Salser SJ et al. (1994) Worm Breeder's Gazette "mab-5 Expression Repeatedly Switches ON and OFF in the V5 Lineage"

Kenyon CJ, Salser SJ

[Worm Breeder's Gazette, 1994]

mab-5 Expression Repeatedly Switches ON and OFF in the V5 Lineage S. Salser and C. Kenvon, UCSF, San Francisco, CA. 94143

Kenyon CJ et al. (1994) Worm Breeder's Gazette "Activity of the polyray-1 Maintenance Gene Must Be Overcome To Allow For Correct Temporal Expression of HOM-C Genes"

Kenyon CJ, Maloof JN

[Worm Breeder's Gazette, 1994]

Activity of the polyray-1 maintenance gene must be overcome to allow for correct temporal expression of HOM-C genes Julin Maloof and Cynthia Kenyon, Dept of Biochemistry, UCSF, San Francisco, CA 94143 0554

Choi, Hailey et al. (2015) International Worm Meeting "Towards an understanding of how embryos cope with stochastic gene expression."

Doan, Kollan, Choi, Hailey, Broitman-Maduro, Gina, Maduro, Morris, Carranza, Francisco

[International Worm Meeting, 2015]

Robust gene expression is crucial for proper embryonic development, and yet gene expression is subject to both extrinsic and intrinsic sources of noise. We are investigating mechanisms by which the C. elegans embryo buffers stochastic variations in gene expression in endoderm specification. Perturbation of the regulators that act in gene regulatory network that specifies E, the endoderm progenitor, causes gut specification to become highly variable. This variability includes both the proportion of embryos making gut, and among those with gut, variations in the number of E descendants that adopt a gut fate. Using existing mutations and single-copy transgenes in which critical transcription factor binding sites have been mutated, we have created a set of strains that experience stochastic E specification. These strains cover a range of probabilities of making gut, from 0% to 100%. Using these strains, we are investigating E lineage phenotypes in the embryo, elucidating phenotypes in adults that survive hypomorphic gut specification, and screening for factors that modulate gut specification in these strains.First, we have found that E can make both gut and non-gut cells in the same embryo, using strains in which we can follow E descendants in the presence of reporter transgenes to mark tissue fates.Second, we have found that surviving adults display phenotypes consistent with caloric restriction. Animals store excess lipid, have defects in morphology and fertility, and exhibit developmental delay.Last, we are performing RNAi screens for maternal factors that modulate gut specification. Using the Vidal feeding library, we have selected ~3000 clones that are known to be expressed in the germline. Thus far, we have found that several diverse maternal pathways, including transcription regulation, metabolism, and apoptosis, influence the ability of progeny embryos to make gut in our partial specification-compromised strains. This suggests that embryonic gene expression is sensitive to many sources of variation.Collectively our data show that gut specification is not an "all-or-none" event, and that if specification does not occur properly, specification defects can persist into the adult intestine. Our results have implications in other developmental pathways in C. elegans, and in any metazoan system in which gene regulatory networks drive developmentally important events.

Robertson FM (2010) IDrugs "High-Content Analysis--CHI's Seventh Annual Conference--Developments in HCA and Pathway Analysis."

Robertson FM

[IDrugs, 2010]

CHI''s Seventh Annual Conference on High-Content Analysis (HCA), held in San Francisco, incorporated topics covering new developments in the field of HCA, including hardware and software updates, new biological models for HCA and pathway analysis. This conference report highlights selected presentations on the use of HCA for the characterization of stem cells, cell-colony analysis, the validation of disease models and the identification of antiparasitic compounds.

Maduro, Morris F. et al. (2013) International Worm Meeting "Life at the edge of robustness: Partial guts suggest that endoderm specification is not all-or-none."

