[
West Coast Worm Meeting,
2002]
Amphetamine as well as other psychostimulants such as cocaine and methylphenidate have a high potential for abuse. Their primary mechanism of action is the inhibition of the clearance of dopamine from the synapse via the dopamine plasma membrane transporter (DAT). The CeDAT has been cloned and shown in vitro to bind both amphetamine and cocaine (LD Jayanthi et al., Mol Pharm 54:601-9, 1998). There is also evidence that even a single exposure to psychostimulants can produce long term potentiation on the mesolimbic dopamine system (Ungless et al., Nature 411:583-587, 2001) which is part of the reward pathway activated by drugs of abuse. These synaptic changes may be important for the subsequent addiction to these types of drugs. We are interested in characterizing further the mechanisms that contribute to the effects of amphetamine modulation on dopaminergic pathways. To examine the effects of amphetamine on synaptic transmission in C. elegans we pretreated worms with amphetamine in liquid culture prior to transferring animals to agar plates for behavioral analysis. We found that amphetamine pretreatment resulted in suppression of locomotion, egg laying, and pharyngeal pumping in a dose dependent manner. These behavioral effects are similar to those produced by exposing animals to exogenous dopamine, suggesting amphetamine is acting on dopaminergic pathways. We then initiated a genetic screen to identify mutants that showed reduced sensitivity to the effects of amphetamine on locomotion. We have identified eight candidate mutants and are in the process of mapping and cloning the genes responsible for their resistance. Most of these mutants are visibly wild type with the exception of two of the mutants which appeared hyperactive for locomotion. This hyperactivity was confirmed by assaying for aldicarb sensitivity. The other mutants were found to be either wild-type or resistant to the effect of aldicarb on movement. One of these mutants also displayed reduced sensitivity to the effects of amphetamine on pharyngeal pumping and two other mutants displayed reduced sensitivity to the effects of amphetamine on egg laying. We are characterizing the mutants from our screen for defects in dopamine mediated behaviors. Preliminary results indicate that two of these mutants are defective in the dopamine dependent basal slowing response on bacteria (Sawin et al., Neuron 26:619-631, 2000).
[
Worm,
2016]
Dorsal intercalation is a coordinated cell migration event that rearranges hypodermal cells during C. elegans embryogenesis, and that resembles cell intercalation in many systems from flies to mice. Despite its conservation, the molecular mechanisms that govern dorsal intercalation in worms have remained elusive. Here, we comment on our recent publication, Walck-Shannon etal.,(1) which begins to spatially map the molecular requirements for intercalation. First, we provide a historical perspective on the factors that have previously hampered the study of dorsal intercalation. Next, we provide a summary of the molecular pathways identified in Walck-Shannon etal.,(1) pointing out surprises along the way. Finally, we consider the potential conservation of the molecular pathway we described and discuss future questions surrounding dorsal intercalation. Despite the challenges, dorsal intercalation is a process poised to advance our understanding of cell intercalation during morphogenesis throughout the animal kingdom.
[
Genome Inform,
2005]
Tandem repeats are an important class of DNA repeats and much research has focused on their efficient identification, their use in DNA typing and fingerprinting, and their causative role in trinucleotide repeat diseases such as Huntington Disease, myotonic dystrophy, and Fragile-X mental retardation. We are interested in clustering tandem repeats into groups or families based on sequence similarity so that their biological importance may be further explored. To cluster tandem repeats we need a notion of pairwise distance which we obtain by alignment. In this paper we evaluate five distance functions used to produce those alignments - Consensus, Euclidean, Jensen-Shannon Divergence, Entropy-Surface, and Entropy-weighted. It is important to analyze and compare these functions because the choice of distance metric forms the core of any clustering algorithm. We employ a novel method to compare alignments and thereby compare the distance functions themselves. We rank the distance functions based on the cluster validation techniques - Average Cluster Density and Average Silhouette Width. Finally, we propose a multi-phase clustering method which produces good-quality clusters. In this study, we analyze clusters of tandem repeats from five sequences: Human Chromosomes 3, 5, 10 and X and C. elegans Chromosome III.
