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Indong RA, Park JM, Hong JK, Lyou ES, Han T, Hong JK, Lee TK, Lee JI. A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory. Front Microbiol 2024; 15:1347797. [PMID: 38476935 PMCID: PMC10929012 DOI: 10.3389/fmicb.2024.1347797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.
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Affiliation(s)
- Rocel Amor Indong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jong Min Park
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Eun Sun Lyou
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Taeman Han
- Korea National Park Research Insitute, Korea National Park Service, Wonju, Republic of Korea
| | - Jong Kwang Hong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
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Lee HK, Lee TY, Lee JI, Park KS, Yoon KH. Precise sensorimotor control impacts reproductive fitness of C. elegans in 3D environments. Neuroreport 2024; 35:123-128. [PMID: 38109381 PMCID: PMC10766090 DOI: 10.1097/wnr.0000000000001986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/20/2023]
Abstract
The ability of animals to sense and navigate towards relevant cues in complex and elaborate habitats is paramount for their survival and reproductive success. The nematode Caenorhabditis elegans uses a simple and elegant sensorimotor program to track odors in its environments. Whether this allows the worm to effectively navigate a complex environment and increase its evolutionary success has not been tested yet. We designed an assay to test whether C. elegans can track odors in a complex 3D environment. We then used a previously established 3D cultivation system to test whether defect in tracking odors to find food in a complex environment affected their brood size. We found that wild-type worms can accurately migrate toward a variety of odors in 3D. However, mutants of the muscarinic acetylcholine receptor GAR-3 which have a sensorimotor integration defect that results in a subtle navigational defect steering towards attractive odors, display decreased chemotaxis to the odor butanone not seen in the traditional 2D assay. We also show that the decreased ability to locate appetitive stimuli in 3D leads to reduced brood size not observed in the standard 2D culture conditions. Our study shows that mutations in genes previously overlooked in 2D conditions can have a significant impact in the natural habitat, and highlights the importance of considering the evolutionary selective pressures that have shaped the behavior, as well as the underlying genes and neural circuits.
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Affiliation(s)
- Hee Kyung Lee
- Department of Physiology, Yonsei University Wonju College of Medicine
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine
- Department of Global Medical Science, Yonsei University Wonju College of Medicine
| | - Tong Young Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus, Wonju, South Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus, Wonju, South Korea
| | - Kyu-Sang Park
- Department of Physiology, Yonsei University Wonju College of Medicine
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine
- Department of Global Medical Science, Yonsei University Wonju College of Medicine
| | - Kyoung-hye Yoon
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine
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Nunn LR, Juang TD, Beebe DJ, Wheeler NJ, Zamanian M. A high-throughput sensory assay for parasitic and free-living nematodes. Integr Biol (Camb) 2023; 15:zyad010. [PMID: 37555835 PMCID: PMC10752570 DOI: 10.1093/intbio/zyad010] [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: 05/18/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023]
Abstract
Sensory pathways first elucidated in Caenorhabditis elegans are conserved across free-living and parasitic nematodes, even though each species responds to a diverse array of compounds. Most nematode sensory assays are performed by tallying observations of worm behavior on two-dimensional planes using agarose plates. These assays have been successful in the study of volatile sensation but are poorly suited for investigation of water-soluble gustation or parasitic nematodes without a free-living stage. In contrast, gustatory assays tend to be tedious, often limited to the manipulation of a single individual at a time. We have designed a nematode sensory assay using a microfluidics device that allows for the study of gustation in a 96-well, three-dimensional environment. This device is suited for free-living worms and parasitic worms that spend their lives in an aqueous environment, and we have used it to show that ivermectin inhibits the gustatory ability of vector-borne parasitic nematodes. Insight box Nematodes are powerful model organisms for understanding the sensory biology of multicellular eukaryotes, and many parasitic species cause disease in humans. Simple sensory assays performed on agarose plates have been the bedrock for establishing the neuronal, genetic, and developmental foundations for many sensory modalities in nematodes. However, these classical assays are poorly suited for translational movement of many parasitic nematodes and the sensation of water-soluble molecules (gustation). We have designed a device for high-throughput nematode sensory assays in a gel matrix. This 'gustatory microplate' is amenable to several species and reveals novel responses by free-living and parasitic nematodes to cues and drugs.
