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Zavagno G, Raimundo A, Kirby A, Saunter C, Weinkove D. Rapid measurement of ageing by automated monitoring of movement of C. elegans populations. GeroScience 2024; 46:2281-2293. [PMID: 37940787 PMCID: PMC10828257 DOI: 10.1007/s11357-023-00998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Finding new interventions that slow ageing and maintain human health is a huge challenge of our time. The nematode Caenorhabditis elegans offers a rapid in vivo method to determine whether a compound extends its 2 to 3-week lifespan. Measuring lifespan is the standard method to monitor ageing, but a compound that extends lifespan will not necessarily maintain health. Here, we describe the automated monitoring of C. elegans movement from early to mid-adulthood as a faster healthspan-based method to measure ageing. Using the WormGazer™ technology, multiple Petri dishes each containing several C. elegans worms are imaged simultaneously and non-invasively by an array of cameras that can be scaled easily. This approach demonstrates that most functional decline in C. elegans occurs during the first week of adulthood. We find 7 days of imaging is sufficient to measure the dose-dependent efficacy of sulfamethoxazole to slow ageing, compared to 40 days required for a parallel lifespan experiment. Understanding any negative consequences of interventions that slow ageing is important. We show that the long-lived mutant age-1(hx546) stays active for longer than the wild type but it moves slower in early adulthood. Thus, continuous analysis of movement can rapidly identify interventions that slow ageing while simultaneously revealing any negative effects on health.
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Affiliation(s)
- Giulia Zavagno
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
- Magnitude Biosciences Limited, NETPark Plexus, Thomas Wright Way, Sedgefield, Durham, TS21 3FD, UK
| | - Adelaide Raimundo
- Magnitude Biosciences Limited, NETPark Plexus, Thomas Wright Way, Sedgefield, Durham, TS21 3FD, UK
| | - Andy Kirby
- Magnitude Biosciences Limited, NETPark Plexus, Thomas Wright Way, Sedgefield, Durham, TS21 3FD, UK
| | - Christopher Saunter
- Magnitude Biosciences Limited, NETPark Plexus, Thomas Wright Way, Sedgefield, Durham, TS21 3FD, UK
| | - David Weinkove
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.
- Magnitude Biosciences Limited, NETPark Plexus, Thomas Wright Way, Sedgefield, Durham, TS21 3FD, UK.
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2
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Wilson IBH, Yan S, Jin C, Dutkiewicz Z, Rendić D, Palmberger D, Schnabel R, Paschinger K. Increasing Complexity of the N-Glycome During Caenorhabditis Development. Mol Cell Proteomics 2023; 22:100505. [PMID: 36717059 PMCID: PMC7614267 DOI: 10.1016/j.mcpro.2023.100505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
Caenorhabditis elegans is a frequently employed genetic model organism and has been the object of a wide range of developmental, genetic, proteomic, and glycomic studies. Here, using an off-line MALDI-TOF-MS approach, we have analyzed the N-glycans of mixed embryos and liquid- or plate-grown L4 larvae. Of the over 200 different annotatable N-glycan structures, variations between the stages as well as the mode of cultivation were observed. While the embryonal N-glycome appears less complicated overall, the liquid- and plate-grown larvae differ especially in terms of methylation of bisecting fucose, α-galactosylation of mannose, and di-β-galactosylation of core α1,6-fucose. Furthermore, we analyzed the O-glycans by LC-electrospray ionization-MS following β-elimination; especially the embryonal O-glycomes included a set of phosphorylcholine-modified structures, previously not shown to exist in nematodes. However, the set of glycan structures cannot be clearly correlated with levels of glycosyltransferase transcripts in developmental RNA-Seq datasets, but there is an indication for coordinated expression of clusters of potential glycosylation-relevant genes. Thus, there are still questions to be answered in terms of how and why a simple nematode synthesizes such a diverse glycome.
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Affiliation(s)
- Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Wien, Austria.
