長形群游細菌的集體運動

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林思寧(Szu-Ning Lin) 查詢紙本館藏

畢業系所

生物物理研究所

論文名稱

長形群游細菌的集體運動
(Collective motions of long swarming bacterial cells)

相關論文

★ 多細菌鞭毛馬達的同步轉動量測	★ Investigation of the Dual Flagellar Motor System
★ Investigating Stators Assembly of Flagellar Motors in Escherichia Coli by PALM	★ 被動粒子在不同的流體型態
★ Lab on the Agar Plates	★ Dynamical Patterns in Vibrio alginolyticus Swarm Plate
★ Probing the Physical Environments of Bacterial Swarm Colony	★ Spiral-coil Formation in Semi-flexible Self-propelled Chain System
★ Real-Time Measurement of Vibrio alginolyticus Polar Flagellar Growth	★ Foraging behavior of Caenorhabditis elegans
★ Investigating the Growth Mechanism of Bacterial Flagella by Real-time Fluorescent Imaging	★ Jamming State of Active Nematics
★ Probing Escherichia coli Energetics under Starvation by Single-Cell Measurements	★ Probing Cell Wall Synthetic Dynamics by Bacterial Flagellar Motor in Escherichia coli
★ Dynamics of sodium-driven stator units in bacterial flagellar motors	★ 高密度二維群游細菌系統之動力學

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摘要(中)

本篇論文主要探討溶藻弧菌的群游動態行為以及群體和單一長型細菌自我推動的運動。自我推動粒子在理論與實驗方面都已被研究，但理想的自我推動粒子系統受限實驗技術，目前理論計算仍領先實驗研究。細菌群游是一種相當良好的方法建立自我推動粒子系統。我們量測了溶藻弧菌的群游行為並建立一套自我推進粒子系統的實驗。
溶藻弧菌是一種擁有兩種鞭毛馬達系統的海洋類細菌，兩種鞭毛馬達分別是單一長在菌體極端由鈉離子驅動的鞭毛（極端鞭毛）和多條分佈在全身的氫離子驅動鞭毛（側邊鞭毛）。當細菌長在洋菜膠培養皿上，菌體會抑制分裂和延長體型，進入群游的型態。我們利用三種基因改良的溶藻弧菌：138-2(擁有兩種鞭毛)、VIO5(只有極端鞭毛)、YM19(只有側邊鞭毛)比較不同種鞭毛在膠狀洋菜膠與水溶液環境的運動。YM19在膠體表面表現活躍的群游動能性，可做為一個理想的細菌群游和自我推動粒子實驗系統。
　　在YM19菌落生長期間，細菌呈現非常多元的運動結構；例如渦流狀、邊界波浪、邊界湧流、塞擠和單層的狀態。我們使用粒子影像速度測量(PIV)的計算方法得到各流場速度和渦度，並藉由時間和空間的頻率次方頻譜描述各行為的特徵。不同的細菌濃度和邊界條件呈現不同的動態樣貌。當菌落邊界被限制前進，會有一帶狀區域銜接在被禁止移動的菌落邊線上做週期擺盪，其頻率約0.8赫茲。驅使的力不僅須由漩渦區提供，同時須要自我推動的細菌群形成波動。在菌落擴張的時候，菌落邊線並不是同步向前推進，而是由後面的細菌推擠。在不同區段突出與追平，菌落內部的運動性和集體運動是菌落擴張的關鍵因素。
　　利用高速攝影機和顯微鏡可以在菌落單層的區域追蹤單隻細菌。相對少量的長型細菌和周遭多數的短型菌體呈現高動態的形體結構。一般而言，細菌的細胞壁相當堅硬以維持菌體形狀，然而短型細菌維持像桿狀的同時，長型細菌被周遭短型細菌擠壓、碰撞卻可以大角度的彎曲。長型細菌的身體兩端呈現獨立的運動。長型細菌還可以自我有序聚的集，變成一個旋轉的螺旋圈。螺旋圈可由旋轉方向和中心結溝分成單層順時(CW) 、單層逆時鐘(CCW)、雙層順時(DCW)和雙層逆時鐘(DCCW)螺旋圈。螺旋圈的長度介32到296微米，旋轉速度2.22到22.96 rad/s。這些螺旋圈的轉速穩定，但整體位移會受短型細菌群的碰撞改變。螺旋圈的形成和拆解是由長型細菌的區域方向改變以及周圍細菌的碰撞造成。穩定旋轉的螺旋圈在主動驅動的系統證實在一不平衡的背景環境，區域性的穩定結構是可以存在的。螺旋圈自我有續聚集的過程或許是一個值得開發的微米技術。

