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Bio 4072/5572: Regenerative and Stem Cell Biology

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Organism Group Process Method(s) Citation (APA 7) Notes
Arthropods       Suzuki, Y., Chou, J., Garvey, S. L., Wang, V. R., & Yanes, K. O. (2019). Evolution and regulation of limb regeneration in arthropods. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-devo: Non-model species in cell and developmental biology (pp. 419-454). Springer, Cham. https://doi.org/10.1007/978-3-030-23459-1_17  
Annelids       Joseph, N. A., Chen, C.-F., Chen, J.-H., & Chen, L.-Y. (2022). Monitoring telomere maintenance during regeneration of annelids. In S. Blanchoud & B. Galliot (Eds.), Whole-body regeneration: Methods and protocols (pp. 467-478). Humana. https://doi.org/10.1007/978-1-0716-2172-1_24  
Salamander Vertebrate Limb regeneration   Kaucka, M., Joven Araus, A., Tesarova, M., Currie, J. D., Bostrom, J., Kavkova, M., Petersen, J., Yao, Z., Bouchnita, A., Hellander, A., Zikmund, T., Elewa, A., Newton, P. T., Fei, J.-F., Chagin, A. S., Fried, K., Tanaka, E. M., Kaiser, J., Simon, A., & Adameyko, I. (2022). Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration. Nature Communications, 13(1), 6949. https://doi.org/10.1038/s41467-022-34266-w  
Mouse Vertebrate   Cre-lox barcoding Pei, W., Wang, J., Rossler, J., Feyerabend, T. B., Hofer, T., & Rodewald, H.-R. (2019). Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nature Protocols, 14(6), 1820-1840. https://doi.org/10.1038/s41596-019-0163-5  
        Regeneration from Cells to Limbs: Past, Present, and Future. Frontiers in Cell and Developmental Biology. https://www.frontiersin.org/research-topics/17983/regeneration-from-cells-to-limbs-past-present-and-future#articles  Collection of 28 articles spanning the topic of regeneration. 
Acoels       Harvard University, Department of Organismic and Evolutionary Biology (2023, January 18). A biological wonder: Harvard researchers discover embryonic origins of adult pluripotent stem cells. SciTechDaily.  Newspaper article. You can also read the original research article in Cell. 
        Model systems for regeneration. The Company of Biologists. https://journals.biologists.com/dev/collection/63/Model-systems-for-regeneration Series of 8 articles highlighting key model systems and species that are currently being used to study tissue and organ regeneration. 
Mouse   Digit tip regeneration scRNAseq Johnson, G. L., Masias, E. J., & Lehoczky, J. A. (2020). Cellular heterogeneity and lineage restriction during mouse digit tip regeneration at single-cell resolution. Developmental Cell, 52(4), 525-540.e5. https://doi.org/10.1016/j.devcel.2020.01.026  
Hydractinia Cnidarian Whole body regeneration Transgenesis    
Parhyale Crustacean Leg regeneration Live imaging, transgenesis Alwes, F., Enjolras, C., & Averof, M. (2016). Live imaging reveals the progenitors and cell dynamics of limb regeneration. eLife, 5. https://doi.org/10.7554/eLife.19766  