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, Wien, Austria; Institut für Parasitologie, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Chunsheng Jin
- Institutionen för Biomedicin, Göteborgs universitet, Göteborg, Sweden
| | | | - Dubravko Rendić
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | | | - Ralf Schnabel
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
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3
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Çelen İ, Jayasinghe A, Doh JH, Sabanayagam CR. Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans and Comparison to Spaceflight Experiments. Cells 2023; 12:270. [PMID: 36672205 PMCID: PMC9856674 DOI: 10.3390/cells12020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Given the growing interest in human exploration of space, it is crucial to identify the effects of space conditions on biological processes. Here, we analyze the transcriptomic response of Caenorhabditis elegans to simulated microgravity and observe the maintained transcriptomic response after returning to ground conditions for four, eight, and twelve days. We show that 75% of the simulated microgravity-induced changes on gene expression persist after returning to ground conditions for four days while most of these changes are reverted after twelve days. Our results from integrative RNA-seq and mass spectrometry analyses suggest that simulated microgravity affects longevity-regulating insulin/IGF-1 and sphingolipid signaling pathways. Finally, we identified 118 genes that are commonly differentially expressed in simulated microgravity- and space-exposed worms. Overall, this work provides insight into the effect of microgravity on biological systems during and after exposure.
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Affiliation(s)
- İrem Çelen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Aroshan Jayasinghe
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Jung H. Doh
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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4
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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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5
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Willis AR, Zhao W, Sukhdeo R, Wadi L, El Jarkass HT, Claycomb JM, Reinke AW. A parental transcriptional response to microsporidia infection induces inherited immunity in offspring. SCIENCE ADVANCES 2021; 7:7/19/eabf3114. [PMID: 33952520 PMCID: PMC8099193 DOI: 10.1126/sciadv.abf3114] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/17/2021] [Indexed: 05/05/2023]
Abstract
Parental infection can result in the production of offspring with enhanced immunity phenotypes. Critically, the mechanisms underlying inherited immunity are poorly understood. Here, we show that Caenorhabditis elegans infected with the intracellular microsporidian parasite N. parisii produce progeny that are resistant to microsporidia infection. We determine the kinetics of the response and show that intergenerational immunity prevents host-cell invasion by Nematocida parisii and enhances survival to the bacterial pathogen Pseudomonas aeruginosa We demonstrate that immunity is induced by the parental transcriptional response to infection, which can be mimicked through maternal somatic depletion of PALS-22 and the retinoblastoma protein ortholog, LIN-35. We find that other biotic and abiotic stresses (viral infection and cadmium exposure) that induce a similar transcriptional response as microsporidia also induce immunity in progeny. Together, our results reveal how a parental transcriptional signal can be induced by distinct stimuli and protect offspring against multiple classes of pathogens.
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Affiliation(s)
- Alexandra R Willis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Winnie Zhao
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ronesh Sukhdeo
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lina Wadi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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6
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Sandner G, König A, Wallner M, Weghuber J. Alternative model organisms for toxicological fingerprinting of relevant parameters in food and nutrition. Crit Rev Food Sci Nutr 2021; 62:5965-5982. [PMID: 33683153 DOI: 10.1080/10408398.2021.1895060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the field of (food) toxicology, there is a strong trend of replacing animal trials with alternative methods for the assessment of adverse health effects in humans. The replacement of animal trials is not only driven by ethical concerns but also by the number of potential testing substances (food additives, packaging material, contaminants, and toxicants), which is steadily increasing. In vitro 2D cell culture applications in combination with in silico modeling might provide an applicable first response. However, those systems lack accurate predictions of metabolic actions. Thus, alternative in vivo models could fill the gap between cell culture and animal trials. In this review, we highlight relevant studies in the field and spotlight the applicability of alternative models, including C. elegans, D. rerio, Drosophila, HET-CAM and Lab-on-a-chip.
