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Sternberg Lab
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    * EDGE: Genomic Tools for Steinernema hermaphroditum Open EDGE: Genomic
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 * cGAL
 * EDGE: Genomic Tools for Steinernema hermaphroditum
   * Why Steinernema?
   * Publications- Steinernema

microPublication Biology
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 * MicroPublications

Lab Members
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 * Alumni Table

Lab Resources
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 * Group Meetings
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WELCOME TO THE STERNBERG LAB!

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Sternberg Lab Homepage
 * Projects
   * cGAL
   * EDGE: Genomic Tools for Steinernema hermaphroditum
     * Why Steinernema?
     * Publications- Steinernema
 * microPublication Biology
   * MicroPublications
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   * Alumni Table
 * Lab Resources
   * Group Meetings
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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.

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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 most notably Steinernema hermaphroditum, 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 to worms navigate up a chemical gradient?
 * How can we best predict gene expression from DNA sequence?
 * What are the functional consequences of variants found in individual with
   autism spectrum disorder and other human phenotyps?
 * 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. elegans molecular 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.


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Ontology
WormBase Alliance of Genome Resources WormBook Textpresso microPublication Gene
Ontology



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Adler R Dillman. (2021). Movie: Dillman_Scarpocapsae_Jumping1 (Version 1.0).
CaltechDATA.





LAB NEWS

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Aidyl is honored as an Explorer!

New Alliance Release with new Textpresso full text, single sentence,
ontology-based search.

Mark Zhang successfully defended his Ph.D. thesis! See preprint of chapter 2

New paper on WormBase transition and Nick's paper on improving enrichment
analysis

Paul Sternberg was awarded Thomas Hunt Morgan Medal of the Genetics Society of
America.

Xuan Wan applied her expertise in analyzing chemotaxis as part of an
interdisciplinary team to improve anti-bacterial catheters, as described on the
Caltech site and a recent paper in Science Advances.

We have a collection of cGAL drivers for C. elegans sensory neurons and
additional effectors, described in a new team paper in the PNAS spearheaded by
Stephanie Nava, Wilber Palma and Xuan Wan.

Drs. Hillel Schwartz and James Tan cloned a mutant locus in the insect-killing
Steinernema hermaphroditum! A just published paper describes this first such
success. The Dumpy mutants defective in this gene were discovered by Hillel,
James, and two summer students, Jackeline Peraza and Krystal Raymundo.

The Global Biodata Coalition announces its first list of Global Core Biodata
Resources. Our very own WormBase and the Alliance of Genome Resources are both
included! See the article in The Caltech Weekly here.

Caltech Green Labs was co-founded by former lab manager Sarah Torres







 * New Publications This Year
 * New microPublications this Year

Enrichment analysis: Markarian N, Van Auken KM, Ebert D, Sternberg PW.
Enrichment on steps, not genes, improves inference of differentially expressed
pathways. PLoS Comput Biol. 2024 Mar 25;20(3):e1011968. doi:
10.1371/journal.pcbi.1011968. PMID: 38527066; PMCID: PMC10994554.

Cloning genes in Steinernema! Schwartz HT, Tan CH, Peraza J, Raymundo KLT,
Sternberg PW. Molecular identification of a peroxidase gene controlling body
size in the entomopathogenic nematode Steinernema hermaphroditum. Genetics. 2023
Dec 11:iyad209. doi: 10.1093/genetics/iyad209. Epub ahead of print. PMID:
38078889.

Many more cGAL reagents! Nava S, Palma W, Wan X, Oh JY, Gharib S, Wang H,
Revanna JS, Tan M, Zhang M, Liu J, Chen CH, Lee JS, Perry B, Sternberg PW. A
cGAL-UAS bipartite expression toolkit for Caenorhabditis elegans sensory
neurons. Proc Natl Acad Sci U S A. 2023 Dec 19;120(51):e2221680120. doi:
10.1073/pnas.2221680120. Epub 2023 Dec 14. PMID:
38096407.https://doi.org/10.1073/pnas.2221680120

CO2 and dauer: Banerjee N, Rojas Palato EJ, Shih PY, Sternberg PW, Hallem EA.
Distinct neurogenetic mechanisms establish the same chemosensory valence state
at different life stages in Caenorhabditis elegans. G3 (Bethesda). 2023 Nov
23:jkad271. doi: 10.1093/g3journal/jkad271. Epub ahead of print. PMID: 38092065.

