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Nogueira M, Golbert DCF, Landeira B, Leão RN. Laser Capture Microdissection Optimization for High-Quality RNA in Mouse Brain Tissue. Curr Protoc 2022; 2:e457. [PMID: 35822833 DOI: 10.1002/cpz1.457] [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] [Indexed: 06/15/2023]
Abstract
Laser Capture Microdissection (LCM) is a method that allows one to select and dissect well-defined structures, specific cell subpopulations, or even single cells from different types of tissue for subsequent extraction of DNA, RNA, or proteins. Its precision allows the dissection of specific groups of cells, avoiding unwanted cells. However, despite its efficiency, several steps can affect the sample RNA integrity. RNA instability represents a challenge in the LCM method, and low RNA integrity can introduce biases, as different transcripts often have different degradation rates. Here we describe an optimized protocol to provide good-concentration and high-quality RNA from specific structures: dentate gyrus and CA1 in the hippocampus, basolateral amygdala, and anterior cingulate cortex of mouse brain tissue. However, the protocol is applicable to other areas of interest. © 2022 Wiley Periodicals LLC. Basic Protocol: Laser capture microdissection of mouse brain tissue.
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Affiliation(s)
- Margareth Nogueira
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Daiane C F Golbert
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Bruna Landeira
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Richardson N Leão
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
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2
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Wang R, Peng G, Tam PPL, Jing N. Integration of computational analysis and spatial transcriptomics in single-cell study. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00084-5. [PMID: 35901961 PMCID: PMC10372908 DOI: 10.1016/j.gpb.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 06/08/2022] [Accepted: 06/19/2022] [Indexed: 04/08/2023]
Abstract
Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell biology. Meanwhile, pioneering explorations in spatial transcriptomics have opened avenues to address fundamental biological questions in health and diseases. Here, we review the technical attributes of single-cell RNA sequencing and spatial transcriptomics, and the core concepts of computational data analysis. We further highlight the challenges in the application of data integration methodologies and the interpretation of the biological context of the findings.
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Affiliation(s)
- Ran Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Patrick P L Tam
- Embryology Research Unit, Children's Medical Research Institute, University of Sydney, Sydney, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2145, Australia
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Guangzhou Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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3
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Perera SN, Williams RM, Lyne R, Stubbs O, Buehler DP, Sauka-Spengler T, Noda M, Micklem G, Southard-Smith EM, Baker CVH. Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach. Glia 2020; 68:2550-2584. [PMID: 32857879 PMCID: PMC7116175 DOI: 10.1002/glia.23870] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022]
Abstract
Olfactory ensheathing cells (OECs) are neural crest-derived glia that ensheath bundles of olfactory axons from their peripheral origins in the olfactory epithelium to their central targets in the olfactory bulb. We took an unbiased laser microdissection and differential RNA-seq approach, validated by in situ hybridization, to identify candidate molecular mechanisms underlying mouse OEC development and differences with the neural crest-derived Schwann cells developing on other peripheral nerves. We identified 25 novel markers for developing OECs in the olfactory mucosa and/or the olfactory nerve layer surrounding the olfactory bulb, of which 15 were OEC-specific (that is, not expressed by Schwann cells). One pan-OEC-specific gene, Ptprz1, encodes a receptor-like tyrosine phosphatase that blocks oligodendrocyte differentiation. Mutant analysis suggests Ptprz1 may also act as a brake on OEC differentiation, and that its loss disrupts olfactory axon targeting. Overall, our results provide new insights into OEC development and the diversification of neural crest-derived glia.
