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Wang Y, Guo K, Wang Q, Zhong G, Zhang W, Jiang Y, Mao X, Li X, Huang Z. Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet. Crit Rev Food Sci Nutr 2022; 64:3167-3185. [PMID: 36200941 DOI: 10.1080/10408398.2022.2130875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.
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Affiliation(s)
- Yuqing Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Kaixin Guo
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Guohuan Zhong
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjun Zhang
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiyi Jiang
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xinliang Mao
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xiaomin Li
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics 2022; 220:iyab170. [PMID: 34791196 PMCID: PMC8733455 DOI: 10.1093/genetics/iyab170] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 11/12/2022] Open
Abstract
Entomopathogenic nematodes (EPNs), including Heterorhabditis and Steinernema, are parasitic to insects and contain mutualistically symbiotic bacteria in their intestines (Photorhabdus and Xenorhabdus, respectively) and therefore offer opportunities to study both mutualistic and parasitic symbiosis. The establishment of genetic tools in EPNs has been impeded by limited genetic tractability, inconsistent growth in vitro, variable cryopreservation, and low mating efficiency. We obtained the recently described Steinernema hermaphroditum strain CS34 and optimized its in vitro growth, with a rapid generation time on a lawn of its native symbiotic bacteria Xenorhabdus griffiniae. We developed a simple and efficient cryopreservation method. Previously, S. hermaphroditum isolated from insect hosts was described as producing hermaphrodites in the first generation. We discovered that CS34, when grown in vitro, produced consecutive generations of autonomously reproducing hermaphrodites accompanied by rare males. We performed mutagenesis screens in S. hermaphroditum that produced mutant lines with visible and heritable phenotypes. Genetic analysis of the mutants demonstrated that this species reproduces by self-fertilization rather than parthenogenesis and that its sex is determined chromosomally. Genetic mapping has thus far identified markers on the X chromosome and three of four autosomes. We report that S. hermaphroditum CS34 is the first consistently hermaphroditic EPN and is suitable for genetic model development to study naturally occurring mutualistic symbiosis and insect parasitism.
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Affiliation(s)
- Mengyi Cao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Zograf JK, Trebukhova YA, Yushin VV, Yakovlev KV. Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00522-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schiffer PH, Polsky AL, Cole AG, Camps JIR, Kroiher M, Silver DH, Grishkevich V, Anavy L, Koutsovoulos G, Hashimshony T, Yanai I. The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression. Proc Natl Acad Sci U S A 2018; 115:4459-4464. [PMID: 29626130 PMCID: PMC5924915 DOI: 10.1073/pnas.1720817115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of development has been studied through the lens of gene regulation by examining either closely related species or extremely distant animals of different phyla. In nematodes, detailed cell- and stage-specific expression analyses are focused on the model Caenorhabditis elegans, in part leading to the view that the developmental expression of gene cascades in this species is archetypic for the phylum. Here, we compared two species of an intermediate evolutionary distance: the nematodes C. elegans (clade V) and Acrobeloides nanus (clade IV). To examine A. nanus molecularly, we sequenced its genome and identified the expression profiles of all genes throughout embryogenesis. In comparison with C. elegans, A. nanus exhibits a much slower embryonic development and has a capacity for regulative compensation of missing early cells. We detected conserved stages between these species at the transcriptome level, as well as a prominent middevelopmental transition, at which point the two species converge in terms of their gene expression. Interestingly, we found that genes originating at the dawn of the Ecdysozoa supergroup show the least expression divergence between these two species. This led us to detect a correlation between the time of expression of a gene and its phylogenetic age: evolutionarily ancient and young genes are enriched for expression in early and late embryogenesis, respectively, whereas Ecdysozoa-specific genes are enriched for expression during the middevelopmental transition. Our results characterize the developmental constraints operating on each individual embryo in terms of developmental stages and genetic evolutionary history.
