Yukiko Yonezawa et al. (2007) International Worm Meeting "Role of the type-b insulin-like genes on larval diapause and adult lifespan in Caenorhabditis elegans."

Yukiko Yonezawa, Yasuo Kimura, Kenji Gouda, Tsuyoshi Kawano

[International Worm Meeting, 2007]

In Caenorhabditis elegans, the insulin/insulin-like growth factor-I signaling (IIS) pathway regulates larval diapause, adult lifespan, fat metabolism, and stress-resistance. C. elegans has 38 putative insulin-like peptides which are grouped into type-<font face=symbol>a</font> , -<font face=symbol>b</font> , and -<font face=symbol>g</font> according to their predicted disulfide bond pattern.1) The type-<font face=symbol>g</font> peptides have the same pattern as mammalian insulin family peptides. On the other hand, the type-<font face=symbol>b</font> peptides have one additional disulfide bond to the canonical three. In 2003, Murphy and co-workers reported that ins-7 categorized into the type-<font face=symbol>b</font> has relevancy on regulation of dauer larva formation and adult lifespan.2) This fact suggested that other type-<font face=symbol>b</font> genes also have physiological functions. Therefore, we attempted to investigate all of the type-<font face=symbol>b</font> genes by RNAi knockdown and/or gene-disruption. In this meeting, we will show positive/nagative regulation of larval diapause and/or adult lifespan by the type-<font face=symbol>b</font> genes. 1) Pierce, S. B., et al. (2001) Genes Dev. 15:672. 2) Murphy, C. T. et al. (2003) Nature 424:277.

Voegtlin, Thomas et al. (2011) International Worm Meeting "An Open-Source Neuromechanical Model of C. Elegans Locomotion."

Cohen, Netta, Voegtlin, Thomas

[International Worm Meeting, 2011]

A neuromechanical model of locomotion in C. elegans was recently proposed by Jordan H. Boyle [1]. One of the main results is that both swimming and crawling can be generated by a single neural circuit, reflexively modulated by the environment. This supports the known experimental results showing that different forms of C. elegans forward locomotion (e.g., swimming and crawling) can be described by a modulation of a single biomechanical gait [2]. The modelling result illustrates the importance and the potential of neuromechanical simulations for the analysis of the worm's behaviour. In order to continue this work, and to make it usable by a broader audience, we have developed a similar neuromechanical model of the worm using CLONES. CLONES (Closed Loop Neural Simulation) is an open source framework for neuromechanical simulations. CLONES implements a communication interface between a neural simulator, called BRIAN [3], and a physics engine for biomedical applications, called SOFA [4]. BRIAN and SOFA are open-source simulators that are easy to use and provide high performance. Our implementation of the worm's locomotion reproduces the neural model described in [1]. However, there are two key differences between the original physical model and our implementation. Firstly, Boyle's model considers that the body of the worm has zero mass (a low Reynolds number approximation). In contrast, the SOFA simulator allows us to integrate equations with mass and inertia. Secondly, the original model uses rigid rods of fixed length orthogonal to the body axis (approximating the incompressibility of the body due to high internal pressure). In SOFA rigid rods are modeled as springs of very high stiffness. The physical system simulated in SOFA is described using a XML syntax. The neural network model interpreted by BRIAN is written in Python, using MATLAB-like syntax. Thus, the model is completely interpreted, and it is possible to visualize/interact with the simulation during runtime. Physical environments containing obstacles or chemical concentration gradients can be defined easily. References 1. Boyle JH: C. elegans locomotion: an integrated approach. PhD thesis, university of Leeds, 2009 2. Berri S, Boyle JH, Tassieri M, Hope IA and Cohen N, Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait HFSP J 3:186, 2009; 3. Goodman DF, Brette R: Brian: a simulator for spiking neural networks in Python. Front Neuroinform 2:5, 2008 4. Allard J, Cotin S, Faure F, Bensoussan PJ, Poyer F, Duriez C, Delingette H, Grisoni L: SOFA - an Open Source Framework for Medical Simulation. Medicine Meets Virtual Reality (MMVR'15), pp. 13-18, 2007.

Frederick Tan et al. (2001) International C. elegans Meeting "Identifying promoter motifs and predicting gene expression patterns in C. elegans using data mining tools."

Dung Phu, Julia Krushkal, Carolina Ruiz, Frederick Tan, Elizabeth Ryder, Ian Pushee, Brian Murphy

[International C. elegans Meeting, 2001]

Kenji Gouda et al. (2007) International Worm Meeting "Redundant function of Caenorhabditis elegans insulin-like genes in larval diapause and adult lifespan."