摘要(英)

The aims of this thesis are investigating the swarming dynamics of Vibrio alginolyticus and studying the collective motions and individual dynamics of self-propelled long bacteria. Self-propelled particle (SPP) has been studied both in theoretical and experimental approaches. However, theoretical works lead experimental works because of the limitation of manufacturing ideal experimental SPP systems. Bacterial swarm is a good candidate for building an experimental SPP system. Here, we survey the swarming behavior of Vibrio alginolyticus and build up swarming protocol to perform self-propelled particle experiments.
Vibrio alginolyticus is a marine bacterium with dual flagellar motor systems, a Na^+-driven polar flagellum and multiple H^+-driven lateral flagella. While growing on agar plate, they elongate without division into swarming phase. Three strains of Vibrio alginolyticus, 138-2 (wild-type), VIO5 (Pof^+), and YM19 (Laf^+) were first examined in both agar plate and aqueous environments. We found that YM19 strain shows very strong surface swarm motility and is an ideal experimental system for both bacterial swarming and self-propelled particle experiments.
During the swarm colony development, YM19 cells shows rich dynamical patterns such as turbulence, edge waving, edge streaming, jamming and mono-layer. We calculate the velocity fields by particle image velocimetry (PIV) and characterize the dynamics of the velocity by power spectra and vorticity calculation. The cells show different dynamical patterns and movement in different cell-densities and boundary conditions. With confined edge, a band of cells anchored on the non-moving contact-line show periodic waving about 0.8 Hz. The driving force is not only from the external turbulence region but also the self-propelled cells in the band. During the colony expansion, the contact-line is not marching together but protruding by a group of cells behind it. Both cell motility and collected motion are critical for the colony expansion.
At mono-layer, single cell can be tracked by microscope and high speed camera. In this region, some long cells are interacting with large amount of short cells and showing very dynamical configurations. The cell wall is rigid to maintain the bacterial shape. However, long cells can be bended by the collisions of short cells. Short cells are like a rigid rod while long cells are bendable and the two ends move independently. Long cells can be self-assembled into rotating spiral coils. Four types of spiral coils can be found featuring by rotational direction and the center structure: single clockwise (SCW), single counterclockwise (SCCW), double clockwise (DCW), and double counterclockwise spiral coil (DCCW) spiral coils. The length of spiral coils cells are between 32 to 296 μm. The rotational speeds are between 2.22 to 22.96 rad/s. These spiral coils rotate stably and the displacement are strongly influenced by the collision of short-cells clusters. The folding and unfolding of spiral coils are the results of the interaction between cells and the change of local moving direction of long cells. The finding of stable spiral coils in the active system indicating the existence of a local stable structure in the non-equilibrium background. The self-assembled process of spiral coil may inspire a new micro manufacturing technology.

關鍵字(中)

★ 細菌
★ 群游
★ 自我推進粒子
★ 群體運動

關鍵字(英)

★ bacterial swarm
★ self-propelled particle
★ Vibrio
★ Vibrio alginolyticus
★ collective motions

