Rocheleau CE (2012) Curr Biol "RNA interference: Systemic RNAi SIDes with endosomes."

Rocheleau CE

[Curr Biol, 2012]

Systemic RNAi, the intercellular spreading of RNAi silencing, requires SID-1 and SID-3 to import silencing signals in Caenorhabditis elegans. How are these signals exported? SID-5, an endosome-associated protein, is a candidate for the job.

(1984) Worm Breeder's Gazette "The CGC needs a Curator"

[Worm Breeder's Gazette, 1984]

The Curator's job involves genetic research, management of the CGC, interaction with numerous research laboratories and participation in meetings. The Curator is important to the C. elegans research community. An important responsibility is the accumulation of genetic data and revision of the genetic map, as well as the continuing evaluation and improvement of our computing capability. The CGC needs a Curator to replace Peg Swanson, who is now at Montana State University.

Paul Sternberg (2002) Worm Breeder's Gazette "Position at Caltech, CA"

Paul Sternberg

[Worm Breeder's Gazette, 2002]

CURATOR. Will annotate gene functions in C. elegans , using Gene Ontology (Nature Genetics [2000], vol. 25, pp. 25-29). Duties include: analysing gene functions in the primary literature; judging the optimal description of these functions in Gene Ontology, inventing new terms for Gene Ontology where necessary; and incorporating these descriptions into Wormbase. A Ph.D. in some area of biology and substantial C. elegans experience are required. The successful job candidate will have broad scientific erudition, verbal articulacy, and creative intelligence as well as patience and a willingness to work hard. Computer literacy in UNIX or Linux is a plus, but is not required. Direct inquiries to Paul Sternberg (pws@its.caltech.edu).

Moya, Nicolas D. et al. (2021) International Worm Meeting "Improved reference genomes for Caenorhabditis briggsae"

Chitrakar, Rojin, Stevens, Lewis, Baugh, L. Ryan, Moya, Nicolas D., Walhout, Marian, Tanny, Robyn E., Dekker, Job, Na, Huimin, Andersen, Erik C.

[International Worm Meeting, 2021]

Decades of research have led to the development of comprehensive genome resources that have been essential to study the Caenorhabditis elegans species. In parallel, the emergence of Caenorhabditis briggsae as a model system has been useful to make interspecies comparisons. Despite the importance of C. briggsae as a model, its genome resources have not been developed to the same extent as C. elegans. The current genome of C. briggsae reference strain AF16 contains thousands of unresolved gaps and numerous mis-assemblies. Because of these issues, C. briggsae gene models remain incomplete and have numerous structural errors in protein-coding genes. We sought to exploit the latest sequencing technologies and computational tools to provide the highest quality C. briggsae genome resources to date. First, we generated high-quality genome assemblies for two strains of C. briggsae: QX1410 (a "tropical" strain isolated in Saint Lucia that is closely related to AF16) and VX34 (a divergent strain isolated in China). These genome assemblies incorporate high coverage Oxford Nanopore PromethION long reads and chromosome conformation capture (Hi-C) data. Second, we genotyped 99 recombinant inbred lines generated from reciprocal crosses between QX1410 and VX34. Using these data, we produced a high-quality recombination map that validated the placement of scaffolds after genome assembly. Third, we sequenced the transcriptomes of each strain to high coverage using Pacific Biosciences SMRT and Illumina platforms. We developed a computational pipeline that leverages long and short RNA reads to generate a genome annotation for each strain. These new genome annotations have improved accuracy and completeness relative to the AF16 genome. Fourth, our research group currently maintains over 1,600 C. briggsae wild strains, comprising the largest collection worldwide. We sequenced the genomes of this entire collection to high coverage using the Illumina platform. We mapped the sequences of all wild strains to the QX1410 genome to call single nucleotide variants across the entire population. These high-quality genome resources will facilitate new avenues of research, including quantitative and population genetic studies of C. briggsae, and enable informative comparisons with C. elegans.

Herman RK (1997) Science "The worm returns."

