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研究生: 江偉立
Kong, Wye Lup
論文名稱: 使用核酸比率作為真核生物生長速度指標的開發研究
Development of Nucleic Acid Ratios as Eukaryote Growth Rate Indices
指導教授: 町田龍二
Machida, Ryuji
口試委員: 蔡怡陞
Tsai, Isheng
王慧瑜
Wang, Hui-Yu
林秀瑾
Lin, Hsiu-Chin
單偉彌
Denis, Vianney
町田龍二
Machida, Ryuji
口試日期: 2022/09/30
學位類別: 博士
Doctor
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2022
畢業學年度: 111
語文別: 英文
論文頁數: 109
英文關鍵詞: Growth rate indices, Ribosomal ratio, mRNA ratio, real-time qPCR, RNA-Seq, Daphnia magna
研究方法: 實驗設計法
DOI URL: http://doi.org/10.6345/NTNU202205215
論文種類: 學術論文
相關次數: 點閱:81下載:7
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  • Quantification of growth is one of the essential steps to understand the flow of elements and energy in food webs. However, in situ estimation of the growth rate, in general, is challenging, especially for zooplankton. In the past, many biochemical indices were developed to estimate animal growth rates by measuring the ratio of certain biochemicals, such as DNA and RNA. Those indices reduce the effort of time series measurement in the field. However, many researchers claimed that the current available biochemical indices are still imperfect and require improvements. Due to proteins encode by mitochondrial genes responsible for energy generation, while nuclear genes encode the rest of the biological processes, including growth, I hypothesized that the ratio between various groups of nuclear and mitochondrial gene RNA abundance capable of growth rate estimation. In this thesis, we explored a total of five nucleic acid ratios as the potential growth rate indices. Daphnia magna were mainly used as the model species to investigate these nucleic acid ratios.
    In chapter 2, I introduced the first nucleic acid ratio, the (1) nuclear and mitochondrial ribosomal ratio (Nuc:Mito-rRNA). Using ribosomal RNA read abundances as the proxy for ribosomes quantities, I measured the ratio between nuclear-encoded cytosolic ribosome and mitochondrial ribosome, and determine the correlation between the ratio and the growth rate. The results of this study showed a significant positive correlation between the proposed ribosomal ratio and somatic growth rate. This demonstrated the potential of the Nuc:Mito-rRNA ratio as a growth rate index.
    Despite the result from chapter 2 showed significant correlation between the ratio and growth rate, there are many genes that translates through nuclear ribosome do not contribute to growth can resulted in unwanted noise. Hence, in chapter 3 I introduced another four mRNA growth rate indices with different level of specificity in term of gene functions, which are (2) nuclear and mitochondrial total mRNA ratio (Nuc:Mito-TmRNA), (3) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito-RPmRNA), (4) gene ontology (GO) term and total mitochondrial mRNA ratio, and (5) nuclear and mitochondrial specific gene mRNA ratio. I investigated these ratios on D. magna RNA-Seq data. These ratios were also tested on RNA-Seq datasets of Saccharomyces cerevisia retrieved from the NCBI Sequence Read Archive to serve as a verification dataset. Using RNA-Seq data, I discovered that both Nuc:Mito-TmRNA and Nuc:Mito-RPmRNA showed significant correlations with the growth rate for both species. I identified that several GO terms and total mitochondrial mRNA ratio showed significant correlations with the growth rate of S. cerevisiae. Lastly, I also identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations with growth rates.
    I foresee future implications of those proposed growth rate indices in metatranscriptome analyses to estimate the growth rate of communities and species. Finally in chapter 4, I discussed this aspect by providing some examples of potential implications of the growth rate indices proposed.

    Abstract iii List of Tables vii List of Figures viii List of Abbreviations xi Chapter 1: General introduction 1 1.1 | Importance of growth rate estimation 1 1.2 | Current states of growth rate estimation approach 2 1.3 | Novel concept in eukaryote growth rate estimation 4 1.4 | Daphnia magna as the model organism 5 1.5 | Thesis aims and outlines 5 Chapter 2: Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate 8 2.1 | Introduction 9 2.2 | Materials and methods 10 2.3 | Results 14 2.4 | Discussions 16 2.5 | Tables 23 2.6 | Figures 27 Chapter 3: Development of transcriptomics-based eukaryotes growth rate indices: Extension of a metatranscriptomics potential 31 3.1 | Introduction 32 3.2 | Materials and methods 33 3.3 | Results 39 3.4 | Discussion 45 3.5 | Tables 53 3.6 | Figures 57 Chapter 4: Conclusions and future perspectives 63 4.1 | Prospect of the proposed indices 65 4.2 | Potential application outside the field of research 66 4.3 | Future studies to address unanswered questions 67 4.4 | General conclusions 67 Reference 69 Appendices 84 Appendix A: Supplementary materials for Chapter 2 84 Appendix B: Supplementary materials for Chapter 3 95

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