論文目次

1 Introduction 1
1.1 Background and motivation 1
1.2 Molecular motors 2
1.3 Flagella filaments 3
1.3.1 Polar filaments 5
1.3.2 Lateral filaments 5
1.4 Experimental techniques review 6
1.4.1 Swimming measurement assays 6
1.4.2 Swarming measurement assays 7
1.4.3 Bacterial flagella features 7
1.5 Introduction to bacterial motility 8
1.5.1 Vibrio alginolyticus 8
1.5.2 Vibrio alginolyticus structure 9
1.5.3 Vibrio alginolyticus energetic 9
1.5.4 Models for motor rotation 10
1.5.5 Models for bacterial swarming 11
2 Experimental Techniques 13
2.1 Microscope system 13
2.1.1 Inverted microscope 13
2.1.2 Charge coupled device 14
2.1.3 Phase contrast attachment 15
2.2 Fluorescence microscopy 16
2.2.1 Coloring cell 16
2.3 Swimming speed measurement 17
2.4 Swarming observation 18
2.4.1 Particle image velocimetry 18
3 Bacteria Swim and Swarm 20
3.1 Experimental aims 20
3.2 Experiment design and analyze 20
3.2.1 V. alginolyticus growth and motility 21
3.3 Swimming in bulk solution 21
3.4 Swarming on nutrient agar 24
3.5 Conclusion and discussion 26
4 Long Cells Swarming: Collective Motions 27
4.1 Experimental aims 27
4.2 Experiment design and analysis 27
4.2.1 Vibrio alginolyticus growth and motility 28
4.3 Result: Collective motions 29
Turbulence state 30
Edge waving 32
Edge streaming 36
Colony expanding and moving contact-line 37
Jamming 39
Dilute and dense monolayer 40
4.4 Conclusion 41
5 Long Cells Swarming: Individual Motions 43
5.2 Results: Individual motions 43
Long cells 43
Spiral coils 45
Interactions 47
Folding and unfolding routes 48
Model 50
5.3 Conclusion and discussion 50
6 Conclusions and outlook 53
6.1 The swim and swarm of Vibrio alginolyticus 53
6.2 The collective motions in Vibrio algynolyticus swarm 54
6.3 The individual motions in Vibrio algynolyticus swarm 54
6.4 Outlooks 55
Bibliography 56

