Pollard, A.K. et al. (2017) International Worm Meeting "Worms in space for outreach on Earth."

Gaffney, C.J., Szewczyk, N.J., Pollard, A.K., Phillips, B.E., Etheridge, T.

[International Worm Meeting, 2017]

Muscle atrophy is one of the main (mal)adaptations associated with prolonged spaceflight. We have previously established C. elegans as a model for studying spaceflight induced alterations in muscle with past experiments demonstrating reproducible expression changes in cytoskeletal and metabolic proteins and their encoding mRNAs. We are currently preparing a European Space Agency sponsored spaceflight experiment that aims to manipulate the stability of integrin based muscle attachment complexes and insulin-like signalling to determine if either or both of these predicted molecular mechanisms causally regulate the gene and protein expression changes observed in response to spaceflight. As spaceflight, particularly launches, captures the public's imagination, we have planned outreach activities to capitalize on this existing interest in spaceflight and to raise the profile of space-based life science research in the United Kingdom (UK). We have divided our outreach messages into three main themes. Firstly, we will describe the advantages of using C. elegans as a model to study biology and highlight some of the impacts on human health that have arisen from studies of the worm. Secondly, we will discuss the use of C. elegans as a model to study space physiology with a focus on how our past and current experiments were physically conducted. Thirdly, we will raise awareness of how the findings from our studies are being translated into new knowledge of the regulation of human muscle both on Earth and in space. We will present examples of how each message will be presented in a poster format for use at our outreach activities and provide electronic versions of these posters for other educators who may wish to use them. Three distinct dissemination routes will be used to maximise the impact of our outreach. Firstly, we will engage with the UK media to produce a video documentary of our experiment to provide the public with deeper understanding of how space experiments are actually conducted. Secondly, outreach days will be run at museums in each of the capital cities in the UK. Thirdly, we will run a number of hands-on workshops at schools in the middle and South West of England. For the outreach days we will employ the three posters described above and an extended version of our school workshop activities. The workshop activities will cover all three of our outreach messages, using wild-type worms and those with mutations relevant to our spaceflight studies (e.g., unc-112 and cha-1), and giving students the opportunity to handle spaceflight experimental hardware. We will discuss the details of our workshop activities for other educators who wish to run similar activities.

Mary Ann Tuli et al. (2006) European Worm Meeting "CGC and WormBase"

Richard Durbin, Robert Herman, Theresa Stiernagle, Mary Ann Tuli, Jonathan Hodgkin

[European Worm Meeting, 2006]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbor Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA).. WormBase is dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C.elegans, and some related nematodes. WormBase can be freely accessed at www.wormbase.org, and is also available for download at ftp://ftp.wormbase.org/pub/wormbase. A new data release is produced every three weeks. The UK WormBase group works closely with the Caenorhabditis Genetics Center (CGC) to curate genetic nomenclature and maintain the C.elegans genetic map. Detailed guidelines are accessible via http://www.cbs.umn.edu/CGC/Nomenclature /nomedguid.htm. All CDSs, transcripts and pseuodgenes are assigned an identifier of the form WBGene00000001. This identifier is unique and remains stable when the gene object is updated. Release WS150 (November 2005) contains 44644 WBGeneIDs of which 25043 are from C.elegans, and 19587 from C.briggsae. The number of CDS objects, which have been assigned a CGC approved gene name is 6638. In release WS140 (March 2005) the Variation class was introduced as a more efficient way to handle most of what was in the Allele and Locus class. The Variation class incorporates the following: Alleles, SNPs (both confirmed and predicted), RFLPs and transposon insertions. Curation of allele data by WormBase biologists is an ongoing project and in response to the WormBase 2005 Users survey (http://www.wormbase.org/announcements/newsletters /pdf/2006-01.pdf) we will curate these more intensely. Allele information is either captured from scientific journals or submitted directly be researchers using the WormBase submission forms at http://wormbase.org/db/curate.base. WormBase is supported by a grant from the National Human Genome Research Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council. CGC is supported by NIH NCRR.

