International C. elegans Meeting "RNAi Screening with a non-redundant cDNA set"

I Maeda, Y Kohara, A Sugimoto, M Yamamoto

[International C. elegans Meeting, 1999]

RNA interference (RNAi) is a powerful tool for the transient inactivation of specific gene expression. We aim to establish a new screening method in which RNAi is performed systematically, to identify genes involved in specific developmental processes. To maximize the efficiency, we use a tag-sequenced, non-redundant cDNA set (made by Y. K.) as templates for preparing dsRNA. To deliver dsRNA into worms, we use the "soaking method" (in which worms are soaked in dsRNA solution) instead of microinjection, so that multiple RNAi can be performed concurrently. Although the soaking method has been known to be less potent and to give variable results, we optimized the condition to achieve a satisfactory efficacy to be used for the screen. In the control experiments, all nine genes tested ( unc-22 , glp-1 , mei-1 , mes-3 , fem-1 , glh-1 , glh-2 , pgl-1 and emo-1 ) with this method exhibited expected phenotypes with high penetrance. We are currently screening for the RNA species that cause sterility or embryonic lethality, however, we will record any other noticeable phenotypes. We plan to make the RNAi data available to the public at the NEXTDB WWW server at NIG (See the abstract by Shin-i et al. ). In the pilot screen, 10/64 gave embryonic lethality of the F1s, and 6/64 resulted in sterility of the P0s. Progress on the screen will be presented.

Hwang, H. et al. (2019) International Worm Meeting "Plasticity of ascr#3 avoidance behavior in C. elegans."

Hwang, H., Kim, K.

[International Worm Meeting, 2019]

Experiences or environmental cues can influence neuronal functions and behaviors. However, the neuronal and molecular mechanisms of behavioral plasticity are not fully understood. Caenorhabditis elegans secretes a mixture of small molecules referred as ascarosides that sense environmental conditions including population density and influence many aspects of development and behavior of C. elegans (Edison, 2009; Srinivasan et al., 2012). Wild-type hermaphrodites are repulsive to ascr#3(asc-?9, C9) while wild-type males are attractive to it (Macosko et al., 2009, Jang et al 2012). Previously, we have shown that ascr#3 avoidance behaviors are modulated by early experience of ascr#3 and feeding state, indicating that ascr#3 avoidance behaviors are plastic (Hong et al., 2017, Ryu et al., 2018). Here, we next investigated whether ascr#3 response is habituated by repeated exposure of ascr#3. We found that wild-type hermaphrodites exhibit normal ascr#3 avoidance to each exposure up to ten times, suggesting that ascr#3 avoidance behavior is not habituated. However, we found that the ascr#3-sensing ADL neurons shows decreased Ca2+ response to ascr#3 upon repeated exposure of ascr#3, indicating that adapted ADL responses to repeated ascr#3 exposure do not lead to habituation of ascr#3 avoidance behavior. In addition, we examined the effects of mating on ascr#3 avoidance and found that mated hermaphrodites appear to exhibit increased ascr#3 avoidance. Understanding how the behaviors are altered upon various experience or condition is the essential step to dissect molecular and neuronal mechanisms of behavioral plasticity.