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Affiliation(s)
- Surangi N Perera
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Ruth M Williams
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Oliver Stubbs
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Dennis P Buehler
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Masaharu Noda
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Japan
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - E Michelle Southard-Smith
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Clare V H Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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Morrison JA, McLennan R, Wolfe LA, Gogol MM, Meier S, McKinney MC, Teddy JM, Holmes L, Semerad CL, Box AC, Li H, Hall KE, Perera AG, Kulesa PM. Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions. eLife 2017; 6:28415. [PMID: 29199959 PMCID: PMC5728719 DOI: 10.7554/elife.28415] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/02/2017] [Indexed: 12/19/2022] Open
Abstract
Neural crest cells migrate throughout the embryo, but how cells move in a directed and collective manner has remained unclear. Here, we perform the first single-cell transcriptome analysis of cranial neural crest cell migration at three progressive stages in chick and identify and establish hierarchical relationships between cell position and time-specific transcriptional signatures. We determine a novel transcriptional signature of the most invasive neural crest Trailblazer cells that is consistent during migration and enriched for approximately 900 genes. Knockdown of several Trailblazer genes shows significant but modest changes to total distance migrated. However, in vivo expression analysis by RNAscope and immunohistochemistry reveals some salt and pepper patterns that include strong individual Trailblazer gene expression in cells within other subregions of the migratory stream. These data provide new insights into the molecular diversity and dynamics within a neural crest cell migratory stream that underlie complex directed and collective cell behaviors.
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Affiliation(s)
- Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, United States
| | - Rebecca McLennan
- Stowers Institute for Medical Research, Kansas City, United States
| | - Lauren A Wolfe
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - Samuel Meier
- Stowers Institute for Medical Research, Kansas City, United States
| | - Mary C McKinney
- Stowers Institute for Medical Research, Kansas City, United States
| | - Jessica M Teddy
- Stowers Institute for Medical Research, Kansas City, United States
| | - Laura Holmes
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - Andrew C Box
- Stowers Institute for Medical Research, Kansas City, United States
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, United States
| | - Kathryn E Hall
- Stowers Institute for Medical Research, Kansas City, United States
| | - Anoja G Perera
- Stowers Institute for Medical Research, Kansas City, United States
| | - Paul M Kulesa
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, United States
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Morrison JA, Box AC, McKinney MC, McLennan R, Kulesa PM. Quantitative single cell gene expression profiling in the avian embryo. Dev Dyn 2016; 244:774-84. [PMID: 25809747 DOI: 10.1002/dvdy.24274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Single cell gene profiling has been successfully applied to cultured cells. However, isolation and preservation of a cell's native gene expression state from an intact embryo remain problematic. RESULTS Here, we present a strategy for in vivo single cell profiling that optimizes cell identification, isolation and amplification of nucleic acids with nominal bias and sufficient material detection. We first tested several photoconvertible fluorescent proteins to selectively mark a cell(s) of interest in living chick embryos then accurately identify and isolate the same cell(s) in fixed tissue slices. We determined that the dual color mDendra2 provided the optimal signal/noise ratio for this purpose. We developed proper procedures to minimize cell death and preserve gene expression, and suggest nucleic acid amplification strategies for downstream analysis by microfluidic reverse transcriptase quantitative polymerase chain reaction or RNAseq. Lastly, we compared methods for single cell isolation and found that our fluorescence-activated cell sorting (FACS) protocol was able to preserve native transcripts and generate expression profiles with much higher efficiency than laser capture microdissection (LCM). CONCLUSIONS Quantitative single cell gene expression profiling may be accurately applied to interrogate complex cell dynamics events during embryonic development by combining photoconversion cell labeling, FACS, proper handling of isolated cells, and amplification strategies.
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Affiliation(s)
| | - Andrew C Box
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Mary C McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri
| | | | - Paul M Kulesa
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, Kansas
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TrkB/BDNF signalling patterns the sympathetic nervous system. Nat Commun 2015; 6:8281. [PMID: 26404565 PMCID: PMC4586040 DOI: 10.1038/ncomms9281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 08/06/2015] [Indexed: 12/16/2022] Open
Abstract
The sympathetic nervous system is essential for maintaining mammalian homeostasis. How this intricately connected network, composed of preganglionic neurons that reside in the spinal cord and post-ganglionic neurons that comprise a chain of vertebral sympathetic ganglia, arises developmentally is incompletely understood. This problem is especially complex given the vertebral chain of sympathetic ganglia derive secondarily from the dorsal migration of ‘primary' sympathetic ganglia that are initially located several hundred microns ventrally from their future pre-synaptic partners. Here we report that the dorsal migration of discrete ganglia is not a simple migration of individual cells but a much more carefully choreographed process that is mediated by extensive interactions of pre-and post-ganglionic neurons. Dorsal migration does not occur in the absence of contact with preganglionic axons, and this is mediated by BDNF/TrkB signalling. Thus BDNF released by preganglionic axons acts chemotactically on TrkB-positive sympathetic neurons, to pattern the developing peripheral nervous system. The signals that pattern the sympathetic nervous system are not fully understood. Here the authors show that the dorsal migration of the primary sympathetic ganglia in chick embryos is orchestrated by BDNF/TrkB signalling and requires contact with preganglionic axons.
