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[
International Worm Meeting,
2015]
Animals in the wild periodically go through phases of feast and famine as resources naturally fluctuate and C. elegans have evolved exceptional survival mechanisms when food sources are scarce. Here, we demonstrate that acute adult starvation of C. elegans induces the depletion of somatic fat but these animals retain their germline fat stores. SKN-1 is an established regulator of cellular and organismal stress responses. Recently, we have reported that SKN-1 is a critical mediator of metabolic adaptation and here we define an unprecedented role for SKN-1 in the depletion of somatic fat phenotype. Notably,
skn-1 gain-of-function mutant animals, which behave as if they are being starved despite eating ad libitum, mobilize their somatic fat, but only late in their reproductive period. The rapid utilization of somatic fat phenotype is a cell non-autonomous organismal response to ensure reproductive success and we have identified a specific eicosanoid signaling pathway that is responsible for this phenotype. Mechanistically, we have found that vitellogenins are essential for lipid mobilization and this phenotype is intimately tied to available nutrients as the lipid depletion phenotype is influenced by diet and can be suppressed with supplemented dietary carbohydrates. Our results describe a novel mechanism to mobilize nutrient stores, which maximizes the fitness for an organism continually challenged by highly variable food availability.
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[
Worm Breeder's Gazette,
1994]
Asymmetric PAR-2 at First Cleavage Lynn Boyd1, Diane Levitan2, and Ken Kemphues1, 1)Section of Genetics and Development, Cornell University; 2) Department of Cellular and Developmental Biology, Harvard University (current address: Columbia University)
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[
Worm Breeder's Gazette,
1992]
In response to the growing interest in worms related to C. elegans for comparative studies, we are coordinating an effort to collect a comprehensive array of cryopreservable species belonging to the order Rhabditida. This collection would be maintained at the Caenorhabditis Genetics Center, would be freely available to all interested scientists, and would provide an excellent resource for worm breeders who are interested in applying a broader phylogenetic viewpoint to comparative biological investigations. Of course, an important advantage of a universally accepted canonical set of living type species is that species identifications can be tested biologically through cross-mating experiments. The utility of such a collection has already been demonstrated in the Drosophila system a remarkable collection of species from around the world is maintained, for example, at the Bowling Green Stock Center in Ohio. We request that interested parties please send their wild isolates to David Fitch, Lynn Carta or Kelley Thomas, along with the following data: the date, source and method of isolation, any ecological information concerning the isolate, pertinent literature references, the names and addresses of the collector, the depositor and the taxonomist(1), and any specifics about stock maintenance. Other data about the species should also be included, such as measurements(2) and male tail characteristics. Scale illustrations and any anatomical, developmental, cytogenetic or molecular data are greatly appreciated. If the isolate is hermaphroditic, males should also be provided, since most of the morphological characters used in species identifications are associated with males. Males may occur spontaneously or can be induced by heat-shocking L4 or young adult hermaphrodites (usually, but not always, at 30 C for 6 hours). Males obtained in this way can be mated to hermaphrodites to maintain a stock containing males. Kelley will provide a molecular "identification tag". David and Lynn will determine if the species has been previously identified in the literature and serve as liaisons to nematologists with taxonomic expertise to help verify the species identification. We will then deposit the species with the CGC. Eventually, we hope to make all of the information associated with each species in the collection available in a database. (See the abstract by Fitch et al. in this issue for the latest information on current CGC species depositions). So hesitate not to share your pet species with us! We think that the effort in building a phylogenetically broad and comprehensive live collection of Rhabditida will be more than compensated by the valuable opportunities it will provide for developing novel approaches to many areas of nematode research.
