Our laboratory is interested in the systems biology of nematodes. We seek to understand how the properties of an organism are encoded in its genome.
We seek to understand how are the properties of an organism – its development, physiology and behavior – are encoded in its genome. We primarily use molecular genetics of the nematode Caenorhabditis elegans but also apply proteomics, computational biology, biochemistry, cell biology, imaging, behavioral analysis, optogenetics, synthetic biology to not only C. elegans but also parasitic nematodes, budding yeast, mice, jellyfish, fungi, and human cells as needed.
Specific areas of current interest are:
- How does the 302-neuron worm brain assess the future environment based on computation of sensory and physiological inputs?
- Does the male worm have a neural representation of its mating partner?
- How can we best predict gene expression from DNA sequence?
- What are the functional consequences of de novo genetic variants found in individual with autism spectrum disorder?
- What changes in the nervous system occur during sleep?
- How do cells migrate accurately during development?
Our major strategy is to perturb the activity of one or more genes and measure how cells or animals misbehave to infer gene function and genetic pathways. We measure gene expression by RNA-seq and transgenic reporters; we measure behavior using automated systems and optogenetics. We focus on intercellular signals and their transduction by the responding cell into transcriptional outputs. Many of the genes we have identified are the nematode counterparts of human genes, and we are leveraging C. elegansmolecular genetics to study human genes with no actionable information and of the consequence of variants found in human individuals, including those with autism spectrum disorder. Nematodes are major health and agricultural problems, so we focus on parasite relevant biology such as dauer/infective juvenile development, using genomics and molecular genetics.
We have a new paper out on microPublication Biology. Read about A Mutation of lips-6 in C. elegans here.
The article, Single cell tools for WormBase is up on bioRxiv now. You can find the article here.
Elizabeth Holman successfully defended her thesis, "Developing Technologies for Real-time Whole Organism Imaging via FTIR Spectromicroscopy" on July 6, 2021. Congratulations!
Congratulations to Sarah Cohen for defending her thesis, "Formation and Function of Ascarosides in Nematodes C. elegans and C. briggsae" on May 17, 2021.
We are proud to announce Cynthia Chai's successful defense of her thesis, "Neurogenetic Analysis of C. elegans Developmental Decision-making" on May 10, 2021.
PNAS has just published our latest research article. Find the full version here.
You can read our most recent publication, "Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature" by clicking here.
Our new paper is now available on microPublication.org. Click here to read all about "Conserved missense variant in ALDH1A3 ortholog impairs fecundity in C. elegans". For a more in depth look at this article, check this out.
One of our newest publications, "Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration" is availalbe online now. Click here for the article.
Now out in Communications Biology, "Autonomous adaptive data acquisition for scanning hyperspectral imaging". Check out the article here, which is covered by Advanced Light Source (ALS) News in their science brief "To Speed Discovery, Infrared Microscopy Goes 'Off the Grid".
Our latest publication, The Gene Ontology resource: enriching a Gold mine is available here.
The paper, Modular metabolite assembly in C. elegans depends on carboxylesterases and formation of lysosome-related organelles has recently come out in eLife. Find the article here.
We now have a table of available cGAL Drive and Effector strains. Click here to check it out.
An exciting article about our newest Molecular Cell paper is currently available here.
Our peer-reviewed, single-result publication platform microPublication Biology is now included in PubMedCentral and indexed in PubMed. The Caltech Library is the publisher. This is the first biology journal designed to help get information into knowledge such as WormBase, ZFIN, SGD, FlyBase, and TAIR.
- Arnaboldi V, Cho J, Sternberg PW. (2021) Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. Database. doi:10.1093/database/baab015.
- Kato M, Kolotuev I, Cunha A, Gharib S, Sternberg PW. (2021) Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration. PNAS. [epub ahead of print]. doi: 10.1073/pnas.1904338118.
- Middelkoop TC, Garcia-Baucells J, Quintero-Cadena P, Pimpale LG, Yazdi S, Sternberg PW, Gross P, Grill SW. 2021. CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left–right symmetry breaking. PNAS. [epub ahead of print]. doi: 10.1073/pnas.2021814118.
- da Viega Beltrame E, Arnaboldi V, Sternberg PW. (2021). Single cell tools for WormBase. bioRxiv. https://doi.org/10.1101/2021.07.04.451030.
- Wong WR, Maher S, Oh JY, Brugman KI, Gharib S, Sternberg PW. (2021). Conserved missense variant in ALDH1A3 ortholog impairs fecundity in C. elegans. microPublication Biology. 10.17912/micropub.biology.000357.
- Cohen, SM; Sun, JJ; Schroeder, FC; Sternberg, PW (2021). Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans. microPublication Biology. 10.17912/micropub.biology.000397.
- Cohen SM, Le HH, Sternberg PW. (2021). A Mutation of lips-6 in C. elegans. microPublication Biology. 10.17912/micropub.biology.000419.