McCloskey, Richard et al. (2015) International Worm Meeting "Food status regulates three behavioral states in Caenorhabditis elegans."

Fang-Yen, Christopher, McCloskey, Richard

[International Worm Meeting, 2015]

Animals switch between behavioral states to adapt to their environments, pursue goals, and to meet energy intake requirements. For example, highly active states are often associated with food or mate searching or predator avoidance while more inactive states are associated with rest or feeding. The nematode C. elegans exhibits behavior states such as dwelling, roaming, and quiescence characterized by low, high, and absent locomotory activity, respectively. It has been observed that food influences the decision to alternately roam or dwell while liquid environments promote a decision to alternate between roaming and quiescence. We investigated the possibility that these three behaviors could exist in any mechanical environment via long-term, longitudinal imaging of C. elegans behavior. We find that roaming, dwelling, and quiescence can occur regardless of the mechanical environment and that fasting induces quiescence by a regulated mechanism that likely depends on neuropeptides. We characterized feeding, locomotion, posture, and egg-laying and find that these stereotypically differ depending on the given behavioral state suggesting that behavioral states reflect the status of multiple neural circuits. We investigated how conserved food-responsive signaling pathways influence behavior state decisions and find that the foraging homolog egl-4 is regulates the architecture of behavioral dynamics while insulin-like signaling is required in the nervous system to regulate decisions over behavior state type. Overall our results show that dwelling, roaming, and fasting quiescence are not just locomotory states but distinct behavior states regulated food availability and evolutionarily conserved signaling pathways involved in nutrition. .

McCloskey, Richard et al. (2009) International Worm Meeting "The Emerging Role of Ubiquitin-Specific Protease MATH-33 in Polarity of the Caenorhabditis elegans Early Embryo."

McCloskey, Richard, Hoose, Wendy A, Morton, Diane G, Kemphues, Kenneth J

[International Worm Meeting, 2009]

The study of partitioning defective (PAR) proteins in the nematode model Caenorhabditis elegans has been instrumental in elucidating conserved mechanisms of cellular polarity. Recently, our lab has used RNAi feeding as a reverse genetic method to uncover additional genes that may be involved in cellular polarity. We found that depletion of the ubiquitin-specific protease MATH-33 increases embryonic lethality and increases the penetrance of polarity phenotypes in weak par-1(zu310ts), par-2(it5ts), and par-4(it57ts) mutants, but does not seem to increase polarity defects in weak par-3 mutants. Generally, these results indicate that MATH-33 protein functions to support polarity in the one-cell embryo, and that it may specifically function with components that are necessary for maintaining the posterior domain. Furthermore, math-33 mutation alone appears to subtly affect the distribution of posteriorly localized cellular components such as PAR-2 and P granules, indicating that its activity may contribute to their localization or activity. Lastly, an antibody created against a C-terminal fragment of MATH-33 has shown that MATH-33 is present in embryo cytoplasm, and is enriched in nuclei, indicating that it could be functioning anywhere the one-cell embryo. My future research will continue to explore the mechanism by which these subtle polarity defects arise and, will address whether MATH-33 is responsible for regulating one or more of the PARs directly.

McCloskey, Richard J. et al. (2011) International Worm Meeting "Putative De-ubiquitylating Enzymes MATH-33 and USP-47 are Required for Polarity Establishment in C. elegans."

McCloskey, Richard J., Kemphues, Kenneth

[International Worm Meeting, 2011]

The C. elegans one-cell embryo polarizes in response to a cue from the sperm centrosome, and this signal leads to a cascade of events that localizes cell fate determinants to execute the developmental program of the worm. In the course of investigating novel genes that may be involved in polarity we found that simultaneous mutation/RNAi of the genes math-33 and usp-47 leads to the inability of embryos to correctly establish and maintain asymmetry as defined by posterior and anterior markers PAR-2 and PAR-3. Protein homology indicates that MATH-33 and USP-47 are putative de-ubiquitylating enzymes whose similar structure and common expression in the germline and early embryos strongly suggests they have functional overlap. We determined that polarity phenotypes result from an impaired establishment phase in which we observe reduced PAR-2 recruitment, and a decrease or failure of posterior to anterior myosin flow. Our observations on the position of the centrosomes lead us to suggest that the centrosomal interaction with the posterior cortex is defective. The polarity defects can be suppressed by compromising the proteasome, suggesting that MATH-33 and USP-47 affect protein stability rather than protein activity. Lastly, we found that USP-46, the homolog of a DUB with a role in polarity in Schizosaccharomyces pombe, is potentially redundant with MATH-33 and USP-47, suggesting that de-ubiquitylation is a required and evolutionarily conserved mechanism to control polarity. .