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Affiliation(s)
- Philipp H Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Avital L Polsky
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Alison G Cole
- Department of Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria
| | - Julia I R Camps
- Molecular Cell Biology, Institute I for Anatomy University Clinic Cologne, University of Cologne, 50937 Cologne, Germany
| | - Michael Kroiher
- Zoological Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - David H Silver
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | | | - Leon Anavy
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Georgios Koutsovoulos
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JW, United Kingdom
| | - Tamar Hashimshony
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Itai Yanai
- Institute for Computational Medicine, NYU School of Medicine, New York, NY 10016
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Kraus C, Schiffer PH, Kagoshima H, Hiraki H, Vogt T, Kroiher M, Kohara Y, Schierenberg E. Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. EvoDevo 2017; 8:16. [PMID: 29075433 PMCID: PMC5648466 DOI: 10.1186/s13227-017-0081-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The free-living nematode Diploscapter coronatus is the closest known relative of Caenorhabditis elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the mode of reproduction, embryonic axis formation and early cleavage pattern (Lahl et al. in Int J Dev Biol 50:393-397, 2006). Our recent genome analysis (Hiraki et al. in BMC Genomics 18:478, 2017) provides a solid foundation to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes. Our genomic data also yielded indications for the view that D. coronatus is a product of interspecies hybridization. RESULTS In a genomic comparison between D. coronatus, C. elegans, other representatives of the genus Caenorhabditis and the more distantly related Pristionchus pacificus and Panagrellus redivivus, certain genes required for central developmental processes in C. elegans like control of meiosis and establishment of embryonic polarity were found to be restricted to the genus Caenorhabditis. The mRNA content of early D. coronatus embryos was sequenced and compared with similar stages in C. elegans and Ascaris suum. We identified 350 gene families transcribed in the early embryo of D. coronatus but not in the other two nematodes. Looking at individual genes transcribed early in D. coronatus but not in C. elegans and A. suum, we found that orthologs of most of these are present in the genomes of the latter species as well, suggesting heterochronic shifts with respect to expression behavior. Considerable genomic heterozygosity and allelic divergence lend further support to the view that D. coronatus may be the result of an interspecies hybridization. Expression analysis of early acting single-copy genes yields no indication for silencing of one parental genome. CONCLUSIONS Our comparative cellular and molecular studies support the view that the genus Caenorhabditis differs considerably from the other studied nematodes in its control of development and reproduction. The easy-to-culture parthenogenetic D. coronatus, with its high-quality draft genome and only a single chromosome when haploid, offers many new starting points on the cellular, molecular and genomic level to explore alternative routes of nematode development and reproduction.
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Affiliation(s)
- Christopher Kraus
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Present Address: Institute for Genetics, Universität zu Köln, Cologne, NRW Germany
| | - Philipp H. Schiffer
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Genetics, Evolution and Environment, University College London, London, WC16BT UK
| | | | | | - Theresa Vogt
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Present Address: Molecular Cell Biology, Institute I for Anatomy University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
| | - Yuji Kohara
- National Institute of Genetics, Mishima, Japan
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Huang L, Lv X, Huang Y, Hu Y, Yan H, Zheng M, Zeng H, Li X, Liang C, Wu Z, Yu X. Identification, sequence analysis, and characterization of serine/threonine protein kinase 17A from Clonorchis sinensis. Parasitol Res 2014; 113:1713-23. [PMID: 24578258 DOI: 10.1007/s00436-014-3816-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/07/2014] [Indexed: 11/24/2022]
Abstract
This is the first report of a novel protein from Clonorchis sinensis (C. sinensis), serine/threonine protein kinase 17A (CsSTK17A), which belongs to a member of the death-associated protein kinase (DAPK) family known to regulate diverse biological processes. The full-length sequence encoding CsSTK17A was isolated from C. sinensis adult cDNA plasmid library. Two transcribed isoforms of the gene were identified from the genome of C. sinensis. CsSTK17A contains a kinase domain at the N-terminus that shares a degree of conservation with the DAPK families. Besides, the catalytic domain contains 11 subdomains conserved among STKs and shares the highest identity with STK from Schistosoma mansoni (55.9%). Three-dimensional structure of CsSTK17A displays the canonical STK fold, including the helix C, P-loop, and the activation loop. We obtained recombinant CsSTK17A (rCsSTK17A) and anti-rCsSTK17A IgG. The rCsSTK17A could be probed by anti-rCsSTK17A rat serum, C. sinensis-infected rat serum and the sera from rats immunized with C. sinensis excretory-secretory products, indicating that it is a circulating antigen possessing a strong immunocompetence. Moreover, quantitative RT-PCR and western blotting analyses revealed that CsSTK17A exhibited the highest mRNA and protein expression level in eggs, followed by metacercariae and adult worms. Intriguingly, in the immunolocalization assay, CsSTK17A was intensively localized to the operculum region of eggs in uterus, as well as the vitelline gland of both adult worm and metacercaria, implying that the protein was associated with the reproduction and development of C. sinensis. Overall, these fundamental studies might contribute to further researches on signaling systems of the parasite.