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McLennan R, Schumacher LJ, Morrison JA, Teddy JM, Ridenour DA, Box AC, Semerad CL, Li H, McDowell W, Kay D, Maini PK, Baker RE, Kulesa PM. Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front. Development 2015; 142:2014-25. [PMID: 25977364 DOI: 10.1242/dev.117507] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 04/09/2015] [Indexed: 12/30/2022]
Abstract
Neural crest (NC) cell migration is crucial to the formation of peripheral tissues during vertebrate development. However, how NC cells respond to different microenvironments to maintain persistence of direction and cohesion in multicellular streams remains unclear. To address this, we profiled eight subregions of a typical cranial NC cell migratory stream. Hierarchical clustering showed significant differences in the expression profiles of the lead three subregions compared with newly emerged cells. Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells. Computational modeling predicted that a small fraction of lead cells that detect directional information is optimal for successful stream migration. Single-cell profiling then revealed a unique molecular signature that is consistent and stable over time in a subset of lead cells within the most advanced portion of the migratory front, which we term trailblazers. Model simulations that forced a lead cell behavior in the trailing subpopulation predicted cell bunching near the migratory domain entrance. Misexpression of the trailblazer molecular signature by perturbation of two upstream transcription factors agreed with the in silico prediction and showed alterations to NC cell migration distance and stream shape. These data are the first to characterize the molecular diversity within an NC cell migratory stream and offer insights into how molecular patterns are transduced into cell behaviors.
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Affiliation(s)
- Rebecca McLennan
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Linus J Schumacher
- Oxford University, Wolfson Centre for Mathematical Biology, Mathematical Institute, Woodstock Road, Oxford OX2 6GG, UK Computer Science, Oxford University, Wolfson Building, Parks Road, Oxford OX1 3QD, UK
| | - Jason A Morrison
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Jessica M Teddy
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Dennis A Ridenour
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Craig L Semerad
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - William McDowell
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA
| | - David Kay
- Oxford University, Wolfson Centre for Mathematical Biology, Mathematical Institute, Woodstock Road, Oxford OX2 6GG, UK Computer Science, Oxford University, Wolfson Building, Parks Road, Oxford OX1 3QD, UK
| | - Philip K Maini
- Oxford University, Wolfson Centre for Mathematical Biology, Mathematical Institute, Woodstock Road, Oxford OX2 6GG, UK
| | - Ruth E Baker
- Oxford University, Wolfson Centre for Mathematical Biology, Mathematical Institute, Woodstock Road, Oxford OX2 6GG, UK
| | - Paul M Kulesa
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
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Kulesa PM, McKinney MC, McLennan R. Developmental imaging: the avian embryo hatches to the challenge. ACTA ACUST UNITED AC 2014; 99:121-33. [PMID: 23897596 DOI: 10.1002/bdrc.21036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 05/31/2013] [Indexed: 01/27/2023]
Abstract
The avian embryo provides a multifaceted model to study developmental mechanisms because of its accessibility to microsurgery, fluorescence cell labeling, in vivo imaging, and molecular manipulation. Early two-dimensional planar growth of the avian embryo mimics human development and provides unique access to complex cell migration patterns using light microscopy. Later developmental events continue to permit access to both light and other imaging modalities, making the avian embryo an excellent model for developmental imaging. For example, significant insights into cell and tissue behaviors within the primitive streak, craniofacial region, and cardiovascular and peripheral nervous systems have come from avian embryo studies. In this review, we provide an update to recent advances in embryo and tissue slice culture and imaging, fluorescence cell labeling, and gene profiling. We focus on how technical advances in the chick and quail provide a clearer understanding of how embryonic cell dynamics are beautifully choreographed in space and time to sculpt cells into functioning structures. We summarize how these technical advances help us to better understand basic developmental mechanisms that may lead to clinical research into human birth defects and tissue repair.