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[
Biochem Soc Trans,
2003]
Despite the central role of the 26 S proteasome in eukaryotic cells, many facets of its structural organization and functioning are still poorly understood. To learn more about the interactions between its different subunits, as well as its possible functional partners in cells, we performed, with Marc Vidal's laboratory (Dana-Farber Cancer Institute, Boston, MA, U.S.A.), a systematic two-hybrid analysis using Caenorhaditis elegans 26 S proteasome subunits as baits (Davy, Bello, Thierry-Mieg, Vaglio, Hitti, Doucette-Stamm, Thierry-Mieg, Reboul, Boulton, Walhout et al. (2001) EMBO Rep. 2, 821-828). A pair-wise matrix of all subunit combinations allowed us to detect numerous possible intra-complex interactions, among which some had already been reported by others and eight were novel. Interestingly, four new interactions were detected between two ATPases of the 19 S regulatory complex and three alpha-subunits of the 20 S proteolytic core. Possibly, these interactions participate in the association of these two complexes to form the 26 S proteasome. Proteasome subunit sequences were also used to screen a cDNA library to identify new interactors of the complex. Among the interactors found, most (58) have no clear connection to the proteasome, and could be either substrates or potential cofactors of this complex. Few interactors (7) could be directly or indirectly linked to proteolysis. The others (12) interacted with more than one proteasome subunit, forming 'interaction clusters' of
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[
Worm Breeder's Gazette,
1990]
A number of improvements have been made in the gm automated DNA sequence analysis system: (1) The ratio of AT-containing to CG-containing dinucleotides has been added as a test for introns. This works better than AT frequency alone in C. elegans.(2) A branch site consensus sequence or an enhanced dinucleotide ratio can be required as an additional test on introns. (3) Predicted amino-acid sequence files are generated in a format appropriate for input to the Dana-Farber motif-identification program plsearch. (4) A graphic interface based on X-windows, version 11 is available as an option. (5) The complete analysis algorithm is significantly faster than the previous version. (6) A greedy model evaluation algorithm is available as an option. This algorithm generates the longest, non-overlapping models that cover a sequence and is much faster than the complete analysis algorithm. The program has been tested on Sun3, Sun4 and VAX machines running Unix (Ultrix on the VAX). Results for a series of tests run on a Sun 4/60 are shown in the table. [See Figure 1] gm can be run remotely on our machine, using the Internet. To do this, telnet to haywire.nmsu.edu, and logon as gm_guest with password gmuser. Read the README file for information on running gm. We are also distributing gm as C source code to nonprofit laboratories, either via anonymous ftp to haywire.nmsu.edu, or on tape. If you would like to receive gm on tape, send a 1/4' cartridge or 1/2' reel tape to: Chris Fields, Box 30001/3CRL, New Mexico State University, Las Cruces, New Mexico 88003-0001, USA; Telephone (505) 646-2848.
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[
International C. elegans Meeting,
1995]
The
par-1 gene is required for many aspects of embryonic polarity including unequal cleavage and the asymmetric distribution of cytoplasmic components. We cloned the
par-1 gene using a combination of YAC transformation rescue and antisense phenocopy. It encodes a putative serine/threonine kinase with strong similarity to kinases identified in yeasts and mammals. Two
par-1 alleles have mutations in invariant kinase residues, suggesting that the kinase activity is crucial for PAR-1 function. PAR-1 protein is localized to the posterior periphery of the zygote. After the first embryonic division, PAR-1 is detected at the P1 periphery but is absent from the AB periphery. As the cell cycle proceeds, the peripheral PAR-1 becomes asymmetrically localized and partitioned into P2. Asymmetric localization of PAR-1 occurs again in P2 and P3, but does not occur in P4. The localization of PAR-1 shows a striking correlation with the distribution of P granules, and thus raises the possibility that PAR-1 is not only required for the early anterior-posterior polarity, but is also involved in later P lineage asymmetric divisions or germ-line development. To better understand interactions among par genes, we examined PAR-1 distribution in other par mutants. Interestingly, in
par-2 mutants, PAR-1 is not detectable at the periphery of the zygote or P lineage blastomeres, but in
par-3 mutants and in
par-2 par-3 double mutants PAR-1 is present around the entire periphery of all cells in the early embryo. These results, together with other results from our lab (see abstracts by B. Etemad-Mogadam and Lynn Boyd), lead us to propose that PAR-1 is restricted to the posterior by PAR-3 activity and that PAR-2 is required to properly localize PAR-3.
