Hubbard EJA et al. (1994) Worm Breeder's Gazette "Genetic Analysis of sel-10."

Hubbard EJA, Greenwald IS

[Worm Breeder's Gazette, 1994]

Genetic analysis of sel-10 E. Jane Albert Hubbard and Iva Greenwald Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, New York, 10032

Sobia Aslam et al. (2002) European Worm Meeting "mab-9/Tbx20 orthologues and the generation of morphological diversity."

Jane Sowden, Alison Woollard, Sobia Aslam

[European Worm Meeting, 2002]

mab-9 (male-abnormal) is essential for patterning of the C. elegans hindgut and for the correct functioning of the nervous system. In mab-9 mutants, two male-specific blast cells B and F, which normally give rise to important copulatory structures of the male tail, adopt the lineage fates of their anterior neighbours, Y and U. This cell fate transformation results in gross abnormality of the male tail. mab-9 hermaphrodites are also abnormal as the B and F cells are structural cells in hermaphrodites and are important in development of the rectum. mab-9 mutants of both sexes are also weakly backwards Unc.

Sobia Aslam et al. (2003) International Worm Meeting "T-box genes and the generation of morphological diversity"

Sara Maxwell, Sobia Aslam, Jane Sowden, Lizzie Clarke, Alison Woollard

[International Worm Meeting, 2003]

The T-box family of transcription factors is phylogenetically conserved and plays important roles during development. There are 20 T-box genes in C. elegans; more than in Drosophila, mice and humans. Most of the C. elegans T-box genes are highly diverged but one of these genes, mab-9(male abnormal), is an orthologue of human and murine Tbx20 and is also closely related to H15 in Drosophila. mab-9, was identified through mutation and functions to specify cell fate during hindgut and male tail development. In addition mab-9 plays a role in the developing nervous system. In mouse and humans, Tbx20 orthologues are expressed during early heart development and in the central nervous system. Vertebrate Tbx20 orthologues in zebrafish and chick show conserved expression patterns (1) and in Drosophila the Tbx20 orthologue, H15, is also expressed during early heart development (2) suggesting an important evolutionary role for Tbx20 in the specification of the heart. Hence, Tbx20 orthologues appear to have acquired diverse functions in chordates and nematodes, despite a common evolutionary origin. However it is also possible that there is an evolutionary parallel between heart and hindgut development. How far are the Tbx20 genetic pathways conserved between chordates and nematodes? We are investigating whether vertebrate Tbx20 can functionally substitute for mab-9 in vivo. Other potential phenotypic parallels in highly conserved T-box genes, for example tbx-2, are also being analysed. The other C. elegans T-box genes are highly diverged but nevertheless some of these have essential functions during development. tbx-23 appears to have no close orthologues within the metazoan phyla however, RNAi for tbx-23 resulted in highly penetrant embryonic lethality. Examination of animals escaping embryonic arrest revealed severe posterior defects, suggesting that tbx-23 may play a role in posterior patterning during embryogenesis. Reporter gene analysis for tbx-23 expression is in progress. 1) Meins et al., Genomics 76, 317-332 (2000) 2) Griffin et al., Dev. Biol 218, 235-247 (2000)

Jane Shingles et al. (2006) European Worm Meeting "Progress of the Localization of Expression Mapping Project"

Jane Shingles, Denis Dupuy, Marc Vidal, Ian Hope, John Reece-Hoyes

[European Worm Meeting, 2006]

Jane Shingles1, John Reece-Hoyes1, Denis Dupuy2, Marc Vidal2 and Ian Hope1. The Promoterome library containing 6500 Caenorhabditis elegans promoter fragments has previously been generated and used to construct promoter ::GFP fusions to allow determination of gene expression patterns in C. elegans. Optimization of the C. elegans micro-particle bombardment transformation technique, to give a medium through-put system, allowed the generation of expression patterns for over 300 C. elegans promoter::GFP fusions. Promoter fusion constructs of transcription factors genes and genes with homology to human genes with no assigned function were selected for the initial analysis and the results are shown. Initial analysis of the results highlights several significant differences between the two sets of genes. Promoters from C. elegans homologues of human genes with no known function were far more likely to yield either no GFP expression (35% vs. 6%) or ubiquitous GFP expression (23% vs. 8%) under the standard laboratory conditions utilized. In contrast, promoters from C. elegans transcription factor genes were far more likely to drive neuronal expression (62% vs.16%).. Full results are presented on the Hope Laboratory Expression Pattern database URL:http://bgypc059.leeds.ac.uk /~web

