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.

Berg, Maureen et al. (2019) International Worm Meeting "Genetic control of Enterobactercommensal abundance and function in C. elegans."

Nelson, Lydia, Berg, Maureen, Shapira, Michael, Monnin, David, Cho, Juhyun

[International Worm Meeting, 2019]

The gut microbiota contributes to host health and fitness, and imbalances in its composition are associated with pathology. However, what shapes microbiota composition is not clear, in particular the role of genetic factors. Previous work in Caenorhabditis elegansdefined a characteristic worm gut microbiota significantly influenced by host genetics. Using synthetic communities and qPCR we subsequently explored the role of genes involved in immune and stress regulation in controlling abundance of core microbiota taxa, revealing a role for the TGF?/BMP pathway. Immune compromised TGF?/BMP mutants showed a bloom specifically of Enterobacterspecies. TGF? overexpression coupled to fluorescent imaging of tdTomato-expressing Enterobacterin turn indicated that TGF?/BMP-exerted control operated primarily in the anterior gut and depended on multi-tissue contributions. Enterobactercommensals are common in the worm gut, accelerating development and enhancing infection resistance. However, disruption of TGF?/BMP signaling turned a normally beneficial Enterobactercommensal to pathogenic. Interestingly, during normal aging worms demonstrated a similar bloom as in TGF?/BMP mutants, but this bloom was independent of the TGF?/BMP pathway. These results demonstrate specificity in gene-microbe interactions underlying gut microbial homeostasis and highlight age-dependent disruption of this homeostasis.

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

Choi, Rebecca et al. (2021) International Worm Meeting "Age-dependent changes in C. elegans gut microbiome composition and their consequences"

Choi, Rebecca, Cho, Juhyun, Shapira, Michael, Baek, Song-Ah, Berg, Maureen, Monnin, David

[International Worm Meeting, 2021]

Aging involves a multi-tissue deterioration. Among other things, it affects the gut microbiome. Changes in gut microbiome composition, in turn, could contribute to age-related pathologies, as imbalances in microbial composition (dysbiosis) are associated with pathology. Identifying central themes in age-dependent microbiome changes is lagging, as is our understanding of their consequences. To examine the bidirectional relationships between host aging and the gut microbiome, we followed age-dependent changes in microbiome composition in worms raised on either natural-like compost microcosms or on well-defined synthetic microbiotas consisting of natural worm gut colonizers. Microbiome composition was analyzed using 16S next generation sequencing or with CFU counts of bacteria cultured on selective media. Additionally, gut colonization at different ages was evaluated using fluorescent microscopy of an RFP-expressing derivative of an Enterobacter commensal. Experiments in both compost microcosms and synthetic microbiotas revealed an expansion of the Enterobacteriaceae family in aging worms, a trend similarly observed in humans. Worms sampled during continuous growth on complex microbiotas showed similar age-dependent changes in their gut microbiomes as worms shifted to complex bacterial communities for a fixed time at advancing ages, suggesting that the aging intestinal niche is more important for determining changes in microbiome composition than the duration of exposure to bacterial communities. Further supporting this expansion, experiments with the RFP-expressing Enterobacter demonstrated increased age-dependent gut colonization. This particular Enterobacter commensal was previously shown to protect young worms from Enterococcus infection, but was found to bloom in immune mutants, reversing its contributions and causing increased pathogen susceptibility (Berg et al. 2019). Indeed, increased commensal colonization in aging worms abolished the commensal's beneficial effects and increased worm susceptibility to infection, as compared to age-matched worms raised on Escherichia coli. Current experiments are underway to examine whether rebalancing of the gut microbiota in aging worms could ameliorate host survival.

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.