-
[
European Worm Meeting,
2008]
Histone methylation is a dynamic process that involves enzymes deposing or. removing methyl marks. Histone H3 lysine methyltransferases (H3KMTs) and. demethylases (H3KDMs) are critical to generate the chromatin structure. necessary to establish the epigenetic program of the cells during. development. High levels of methylation on H3K4 or H3K27 are associated to. either activation or repression of transcription, respectively. These marks. are also responsible for the formation of bivalent domains, a chromatin. state regulating expression of key developmental genes. Interestingly, the. enzymes that regulate the methylation levels of these marks can be found. within the same protein complex. This suggests that they may share. biological functions. Here we investigate the role of the H3K4MT, SET-16. MLL3, and the H3K27DM, UTX-1, during vulval development. Using a. hypersensitive background for Ras signalling, we show that both enzymes. prevent erroneous adoption of the vulval fate, and that either enzyme. attenuates LET-23 EGFR (epidermal growth factor receptor) signalling. We. have also found that SET-16 MLL3 or UTX-1 positively regulate expression of.
ajm-1, an apical junction molecule. Importantly, RNAi of
ajm-1 causes a. synthetic multivulvae phenotype identical to the one caused by
set-16.
mll3(RNAi) or
utx-1(RNAi). These results suggest that UTX-1 and the SET-16. MLL3 complex regulate vulval fate adoption, at least in part by activation. of
ajm-1 expression, and by regulating H3K4 or H3K27 methylation levels.. Do not add objects such as pictures, boxes, headers, footers, footnotes,. etc.
-
[
European Worm Meeting,
2008]
The LET-23 EGFR (epidermal growth factor receptor) signaling pathway plays. a critical role in the development of the Caenorhabditis elegans vulva.. Mutations in genes that regulate this pathway result in abnormal vulva. phenotypes. Furthermore, the fact that the LET-23 pathway is often. dysregulated in cancers means that to fully elucidate this pathway would. have an impact on cancer research. RNA interference (RNAi) is an extremely. effective tool in studying gene function in vivo. Using this technique we. have performed a large-scale RNAi screen in a
gap-1 background in order to. identify novel attenuators of the LET-23 signaling pathway. Mutated genes. that negatively regulate this pathway can result in a multivulva phenotype. (Muv) or synthetic Muv (synMuv). We have screened ~8,500 genes, looking for. those that resulted in a synMuv phenotype with
gap-1. From this screen we. have identified roughly 200 candidates of which, 36 were high confidence. attenuators of the LET-23 signaling pathway. Within this group there were. genes involved in chromatin remodeling, cell signaling, sumolylation and. the cell cycle. These 36 genes were then further analysed for persistent. expression of EGL-17::CFP (an indicator of high levels of Ras signaling) in. the secondary cells of the vulva. By screening ~40% of C.elegans genome. using RNAi we have identified novel components of the LET-23 signaling. pathway. It may be possible to now go on to identify further attenuators by. mining databases such as WormNet (www.functionalnet.org/wormnet/).
-
[
C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany,
2010]
The conserved Mixed Lineage Leukaemia (MLL) complex deposits activating methyl marks on histone tails through a methyltransferase (MT) activity. Here we provide in vivo evidence that in addition to methylation, the C. elegans MLL-like complex can remove specific methyl marks linked to repression of transcription. This supports the proposed model in which the MLL complex orchestrates both the deposition and the removal of methyl marks to activate transcription. We have uncovered the MLL-like complex in a large-scale RNAi screen designed to identify attenuators of RAS signalling during vulval development. We have also found that the histone acetyltransferase complex, NuA4/TIP60, cooperates with the C. elegans MLL-like complex in the attenuation of RAS signalling. Critically, we show that both complexes regulate a common novel target and attenuator of RAS signalling, AJM-1 (Apical Junction Molecule-1). Therefore, the C. elegans MLL-like complex cooperates with the NuA4/TIP60 complex to regulate the expression of a novel effector, AJM-1.