Keiko Gengyo-Ando, Yasuo Kimura, Kenji Gouda, Yohei Matsunaga, Tsuyoshi Kawano, Shohei MItani

[International Worm Meeting, 2007]

The insulin/insulin-like growth factor-I signaling (IIS) pathway regulates larval diapause and adult lifespan in Caenorhabditis elegans. To date, many of the 38 insulin-like genes have been identified1), and a few of the genes have been investigated to identify their physiological function by RNAi knockdown. For instance, Murphy and co-workers reported that ins-7 RNAi knockdown induces larva diapause and an extended lifespan.2) In our previous study, we disrupted Ceinsulin-1 (ins-18) and Ceinsulin-2 (ins-17), and elucidated their function on larval diapause and adult lifespan. Disruption of ins-17 and/or ins-18 reduced dauer larva formation caused by a crude extract of dauer-inducing pheromone, while the disruption showed no effect on adult lifespan. To investigate redundant function of the insulin-like genes, we disrupted the ins-7, and then established multiple-gene-disrupted animals. Disruption of ins-7 induced an extended lifespan as expected. Disruption of ins-7 and ins-17 also revealed lifespan extension, suggesting that ins-17 is not relevant to lifespan regulation. On the other hand, disruption of ins-7 and ins-18 revealed no lifespan extension, indicating that ins-18 is necessary for lifespan extension induced by the gene-disruption of ins-7. Now we are measuring lifespan of each gene-disrupted animal under daf-2(-) conditions. 1) Pierce, S. B. et al. (2001) Genes Dev. 15:672. 2) Murphy, C. T. et al. (2003) Nature 424:277.

Yueyi I Liu et al. (2004) West Coast Worm Meeting "Global Identification of C. elegans Regulatory Motifs"

Stuart K Kim, Yueyi I Liu

[West Coast Worm Meeting, 2004]

Regulatory motifs are short sequences of DNA that regulate the level, timing, and location of gene expression. Identifying these motifs and their functions is crucial in our understanding of gene regulation and disease processes. We developed CompareProspector, a motif-finding program that takes advantage of cross-species sequence comparison to identify putative regulatory motifs from sets of co-regulated genes [1] . We applied CompareProspector to 30 sets of genes with very similar patterns of expression, identified from the C. elegans topomap [2] and individual DNA microarray experiments. The statistical significance of each candidate motif identified was evaluated using criteria such as motif enrichment-the ratio of prevalence of the motif in a given set of promoters to its prevalence elsewhere in the genome, and the expression coherence of genes with the motif. We identified twelve significant regulatory motifs, three of which have literature evidence confirming they are true regulatory motifs. Overall, these twelve motifs are found in the upstream regulatory regions of 2970 different genes, and may be involved in gene regulation in 24 clusters of co-expressed genes. The first known motif, with the consensus TGATAA, matches the consensus of known binding sites for GATA factors. As GATA factors are known to be involved in worm intestine development [3] and hyperdermis development, it is not surprising that the GATA motif is identified from a set intestine-specific genes (F. Pauli, unpublished), mount08 of the topomap, which is enriched in genes from the intestine, and several collagen-related datasets (mount14, 17, and 35 of the topomap). We correctly identified GATA sites in the promoters of genes known to be regulatory by GATA factors. Interestingly, the GATA motif is also identified from several data sets involved in the aging process. This result parallels that of Murphy and colleagues, who independently identified this motif from their data set of DAF-16 target genes [4] . Both our result and the result from Murphy suggest that GATA factors may be involved in worm aging. Motif 2, which is identified in the two heat shock-related data sets, matches the consensus of known binding sites for heat shock factors [5] . Motif 3 matches the consensus of heat shock associated sites (HSAS), a motif that was first predicted computationally to be involved in the heat shock process [6] and later experimentally validated to be involved in ethanol stress response (14 th International C. elegans Conference abstract 1113C). We are currently in the process of validating the rest of the motifs and their individual binding sites using mutagenesis studies of promoters with predicted motifs. 1. Liu, Y., Liu, X.S., Wei, L., Altman, R.B. and Batzoglou, S. (2004) Eukaryotic regulatory element conservation analysis and identification using comparative genomics . Genome Res. 14 , 451-8. 2. Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J.M., Eizinger, A., Wylie, B.N. and Davidson, G.S. (2001) A gene expression map for Caenorhabditis elegans . Science. 293 , 2087-92. 3. Maduro, M.F. and Rothman, J.H. (2002) Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm . Dev Biol. 246 , 68-85. 4. Murphy, C.T., McCarroll, S.A., Bargmann, C.I., Fraser, A., Kamath, R.S., Ahringer, J., Li, H. and Kenyon, C. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans . Nature. 424 , 277-83. 5. Amin, J., Ananthan, J. and Voellmy, R. (1988) Key features of heat shock regulatory elements . Mol Cell Biol. 8 , 3761-9. 6. GuhaThakurta, D., Palomar, L., Stormo, G.D., Tedesco, P., Johnson, T.E., Walker, D.W., Lithgow, G., Kim, S. and Link, C.D. (2002) Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods . Genome Res. 12 , 701-12 .

