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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 郭典翰 | zh_TW |
| dc.contributor.advisor | Dian-Han Kuo | en |
| dc.contributor.author | 歐穎潔 | zh_TW |
| dc.contributor.author | Ying-chieh Ou | en |
| dc.date.accessioned | 2025-08-21T16:55:59Z | - |
| dc.date.available | 2025-08-22 | - |
| dc.date.copyright | 2025-08-21 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-08-06 | - |
| dc.identifier.citation | Alexa, A., & Rahnenfuhrer, J. (2024). topGO: enrichment analysis for gene ontology. https://doi.org/10.18129/B9.bioc.topGO
Bessodes, N., Haillot, E., Duboc, V., Rottinger, E., Lahaye, F., & Lepage, T. (2012). Reciprocal signaling between the ectoderm and a mesendodermal left-right organizer directs left-right determination in the sea urchin embryo. PLoS Genet, 8(12), e1003121. https://doi.org/10.1371/journal.pgen.1003121 Bocci, F., Onuchic, J. N., & Jolly, M. K. (2020). Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models. Front Physiol, 11, 929. https://doi.org/10.3389/fphys.2020.00929 Bruno Pernet, Livingston, B. T., Sojka, C., & Lizárraga, D. (2017). Embryogenesis and larval development of the seastar Astropecten armatus. Invertebrate Biology, 136(2), 121-133. https://doi.org/10.1111/ivb.12172 Cameron, C. B., Garey, J. R., & Swalla, B. J. (2000). Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla. Proc Natl Acad Sci U S A, 97(9), 4469-4474. https://doi.org/10.1073/pnas.97.9.4469 Chen, J. H., Luo, Y. J., & Su, Y. H. (2011). The dynamic gene expression patterns of transcription factors constituting the sea urchin aboral ectoderm gene regulatory network. Dev Dyn, 240(1), 250-260. https://doi.org/10.1002/dvdy.22514 D'Souza, B., Meloty-Kapella, L., & Weinmaster, G. (2010). Canonical and non-canonical Notch ligands. Curr Top Dev Biol, 92, 73-129. https://doi.org/10.1016/S0070-2153(10)92003-6 Duboc, V., Rottinger, E., Lapraz, F., Besnardeau, L., & Lepage, T. (2005). Left-right asymmetry in the sea urchin embryo is regulated by nodal signaling on the right side. Dev Cell, 9(1), 147-158. https://doi.org/10.1016/j.devcel.2005.05.008 Formery, L., Wakefield, A., Gesson, M., Toisoul, L., Lhomond, G., Gilletta, L., Lasbleiz, R., Schubert, M., & Croce, J. C. (2022). Developmental atlas of the indirect-developing sea urchin Paracentrotus lividus: From fertilization to juvenile stages. Front Cell Dev Biol, 10, 966408. https://doi.org/10.3389/fcell.2022.966408 Fuss, B., Josten, F., Feix, M., & Hoch, M. (2004). Cell movements controlled by the Notch signalling cascade during foregut development in Drosophila. Development, 131(7), 1587-1595. https://doi.org/10.1242/dev.01057 Gazave, E., Guillou, A., & Balavoine, G. (2014). History of a prolific family: the Hes/Hey-related genes of the annelid Platynereis. Evodevo, 5, 29. https://doi.org/10.1186/2041-9139-5-29 Gonzalez, P., & Lessios, H. A. (1999). Evolution of sea urchin retroviral-like (SURL) elements evidence from 40 echinoid species. Molecular Biology and Evolution, 16(7), 938-952. He, X., Wu, F., Zhang, L., Li, L., & Zhang, G. (2021). Comparative and evolutionary analyses reveal conservation and divergence of the notch pathway in lophotrochozoa. Sci Rep, 11(1), 11378. https://doi.org/10.1038/s41598-021-90800-8 Heyland, A., & Hodin, J. (2014). A detailed staging scheme for late larval development in Strongylocentrotus purpuratus focused on readily-visible juvenile structures within the rudiment. BMC Dev Biol, 14, 22. https://doi.org/10.1186/1471-213X-14-22 Howard-Ashby, M., Materna, S. C., Brown, C. T., Chen, L., Cameron, R. A., & Davidson, E. H. (2006). Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. Dev Biol, 300(1), 90-107. https://doi.org/10.1016/j.ydbio.2006.08.033 Jackson, E. W., Romero, E., Kling, S., Lee, Y., Tjeerdema, E., & Hamdoun, A. (2024). Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin Lytechinus pictus. Development, 151(20). https://doi.org/10.1242/dev.202991 Kopan, R., & Ilagan, M. X. (2009). The canonical Notch signaling pathway: unfolding the activation mechanism. Cell, 137(2), 216-233. https://doi.org/10.1016/j.cell.2009.03.045 Li, T., Zhang, Y., Patil, P., & Johnson, W. E. (2021). Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference. Biostatistics, 24(3), 635-652. https://doi.org/10.1093/biostatistics/kxab039 Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8 Luo, Y. J., & Su, Y. H. (2012). Opposing nodal and BMP signals regulate left-right asymmetry in the sea urchin larva. PLoS Biol, 10(10), e1001402. https://doi.org/10.1371/journal.pbio.1001402 Lv, Y., Pang, X., Cao, Z., Song, C., Liu, B., Wu, W., & Pang, Q. (2024). Evolution and function of the Notch signaling pathway: an invertebrate perspective. International Journal of Molecular Sciences, 25(6), 3322. Minokawa, T., Rast, J. P., Arenas-Mena, C., Franco, C. B., & Davidson, E. H. (2004). Expression patterns of four different regulatory genes that function during sea urchin development. Gene Expr Patterns, 4(4), 449-456. https://doi.org/10.1016/j.modgep.2004.01.009 Minsuk, S. B., Turner, F. R., Andrews, M. E., & Raff, R. A. (2009). Axial patterning of the pentaradial adult echinoderm body plan. Dev Genes Evol, 219(2), 89-101. https://doi.org/10.1007/s00427-009-0270-3 Nesbit, K. T., Fleming, T., Batzel, G., Pouv, A., Rosenblatt, H. D., Pace, D. A., Hamdoun, A., & Lyons, D. C. (2019). The painted sea urchin, Lytechinus pictus, as a genetically-enabled developmental model. Methods Cell Biol, 150, 105-123. https://doi.org/10.1016/bs.mcb.2018.11.010 Nesbit, K. T., & Hamdoun, A. (2020). Embryo, larval, and juvenile staging of Lytechinus pictus from fertilization through sexual maturation. Dev Dyn, 249(11), 1334-1346. https://doi.org/10.1002/dvdy.223 Rahman, I. A., & Zamora, S. (2024). Origin and early evolution of echinoderms. Annual Review of Earth and Planetary Sciences, 52(1), 295-320. https://doi.org/10.1146/annurev-earth-031621-113343 Rozhnov, S. V. (2012). The anteroposterior axis in echinoderms and displacement of the mouth in their phylogeny and ontogeny. Biology Bulletin, 39(2), 162-171. https://doi.org/10.1134/S1062359012020094 Schurch, N. J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M., & Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA, 22(6), 839-851. https://doi.org/10.1261/rna.053959.115 Sherwood, D. R., & McClay, D. R. (1997). Identification and localization of a sea urchin Notch homologue: insights into vegetal plate regionalization and Notch receptor regulation. Development, 124(17), 3363-3374. https://doi.org/10.1242/dev.124.17.3363 Sherwood, D. R., & McClay, D. R. (1999). LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo. Development, 126(8), 1703-1713. https://doi.org/10.1242/dev.126.8.1703 Sherwood, D. R., & McClay, D. R. (2001). LvNotch signaling plays a dual role in regulating the position of the ectoderm-endoderm boundary in the sea urchin embryo. Development, 128(12), 2221-2232. https://doi.org/10.1242/dev.128.12.2221 Slota, L. A., Miranda, E. M., & McClay, D. R. (2019). Spatial and temporal patterns of gene expression during neurogenesis in the sea urchin Lytechinus variegatus. Evodevo, 10, 2. https://doi.org/10.1186/s13227-019-0115-8 Smith, A. B. (1988). Phylogenetic relationship, divergence times, and rates of molecular evolution for camarodont sea urchins Molecular Biology and Evolution, 5(4), 345-365. Smith, A. B. (1997). Echinoderm larvae and phylogeny. Annual Review of Ecology and Systematics, 28, 219-241. Smith, M. M., Cruz Smith, L., Cameron, R. A., & Urry, L. A. (2008). The larval stages of the sea urchin, Strongylocentrotus purpuratus. J Morphol, 269(6), 713-733. https://doi.org/10.1002/jmor.10618 Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., Coffman, J. A., Dean, M., Elphick, M. R., Ettensohn, C. A., Foltz, K. R., Hamdoun, A., Hynes, R. O., Klein, W. H., Marzluff, W.,…Wright, R. (2006). The genome of the sea urchin Strongylocentrotus purpuratus. Science, 314(5801), 941-952. https://doi.org/10.1126/science.1133609 Steinbuck, M. P., & Winandy, S. (2018). A review of Notch processing with new