Mary Ann Tuli et al. (2005) International Worm Meeting "CGC and WormBase"

Theresa Stiernagle, Robert Herman, Jonathan Hodgkin, Richard Durbin, Mary Ann Tuli

[International Worm Meeting, 2005]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbour Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA). WormBase is dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C.elegans and some related nematodes. WormBase can be freely accessed at www.wormbase.org and is also available for download at ftp://ftp.wormbase.org/pub/wormbase/. A new database release is produced every three weeks. The UK WormBase group works closely with the Caenorhabditis Genetics Center (CGC) to curate genetic nomenclature and maintain the C.elegans genetic map. Detailed guidelines are accessible via http://www.cbs.umn.edu/CGC/Nomenclature/nomenguid.htm Since WS126 (June 2004) all CDSs, transcripts and pseudogenes have been assigned an identifier of the form WBGene00000001. This identifier is unique and remains stable when the gene object is updated. Release WS140 (March 2005) contains 44107 WBGeneIDs of which 24506 are from C.elegans, and 19587 from C.briggsae. The number of CDS objects which have been assigned a CGC approved gene name is 5707. In release WS140 (March 2005) the Variation class was introduced as a more efficient way to handle most of what was in the Allele and Locus classes. The Variation class incorporates the following: Alleles, SNPs (both confirmed and predicted), RFLPs and transposon insertions. Curation of allele data by WormBase biologists is an ongoing project and recent efforts have seen the number of Allele objects in the database increase from about 9000 in WS110 (October 2003) to about 11200 in WS140 (March 2005). Allele information is either captured from scientific journals or submitted directly by researchers using the WormBase submission forms at http://wormbase.org/db/curate/base WormBase is supported by a grant from the National Human Genomes Reseach Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council. CGC is supported by NIH NCRR.

Funda Sar et al. (2007) International Worm Meeting "Genome-wide RNAi screen to map genetic interactions of miRNA genes."

Eric Miska, Funda Sar

[International Worm Meeting, 2007]

Small non-coding RNAs regulate several biological processes through post-transcriptional and/or transcriptional gene silencing. MicroRNAs (miRNAs) have been implicated in developmental processes, apoptosis and cancer. Extensive efforts have been made to understand the biogenesis, and in vivo functions of miRNAs. However, a large-scale deletion study found that many miRNA genes do not have obvious abnormal loss-of-function phenotypes (Miska et al., unpublished results). This is potentially due to redundancy between miRNA genes and/or other complex regulatory interactions of miRNA and target genes. Therefore, it is important to identify genetic interactors of miRNA genes to enhance our understanding of how miRNAs function. RNA interference technology and the existence of an RNAi library representing 86% of known coding genes enables us to perform a large scale high-throughput analysis of interactions in C.elegans. Synthetic enhancement of phenotypes resulting from a defined mutation in a miRNA gene in combination with knockdown of a library gene will indicate a genetic interaction between these two genes. The preliminary genetic map for miRNA genes will be presented and initial functional analysis of these interactions will be discussed. This work is supported by Cancer Research UK. .

Mary-Ann Tuli et al. (2007) International Worm Meeting "CGC and WormBase."

Jonathan Hodgkin, Theresa Stiernagle, Robert Herman, Mary-Ann Tuli, Richard Durbin

[International Worm Meeting, 2007]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbour Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA). The UK WormBase group works closely with the Caenorhabditis Genetics Center (CGC) to curate genetic nomenclature and maintain the C.elegans genetic map. Detailed guidelines are accessible via http://www.cbs.umn.edu/CGC/Nomenclature/nomenguid.htm Release WS170 (Jan 2007) contains 54213 WBGeneIDs (unique gene identifiers) of which 25533 are from C.elegans and 19666 from C.briggsae. The number of CDS objects which have been assigned a CGC approved gene name in release WS170 (Jan 2007) is 7300 (compared to 5707 in release WS140 (March 2005). Strain data is sent to WormBase from the CGC in Minneapolis every month. The extensive cross referencing within these objects allows users to easily find information relating to a specific strain. The number of strains in WS170 is 13000 of which 8000 are stored at the CGC. Manual curation of allele data by WormBase biologists is an ongoing project and recent efforts have seen the backlog of post-2001 publications cleared. Many of these alleles have details of the strain carrying the mutation and a description of the lesion. If we know the location of a mutation, we are now able to automatically attach an accurate description of how it affects a gene and give the amino acid change if applicable. This has considerably enhanced allele representation in WormBase. We are now able to start working on pre-2001 publications. Allele information is either captured from scientific journals or submitted directly by researchers using the WormBase submission forms at http://wormbase.org/db/curate/online_forms We continue our long term collaboration with the C. elegans Gene Knockout Consortium ( http://celeganskoconsortium.omrf.org/ ) and the National Bioresource Deletion Mutant Project ( http://shigen.lab.nig.ac.jp/c.elegans/index.jsp ) A link to the source database from WormBase allows users to view more detailed information about individual alleles. Since WS153 (Dec 2005) WormBase has been collaborating with the NemaGENETAG Mos insertion project ( http://elegans.imbb.forth.gr/nemagenetag/ ) and in WS174 had over 4000 alleles including full details of the Mos insertion site. We have developed a web form where collaborators can upload their data which has streamlined the submission procedure. WormBase is supported by a grant from the National Human Genomes Reseach Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council. CGC is supported by NIH NCRR.