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Affiliation(s)
- Lisi Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, People's Republic of China
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Functional transcriptomics of a migrating cell in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2012; 109:16246-51. [PMID: 22991463 DOI: 10.1073/pnas.1203045109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In both metazoan development and metastatic cancer, migrating cells must carry out a detailed, complex program of sensing cues, binding substrates, and moving their cytoskeletons. The linker cell in Caenorhabditis elegans males undergoes a stereotyped migration that guides gonad organogenesis, occurs with precise timing, and requires the nuclear hormone receptor NHR-67. To better understand how this occurs, we performed RNA-seq of individually staged and dissected linker cells, comparing transcriptomes from linker cells of third-stage (L3) larvae, fourth-stage (L4) larvae, and nhr-67-RNAi-treated L4 larvae. We observed expression of 8,000-10,000 genes in the linker cell, 22-25% of which were up- or down-regulated 20-fold during development by NHR-67. Of genes that we tested by RNAi, 22% (45 of 204) were required for normal shape and migration, suggesting that many NHR-67-dependent, linker cell-enriched genes play roles in this migration. One unexpected class of genes up-regulated by NHR-67 was tandem pore potassium channels, which are required for normal linker-cell migration. We also found phenotypes for genes with human orthologs but no previously described migratory function. Our results provide an extensive catalog of genes that act in a migrating cell, identify unique molecular functions involved in nematode cell migration, and suggest similar functions in humans.
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Wang X, Chen W, Huang Y, Sun J, Men J, Liu H, Luo F, Guo L, Lv X, Deng C, Zhou C, Fan Y, Li X, Huang L, Hu Y, Liang C, Hu X, Xu J, Yu X. The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. Genome Biol 2011; 12:R107. [PMID: 22023798 PMCID: PMC3333777 DOI: 10.1186/gb-2011-12-10-r107] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 09/13/2011] [Accepted: 10/24/2011] [Indexed: 02/07/2023] Open
Abstract
Background Clonorchis sinensis is a carcinogenic human liver fluke that is widespread in Asian countries. Increasing infection rates of this neglected tropical disease are leading to negative economic and public health consequences in affected regions. Experimental and epidemiological studies have shown a strong association between the incidence of cholangiocarcinoma and the infection rate of C. sinensis. To aid research into this organism, we have sequenced its genome. Results We combined de novo sequencing with computational techniques to provide new information about the biology of this liver fluke. The assembled genome has a total size of 516 Mb with a scaffold N50 length of 42 kb. Approximately 16,000 reliable protein-coding gene models were predicted. Genes for the complete pathways for glycolysis, the Krebs cycle and fatty acid metabolism were found, but key genes involved in fatty acid biosynthesis are missing from the genome, reflecting the parasitic lifestyle of a liver fluke that receives lipids from the bile of its host. We also identified pathogenic molecules that may contribute to liver fluke-induced hepatobiliary diseases. Large proteins such as multifunctional secreted proteases and tegumental proteins were identified as potential targets for the development of drugs and vaccines. Conclusions This study provides valuable genomic information about the human liver fluke C. sinensis and adds to our knowledge on the biology of the parasite. The draft genome will serve as a platform to develop new strategies for parasite control.
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Affiliation(s)
- Xiaoyun Wang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, PR China
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Singaravelu G, Singson A. New insights into the mechanism of fertilization in nematodes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 289:211-38. [PMID: 21749902 PMCID: PMC3273857 DOI: 10.1016/b978-0-12-386039-2.00006-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fertilization results from the fusion of male and female gametes in all sexually reproducing organisms. Much of nematode fertility work was focused on Caenorhabditis elegans and Ascaris suum. The C. elegans hermaphrodite produces a limited number of sperm initially and then commits to the exclusive production of oocytes. The postmeiotic differentiation called spermiogenesis converts sessile spermatids into motile spermatozoa. The motility of spermatozoa depends on dynamic assembly and disassembly of a major sperm protein-based cytoskeleton uniquely found in nematodes. Both self-derived and male-derived spermatozoa are stored in spermatheca, the site of fertilization in hermaphrodites. The oocyte is arrested in meiotic prophase I until a sperm-derived signal relieves the inhibition allowing the meiotic maturation to occur. Oocyte undergoes meiotic maturation, enters into spermatheca, gets fertilized, completes meiosis, and exits into uterus as a zygote. This review focuses on our current understanding of the events around fertilization in nematodes.
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