[
Anesthesiology,
2018]
WHAT WE ALREADY KNOW ABOUT THIS TOPIC: WHAT THIS ARTICLE TELLS US THAT IS NEW: BACKGROUND:: Previous work on the action of volatile anesthetics has focused at either the molecular level or bulk neuronal measurement such as electroencephalography or functional magnetic resonance imaging. There is a distinct gulf in resolution at the level of cellular signaling within neuronal systems. We hypothesize that anesthesia is caused by induced dyssynchrony in cellular signaling rather than suppression of individual neuron activity. METHODS: Employing confocal microscopy and Caenorhabditis elegans expressing the calcium-sensitive fluorophore GCaMP6s in specific command neurons, we measure neuronal activity noninvasively and in parallel within the behavioral circuit controlling forward and reverse crawling. We compare neuronal dynamics and coordination in a total of 31 animals under atmospheres of 0, 4, and 8% isoflurane. RESULTS: When not anesthetized, the interneurons controlling forward or reverse crawling occupy two possible states, with the activity of the "reversal" neurons AVA, AVD, AVE, and RIM strongly intercorrelated, and the "forward" neuron AVB anticorrelated. With exposure to 4% isoflurane and onset of physical quiescence, neuron activity wanders rapidly and erratically through indeterminate states. Neuron dynamics shift toward higher frequencies, and neuron pair correlations within the system are reduced. At 8% isoflurane, physical quiescence continues as neuronal signals show diminished amplitude with little correlation between neurons. Neuronal activity was further studied using statistical tools from information theory to quantify the type of disruption caused by isoflurane. Neuronal signals become noisier and more disordered, as measured by an increase in the randomness of their activity (Shannon entropy). The coordination of the system, measured by whether information exhibited in one neuron is also exhibited in other neurons (multiinformation), decreases significantly at 4% isoflurane (P = 0.00015) and 8% isoflurane (P = 0.0028). CONCLUSIONS: The onset of anesthesia corresponds with high-frequency randomization of individual neuron activity coupled with induced dyssynchrony and loss of coordination between neurons that disrupts functional signaling.
Grove, Christian, Chan, Juancarlos, Van Auken, Kimberly, Gao, Sibyl, Cho, Jaehyoung, Sternberg, Paul W.
[
MicroPubl Biol,
2018]
Protein interaction is an important data type to understand the biological function of proteins involved in the interaction, and helps researchers to deduce the biological nature of unknown proteins from the well-characterized functions of their interaction partners. High-throughput studies, coupled with the aggregation of individual experiments, provides a global 'snapshot' of the protein interactions occurring at all levels of biological processes or circumstances. This snapshot of the interaction network, the interactome, is important to understand the overall events up to the level of comparison between species or pathway simulation, or to find new factors yet undefined in the processes, or to add details to the biological processes and pathways.
As of September 2018, WormBase (www.wormbase.org) (Lee et al. 2018) contains 28,279 physical protein-protein interactions for the roundworm Caenorhabditis elegans. Among these, 1500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, 17,990 protein-protein interactions are unique, and 6,079 unique genes are involved in these interactions. In order to visualize the overall interaction map, a network diagram for all the unique interactions was generated by using the Cytoscape program, version 3.6.1 (Shannon et al. 2003) (Figure 1A). These numbers represent a 108% increase in the number of interaction annotations since last year, 2017. These interaction data were curated from 1,251 peer-reviewed papers, which were selected from the literature by Textpresso Central using automatic SVM (Support Vector Machine)-based text mining approaches (Fang et al. 2012; Mller et al. 2018) and manual verification. Compared to other databases providing C. elegans protein-protein interaction, WormBase now presents the largest data set, which has 1.72-fold more interaction annotations than IMEx (Orchard et al. 2012) and 4.51-fold more than BioGRID (Chatr-Aryamontri et al. 2017) (Figure 1B). Most significantly, WormBase now houses the complete protein interaction data from almost all of the C. elegans literature published from 1993 to 2018. The data sets presented at IMEx and BioGRID are annotated from 253 and 174 papers, respectively. All the physical interaction data in WormBase are supported by experimental evidence from original research papers. The statistics of the detection methods used as experimental evidence are shown in Figure 1C. The majority of the interaction data came from high throughput analysis such as large-scale yeast two-hybrid assays or mass-spectrometry, however, a significant portion of the data (13.1%) are supported by more direct detection methods using small-scale, low throughput methods such as co-immunoprecipitation or co-crystallography (Figure 1C).
In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the Interactions widget on the gene report page. The Interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions. All the interaction data are represented together in a graph created with Cytoscape.js and a table. In the table, the gene names of interaction partners (bait-target) in the interaction are displayed along with the publication. The interaction details including the detection method are also captured in the summary and the remark field in the Interactions page. Users can query the data by using the search bar on the WormBase front page or download all the available data files from the WormBase FTP site (ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758
/annotation/c_elegans.PRJNA13758.WSXXX.interactions.txt.gz, where WSXXX is the database version release, like WS267).
All the interaction data in WormBase will be available soon at the new information resource for multiple model organisms, the Alliance of Genome Resources (https://www.alliancegenome.org/). This site will integrate all the interaction data from human and from model organisms C. elegans, budding yeast (Saccharomyces cerevisiae), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus) and rat (Rattus norvegicus). Integrated views of interaction data from diverse model organisms will be extremely helpful to build interaction databases for species-to-species comparison, and to establish a disease model quickly based on the database. For the most efficient analysis of the interaction data in WormBase, we are now working on developing a new Venn diagram tool and integrating the Gene Set Enrichment Analysis tool (https://wormbase.org/tools/enrichment/tea/tea.cgi) into the Interactions widget. We will continue to curate other types of macro-molecular interactions including protein-DNA, protein-RNA and RNA-RNA interactions, as well as newly reported protein-protein interaction data to serve our research community.