Dynamical Patterns in Vibrio alginolyticus Swarm Plate

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許慈容(Tzu-Jung Hsu) 查詢紙本館藏

畢業系所

生物物理研究所

論文名稱

(Dynamical Patterns in Vibrio alginolyticus Swarm Plate)

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
★ 長形群游細菌的集體運動	★ 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
★ 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)

本篇論文主要從自我推進粒子集體運動的物理和生物方面，探討溶藻弧菌的群游動態、菌落擴張以及細胞分裂。
溶藻弧菌是一種擁有兩種鞭毛馬達系統的海洋細菌，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）。當細胞從液體轉換到洋菜膠或粘性較高的介質時，細胞表面的鞭毛數量會增加，在膠體表面有較高的運動性。側邊鞭毛只會在固體表面上表達群游動能性。為了更清楚地了解極端和側邊鞭毛馬達的功能，我們使用三種基因改變的溶藻弧菌：138-2(擁有兩種鞭毛)、VIO5(只有極端鞭毛)、YM19(只有側邊鞭毛)。
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。在本篇論文中，我們的研究專注於邊界波浪和塞擠狀態。
1.邊界波浪: 當細胞伸長且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。我們使用粒子影像速度測量(PIV)的計算方法來研究波浪擺盪的機制。波浪擺盪頻率與細胞長度成反比。波浪擺盪是由於細胞的一端被固定於菌落邊線上的自我推進運動。
2. 塞擠狀態: 塞擠狀態是一個很有趣的現象，在菌落內部可以發現具有高密度的單層區域。各個細胞都具有高動能性，但當密度增加時，所有的細菌會形成非移動性向列模式。我們追蹤單一細胞的運動，並計算均方位移(MSD)來研究塞擠形成的過程。塞擠狀態的形成類似於相變的現象。
3. 菌落可以1.03微米/秒的速度迅速擴張。我們發現菌落邊線的移動速度與邊線後面細菌的集體運動有關。我們提出了一個簡單的物理模型來解釋菌落擴張的原因。
4.細胞分裂:群游細胞會抑制細胞分裂。一但將長型細胞轉移到液體環境中，細胞將會分裂回短桿狀。我們設計了一個新的洋菜膠平板系統，在液體中觀察細胞分裂的過程。我們發現細胞能從一端依序分裂，形成正確的大小; 也可以從其他位置分裂成不同大小。

摘要(英)

The aim of this thesis is investigating the swarming dynamics of Vibrio alginolyticus from physical and biological aspects of self-propelled particles collective motions, colony expansion and cell division.
Vibrio alginolyticus is a marine bacterium with dual flagellar motor systems which are single Na+ driven polar flagellum and multiple H+ driven lateral flagella. When cells transfer from liquid to agar or high viscosity medium, the number of flagella on the cell surface increases, become highly motile on agar surface. The lateral flagella are expressed for swarm motility on the surface. To give a clear understanding of the functions of polar and lateral flagellar motors, three strains of Vibrio alginolyticus were used: 138-2 ( Pof + Laf + ), VIO5 ( Pof + Laf -), and YM19 ( Pof - Laf + ); wild type with single polar and many lateral filaments, polar only and lateral only, respectively.
During the swarm colony development, YM19 cells shows rich dynamical patterns such as turbulence, edge waving, edge streaming, jamming and mono-layer. In this thesis, I focus on the two collective patterns, edge waving and jamming.
1. Edge waving: The edge waving is happed when the cells are elongated and confined to the edge, a band of cells anchored on the non-moving contact-line show periodic waving. We calculate the velocity by particle image velocimetry (PIV) to study the mechanism of the waving patterns. The waving frequency is inverse proportional to the cell length. The mechanical origin of waving is the self-propelled motion of these cells with one end fixed on the edge of the colony.
2. Jamming: Jamming state is a very interesting phenomenon which can be found at inner region of colony with high density in single layer. Individual cells have high motility but all packed with other neighbors into a non-moving nematic patterns. We track the motion of single cell and calculate the MSD to study the jamming forming process. The jamming state formation is similar to the phase transition phenomenal.
3. The colony could expand rapidly at 1.03 μm/s. We found the local edge moving speed is correlated to the collective motion behind it. There is a high motility active region behind contact line. We propose a colony expanding model based on simple physical mechanism.
4. Cell division: Swarming cells suppress their cell division. Once the cells return to bulk liquid environment, the filamentous cells would return to Planktonic cell type quickly. We design a new agar plate system with bulk liquid environments to observe the dynamical process of cell division in vitro. We found the cells divide with correct size from one end sequentially and also other position of different size.

