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.
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.
Undergraduate Student Sophie Walton has been awarded a Hertz Fellowship. Click here to read all about her amazing accomplishment.
May 15, 2020. Porfirio Quintero Cadena defended his thesis "Mechanism and Scaling of Eukaryotic Transcription Activaton". Congratulations, Porfirio!
May 11, 2020. Katherine Brugman defended her thesis "pezo-1 function in Caenorhabditis elegans". Great work, Katie!
Our newest paper about Mono Lake worms in out now. Click on the following links to read all about it:
We are proud to announce Dr. Han Wang will start his own lab at the University of Wisconsin, Madison in January 2020. He will be a part of the Department of Integrative Biology. You can learn more about his new lab at www.hanwanglab.com.
- Quintero-Cadena P, Lenstra TL, Sternberg PW. (2020). RNA pol II length and disorder enable cooperative scaling of transcriptional bursting. Mol Cel [epub ahead of print]. doi: 10.1016/j.molcel.2020.5.030.
- Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. (2020). Caenorhabditis elegans AF4/FMR2 family homolog affl-2 regulates heat shock induced gene expression. Genetics. [epub ahead of print]. doi: 10.1534/genetics.120.302923.
- Bai X, Bouffard JW, Lord A, Brugman K, Sternberg PW, Cram EJ, Golden A. (2020). Caenorhabditis elegans PIEZO channel coordinates multiple reproductive tissues to govern ovulation. Elife. [epub ahead of print]. doi: 10.7554/eLife.53603.
- Arnaboldi V, Raciti D, Van Auken K, Chan JN, Müller HM, Sternberg PW. (2020). Text mining meets community curation: a newly designed curation platform to improve author experience at WormBase. Database (Oxford). [epub ahead of print] doi: 1093/database/baaa006. PMCID: PMC7078066.
- Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, the Alliance of Genome Resources. (2020) Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford). [epub ahead of print]. doi: 10.1093/database/baaa037.