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Otalora K, Riera JL, Tavecchia G, Rotger A, Igual JM, Trotta JP, Baldo L. Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data. Ecol Evol 2024; 14:e11407. [PMID: 38799398 PMCID: PMC11116764 DOI: 10.1002/ece3.11407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
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Affiliation(s)
- Katherin Otalora
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Fundación FUNMAJO, EBA, RAIEC, Biodiversity BranchTunjaBoyacáColombia
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Andreu Rotger
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - José Manuel Igual
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Jean‐Remi Paul Trotta
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Institute for Research on Biodiversity (IRBio)University of Barcelona (UB)BarcelonaSpain
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Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
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Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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Alibardi L. Immunolocalization of Adenomatous Polyposis Coli protein (apc) in the regenerating lizard tail suggests involvement in tissue differentiation and regulation of growth. J Morphol 2022; 283:677-688. [PMID: 35195910 DOI: 10.1002/jmor.21465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 11/07/2022]
Abstract
Lizard tail regeneration is likely regulated by the balanced activity of oncogenes and tumor suppressors that control cell proliferation avoiding tumorigenic degeneration. One of the main tumor suppressor genes present in the regenerating tail is the "adenomatous polyposis coli (apc)" but the localization of its coded protein (apc) is not known. This protein may be involved in regulation of apical-basal tail regeneration in lizards. The present immunohistochemical study shows that apc is localized in apical wound epidermis and regenerating ependyme, two tissues that proliferate and also express onco-genes. Apc is not present in blastema cells but localizes in differentiating cells of regenerating scales, muscles and less intensely in the non-apical ependymal epithelium and cartilage. This suggests that apc is involved in the induction of their differentiation. The apc immunolabeling is mainly nuclear in the basal epidermal layer of the apical wound epidermis where it may be involved in modulating keratinocytes proliferation, like in the forming scales. In regenerating muscle and cartilage apc is mainly cytoplasmic while sparse labeled nuclei are seen in proliferative areas of these tissues. In the regenerating spinal cord, the nuclear and cytoplasmic apc labeling is present in ependymal cells of the distal-most ependymal ampulla but the labeling fades in more proximal regions and mainly remains in the cytoplasm facing the central canal and in sparse nuclei. It is suggested that the pattern of immunolabeling for apc indicates that this tumor suppressor may contribute to tissue differentiation within the regenerating tail. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova and Department of Biology of the University of Bologna
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Alibardi L. Review: Regeneration of the tail in lizards appears regulated by a balanced expression of oncogenes and tumor suppressors. Ann Anat 2021; 239:151824. [PMID: 34478856 DOI: 10.1016/j.aanat.2021.151824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tail regeneration in lizards is the only case of large multi-tissue organ regeneration in amniotes. METHODS The present Review summarizes numerous immunolocalization and gene-expression studies indicating that after tail amputation in lizards the stump is covered in 7-10 days by the migration of keratinocytes. This allows the accumulation of mesenchymal-fibroblasts underneath the wound epidermis and forms a regenerative blastema and a new tail. RESULTS During migration keratinocytes transit from a compact epidermis into relatively free keratinocytes in a process of "Epithelial Mesenchymal Transition" (EMT). While EMT has been implicated in carcinogenesis no malignant transformation is observed during these cell movements in the regenerative blastema. Immunolabeling for E-cadherin and snail shows that these proteins are present in the cytoplasm and nuclei of migrating keratinocytes. The basal layer of the wound epithelium of the apical blastema express onco-proteins (wnt2b, egfr, c-myc, fgfs, fgfr, rhov, etc.) and tumor suppressors (p53/63, fat2, ephr, apc, retinoblastoma, arhgap28 etc.). This suggests that their balanced action regulates proliferation of the blastema. CONCLUSIONS While apical epidermis and mesenchyme are kept under a tight proliferative control, in more proximal regions of the regenerating tail the expression of tumor-suppressors triggers the differentiation of numerous tissues, forming the large myomeres, axial cartilage, simple spinal cord and nerves, new scales, arteries and veins, fat deposits, dermis and other connective tissues. Understanding gene expression patterns of developmental pathways activated during tail regeneration in lizards is useful for cancer research and for future attempts to induce organ regeneration in other amniotes including humans.
