Frederick Tan et al. (2001) International C. elegans Meeting "Identifying promoter motifs and predicting gene expression patterns in C. elegans using data mining tools."

Dung Phu, Julia Krushkal, Carolina Ruiz, Frederick Tan, Elizabeth Ryder, Ian Pushee, Brian Murphy

[International C. elegans Meeting, 2001]

Papp, Andy et al. (2009) International Worm Meeting "Investigation of Low-cost GFP Microscopy."

Papp, Andy, Aldrich, Chris, Bangalore, Srikanth, Perry, David

[International Worm Meeting, 2009]

The Green Fluorescent Protein (GFP) gene from the fluorescent jellyfish Aequorea victoria, and its variants (such as EGFP), are used extensively to study the location and timing of gene expression in transgenic animals and plants (Chalfie et al, 1994). Resultant GFP fusion proteins are especially well-suited to studying in vivo gene expression patterns in the transparent nematode, C. elegans and the transparent larva of the fly D. melanogaster. Perhaps one of the most significant limitations to its use in large-scale genetic screens is the high cost of equipment needed to observe GFP microscopically - namely the Fluorescence Dissecting Stereomicroscope for screening and picking mutants and upright and inverted epi-fluorescent compound microscopes for more detailed studies. Commercially available Fluorescence Dissecting Stereomicroscopes typically sell in the midrange between US$10,000 and US$20,000. They are offered by only the "high-end" microscope companies, based upon their most expensive dissecting scopes, and incorporate their premium-priced mercury arc-lamp illuminators, power supplies and epi-fluorescence modules. This leads us to wonder whether it is possible to cut corners without sacrificing utility, and which corners can be cut. Since the inception of GFP-based expression screens, a variety of researchers have produced custom-made and home-made GFP dissecting scopes. These include, for example, Welcome Bender (Harvard Medical School, pers. comm.) and Ian Chin-Sang (Chin-Sang, 2004). There are several possibilities to consider toward lowering the cost of a Fluorescence Dissecting Stereomicroscope. It may be possible to get sufficient light from relatively inexpensive, long-lived, lower-power-consuming Light Emitting Diodes (LEDs) vs. mercury arc lamps. Depending upon the spectral specificity of the LEDs, filters or dichroic mirrors might be omitted. Getting enough light intensity of the precise wavelengths that excite GFP fluorescence focused onto the sample is important. The exciting beam can be provided directly or focused backward through the microscope using "epi-illumination". We will explore these possibilities and report (and possibly demonstrate) the results. Chin-Sang, Ian. (2004) GFP Stereoscope Using LED light source. Queen''s University, Kingston, ON, Canada. http://130.15.90.245/gfp_stereoscope.htm.

Biron RW et al. (1996) East Coast Worm Meeting "gon-2: Expression and Function by Inference."

Sun Y-a, Biron RW, Lambie EJ

[East Coast Worm Meeting, 1996]

The somatic gonad of C. elegans develops entirely from the postembryonic blast cells, Z1 and Z4. gon-2 is required for the division and differentiation of these cells. All of the alleles of gon-2 that we have isolated cause a partial maternal-effect gonadless (Gon) phenotype. Tissues other than the somatic gonad appear unaffected. The degree of gonad development is variably penetrant for all alleles; in some animals, Z1 and Z4 fail to divide at all. Cell lineage and pes-1::lacZ expression studies in Gon animals suggest that gon-2 acts to regulate the timing of division of Z1, Z4 and their descendants (thanks to Ian Hope for pes-1::lacZ). q388 is temperature sensitive, and has a more penetrant phenotype than any of the other alleles. The TSP of the Gon phenotype of q388 suggests that gon-2 translation may begin early in embryogenesis, well before the birth of Z1 and Z4. We are currently using a cosmid that rescues gon-2 for mosaic analysis. At the moment, the genome project ftp site is only one cosmid away from gon-2. So, by the time of the meeting we should have some idea about the possible sequence of the gene.