-
Vintilla, Adriana, Fisher, Kate, Whitmarsh, Alan, Samsudin, Nurulhafizah, Fei, Pang Yoke, Velichkova, Gabriel, Poulin, Gino
[
International Worm Meeting,
2021]
Histone 3 lysine 4 methylation (H3K4me) is an epigenetic mark regulating transcription, metabolism, and longevity. H3K4me necessitates, in addition to KMT2 enzymes, the conserved core components WDR5, ASH2, and RBBP5. In C. elegans, deficiency in WDR-5 or ASH-2 reduces H3K4me3 levels and extends lifespan. Transgenerational experiments whereby only the parental generation is deficient in WDR-5 or ASH-2 leads to incomplete reprogramming of the next generation resulting in long-lived descendants. Whether RBBP-5 has similar functions remains unclear. Herein, using spike in ChIP-seq, we show that RBBP-5 is required for H3K4 mono- and multi-methylation and adults lacking RBBP-5 are short-lived. In contrast with WDR-5 or ASH-2 deficiencies, our transgenerational experiments show that reprogramming of the next wild type generation is normal. Instead, we revealed that RBBP-5-deprived descendants originating from mothers heterozygous for the
rbbp-5 deficiency inherit a wild type lifespan. However, at the fifth generation the
rbbp-5(-) short-lived phenotype fully manifest. Using RNA-seq and reporter assays, we found that RBBP-5 is important to maintain mitochondrial bioenergetic and core translational functions. We also show that restoring RBBP-5 expression in the soma is sufficient to recapitulate the wild type lifespan, hence ruling out the germlines as the primary site for H3K4me longevity promoting functions. Collectively, this work shows RBBP-5 regulated H3K4me promotes longevity and wild type lifespan can be epigenetically transmitted to H3K4me-depleted descendants most likely by a mechanism alleviating mitochondrial and translational dysfunctions in somatic cells.
-
[
Vet Res,
2015]
The poultry-associated bacterium Mycoplasma iowae colonizes multiple sites in embryos, with disease or death resulting. Although M. iowae accumulates in the intestinal tract, it does not cause disease at that site, but rather only in tissues that are exposed to atmospheric O2. The activity of M. iowae catalase, encoded by katE, is capable of rapid removal of damaging H2O2 from solution, and katE confers a substantial reduction in the amount of H2O2 produced by Mycoplasma gallisepticum katE transformants in the presence of glycerol. As catalase-producing bacteria are often beneficial to hosts with inflammatory bowel disease, we explored whether M. iowae was exclusively protective against H2O2-producing bacteria in a Caenorhabditis elegans model, whether its protectiveness changed in response to O2 levels, and whether expression of genes involved in H2O2 metabolism and virulence changed in response to O2 levels. We observed that M. iowae was in fact protective against H2O2-producing Streptococcus pneumoniae, but not HCN-producing Pseudomonas aeruginosa, and that M. iowae cells grown in 1% O2 promoted survival of C. elegans to a greater extent than M. iowae cells grown in atmospheric O2. Transcript levels of an M. iowae gene encoding a homolog of Mycoplasma pneumoniae CARDS toxin were 5-fold lower in cells grown in low O2. These data suggest that reduced O2, representing the intestinal environment, triggers M. iowae to reduce its virulence capabilities, effecting a change from a pathogenic mode to a potentially beneficial one.
-
[
PLoS One,
2014]
Mycoplasma iowae is a well-established avian pathogen that can infect and damage many sites throughout the body. One potential mediator of cellular damage by mycoplasmas is the production of H2O2 via a glycerol catabolic pathway whose genes are widespread amongst many mycoplasma species. Previous sequencing of M. iowae serovar I strain 695 revealed the presence of not only genes for H2O2 production through glycerol catabolism but also the first documented mycoplasma gene for catalase, which degrades H2O2. To test the activity of M. iowae catalase in degrading H2O2, we studied catalase activity and H2O2 accumulation by both M. iowae serovar K strain DK-CPA, whose genome we sequenced, and strains of the H2O2-producing species Mycoplasma gallisepticum engineered to produce M. iowae catalase by transformation with the M. iowae putative catalase gene, katE. H2O2-mediated virulence by M. iowae serovar K and catalase-producing M. gallisepticum transformants were also analyzed using a Caenorhabditis elegans toxicity assay, which has never previously been used in conjunction with mycoplasmas. We found that M. iowae katE encodes an active catalase that, when expressed in M. gallisepticum, reduces both the amount of H2O2 produced and the amount of damage to C. elegans in the presence of glycerol. Therefore, the correlation between the presence of glycerol catabolism genes and the use of H2O2 as a virulence factor by mycoplasmas might not be absolute.