Ghamsari, Farhad, Maduro, Morris F., Broitman-Maduro, Gina, Carranza, Francisco, Walia, Gurjot

[International Worm Meeting, 2013]

The C. elegans intestine is derived from the embryonic blastomere E. The paradigm for E specification is that maternal SKN-1- and POP-1-dependent input cause activation of the E-specific gut specification factors end-1 and end-3. After reaching a threshold of expression, these activate elt-2, which maintains its expression by autoregulation and drives the commitment to gut differentiation. Prior work suggests that gut specification may not be all-or-none, and that some of the descendants of E are capable of adopting a gut fate independently of others. We have created strains in which E is specified by single-copy transgene forms of end-1 and/or end-3 that are mutated for binding sites for the MED-1,2 GATA factors, themselves direct targets of SKN-1. In such strains, different embryos make variable numbers of apparently normal-sized gut cells, suggesting that specification has become subject to stochastic variations among embryos, and that commitment to a gut fate can occur later in the E lineage. Counting of embryonic elt-2 transcripts by single-molecule FISH suggests that activation of elt-2 is more graded in these strains, as opposed to an all-or-none mode as was previously reported for SKN-1-depleted embryos (Raj et al., 2010). As these effects are confined to the E lineage due to the nature of the strains constructed, we are able to evaluate adults derived from embryos in which functional guts were made. We find that such adults store lipids at significantly higher levels and display other variable pleiotropic phenotypes, suggestive of primary defects in gut function. Together, these results build a picture in which specification of gut is not an all-or-none event, and that in animals that do make an intestine, the endoderm differentiation network is not fully self-correcting for partially compromised specification. We will present these results, including the outcome of an attempt to computationally model the stochasticity of elt-2 activation.

Broitman-Maduro, Gina et al. (2013) International Worm Meeting "Enhanced RNA virus susceptibility results from defects in lipid metabolism."

Ding, Shou-wei, Coffman, Stephanie, Guo, YuanYuan, Carranza, Francisco, Maduro, Morris, Pompura, Saige, Broitman-Maduro, Gina

[International Worm Meeting, 2013]

Prior work has shown that C. elegans can support replication of (+) strand RNA viruses, including the Flock House Virus (FHV), and the Orsay virus. We have previously reported that transgene expression of FHV RNA1, which encodes the viral RdRP and a viral suppressor of RNAi (B2), can direct its own replication (Lu et al., 2005). By replacing the coding region of B2 with that of GFP (FR1gfp) we can visualize viral replication in backgrounds that are virus-susceptible. In an RNAi screen for factors that influence replication of FR1gfp (see abstract by Stephanie Coffman), we identified genes that are known to affect storage or metabolism of lipids, such as nhr-68 (Ashrafi et al., 2003). To evaluate the relationship between lipid storage and RNA virus replication, we examined fat stores using Oil Red O in chromosomal mutants for other genes identified by the screen, and directly assessed viral replication in strains that are known to have fat storage defects. Our results confirm that conditions known to cause increases in fat stores, such as the germlineless glp-4(bn2) background, result in a significant increase in viral replication. As lipid storage defects have been recently shown to be correlated with autophagy (Hansen et al., 2013), we have tested the role of autophagy in lipid storage-mediated viral susceptibility. Overexpression of the lipase lipl-4 appears to be sufficient to increase viral susceptibility, in a manner that is partially dependent on the autophagy gene atg-1. The connection between lipid storage and susceptibility to RNA virus replication is not immediately obvious, and our data suggest that the interactions are complex, though one possibility is that autophagy regulates some components of the RNAi machinery (Gibbings et al., 2012). Results of characterization of viral replication (both FR1gfp and Orsay virus) in various mutant backgrounds will be presented.

Gogonea CB et al. (1999) J Mol Graph Model "Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family."

Ali YM, Gogonea V, Merz KM, Gogonea CB, Siddiqui SS

[J Mol Graph Model, 1999]

In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caenorhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma-tubulin). We obtained their tertiary structures by computationally modifying the X-ray crystal structure of the pig brain alpha/beta-tubulin dimer published by Nogales et al. [Nature (London) 1998;391:199-203]. Our computational protocol involves changing the amino acids (with MIDAS; Jarvis et al., UCSF MIDAS. University of California, San Francisco, 1986) in the 3D structure of pig brain alpha/beta-tubulin dimer followed by geometry optimization with the AMBER force field (Perlman et al., AMBER 4. University of California, San Francisco, 1990). We subsequently analyze and compare the resulting structures in terms of the differences in their secondary and tertiary structures. In addition, we compare the pattern of hydrogen bonds and hydrophobic contacts in the guanosine triphosphate (GTP)-binding site for all members of the tubulin family. Our computational results show that, except for gamma-tubulin, all members of the C. elegans tubulin family have similar secondary and 3D structures and that the change in the pattern of hydrogen bonds in the GTP-binding site may be used to assess the relative stability of different alpha/beta-tubulin dimers formed by monomers of the tubulin family.

