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Persaud R, Jackson JL, Seidel HS, Stevens L, Chitrakar R, Moya ND, Moscatelli M, Braendle C, Yuen J, Rockman MV, Andersen EC, Noble LM, Baugh LR, Zhang G
[
Elife,
2021]
Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three <i>Caenorhabditis</i> species provides a powerful lens to examine causes and consequences of mating system transitions. Among the selfers, <i>C. tropicalis</i> is the least genetically diverse and most afflicted by outbreeding depression. We generated a chromosomal-scale genome for <i>C. tropicalis</i> and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is caused largely by multiple Medea-like elements, genetically consistent with maternal toxin/zygotic antidote systems. Loci with Medea activity harbor novel and duplicated genes, and their activity is modified by mito-nuclear background. Segregating Medea elements dramatically reduce fitness, and simulations show that selfing limits their spread. Frequent selfing in <i>C. tropicalis</i> may therefore be a strategy to avoid Medea-mediated outbreeding depression.
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[
MicroPubl Biol,
2023]
<i>Caenorhabditis</i> <i>elegans</i> is an excellent genetic model system with a large arsenal of forward and reverse genetic techniques. However, not all approaches are easily ported to related <i>Caenorhabditis</i> species (which are useful for gene conservation and gene pathway evolution studies). For CRISPR/Cas9 genetic editing, an easily screenable and dominant co-transformation marker is required - a secondary mutation that won't impact the phenotype of a desired mutation but is capable of being screened for in heterozygous mutants. We describe here the adaptation of a dominant dumpy/roller CRISPR/Cas9-induced mutation in the <i>C. tropicalis</i> <i>
dpy-10</i> orthologue.
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Serpa R, Brilhante RS, Silva AL, Sidrim JJ, Castelo-Branco Dde S, Oliveira JS, Pereira-Neto WA, Rocha MF, Evangelista AJ, Cordeiro Rde A, Pereira VS, Aguiar FR
[
Vet Microbiol,
2016]
The aim of this study was to evaluate the in vitro hemolytic activity and biofilm antifungal susceptibility of veterinary and human Candida tropicalis strains, as well as their pathogenesis against Caenorhabditis elegans. Twenty veterinary isolates and 20 human clinical isolates of C. tropicalis were used. The strains were evaluated for their hemolytic activity and biofilm production. Biofilm susceptibility to itraconazole, fluconazole, voriconazole, amphotericin B and caspofungin was assessed using broth microdilution assay. The in vivo evaluation of strain pathogenicity was investigated using the nematode C. elegans. Hemolytic factor was observed in 95% of the strains and 97.5% of the isolates showed ability to form biofilm. Caspofungin and amphotericin B showed better results than azole antifungals against mature biofilms. Paradoxical effect on mature biofilm metabolic activity was observed at elevated concentrations of caspofungin (8-64g/mL). Azole antifungals were not able to inhibit mature C. tropicalis biofilms, even at the higher tested concentrations. High mortality rates of C. elegans were observed when the worms were exposed to with C. tropicalis strains, reaching up to 96%, 96h after exposure of the worms to C. tropicalis strains. These results reinforce the high pathogenicity of C. tropicalis from veterinary and human sources and show the effectiveness of caspofungin and amphotericin B against mature biofilms of this species.
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Costa Sidrim JJ, de Alencar LP, Aguiar Cordeiro R, Silva Franco JD, Nogueira Brilhante RS, Serpa R, Souza Collares Maia Castelo-Branco D, Colares de Andrade AR, Leite Mendes PB, de Jesus Evangelista AJ, Carneiro Camara LM, de Oliveira JS, Gadelha Rocha MF, Sales JA
[
Future Microbiol,
2018]
AIM: To investigate the direct effect of antibiotics on growth and virulence of the major Candida species associated with invasive infections. MATERIALS & METHODS: Cefepime, imipenem, meropenem, amoxicillin and vancomycin were tested at twofold the peak plasma concentration (2x PP) and the peak plasma concentration (PP). The effects of antibiotics on Candida albicans, Candida parapsilosis, Candida krusei and Candida tropicalis were investigated by colony counting, flow cytometry, proteolytic activity and virulence in Caenorhabditis elegans. RESULTS: Antibiotics increase growth and proteolytic activity of Candida spp; In addition, amoxicillin potentiates virulence ofC. krusei and C. tropicalis against Caenorhabditis elegans. CONCLUSION: These results suggest that antimicrobial therapy may have a direct effect on the pathophysiology of invasive fungal infections in patients at risk.