Parhyale Crustacean Leg regeneration Cell lineage tracing, CRISPR Cevrim, B. C. (2020). Tracking cell fates during limb regeneration (2021LYSEN006). [Doctoral dissertation, University of Lyon].   
Planaria   Whole body regeneration scRNAseq Benham-Pyle, B. W., Brewster, C. E., Kent, A. M., Mann Jr, F. G., Chen, S., Scott, A. R., Box, A. C., & Alvarado, A. S. (2021). Identification of rare post-mitotic cell states induced by injury and required for whole-body regeneration in Schmidtea mediterranea. Nature Cell Biology, 23(9), 939-952. https://doi.org/10.1038/s41556-021-00734-6  
Planaria   Regeneration   Reddien, P. W. (2018). The cellular and molecular basis for planarian regeneration. Cell, 175(2), 327-345. https://doi.org/10.1016/j.cell.2018.09.021 Review article. 
Planaria   Regeneration Press and split planaria Arnold, C. P., Benham-Pyle, B. W., Lange, J. J., Wood, C. J., & Alvarado, A. S. (2019). Wnt and TGFβ coordinate growth and patterning to regulate size-dependent behaviour. Nature, 572(7771), 655-659. https://doi.org/10.1038/s41586-019-1478-7  
        Holstein, T. W. (2019, August 14) What makes flatworms go to pieces. News and Views. https://www.nature.com/articles/d41586-019-02376-z Commentary on above paper. 
Planaria   Techniques scRNAseq Garcia-Castro, H. & Solana, J. (2022). Single-cell transcriptomics in planaria: New tools allow new insights into cellular and evolutionary features. Biochemical Society Transactions, 50(5), 1237-1246. https://doi.org/10.1042/BST20210825 Review article. 
Planaria       Ivankovic, M., Haneckova, R., Thommen, A., Grohme, M. A., Vila-Farre, M., Werner, S., & Rink, J. C. (2019). Model systems for regeneration: planarians. Development, 146(17). https://doi.org/10.1242/dev.167684 Review article. 
Planaria   Regeneration competent and incompetent Comparative, RNAi, bulk RNAseq Sikes, J. M. & Newmark, P. A. (2013). Restoration of anterior regeneration in a planarian with limited regenerative ability. Nature, 500(7460), 77-80. https://doi.org/10.1038/nature12403  
Hydra Cnidarian Hydra regeneration   Juliano, C. [Carnegie Science Embryology]. (2020, October 2). Mechanisms of Development and Regeneration in Hydra (Celia Juliano) // 2020 Minisymposium - Keynote [Video]. YouTube. https://www.youtube.com/watch?v=hmkeZ7_6owI   
Zebrafish Vertebrate Hair cell regeneration scRNAseq Lush, M. E., Diaz, D. C., Koenecke, N., Baek, S., Boldt, H., St. Peter, M. K., Gaitan-Escudero, T., Romero-Carvajal, A., Busch-Nentwich, E. M., Perera, A. G., Hall, K. E., Pak, A., Haug, J. S., & Piotrowski, T. (2019). scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. eLife, 8. https://doi.org/10.7554/eLife.44431  
        Lu, S., Schneider, I., Zeng, H., & He, S. (2023). The use of single-cell sequencing to reveal stem/progenitor cells in animal organ regeneration. Water Biology and Security, 2(1). https://doi.org/10.1016/j.watbs.2022.100081 Review of scRNAseq in regeneration. 
Zebrafish Vertebrate Heart regeneration scRNAseq

