Martin, Jack et al. (2021) International Worm Meeting "The kynurenine pathway is a major modulator of E. faecalis infection in C. elegans"

Whittingham-Dowd, Jayde, Cetnar, Kalina, Rezwana, Ruhi, Norvaisas, Povilas, Kosztelnik, Monika, Parry, Jackie, Au, Catherine, Martin, Jack, Cabreiro, Filipe, Zarate Potes, Alejandra, Urbaniak, Mick, Gems, David, Fathallah, Nadin, Hardgrave, Alex, Benedetto, Alexandre

[International Worm Meeting, 2021]

Key words Kynurenine pathway, E. faecalis, gut infection, microbiota, lysosome-related organelles autofluorescence. Abstract The kynurenine pathway (KP), main catabolic route for the essential amino-acid tryptophan, is well-known for its immunomodulatory role in mammals. While investigating death fluorescence in C. elegans, anthranilic acid (AA)-loaded lysosome-related organelles (LROs) were previously found responsible for the blue auto-fluorescence seen in the worm gut (Coburn et al. PLOS Biol. 2013). Given the bacteriostatic potential of AA and other kynurenine pathway compounds, we hypothesised that LROs and the KP play a key role in C. elegans gut microbial control. To test this idea, we exposed C. elegans to a worm-pathogenic strain of E. faecalis (OG1RF) and observed changes in gut morphology and autofluorescence dynamics upon infection. Transcriptomics and targeted metabolomics analyses further showed that KP activity is modulated upon E. faecalis infection. Using a combination of KP mutants from the Nollen lab (Van Der Goot et al. PNAS 2012), we observed that inhibition of various KP enzymes differentially affect C. elegans resistance to E. faecalis infection. E. faecalis growth on KP mutant worm extracts confirmed that resistant mutants produce bacteriostatic compounds, which we measured by HPLC. This was verified by the delayed or reduced gut colonisation of OG1RF-GFP (gifted by D. Garsin), and the ability for some mutants to thrive on OG1RF loans. We are currently investigating a broader role for the KP in C. elegans gut microbiota control, notably using newly generated CeMBio fluorescent strains.

consortium, modERN et al. (2015) International Worm Meeting "Comprehensive identification of worm and fly transcription factor binding sites."

Gerstein, M, White, KP, consortium, modERN, Celnicker, S, Reinke, V, Waterston, RH

[International Worm Meeting, 2015]

Studies of the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster have vastly increased our understanding of metazoan biology. Both organisms have provided test beds for genome sequencing strategies, and since the publication of their genome sequences at the turn of the century, efforts at understanding the information content of these key genomes have been at the forefront. As members of modENCODE, we established ChIP-seq pipelines and identified binding sites for about 100 transcription factors or chromatin modifiers in each organism. We have now combined efforts and work together as the modERN (model organism encyclopedia of regulatory networks) consortium. We have created a merged, more efficient pipeline to systematically and comprehensively identify binding sites for the remaining ~600 transcription factors (TFs) in each organism. Since the project began in Sept 2013, we have analyzed about 100 additional factors for each organism. We are also embarked on efforts to assign TF binding sites to regulated genes using RNA-seq to monitor gene expression changes in TF loss-of-function animals. We will map these results to a network framework to provide functional validation. In addition, we will perform targeted bioinformatic analyses to examine the association of binding sites between factors, their distribution in the genome, and how they are linked with changes in gene expression from the RNAi experiments. All strains are being deposited in the stock centers. All data are being incorporated in the ENCODE database (www.encodeproject.org) and will be made available through WormBase and FlyBase.

M Reigl et al. West Coast Worm Meeting "Search for computational modules in the C. elegans brain."

U Alon, M Reigl, D B Chklovskii

[West Coast Worm Meeting]

Are there multi-neuron computational modules in the C. elegans nervous system? We attempt to answer this question by applying a systematic statistical approach to the C. elegans wiring diagram (White et al. 1976). Our approach is to identify multi-neuron inter-connectivity patterns that are significantly over-represented in the actual wiring diagram compared to the randomized wiring diagram, which preserves the number of synapses per neuron but not the identity of connections. To do this we compute the numbers of occurrences of all n-neuron (n=2...5) inter-connectivity patterns in the actual and randomized wiring diagrams. This statistical approach confirms previous reports of the over-abundance of reciprocal connections and triangular connectivity patterns (White et al. 1976). Moreover, we discover several new four-neuron and five-neuron inter-connectivity patterns that appear significantly more often in C. elegans than in randomized wiring diagrams. We suggest that these inter-connectivity patterns may serve as computational modules that perform stereotypical functions.