-
[
Mol Brain,
2021]
Aim: Experimental animals, such as non-human primates (NHPs), mice, Zebrafish, and Drosophila, are frequently employed as models to gain insights into human physiology and pathology. In developmental neuroscience and related research fields, information about the similarities of developmental gene expression patterns between animal models and humans is vital to choose what animal models to employ. Here, we aimed to statistically compare the similarities of developmental changes of gene expression patterns in the brains of humans with those of animal models frequently used in the neuroscience field.Methods: The developmental gene expression datasets that we analyzed consist of the fold-changes and P values of gene expression in the brains of animals of various ages compared with those of the youngest postnatal animals available in the dataset. By employing the running Fisher algorithm in a bioinformatics platform, BaseSpace, we assessed similarities between the developmental changes of gene expression patterns in the human (Homo sapiens) hippocampus with those in the dentate gyrus (DG) of the rhesus monkey (Macaca mulatta), the DG of the mouse (Mus musculus), the whole brain of Zebrafish (Danio rerio), and the whole brain of Drosophila (D. melanogaster).Results: Among all possible comparisons of different ages and animals in developmental changes in gene expression patterns within the datasets, those between rhesus monkeys and mice were highly similar to those of humans with significant overlap P-value as assessed by the running Fisher algorithm. There was the highest degree of gene expression similarity between 40-59-year-old humans and 6-12-year-old rhesus monkeys (overlap P-value = 2.1 10- 72). The gene expression similarity between 20-39-year-old humans and 29-day-old mice was also significant (overlap P = 1.1 10- 44). Moreover, there was a similarity in developmental changes of gene expression patterns between 1-2-year-old Zebrafish and 40-59-year-old humans (Overlap P-value = 1.4 10- 6). The overlap P-value of developmental gene expression patterns between Drosophila and humans failed to reach significance (30 days Drosophila and 6-11-year-old humans; overlap P-value = 0.0614).Conclusions: These results indicate that the developmental gene expression changes in the brains of the rhesus monkey, mouse, and Zebrafish recapitulate, to a certain degree, those in humans. Our findings support the idea that these animal models are a valid tool for investigating the development of the brain in neurophysiological and neuropsychiatric studies.
-
[
CBE Life Sci Educ,
2008]
The skill set required of biomedical researchers continues to grow and evolve as biology matures as a natural science. Science necessitates creative yet critical thinking, persuasive communication skills, purposeful use of time, and adeptness at the laboratory bench. Teaching these skills can be effectively accomplished in an inquiry-based, active-learning environment at a primarily undergraduate institution. Cell Biology Techniques, an upper-level cell biology laboratory course at St. John Fisher College, features two independent projects that take advantage of the biology of the nematode Caenorhabditis elegans, a premier yet simple model organism. First, students perform a miniature epigenetic screen for novel phenotypes using RNA interference. The results of this screen combined with literature research direct students toward a singe gene that they attempt to subclone in the second project. The biology of the chosen gene/protein also becomes an individualized focal point with respect to the content of the laboratory. Progress toward course goals is evaluated using written, oral, and group-produced assignments, including a concept map. Pre- and postassessment indicates a significant increase in the understanding of broad concepts in cell biological research.