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[
Front Pharmacol,
2017]
Candida species causes superficial and life-threatening systemic infections and are difficult to treat due to the resistance of these organism to various clinically used drugs. Protolichesterinic acid is a well-known lichen compound. Although the antibacterial activity of protolichesterinic acid has been reported earlier, the antifungal property and its mechanism of action are still largely unidentified. The goal of the present investigation is to explore the anticandidal activity and mechanism of action of protolichesterinic acid, especially against Candida tropicalis. The Minimum Inhibitory Concentration (MIC) value was established through microdilution techniques against four Candida species and out of four species tested, C. tropicalis showed a significant effect (MIC: 2 g/ml). In the morphological interference assay, we observed the enhanced inhibition of hyphae when the cells were treated with protolichesterinic acid. Time-kill assay demonstrated that the maximum rate of killing was recorded between 2 and 6 h. C. tropicalis exposed to protolichesterinic acid exhibited an increased ROS production, which is one of the key factors of fungal death. The rise in ROS was due to the dysfunction of mitochondria caused by protolichesterinic acid. We confirmed that protolichesterinic acid-induced dysfunction of mitochondria in C. tropicalis. The damage of cell membrane due to protolichesterinic acid treatment was confirmed by the influx of propidium iodide and was further confirmed by the release of potassium ions. The treatment of protolichesterinic acid also triggered calcium ion signaling. Moreover, it commenced apoptosis which is clearly evidenced by Annexin V and propidium iodide staining. Interestingly protolichesterinic acid recorded excellent immunomodulatory property when tested against lymphocytes. Finally protolichesterinic acid showed low toxicity toward a normal human cell line Foreskin (FS) normal fibroblast. In in vivo test, protolichesterinic acid significantly enhanced the survival of C. tropicalis infected Caenorhabditis elegans. This investigation proposes that the protolichesterinic acid induces apoptosis in C. tropicalis via the enhanced accumulation of intracellular ROS and mitochondrial damage, which leads fungal cell death via apoptosis. Our work revealed a new key aspect of mechanisms of action of protolichesterinic acid in Candida species. This article is the first study on the antifungal and mechanism of action of protolichesterinic acid in Candida species.
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Crombie TA, Cook DE, Zhang G, Evans KS, Roberto NM, Andersen EC, Tanny RE, Stinson LA, Hodgins KA, Buchanan CM, Battlay P, Ailion M, Zdraljevic S, Dilks CM, Lee D
[
Mol Ecol,
2022]
The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. To characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three-year period, measured various environmental parameters at each sampling site, and whole-genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche comprises moderately moist native forests at high elevations (500 to 1500 meters) where ambient air temperatures are cool (15 to 20C). Compared to other Caenorhabditis species found on the Hawaiian Islands (e.g., Caenorhabditis briggsae and Caenorhabditis tropicalis), we found that C. elegans were enriched in native habitats. We measured levels of genetic diversity and differentiation among Hawaiian C. elegans and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyper-divergent regions, which are likely maintained by balancing selection and enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and contribute to our understanding of the forces that shape genetic diversity on the most remote volcanic archipelago in the world.
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[
PLoS One,
2013]
During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of transcription factors (TFs). This study sought to compare TF expression during embryonic development in a diverse group of metazoan animals: representatives of vertebrates (Danio rerio, Xenopus tropicalis), a chordate (Ciona intestinalis) and invertebrate phyla such as insects (Drosophila melanogaster, Anopheles gambiae) and nematodes (Caenorhabditis elegans) were sampled, The different species showed overall very similar TF expression patterns, with TF expression increasing during the initial stages of development. C2H2 zinc finger TFs were over-represented and Homeobox TFs were under-represented in the early stages in all species. We further clustered TFs for each species based on their quantitative temporal expression profiles. This showed very similar TF expression trends in development in vertebrate and insect species. However, analysis of the expression of orthologous pairs between more closely related species showed that expression of most individual TFs is not conserved, following the general model of duplication and diversification. The degree of similarity between TF expression between Xenopus tropicalis and Danio rerio followed the hourglass model, with the greatest similarity occuring during the early tailbud stage in Xenopus tropicalis and the late segmentation stage in Danio rerio. However, for Drosophila melanogaster and Anopheles gambiae there were two periods of high TF transcriptome similarity, one during the Arthropod phylotypic stage at 8-10 hours into Drosophila development and the other later at 16-18 hours into Drosophila development.