Simon C Harvey et al. (2005) International Worm Meeting "The genetics and fitness consequences of phenotypic plasticity of dauer larvae development"

Mark E Viney, Simon C Harvey, Alison Shorto

[International Worm Meeting, 2005]

The choice between dauer and non-dauer development is an example of phenotypic plasticity, in which environmental conditions determine developmental fate. Comparison of the plasticity of dauer larvae development in different wild isolates of Caenorhabditis elegans reveals considerable variation in this plasticity in response to both food and pheromone conditions. Additionally, recombinant-inbred lines (RILs) created from crosses between N2 (which shows a high plasticity) and DR1350 (a wild isolate which show a low plasticity) show a range of plasticities greater than that of the parental lines. To understand the genetics of this variation in plasticity, we have used two complementary approaches. Firstly, quantitative trait loci (QTL) mapping to identify the genomic regions controlling the variation in plasticity. This has identified several regions containing candidate QTLs affecting the plasticity of dauer development. Secondly, a comparison of various aspects of the life histories of the RILs to address the fitness consequences of the variation in plasticity. This has identified a positive correlation between the population growth rate and plasticity. These data have therefore developed a clearer picture of the genetics behind variation in a complex trait and additionally are suggesting the selective forces that may act to produce and maintain that variation. This work is supported by a grant from the Natural Environment Research Council, UK.

Samantha J Broad et al. (2005) International Worm Meeting "Profiling the induced response of C. elegans to applied xenobiotic compounds"

Mike Robinson, Ian Hope, Pe Urwin, Samantha J Broad, Anthony Flemming

[International Worm Meeting, 2005]

An estimated 42% of potential global crop production is lost to pests before harvest (Oerke, 1994). Many pesticides are hazardous to the environment and pose a threat to public health. The UK Environment Agency estimates that around 120m pa is spent cleaning up pesticide residue in the UK. The requirement for more effective and environmentally friendly pesticides is increasingly urgent as some of the most effective broad spectrum pesticides such as dazomet, aldicarb and methyl bromide are currently either subject to a total ban or are being phased out. This project will develop a high throughput, informative frontline screen for the discovery of novel pesticides. Initial studies of the effects of 19 xenobiotic chemicals on wild type C. elegans (N2) and selected mutant strains have been carried out. Bioassay data have been collected and LD50 values taken as a concise measure of efficacy of each chemical. The effect of each chemical on growth of the E. coli OP50 foodsource has been assessed. Juglone was found to cause cell lysis, and was the only chemical to reduce the growth rate significantly (p &#8805; 0.05). Each strain (N2, the ndg4 mutant and the loss of function mutants nhr-8, age-1, age-1/daf-16, fat-2, mrp-1, mev-1, cnb-1 and pgp-3 mutant strains) was assayed against 2, 1, 0.5, 0.25, 0.13 and 0.06 mM concentrations of each chemical in microtitre plates, at 20<sym05>C, in liquid S basal media with OP50. At 1, 24, 48 and 72 hour timepoints the numbers of dead and live individuals were counted. The results of triplicate assays were pooled and the LD50 values were calculated using probit analysis. Observations of the phenotypic effects of each chemical on fitness, behaviour, locomotion, chemo-attraction and fecundity have been performed using radial dispersal rates, a point source gradient assay and viable egg counts. Based on these data microarray analyses are underway to compare gene expression levels of wild-type C. elegans following exposure to a subset of 7 of these chemicals (thiabendazole, juglone, 46;-naphthoflavone, fluoxetine, dazomet, imidochloprid and colchicine) or under general stresses such as osmotic stress and heat stress. This data will be used to identify genes specifically involved in the response to xenobiotic exposure. Promoter regions of responsive genes will be cloned and used to generate reporter-expression constructs. These will be used to create a number of C. elegans reporter lines which can be used to identify responses induced by novel compounds.