Apfeld J et al. (1999) Nature "Regulation of lifespan by sensory perception in Caenorhabditis elegans."

Kenyon CJ, Apfeld J

[Nature, 1999]

Caenorhabditis elegans senses environmental signals through ciliated sensory neurons located primarily in sensory organs in the head and tail. Cilia function as sensory receptors, and mutants with defective sensory cilia have impaired sensory perception. Cilia are membrane-bound microtubule-based structures and in C. elegans are only found at the dendritic endings of sensory neurons. Here we show that mutations that cause defects in sensory cilia or their support cells, or in sensory signal transduction, extend lifespan. Our findings imply that sensory perception regulates the lifespan of this animal, and suggest that in nature, its lifespan may be regulated by environmental cues.AD - Department of Biochemistry and Biophysics, University of California at San Francisco, 94143-0448, USA.FAU - Apfeld, JAU - Apfeld JFAU - Kenyon, CAU - Kenyon CLA - engPT - Journal ArticleCY - ENGLANDTA - NatureJID - 0410462RN - 0 (DAF-16 transcription factor)RN - 0 (DAF-2 protein)RN - 0 (Helminth Proteins)RN - 0 (Transcription Factors)RN - EC 2.7.11.- (Receptor, Insulin)SB - IM

Ellis HM et al. (1983) Worm Breeder's Gazette "monoclonal antibodies directed against the Drosophila nervous system cross-react with C elegans."

Yuan JY, Horvitz HR, Ellis HM

[Worm Breeder's Gazette, 1983]

We have begun to screen a collection of monoclonal antibodies that were generated against Drosophila embryos and stain a variety of Drosophila nervous tissues. These antibodies were kindly provided by Lily and Yuh Nung Jan of the University of California at San Francisco. Worms were fixed overnight at 4 C in 2% Formaldehyde, squashed, frozen and fractured as described by Albertson et al. (W.B.G. Vol.7 No.1) and transferred through a series of alchohols (95,70,50% EtOH). Three out of nine monoclonal antibodies that we have tested so far stain C. elegans. 20B6-B6* stains many nerve processes including dorsal and ventral cords, sub-lateral cords, cord commissures, amphid commissures and processes in the head. It is not yet clear whether this antibody stains all or only some processes. 18H12-C3* stains processes in a manner similar to 20B6-B6* as well as sperm and muscle ( or a structure with a muscle-like staining pattern). 21A4-E4 stains sperm and early (pre-morphogenetic) eggs. This staining is non- nuclear in both sperm and eggs and appears to be symmetrically distributed within eggs.

De Bono M et al. (1998) Cell "Natural variation in a neuropeptide Y receptor homolog modifies social behavior and food response in C. elegans."

Bargmann CI, De Bono M

[Cell, 1998]

Natural isolates of C. elegans exhibit either solitary or social feeding behavior. Solitary foragers move slowly on a bacterial lawn and disperse across it, while social foragers move rapidly on bacteria and aggregate together. A loss-of-function mutation in the npr-1 gene, which encodes a predicted G protein-coupled receptor similar to neuropeptide Y receptors, causes a solitary strain to take on social behavior. Two isoforms of NPR-1 that differ at a single residue occur in the wild. One isoform, NPR-1 215F, is found exclusively in social strains, while the other isoform, NPR-1 215V, is found exclusively in solitary strains. An NPR-1 215V transgene can induce solitary feeding behavior in a wild social strain. Thus, isoforms of a putative neuropeptide receptor generate natural variation in C. elegans feeding behavior.AD - Howard Hughes Medical Institute, Department of Anatomy, The University of California, San Francisco 94143-0452, USA.FAU - de Bono, MAU - de Bono MFAU - Bargmann, C IAU - Bargmann CILA - engSI - GENBANK/U49944PT - Journal ArticleCY - UNITED STATESTA - CellJID - 0413066RN - 0 (Helminth Proteins)RN - 0 (Receptors, Neuropeptide Y)RN - EC 3.6.1.- (GTP-Binding Proteins)SB - IM