Herman RK

[Science, 1997]

When I began working on the small nematode Caenorhabditis elegans in the early '70s, not long after Sydney Brenner had chosen it as a model organism for studying animal development and behavior, one could read most of the essentials then published about the creature in an afternoon. As more people joined the worm community and wrote papers that demanded attention, newcomers and interested spectators faced an ever bigger job trying to familiarize themselves with the field. In 1988, a book, The Nematode Caenorhabditis elegans, came to the rescue. "Worm I" reviewed the worm's genome, anatomy, embryology, sex determination, muscle development, and behavior, among other things. Appendixes contained a list of all 959 somatic hermaphrodite cells and their lineages, a list of 774 mapped genes and mutant phenotypes, and a compilation of laboratory methods. "Worm I" has aged gracefully but is irrevocably stuck at 1988. Enter "Worm II".

Aoki ST et al. (2016) Proc Natl Acad Sci U S A "PGL germ granule assembly protein is a base-specific, single-stranded RNase."

Aoki ST, Kimble J, Wickens M, Bingman CA, Kershner AM

[Proc Natl Acad Sci U S A, 2016]

Cellular RNA-protein (RNP) granules are ubiquitous and have fundamental roles in biology and RNA metabolism, but the molecular basis of their structure, assembly, and function is poorly understood. Using nematode "P-granules" as a paradigm, we focus on the PGL granule scaffold protein to gain molecular insights into RNP granule structure and assembly. We first identify a PGL dimerization domain (DD) and determine its crystal structure. PGL-1 DD has a novel 13 -helix fold that creates a positively charged channel as a homodimer. We investigate its capacity to bind RNA and discover unexpectedly that PGL-1 DD is a guanosine-specific, single-stranded endonuclease. Discovery of the PGL homodimer, together with previous results, suggests a model in which the PGL DD dimer forms a fundamental building block for P-granule assembly. Discovery of the PGL RNase activity expands the role of RNP granule assembly proteins to include enzymatic activity in addition to their job as structural scaffolds.

Jiang X et al. (2020) J Fluoresc "A Water-Soluble Fluorescent Probe for the Selective Sensing of Ag+ and its Application in Imaging of Living Cells and Nematodes."

Deng M, Wu J, Jiang X, Li H, Yang Y, Zhou X, Qi X, Lu M, Liang S

[J Fluoresc, 2020]

In this study, an imidazole-coumarin based fluorescent probe was developed for the selective and sensitive detection of Ag⁺ in aqueous solution. Using a combination of Job plot, NMR titrations, and DFT calculations, the binding properties between Ag⁺ and the probe were deeply investigated, and the results revealed a 1:1 binding stoichiometry between the probe and Ag⁺ with a binding constant of 1.02x10⁶M^-1. The detection limit was found to be 150nM, which satisfies the requirement for the quantitative detection of Ag⁺ in real water samples. Moreover, the new probe, Ic, was successfully applied to sense Ag⁺ in HeLa and HepG2 cells as well as in C. elegans, indicating that it could be a useful tool for the environmental monitoring of Ag⁺ pollution. These results demonstrated that Ic could serve as a high-efficiency and low-cost fluorescent probe for tracking Ag⁺ in an aquatic environment and biological organisms.

Sullivan-Brown, Jessica et al. (2021) International Worm Meeting "Characterization of RNAi phenotypes in C. elegans from understudied genes in a Cell and Molecular Biology course"

Sowa, Jessica, Sullivan-Brown, Jessica

[International Worm Meeting, 2021]

The characterization of relatively understudied genes in C. elegans using RNA interference is an excellent approach for designing undergraduate research-based labs. Here we describe a successful lab course in which Cell and Molecular Biology students at West Chester University of Pennsylvania (WCU) make novel discoveries associated with knock down of dcaf-13, a likely oncogene in humans. Each class represents the flow of a typical study of gene function, beginning with a journal club reading the primary literature. Then students use bioinformatics to identify the human protein sequence of DCAF13, perform a BLAST search to find C. elegans homologs, and use WormBase to identify the C. elegans gene sequence. An RNAi knock down experiment is then performed with dcaf-13. Throughout the lab, students characterize the resulting phenotypes, using IMAGEJ/FIJI for quantification of worm length and fluorescence microscopy for GFP analysis of an intestinal cell fate marker. Students then isolate RNAs using Trizol RNA extraction and perform cDNA synthesis. Students then design primers to test if dcaf-13 knock down affects the expression of different cell cycle genes by performing RT-PCR. At the end of the course, students present their work orally in a poster presentation and in written communication in a primary research style paper. We have recently added a component in which students design a future experiment in the format of a small grant proposal and after peer review, two projects are chosen to perform in lab. The lab serves two primary functions: to provide students opportunities to advance their experimental techniques so they are competitive in the job market and create an experience that mimics a typical research project by making real contributions to science. Our goals are to publish the work the students generated. Importantly, this framework can be applied to other understudied genes in C. elegans in which the RNAi phenotypes are not well documented, benefiting both students and the C. elegans community.