May Tran et al. (2005) International Worm Meeting "RNAi knockout of the mitochondrial carrier protein ucp-4: effects on metabolism"

May Tran, Craig LaMunyon, Aidyl Gonzalez-Serricchio

[International Worm Meeting, 2005]

We are investigating the phenotype of ucp-4 RNAi knockout worms. Mitochondrial uncoupling protein (UCP) function in humans has been linked to obesity. UCPs are mitochondrial carrier proteins, and human UCP-1, -2, and -3 are protonophores, transporting protons from the intermembrane space to the matrix, bypassing ATP synthase, and thereby raising resting metabolic rate in response to certain cues. The function of human UCP-4 is not clear, but it may be a mitochondrial fatty-acid transporter, and it is a homolog to the C. elegans ucp-4 (K07B1.3). Initial RNAi experiments by Dr. Julie Ahringers lab deemed knockout worms to be wild-type. However, we wondered if the RNAi phenotype might be a subtle alteration of metabolic activity. We obtained Dr. Ahringers RNAi feeding clone from the UK HGMP Resource Centre and measured egg laying and defecation rates. Compared to control worms fed HT115 bacteria containing the empty feeding vector, ucp-4 RNAi fed young adults that were exposed beginning as L1 larvae laid eggs at a significantly slower rate, although preliminary data on defecation rate suggests no difference between these treatments. If the trends in these data hold, it would suggest that ucp-4 RNAi knockout worms are processing food at the same rate, but converting that energy into offspring at a reduced rate.

Li, C.C.Y. et al. (2017) International Worm Meeting "Towards a unified global C. elegans Metabolic Reconstruction Model."

Li, C.C.Y., Witting, M., Kaleta, C., Casanueva, O, Hastings, J., Le Novere, N.

[International Worm Meeting, 2017]

C. elegans has recently been advanced as a premier metazoan model organism for the study of metabolism, with the publication of two whole-genome metabolic models (1, 2). Using these models together with -omics data allows the in-depth data-driven exploration of systems-level metabolism using in silico simulations. In a GENiE workshop to be held April 2017 at the Babraham Institute, Cambridge, UK, the relationships between these two existing metabolic models will be explored with the objective of generating a consensus model. Because the two reconstructions are still incomplete, and certain important pathways and areas of metabolism are currently under-annotated, we aim to identify specific areas that are relevant to the C. elegans community and prioritise them for further annotation in a follow-up community-driven "annotation jamboree" workshop. This poster will describe the main objectives set by the first workshop and opens the invitation to the C. elegans metabolic research community to contribute to the follow-up annotation efforts. 1. Gebauer, J.; Gentsch, C.; Mansfeld, J.; Schmei beta er, K.; Waschina, S.; Brandes, S.; Klimmasch, L.; Zamboni, N.; Zarse, K.; Schuster, S.; Ristow, M.; Schauble, S. & Kaleta, C. (2016), 'A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.', Cell Syst 2(5), 312--322. 2. Yilmaz, L. S. & Walhout, A. J. M. (2016), 'A Caenorhabditis elegans Genome-Scale Metabolic Network Model.', Cell Syst 2(5), 297--311.

Paul Davis et al. (2007) International Worm Meeting "Caenorhabditae Genome Curation - WormBase."

Paul Davis, John Spieth, Darin Blasiar, Tamberlyn Bieri, Gary Williams, Anthony Rogers, Philip Ozersky

[International Worm Meeting, 2007]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbor Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA). WormBase (http://www.wormbase.org) is a freely available information resource primarily for the nematode Caenorhabditis elegans but is continually expanding to include data from other related nematodes such as C. briggsae and C. remanei. Although the genome sequence and associated gene set of C. elegans has been annotated and curated for over a decade, corrections are still regularly made with each tri-weekly release. WormBase sequence curators rely on many sources of evidence for identifying gene refinements and additions, an important one being our users. We would like to point out that we appreciate feedback from the Worm Community and suggested modifications are always given top priority. Here we illustrate some of the sources of gene modifications/additions, tools that have been developed to aid curators in their work as well as highlight some issues (positive and negative) that our users should be aware of. As other Caenorhabitae sequencing projects progress to yield reliable assemblies and gene sets (utilising the knowledge gained from the nGASP project), WormBase aims to start limited curation and maintenance of these genomes. This has already begun for C. briggsae where the new genetic map based Ultra/Super contig assembly has been adopted and the backlog of community suggested corrections are being processed.