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.

Vargas, Elizabeth et al. (2017) International Worm Meeting "Trisomy correction occurs during both meiosis I and meiosis II."

Korf, Ian, Friedman, Jacob, McNally, Francis, McNally, Karen, Vargas, Elizabeth, Wang, David

[International Worm Meeting, 2017]

The vast majority of eukaryotes have exactly two copies of each chromosome and reproduce sexually through the process of meiosis. Accurate chromosome segregation requires the physical attachment of exactly two homologous chromosomes by a crossover so that each homologous chromosome can form attachments to opposite poles of a bipolar spindle. Thus a third copy of a chromosome might be expected to segregate randomly, resulting in 50% of progeny inheriting the extra chromosome. Hodgkin et al. (Genetics 91:67) reported that C. elegans with a third copy of the X chromosome have far fewer than 50% trisomic progeny. Cortes et al. (Elife 4:e06056) found that the preferential elimination of the extra X occurs during anaphase I of female meiosis. To test whether extra copies of all C. elegans chromosomes are preferentially eliminated, we scored the inheritance of three different DNA polymorphisms for each autosome among the progeny of triploid hermaphrodites mated with diploid males. For all 5 autosomes, the frequency of trisomic offspring was significantly less than expected from random segregation. Preferential elimination of the extra copy of chromosome V was confirmed by FISH. We also generated a trisomy IV worm strain and when trisomy IV hermaphrodites were mated to diploid males, the frequency of triplo IV progeny was again much lower than expected from random segregation. Cortes et al. (2015) found that univalent X chromosomes do not lose cohesion during anaphase I and thus lag before being preferentially captured by the polar body. Counting of mCherry:histone-labeled chromosomes in triploids revealed that chromosome number decreased between metaphase I and metaphase II and decreased again between metaphase II and diakinesis in the adult progeny. Data from live imaging of anaphase chromosome segregation and REC-8 staining of fixed meiotic spindles support a model in which some univalents remain intact during anaphase I whereas other univalents segregate apart at anaphase I. The resulting single chromatids then lag during anaphase II and are preferentially captured by the second polar body. These data demonstrate that asymmetric female meiotic divisions can correct triploidy and trisomy in C. elegans.

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

Thomas, Cristel G et al. (2011) International Worm Meeting "Evolution of Sex-biased Expression in the Caenorhabditis genus."

Korf, Ian, Smith, Harold E, Li, Renhua, Thomas, Cristel G, Haag, Eric S, Oliver, Brian

[International Worm Meeting, 2011]

Mating systems shape genome structures, both indirectly through their effects on population genetics and directly due to the genetic control of reproductive traits. Most extant Caenorhabditis species are gonochoristic (male/female), while the most studied species, C. elegans and C. briggsae, are androdioecious (self-fertile hermaphrodite/male). Both selfing species display an overall reduced ability to mate, suggesting that the selective pressure on maintaining efficient mating was weakened as selfing arose. The genes underlying these traits were likely to have been expressed in a sex-biased fashion in the gonochoristic ancestor, and we hypothesized that as selfing emerged their regulation was modified or they were lost altogether. This hypothesis is especially interesting given that selfing species have consistently smaller genome sizes than their gonochoristic relatives. We sought to address whether a disproportionate loss of genes with sex-biased expression accompanies the loss of mating-related traits in Caenorhabditis hermaphrodites. One approach uses RNA-seq to perform a comprehensive survey of adult sex-biased transcripts in C. japonica, C. brenneri, C. remanei and C. elegans fog-2(q71). This allows us to determine the overall number and fraction of sex-biased genes for each species, and hence test the above hypothesis genome-wide. Another approach involves identification and characterization of specific male genes lost in one or more hermaphrodites. Taken together, our results indicate a substantial erosion of reproductive genes has occurred in selfing lineages. We suggest that, with respect to reproductive biology, C. elegans and C. briggsae are actually rather poor models for the rest of Caenorhabditis.

Kelly WG et al. (1998) Development "Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans."

Fire A, Kelly WG

[Development, 1998]

The germline of the nematode Caenorhabditis elegans exhibits a remarkable ability to specifically silence transgenic DNA. We have shown that this silencing mechanism is disrupted in animals mutant for the maternal effect sterile genes mes-2, mes-3, mes-4 and mes-6. The proteins encoded by mes-2 and mes-6 have been shown to be related to the Polycomb Group of transcriptional repressors (Holdeman, R., Nehrt, S. and Strome, S. (1998). Development 125, 2457-2467; Korf, I., Fan, F. and Strome, S. (1998). Development 125, 2469-2478). These results suggest that a genetic silencing process is essential for sustained germline function, and that this silencing is mediated, at least in part, by Polycomb Group proteins.