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Affiliation(s)
- Leonardo R. Nunn
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Terry D. Juang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - David J. Beebe
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - Nicolas J. Wheeler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, WI USA
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
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Xie S, Dierlam C, Smith E, Duran R, Williams A, Davis A, Mathew D, Naslavsky N, Iyer J, Caplan S. The retromer complex regulates C. elegans development and mammalian ciliogenesis. J Cell Sci 2022; 135:jcs259396. [PMID: 35510502 PMCID: PMC9189432 DOI: 10.1242/jcs.259396] [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: 09/24/2021] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
The mammalian retromer consists of subunits VPS26 (either VPS26A or VPS26B), VPS29 and VPS35, and a loosely associated sorting nexin (SNX) heterodimer or a variety of other SNX proteins. Despite involvement in yeast and mammalian cell trafficking, the role of retromer in development is poorly understood, and its impact on primary ciliogenesis remains unknown. Using CRISPR/Cas9 editing, we demonstrate that vps-26-knockout worms have reduced brood sizes, impaired vulval development and decreased body length, all of which have been linked to ciliogenesis defects. Although preliminary studies did not identify worm ciliary defects, and impaired development limited additional ciliogenesis studies, we turned to mammalian cells to investigate the role of retromer in ciliogenesis. VPS35 localized to the primary cilium of mammalian cells, and depletion of VPS26, VPS35, VPS29, SNX1, SNX2, SNX5 or SNX27 led to decreased ciliogenesis. Retromer also coimmunoprecipitated with the centriolar protein, CP110 (also known as CCP110), and was required for its removal from the mother centriole. Herein, we characterize new roles for retromer in C. elegans development and in the regulation of ciliogenesis in mammalian cells, suggesting a novel role for retromer in CP110 removal from the mother centriole.
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Affiliation(s)
- Shuwei Xie
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carter Dierlam
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Ellie Smith
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Ramon Duran
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Allana Williams
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Angelina Davis
- School of Science and Mathematics, Tulsa Community College, Tulsa, OK 74115, USA
| | - Danita Mathew
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jyoti Iyer
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Guisnet A, Maitra M, Pradhan S, Hendricks M. Three-Dimensional Fruit Tissue Habitats for Culturing Caenorhabditis elegans. Curr Protoc 2021; 1:e288. [PMID: 34767311 DOI: 10.1002/cpz1.288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Environmental factors influence many traits of biological interest, but reproducing an animal's natural habitat in a controlled laboratory environment is challenging. Environmental enrichment-adding complexity to the usually simplistic conditions under which laboratory animals are raised-offers a potential tool for better understanding biological traits while maintaining controlled laboratory conditions. For the model nematode Caenorhabditis elegans, the contrast between the natural environment and the laboratory conditions in which they are raised is enormous. Although several methods have been developed in an effort to complexify C. elegans laboratory conditions, there is still a need for an enriched controlled laboratory habitat in which C. elegans can be raised over several generations, the bacterial food availability is similar to that in traditional agar plates, and the animals are crawling as opposed to swimming or burrowing. To this end, we describe here a standardized protocol for creating controlled, reproducible, three-dimensional environments for multigenerational maintenance of C. elegans in the laboratory. These environments are derived from decellularized apple hypanthium tissue and have bacterial food uniformly distributed throughout. We also describe how traditional C. elegans methods of collecting synchronized eggs, cleaning contaminated stocks, and collecting animal populations are adapted to our scaffold environment. These methods can be adapted to host different bacteria or bacterial populations, and the resulting scaffolds can be used in a range of experimental designs for behavioral and phenotypical studies in C. elegans and other nematodes. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Decellularization and storage of apple tissue Basic Protocol 2: Preparation of plates from decellularized apple scaffolds Basic Protocol 3: Synchronization of eggs or animals and cleaning contaminated stocks from scaffold plates Alternate Protocol: Collection of non-synchronized larvae and adults from scaffold plates.