Reigl M et al. (2002) West Coast Worm Meeting "Search for computational modules in the C. elegans brain"

Reigl M, Chklovskii DB, Alon U

[West Coast Worm Meeting, 2002]

Are there multi-neuron computational modules in the C. elegans nervous system? We attempt to answer this question by applying a systematic statistical approach to the C. elegans wiring diagram (White et al. 1976). Our approach is to identify multi-neuron inter-connectivity patterns that are significantly over-represented in the actual wiring diagram compared to the randomized wiring diagram, which preserves the number of synapses per neuron but not the identity of connections. To do this we compute the numbers of occurrences of all n-neuron (n=2...5) inter-connectivity patterns in the actual and randomized wiring diagrams. This statistical approach confirms previous reports of the over-abundance of reciprocal connections and triangular connectivity patterns (White et al. 1976). Moreover, we discover several new four-neuron and five-neuron inter-connectivity patterns that appear significantly more often in C. elegans than in randomized wiring diagrams. We suggest that these inter-connectivity patterns may serve as computational modules that perform stereotypical functions.

Brittin, Christopher et al. (2015) International Worm Meeting "A 3D Analysis of the Mind of the Worm Connectome."

Brittin, Christopher, Emmons, Scott, Cook, Steven, Cohen, Netta, Hall, David

[International Worm Meeting, 2015]

A connectome is a comprehensive map of all neural connections in an organism's nervous system. The first connectome was published almost 30 years ago by White et al. (1986) and described the structure of the nervous system of the nematode C. elegans adult hermaphrodite. Subsequent network analyses of this data have focused only on the synaptic connectivity of the nervous system, while neglecting much of the spatial information in the data. Initial spatial analyses of the C. elegans connectome reported in (White et al., 1983; Durbin, 1987) used only a sparse sampling of physical neuron contacts. Using the original electron micrographs from (White et al., 1986), we have extended this analysis by performing a 3D reconstruction of every neuron in the C. elegans nerve ring in both the L4 and adult. This represents the first complete volumetric reconstruction of the main neuropil of any animal from multiple developmental stages. With this enriched data set, we have been able to do a comparative analysis of synaptic connectivity, characterize the spatial distribution of synapses for each neuron and analyse the relationship between neuron contact and synapse formation in the C. elegans nerve ring. Similar to (White et al., 1983), we found that ~40% of all possible physical contacts result in a synapse or gap junction. We also found a positive correlation between the frequency of synapse formation and the amount of physical contact between neurons. Specifically, the frequency of synapse formation between two neurons approaches ~0.7 as the amount of physical contact approaches 10% of a neuron's total measured surface area. However, like (Durbin, 1987), we find that synapse probability and synapse number between any pair neurons does not depend strongly on the amount of shared physical contact. Furthermore, synapse volumes appear to be conserved between the L4 and adult, while the number of synapses between any two neurons appear to be, on average, greater in the adult. This could suggest that during late nervous system development, synaptic partnerships are reinforced by creating additional small synapses between neurons rather than enlarging the volume of current synapses. .

Ken-ichi Oshio et al. (2002) Japanese Worm Meeting "Revision of synaptic connectivity database"

Eizo Akiyama, Yuishi Iwasaki, Yuko Osana, Ken-ichi Oshio, Sohei Gomi, Satoru Morita, Kotaro Oka, Kazumi Omata

[Japanese Worm Meeting, 2002]

The synaptic connectivity of C. elegans is well known from observations of the somatic system by White et al. and those of the pharyngeal system by Albertson et al. So far, three databases were constructed for computational usage by Achacoso et al. and Durbin, and recently in WormBase. However, they lack some data such as those in tables of White's paper and those in figures of Albertson's book. Our database (K. Oshio, S. Morita, Y. Osana and K. Oka: Technical Report of CCEP, Keio Future No.1, 1998) includes all data described in White's paper and Albertson's book. Unfortunately, some mistakes were found in the database through private communications with John White who is the author of White's paper and with the users of the database. Thus we have been proceeding with the revision to make it perfect one. We are planning to complete the revision in September 2002. The database should be worthwhile not only for neurophysiological studies, but also for post-genomic interests mediating genomes and behavior.

Zeyu Zheng et al. (2007) International Worm Meeting "Quantitative 4D analysis of centrosome movement in early embryos."

Asako Sugimoto, Yumi Iida, Takafumi Konishi, Zeyu Zheng

[International Worm Meeting, 2007]

Caenorhabditis elegans embryos undergo stereotypic cell division patterns. Because the cleavage plane for each cell division is defined by the orientation of the mitotic spindle, positioning of spindle poles, or centrosomes, is crucial to regulate cell division patterns. Previous reports revealed that centrosomes are positioned by interactions between microtubules and the particular region of the cell cortex (1-3). However, a detailed mechanistic understanding of centrosome movement is still limited. As a step to better understand the regulation of centrosome movement in early cell divisions, we are developing a quantitative approach to analyze dynamic movement of centrosomes at high spatial and temporal resolution. 4D images of embryos expressing GFP markers visualizing centrosomes and cell membrane are acquired using a spinning-disc confocal microscope, and positions of individual centrosomes are extracted from each image. Using these positional data, direction and speed of each centrosome movement, and rotation angle and distance of each centrosome pair are quantitatively and statistically analyzed in a 3-dimensional space. We will present our progress on the analysis of wild-type and mutant embryos having spindle orientation defects. 1.Hyman and White (1987) J. Cell Biol. 105:2123-2135. 2.Hyman (1989) J. Cell Biol. 109:1185-1193. 3.Keating and White (1998) J. Cell Sci. 111:3027-3033. .