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Affiliation(s)
- Georg Sandner
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, Austria
| | - Alice König
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, Austria.,FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Melanie Wallner
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, Austria.,FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Julian Weghuber
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, Austria.,FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
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7
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Willis AR, Sukhdeo R, Reinke AW. Remembering your enemies: mechanisms of within-generation and multigenerational immune priming in Caenorhabditis elegans. FEBS J 2020; 288:1759-1770. [PMID: 32767821 DOI: 10.1111/febs.15509] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
Abstract
Pathogens are abundant and drive evolution of host immunity. Whilst immune memory is classically associated with adaptive immunity, studies in diverse species now show that priming of innate immune defences can also protect against secondary infection. Remarkably, priming may also be passed on to progeny to enhance pathogen resistance and promote survival in future generations. Phenotypic changes that occur independent of DNA sequence underlie both 'within-generation' priming and 'multigenerational' priming. However, the molecular mechanisms responsible for these phenomena are still poorly understood. Caenorhabditis elegans is a simple and genetically tractable model organism that has enabled key advances in immunity and environmental epigenetics. Using both natural and human pathogens, researchers have uncovered numerous examples of innate immune priming in this animal. Viral infection models have provided key evidence for a conserved antiviral RNA silencing mechanism that is inherited in progeny. Bacterial infection models have explored mechanisms of within-generation and multigenerational priming that span chromatin modification and transcriptional changes, small RNA pathways, maternal provisioning and pathogen avoidance strategies. Together, these studies are providing novel insight into the immune reactivity of the genome and have important consequences for our understanding of health and evolution. In this review, we present the current evidence for learned protection against pathogens in C. elegans, discuss the significance and limitations of these findings and highlight important avenues of future investigation.
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Affiliation(s)
| | - Ronesh Sukhdeo
- Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, ON, Canada
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8
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Bulterijs S, Braeckman BP. Phenotypic Screening in C. elegans as a Tool for the Discovery of New Geroprotective Drugs. Pharmaceuticals (Basel) 2020; 13:E164. [PMID: 32722365 PMCID: PMC7463874 DOI: 10.3390/ph13080164] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/10/2023] Open
Abstract
Population aging is one of the largest challenges of the 21st century. As more people live to advanced ages, the prevalence of age-related diseases and disabilities will increase placing an ever larger burden on our healthcare system. A potential solution to this conundrum is to develop treatments that prevent, delay or reduce the severity of age-related diseases by decreasing the rate of the aging process. This ambition has been accomplished in model organisms through dietary, genetic and pharmacological interventions. The pharmacological approaches hold the greatest opportunity for successful translation to the clinic. The discovery of such pharmacological interventions in aging requires high-throughput screening strategies. However, the majority of screens performed for geroprotective drugs in C. elegans so far are rather low throughput. Therefore, the development of high-throughput screening strategies is of utmost importance.
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Affiliation(s)
- Sven Bulterijs
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Bart P. Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
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9
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Preez GD, Fourie H, Daneel M, Miller H, Höss S, Ricci C, Engelbrecht G, Zouhar M, Wepener V. Oxygen consumption rate of Caenorhabditis elegans as a high-throughput endpoint of toxicity testing using the Seahorse XF e96 Extracellular Flux Analyzer. Sci Rep 2020; 10:4239. [PMID: 32144330 PMCID: PMC7060326 DOI: 10.1038/s41598-020-61054-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/17/2020] [Indexed: 12/25/2022] Open
Abstract
Caenorhabditis elegans presents functioning, biologically relevant phenotypes and is frequently used as a bioindicator of toxicity. However, most C. elegans in vivo effect-assessment methods are laborious and time consuming. Therefore, we developed a novel method to measure the oxygen consumption rate of C. elegans as a sublethal endpoint of toxicity. This protocol was tested by exposing 50 larval stage one C. elegans individuals for 48 h (at 20 °C) to different concentrations of two toxicants i.e. benzylcetyldimethylammonium chloride (BAC-C16) and cadmium (Cd). Following exposures, the oxygen consumption rate of the C. elegans individuals were measured using the high-throughput functionality of the Seahorse XFe96 Extracellular Flux Analyzer. Dose-response curves for BAC-C16 (R2 = 0.93; P = 0.001) and Cd (R2 = 0.98; P = 0.001) were created. Furthermore, a strong, positive correlation was evidenced between C. elegans oxygen consumption rate and a commonly used, ecologically relevant endpoint of toxicity (growth inhibition) for BAC-C16 (R2 = 0.93; P = 0.0001) and Cd (R2 = 0.91; P = 0.0001). The data presented in this study show that C. elegans oxygen consumption rate can be used as a promising functional measurement of toxicity.
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Affiliation(s)
- G Du Preez
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa.