-
[
Worm Breeder's Gazette,
1992]
After tabulating the results of the Worm Plate Survey. we have come up with some interesting results. Most notably. the high variability in prices that labs are paying for their plates, even for the exact same plates from the same supplier, and the fact that most plates are marked up considerably over the actual cost. The replies can be separated into 4 categories: Labs that get plates from Fisher ($29-$58). but wish they had non-vented plates Labs that get non-vented plates via Applied Scientific (~$38) Labs that get plates from Falcon (vented) or Nunc (non-vented) and pay much more Most labs' plates were "slipable" or "semi-stackable", but all labs wanted plates that stack well for easy manual pouring, seeding, carrying, and using. Everyone wanted plates with shallow lids such that the bottoms can be lifted out of the tops for inverted use. Some labs expressed an interest in plates slightly smaller than "60 mm". That number is in quotes because all of the companies' plates have bottoms smaller than 60 mm (e.g. Fisher -54 x 14 mm). We have negotiated with the plastic companies that really make the plates for Fisher, Applied Scientific, etc. (that actually just resell them to you). I have come to the conclusion that we can provide you with better worm plates, the same worm plates cheaper, or in most cases better worm plates cheaper. This is true for every lab. The bottom line is that we can get you top quality non-vented "60 mm" plates (like Applied Scientific's, except fully stackable) for about $29 per 500 case INCLUDING shipping depending on your usage and how many cases you can receive at one time. Several labs have found the non-vented plates last longer without drying out or getting contaminated, compared with normal vented plates, so you should save that way, too. We offer full service shipping (e.g. standing orders and same-day telephone orders, free. Similarly low prices are available on 100 mm and 150 mm plates that exceed industry standards for flatness (reducing media usage) and clarity. The 100 mm are about $27 per 500 case plus shipping; The 150 mm dishes (good for DNA & RNA preps and library platings, with more than 2.25x the surface area of 100 mm dishes) are made thicker and deeper than industry standards and are about $21.50 per 100 case plus shipping. The shipping charge is very low for labs, or groups of labs in one city, that can take delivery of many cases in a single shipment. You can even suggest that your stockroom order plates from us. Call us for an exact price quote depending on your usage and how many cases you can receive at one time. In any case, we'll work things out to save you money. In the future, we can offer inexpensive 35 mm dishes if the community at large can order about 2000 cases per year, so let me know about your needs for other sizes. The response was very mixed about pre-poured plates. We may set that up later, but for now we can help the most by saving you lots on empty petri dishes (and later, maybe media .supplies). We are happy to send out free samples so you can examine the dishes. If we haven't contacted you yet, just give us a call. Respondents: 38 (including 5 anonymous) "Winners": Horvitz = 550, Meyer = 400, Thomas = 400, Greenwald = 300 200-299 cases 8 labs 100-199 cases 7 labs 4-99 cases 19 labs Highest price per case: US = 118.75, Canada = $117 (non-vented) Lowest price per case: US = $29, Canada = $25 (vented) Farthest away response: Malta! No responses from MRC or anyone else in Europe or Asia. It is possible that we can save money and/or provide better plates for these labs, including, shipping, too. Let us know.
-
Sternberg PW, Ansell BRE, Andrews KT, Nowell C, Chang BCH, Hofmann A, Crawford S, Korhonen PK, Baell J, Gijs MAM, Fisher GM, Young ND, Preston S, Mouchiroud L, Gasser RB, Jabbar A, Auwerx J, Davis RA, McGee SL, Cornaglia M
[
FASEB J,
2017]
As a result of limited classes of anthelmintics and an over-reliance on chemical control, there is a great need to discover new compounds to combat drug resistance in parasitic nematodes. Here, we show that deguelin, a plant-derived rotenoid, selectively and potently inhibits the motility and development of nematodes, which supports its potential as a lead candidate for drug development. Furthermore, we demonstrate that deguelin treatment significantly increases gene transcription that is associated with energy metabolism, particularly oxidative phosphorylation and mito-ribosomal protein production before inhibiting motility. Mitochondrial tracking confirmed enhanced oxidative phosphorylation. In accordance, real-time measurements of oxidative phosphorylation in response to deguelin treatment demonstrated an immediate decrease in oxygen consumption in both parasitic (Haemonchus contortus) and free-living (Caenorhabditis elegans) nematodes. Consequently, we hypothesize that deguelin is exerting its toxic effect on nematodes as a modulator of oxidative phosphorylation. This study highlights the dynamic biologic response of multicellular organisms to deguelin perturbation.-Preston, S., Korhonen, P. K., Mouchiroud, L., Cornaglia, M., McGee, S. L., Young, N. D., Davis, R. A., Crawford, S., Nowell, C., Ansell, B. R. E., Fisher, G. M., Andrews, K. T., Chang, B. C. H., Gijs, M. A. M., Sternberg, P. W., Auwerx, J., Baell, J., Hofmann, A., Jabbar, A., Gasser, R. B. Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain.