Jordan, David et al. (2017) International Worm Meeting "Statistical measurements of phenotypic variation to study genome and environment interactions C. elegans."

Miska, Eric, Jordan, David

[International Worm Meeting, 2017]

Phenotypic diversity is the raw material for natural selection. If such variations can be inherited, they can play a role in evolutionary change. The study of phenotypic diversity must begin by quantifying such variation. For example, one may ask how many phenotypes can be generated from a single genotype in a fixed environment. However, quantifying phenotypes may be ill-posed, e.g. if traits are continuous, the answer may infinite. Instead, we propose to ask a related question, how many parameters are necessary to describe the space of phenotypic variation. To do this have collected a variety of phenotypic measurements from small populations of C. elegans, including details of their development, growth rate, movement, brood size, and lifespan. We collect these measurements with a set of custom video microscopes that can record and track the movements and sizes of 40 animals from eggs to adults (~3 days). Starting with the simplest case, a single genotype, in a fixed environment, first we explore the local phenotypic space with perturbations in temperature, food availability, and stress. We then expand both the genetic diversity, using a collection of C. elegans strains isolated from the wild, as well as the environmental diversity, using a variety of bacterial food sources also isolated from C. elegans natural habitats. To understand the relationships, if any, between these phenotypic measurements, we proprose to use methods of dimensionality reduction to directly answer the question of how many parameters are necessary to capture the observable phenotypic diversity. Furthermore, we intend to explore how that changes under both genetic, and environmental perturbations. While the mechanism of inheritance of phenotypic variation due to genetic change is well understood, whether variation resulting from other sources can be inherited, and if so what the mechanism might be, is less well understood. Using the map of phenotypic space we have constructed, we intend to explore how populations move in this space in response to environmental stresses, such as heat shock, starvations, osmotic stress, and pathogen infection. We can then monitor the relaxation of the population distribution to its unperturbed state to assess whether any such variation can be inherited and if so, on which time scales. We hope that these studies will add both new methods, new data, and new ways of thinking to evolutionary, and ecological studies.

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

Hibshman JD et al. (2021) STAR Protoc "Liquid-culture protocols for synchronous starvation, growth, dauer formation, and dietary restriction of Caenorhabditis elegans."

Hibshman JD, Baugh LR, Webster AK

[STAR Protoc, 2021]

Standard laboratory culture of <i>Caenorhabditis elegans</i> utilizes solid growth media with a bacterial food source. However, this culture method limits control of food availability and worm population density, factors that impact many life-history traits. Here, we describe liquid-culture protocols for precisely modulating bacterial food availability and population density, facilitating reliable production of arrested L1 larvae, dauer larvae, dietarily restricted worms, or well-fed worms. Worms can be grown in small quantities for standard assays or in the millions for other applications. For complete details on the use and execution of these protocols, please refer to Hibshman etal. (2016), Webster etal. (2018), and Jordan etal. (2019).

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.