Oh S et al. (2012) J Appl Microbiol "The bacterial signalling molecule indole attenuates the virulence of the fungal pathogen Candida albicans."

Oh S, Kim Y, Go GW, Mylonakis E

[J Appl Microbiol, 2012]

AIMS: Indole is a signalling molecule, produced by a number of Gram-positive and Gram-negative bacteria both in nature as well as clinical environments. Here, we explored the effect of bacterial indole and one of its main derivatives on the virulence of the fungal pathogen Candida albicans. METHODS AND RESULTS: We found that indole and its derivate indole-3-acetonitrile (IAN) did not affect the viability of C. albicans. Interestingly, indole and IAN repressed C. albicans biofilm formation as well as the attachment of C. albicans to intestinal epithelial HT-29 cells and inhibited the ability of the yeast to make filaments that are the main virulence factor of C. albicans. In addition, we used the heterologous model host Caenorhabditis elegans to demonstrate in vivo that the presence of indole or IAN attenuates C. albicans infection (P = 0.0188 and P < 0.0001 for indole and IAN, respectively, compared to worms exposed to C. albicans DAY185 alone) and decreases fungal colonization in the nematode gut. Importantly, quantitative real-time polymerase chain reaction (qRT-PCR) results showed that in C. albicans, indole and IAN strongly stimulated the transcription of NRG1. CONCLUSIONS: Indole and IAN attenuates fungal virulence by regulating the transcription of NRG1, a transcriptional factor that influences filamentation and biofilm formation in C. albicans. SIGNIFICANCE AND IMPACT OF THE STUDY: Our findings indicate that the bacterial signalling molecules indole and its derivatives play an inter-kingdom role in dynamic network of microbiota and directly modulate the virulence of fungal C. albicans via NRG1.

James H Mapes et al. (2005) International Worm Meeting "Characterization of C. elegans annexins, a family of calcium dependent phospholipid binding proteins."

James H Mapes, Ian Arnold, Ding Xue

[International Worm Meeting, 2005]

Alteration of phospholipid asymmetry plays an important role in regulating several important biological processes such as blood coagulation and recognition of apoptotic cells during phagocytosis. Phosphatidylserine (PS) is normally restricted to the inner leaflet of plasma membrane but is externalized during apoptosis. Externalized PS has been suggested to be an eat-me signal for phagocytosis of apoptotic cells. We are interested in understanding how phospholipid asymmetry is generated, recognized, and interpreted during various biological processes. Annexins are a family of calcium-dependent phospholipid binding proteins that may be involved in interpreting phospholipid asymmetry. There are four annexin genes in C. elegans, nex-1, nex-2, nex-3 and nex-4. RNAi treatment of nex-1 causes defects in the clearance of apoptotic cells (1). Interestingly, human Annexin I serves as an adaptor between externalized PS on apoptotic cells and engulfment receptors on macrophages (1). In order to understand the potential functions of the four C. elegans nex genes, we characterized their expression and subcellular localization patterns using GFP fusion proteins and the phenotypes of RNAi-treated animals or deletion mutants. We found that NEX-1, NEX-2, and NEX-3 were broadly expressed in C. elegans and had significant overlaps in their expression patterns. The expression of NEX-4 was restricted to several neurons in the head and tail. The expression of all four NEX genes was not readily apparent until the 4-fold embryonic stage, after most cell deaths and clearance of corpses have occurred. Examination of RNAi-treated animals or two nex gene deletion mutants, nex-1(gk148) and nex-4(gk102), did not reveal any defect in apoptosis, cell corpse engulfment, or other detectable phenotypes. Construction and characterization of double, triple, or quadruple mutants that are defective in multiple nex genes may be important to reveal if nex genes play a role in cell corpse removal or other biological processes. (1) Arur S, Uche UE, Rezaul K, Fong M, Scranton V, Cowan AE, Mohler W, and Han DK (2003). Annexin I is an endogenous ligand that mediates apoptotic cell engulfment. Dev. Cell 4:587-598.

Brownlee DJA et al. (1996) Parasitol Today "Nematode neuropeptides: Localization, isolation and functions."

Holden-Dye L, Brownlee DJA, Walker RJ, Fairweather I

[Parasitol Today, 1996]

Historically, peptidergic substances (in the form of neurosecretions) were linked to moulting in nematodes. More recently, there has been a renewal of interest in nematode neurobiology, initially triggered by studies demonstrating the localization of peptide immunoreactivities to the nervous system. Here, David Brownlee, Ian Fairweather, Lindy Holden-Dye and Robert Walker will review progress on the isolation of nematode neuropeptides and efforts to unravel their physiological actions and inactivation mechanisms. Future avenues for research are suggested and the potential exploitation of peptidergic pathways in future therapeutic strategies

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/.