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

Francesca Palladino et al. (1997) International C. elegans Meeting "Towards the isolation of a cec-1 mutant"

Fritz Mueller, Francesca Palladino

[International C. elegans Meeting, 1997]

The chromo domain was originally identified in Drosophila as a sequence motif common to the Polycomb repressor protein (PC) and the heterochromatin-associated protein HP1. Other proteins containing this motif have subsequently been identified in a number of species from plants to mammals. This conserved domain appears to be common to chromatin-associated proteins. The C. elegans gene cec-1 encodes a chromo domain-containing nuclear protein present in all somatic cells from the 50-80 cell-stage onwards to adult animals. CEC-1 protein is not detected in early embryos and germ cells, while cec-1 mRNA is present in all blastomeres of the early embryo. Immunolocalization experiments show a homogeneous distribution of CEC-1 within interphase nuclei. The expression pattern of CEC-1 suggests that it represents a novel chromosome-associated protein in C. elegans. (Agostoni et al. 1996) In order to study the function of cec-1, we are attempting to isolate a mutation in this gene. A Tc1 insertion was isolated in the laboratory of Dr. Ian Hope (Leeds University) from which we are trying to isolate a deletion derivative. As a parallel approach, we are also testing the possibility that the cec-1 coding region rescues candidate lethal mutations in transgenic strains.

Karishma Sadikot et al. (2006) Development & Evolution Meeting "A Novel Dosage Compensation Protein with Chromosome Segregation Functions"

Karishma Sadikot, Barbara Meyer, Nizar Taki, Gyorgyi Csankovszki, Emily Petty

[Development & Evolution Meeting, 2006]

The C. elegans dosage compensation complex (DCC) assembles on hermaphrodite X chromosomes to downregulate gene expression two-fold. This ensures equal amounts of X-linked gene products in XX hermaphrodites and XO males. The DCC is similar to the 13S condensin complex, which is essential for mitotic and meiotic chromosome segregation. The four known DCC subunits are homologous to four of the five condensin proteins. In search of the fifth DCC subunit, antibodies against the unique dosage compensation protein, DPY-27, were used to immunoprecipitate the DCC from embryonic extracts. In collaboration with Ian McLeod and John R. Yates III, MUD-PIT analyses of precipitated proteins identified a novel DCC subunit, the protein encoded by F29D11.2. PSI -BLAST identified F29D11.2 as the homolog of the condensin subunit CAP-G. Using RNAi, we confirmed that this protein plays a role in dosage compensation. F29D11.2 is required for localization of other DCC subunits, and it will only localizes to the X in the presence of all other subunits, indicating that the protein is an integral member of the worm DCC. Interestingly, F29D11.2 appears to also interact with the worm mitotic condensin. Our preliminary results indicate that the protein is present in immunoprecipitated mitotic condensin complexes. The protein also appears to localize to germline nuclei. Furthermore, animals homozygous for a null mutation in F29D11.2 arrest during larval development with chromosome segregation defects, including chromatin bridges connecting interphase nuclei. These results suggest that F29D11.2 may function in both dosage compensation and mitotic and meiotic chromosome segregation.

Polinko E et al. (1997) International C. elegans Meeting "The Role of CKS-1 in Embryogenesis"

Strome S, Korf I, Polinko E

[International C. elegans Meeting, 1997]

The cks-1 (cyclin-dependent kinase subunit) gene product has been implicated in regulation of the cell cycle in organisms from yeast to frogs. Although it is known that cks-1 is an essential gene in yeast, whose product physically interacts with both cdk (cyclin-dependent kinase) and cyclins, a clear picture of the exact role of cks-1 in the cell cycle has yet to be uncovered. Our lab obtained a C. elegans cks-1 homolog as a downstream gene in an operon with mes-6 (cloned by Ian Korf). This C. elegans homolog provides an opportunity to analyze the in vivo role of cks-1 in both meiosis and mitosis in a multicellular organism. Toward this end, we have injected antisense cks-1 RNA into the germline of wild-type hermaphrodites and analyzed their progeny. We have analyzed the development of these "antisensed embryos" by Nomarski, as well as by immuno- fluorescence staining of centrosomes, microtubules, and DNA. These embryos show a delay/block in the completion of meiosis and in progression through mitosis. The mitosis defect appears to be an arrest of chromosomes at a stage before anaphase, although the MTOCs continue to duplicate and set up new spindles. Our results support the hypothesis that C. elegans CKS-1 serves an essential role in both meiosis and mitosis, and that the mitosis role may be at the metaphase-to-anaphase transition. We are currently investigating at what point the delays/blocks in meiosis and mitosis occur, and we are attempting to immunolocalize CKS-1 in C. elegans.