- Agricultural Research Council - Institute for Tropical and Subtropical Crops, Private Bag X11208, Nelspruit, 1200, South Africa.
| | - H Fourie
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - M Daneel
- Agricultural Research Council - Institute for Tropical and Subtropical Crops, Private Bag X11208, Nelspruit, 1200, South Africa
| | - H Miller
- Human Metabolomics, Faculty of Natural Sciences, North-West University, Potchefstroom, 2520, South Africa
| | - S Höss
- Ecossa, Giselastrasse 6, 82319, Starnberg, Germany
- University of Bielefeld, Department of Animal Ecology, Konsequenz 45, 33615, Bielefeld, Germany
| | - C Ricci
- Centre of Excellence for Nutrition (CEN), North-West University, Potchefstroom, South Africa
- Pediatric Epidemiology, Department of Pediatrics, University Medicine Leipzig, Leipzig, Germany
| | - G Engelbrecht
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - M Zouhar
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Plant Protection, Kamycka 129, 165 21, Prague, Czech Republic
| | - V Wepener
- Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
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10
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Kuijper B, Hanson MA, Vitikainen EIK, Marshall HH, Ozanne SE, Cant MA. Developing differences: early-life effects and evolutionary medicine. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190039. [PMID: 30966882 DOI: 10.1098/rstb.2019.0039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation in early-life conditions can trigger developmental switches that lead to predictable individual differences in adult behaviour and physiology. Despite evidence for such early-life effects being widespread both in humans and throughout the animal kingdom, the evolutionary causes and consequences of this developmental plasticity remain unclear. The current issue aims to bring together studies of early-life effects from the fields of both evolutionary ecology and biomedicine to synthesise and advance current knowledge of how information is used during development, the mechanisms involved, and how early-life effects evolved. We hope this will stimulate further research into early-life effects, improving our understanding of why individuals differ and how this might influence their susceptibility to disease. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Bram Kuijper
- 1 Environment and Sustainability Institute , Penryn Campus, University of Exeter, Penryn TR10 IEZ , UK
| | - Mark A Hanson
- 3 Institute of Developmental Sciences and NIHR Southampton Biomedical Research Centre, Southampton University Hospital and University of Southampton , UK
| | - Emma I K Vitikainen
- 2 Centre for Ecology and Conservation , Penryn Campus, University of Exeter, Penryn TR10 IEZ , UK.,4 Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki , Helsinki , Finland
| | - Harry H Marshall
- 2 Centre for Ecology and Conservation , Penryn Campus, University of Exeter, Penryn TR10 IEZ , UK.,5 Department of Life Sciences, University of Roehampton , London SW15 4JD , UK
| | - Susan E Ozanne
- 6 University of Cambridge - Department of Clinical Biochemistry , Hills Road, Addenbrookes Level 4, Box 232 Cambridge CB2 2QR , UK
| | - Michael A Cant
- 2 Centre for Ecology and Conservation , Penryn Campus, University of Exeter, Penryn TR10 IEZ , UK
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11
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Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology. Biochem Soc Trans 2019; 47:887-896. [PMID: 31127069 DOI: 10.1042/bst20190001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Abstract
Reproducibility is critical for the standardization, interpretation, and progression of research. However, many factors increase variability and reduce reproducibility. In Caenorhabditis elegans research, there are many possible causes of variability that may explain why experimental outcomes sometimes differ between laboratories and between experiments. Factors contributing to experimental variability include the genetic background of both C. elegans and its bacterial diet, differences in media composition, intergenerational and transgenerational effects that may be carried over for generations, and the use of chemicals or reagents that may have unexpected consequences. This review summarizes sources of variability in C. elegans research and serves to identify laboratory practices that could influence reproducibility.
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12
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Lev I, Gingold H, Rechavi O. H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes. eLife 2019; 8:e40448. [PMID: 30869075 PMCID: PMC6417860 DOI: 10.7554/elife.40448] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/26/2019] [Indexed: 12/17/2022] Open
Abstract
In Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via small RNAs. RNAi inheritance is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing requires a feed-forward loop between H3K9me3 and small RNAs. Here, we show that in C. elegans not only is H3K9me3 unnecessary for inheritance, the modification's function depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that endo-siRNAs that depend on SET-25 and SET-32 target newly acquired and highly H3K9me3 marked genes. Thus, 'repressive' chromatin marks could be important specifically for heritable silencing of genes which are flagged as 'foreign', such as gfp. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
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