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Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova and Dipartmento di Biologia, Universita' di Bologna, Italy.
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Dong Z, Coates D. Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration. J Proteome Res 2021; 20:2167-2181. [PMID: 33769828 DOI: 10.1021/acs.jproteome.1c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.
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Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration. Sci Rep 2021; 11:3675. [PMID: 33574494 PMCID: PMC7878758 DOI: 10.1038/s41598-021-83283-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/28/2021] [Indexed: 11/08/2022] Open
Abstract
Epimorphic regeneration of appendages is a complex and complete phenomenon found in selected animals. Hemidactylus frenatus, house gecko has the remarkable ability to regenerate the tail tissue upon autotomy involving epimorphic regeneration mechanism. This study has identified and evaluated the molecular changes at gene and protein level during the initial stages, i.e., during the wound healing and repair mechanism initiation stage of tail regeneration. Based on next generation transcriptomics and De novo analysis the transcriptome library of the gecko tail tissue was generated. A total of 254 genes and 128 proteins were found to be associated with the regeneration of gecko tail tissue upon amputation at 1, 2 and 5-day post amputation (dpa) against control, 0-dpa through differential transcriptomic and proteomic analysis. To authenticate the expression analysis, 50 genes were further validated involving RTPCR. 327 genes/proteins identified and mapped from the study showed association for Protein kinase A signaling, Telomerase BAG2 signaling, paxillin signaling, VEGF signaling network pathways based on network pathway analysis. This study empanelled list of transcriptome, proteome and the list of genes/proteins associated with the tail regeneration.
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Daponte V, Tylzanowski P, Forlino A. Appendage Regeneration in Vertebrates: What Makes This Possible? Cells 2021; 10:cells10020242. [PMID: 33513779 PMCID: PMC7911911 DOI: 10.3390/cells10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ability to regenerate amputated or injured tissues and organs is a fascinating property shared by several invertebrates and, interestingly, some vertebrates. The mechanism of evolutionary loss of regeneration in mammals is not understood, yet from the biomedical and clinical point of view, it would be very beneficial to be able, at least partially, to restore that capability. The current availability of new experimental tools, facilitating the comparative study of models with high regenerative ability, provides a powerful instrument to unveil what is needed for a successful regeneration. The present review provides an updated overview of multiple aspects of appendage regeneration in three vertebrates: lizard, salamander, and zebrafish. The deep investigation of this process points to common mechanisms, including the relevance of Wnt/β-catenin and FGF signaling for the restoration of a functional appendage. We discuss the formation and cellular origin of the blastema and the identification of epigenetic and cellular changes and molecular pathways shared by vertebrates capable of regeneration. Understanding the similarities, being aware of the differences of the processes, during lizard, salamander, and zebrafish regeneration can provide a useful guide for supporting effective regenerative strategies in mammals.