Church DL et al. (1991) International C. elegans Meeting "SPECIFICITY OF TRANS-SPLICING IN C. ELEGANS"

Church DL, Wickens MP

[International C. elegans Meeting, 1991]

Trans-splicing attaches a 22-nt leader to the 5' end of 1020% of mRNAs in the nematode, C. elegans. We are studying the specificity of the reaction, by which a given pre-mRNA receives, predominantly, only one of two spliced leaders (SLl or SL2). Is the specificity for SLl vs. SL2 conferred by the sequence immediately upstrearn of the trans-splice acceptor site? We have constructed a chimeric gene (tra-2/unc-54) comprising 70 nt upstream of the first exon of a trans-spliced gene (tra-2, which predominantly receives SL2) followed by the 'body' of a nontrans-spliced gene (unc- 54). We have analyzed trans-splicing in a stable transgenic strain carrying the tra2/uncS4 construction. PCR analysis suggests that both the endogenous tra2 message and the tra2/unc54 RNA receive SLl and SL2. Primer extension studies indicate that most of the tra2/unc54 RNA is not trans-spliced.To study the 5' ends of the .trans-spliced tra2/unc54 RNAs, we have used the RACE ('rapid amplification of DNA ends') method. By cloning, screening and sequencing RACE products, we have verified that SLl is trans-spliced to the tra2 acceptor site of at least some tra2/unc54 RNAs. Taken together, the data suggest that the tra2 sequence contained in the tra2/unc54 RNA does not direct the preferential trans-splicing of SL2. (D.C. is supported by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fund for Medical Research.)

John Reece-Hoyes et al. (2006) European Worm Meeting "wTF2.0: A Fundamental First Step for Mapping the Caenorhabditis elegans Transcription Factor Localizome"

Jane Shingles, A.J. Marian Walhout, Denis Dupuy, Bart Deplancke, Ian Hope, John Reece-Hoyes, Marc Vidal, Christian Grove

[European Worm Meeting, 2006]

John Reece-Hoyes1, Bart Deplancke2, Jane Shingles1, Christian Grove2, Denis Dupuy3, A.J. Marian Walhout2, Marc Vidal3 and Ian Hope1. The Localization of Expression Mapping Project (LEMP) aims to use cloned C.elegans promoter fragments to generate a genome-wide set of expression patterns termed the Localizome. The Promoterome currently contains promoter fragments of up to 2kb from about 6,500 of the approximately 20,000 identified genes in the C.elegans genome. Using the Multisite Gateway system these promoter fragments are re-cloned upstream of GFP within an unc-119 rescue vector and the resulting constructs used to transform unc-119 mutant nematodes by a modified ballistic DNA transfer technique. The current focus of the LEMP is on C.elegans transcription factor genes with the view that these expression pattern data will be essential for mapping transcription regulatory networks. While C.elegans gene models have undergone continuous refinement, the extant lists of predicted C.elegans transcription factors (collectively referred to as wTF1.0) were in need of updating. We have identified a compendium of 934 transcription factor genes (referred to as wTF2.0) by interrogating Wormbase version 140 for proteins with appropriate Gene Ontology (GO) terms and then manually removed false positives (369) and added false negatives (373). The results of various bioinformatic analyses using wTF2.0 as well as how the list can be used to investigate regulatory networks will be discussed. We expect wTF2.0 to be a dynamic resource due to regular updating of the C.elegans genome annotation as well as changes in the functional annotations of protein domains. wTF2.0 will be accessible to the scientific community via an online interface where input is possible. wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function.

H Van Luenen et al. (1999) International C. elegans Meeting "World-wide worm SNPs: Dissecting the molecular evolution of the species using a high density SNP map"

R Plasterk, R Koch, H Van Luenen

[International C. elegans Meeting, 1999]

