Marcelo C Santos et al. (2003) Worm Breeder's Gazette "Modelling of C. elegans pharyngeal neural network"

Marc Pilon, Kristian Lindgren, Marcelo C Santos

[Worm Breeder's Gazette, 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.

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-Ocana C et al. (2002) J Biol Chem "Uptake of exogenous coenzyme Q and transport to mitochondria is required for bc1 complex stability in yeast coq mutants."

Clarke CF, Santos-Ocana C, Padilla S, Navas P, Do TQ

[J Biol Chem, 2002]

Coenzyme Q (Q) is an essential component of the mitochondrial respiratory chain in eukaryotic cells but also is present in other cellular membranes where it acts as an antioxidant. Because Q synthesis machinery in Saccharomyces cerevisiae is located in the mitochondria, the intracellular distribution of Q indicates the existence of intracellular Q transport. In this study, the uptake of exogenous Q(6) by yeast and its transport from the plasma membrane to mitochondria was assessed in both wild-type and in Q-less coq7 mutants derived from four distinct laboratory yeast strains. Q(6) supplementation of medium containing ethanol, a non-fermentable carbon source, rescued growth in only two of the four coq7 mutant strains. Following culture in medium containing dextrose, the added Q(6) was detected in the plasma membrane of each of four coq7 mutants tested. This detection of Q(6) in the plasma membrane was corroborated by measuring ascorbate stabilization activity, as catalyzed by NADH-ascorbate free radical reductase, a transmembrane redox activity that provides a functional assay of plasma membrane Q(6). These assays indicate that each of the four coq7 mutant strains assimilate exogenous Q(6) into the plasma membrane. The two coq7 mutant strains rescued by Q(6) supplementation for growth on ethanol contained mitochondrial Q(6) levels similar to wild type. However, the content of Q(6) in mitochondria from the non-rescued strains was only 35 and 8%, respectively, of that present in the corresponding wild-type parental strains. In yeast strains rescued by exogenous Q(6), succinate-cytochrome c reductase activity was partially restored, whereas non-rescued strains contained very low levels of activity. There was a strong correlation between mitochondrial Q(6) content, succinate-cytochrome c reductase activity, and steady state levels of the cytochrome c(1) polypeptide. These studies show that transport of extracellular Q(6) to the mitochondria operates in yeast but is strain-dependent. When Q biosynthesis is disrupted in yeast strains with defects in the intracellular transport of exogenous Q, the bc(1) complex is unstable. These results indicate that delivery of exogenous Q(6) to mitochondria is required fore activity and stability of the bc(1) complex in yeast coq mutants.

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.

Rodrigues AJ et al. (2007) FASEB J "Functional genomics and biochemical characterization of the C. elegans orthologue of the Machado-Joseph disease protein ataxin-3."

Ailion M, Rodrigues AJ, Maciel P, Geschwind DH, Coppola G, Santos C, Costa MD, Sequeiros J

[FASEB J, 2007]

Machado-Joseph disease (MJD) is the most common dominant spinocerebellar ataxia. MJD is caused by a CAG trinucleotide expansion in the ATXN3 gene, which encodes a protein named ataxin-3. Ataxin-3 has been proposed to act as a deubiquitinating enzyme in the ubiquitin-proteasome pathway and to be involved in transcriptional repression; nevertheless, its precise biological function(s) remains unknown. To gain further insight into the function of ataxin-3, we have identified the Caenorhabditis elegans orthologue of the ATXN3 gene and characterized its pattern of expression, developmental regulation, and subcellular localization. We demonstrate that, analogous to its human orthologue, C. elegans ataxin-3 has deubiquitinating activity in vitro against polyubiquitin chains with four or more ubiquitins, the minimum ubiquitin length for proteasomal targeting. To further evaluate C. elegans ataxin-3, we characterized the first known knockout animal models both phenotypically and biochemically, and found that the two C. elegans strains were viable and displayed no gross phenotype. To identify a molecular phenotype, we performed a large-scale microarray analysis of gene expression in both knockout strains. The data revealed a significant deregulation of core sets of genes involved in the ubiquitin-proteasome pathway, structure/motility, and signal transduction. This gene identification provides important clues that can help elucidate the specific biological role of ataxin-3 and unveil some of the physiological effects caused by its absence or diminished function.--Rodrigues, A-J., Coppola, G., Santos, C., do Carmo Costa, M., Ailion, M., Sequeiros, J., Geschwind, D. H., Maciel, P. Functional genomics and biochemical characterization of the C. elegans orthologue of the Machado-Joseph disease protein ataxin-3.

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.

Winkenbach LP et al. (2019) RNA Biol "Todos Santos small RNA symposium."

Claycomb JM, Doser R, Pasquinelli AE, Winkenbach LP, Reed KJ, Phillips CM

[RNA Biol, 2019]

Worm biologists from the United States, Canada, and the United Kingdom gathered at the Colorado State University Todos Santos Center in Baja California Sur, Mexico, April 3-5, 2019 for the Todos Santos Small RNA Symposium. Meeting participants, many of whom were still recovering from the bomb cyclone that struck a large swath of North America just days earlier, were greeted by the warmth and sunshine that is nearly ubiquitous in the sleepy seaside town of Todos Santos. With only 24 speakers, the meeting had the sort of laid-back vibe you might expect amongst the palm trees and ocean breeze of the Pacific coast of Mexico. The meeting started with tracing the laboratory lineages of participants. Not surprisingly, the most common parental lineages represented at the meeting were Dr. Craig Mello, Dr. Gary Ruvkun, and Dr. Victor Ambros, whom, together with Dr. Andy Fire and Dr. David Baulcombe, pioneered the small RNA field. In sad irony, on the closing day of the meeting, participants were met with the news of Dr. Sydney Brenner's passing. By establishing the worm, <i>Caenorhabditis elegans</i>, as a model system Dr. Brenner paved the way for much of the research discussed here.

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.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.