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Affiliation(s)
- Aurélie Guisnet
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Malosree Maitra
- Integrated Program in Neuroscience, McGill University, Montréal, Québec, Canada
| | - Sreeparna Pradhan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts
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Paper-Supported High-Throughput 3D Culturing, Trapping, and Monitoring of Caenorhabditis Elegans. MICROMACHINES 2020; 11:mi11010099. [PMID: 31963416 PMCID: PMC7020171 DOI: 10.3390/mi11010099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/19/2022]
Abstract
We developed an innovative paper-based platform for high-throughput culturing, trapping, and monitoring of C. elegans. A 96-well array was readily fabricated by placing a nutrient-replenished paper substrate on a micromachined 96-well plastic frame, providing high-throughput 3D culturing environments and in situ analysis of the worms. The paper allows C. elegans to pass through the porous and aquatic paper matrix until the worms grow and reach the next developmental stages with the increased body size comparable to the paper pores. When the diameter of C. elegans becomes larger than the pore size of the paper substrate, the worms are trapped and immobilized for further high-throughput imaging and analysis. This work will offer a simple yet powerful technique for high-throughput sorting and monitoring of C. elegans at a different larval stage by controlling and choosing different pore sizes of paper. Furthermore, we developed another type of 3D culturing system by using paper-like transparent polycarbonate substrates for higher resolution imaging. The device used the multi-laminate structure of the polycarbonate layers as a scaffold to mimic the worm’s 3D natural habitats. Since the substrate is thin, mechanically strong, and largely porous, the layered structure allowed C. elegans to move and behave freely in 3D and promoted the efficient growth of both C. elegans and their primary food, E. coli. The transparency of the structure facilitated visualization of the worms under a microscope. Development, fertility, and dynamic behavior of C. elegans in the 3D culture platform outperformed those of the standard 2D cultivation technique.
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Lesanpezeshki L, Hewitt JE, Laranjeiro R, Antebi A, Driscoll M, Szewczyk NJ, Blawzdziewicz J, Lacerda CMR, Vanapalli SA. Pluronic gel-based burrowing assay for rapid assessment of neuromuscular health in C. elegans. Sci Rep 2019; 9:15246. [PMID: 31645584 PMCID: PMC6811592 DOI: 10.1038/s41598-019-51608-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/03/2019] [Indexed: 12/26/2022] Open
Abstract
Whole-organism phenotypic assays are central to the assessment of neuromuscular function and health in model organisms such as the nematode C. elegans. In this study, we report a new assay format for engaging C. elegans in burrowing that enables rapid assessment of nematode neuromuscular health. In contrast to agar environments that pose specific drawbacks for characterization of C. elegans burrowing ability, here we use the optically transparent and biocompatible Pluronic F-127 gel that transitions from liquid to gel at room temperature, enabling convenient and safe handling of animals. The burrowing assay methodology involves loading animals at the bottom of well plates, casting a liquid-phase of Pluronic on top that solidifies via a modest temperature upshift, enticing animals to reach the surface via chemotaxis to food, and quantifying the relative success animals have in reaching the chemoattractant. We study the influence of Pluronic concentration, gel height and chemoattractant choice to optimize assay performance. To demonstrate the simplicity of the assay workflow and versatility, we show its novel application in multiple areas including (i) evaluating muscle mutants with defects in dense bodies and/or M-lines (pfn-3, atn-1, uig-1, dyc-1, zyx-1, unc-95 and tln-1), (ii) tuning assay conditions to reveal changes in the mutant gei-8, (iii) sorting of fast burrowers in a genetically-uniform wild-type population for later quantitation of their distinct muscle gene expression, and (iv) testing proteotoxic animal models of Huntington and Parkinson’s disease. Results from our studies show that stimulating animals to navigate in a dense environment that offers mechanical resistance to three-dimensional locomotion challenges the neuromuscular system in a manner distinct from standard crawling and thrashing assays. Our simple and high throughput burrowing assay can provide insight into molecular mechanisms for maintenance of neuromuscular health and facilitate screening for therapeutic targets.