Martinelli SD et al. (1995) International C. elegans Meeting "ACEDB"

Durbin RM, Martinelli SD

[International C. elegans Meeting, 1995]

We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.

Chao-I Chen et al. (2004) West Coast Worm Meeting "A Bayesian approach toward analyzing the network of genes involved in C. elegans programmed cell death"

Chao-I Chen, Vebjorn Ljosa, S Rao Jammalamadaka, Chiou-Wei Tsai, Ambuj K Singh, Thomas A McCloskey, Xiaofang Lei, Joel H Rothman

[West Coast Worm Meeting, 2004]

From an RNAi screen for genes that repress apoptosis, we have identified a set of about 130 candidates (see abstract by McCloskey et al.). We are using computational methods in an effort to predict functional networks through which these genes may act and to identify additional candidates and their relationships within the postulated networks. We are initially working with a number of datasets as the basis for our predictions: microarray expression data, the physical orientation of genes within the worm genome, phylogenetic profile data, and PSORT predictions of protein localization. The datasets are normalized according to their overlap with the worm interactome and Wormbase subcellular localization data. They are then combined using a nave Bayesian network, to yield a set of potential functionally interacting protein pairs along with a likelihood score for each pair. Finally, we construct network maps of the protein pairs that fall above a desired likelihood ratio. Our initial efforts suggest a cluster of functional interactions that are predicted from the gene set identified by the RNAi screen; refinements of the computational methods are in progress.

Consortium Wormbase et al. (2000) West Coast Worm Meeting "From ACeDB to a more complete and usable database"

Consortium Wormbase, Foltz NL, Schwarz EM, Sternberg PW

[West Coast Worm Meeting, 2000]

We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.

Consortium Wormbase (2000) Worm Breeder's Gazette "Update on the C. elegans database WormBase"

Consortium Wormbase

[Worm Breeder's Gazette, 2000]

WormBase (www.wormbase.org) is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. WormBase builds upon the existing ACeDB database of the C. elegans genome by providing curation from the literature, an expanded range of content and a user friendly web interface. The team that developed and maintained ACeDB (Richard Durbin, Jean Thierry-Mieg) remains an important part of WormBase. Lincoln Stein and colleagues at Cold Spring Harbor are leading the effort to develop the user interface, including visualization tools for the genome and genetic map. Teams at Sanger Centre (led by Richard Durbin) and the Genome Sequencing Center at Washington University, St. Louis (led by John Spieth) continue to curate the genomic sequence. Jean and Danielle Thierry-Mieg at NCBI spearhead importation of large-scale data sets from other projects. Paul Sternberg and colleagues at Caltech will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level; and gene interactions. Paul Sternberg assumes overall responsibility for WormBase, and is delighted to hear feedback of any sort. WormBase has recently received major funding from the National Human Genome Research Institute at the US National Institutes of Health, and also receives support from the National Library of Medicine/NCBI and the British Medical Research Council. WormBase is an expansion of existing efforts, and as such continues to need you help and feedback. Even with the increased scope and funding, all past contributors to ACeDB remain involved. The Caenorhabditis Genetics Center (Jonathan Hodgkin and Sylvia Martinelli) collaborate with WormBase to curate the genetic map and related topics. Ian Hope and colleagues continue to supply expression data to WormBase. Leon Avery will continue his superb website and serves as one advisor to WormBase. While the major means of access to WormBase is via the world wide web, downloadable versions of WormBase as well as the acedb software engine will continue to be available.