關鍵字(中)

★ 群游
★ 邊界波浪
★ 塞擠
★ 側邊鞭毛
★ 自我推進粒子
★ 溶藻弧菌

關鍵字(英)

★ swimming
★ swarming
★ edge waving
★ jamming
★ lateral flagella
★ contact line
★ self-propelled particle
★ vibrio alginolyticus

論文目次

1 Introduction 1
1.1 Background 1
1.2 Flagellar Motors 2
1.3 Flagella Filaments 3
1.3.1 Polar Filaments 5
1.3.2 Lateral Flagella 6
1.4 Bacterial Motion 7
1.5 Vibrio alginolyticus 9
1.5.1 Vibrio alginolyticus Structure 9
1.5.2 Vibrio alginolyticus Energetic 10
1.5.3 Bacterial Swarming 10
1.6 Self-Propelled Particle 11
1.7 Cell Division 15
2 Experimental Techniques 18
2.1 Microscopy System 18
2.1.1 Inverted Microscopy 18
2.1.2 Charge Coupled Device (CCD) 19
2.1.3 Phase Contrast Attachment 20
2.2 Fluorescence Microscope 21
2.3 Bacterial strains/growth media/agar preparation
23
2.4 Swimming Speed Measurement 24
2.5 Swarming Observation 25
2.6 Particle Image Velocimetry (PIV) 26
2.7 Cell Divide Observation 27
3 Bacteria Swimming Speed 28
3.1 Experiment Design and Analysis 28
3.2 Swimming in Medium 30
3.3 Conclusion and Discussion 32
4 Bacteria Swarming 33
4.1 Experiment Design and Analysis 33
4.1.1 Vibrio alginolyticus Growth and Motility
34
4.1.2 Swarm Structure Overview 35
4.2 Collective Motions 36
4.2.1 Edge Waving 37
4.2.2 Waving Model 39
4.2.3 Jamming 40
4.3 Discussion 45
5 Bacteria Division and Contact Line 46
5.1 Experimental Design of Bacterial Division
46
5.1.1 Experimental Results 46
5.2 Contact Line 50
5.3 Discussion 54
6 Conclusions and Outlooks 55
6.1 Bacteria Swimming Speed 55
6.2 Bacteria Swarming 55
6.3 Bacteria Division and Contact Line 56
6.4 Outlooks 57
Reference 58

參考文獻

Angelini, T. E., Hannezo, E., Trepat, X., Marquez, M., Fredberg, J. J., and Weitz, D.A. (2011) Glass-like dynamics of collective cell migration. PNAS, 108, 4714-4719.

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. JOURNAL OF BACTERIOLOGY, 178, 5024-5026.

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. Journal of Bacteriology, 178, 5024-5026.

Berg, H. C. (2003) The rotary motor of bacterial flagella. Annu. Rev. Biochem, 72, 19-54.

Baskaran, A. and Marchetti. M. C. (2009) Statistical mechanics and hydrodynamics
of bacterial suspensions. PNAS, 160, 15567-15572.

Be’er, A., Smith, R. S., Zhang. H. P., Florin. E. L., Payne, S. M. and Swinney H. L. (2009) Paenibacillus dendritiformis Bacterial Colony Growth Depends on
Surfactant but Not on Bacterial Motion. Journal of Bacteriology, 191, 5758-5764.

Bialke´, J., Speck, T. and Löwen, H. (2012) Crystallization in a Dense Suspension of Self-Propelled Particles. PHYSICALREVIEW LETTERS, 108, 168301-1-5

Chelakkot, R., Gopinath, A., Mahadevan, L. and Hagan M.F. (2013) Flagellar dynamics of a connected chain of active, polar, Brownian particles. Journal of The Royal Society Interface, 11, 20130884.

Darnton, N. C., Turner, L., Rojevsky S., and Berg, H. C. (2010) Dynamics of Bacterial Swarming. Biophysical Journal, 98, 2082-2090.

Filho, F. G. (2007) Chapter 4: Cell Division. Bacillus: Cellular and Molecular, ISBN: 978-1-904455-12-7

Fily, Y., Henkes, S. and Marchetti, M. C. (2014) Freezing and phase separation of self-propelled disks. Soft Matter, 10, 2132-2140.

Galli, E. (2011) Characterization of the Cell Division Factor ZapB of Escherichia coli. Newcastle University Institute for Cell and Molecular Biosciences.

Hallatschek, O., Hersen, P., Ramanathan, S. and Nelson, D. R. (2008) Genetic drift at expanding frontiers promotes gene segregation. PNAS, 105, 19926-19930.

Homma, M., Oota, H., Kojima, S., Kawagish, I. and Imae, Y. (1996) Chemotactic responses to an attractant and a repellent by the polar and lateral flagellar systems of Vibrio alginolyticus. Microbiology, 142, 2777-2783.

