Probing the Physical Environments of Bacterial Swarm Colony

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廖志揚(Jhih-yang Liao) 查詢紙本館藏

畢業系所

物理學系

論文名稱

(Probing the Physical Environments of Bacterial Swarm Colony)

相關論文

★ 多細菌鞭毛馬達的同步轉動量測	★ 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
★ Spiral-coil Formation in Semi-flexible Self-propelled Chain System	★ Real-Time Measurement of Vibrio alginolyticus Polar Flagellar Growth
★ Foraging behavior of Caenorhabditis elegans	★ 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
★ Deformation Dynamics of Active 2D Tetragonal Pseudo-Crystal	★ Probing Ion-Flux of Bacterial Flagellar Motors by Correlative Microscopy
★ Aliivibrio fischeri in Motion	★ 主動粒子的擴張行為

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摘要(中)

細菌菌落生長的第一步是感染和侵入，洋菜膠體是用來模擬細菌生長的環境，接種少量的細菌在洋菜膠表面上，細菌開始生長、增加活動力然後向外擴，這是一種低維度的高度動態過程。然而在細菌群游菌落中的物理環境知道得很少，三個群游細菌的主要特色細菌增長、鞭毛大量增生和細菌生長停滯期可以幫助我們了解群游菌落的動態發展，我們量測菌落的表面輪廓、接觸角和菌落環境中有效的黏滯係數來說明群游菌落中的流體機制。
1. 菌落接觸角、表面輪廓及生長停滯期
細菌菌落為超親水性且邊界會隨著菌落發展而向前移動，我們使用的細菌是溶藻弧菌，品種為只有側鞭毛的YM19，YM19在洋菜膠體表面有良好的活動性，在YM19菌落發展的期間，菌落邊界會停滯然後隨著細菌向外擴而改變形狀。我們藉由共軛焦顯微鏡雷射掃描影像方法，重建出薄膜表面輪廓的三維結構，這種方法在量測菌落邊界附近的表面輪廓有極高的解析度，細菌的菌落會隨著時間不斷改變，而不像表面上熱平衡的液滴，細菌的邊界在發展的過程中會出現滯留的現象。
2. 有效的黏滯細數及細菌鞭毛大量增生
細菌菌落表面上含有一層薄薄的，流變的條件建立在液-氣交界及底部液-洋菜膠體交界的平衡，菌落中有效黏滯係數會隨著時間增加而增加，我們利用微米聚苯乙烯珠子的擴散來量測菌落中局部的有效黏滯係數，數據顯示越接近表面的有效黏滯係數越大，我們猜測細菌鞭毛大量增生是為了產生更多的推力來克服表面黏滯係數的增加。
3. 細菌增長在流體中的好處
我們比較擁有相同鞭毛密度的長桿狀細菌的阻力係數及推力，我們發現群游細菌的增長在表面流體環境可以得到數倍的推力比。
這篇論文的目標是想利用物理的角度了解群游菌落中的環境特色，所有的現象都可以利用流體的機制解釋，結合物理的參數、流變的量測及電腦數值模擬，我們可以建立出全物理的模型來說明群游細菌菌落的動態發展，例如溶藻弧菌。

摘要(英)

