Marcelo C Santos et al. (2003) International Worm Meeting "Modelling of C. elegans pharyngeal neural network"

Marcelo C Santos, Kristian Lindgren, Marc Pilon

[International Worm Meeting, 2003]

This work describes a dynamical model of the neural circuitry and muscles for the pharynx of C. elegans. Our goal is to build a model of the pharyngeal neural network dynamics with respect to the generation of signals (action potentials) for controlling the feeding. We also include in the model the processing of feedback from the sensory endings in the muscles. A dynamical system of two variables is used to mimic the myogenic rhythm of the pharyngeal muscles.A set of simulations is described in detail where some connections are tuned to mimic apropriate behaviour. We also try to use a genetic algorithm to tune parameters for the system, where a population of pharynx models is evolved through random mutation and crossover.Our model is limited by the information about the pharynx dynamics that we could gather from published literature, and we were successfull in building and simulating a simple model. The simulations mimic some behaviours observed in the laboratory with respect to feeding and its control by the pharyngeal neural circuitry. In the poster, we give a detailed description of the pharyngeal aspects and behaviour that we would like to model, and describe what we can model using only published data.

Santos S I C O et al. (2008) European Worm Meeting "Ultra-fast optics: a novel tool to study C. elegans"

Mathew M, Santos S I C O

[European Worm Meeting, 2008]

In the last decade nonlinear techniques using ultra-fast optics has emerged. as a novel tool for biological investigation. We present the use of these. techniques in studying C. elegans viz. Two Photon Microscopy (TPEFM),. Harmonic Generation Microscopy (SHGM & THGM) and Ultra-fast laser Induced. Nanosurgery.. Nonlinear imaging techniques are superior to commonly used techniques with. respect to penetration depth, photobleaching and signal to noise ratio,. owing to the use of very high intensity low average power ultra-short near. infra red (NIR) pulses.. In the last few years these high intensity NIR pulses have also been used. to precisely target, cut and manipulate sub-cellular structures with sub-. micrometer resolution. This offers the possibility of in vivo surgery. without collateral damage.

P Dal Santo et al. (1999) International C. elegans Meeting "The IP3 Receptor is a Timekeeper for the Defecation Cycle Rhythm"

EM Jorgensen, P Dal Santo, MA Logan, AD Chisholm

[International C. elegans Meeting, 1999]

The C. elegans defecation cycle is characterized by the activation of three distinct muscle contractions every 45-50 seconds. How is cycle time maintained? To address this question we identified and characterized mutants with abnormal cycle times. Specifically, we cloned the dec-4 gene and demonstrated that it encodes the inositol trisphosphate receptor (IP 3 receptor). Mutations in the IP 3 receptor alter the timing of the defecation cycle. Null mutations eliminate the cycle, hypomorphic mutants have a slow cycle, and overexpression of the protein results in a fast cycle time. The IP 3 receptor is expressed in several different tissues including the pharynx, the somatic gonad, and the intestine. Using mosaic analysis we demonstrated that IP 3 receptor expression in the intestine is necessary and sufficient for normal timing of the cycle. This indicates that the periodic muscle contractions can be controlled non-autonomously from the intestine. IP 3 receptors are localized to the endoplasmic reticulum and are known to function as calcium release channels. Activation of the channel by a phospholipid signaling pathway leads to the production of temporally and spatially regulated calcium oscillations. Our current data predicts a model in which calcium oscillations in the intestine trigger the defecation motor program. To test this model we injected calcium-sensitive dyes into the posterior intestinal cells of adult animals. Our results demonstrate that calcium oscillations occur in the intestine. The frequency of calcium oscillations are consistent with the timing of the defecation cycle and peak calcium levels occur just before the onset of the muscle program. We conclude that periodic calcium release in the intestinal cells initiates the muscle contractions of the defecation cycle and that the IP 3 receptor is a central component of the timekeeping mechanism that regulates this behavioral rhythm.

Paola Dal Santo et al. (2001) International C. elegans Meeting "pbo-4 and pbo-5 define a novel signaling pathway required to initiate the posterior body contraction"

Paola Dal Santo, Erik M Jorgensen

[International C. elegans Meeting, 2001]

