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Rueda-Alaña E, Grillo M, Vázquez E, Salas SM, Senovilla-Ganzo R, Escobar L, Quintas A, Benguría A, Aransay AM, Bengoa-Vergniory N, Dopazo A, Encinas JM, Nilsson M, García-Moreno F. BirthSeq, a new method to isolate and analyze dated cells in different vertebrates. Development 2024; 151:dev202429. [PMID: 38856078 DOI: 10.1242/dev.202429] [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: 10/19/2023] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a crucial role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via fluorescence-activated cell sorting, and analysis using high-throughput techniques. We calibrated the BirthSeq method for developmental organs across three vertebrate species (mouse, chick and gecko), and utilized it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organisms, aiding developmental biology research by targeting cells and their temporal cues.
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Affiliation(s)
- Eneritz Rueda-Alaña
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Marco Grillo
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Enrique Vázquez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Rodrigo Senovilla-Ganzo
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Laura Escobar
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Ana Quintas
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Ana María Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Nora Bengoa-Vergniory
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Juan Manuel Encinas
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
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Ligasová A, Koberna K. DNA Replication: From Radioisotopes to Click Chemistry. Molecules 2018; 23:molecules23113007. [PMID: 30453631 PMCID: PMC6278288 DOI: 10.3390/molecules23113007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
The replication of nuclear and mitochondrial DNA are basic processes assuring the doubling of the genetic information of eukaryotic cells. In research of the basic principles of DNA replication, and also in the studies focused on the cell cycle, an important role is played by artificially-prepared nucleoside and nucleotide analogues that serve as markers of newly synthesized DNA. These analogues are incorporated into the DNA during DNA replication, and are subsequently visualized. Several methods are used for their detection, including the highly popular click chemistry. This review aims to provide the readers with basic information about the various possibilities of the detection of replication activity using nucleoside and nucleotide analogues, and to show the strengths and weaknesses of those different detection systems, including click chemistry for microscopic studies.
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Affiliation(s)
- Anna Ligasová
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
| | - Karel Koberna
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
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Rahim RS, St John JA, Crane DI, Meedeniya ACB. Impaired neurogenesis and associated gliosis in mouse brain with PEX13 deficiency. Mol Cell Neurosci 2017; 88:16-32. [PMID: 29187321 DOI: 10.1016/j.mcn.2017.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/04/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
Zellweger syndrome (ZS), a neonatal lethal disorder arising from defective peroxisome biogenesis, features profound neuroanatomical abnormalities and brain dysfunction. Here we used mice with brain-restricted inactivation of the peroxisome biogenesis gene PEX13 to model the pathophysiological features of ZS, and determine the impact of peroxisome dysfunction on neurogenesis and cell maturation in ZS. In the embryonic and postnatal PEX13 mutant brain, we demonstrate key regions with altered brain anatomy, including enlarged lateral ventricles and aberrant cortical, hippocampal and hypothalamic organization. To characterize the underlying mechanisms, we show a significant reduction in proliferation, migration, differentiation, and maturation of neural progenitors in embryonic E12.5 through to P3 animals. An increasing reactive gliosis in the PEX13 mutant brain started at E14.5 in association with the pathology. Together with impaired neurogenesis and associated gliosis, our data demonstrate increased cell death contributing to the hallmark brain anatomy of ZS. We provide unique data where impaired neurogenesis and migration are shown as critical events underlying the neuropathology and altered brain function of mice with peroxisome deficiency.
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Affiliation(s)
- Rani Sadia Rahim
- Griffith Institute for Drug Discovery, School of Natural Sciences, Griffith University, Qld, Australia
| | - James A St John
- Griffith Institute for Drug Discovery, School of Natural Sciences, Griffith University, Qld, Australia; Clem Jones Centre for Neurobiology and Stem Cell Research, Australia; Menzies Health Institute Queensland, Griffith University, Qld, Australia
| | - Denis I Crane
- Griffith Institute for Drug Discovery, School of Natural Sciences, Griffith University, Qld, Australia.
| | - Adrian C B Meedeniya
- Menzies Health Institute Queensland, Griffith University, Qld, Australia; Interdisciplinary Centre for Innovations in Biotechnology & Neurosciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka.
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