Bacterial colonization is the first step of infection and invasion. Agar plate is a model system to study bacterial colonization. After inoculating few cells on the two dimensional agar surface, bacteria will start to grow and then expand by their swarm motility. This is a highly dynamical process in a reduced dimension system. However, very little is known regarding the physical environments of swarm colony. Three major characteristic features among different swarming cells are cell length elongation, hyperflagellation and swarming lag. To study the dynamics of bacterial colony development, we measured colony profiles, contact angles, and effective viscosity to clearly the hydrodynamical mechanisms of these three major swarming cell features.
1. Contact angle and surface profile and swarming lag:
The surface is super-hydrophilic and the contact line is moving as the colony develops. We use the strain of Vibrio alginolyticus, YM19, which only have lateral filament. YM19 have great surface swarm motility on agar plate. During the YM19 colony development, the contact line of the development process will change with the colony expansion. We design a confocal surface profile measurement method on thin film system to reconstruct the three dimensional structures from the laser scanning images. Thus we can measure the high resolution surface profiles near contact lines during the colony development. Unlike thermal equilibrium droplet on the surface, bacterial colony changes dynamically with time. The contact angle shows a hysteresis during the colony devilment indicating a pinning effect of the contact line.
2. Effective viscosity and hyperflagellation:
The colony is a thin layer of liquid above agar surface. The rheological condition is within a top air-liquid interface and a bottom liquid-agar interface. The effective viscosity in the colony varies as time increases. We measure the local effective viscosity by measuring diffusion of micron size polystyrene beads within the simulated colony. The result shows an increscent of effective viscosity near the agar surface. Therefore we suspect the swarming-cell hyperflagellation is the results of increasing thrusting force near the surface.
3. Hydrodynamical advantage of cell length elongation.
We compare the drag coefficient of long rods and the thrusting force of long rods with uniform flagella density. We found that the elongation is hydrodynamically beneficial for swarming cells to have up to several times thrusting force ratio.
The aim of this thesis is to understand the physical origin of the three major swarm cells characteristic features. All of them can be explained by hydrodynamical mechanism. Combining physical parameter measurements, rheological measurements and computation simulation, we are able to build up a complete physical model to understand the dynamical development of swarming colony such as Vibrio alginolyticus.

關鍵字(中)

★ 群游菌落

關鍵字(英)

★ Swarm colony

論文目次

CHAPTER 1 Introduction……………………………………….……1
1.1 Background and Motivation……………………………………………….……….1
1.2 Bacterial Strain and Motility………………………………………………..………2
1.2.1 Vibrio alginolyticus……………………………………………………..….……….2
1.2.2 Flagella Filaments……………………………………………………….……..……3
1.2.3 Flagellar Motor and Energetic………………………………………………….5
1.2.4 Bacteria Swimming and Swarming…………………………………..……...7
1.3 Environment of Agar Plate………………………………………..…………………9
1.3.1 Reynolds Number………………………………………………………..…………..9
1.3.2 Viscosity…………………………………………………………………….….…………9
1.3.3 Effective Viscosity…………………………………………………….…….………11
1.3.4 Diffusion…………………………………………………………..…….…….………..12
1.3.5 Contact Angle and Surface Tension………………………….……………..13
1.3.6 Response of Bacteria in this Environment………………………………14
CHAPTER 2 Experimental Apparatus…………………………17
2.1 Confocal Microscope…………………………………………………..……………..17
2.1.1 Principle…………………………………………………………………………………18
2.1.2 3D Surface Profile Reconstruction………………………………………….19
2.1.3 Calibration……………………………………………………………………………..20
2.2 Optical Microscope…………………………………………………………………….21
2.2.1 Phase Contrast……………………………………………….………………………22
CHAPTER 3 Experimental Materials and Techniques…24
3.1 Bacterial Strain………………………………………………………..………………..24
3.2 Surface Profile and Contact Angle Measurement Method…………..25
3.2.1 Confocal Microscopy Reflection Measurement Method………….25
3.2.2 Fluorescent Measurement Method…………………………………………27
3.3 Single Particle Tracking……………………………………………………………….28
3.4 Mean Square Displacement……………………………………………..…………30
3.5 Height Calibration of Single Particle…………………………………………….32
CHAPTER 4 Experimental Results………………………………35
4.1 Evolution of the Colony………………………………………………………………35
4.1.1 Experimental Preparation………………………………….……………………35
4.1.2 Surface Profile…………………………………………………………………..……36
4.1.3 Contact Angles………………………………………………………………………..39
4.1.4 Discussion……………………………………………………………………………….41
4.2 Effective Viscosity of the Colony………………………………………………….42
4.2.1 Drag Coefficient in an Unbounded Solution…………………….………42
4.2.2 Polar Flagella are Ineffective in the Thin Layer………………………..44
4.2.3 Effective Viscosity in the Colony……………………………………………..46
4.3 Discussions………………………………………………………………………………….49
CHAPTER 5 Conclusion………………………………..……………51
Reference………………………………………………………………...53

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指導教授

羅健榮(Chien-Jung Lo)

審核日期

2015-7-29

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