臺灣博碩士論文加值系統

在台灣，克雷伯氏肺炎桿菌常出現在糖尿病患者，進而引起肺炎、敗血症、肝膿瘍等等併發症。莢膜是主要的致病因子。莢膜多醣體屬於水溶性，偏酸性，莢膜多醣體之組成被發現有具有極高的變異度。

本篇論文希望能藉由比較10種菌株(NTUH-2044、K1、K2、K5、K9、K14、K52、NK8、NK29、NK245)的莢膜多醣體，並觀察10株中在哪些基因片段相似度較高；之後藉由不同演算法來建立演化樹，並且利用Robinson-foulds distance來找出在三種演算法中，何種演算法建立出來的為『相對最佳演化樹』。

由多重序列比較的結果來看，各序列在galf、wzi、gnd、和ugd的基因區段相似度較高。而在莢膜多醣體去除5’和3’端的情況下，普遍相似度不高。但在wzc和wcal區段有不錯的相似度。在計算演化樹的距離上，最大簡約法在未除去5’和3’跟已除去5’和3’狀態下中RF距離的數值是相對最小的，所以其產生的演化樹在三種演算法下是相對最佳演化樹。

In Taiwan, Klebsiella pneumonia is prominent in people who have diabetes and causes complications including pneumonia, sepsis, liver abscess, etc. Capsular is the main etiological factor. Also, capsular polysaccharide belongs to water-soluble and meta-acidic and its compositions are found to have highly variability.

In this thesis, we want to find out in which algorithms the local optimal phylogentic tree is constructed by comparing ten strains of Klebsiella pneumonia of capsular polysaccharides, including NTUH-2044、K1、K2、K5、K9、K14、K52、NK8、NK29、NK245, observing similarities of genes among ten strains, constructing phylogenetic trees by various algorithms and then using the Robinson-foulds distance.

According to the result of comparative sequence analysis overview, sequences in galf, wzi, gnd and ugd regions have higher similarities. However, the similarity in cps without 5'' and 3'' is low in general but in wzc and wcal region are higher. When calculating the distance of phylogenetic trees, the RF distance is relatively low under the situation of maximum parsimony method with whole cps and without 5'' and 3''; therefore, the phylogenetic trees constructed by them are the local optimal phylogenetic tree among three algorithms.

致謝 i
中文摘要 ii
Abstract iii
Contents iv
List of Figures vi
List of Tables viii

Chapter 1 Introduction 1
1.1 Klebsiella Peneumoniae . . . . . . . . . . . . . . . 1
1.2 Capsular types of Klebsiella Peneumoniae . . . . . . 2
1.3 Objectives . . . . . . . . . . . . . . . . . . . . 3
1.4 Organization . . . . . . . . . . . . . . . . . . . . 3

Chapter 2 Preliminaries 4
2.1 Structure of DNA . . . . . . . . . . . . . . . . . . 4
2.2 Sequence alignment . . . . . . . . . . . . . . . . . 5
2.3 Phylogenetic tree . . . . . . . . . . . . . . . . . .7
2.3.1 Distance–based method . . . . . . . . . . . . . . .7
2.3.1.1 Neighbor-joining . . . . . . . . . . . . . . . . .8
2.3.2 Character-based method . . . . . . . . . . . . . .10
2.3.2.1 Maximum Parsimony . . . . . . . . . . . . . . . .10
2.3.2.2 Maximum-likelihood . . . . . . . . . . . . . . . 11
2.4 Robinson-foulds distance . . . . . . . . . . . . . . 11

Chapter 3 Materials and Methods 13
3.1 Strains selection . . . . . . . . . . . . . . . . . .13
3.2 Comparative sequences . . . . . . . . . . . . . . . .14
3.3 Experiment workflow . . . . . . . . . . . . . . . . .14

Chapter 4 Results 16
4.1 Comparative sequence analysis overview . . . . . . .16
4.2 Construction of phylogenetic trees . . . . . . . . .18
4.3 Calculate the Robinson-foulds distance . . . . . .. .21