Banerjee N, Shih PY, Rojas Palato EJ, Sternberg PW, Hallem EA. Differential
processing of a chemosensory cue across life stages sharing the same valence
state in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2023 May
9;120(19):e2218023120. doi: 10.1073/pnas.2218023120. Epub 2023 May 1. PMID:
37126715; PMCID: PMC10175840.

mating behavior: Weng JW, Park H, Valotteau C, Chen RT, Essmann CL, Pujol N,
Sternberg PW, Chen CH. Body stiffness is a mechanical property that facilitates
contact-mediated mate recognition in Caenorhabditis elegans. Curr Biol. 2023 Jul
28:S0960-9822(23)00927-2. doi: 10.1016/j.cub.2023.07.020. Epub ahead of print.
PMID: 37541249.

Reilly DK, Schwarz EM, Muirhead CS, Robidoux AN, Narayan A, Doma MK, Sternberg
PW, Srinivasan J. Transcriptomic profiling of sex-specific olfactory neurons
reveals subset-specific receptor expression in Caenorhabditis elegans. Genetics.
2023 Apr 6;223(4):iyad026. doi: 10.1093/genetics/iyad026. PMID: 36801937; PMCID:
PMC10319972.

Cell biology: Tan C-H, Chen K-W, Park H, Sternberg PW, Chou T-F. (2023).
LINKIN-associated proteins necessary for tissue integrity during collective cell
migration. bioRxiv https://doi.org/10.1101/2023.02.02.527750

Alliance preprint: Alliance of Genome Resources Consortium. Updates to the
Alliance of Genome Resources Central Infrastructure. bioRxiv [Preprint]. 2023
Nov 22:2023.11.20.567935. doi: 10.1101/2023.11.20.567935. PMID: 38045425; PMCID:
PMC10690154.

GO: Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics.
2023 May 4;224(1):iyad031. doi: 10.1093/genetics/iyad031. PMID: 36866529; PMCID:
PMC10158837.

knowledge modeling: Prakash SJ, Van Auken KM, Hill DP, Sternberg PW. Semantic
Representation of Neural Circuit Knowledge in Caenorhabditis elegans. Brain Inf.
10, 30 (2023). doi: 10.1101/2023.04.28.538760. PMID: 37162850; PMCID:
PMC10168330.

transcriptomics: Truong L, Chen YW, Barrere-Cain R, Levenson MT, Shuck K, Xiao
W, da Veiga Beltrame E, Panter B, Reich E, Sternberg PW, Yang X, Allard P.
Single-nucleus resolution mapping of the adult C. elegans and its application to
elucidate inter- and trans-generational response to alcohol. Cell Rep. 2023 May
23;42(6):112535. doi: 10.1016/j.celrep.2023.112535. Epub ahead of print. PMID:
37227821.

Imaging: Holman EA, Krishnan H, Holman DR, Holman HN, Sternberg PW. Toward
implementing autonomous adaptive data acquisition for scanning hyperspectral
imaging of biological systems. Appl Phys Rev. 2023 Mar 28;(10)1:011319.

weird photochemistry artifact analyzed: Chieh-Hsiang Tan, Keke Ding, Mark
G Zhang, Paul W. Sternberg. Fluorescence dynamics of lysosomal-related organelle
flashing in the intestinal cells of Caenorhabditis elegans. bioRxiv [Preprint].
2023. doi: https://doi.org/10.1101/2023.10.16.562538

data standards: Wright A, Wilkinson MD, Mungall C, Cain S, Richards S, Sternberg
P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. DATA
RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard.
bioRxiv [Preprint]. 2023 Dec 1:2023.11.29.569306. doi:
10.1101/2023.11.29.569306. PMID: 38076838; PMCID:
PMC10705436.doi: https://doi.org/10.1101/2023.11.29.569306





Rodak, NY; Tan, CH; Sternberg, PW (2024). An improved solid medium-based
culturing method for <i>Steinernema hermaphroditum</i>. microPublication
Biology. <a href="https://doi.org/10.17912/micropub.biology.001110"
target="_blank" rel="noopener noreferrer">10.17912/micropub.biology.001110</a>.




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