Mary C Abraham et al. (2003) International Worm Meeting "Was it the butler? The curious case of linker cell murder."

Mary C Abraham, Shai Shaham

[International Worm Meeting, 2003]

Apoptosis sculpts tissues during development, is required to remove self-reactive immune cells and can act as a defense mechanism against cancer. Apoptosis occurs in these very diverse contexts across many different organisms, yet at its core lies conservation of molecules and morphology of cell death. The C. elegans linker cell death is an example of a developmentally regulated cell death. The linker cell migrates as a leader cell guiding the male gonad as it grows and develops. It dies at the late L4 stage when its migratory job is complete and the gonad is about to reach and fuse with the proctodeum, allowing the cloaca to act as a sperm exit channel. There are two particularly striking observations about linker cell death compared with other cell deaths in C. elegans. First, the linker cell is the only known example of a C. elegans cell that consistently dies in animals harboring a strong ced-3/caspase loss-of-function mutation (1). This observation suggests the linker cell may have a caspase-independent cell death pathway. Second, the signal initiating linker cell death may come from outside the cell. Specifically, ablation of the U cell prevents linker cell death (2). It is thought, therefore, that a signal from the U cell descendants, which neighbor the linker cell at the moment of its demise, commits cellular murder. No intercellular pathways initiating apoptosis have been identified in C. elegans. Work reported will include further analysis of linker cell death in a variety of mutants, including the cell death pathway mutants, engulfment mutants and linker cell migration mutants. Engulfment of the linker cell was studied using GFP markers such as EGL-5::GFP expressed in the engulfing U cell descendant. Current progress will be reported on an EMS mutagenesis screen, using a strain with LAG-2::GFP to mark the linker cell, aimed at finding mutants defective in linker cell death. References: (1) Ellis H.M. and Horvitz H.R. (1986) Genetic Control of programmed cell death in the nematode C. elegans. Cell, 44:817-29; (2) Sulston J.E., Albertson D.G and Thompson J. N. (1980) The Caenorhabditis elegans male: postembryonic development of nongonadal structures. Dev Biol, 78:542-76.

Riddle DL et al. (1980) Worm Breeder's Gazette "announcements"

Swanson MM, Riddle DL

[Worm Breeder's Gazette, 1980]

The Caehorhabditis Genetics Center (CGC), sponsored by the National Institute on Aging, was funded on September 30, 1979. Dr. Don Murray is the NIA Project Officer. As you know, the CGC is to be responsible for strain acquisition, banking and distribution. Strains will be available without cost to all qualified investigators pursuing genetics-related studies with C. elegans. Other CGC functions will include maintenance of the genetic map, coordination of genetic nomenclature and maintenance of a current data bank on all strains, including bibliographic information. During the first year, we will be developing a computerized system for storage and retrieval of this information. The program will be designed to allow other labs with CRT terminals remote access to the computer data files. We have recently mailed a questionnaire regarding your anticipated use of the Center's services. Since your responses may help us to modify the design of the services to be offered, we would appreciate your returning those questionnaires as soon as possible if you have not already done so. If you did not receive our mailing and anticipate using the CGC, please contact us. We plan to maintain a complete library of articles on Caenorhabditis, so we would appreciate it if you also would send us one copy of each of your Caenorhabditis publications. We have recently done a retrospective search of the literature and will soon be distributing a complete C. elegans bibliography as a supplement to this Newsletter. The new bibliography contains about 350 references, and we plan to update it with each future issue of the Newsletter. We would like to thank Bob Herman for the excellent job he has done as a volunteer stock distribution center. The immensely valuable work that Bob Herman and Bob Horvitz have done on the genetic map surely is apparent to everyone. Bob Herman will be supplying us with many strains he has received from other laboratories and we hope to have a relatively up-to-date C. elegans collection in a few months. The CGC is scheduled to be fully operational by the Fall of 1980, but some services are available now.