Lin, Dawei et al. (2010) Worm Breeder's Gazette "A Web-based bioinformatics solution integrated with next generation sequencing to identify molecular lesions of a C. elegans mutant"

Nicolet, Charles, Starr, Daniel, Lu, Zhiwei, Boveda, Jose, Chang, Yu-Tai, Korf, Ian, Lin, Dawei

[Worm Breeder's Gazette, 2010]

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.

Yin, Da et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "GENOMIC AND FUNCTIONAL CHARACTERIZATION OF GENOME SHRINKAGE IN CAENORHABDITIS"

Meyer, Barbara J., Haag, Eric S., Schartner, Caitlin M., Ralston, Edward J., Korf, Ian, Thomas, Cristel G., Yin, Da, Schwarz, Erich M.

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Sexual mode evolves rapidly in some eukaryotic lineages. This is expected to have pronounced consequences for population genetics, sexual differentiation and the nature and intensity of sexual selection, all of which may be reflected in the genome. C. elegans is a self-fertile species, derived recently from an obligately outcrossing male-female ancestor.This trait has evolved in at least two other species of the Elegans sub-genus, C. briggsae and C. sp. 11 (Kiontke et al. 2011). Previous studies indicate that selfing species have smaller genomes and several thousand fewer protein-coding genes than their outcrossing ancestors (Thomas et al. 2012). This reproducibility may be stimulated by an interaction between partial selfing and segregation distortion affecting large indels in male meiosis (Wang et al. 2010). However, the size, location, and gene content of specific deletions remain unknown for any natural system. To characterize the process of genome shrinkage, we have produced a genome assembly from the closest known outcrossing relative of C. briggsae, C. nigoni (formerly C.sp. 9; Felix et al. 2014). The C. nigoni genome is roughly 20 Mb (20%) larger than that of C. briggsae. By comparing C. nigoni contigs with the chromosome-level assembly for C. briggsae, we created an approximation of the C. nigoni physical map. Genome-wide sequence alignment showed the majority of the size reduction is located on the two arms of the five autosomes. Using C. sp.5 as an outgroup, we are able to identify gene family reductions, as well as specific genes recently lost in the C. briggsae lineage. Finally, we present detailed characterization of a family of rapidly evolving proteins that were independently lost in C. elegans and C. briggsae, the MSS (male-specific secreted) family, We have characterized their temporal and spatial expression, and find they are likely to be transferred to the female reproductive tract. We are now developing assays to reveal potential physiological responses to MSS proteins in females, including using calcium imaging to localize putative responder cells in female reproductive tract. References Felix, M.-A., C. Braendle, et al. (2014). "A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species." PLoS One 9: e94723.Kiontke, K., M.-A. Felix, et al. (2011). "A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits." BMC Evol Biol 11: 339.Thomas, C. G., R. Li, et al. (2012). "Simplification and desexualization of gene expression in self-fertile nematodes." Curr Biol 22: 2167-2172.Wang, J., P. J. Chen, et al. (2010). "Chromosome size differences may affect meiosis and genome size." Science 329: 293.

Korf I et al. (1994) Worm Breeder's Gazette "Cloning mes-6."

Strome S, Korf I

[Worm Breeder's Gazette, 1994]

Cloning mes-6 Ian Korf and Susan Strome Department of Biology, Indiana University, Bloomington, Indiana, 47405 mes-6 was identified through screens for maternal effect sterile loci. Its phenotype is similar to that of mes-2, mes- 3. and mes-4. Homozygous mutants at these loci produce progeny with few germ nuclei and no gametes. We are cloning these genes to better understand their function. mes-6 is located between unc-24 and fem-3 on LG IV. The physical map of this region is shown in Figure 1. Using transformation rescue, we were able to identify a YAC (Y59Hl 1) and a cosmid (T12D3) that contain mes-6. Single restriction fragments of T12D3 did not rescue but a curious phenomenon was observed: a 7.2 kb Eco RV fragment induced an array-dependent dominant sterile phenotype. We hypothesized that this may be due to a portion of the gene acting in a dominant negative manner. A mixture of the Eco RV fragment and an overlapping Pst I fragment rescued mes-6. These fragments were used to probe a Northern blot. Only one transcript hybridized to both restriction fragments. This 2.0 kb transcript is enriched in strains containing oocytes (N2 and fem-2 lf) relative to those without a germ line or containing only sperm (glp-4 and fem-3 gf). This maternal expression is consistent with the mutant's maternal-effect phenotype. The Pst I restriction fragment detected another 1.2 kb maternal transcript. The cDNA corresponding to this transcript maps very close to the 2.0 kb transcript and they may define an operon. In order to prove that the 2.0 kb transcript is mes-6. we translationally fused a 3.1 kb Sac I genomic fragment, containing the 5' half of the gene and upstream sequences, to a 1.0 kb cDNA fragment containing the 3' half. This construct rescues mes-6. The data are surnmarized in Figure 2. Sequencing of both and the neighboring gene is in progress.

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.