The C. elegans defecation cycle is characterized by the activation of three distinct muscle contractions. Every 50 seconds, a cycle begins with the posterior body contraction, followed by the anterior body contraction, and finally, by the enteric muscle contraction. Laser ablation studies have shown that two GABAergic motor neurons, AVL and DVB, are required the anterior body contraction and the enteric muscle contraction. Neuronal ablations did not affect cycle timing or the execution of the posterior body contraction. In addition, mutations that disrupt neurotransmission and secretion also have no effect on the posterior body contraction. Together, these results suggest that a non-neuronal signal is required for proper timing of the cycle and initiation of the posterior body contraction. We demonstrated that the defecation cycle is regulated by an endogenous clock that resides in the intestine. Specifically, mutations in the inositol trisphosphate (IP 3 ) receptor, an intracellular calcium channel, eliminate clock function. Moreover, we observe calcium spikes in the intestine that correlate with the timing of the cycle and immediately precede a posterior body contraction. These data suggest that a calcium spike may stimulate the release of a signal from the intestine that could then be received by the body muscles. How does a calcium signal in the intestine trigger a muscle contraction without a neuronal intermediate? To identify the nature of the signal and its target, we screened for mutations that specifically eliminate the posterior body contraction. From this screen we identified the pbo-4 and pbo-5 genes. We cloned pbo-4 and demonstrated that it encodes a protein homologous to Na + /H + exchangers (NHEs). Plasma membrane NHEs mediate the exchange of one Na + ion into the cell for one H + ion out, and thus acidify the extracellular environment. In mammalian cells, some isoforms are activated by calcium via calmodulin binding. Similarly, PBO-4 contains a potential Ca 2+ /calmodulin binding domain on the C-terminal, cytosolic portion of the protein that could mediate calcium signaling. Interestingly, pbo-4 expression is restricted to the posterior intestine. This suggests that PBO-4 activity is part of the signal that initiates the posterior body contraction. What is the target? pbo-5 encodes a novel, ligand-gated ion channel that is distantly related to acetylcholine receptors. pbo-5 expression is restricted to the posterior muscles that lie adjacent to the PBO-4 expressing cells. These data predict a model in which a calcium spike activates PBO-4 to secrete protons from the intestine. PBO-5 might then recognize this signal, depolarize the body muscles, and initiate the posterior body contraction. We are currently characterizing the electrophysiological properties of PBO-5 to determine whether it forms a homomeric channel and to test whether changes in pH affect receptor activation.

Dal Santo P et al. (1997) International C. elegans Meeting "pbo-4 AND pbo-5 DEFINE FIVE COMPLENTATION GROUPS REQUIRED TO INITIATE THE POSTERIOR BODY CONTRACTION OF THE DEFECATION CYCLE."

Dal Santo P, Jorgensen EM

[International C. elegans Meeting, 1997]

The C. elegans defecation cycle is characterized by three sequential muscle contractions, the posterior body contraction, the anterior body contraction, and the enteric muscle contraction. Every 50 seconds a cycle is initiated by a posterior body contraction which begins at the tip of the tail and is propagated anteriorly toward the vulva. Mutants defective in synthesis and secretion of neurotransmitter, axon outgrowth and muscle excitability disrupt the anterior body contraction or enteric muscle contraction but do not affect the posterior body contraction. Similarly, ablation of neurons in the tail do not disrupt the posterior body contraction. These data suggest that the posterior body contraction is not initiated by an excitatory signal from a neuron, but rather, by secretion of a diffusible signal or by transmission of a signal through the gap junctions of individual muscle cells. To identify this potentially novel signal and the mechanism by which it initiates a cycle, we screened for mutations that specifically eliminate the posterior body contraction. We identified 20 new pbo alleles. In addition to those previously isolated, we have a total of 34 alleles that map to two genetic loci, pbo-4 and pbo-5. Complementation analysis between alleles revealed that pbo-5 can be further divided into four complementation groups. Some mutations eliminate multiple complementation groups and exhibit a polar effect such that downstream complementation groups are also eliminated. These data suggest an unusual organization of the pbo-5 locus. We are currently conducting a molecular characterization of pbo-5 to determine whether it is a single gene encoding a multifunctional protein, whether four different products arise from complex splicing, or whether pbo-5 represents four separate but tightly linked genes.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Oomura, S. et al. (2019) International Worm Meeting "Early embryogenesis of C. inopinata, a sibling species of C.elegans."

Matsumura, Y., Haruta, N., Hoshi, Y., Sugimoto, A., Oomura, S.

[International Worm Meeting, 2019]

C. inopinata is a newly discovered sibling species of C. elegans. Despite their phylogenetic closeness, they have many differences in morphology and ecology. For example, while C. elegans is hermaphroditic, C. inopinata is gonochoristic; C. inopinata is nearly twice as long as C. elegans. A comparative analysis of C. elegans and C. inopinata enables us to study how genomic changes cause these phenotypic differences. In this study, we focused on early embryogenesis of C. inopinata. First, by the microparticle bombardment method we made a C. inopinata line that express GFP::histone in whole body, and compared the early embryogenesis with C. elegans by DIC and fluorescent live imaging. We found that the position of pronuclei and polar bodies were different between these two species. In C. elegans, the female and male pronuclei first become visible in anterior and posterior sides, respectively, then they meet at the center of embryo. On the other hand, the initial position of pronuclei were more closely located in C. inopinata. Also, the polar bodies usually appear in the anterior side of embryo in C. elegans, but they appeared at random positions in C. inopinata. Therefore, we infer that C. inopinata may have a different polarity formation mechanism from that in C. elegans. We are also analyzing temperature dependency of embryogenesis in C. inopinata, whose optimal temperature is ~7 degree higher than that in C. elegans.