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Affiliation(s)
- Valentina Daponte
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
| | - Przemko Tylzanowski
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, University of Leuven, 3000 Leuven, Belgium;
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Antonella Forlino
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
- Correspondence: ; Tel.: +39-0382-987235
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Dong Z, Haines S, Coates D. Proteomic Profiling of Stem Cell Tissues during Regeneration of Deer Antler: A Model of Mammalian Organ Regeneration. J Proteome Res 2020; 19:1760-1775. [DOI: 10.1021/acs.jproteome.0c00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Stephen Haines
- Proteins & Metabolites, AgResearch Lincoln Research Centre, Lincoln, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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Alibardi L. Review: The Regenerating Tail Blastema of Lizards as a Model to Study Organ Regeneration and Tumor Growth Regulation in Amniotes. Anat Rec (Hoboken) 2018; 302:1469-1490. [DOI: 10.1002/ar.24029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova and Department of Biology at University of Bologna Bologna Italy
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Alibardi L. Immunolocalization of serpins in the regenerating tail of lizard suggests a role for epidermal and neural barrier formation. ZOOLOGY 2018; 131:1-9. [DOI: 10.1016/j.zool.2018.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
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Alibardi L. Immunolocalization of Matrix Metalloproteinases in regenerating lizard tail suggests that an intense remodelling activity allows for apical tail growth. ACTA ZOOL-STOCKHOLM 2018. [DOI: 10.1111/azo.12277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab and Department of Biology University of Bologna Bologna Italy
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Alibardi L. Immunodetection of High Mobility Group Proteins in the regenerating tail of lizard mainly indicates activation for cell proliferation. ACTA ZOOL-STOCKHOLM 2018. [DOI: 10.1111/azo.12259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova and Department of BiologyUniversity of Bologna Bologna Italy
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Alibardi L. Ultrastructural analysis of early regenerating lizard tail suggests that a process of dedifferentiation is involved in the formation of the regenerative blastema. J Morphol 2018; 279:1171-1184. [DOI: 10.1002/jmor.20838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab, Padova, and Department of Biology; University of Bologna; Bologna Italy
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Alibardi L. Temporal distribution of 5BrdU‐labelled cells suggests that most injured tissues contribute proliferating cells for the regeneration of the tail and limb in lizard. ACTA ZOOL-STOCKHOLM 2018. [DOI: 10.1111/azo.12255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab and Department of BiologyUniversity of Bologna Bologna Italy
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Alibardi L. Epidermal Growth Factor and EGF Receptors are mainly expressed in the wound epidermis and proliferating ependyma of the regenerating tail of lizards. ACTA ZOOL-STOCKHOLM 2017. [DOI: 10.1111/azo.12235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab; Padova Italy
- Department of Biology; University of Bologna; Bologna Italy
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Alibardi L. Review: Biological and Molecular Differences between Tail Regeneration and Limb Scarring in Lizard: An Inspiring Model Addressing Limb Regeneration in Amniotes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:493-514. [DOI: 10.1002/jez.b.22754] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 05/16/2017] [Accepted: 05/24/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab and Department of Biology; University of Bologna; Bologna Italy
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Immunolocalization of FGF8/10 in the Apical Epidermal Peg and Blastema of the regenerating tail in lizard marks this apical growing area. Ann Anat 2016; 206:14-20. [PMID: 27113329 DOI: 10.1016/j.aanat.2016.03.010] [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: 01/10/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/20/2022]
Abstract
Previous studies have shown that Fibroblast Growth Factors are present in the regenerating tail tissues of lizards where they may stimulate the process of regeneration. The present study is focused on the immunolocalization of FGF8 and FGF10 in the regenerating lizard tail, two signaling proteins of the apical epidermal cup/ridge and mesenchymal blastema sustaining tail and limb regeneration in amphibians and the development of the tail and limbs in vertebrate embryos. Main immunoreactive protein bands at 15-18kDa for FGF8/10 are detected in the regenerating epidermis and only a band at 30 or 35kDa in the underlying connective tissues. FGF8 appears particularly localized in cells and nuclei of the apical epidermal peg and of the ependymal ampulla present at the tip of the regenerating tail. FGF10 is also immuno-localized in the apical epidermis but is particularly intensely localized in the mesenchyme of the apical blastema. In accordance with previous studies, the present observations supports the hypothesis that the apical epidermal peg and the ependymal tube with the few regenerated neurons present within it, release FGF8/10 that may contribute to maintenance of cell proliferation in the apical front of the mesenchyme for the growth of the regenerating tail.
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Alibardi L. Cell proliferation in the amputated limb of lizard leading to scarring is reduced compared to the regenerating tail. ACTA ZOOL-STOCKHOLM 2016. [DOI: 10.1111/azo.12161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab and Dipartimento di Bigea; Università di Bologna; via Selmi 3 Bologna 40126 Italy
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