Zarkower D et al. (1994) Worm Breeder's Gazette "mab-3 YAC Rescue"

De Bono M, Hodgkin JA, Zarkower D

[Worm Breeder's Gazette, 1994]

mab-3 YAC rescue David Zarkower, Mario de Bono, and Jonathan Hodgkin MRC Laboratory of Molecular Biology, Cambridge, England

Weinkove D (2018) BMC Biol "On microbes, aging and the worm: an interview with David Weinkove."

Weinkove D

[BMC Biol, 2018]

David Weinkove is an associate professor at Durham University, UK, studying host-microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiology of their hosts, including the process of aging. In this interview, he discusses the questions shaping his research, how they evolved over the years, and his guiding principles for leading a lab.

Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710

Grenache DG et al. (1993) Worm Breeder's Gazette "Differential Effects of Dauer-Defective Mutations in L1-Specific Surface Antigen Switching"

Politz SM, Grenache DG

[Worm Breeder's Gazette, 1993]

DIFFERENTIAL EFFECTS OF DAUER-DEFECTIVE MUTATIONS ON L1- SPECIFIC SURFACE ANTIGEN SWITCHING. David G. Grenache and Samuel M. Politz, Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA.

Emmons SW et al. (1994) Worm Breeder's Gazette "Strain Names for non-C. elegans Species."

Emmons SW, Fitch DHA, Leroi AM

[Worm Breeder's Gazette, 1994]

Strain names for non-C. elegans species Scott W. Emmonst, Armand Leroit, and David Fitch, Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, Department of Biology, New York University, RmlOO9 Main Bldg., Washington Square, New York, NY 10003

Hall DH et al. (1994) Worm Breeder's Gazette "Cytology of Degenerin-Induced Cell Death in the PVM Neuron"

Driscoll MA, Chalfie M, Gu GQ, Hall DH, Gong L

[Worm Breeder's Gazette, 1994]

Cytology of degenerin-induced cell death in the PVM neuron David H. Hall, Guoqiang Gu+, Lei Gong#, Monica Driscoll#, and Martin Chalfie+, * Dept. Neuroscience, Albert Einstein College of Medicine, Bronx, N.Y. 10461 + Dept. Biological Sciences, Columbia University, New York, N.Y. 10027 # Dept. Molecular Biology and Biochemistry, Rutgers University, Piscataway, N.J. 08855

Amrit FRG et al. (2017) J Vis Exp "Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project."

Ghazi A, Amrit FRG

[J Vis Exp, 2017]

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. However, for first-time users and bioinformatics' amateurs, self-learning and familiarization with these platforms can be time-consuming and daunting. We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples.

Vogel G (2002) Science "Neuroscience. Genes keep neurons' house in order."

Vogel G

[Science, 2002]

As any homeowner knows, timely maintenance is vital for keeping a building functioning properly after construction is finished. The same is evidently true for the complex architecture of the nervous system - at least in the roundworm. On page 686, neuroscientists Oliver Hobert, Oscar Aurelio, and David Hall describe a new family of proteins that help keep the wiring of the worm's nervous system tangle free.

Victor R Ambros et al. (2003) International Worm Meeting "MicroRNAs and other tiny endogenous RNAs in C. elegans"

Ann Lavanway, Christopher M Hammell, Rosalind C Lee, Victor R Ambros, Peter T Williams, David Jewell

[International Worm Meeting, 2003]

MicroRNAs (miRNAs) are very small (~22 nt long) noncoding RNAs that are generated from hairpin precursor transcripts by Dicer-dependent processing. miRNAs likely inhibit translation of mRNAs via imprecise antisense base-pairing. Small interfering RNAs (siRNAs) are similar in size to miRNAs, but they recognize targets by precise complementarity, and elicit RNA-mediated interference (RNAi). To identify as many of the C. elegans miRNA genes as possible, and other kinds of ~22 nt endogenous RNAs expressed in C. elegans, we employed phylogenetic comparisons of noncoding genomic sequences, and sequencing of size-selected cDNA libraries. Among the new small RNAs detected are 21 distinct miRNA sequences that were not previously described in C. elegans. We estimate the size of the C. elegans miRNA gene family to be somewhat more than 100 distinct gene; about 80% of these are conserved in a C. briggsae, and about 30% have apparent homologs in insects and/or vertebrates. We also identified 33 distinct members of a second class of small RNA, which we call tiny noncoding RNAs (tncRNAs). tncRNAs are similar in length to miRNAs, but unlike miRNAs, they are apparently not processed from short hairpin precursors. However, like miRNAs, tncRNAs are transcribed from noncoding genomic sequence, and in some cases, exhibit developmentally regulated expression. tncRNAs also resemble miRNAs in their lack of precise complementarity to any worm mRNA. Therefore, tncRNAs could act in a fashion exemplified by the canonical miRNAs, lin-4 and let-7, and recognize RNA targets through imprecise antisense base-pairing. Finally, we identified a third class of ~22 nt RNAs in C. elegans that are produced directly from protein coding sequences and are predicted to have precise antisense complementarity to messenger RNAs. These apparent endogenous siRNAs represent sequences from more than 500 different protein-coding genes, including prominently transposons, kinases, transcription factors, and F-box proteins. Preliminary analysis of worms deficient in Dicer, alg-1/alg-2 or rde- genes indicates that the accumulation of miRNAs, tncRNAs and siRNAs depend on distinct pathways. These results suggest that RNA-mediated gene regulation and gene silencing may be broadly deployed in normal worm cells through the action of diverse classes of small RNAs.

Brownlee DJA et al. (1996) Parasitol Today "Nematode neuropeptides: Localization, isolation and functions."

Holden-Dye L, Brownlee DJA, Walker RJ, Fairweather I

[Parasitol Today, 1996]

Historically, peptidergic substances (in the form of neurosecretions) were linked to moulting in nematodes. More recently, there has been a renewal of interest in nematode neurobiology, initially triggered by studies demonstrating the localization of peptide immunoreactivities to the nervous system. Here, David Brownlee, Ian Fairweather, Lindy Holden-Dye and Robert Walker will review progress on the isolation of nematode neuropeptides and efforts to unravel their physiological actions and inactivation mechanisms. Future avenues for research are suggested and the potential exploitation of peptidergic pathways in future therapeutic strategies