臺灣博碩士論文加值系統

由於鯨豚類從陸地生活演化成水中生活，其皮膚結構在很多方面與其他陸生哺乳類皮膚結構有明顯的差異，表皮由三個層面組成，由外而內分別是角質層、棘層、基底層，與陸生哺乳類相比，缺少了顆粒層，在皮膚中也沒有發現汗腺與皮脂腺，體表上大部分也沒有毛髮覆蓋。鯨豚擱淺是指鯨豚因為某些原因受困淺灘而無法自行返回海中，若是鯨豚擱淺沒有及時發現，鯨豚就很有可能因為脫水，體重壓迫，疾病等原因導致鯨豚死亡。侏儒抹香鯨是台灣常見的擱淺鯨豚類之一，且歸類在抹香鯨家族中，而關於牠的研究非常稀少，大部分的資料獲得方式都是由於侏儒抹香鯨擱淺死亡得知。
本研究中利用擱淺死亡的侏儒抹香鯨新鮮皮膚RNA進行RNA-seq，得到了61,742,824條reads，在經過一系列處理後發現31,668個蛋白質可以被對應到NCBI中瓶鼻海豚資料庫。我們進行了基因表現量分析、gene ontology (GO)，並畫出與其他七個物種的演化樹。另外，也將侏儒抹香鯨表皮與牛皮膚進行GO enrichment比較，發現在biological process的部分有三個enriched GO term；而molecular function部分有六個enriched GO term。之後將enriched的GO term中各挑出一個基因，並畫出其演化樹觀察。最後，擱淺的鯨豚類時常伴隨著脫水的情況發生，而在發現enriched GO term (transmembrane transporter activity)中有許多SLC protein family，推測SLC protein family在侏儒抹香鯨脫水時的離子調控有著一定程度的影響。

Cetaceans are composed of whales, dolphins, porpoises. The ancestors of the cetaceans were branched from Artiodactyla 65 million years ago. The cetacean skin structure is different from terrestrial mammals, which reflected their adaptation from land to sea. Their epidermis consists of three layers, the stratum corneum, the stratum spinosum and the stratum basale. The dwarf sperm whale is one of the common stranded whales in Taiwan. The study of the dwarf sperm whale is very rare. Most of the data was due to the dwarf sperm whale stranded and died. In this study, RNA was obtained from fresh skin of the dwarf sperm whale. After RNA-seq, 61,742,824 reads were found. After a series of process, 31,668 proteins were found to correspond to the NCBI bottlenose dolphin database. We performed gene expression analysis, gene ontology (GO), and phylogenetic tree of dwarf sperm whale with seven other mammals. In addition, we found the enriched GO term between dwarf sperm whale skin and the bovine skin. Then, we select one gene from each of the enriched GO terms and observe its evolutionary tree. Finally, it occurred to us that stranded whales are often stranded accompanied with dehydration. In our data, there are many SLC proteins in the enriched GO term. The SLC family is the protein responsible for transporting solutes, which indicating that the SLC family is important during the dehydration of dwarf sperm whales.

目錄
摘要 I
致謝 IV
目錄 V
表目錄 VII
圖目錄 VII
前言 1
1. 鯨豚類(Cetacean). 1
2. 侏儒抹香鯨(Kogia sima) 3
3. 皮膚 4
4. 轉錄組(Transcriptome) 7
研究目的 8
材料與方法 9
1.侏儒抹香鯨皮膚採樣 9
2. RNA萃取 9
3. cDNA library建立與定序 10
4.序列組裝及註解 10
5.侏儒抹香鯨基因表現量 11
6.侏儒抹香鯨gene ontology(level 5)註解 12
7.侏儒抹香鯨與其他物種演化樹(phylogenetic tree) 12
8.牛皮膚transcriptome組裝、註解及表現量分析 13
9.侏儒抹香鯨與牛GO富集分析(GO enrichment) 13
10.侏儒抹香鯨與其他物種同源角蛋白演化樹分析 14
結果 15
1.擱淺之侏儒抹香鯨 15
2.侏儒抹香鯨序列資訊 15
3.侏儒抹香鯨基因表現量前10名 15
4.侏儒抹香鯨皮膚與牛皮膚GO (level 5) 16
5.侏儒抹香鯨與其他物種演化樹 19
6.侏儒抹香鯨皮膚與牛皮膚基因差異 19
7.角蛋白基因演化樹 24
討論 26
1.RNA-seq與DNA微陣列(Microarray)差異 26
2.侏儒抹香鯨基因註解 27
3.陸生哺乳類與海生哺乳類皮膚差異 29
4.物種演化樹 31
5.擱淺、脫水與相關GO term基因 32
結論 36
參考文獻 37
 
表目錄
表一：序列處理過程及數量。 49
表二：侏儒抹香鯨基因表現量前10名。 50
表三：所有GO enrichment 的GO term表格。 51
圖目錄
圖一：侏儒抹香鯨照片及擱淺事件時間軸。 52
圖二：侏儒抹香鯨GO(level5) biological process、molecular function、cellular component前十GO term。 53
圖三：牛GO(level5) biological process、molecular function、cellular component前十GO term。 54
圖四：侏儒抹香鯨與其他七物種系統發生樹。 55
圖五：rRNA metabolic process and rRNA processing中瓶鼻海豚(Tursiops truncatus)、侏儒抹香鯨(Kogia sima)與牛(Bos taurus)各基因表現量。 56
圖六：carboxylic acid transport中瓶鼻海豚(Tursiops truncatus)、侏儒抹香鯨(Kogia sima)與牛(Bos taurus)各基因表現量。 57
圖七： DNA helicase activity、helicase activity and catalytic activity, acting on DNA中瓶鼻海豚(Tursiops truncatus)、侏儒抹香鯨(Kogia sima)與牛(Bos taurus)各基因表現量。 58
圖八：secondary active transmembrane transporter activity、organic acid transmembrane transporter activity、carboxylic acid transmembrane transporter activity中瓶鼻海豚(Tursiops truncatus)、侏儒抹香鯨(Kogia sima)與牛(Bos taurus)各基因表現量。 59
圖九：K13、K14、K17、K28基因演化樹。 60
圖十：K13、K14、K17基因演化樹。 61
圖十一：K5、K6基因演化樹。 62
圖十二：侏儒抹香鯨KRT基因表現量。 63

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