Henkes, S., Fily, Y. and Marchetti, M. C. (2011) Active jamming: Self-propelled soft particles at high density. PHYSICAL REVIEW, 84, 1539-3755.

Kearns, B. D. (2010) A field guide to bacterial swarming motility. Nat Rev Microbiol, 8(9), 634-644

Kumar, A. and Wu, J. (2004) Jamming phase diagram of colloidal dispersions by molecular dynamics simulations. Applied Physics Letters, 84, 4565-4567.

Kudo, S., Imai, N., Nishitoba, M., Sugiyama, S. and Magariyama, Y. (2005) Asymmetric swimming pattern of Vibrio alginolyticus cells with single polar ﬂagella. FEMS Microbiology Letters, 242, 221-225.

KOGURE, K., IKEMOTO, E. and MORISAKI, H. (1998) Attachment of Vibrio alginolyticus to Glass Surfaces Is Dependent on Swimming Speed. Journal of Bacteriology, 180, 932-937.

Kawagishi, I., Imagawa, M., Irnae, Y. McCarte, L. and Homma, M. (1996) The sodium-driven polar flagellar motor of marine Vibrio as the mechanosensor that regulates lateral flagellar expression. Molecular Microbiology, 20, 693-699.

KAWAGISHI, I., MAEKAWA, Y., ATSUMI, T., HOMMA, M. and IMAE, Y. (1995) Isolation of the Polar and Lateral Flagellum-Defective Mutants in Vibrio alginolyticus and Identiﬁcation of Their Flagellar Driving Energy Sources. Journal of Bacteriology, 177, 5158-5160.

Kojima, M., Kubo, R., Yakushi, T., Homma, M, and Kawagishi, I. (2007) The bidirectional polar and unidirectional lateral ﬂagellar motors of Vibrio alginolyticus are controlled by a single CheY species. Molecular Microbiology, 64, 57-67.

Lele, U. N., Baig, U. I. and Watve, M. G. (2011) Phenotypic Plasticity and Effects of Selection on Cell Division Symmetry in Escherichia coli. PLoS ONE:Bacterial Division Symmetry, 6, e141516.

McCarter, L. L. (2010) Bacterial Acrobatics on a Surface: Swirling Packs, Collisions, and Reversals during Swarming. JOURNAL OF BACTERIOLOGY, 192, 3246-3248.

McCarter, L. L. (2001) Polar flagellar motility of the Vibrionaceae. Microbiol. Mol. Biol. Rev. 65, 445–462.

Narayan, V., Menon, N. and Ramaswamy, S. (2005) Nonequilibrium steady states in a vibrated-rod monolayer: tetratic, nematic, and smectic correlations. Journal of Statistical Mechanics: Theory and Experimentsissa.

Ping, L., Wu, Y., Hosu, B. G., Tang, J. X. and Berg, H. C. (2014) Osmotic Pressure in a Bacterial Swarm. Biophysical Journal, 107, 871-878.

Partridge, J. D. and Harshey, R. M. (2013) Swarming: Flexible Roaming Plans. Journal of Bacteriology, 195, 909-918.

Rowlett, V. W. and Margolin, W. (2014) Asymmetric Constriction of Dividing Escherichia coli Cells Induced by Expression of a Fusion between Two Min Proteins. Journal of Bacteriology, 196, 2089-2100.

Sadati, M., Nourhani, A., Fredberg, J. J. and Qazvini, N. T. (2014) Glass-like dynamics in the cell and in cellular collectives. WIREs: Systems Biology and Medicine, 6(2), 137-149.

Sullivan, S. M., and Maddock J. R. (2000) Bacterial division: Finding the dividing line. Current Biology, 10, R249-R252.

Steager, E. B., Kim, C. B. and Kin, M. J. (2008) Dynamics of pattern formation in bacterial swarms. PHYSICS OF FLUIDS, 20, 073601:1-5.

Skoog, K. (2011) Cell division in Escherichia coli. ISBN 978-91-7447-339-1.

Takekawa, N., Kojima, S. and Homma, M. (2014) Contribution of Many Charged Residues at the Stator-Rotor Interface of the Na+-Driven Flagellar Motor to Torque Generation in Vibrio alginolyticus. Journal of Bacteriology, 196, 1377-1385.

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. PNAS, 109, 14308-14313.

Wensink, H. H. and Löwen, H. (2012) Emergent states in dense systems of active rods: from swarming to turbulence. Journal of Physics: Condensed Matter, 24, 464130.

Wu, Y., and Berg H. C. (2012) Water reservoir maintained by cell growth
fuels the spreading of a bacterial swarm. PNAS, 109, 4128-4133.

指導教授

羅健榮(Chien-Jung Lo)

審核日期

2015-7-29

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