參考文獻

Albada, S. B. V., Tǎnase-Nicola, S., and Wolde, P. R. T. (2009) The switching dynamics of the bacterial flagellar motor. Molecular Systems Biology. 5, 1-8.
Atsumi, T., Maekawa, Y., Yamada, T., Kawagishi, I., Imae, Y., and Homma, M. (1996) Effect of viscosity on swimming by the lateral and polar flagella of Vibrio alginolyticus. J. Bacteriol. 178, 5024-4026.
Be’er, A. and Harshey, R. M. (2011) Collective motion of surfactant-producing bacteria imparts superdiffusivity to their upper surface. Biophys J.101, 1017-1024. Berg, H. C. (2003) E. coli in motion.
Boer, W. E. D., Golten, C. and Scheffers,W. A. (1975) Effects of some physical factors on flagellation and swarming of Vibrio alginolyticus. Neth. J. Sea Res. 9, 197-213.
Belas, M. R. and Colwell, R. R. (1982) Scanning electron microscope observation of the swarming phenomenon of Vibrio parahamemolytiucs. J. Bacteriol. 150, 956-959.
Belas, R., Simon, M., and Silverman, M. (1986) Regulation of lateral flagella gene transcription in Vibrio parahamemolytiucs. J. Bacteriol. 167, 210-218.
Chattopadhyay, S., Moldovan, R., Yeung, C., and Wu, X. L. (2006) Swimming efficiency of bacterium Escherichia coli. Proc. Natl Acad. Sci. 103, 13712-13717.
Copeland, M. F. and Weibel, D. B. (2009) Bacterial swarming: a model system for studying dynamic self-assembly. Soft Matter. 5, 1174-1187.
Darnton, N. C., Turner, L., Rojevsky S., and Berg, H. C. (2010) Dynamics of bacterial swarming. Biophys J. 98, 2082-2090.
Fujii, M., Shibata, S. and Aizawa, S. (2008) Polar, peritrichous, and lateral flagella belong to three distinguishable flagellar families. J. Mol. Biol. 379, 273-283.
Furuno, M., Atsumi, T., Yamda, T., Kojima, S., Nishioka, N., Kawagishi, I., and Homma, M. (1997) Characterization of polar-flagellar-length mutants in Vibrio alginolyticus. Microbiology. 143, 1615-1621.
Gillis, A., Dupres, V., Machillon, J., and Dufrêne, Y. R. (2012) Atomic force
microscopy: A powerful tool for studying bacterial swarming motility. Micron. 43, 1304-1311.
Hiratsuka, Y., Miyata, M., Tada, T., and Uyeda, T. Q. P. (2006) A microrotary motor powered by bacteria. Proc. Natl Acad. Sci. 103, 13618-13623.
Kearns, B. D. (2010) A field guide to bacterial swarming motility. NIH. 8, 634-644.
Kikuchi, N., Ehrlicher, A., Koch, D., Käs, J. A., Ramaswamy, S., and Rao, M. (2009) Buckling, stiffening, and negative dissipation in the dynamics of a biopolymer in an active medium. Proc. Natl Acad. Sci. 106, 19776-19779.
Kojima, M., Kubo, R., Yakushi, T., Homma, M, and Kawagishi, I. (2007) The bidirectional polar and unidirectional interal flagellar motors of Vibrio alginolyticus are controlled by a single CheY species. Mol. Microbiol. 64, 57-67.
Leonardo, R. D., Angelani, L., Arciprete, D. D., Ruocco, G., Iebba, V., Schippa, S., Conte, M. P., Mecarini, F., Angelis, F. D., and Fabrizio, E. Di. (2010) Bacterial ratchet motors. Proc. Natl Acad. Sci.
Li, N. Kojima, S. and Homma, M. (2011). Sodium-driven motor of the polar flagellum in marine bacteria Vibrio. Genes Cells. 16, 985-999.
Liu, J. Z., Dapice, M., and Khan, S. (1990) Ion selectivity of the Vibrio alginolyticus flagellar motor. J. Bacteriol. 172, 5236-5244.
Maki, N., Gestwicki, J. E., Lake, E. M., Kiessling, L. L., and Adler, J. (2000) Motility and Chemotaxis of Filamentous Cells of Escherichia coli. J. Bacteriol. 182, 4337-4342.
Matsushita, M., Hiramatsu, F., Kobayashi, N., Ozawa, T., Yamazaki, Y., and Matsuyama, T. (2005) Colony formation in bacteria: experiments and modeling. Biofilms. 1, 305-317.
McCarter, L. L. (2001) Polar flagellar motility of the Vibrionaceae. Microbiol. Mol. Biol. R. 65, 445-462.
Minamino, T., Imada, K., and Namba, K. (2008) Molecular motors of the bacterial flagella. Curr. Opin. Microbiol.18, 693-701.
Partridge, J. D. and Harshey, R. M. (2013) Swarming: Flexible roaming plans. J. Bacteriol. 195, 909-918.
Sharma, M. and Anand, S. K. (2002) Swarming: A coordinated bacterial activity. Curr Sci. India. 83, 707-15.
Sokolov, A., Apodaca, M. M., Grzybowski, B. A., and Aranson, I. S. (2009) Swimming bacteria power microscopic gears. Proc. Natl Acad. Sci. 107, 969-974.
Stewart, B. J. and McCarter, L. L. (2003) Lateral Flagellar Gene System of Vibrio parahaemolyticus. J Bacteriol. 185, 4508-4518.
Terashima, H., Kojima, S., and Homma, M. (2008) Flagellar motility in bacteria: Structure and function of flagellar motor. Int. Rev. Cell Mol. Biol. 270, 39-85.
Turner, L., Ryu, W. S., and Berg, H. C. (2000) Real-time imaging of fluorescent flagellar filaments. J Bacteriol. 182, 2793-2801.
Turner, L., Zhang, R., Darnton, N. C., and Berg, H. C. (2010) Visualization of Flagella during bacterial Swarming. J. Bacteriol. 192, 3259-3267.
Wensink, H. H. and Löwen, H. (2012) Emergent states in dense systems of active rods: from swarming to turbulence. J. Phys.: Condens. Matter. 24, 464130.
Wensink, H. H., Dunkel, J., Heidenreich, S. Drescher, K. , Goldstein, R. E., Löwen, H., and Yeomans J. M. (2012) Meso-scale turbulence in living fluids. Proc. Natl Acad. Sci.
Wu, Y., and Berg H. C. (2012) Water reservoir maintained by cell growth fuels the spreading of a bacterial swarm. Proc. Natl Acad. Sci. 109, 4128-4133.
Yang, Y., Marceau, V., and Gompper, G. (2010) Swarm behavior of self-propelled rods and swimming flagella. Phy. Rev. E. 82, 031904.
Zhang, H. P., Be’er, A., Florin, E. L., and Swinney, G. L. (2010) Collective motion and density fluctuations in bacterial colonies. Proc. Natl Acad. Sci. 107, 13626-13630.
Zhang, H. P., Be’er, A., Smith, R. S., Florin, E. –L., and Swinney, H. L. (2009) Swarming dynamics in bacterial colonies. EPL. 87, 48011.

指導教授

羅健榮(Chien-Jung Lo)

審核日期

2013-7-9

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