Honkoop, H., de Bakker, D. E. M., Aharonov, A., Kruse, F., Shakked, A., Nguyen, P. D., de Heus, C., Garric, L., Muraro, M. J., Shoffner, A., Tessadori, F., Craiger Peterson, J., Noort, W., Bertozzi, A., Weidinger, G., Posthuma, G., Grun, D., van der Laarse, W. J., Klumperman, J., . . . Baakers, J. (2019). Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. eLife, 8. https://doi.org/10.7554/eLife.50163

  
Axolotl Vertebrate Limb regeneration scRNAseq Gerber, T., Murawala, P., Knapp, D., Masselink, W., Schuez, M., Hermann, S., Gac-Santel, M., Nowoshilow, S., Kageyama, J., Khattak, S., Currie, J. D., Camp, J. G., Tanaka, E. M., & Treutlein, B. (2018). Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. Science, 362(6413), 421. https://doi.org/10.1126/science.aaq0681  
        Srivastava, M. (2021). Beyond casual resemblance: Rigorous frameworks for comparing regeneration across species. Annual Review of Cell and Developmental Biology, 37(1), 415-440. https://doi.org/10.1146/annurev-cellbio-120319-114716 Framework for comparing regeneration across animals. 
Stentor       Marshall, W. F. (2021). Regeneration in Stentor coeruleus. Frontiers in Cell and Developmental Biology, 9, 753625. https://doi.org/10.3389/fcell.2021.753625  
C. elegans Nematode Axon regeneration   Hammarlund, M. & Jin, Y. (2014). Axon regeneration in C. elegans. Current Opinion in Neurobiology, 27, 199-207. https://doi.org/10.1016/j.conb.2014.04.001  
Sea star Echnioderm     Meyer, A, & Hinman, V. (2022). Chapter eighteen - The arm of the starfish: The far-reaching applications of Patiria miniata as a model system in evolutionary, developmental, and regenerative biology. In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (pp. 523-543). Elsevier. https://doi.org/10.1016/bs.ctdb.2022.01.006  
Drosophila       Hariharan, I. K. & Serras, F. (2017). Imaginal disc regeneration takes flight. Current Opinion in Cell Biology, 48, 10-16. https://doi.org/10.1016/j.ceb.2017.03.005  
African spiny mouse       Seifert, A. W. & Temple-Smith, P. (2022). Chapter twenty-three - A remarkable rodent: Regeneration and reproduction in spiny mice (Acomys). In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (659-707). Elsevier. https://doi.org/10.1016/bs.ctdb.2021.12.017 Review. 
Axolotl       Echeverri, K., Fei, J. & Tanaka, E. M. (2022). Chapter twenty-two - The axolotl's journey to the modern molecular era. In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (631-658). Elsevier. https://doi.org/10.1016/bs.ctdb.2021.12.010 Review. 
Pristina leidyi Annelid     Bely, A. E. (2022). Chapter sixteen - Journey beyond the embryo: The beauty of Pristina and naidine annelids for studying regeneration and agametic reproduction. In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (469-495). Elsevier. https://doi.org/10.1016/bs.ctdb.2021.12.020 Review. 
Platynereis dumerilii Annelid    

Ozpolat, B. D., Randel, N., Williams, E. A., Bezares-Calderon, L. A., Andreatta, G., Balavoine, G., Bertucci, P. Y., Ferrier, D. E. K., Gambi, M. C., Gazave, E., Handberg-Thorsager, M., Hardege, J., Hird, C., Hsieh, Y.-W., Hui, J., Mutemi, K. N., Schneider, S. Q., Simakov, O., Vergara, H. M., . . . Arendt, D. (2021). The Nereid on the rise: Platynereis as a model system. EvoDevo, 12(1), 10. https://doi.org/10.1186/s13227-021-00180-3

 Review.
Syllids Annelid     Ribeiro, R. P., Bleidorn, C., & Aguado, M. T. (2018). Regeneration mechanisms in Syllidae (Annelida). Regeneration, 5(1), 26-42. https:/doi.org/10.1002/reg2.98 Review. 
Planaria       Newmark, P. A. & Sanchez Alvarado, A. (2022). Chapter eleven - Schmidtea happens: Re-restablishing the planarian as a model for studying the mechanisms of regeneration. In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (307-344). Elsevier. https://doi.org/10.1016/bs.ctdb.2022.01.002 Review. 
Acoels       Srivastava, M. (2022). Chapter six - Studying development, regeneration, stem cells, and more in the acoel Hofstenia miamia. In B. Goldstein & M. Srivastava (Eds.), Emerging model systems in developmental biology (153-172). Elsevier. https://doi.org/10.1016/bs.ctdb.2022.01.003 Review. 
Ascidians       Vanni, V., Ballarin, L., Gasparini, F., Peronato, A., & Manni, L. (2022). Studying regeneration in ascidians: An historical overview. In In S. Blanchoud & B. Galliot (Eds.), Whole-body regeneration: Methods and protocols (pp. 27-48). Humana. https://doi.org/10.1007/978-1-0716-2172-1_2 Review. 
Zebrafish       Gonzalez-Rosa, J. M., Burns, C. E., & Burns, C. G. (2017). Zebrafish heart regeneration: 15 years of discoveries. Regeneration, 4(3), 105-123. https://doi.org/10.1002/reg2.83 Review on heart regeneration.
Mouse       Dolan, C. P., Dawson, L. A., & Muneoka, K. (2018). Digit tip regeneration: Merging regeneration biology with regenerative medicine. Stem Cells Translational Medicine, 7(3), 262-270. https://doi.org/10.1002/sctm.17-0236 Review on digit tip regeneration.