Lee, Inhwan et al. (2013) International Worm Meeting "Epigentic regulation of L1 longevity."

You, Young-jai, Lee, Inhwan

[International Worm Meeting, 2013]

Animals encounter food infrequently and starvation is a common physiological state in their natural circumstance [1]. Hatching in the absence of food, worms arrest their development at the L1 stage and survive starvation more than two weeks [2]. It was shown that adult longevity is regulated epigenetically by chromatin alterations and the genes that regulate epigenetics [3]. Here, we investigate whether L1 longevity is also regulated epigenetically. When we measured various histone modifications using Western blot, we found histone 3 lysine 4 tri-methylation, known to be a modification to activate gene transcription, is increased in L1 starvation. Moreover, mutants of set-2, which encodes a histone 3 lysine 4 tri-methyl transferase that functions in adult longevity [3], has reduced L1 longevity. There are several genes essential for normal L1 longevity, such as aak-2 and daf-16. Based on our data, we hypothesize that chromatin remodeling through histone 3 lysine 4 tri-methylation regulates transcription of genes involved in L1 longevity. Currently we are testing this hypothesis by measuring expression levels these genes by ChIP-qPCR during L1 starvation in set-2 mutant. References [1] Brian H. Lee, Plus Genetics, 2008 [2] Inhwan Lee, Plus One, 2012 [3] Eric L. Greer, Nature, 2010.

Diana David-Rus et al. (2004) East Coast Worm Meeting "Tracking the mid-life crisis of C. elegans"

Uri Einav, Patrick Nef, Eytan Domany, Peter J Schmeissner, Monica Driscoll, Diana David-Rus, Christophe Grundschober, Beate Hartmann, Garth Patterson

[East Coast Worm Meeting, 2004]

In an effort to better understand the biology of aging with an emphasis on mid-life changes that influence healthspan, we have undertaken a DNA microarray analysis of global gene expression profiles over time using Affymetrix gene chip arrays. Our experiment includes time points including the reproductive and post-reproductive periods, with a series of consecutive mid-life time points being covered. Studies in our lab and others have suggested that critical events during the mid-life of the nematode can influence the aging of this organism. For our analyses, we used supervised and unsupervised methods, including a clustering method developed in the Domany lab. Interestingly, we find a sharp change in the transcriptional levels of numerous genes at about 10 days post egg-lay. This abrupt change in gene expression on day 10 is consistent with a window of time identified previously by our lab as a time when mutations in the age-1 gene are able to delay the deterioration of muscle tissue (Herndon et al., 2002, Nature, 419: 808-14). The abrupt change also correlates with a transition point at which autofluorescent biomarkers accumulate (see abstract by Gerstbrein et al., this volume). Since two similar microarray experiments already have been performed (Lund et al., 2001, Curr Biol. 12(18): 1566-73; Murphy et al., 2003, Nature, 424(6946):277-83), we attempted a detailed cross-comparison between data from all three experiments, using non-parametric techniques. Again, a dramatic change in gene expression was observed for some genes at time points corresponding to our day 10 time point. Approximately 100 genes show significant changes in gene expression over adulthood in all three studies. These expression changes might be relevant to rapid end-stage deterioration in old nematodes.

Diana David-Rus et al. (2004) East Coast Worm Meeting "Tracking the mid-life crisis of C. elegans"

Christophe Grundschober, Garth Patterson, Uri Einav, Eytan Domany, Beate Hartmann, Patrick Nef, Peter J Schmeissner, Diana David-Rus, Monica Driscoll

[East Coast Worm Meeting, 2004]