Chapter 5 Concluding Remarks 25

Bibliography 26

Bibliography
[1] Doo Ryeon Chung, Ha Rim Lee, Seung Soon Lee, Shin Woo Kim, Hyun-Ha Chang, Sook-In Jung, Myoung-don Oh, Kwan Soo Ko, Cheol-In Kang, Kyong Ran Peck, andJae-HoonSong. EvidenceforclonaldisseminationoftheserotypeK1Klebsiella pneumoniae strain causing invasive liver abscesses in Korea. Journal of clinical microbiology, 46(12):4061–3, 2008.
[2] C-P Fung, F-Y Chang, S-C Lee, B-S Hu, B I-T Kuo, C-Y Liu, M Ho, and L K Siu. A global emerging disease of Klebsiella pneumoniae liver abscess: is serotype K1 an important factor for complicated endophthalmitis? Gut, 50(3):420–4, 2002.
[3] Y. Arakawa, R. Wacharotayankun, T. Nagatsuka, H. Ito, N. Kato, and M. Ohta. Genomicorganization of the Klebsiella pneumoniae cps region responsible for serotype K2 capsular polysaccharide synthesis in the virulent strain chedid. Journal of Bacteriology, 177(7):1788–1796, 1995.
[4] Yi-Jiun Pan, Han-Chi Fang, Hui-Ching Yang, Tzu-Lung Lin, Pei-Fang Hsieh, Feng-Chiao Tsai, Yoav Keynan, and Jin-Town Wang. Capsular polysaccharide synthesis regions in Klebsiella pneumoniae serotype K57 and a new capsular serotype. Journal of clinical microbiology, 46(7):2231–40, 2008.
[5] Hung Yu Shu, Chang Phone Fung, Yen Ming Liu, Keh Ming Wu, Ying Tsong Chen, Ling Hui Li, Tze Tze Liu, Ralph Kirby, and Shih Feng Tsai. Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates. Microbiology, 155(2009):4170–4183, 2009.
[6] Wolfram Saenger. Principles of Nucleic Acid Structure. 1984.
[7] James D Watson and Francis H C Crick. Molecular structure of nucleic acids, 1953.
[8] Tristan Cazenave. Overestimation for Multiple Sequence Alignment. (Cibcb):159-164, 2007.
[9] WLChang, MinyiGuo, andMSHHo. Fast Parallel Molecular Algorithms for DNA-Based Computation: Factoring Integers. IEEE Transactions on Nanobioscience, 4(2):149–163, 2005.
[10] D L Swofford and G J Olsen. Phylogeny reconstruction. In ? Molecular Systematics.(Eds DM Hillis and C. Moritz.) pp. 411–501. Sinauer Associates: Sunderland, Massachusetts, 1990.
[11] Chuang Peng. Distance Based Methods in Phylogenetic Tree Construction. Neural Parallel and Scientific, pages 1–11, 2007.
[12] NSaitou and MNei. The neighbor-joiningmethod: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4(4):406–25, 1987.
[13] Radu Mihaescu, Dan A N Levy, and Lior Pachter. Why Neighbor-Joining Works. Algorithmica, 54(1):1–24, 2007.
[14] Joanna Komorek and Rafal Morga. Relationship between the maximum and the random reflectance of vitrinite for coal from the Upper Silesian Coal Basin (Poland). Fuel, 81(7):969–971, 2002.
[15] Kei Takahashi and Masatoshi Nei. Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony , Minimum Evolution , and Maximum Likelihood When a Large Number of Sequences Are Used. pages 1251-1258, 1987.
[16] Benny Chor and Tamir Tuller. Maximum likelihood of evolutionary trees : hardness and approximation. 21:97–106, 2005.
[17] D. F. Robinson and L. R. Foulds. Comparison of phylogenetic trees. Mathematical Biosciences, 53(1-2):131–147, 1981.
[18] Koun-tem Sun, Jr-shiuan Wei, Ting-tsung Chang, Wen-chun Liu, and Yi-yu Hsu. The Study of Computing Evolutionary distance. 2007.
[19] Chi-tai Fang, Shau-yan Lai, Wen-ching Yi, Po-ren Hsueh, Kao-lang Liu, and Shan-chwen Chang. Klebsiella pneumoniae Genotype K1 : An Emerging Pathogen That Causes Septic Ocular or Central Nervous System Complications from Pyogenic Liver Abscess. 45, 2007.
[20] Robert C Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5):1792–7, 2004.
[21] Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, and Sudhir Kumar. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12):2725–2729, 2013.