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Affiliation(s)
- Paul M Kulesa
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
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Yee JY, Limenta LMG, Rogers K, Rogers SM, Tay VSY, Lee EJD. Ensuring good quality RNA for quantitative real-time PCR isolated from renal proximal tubular cells using laser capture microdissection. BMC Res Notes 2014; 7:62. [PMID: 24467986 PMCID: PMC3905289 DOI: 10.1186/1756-0500-7-62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/24/2014] [Indexed: 01/14/2023] Open
Abstract
Background In order to provide gene expression profiles of different cell types, the primary step is to isolate the specific cells of interest via laser capture microdissection (LCM), followed by extraction of good quality total RNA sufficient for quantitative real-time polymerase chain reaction (qPCR) analysis. This LCM-qPCR strategy has allowed numerous gene expression studies on specific cell populations, providing valuable insights into specific cellular changes in diseases. However, such strategy imposed challenges as cells of interests are often available in limited quantities and quality of RNA may be compromised during long periods of time spent on collection of cells and extraction of total RNA; therefore, it is crucial that protocols for sample preparation should be optimised according to different cell populations. Findings We made several modifications to existing protocols to improve the total RNA yield and integrity for downstream qPCR analyses. A modified condensed hematoxylin and eosin (H&E) staining protocol was developed for the identification of rat renal proximal tubular cells (PTCs). It was then determined that a minimal of eight thousands renal PTCs were required to meet the minimal total RNA yield required for downstream qPCR. RNA integrity was assessed using at every progressive step of sample preparation. Therefore, we decided that the shortened H&E staining, together with microdissection should be performed consecutively within twenty minutes for good quality for gene expression analysis. These modified protocols were later applied on six individual rat samples. A panel of twenty rat renal drug transporters and five housekeeping genes showed Ct values below thirty-five, confirming the expression levels of these drug transporters can be detected. Conclusions We had successfully optimized the protocols to achieve sufficient good quality total RNA from microdissected rat renal PTCs for gene expression profiling via qPCR. This protocol may be suitable for researchers who are interested in employing similar applications for gene expression studies.
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Affiliation(s)
- Jie Yin Yee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, MD11 10 Medical Drive #05-09, Singapore 117597, Singapore.
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McKinney MC, Fukatsu K, Morrison J, McLennan R, Bronner ME, Kulesa PM. Evidence for dynamic rearrangements but lack of fate or position restrictions in premigratory avian trunk neural crest. Development 2013; 140:820-30. [PMID: 23318636 DOI: 10.1242/dev.083725] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Neural crest (NC) cells emerge from the dorsal trunk neural tube (NT) and migrate ventrally to colonize neuronal derivatives, as well as dorsolaterally to form melanocytes. Here, we test whether different dorsoventral levels in the NT have similar or differential ability to contribute to NC cells and their derivatives. To this end, we precisely labeled NT precursors at specific dorsoventral levels of the chick NT using fluorescent dyes and a photoconvertible fluorescent protein. NT and NC cell dynamics were then examined in vivo and in slice culture using two-photon and confocal time-lapse imaging. The results show that NC precursors undergo dynamic rearrangements within the neuroepithelium, yielding an overall ventral to dorsal movement toward the midline of the NT, where they exit in a stochastic manner to populate multiple derivatives. No differences were noted in the ability of precursors from different dorsoventral levels of the NT to contribute to NC derivatives, with the exception of sympathetic ganglia, which appeared to be 'filled' by the first population to emigrate. Rather than restricted developmental potential, however, this is probably due to a matter of timing.
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Affiliation(s)
- Mary C McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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