Edgley ML et al. (1995) International C. elegans Meeting "CYBERWORMS"

Collins D, Bryer J, Baillie DL, Edgley ML, Rose AM

[International C. elegans Meeting, 1995]

We are engaged in two projects to improve the alignment of the genetic and physical maps for C. elegans. The Genetic Toolkit project uses PCR to tie the endpoints of balanced deficiencies to the physical map; and the CGAT project uses microinjection of cloned cosmids from the worm sequencing project to generate transgenic arrays that are used to rescue mapped, balanced lethal mutations. Both projects are generating large amounts of genetic map information, which is being integrated into the CGC map (compiled by Jonathan Hodgkin) using the ACEDB program (Richard Durbin and Jean Thierry-Mieg). We also have established a World-Wide Web hypertext server to provide access to information generated by these projects. This Genetic Toolkit web site (http: genetic balancers and transgenic strains available from our laboratories. For stable transgenic strains, listed cosmids are linked to modified GenBank entries describing the sequence. This work is funded by the NIH National Center for Research Resources (NCRR) and the Canadian Genome Analysis and Technology Program (CGAT).

Ling Chen et al. (2004) West Coast Worm Meeting "Functional Characterization of a Putative Apoptotic Suppressor, tfg-1, in C. elegans"

Joel H Rothman, Ling Chen, Tom McCloskey

[West Coast Worm Meeting, 2004]

Among the genes identified in genome-wide RNAi screens for novel apoptotic regulators (see abstract by McCloskey and Rothman) is tfg-1 , the C. elegans homologue of human TFG (TRK-fused gene). TFG was originally identified on the basis of its rearrangement in chromosomal translocations present in papillary thyroid carcinomas and anaplastic large cell lymphomas. These rearrangements create in-frame fusions of TFG coding sequences with the receptor tyrosine kinase, ALK (anaplastic lymphoma kinase). TFG transcription is also up-regulated in response to activation of the TNF receptor family member TALL-1, which promotes proliferation of B lymphocytes and autoimmunity. We have found that that loss of tfg-1 activity results in a slight increase in CED-3-independent cell death. While this effect is mild, we also observed that RNAi of tfg-1 results in small, uncoordinated, and sterile phenotypes, all three of which are suppressed by a ced-4 , but not a ced-3 mutation. Thus, the Sma Unc Ste phenotypes might be the result of CED-4-dependent apoptosis, as is seen in icd-1 and icd-2 mutants (see abstract by Bloss and Rothman). While the function of human TFG in tumorigenesis is unknown, these results suggest that tfg-1 might act to suppress apoptosis, leading to the hypothesis that TFG might contribute to tumor formation by inappropriately repressing apoptosis, in analogy to the action of the anti-apoptotic factor, Bcl-2, in promoting lymphomas. Such an anti-apoptotic function could also explain a role for TFG in autoimmunity. Current studies are directed at illuminating the action of tfg-1 in repression of apoptosis.

Heimbucher, Thomas et al. (2013) International Worm Meeting "MATH-33, a conserved DUB required for DAF-16/FOXO stabilization and function."

Carrano, Andrea, Fonslow, Bryan R., McCloskey, Richard, Dillin, Andrew, Klammt, Christian, Riedel, Christian G., Riera, Celine, Kemphues, Kenneth, Lillemeier, Bjorn F., Liu, Zheng, Yates III, John R., Bossard, Carine, Heimbucher, Thomas, Hunter, Tony, O'Shea, Clodagh

[International Worm Meeting, 2013]

The FOXO transcription factor DAF-16, a downstream effector of Insulin/IGF-1 signaling (IIS), is a critical longevity determinant in diverse organisms. However, the molecular basis of its regulation is still largely unknown. By mass spectrometry of affinity-purified DAF-16-associated factors, we have identified the deubiquitylating enzyme MATH-33 as a co-regulator for DAF-16 activity. We show that MATH-33 stabilizes DAF-16 protein levels in C. elegans under conditions when IIS is downregulated and DAF-16 is transcriptionally active. In addition, MATH-33 is required for maintaining DAF-16 function to regulate early developmental decisions and life span. Disruption of math-33 expression in C. elegans significantly reduces DAF-16 protein levels under low IIS conditions without affecting daf-16 mRNA levels. Genetic ablation of both math-33 and rle-1, a previously identified DAF-16 ubiquitin E3 ligase, is able to partially rescue DAF-16 activity, indicating an epistatic relationship between both factors for regulating DAF-16 levels. Finally, we demonstrate that expression of a catalytically inactive form of MATH-33 in cultured mammalian cells results in an increase of ubiquitylated DAF-16. Our data support a model in which MATH-33 acts as a deubiquitylating enzyme to stabilize DAF-16 protein levels when IIS is downregulated.