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Faculty List
Paul W. Sternberg
pws@caltech.edu
Ph.D., 1984, Massachusetts Institute of Technology
WormBook (online book about C. elegans and other nematodes)
Neuroscience Information Framework
Predicting Genetic Interactions (GeneOrienteer)
Nematode Systems Biology
We seek to understand how a genome controls development, behavior and physiology. We use C. elegans molecular genetics to understand detailed mechanisms, and functional genomics to obtain global views of development and behavior. We tightly couple computation and experimental data, in part to use computation to make experimental tests more efficient. Moreover, we study other genomes, genetics, and biology of other nematodes to help us comprehend C. elegans, to learn how development and behavior evolve, and to learn how to control parasitic and pestilent nematodes.
Our efforts in genomics are experimental and computational. We worked with Caltech’s Millard and Muriel Jacobs Genetics and Genome Laboratory to determine the genomic sequence of several nematode species using only short sequencing reads. The first was a new Caenorhabditis species (angaria) that is an outgroup for the five existing sequenced species of this genus. We used cDNA sequence data to help assemble larger than gene-size pieces of this genome. By comparing the C. angaria genome to other Caenorhabditis species, we identified thousands of short, high conserved sequences that we hypothesis are regulatory. In addition, we have sequenced, assembled and annotated the genome of Steinernema carpocapsae, an insect-killing nematode that can jump onto hosts (see below) and four other Steinernema species. We are also helping to sequence and analyze the genome and transcriptomes of the sheep parasite Haemonchus contortus and related animal parasites. For comparison we are analyzing genomes of several other free-living nematodes, including Panagrellus redivivus.
Our behavioral studies focused this year on sexual attraction, sleep, and host finding by parasitic nematodes. We have continued to study the chemicals (ascarosides) that constitute mating pheromone made by hermaphrodites (morphologically females but that make sperm for internal self-fertilization) and sensed by males. We hypothesize that ascarosides are a diverse family of nematode signaling molecules. To test this hypothesis we are continuing our collaboration with the labs of Art Edison and Frank Schroeder to purify mating cues from other nematode species. To study parasite behaviors, we are using three genera of insect killing nematodes that are used in insect biocontrol because they deliver toxic bacteria to their hosts. One key discovery this year is that Heterorhabditis bacteriophora and Steinernema carpocapsae use the same sensory neuron as C. elegans to respond to carbon dioxide. Steinernema carpocapsae is able to jump onto insects, and we are trying to understand the genetic and cellular basis for this amazing behavior, as well as its evolutionary origin, as only members of this genus can jump.
We have used channel rhodopsin to faithfully activate a neuron, as evidenced by whole-cell patch electrophysiology neuronal activity in a pre-synaptic cell expressing channel rhodopsin and then in its post-synaptic partner. Now that this system is validated, we are expressing channel rhodopsin and a genetically-encoded calcium sensor in a range of specific neurons to be able to examine neuronal circuit properties.
The infective juveniles (IJs) of H. bacteriophora and S. carpocapsae are analogous to the dauer larvae of C. elegans. Developing C. elegans larvae choose between proceeding directly to reproductive development or to arrest development as dauer larvae, depending on population density (signaled by several ascarosides) and the amount of food available. We are studying how larvae make this all-or-none decision. As worms exit the dauer stage they resume reproductive development and we have analyzed how the organization of genes into operon might facilitate a rapid transition to growth.
In the area of cell regulation, we have continued to study WNT and EGF signaling to define new components, how these two pathways interact, and what determines the specific outcomes of common signals. For this study we focus on the C. elegans vulva, a paradigm for analyzing organogenesis. In one project, we are using the polarity of the vulval secondary lineage to study how multiple types of WNT receptors act in concert or antagonistically. This year we discovered that fibroblast growth factor (FGF) signaling works with WNT in this process. EGF controls development via the RAS/MAPkinase pathway and behavior via phospholipase C-gamma pathway. We had previously found that the EGF-receptor acts in a single neuron, ALA, to control a sleep-like state. We are testing other conserved signaling pathways for common roles in sleep regulation, and using calcium imaging to examine neuronal function during worm sleep. We had discovered that a network of three homeobox containing transcriptional regulatory proteins regulate expression of the EGF-receptor and other genes in the ALA neuron, and are now defining the cis-regulatory elements that respond to these homeobox proteins.
We are trying to learn how to efficiently define cis-regulatory elements using functional assays. We have established establishing pipelines for cis-regulatory computational analysis to define genomic elements that we test in transgenic C. elegans. For example, we tested some of our methods on elements that direct expression in the DVA neuron, which we had previously shown to control the extent of body flexion during locomotion.
We are developing new assays for regulatory elements. For a number of projects, we want to identify all the genes that are expressed in a particular cell at a particular time. We thus are trying different methods of obtaining a transcriptional profile from a single cell; the male linker cell is our first test case.
We started a new project on cell migration to understand both normal organogenesis and potential migratory programs that might be accessed by metastatic tumor cells. The C. elegans male linker cell (LC) undergoes a complex migration with changes in direction, speed, and morphology. An initial functional screen for genes involved in LC migration identified the Tlx ortholog nhr-67 as being necessary for the middle parts of the migratory program, such as negative regulation of the netrin receptor unc-5 to allow a ventral turn. We have profiled the transcriptome of individual LCs by microdissection, amplification, and cDNA deep sequencing. This study identified about 800 LC-enriched genes whose functions we are now analyzing, including a number of conserved proteins of unknown function that we predict will have roles in migration in human cells.
We examined several molecular aspects of nematode life-cycle decisions. We used L1 larval arrest to study nutritional control of these decisions, and went on to use microarrays and NanoString technology to examine transcriptional changes. We were early adopters of chromatin immunoprecipitation analyzed by deep sequencing (ChIP-seq) and discovered that RNA polymerase accumulates at the 5' end of transcriptional units during L1 arrest. We then examined the genomic organization related to arrested states and the transition back to growth. We used this analysis to develop a model for the selective advantage of operons in metazoans, namely that operons decrease the need for transcriptional resources in the initial stages of transition to growth, either release from L1 arrest or recovery from dauer larvae. We are now examining how the entry into dauer is controlled by dauer pheromones (mixture of ascarosides) and steroid hormones (dafachronic acid). We collaborated with Adam Anteb (Max-Planck-Institute for Biology of Ageing) to analyze the role of dafachronic acid in pheromone response, in particular how worms respond to a shift form high to low pheromones when larvae are deciding to undergo reproductive or dauer development.
We continue to organize, store, and display information about C. elegans and to extend these efforts to other nematodes. With our international team of collaborators, we present this information in an Internet-accessible database, WormBase (www.wormbase.org). Our major contribution is to extract information from the literature, focusing on gene, protein, and cell function; gene expression; gene-gene interactions; and functional genomics data. Annotation of gene function includes use of the Gene Ontology (GO; www.geneontology.org, and we are developing these ontologies as part of the GO Consortium. To facilitate these processes, we have developed Textpresso (www.textpresso.org), a search engine for biological literature. In collaboration with other model organism databases, we have applied Textpresso to the literature of C. elegans, Drosophila, Arabidopsis, mouse, and several human diseases. We use this system to automate some steps in the extraction of information from full-text papers. Extension of Textpresso to neuroscience is part of the Neuroscience Information Framework. Lastly, we are exploring ways of visualizing biological information.