German EA et al. (1998) East Coast Worm Meeting "CROSSED WIRES IN UNC-37 VENTRAL CORD"

Hall DH, Miller DM, German EA

[East Coast Worm Meeting, 1998]

Uncoordinated movement in unc-37 adults is superficially similar to the impairment observed in unc-4 animals (1). In unc-4, loss of coordination results from a specific wiring deficit between interneurons and motorneurons in the ventral nerve cord (3,4). We are currently analyzing the detailed synaptic pattern in an adult unc-37 nerve cord from serial thin sections. Preliminary data were discussed previously (2). We have now identified the major interneurons and 20 motorneurons in the anterior ventral nerve cord, and have determined their synaptic interactions. The morphological phenotype of unc-37 is not as limited as the specific wiring defect in unc-4. Many neurons show minor changes in branching or axon caliber, and there is a wider variety of wiring changes. However, in both mutations the AVB interneurons form inappropriate gap junctions onto class A targets, while AVAs fail to make normal junctions onto these targets. This specific change may explain the similarity in their gross behavioral phenotypes. 1. Pflugrad et al. (1997) Development 124:1699-1709. 2. Hall, German and Miller (1997) 11th Annual C. elegans meeting. 3. J.G. White et al. (1986) Phil. Trans. R. Soc. Lond 314:1-340. 4. J.G. White et al. (1992) Nature 355:838-41.

K Oshio et al. (1999) International C. elegans Meeting "Analysis of neuronal connectivity of C. elegans using random walker"

Y Osana, K Kawamura, S Morita, Y Funabashi, K Oshio, K Oka

[International C. elegans Meeting, 1999]

From the detailed report of White et al. and Albertson et al. , we have almost complete knowledge about the synaptic connectivity of C. elegans with the type of synapse (electric junction or chemical synapse). However, the type of each chemical synapse (excitatory or inhibitory one) is not described. Conventional electrophysiological methods for C. elegans is difficult because the size of the neurons is too small to penetrate the intracellular electrode. On the other hand, computational studies of neuronal circuit are now possible by virtue of the above mentioned elaborate experimental studies of neuroanatomists. We have built a new data base of the whole neuronal circuit including pharyngeal neurons only from the article of White et al. and Albertson et al. There exist two other data bases to the knowledge of the present authors. The first data base was constructed by Achacoso and Yamamoto who also analyzed the properties of the network. Another data base was constructed from the article of White et al. by Durbin, which is available on the internet homepage. To begin understanding signal processing on the nervous system, we have investigated the neuronal connectivity by putting random walkers on certain neurons of the network. Here we ignore internal structure of neurons. Random walker is a particle which moves among neurons randomly, and can be considered to be transmitted signal. In our simulation, random walkers are put on certain sensory neurons at each time step, this corresponds to stimulation which sensory neurons accept. We removed random walkers at certain motor neurons, this means, for instance, signals are transmitted to muscles which cause normal action. As a result, we have found that the degree of relation of each neuron for input neurons can be known from the probability to find random walker, although the difference between excitatory and inhibitory of chemical synapses is not taken into account. The simulational results will be shown comparing with real function such as the touch sensitivity. E-mail: oshio@future.st.keio.ac.jp

N Mandhana et al. (2004) European Worm Meeting "DEVELOPMENT OF CHIP CHIP FOR C. ELEGANS FOR FINDING IN VIVO BINDING SITES OF CHROMATIN FACTORS"

M Vidal, J Ahringer, D Dupuy, N Mandhana

[European Worm Meeting, 2004]

Chromatin-modifying complexes are important for transcriptional control, but their roles in the regulation of development remains poorly understood. We are interested in elucidating how chromatin regulatory complexes function in developmental decisions. The synthetic multivulva (synMuv) genes negatively regulate vulval induction and a sub-set of these genes are components of histone deacetylase (HDAC) complexes (e.g., Rb and NuRD). HDACs are are thought to be recruited to target genes by sequence specific transcription factors, where they locally deacetylate histone H3 tails, and bring about transcriptional repression. We are trying to understand how chromatin-remodelling complexes are integrated into signalling and developmental pathways. To this end, we are currently constructing a C. elegans promoter DNA array which will be used in ChIP-chip (Chromatin immunoprecipitation with DNA Microarray) experiments to identify binding sites for chromatin factors and sequence specific binding proteins. We are spotting ~9000 intergenic PCR fragments generated for the promoterome project in the Vidal Lab. These PCR products are amplified upstream DNA sequences and cover approximately 1.5 - 2.2 kp long sequences from the translation start site. We are also comparing the gene expression profiles of synMuv mutants using the Afffymetrics gene system to look for change of gene expression in these mutants compared to wildtype.