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Affiliation(s)
| | - Jennifer E Hewitt
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, USA.,Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ricardo Laranjeiro
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Adam Antebi
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Nathaniel J Szewczyk
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, United Kingdom & National Institute for Health Research Nottingham Biomedical Research Centre, Derby, UK
| | - Jerzy Blawzdziewicz
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX, USA
| | - Carla M R Lacerda
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, USA
| | - Siva A Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, USA.
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Lee TY, Yoon KH, Lee JI. Cultivation of Caenorhabditis elegans in Three Dimensions in the Laboratory. J Vis Exp 2016. [PMID: 28060308 DOI: 10.3791/55048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The use of genetic model organisms such as Caenorhabditis elegans has led to seminal discoveries in biology over the last five decades. Most of what we know about C. elegans is limited to laboratory cultivation of the nematodes that may not necessarily reflect the environments they normally inhabit in nature. Cultivation of C. elegans in a 3D habitat that is more similar to the 3D matrix that worms encounter in rotten fruits and vegetative compost in nature could reveal novel phenotypes and behaviors not observed in 2D. In addition, experiments in 3D can address how phenotypes we observe in 2D are relevant for the worm in nature. Here, a new method in which C. elegans grows and reproduces normally in three dimensions is presented. Cultivation of C. elegans in Nematode Growth Tube-3D (NGT-3D) can allow us to measure the reproductive fitness of C. elegans strains or different conditions in a 3D environment. We also present a novel method, termed Nematode Growth Bottle-3D (NGB-3D), to cultivate C. elegans in 3D for microscopic analysis. These methods allow scientists to study C. elegans biology in conditions that are more reflective of the environments they encounter in nature. These can help us to understand the overlying evolutionary relevance of the physiology and behavior of C. elegans we observe in the laboratory.
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Affiliation(s)
- Tong Y Lee
- Division of Biological Science and Technology, Yonsei University
| | - Kyoung-Hye Yoon
- Division of Biological Science and Technology, Yonsei University
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University;
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Kalichamy SS, Lee TY, Yoon KH, Lee JI. Hypergravity hinders axonal development of motor neurons in Caenorhabditis elegans. PeerJ 2016; 4:e2666. [PMID: 27833821 PMCID: PMC5101602 DOI: 10.7717/peerj.2666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/08/2016] [Indexed: 12/29/2022] Open
Abstract
As space flight becomes more accessible in the future, humans will be exposed to gravity conditions other than our 1G environment on Earth. Our bodies and physiology, however, are adapted for life at 1G gravity. Altering gravity can have profound effects on the body, particularly the development of muscles, but the reasons and biology behind gravity’s effect are not fully known. We asked whether increasing gravity had effects on the development of motor neurons that innervate and control muscle, a relatively unexplored area of gravity biology. Using the nematode model organism Caenorhabditis elegans, we examined changes in response to hypergravity in the development of the 19 GABAergic DD/VD motor neurons that innervate body muscle. We found that a high gravity force above 10G significantly increases the number of animals with defects in the development of axonal projections from the DD/VD neurons. We showed that a critical period of hypergravity exposure during the embryonic/early larval stage was sufficient to induce defects. While characterizing the nature of the axonal defects, we found that in normal 1G gravity conditions, DD/VD axonal defects occasionally occurred, with the majority of defects occurring on the dorsal side of the animal and in the mid-body region, and a significantly higher rate of error in the 13 VD axons than the 6 DD axons. Hypergravity exposure increased the rate of DD/VD axonal defects, but did not change the distribution or the characteristics of the defects. Our study demonstrates that altering gravity can impact motor neuron development.
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Affiliation(s)
| | - Tong Young Lee
- Division of Biological Science and Technology, Yonsei University , Wonju , South Korea
| | - Kyoung-Hye Yoon
- Division of Biological Science and Technology, Yonsei University , Wonju , South Korea
| | - Jin Il Lee
- Division of Biological Science and Technology, Yonsei University , Wonju , South Korea
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