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Panchal, Henali, Attix, Haley, Cho, Martin, Zarilla, Kathy, George, Alex, Hastie, Eric, Cortez, Angel
[
MicroPubl Biol,
2021]
Research experiences in community college lead to increased retention in science, technology, engineering, and mathematics (STEM) (Nerio et al., 2019). This two week undergraduate research experience (URE) was designed to enhance laboratory skills in students with limited prior exposure, introduce developmental biology and genetics in a model organism system (C. elegans), and encourage participation in generation of data for a micropublication. The University of North Carolina at Chapel Hill and Durham Technical Community College partnered to host the URE for two weeks, for two hours, 4 days a week to limit lab time for students who work full time jobs. Here, we report our findings comparing early developmental cell division of wild type N2 embryos and a wild caught strain that was obtained from soil outside of Loeb Hall in Woods Hole, MA in 2017. The strain, originally called WH strain, was grown on OP50 and survived, suggesting it is a bacteriovore. The WH nematode lays embryos at the one cell stage, making early divisions observable without the dissection or bleaching required for the N2 strain. Students used primers to amplify the 18S ribosomal subunit geneused in phylogenetic analysis of taxafrom extracted genomic DNA and sent the product for sequencing (Floyd et al., 2005). The hairpin 17 region was selected to display a comparison because of high conservation (Nyaku et al., 2013). BLAST results for the N2 strain matched N2 and results for the wild caught WH strain matched with the nematode strain Acrobeloides sp. LKC 27 (a match of 99.7% and E value of 0), available from the Caenorhabditis Genetics Center. LKC 27 was isolated from a western corn rootworm from a Brookings, SD insectary in 2003 (personal communication with Dr. Lynn Carta, USDA-ARS). Students concluded that additional loci need to be examined to determine the relationship of the WH strain to LKC 27.
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[
International C. elegans Meeting,
2001]
A simple lab has been designed for use in a sophomore genetics course. There are four primary objectives for this laboratory exercise: 1) students predict genotypes based on phenotype 2) students design primers for PCR 3) students use the PCR technique 4) students analyze results using gel electrophoresis The learning elements of the lab can be broken down into two main areas. First, it serves as a demonstration of the relationship between genotype and phenotype. Students observe the phenotype of worms and then make predictions about the genotype which they subsequently test. A second valuable learning element has been having the students design primers for PCR. Students must have a good understanding of both DNA structure and DNA polymerase activity to design primers successfully. This laboratory exercise makes use of a
dpy-5 mutation that contains a deletion of 1009 bp (gracious thanks to Colin Thacker and Ann Rose for supplying the strain).. The mutation (
e907) is semidominant. Therefore, students can identify all three genotypes in a population of worms containing the wild type and
e907 alleles (+/+; +/e907;
e907/e907). The investigation occurs over three lab periods. In the first lab, students become familiar with observing the Dpy phenotype and with picking worms. They also design primer pairs that will amplify both the wild type and
e907 alleles. In the second lab, students use these primer pairs in single worm PCR reactions. They are asked to pick worms that represent each of the three genotypes and use these for PCR. In the third period, an agarose gel is run of the PCR reactions. Students determine the genotypes of the worms they chose and find out if their genotype predictions were correct. I have found that sophomore students are able to do this lab with a high percentage of success. If you would like more information or would like the lab handout, please contact Lynn Boyd at boydl@uah.edu.
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Kohara Y, Tzellas N, Thierry-Mieg N, Jackson C, Temple GF, Hill DE, Vidal M, Lamesch PE, Thierry-Mieg D, Vandenhaute J, Brasch MA, Vaglio P, Doucette-Stamm L, Moore T, Hartley JL, Shin-i T, Lee H, Reboul J, Hitti J, Thierry-Mieg 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