insights into ligand-independent Notch signaling in T-cells. Front Immunol, 9, 1230. https://doi.org/10.3389/fimmu.2018.01230 Sweet, H. C., Azriel, G., Jaff, N., Moser, J., Riola, T. A., Ideman, C., Barton, M., Nelson, J., & Lenhart, M. M. (2022). Formation of coelomic cavities during abbreviated development of the brittle star ophioplocus esmarki. Biol Bull, 243(3), 283-298. https://doi.org/10.1086/721954 Telmer, C. A., Karimi, K., Chess, M. M., Agalakov, S., Arshinoff, B. I., Lotay, V., Wang, D. Z., Chu, S., Pells, T. J., & Vize, P. D. (2024). Echinobase: a resource to support the echinoderm research community. Genetics, 227(1), iyae002. Tiemeijer, L. A., Sanlidag, S., Bouten, C. V. C., & Sahlgren, C. M. (2022). Engineering tissue morphogenesis: taking it up a Notch. Trends Biotechnol, 40(8), 945-957. https://doi.org/10.1016/j.tibtech.2022.01.007 Tu, Q., Cameron, R. A., Worley, K. C., Gibbs, R. A., & Davidson, E. H. (2012). Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res, 22(10), 2079-2087. https://doi.org/10.1101/gr.139170.112 Turbeville, J. M., Schulz, J. R., & Raff, R. A. (1994). Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology. Mol Biol Evol, 11(4), 648-655. https://doi.org/10.1093/oxfordjournals.molbev.a040143 Udagawa, S., Nagai, A., Kikuchi, M., Omori, A., Tajika, A., Saito, M., Miura, T., Irie, N., Kamei, Y., & Kondo, M. (2022). The pentameric hydrocoel lobes organize adult pentameral structures in a sea cucumber, Apostichopus japonicus. Dev Biol, 492, 71-78. https://doi.org/10.1016/j.ydbio.2022.09.002 Vacquier, V. D., & Hamdoun, A. (2024). Cold storage and cryopreservation methods for spermatozoa of the sea urchins Lytechinus pictus and Strongylocentrotus purpuratus. Dev Dyn, 253(8), 781-790. https://doi.org/10.1002/dvdy.691 Wada, H., & Satoh, N. (1994). Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA. Proc Natl Acad Sci U S A, 91(5), 1801-1804. https://doi.org/10.1073/pnas.91.5.1801 Walton, K. D., Croce, J. C., Glenn, T. D., Wu, S. Y., & McClay, D. R. (2006). Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development. Dev Biol, 300(1), 153-164. https://doi.org/10.1016/j.ydbio.2006.08.064 Wang, M. M. (2011). Notch signaling and Notch signaling modifiers. Int J Biochem Cell Biol, 43(11), 1550-1562. https://doi.org/10.1016/j.biocel.2011.08.005 Zhou, M., Yan, J., Ma, Z., Zhou, Y., Abbood, N. N., Liu, J., Su, L., Jia, H., & Guo, A. Y. (2012). Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events. PLoS One, 7(7), e40649. https://doi.org/10.1371/journal.pone.0040649 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/99237 | - |
| dc.description.abstract | 棘皮動物門如海膽以成體具有獨特的五輻對稱性為人所知，但其實他們皆是從兩側對稱的幼生發育而來。在海膽中，五輻對稱性最早展現在幼生左側一個叫雛體 (adult rudiment) 的構造，但目前仍不知其背後形成的分子機制。先前在加州紫海膽 (Strongylocentrotus purpuratus) 中轉錄體分析發現部分參與Delta/ Notch 訊息傳遞的基因在幼生左側有較高的表現，因此我在此研究中進一步的了解Delta/Notch訊息傳遞在海膽雛體發育過程中的作用為何。我透過原位雜交實驗 (in situ hybridization) 釐清SpDelta、SpNotch、和SpHes和SpHet1基因在雛體中的表現，並發現以DAPT抑制Notch訊息傳遞會使雛體的初始管足 (primary podia) 構造無法正常發育。此外，為了瞭解雛體發育在演化上保守的分子機制，我比較加洲紫海膽和彩繪海膽 (Lytechinus pictus) 的雛體相關轉錄體，發現FGF、Wnt 以及 Notch 訊息傳遞路徑中的多個基因在兩物種中皆呈現差異性表現，顯示這些訊息途徑皆可能參與雛體發育的調控。最後，我確認 Notch 訊息傳遞的功能及其表現模式在彩繪海膽中具有保守性。綜合以上結果，本研究證實 Delta/Notch 訊息傳遞在海膽雛體形成過程中為初始管足發育所必須，並為理解棘皮動物雛體發育的分子機制提供了新的見解。 | zh_TW |
| dc.description.abstract | Echinoderms, such as sea urchins, are unique in possessing pentaradial symmetry as adults, despite developing from bilaterally symmetric larvae. In sea urchins, this transition first appears in the formation of the adult rudiment on the larval left side. However, the molecular mechanisms underlying rudiment development remain poorly understood. Preliminary transcriptomic analysis in Strongylocentrotus purpuratus revealed left-sided enrichment of several Delta/Notch signaling components, prompting further investigation into the role of this pathway. In this study, I examined the spatial expression of SpDelta, SpNotch, SpHes, and SpHey1 in rudiments using whole-mount in situ hybridization (WMISH), and demonstrated that Notch signaling inhibition via