Karin Kiontke et al. (2008) Development & Evolution Meeting "New Phylogeny Of Caenorhabditis Including Recently Discovered Species"

David Fitch, Karin Kiontke, Marie-Anne FELIX

[Development & Evolution Meeting, 2008]

Recently, seven new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to 17, 10 of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10, 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Whereas none of them is likely to be the sister species of C. elegans, we now know of two close relatives of C. briggsae-C. sp. 5 and C. sp. 9. C. sp. 9 can hybridize with C. briggsae in the laboratory [see abstract by Woodruff et al.]. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. This species is easier to cultivate than C. japonica and may be a better candidate for comparative experimental work. Two of the new species branch off before C. japonica as sister species of C. sp. 3 and C. drosophilae+C. sp. 2, respectively. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and five from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last two years. There is no indication that we are even close to knowing all species in this genus.

Schartner, Caitlin M. et al. (2015) International Worm Meeting "X-chromosome evolution: divergence of X-sequence motifs that drive dosage compensation across Caenorhabditis species."

Meyer, Barbara J., Lo, Te-Wen, Schartner, Caitlin M.

[International Worm Meeting, 2015]

Dosage compensation (DC) across Caenorhabditis species exemplifies an essential process that has undergone rapid co-evolution of protein-DNA interactions central to its mechanism. In C. elegans, recruitment elements on X (rex sites) recruit a condensin-like DC complex (DCC) to hermaphrodite X chromosomes to balance gene expression between the sexes. Recruitment assays in vivo showed that C. elegans rex sites do not recruit the DCC of C. briggsae, and vice versa. To understand how DC complexes and X chromosomes evolved to use different X targeting sequences, we compared DCC subunits and binding sites in C. elegans to those in three species of the C. briggsae clade (15-30 MYR diverged): C. briggsae, its close relative C. nigoni (C. sp. 9), and C. tropicalis (C. sp. 11). By raising antibodies and introducing endogenous tags with TALENs or CRISPR/Cas9, we showed that homologs of both SDC-2, the pivotal X targeting factor, and DPY-27, a DCC-specific condensin subunit, bind X chromosomes of XX animals. Although the DCC shares key components across these four species, the binding sites differ. First, ChIP-seq studies in C. briggsae and C. nigoni identified DCC binding sites that are homologous across these close relatives but differ from C. elegans sites in sequence and location. Second, C. elegans sites use motifs enriched on X (MEX and MEXII) to drive DCC binding, but these motifs are not in C. briggsae or C. nigoni DCC sites and are not X-enriched. Third, we found an X-enriched motif at DCC binding sites of C. briggsae and C. nigoni that is not X-enriched in C. elegans. An oligo with the C. briggsae motif recruits the DCC in C. briggsae, but a similar oligo lacking the motif fails to recruit, establishing the importance of the motif. Fourth, another motif was found in C. briggsae and C. nigoni that shares a few nucleotides with MEX, but its functional divergence was shown by C. elegans recruitment assays. Fifth, two endogenous C. briggsae X-chromosome regions with strong C. elegans MEX motifs fail to recruit the C. briggsae DCC, as assayed by ChIP-seq and recruitment assays. None of these DCC motifs is enriched on the C. tropicalis draft X sequence, supporting further binding site divergence within the C. briggsae clade. Ongoing ChIP-seq studies in C. tropicalis will help determine how C. elegans and C. briggsae clade motifs are evolutionarily related. Comparison of DCC targeting mechanisms across these four species allows us to characterize a rarely captured event: the recent co-evolution of a protein complex and its rapidly diverged target sequences across an entire X chromosome.

Kiontke, Karin C. et al. (2009) International Worm Meeting "New Caenorhabditis species: phylogeny and evolution."

Fitch, David H. A., Felix, Marie-Anne, Kiontke, Karin C.

[International Worm Meeting, 2009]

Recently, nine new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to nineteen, eleven of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10 and 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Although none of them is the sister species of C. elegans, C. sp. 5 and C. sp. 9 are close relatives of C. briggsae. C. sp. 9 can hybridize with C. briggsae in the laboratory. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. Three of these species, C. sp. 7, C. sp. 9 and C. sp. 11 have been chosen for genome sequencing. Four further new species branch off before C. japonica within a monophyletic clade which also comprises C. sp. 3 and C. drosophilae. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and seven from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. Other characters, like the shape of the stoma and the male tail, introns, susceptibility to RNAi and genome size are being evaluated in the context of the phylogeny. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last few years. There is no indication that we are even close to knowing all species in this genus.