Martinelli SD et al. (1997) International C. elegans Meeting "ACEDB IN 1997"

Thierry-Mieg J, Durbin RM, Martinelli SD

[International C. elegans Meeting, 1997]

The ACEDB worm genome database has been released more frequently since 1995, approaching monthly. It currently uses 500 MB disk space, having doubled since May 1996, and we expect this to double again in the next year as the genomic sequence is finished (more space is required when building from updates). For those not requiring the genomic sequence, we now also make available a smaller database of around 60MB containing all other information. Regular data sources include bibliography, address and strain lists (CGC), genomic sequence and analysis (Consortium), WBG and WM abstracts (Leon Avery), physical map (Alan Coulson), EMBL sequences. Genetic data and gene expression data come to us continuously but irregularly, either from members of the worm community or from a literature search. Data from the current call for genetic data (WBG 14.5) will be included this summer, in conjunction with the new map from the CGC. In 1996, new classes were added for gene expression information: Expr_pattern, Life_stage, Cell_group. Our thanks to Ian Hope for initiating this, and to his lab and Donna Albertson for early data. More extensive use of these classes requires more active input from the community. We are endeavouring to provide connections between Genes/Strains/Clones/Sequences and expression data, as well as to Papers/WBG articles. We plan during this year to provide graphical WWW access to ACEDB. We would value other suggestions for new user interfaces, new types of data, further connections between classes or improved terminology. ACEDB ftp sites are ncbi.nlm.nih.gov/repository/acedb/, ftp.sanger.ac.uk/pub/acedb/, lirmm.lirmm.fr/genome/acedb/.

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.

Consortium Wormbase (2000) Worm Breeder's Gazette "Update on the C. elegans database WormBase"

Consortium Wormbase

[Worm Breeder's Gazette, 2000]

WormBase (www.wormbase.org) is an international consortium of biologists and computer scientists 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 builds upon the existing ACeDB database of the C. elegans genome by providing curation from the literature, an expanded range of content and a user friendly web interface. The team that developed and maintained ACeDB (Richard Durbin, Jean Thierry-Mieg) remains an important part of WormBase. Lincoln Stein and colleagues at Cold Spring Harbor are leading the effort to develop the user interface, including visualization tools for the genome and genetic map. Teams at Sanger Centre (led by Richard Durbin) and the Genome Sequencing Center at Washington University, St. Louis (led by John Spieth) continue to curate the genomic sequence. Jean and Danielle Thierry-Mieg at NCBI spearhead importation of large-scale data sets from other projects. Paul Sternberg and colleagues at Caltech will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level; and gene interactions. Paul Sternberg assumes overall responsibility for WormBase, and is delighted to hear feedback of any sort. WormBase has recently received major funding from the National Human Genome Research Institute at the US National Institutes of Health, and also receives support from the National Library of Medicine/NCBI and the British Medical Research Council. WormBase is an expansion of existing efforts, and as such continues to need you help and feedback. Even with the increased scope and funding, all past contributors to ACeDB remain involved. The Caenorhabditis Genetics Center (Jonathan Hodgkin and Sylvia Martinelli) collaborate with WormBase to curate the genetic map and related topics. Ian Hope and colleagues continue to supply expression data to WormBase. Leon Avery will continue his superb website and serves as one advisor to WormBase. While the major means of access to WormBase is via the world wide web, downloadable versions of WormBase as well as the acedb software engine will continue to be available.