DAPT treatment disrupts primary podia formation. To explore evolutionary conserved regulatory programs, I analyzed rudiment-associated transcriptomes in S. purpuratus and Lytechinus pictus. Comparative analyses revealed differential expression of genes in the FGF, Wnt, and Notch pathways, suggesting their involvement in rudiment formation. Finally, I confirmed that Notch signaling function and expression patterns are conserved in L. pictus. These findings highlight Delta/Notch signaling as a key regulator essential for primary podia formation in sea urchin larvae and provide new insights into the molecular basis of rudiment development in echinoderms. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-08-21T16:55:59Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-08-21T16:55:59Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | Abstract i
摘要 ii Table of Contents iii List of Figures v List of Tables vii Introduction 1 The uniqueness of the five-fold symmetry 1 Formation of the rudiment and the appearance of pentaradial symmetry in S. purpuratus 2 Lytechinus pictus is a newly developed model organism 4 Left/Right transcriptomes of S. purpuratus larvae suggest roles of Delta/Notch pathway in 5-fold symmetry 5 Nodal perturbation transcriptome of L. pictus 8 Purposes of the present study 9 Materials and Methods 11 Animals and larval culturing 11 Drug treatment 11 Gene cloning and probe synthesis 12 Whole-mount in situ hybridization 14 Sample collections for RNA-sequencing and bioinformatics 15 Results 17 SpDelta, SpNotch, SpHes and SpHey1 are expressed in sea urchin rudiment 17 Inhibition of Notch signaling suppressed development of the primary podia in the rudiment 19 DAPT altered expression patterns of genes related to Notch signaling 21 Stage and batch effects masked the effect of Nodal signaling perturbation in L. pictus transcriptomes 24 Gene ontology analysis suggests developmental roles for genes upregulated by SB431542 and downregulated by hActivin 27 Comparative analysis between S. purpuratus and L. pictus revealed Notch and FGF signaling pathways might play a conserved role in rudiment formation 30 The function of Notch signaling was conserved in L. pictus despite the slightly different expression pattern 35 Discussion 38 The regulation of Delta/Notch signaling is region-specific within the rudiment in S. purpuratus 38 Delta/Notch signaling mediates signaling between the ectodermal vestibule and the mesodermal hydrocoel required for primary podia morphogenesis 42 Technical and methodological factors influencing transcriptome comparisons between S. purpuratus and L. pictus 44 Comparison of Notch signaling between S. purpuratus and L. pictus suggests a conserved role in rudiment development despite divergence in gene expression patterns 46 References 49 Figures 54 Tables 94 Appendixes 104 | - |
| dc.language.iso | en | - |
| dc.subject | 雛體發育 | zh_TW |
| dc.subject | 海膽 | zh_TW |
| dc.subject | Delta/Notch訊息傳遞 | zh_TW |
| dc.subject | Delta/Notch signaling | en |
| dc.subject | sea urchin | en |
| dc.subject | rudiment development | en |
| dc.title | Delta/Notch訊息傳遞對海膽雛體初始管足發育的必要性 | zh_TW |
| dc.title | Delta/Notch Signaling is Required for the Development of Primary Podia during Sea Urchin Rudiment Formation | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.coadvisor | 蘇怡璇 | zh_TW |
| dc.contributor.coadvisor | Yi-Hsien Su | en |
| dc.contributor.oralexamcommittee | 游智凱;駱乙君;張俊哲 | zh_TW |
| dc.contributor.oralexamcommittee | Jr-Kai Yu;Yi-Jyun Luo;Chun-Che Chang | en |
| dc.subject.keyword | 海膽,雛體發育,Delta/Notch訊息傳遞, | zh_TW |
| dc.subject.keyword | sea urchin,rudiment development,Delta/Notch signaling, | en |
| dc.relation.page | 105 | - |
| dc.identifier.doi | 10.6342/NTU202503340 | - |
| dc.rights.note | 同意授權(全球公開) | - |
| dc.date.accepted | 2025-08-09 | - |
| dc.contributor.author-college | 生命科學院 | - |
| dc.contributor.author-dept | 生命科學系 | - |
| dc.date.embargo-lift | 2025-08-22 | - |
| 顯示於系所單位： | 生命科學系 | |
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