We would like to reconstruct the history of the C. elegans species at the genome level, therefore we sampled the genomes of four natural isolates (strain CB4857 isolated in Claremont, California, RC301 from Freiburg, Germany, TR403 from Madison, Wisconsin and AB1 from Adelaide, Australia) for single nucleotide polymorphisms (SNPs). Random genomic DNA fragments from the 4 strains were shotgun cloned and sequenced. There was no selection for transcribed or non-transcribed regions of the genome. In total we sequenced 1572 clones resulting in over 1 Mb of sequence information. The sequences are compared to the canonical Bristol N2 sequence to ask the question whether the clone maps to a unique sequence, and -if so- whether it contains polymorphisms. Once a SNP is identified we check other strains for the presence of the same polymorphism by PCR amplification and sequence analysis. In an initial experiment we found approximately one SNP per 3000 bp sequenced. The SNPs are randomly spread over the genome. Based on these observations we expect to find approximately 500 SNPs, one in every 200 kb. In the initial experiment we found, as expected, that several SNPs initially detected in one strain were also present in some but not all other strains. For example: a T in the Australian AB1, is a G at the same position in Bristol N2 in cosmid K10D2 at position 27946, and we found it to be like AB1 in the Californian CB4857 strain and the German RC301 strain, while the TR403 strain from Wisconsin resembles the Bristol N2 strain. Thus different patches of the genome have different ancestors. With our high density SNP map we will generate a genome map for each isolate which will show how each genome is patched together from a limited set of parental strains. The SNP's will be added to ACeDB, and can also be used as markers on the genetic map. They can be recognised by PCR followed by sequencing, but we also found that the SNPs we looked at could be visualised by SSCP analysis. We thank Jane Rogers and Amanda McMurray for their assistance in sequencing the clones.

Masahiro Matsuki et al. (2003) International Worm Meeting "GOA-1 participates in odorant avoidance and olfactory adaptation in C.elegans"

Masahiro Matsuki, Hirofumi Kunitomo, Yuichi Iino

[International Worm Meeting, 2003]

The Go class of heterotrimeric G proteins is abundantly expressed in mammalian brain. The nematode Caenorhabditis elegans has one gene, goa-1, encoding a homologue of the alpha subunit of Go, which is expressed throughout the C.elegans nervous system. Previous genetic and pharmacological studies showed that GOA-1 (Go) and EGL-30 (Gq) act antagonistically in modulating the neurotransmitter release at neuromuscular junctions. However, molecular functions of GOA-1 in sensory neurons and interneurons remain mostly unexplored. Here we focused on odorant chemotaxis, which is a complex behavior mediated by sensory neurons and interneurons, and tested whether GOA-1 participates in odor perception and/or processing of odor signals. A loss-of-function mutant of goa-1, goa-1(n1134), exhibited diminished long-range avoidance of the volatile repellent 2-nonanone, but showed enhanced avoidance of 1-octanol. Experiments using a heat-shock promoter to drive goa-1(+) in the goa-1(n1134) mutant indicated that GOA-1 activity supplied in the adult stage was sufficient for avoidance of 2-nonanone. In addition to the defects in odorant avoidance,we found that goa-1(n1134) mutants also have a defect in adaptation to the AWC-sensed odorant benzaldehyde. When goa-1(+) was expressed widely in the nervous system using the goa-1 or tax-6 promoter, adaptation defect of goa-1 mutants were fully rescued. On the other hand, expression using the promoter of che-2, which is expressed in all the amphid sensory neurons except AFD, did not readily rescue the defect, suggesting that GOA-1 may act in interneurons to process the adaptation signals. We continue our attempts to narrow down the cells in which goa-1 acts for benzaldehyde adaptation. To clarify whether the EGL-30 (Gq) signaling pathway is also required for odor adaptation, we tested the EGL-30 signaling mutants. eat-16 encodes an RGS, regulator of G protein signaling, which negatively regulates the EGL-30 (Gq). eat-16 mutants and animals in which egl-30(+) was overexpressed were defective in adaptation, suggesting that the EGL-30 (Gq) signaling pathway is also important for odor adaptation. We are grateful to Jane Mendel and Paul Sternberg for the goa-1 clones and the syIs36[egl-30(+)] strain, and Ikue Mori for the tax-6 promoter.

Sternberg, Paul et al. (2015) International Worm Meeting "WormBase 2015."