In an effort to better understand the biology of aging with an emphasis on mid-life changes that influence healthspan, we have undertaken a DNA microarray analysis of global gene expression profiles over time using Affymetrix gene chip arrays. Our experiment includes time points including the reproductive and post-reproductive periods, with a series of consecutive mid-life time points being covered. Studies in our lab and others have suggested that critical events during the mid-life of the nematode can influence the aging of this organism. For our analyses, we used supervised and unsupervised methods, including a clustering method developed in the Domany lab. Interestingly, we find a sharp change in the transcriptional levels of numerous genes at about 10 days post egg-lay. This abrupt change in gene expression on day 10 is consistent with a window of time identified previously by our lab as a time when mutations in the age-1 gene are able to delay the deterioration of muscle tissue (Herndon et al., 2002). The abrupt change also correlates with a transition point at which autofluorescent biomarkers accumulate (see abstract by Gerstbrein et al., this volume). Since two similar microarray experiments already have been performed (Lund et al., 2001, Curr Biol. 12(18): 1566-73; Murphy et al., 2003, Nature, 424(6946):277-83), we attempted a detailed cross-comparison between data from all three experiments, using non-parametric techniques. We found approximately 100 genes showing changes in gene expression over adulthood common to all three studies. These expression changes might be relevant to rapid end-stage deterioration in old nematodes.

Diana David-Rus et al. (2005) International Worm Meeting "A search for mid-life gene expression changes that might influence healthspan"

Patrick Nef, Peter J Schmeissner, Beate Hartmann, Diana David-Rus, Monica Driscoll, Eytan Domany, Christophe Grundschober, Garth Patterson, Uri Einav

[International Worm Meeting, 2005]

Studies in our and other labs have suggested that critical events during the mid-life of the nematode can influence the aging and lifespan of this organism. In an effort to better understand the biology of aging with an emphasis on mid-life changes that influence healthspan, we performed a DNA microarray analysis of global gene expression profiles over time using Affymetrix gene chip arrays. Our experiment includes time points covering the reproductive and post-reproductive periods, with a series of consecutive mid-life time points. For our analyses, we used unsupervised methods, including a clustering method called Two-Way SPC (see. Domany et al.,Phys. Rev.Lett 76,3521). The method is actually a new approach to clustering, based on rules which can be described with help of statistical mechanics. Interestingly, we do find a sharp change in the transcriptional levels of numerous genes at about 10 days post egg-lay. This abrupt change in gene expression on day 10 of adulthood is consistent with a transition point at which potentially harmful autofluorescent biomarkers accumulate at accelerated rates (see abstract by Gerstbrein et al.) and at which age-related muscle decline may also accelerate. Since similar microarray experiments have been published (Lund et al., 2001, Curr Biol. 12(18): 1566-73; Murphy et al., 2003, Nature, 424(6946):277-83), we attempted a detailed cross-comparison between data from all three experiments, using again unsupervised, as well as supervised techniques. From the supervised technique we found approximately 100 genes that change expression during adult lifespan that are common to all three studies. We consider that these expression changes might be relevant to rapid end-stage deterioration in old nematodes.

Paramita Ray et al. (2004) Mid-west Worm Meeting "ceh-28 is required for feeding in C. elegans"

Peter G Okkema, Paramita Ray

[Mid-west Worm Meeting, 2004]

NK-2 family homeobox genes are important developmental regulators in many organisms. The C. elegans genome contains 4 members of this gene family ( ceh-22, ceh-24, ceh-27 and ceh-28 ). ceh-22 is expressed in the pharyngeal muscles where it regulates gene expression with the pan-pharyngeal factor PHA-4, and we are determining if additional NK-2 family members function similarly in other pharyngeal cell types. Brian Harfe and Andy Fire have previously shown a ceh-28::gfp transcriptional fusion is expressed exclusively in the M4 pharyngeal neuron. We have similarly found a ceh-28::gfp translational fusion containing 3.7 kb of 5' flanking DNA is expressed in M4. Expression initiates during embryogenesis in two cells, and we speculate these cells are M4 and its sister cell, which dies during normal development. We are currently verifying the expression pattern of the endogenous ceh-28 gene using anti-CEH-28 antibodies. M4 is a motor neuron essential for pharyngeal isthmus peristalsis and feeding. To functionally characterize ceh-28 , we have isolated a deletion mutant ceh-28(cu11) . This deletion removes much of the ceh-28 homeobox and is likely a null allele. Homozygous ceh-28(cu11) strains can be maintained, although these mutants appear starved and exhibit slow growth and partially penetrant larval lethality. Similar phenotypes were observed in ceh-28(RNAi) animals. All ceh-28 mutant worms have a stuffed pharynx phenotype similar to animals in which M4 has been killed by laser ablation (Avery and Horvitz, 1987), suggesting M4 is defective. We are currently examining M4 differentiation, morphology and function in ceh-28(cu11) mutants to understand the role of ceh-28 in pharyngeal development.