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Phillips, Patrick C, Driscoll, Monica, Jones, E Grace, Guo, Max, Garrett, Theo, Lithgow, Gordon, Sedore, Christine A, Hall, David, Plummer, W Todd, Lucanic, Mark, Morshead, Mackenzie L
[
microPublication Biology,
2020]
The Caenorhabditis Intervention Testing Program (CITP) is a multi-institutional, National Institute on Aging (NIA)-funded consortium. The goal of the program is to identify chemical compounds that extend lifespan robustly and reproducibly across genetically diverse Caenorhabditis strains (Lucanic et al. 2017). The CITP test compounds are selected if they are consistently highly ranked via computational prediction for lifespan or healthspan effects (Coleman-Hulbert et al. 2019), if they are predicted or known to interact with known lifespan-regulating pathways, or if they have previously been reported as extending lifespan or healthspan in laboratory animals. Obeticholic acid is an analog of the natural bile acid chenode oxycholic acid, which acts as an agonist of the farnesoid X receptor (FXR) (Neuschwander-Teri et al. 2015), a nuclear receptor (NR) closely involved with hepatic triglyceride homeostasis. Obeticholic acid is most commonly used to treat the autoimmune liver disease, primary biliary cholangitis. The most likely homolog of FXR in C. elegans is DAF-12, which can bind and be activated by human bile acids (Held et al. 2006; Zhi et al. 2011). DAF-12 modulation is of particular interest because it is closely linked to dauer formation, lifespan extension, and metabolism homeostasis (Antebi 2015).
We assayed lifespan in response to different concentrations of obeticholic acid exposure in three Caenorhabditis species using the flatbed scanner-based Automated Lifespan Machine (ALM) workflow previously published (Banse et al. 2019). To summarize, the worms were age synchronized by egg-lays on standard 60 mm diameter Nematode Growth Media (NGM) plates with lawns of Escherichia coli OP50-1, and transferred to compound-treated 38 mm NGM plates containing 51 M 5-Fluoro-2-deoxyuridine (FUdR) at a density of 50 worms per plate on day one of adulthood. For treatment plates, we used standardized protocols (Caenorhabditis Intervention Testing Program 2020); in short, obeticholic acid (Apexbio Technology) was dissolved in dimethyl sulfoxide (DMSO) and diluted appropriately such that addition of 7.5 l of stock solution and 125 l water for 35 mm diameter plates, and 17.5 l of stock solution and 232.5 l water for 50 mm diameter scanner plates would generate 50, 100, and 150 M final obeticholic acid concentrations. For control plates, DMSO was added instead of stock solution using the same method. The worms were maintained at 20C and transferred to new treatment plates again on day two of adulthood. One week after age-synchronization (day five of adulthood for C. elegans and C. briggsae, day four for C. tropicalis), the worms were transferred to compound-treated scanner plates and loaded onto the ALM. At this point, automated survival monitoring began, and the scanner data was collected and analyzed using Lifespan Machine software (https://github.com/nstroustrup/lifespan; Stroustrup et al.. 2013).
Our results indicate that obeticholic acid does not have a consistent beneficial effect on lifespan in any of the C. elegans or C. briggsae strains tested at the concentrations used. Although we did see some significant differences from the control for some of the concentrations in the C. tropicalis strains, overall the difference was not robust. We actually saw a significant decrease in lifespan in C. tropicalis JU1630, a weakly significant increase in C. tropicalis QG834 at some concentrations, and a relatively significant increase in C. tropicalis JU1373, but with only a 5.7-7.9% change in mean survival from the control (Fig. 1). In summary, our results do not indicate a robust effect of obeticholic acid on Caenorhabditis lifespan. This conclusion is based upon two biological replicates at each concentration performed in one lab, resulting in an average of 104 individuals measured per strain and concentration, and should be considered preliminary. The effect on lifespan in this study may pertain to a lack of physiological relevance of obeticholic acid to Caenorhabditis. Obeticholic acid was of interest to the CITP because of its effect on the mammalian NR FXR. Although DAF-12 has been identified as a potential Caenorhabditis homolog of FXR and other bile acids have been shown to bind with DAF-12 (Zhi et al. 2011), it is possible that obeticholic acid was not able to bind with high affinity to the receptor, therefore eliciting little to no effect on lifespan. Alternatively, obeticholic acid may be rapidly metabolized in Caenorhabditis.
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[
BMC Ecol,
2017]
BACKGROUND: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar external morphology despite deep genomic divergence. METHODS: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats. RESULTS: We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity. CONCLUSION: Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables a dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.
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Gibson SB, Chitrakar R, Andersen EC, Tracey A, Baugh LR, Walhout AJM, Stevens L, Tanny RE, Moya ND, Dekker J, Na H
[
Genome Biol Evol,
2022]
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.