Berriman, Matt, Howe, Kevin, Kersey, Paul, Stein, Lincoln, Harris, Todd, Sternberg, Paul, Schedl, Tim

[International Worm Meeting, 2015]

WormBase has existed for 15 years and has evolved in many ways. The new website is fully operational and has made the process of adding new data types, displays, and tools easier. Behind the scenes we are piloting an overhaul of the underlying database infrastructure to allow us to handle the ever increasing data, have the website perform faster, and allow more frequent updates of information. This is a critical time for the project, as we face considerable pressure from two directions. The first is that our funders really want us to do more with less. We are responding to this by leading the way in making curation (the process of extracting information from papers and data sets into computable form) more efficient using a new version of Textpresso (to be released later this calendar year); by discussing with other model organism information resources ways to work together to be more efficient and inter-connected; and by seeking additional sources of funding. The second, delightful, pressure is an increase in data and results generated by the C. elegans and nematode communities. While we are handling this increase by changes in our software for curation, the database infrastructure, and the website, we do need your help. Many of you have helped us over the last few years to identify data in your papers or by sending us data directly. We now need you to help with a few types of information by submitting the data via specially designed, user-friendly forms that ensure good quality and the use of standard terminology. In particular, we have a large backlog of uncurated information associating alleles with phenotypes. We pledge to make this process as painless as possible, and to improve WormBase's description of phenotypes with your feedback, starting at this meeting at the WormBase booth, workshops and posters. With your help, continual improvement of our efficiency, and additional sources of funding, we are optimistic that we can do much more with even somewhat less effort.Consortium: Paul Davis, Michael Paulini, Gary Williams, Bruce Bolt, Thomas Down, Jane Lomax, Todd Harris, Sibyl Gao, Scott Cain, Xiaodong Wang, Karen Yook, Juancarlos Chan, Wen Chen, Chris Grove, Mary Ann Tuli, Kimberly Van Auken, D. Wang, Ranjana Kishore, Raymond Lee, John DeModena, James Done, Yuling Li, H.-M. Mueller, Cecilia Nakamura, Daniela Raciti, Gary Schindelman.

Masahiro Matsuki et al. (2005) International Worm Meeting "GOA-1 Go, EGL-30 Gq and the control of DAG levels are important for olfactory adaptation in C. elegans"

Yuichi Iino, Hirofumi Kunitomo, Masahiro Matsuki

[International Worm Meeting, 2005]

In the nematode Caenorhabditis elegans, a homolog of the alpha subunit of Go, encoded by the goa-1 gene, is known to negatively modulate the neurotransmitter release at neuromuscular junctions. However, molecular functions of GOA-1 in sensory neurons and interneurons remain mostly unexplored.We found that the loss-of-function mutant, goa-1(n1134), has a defect in adaptation to benzaldehyde. To identify the neurons in which goa-1 functions, expression of goa-1 was driven by various promoters in goa-1 mutants. When goa-1(+) was expressed in AWC chemosensory neurons using gcy-10, odr-3 or gpa-13 promoters, adaptation defects of goa-1 mutants were partially rescued. These results indicate that goa-1 functions mainly in AWC neurons to negatively modulate neuronal activity, although goa-1 may also function in some unidentified neurons.We further found that the syIs36 animals, in which egl-30 Gq gene is overexpressed, showed an adaptation defect. Overexpression of egl-30(gf) in AWC was sufficient to cause a severe defect in adaptation. Therefore, in AWC neurons, GOA-1 and EGL-30 signaling pathways modulate olfactory responses in opposite directions.Diacylglycerol (DAG) acts downstream of the Gq-PLC pathway. We found that exogenous phorbol ester, a DAG analogue, effectively disrupted olfactory adaptation. Previous reports revealed that dgk-1 gene encodes a DAG kinase (DGK) and therefore DAG levels are thought to be elevated in dgk-1 mutants. We tested whether dgk-1 also participates in modulating olfactory adaptation. Unexpectedly, olfactory adaptation in dgk-1 mutants was almost normal. In addition to dgk-1 mutants, mutants of dgk-3, which encodes a DGK and is expressed in a few sensory neurons including AWC, also showed normal adaptation. However, dgk-3;dgk-1 double mutants exhibited a severe adaptation defect, suggesting that DGK-1 and DGK-3 redundantly function to decrease the DAG levels in AWC neurons. These results indicate that a down-regulation of DAG levels through an inhibition of EGL-30 and/or activation of DGK is important for olfactory adaptation, and we propose that part of these processes are mediated by the GOA-1 Go signaling pathway.We are grateful to Jane E. Mendel and Paul W. Sternberg for goa-1 clones and syIs36[egl-30(+)] strain; Motomichi Doi and Kouichi Iwasaki for egl-30(gf) plasmids.