http://2009.igem.org/wiki/index.php?title=Special:Contributions/Utopian&feed=atom&limit=50&target=Utopian&year=&month=2009.igem.org - User contributions [en]2024-03-28T12:03:41ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:HKU-HKBU/BrainstormingTeam:HKU-HKBU/Brainstorming2009-10-22T03:52:02Z<p>Utopian: /* Methane-consuming bacteria */</p>
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=Brainstorming=<br />
The brainstorming for our team started at the beginning of June, 2009. All the team members racked their brains and we have come up with many exciting ideas during this process. We mainly focused on developing engineered bacteria that can benefit our society and promote human health. A list of ideas that we came up with during our brainstorming sessions is provided below.<br />
<br />
====Mosquito-repelling bacteria====<br />
Bacteria that can kill mosquitoes or expel mosquitoes away by releasing some 'anti-mosquito' chemicals and thus can be used to reduce malaria. The engineered bacteria can be distributed to malaria-afflicted area and control the population of the malaria-bearing mosquitoes. We need to manipulate the existing metabolic pathway of bacteria to produce organic repellent such as N,N-Diethyl-meta-toluamide, or DEET in abbreviation. Alternatively, we can also introduce metabolic pathways that enable bacteria to generate mosquito attracting chemical as well as mosquitoe killing agents. However, we found out that this is quite a comprehensive project and we only have 3 months! We decided to follow this project after the iGEM.<br />
<br />
====Bacteria radio====<br />
Bacteria conjugated with nanotubes that can sense the electromagnetic waves and thus wirelessly-controllable. It would be awesome if we were able to wirelessly control a bacterium! We can implant these wireless controlled 'robots' into the human body and guide them to do the cleaning work and even release therapeutic agents according to our design. Researchers at [http://www.physics.berkeley.edu/research/zettl/projects/nanoradio/radio.html UC Berkeley] have successfully developed a nanotube radio using carbon nanotube as the antenna. We want to incorporate the nanotube into our bacteria by conjugating it with a surface protein. When electromagnetic wave arrives at the nanotube, it will produce high frequency mechanical vibration on the nanotube and the signal will be transmitted to the linked protein, causing changes in its conformation. A signal-transduction pathway can be constructed to achieve intracellular amplification of the signal and the bacterium will produce further biochemical response. It is an amazing idea; but owing to the time limit and the difficulties , we have to give up and move on to a more do-able idea.<br />
<br />
====Bacteria arm====<br />
Bacteria connected at ends to form a chain so that their movements are synchronized. Single-cell bacteria like ''E. coli'' swim on their own. It will be great if we can organize a bunch of bacteria into a chain or a matrix and synchronize their movements to generate large enough forces to power other devices. The function of this bacteria arm is also implicated in our ‘bacteria signaling chain’ mentioned below.<br />
<br />
====Desalinating bacteria====<br />
Bacteria that can neutralize acidic soil or can convert soluble salts into insoluble precipitation by releasing ions. This will be extremely helpful as China is suffering severe loss of arable soil due to salinization. However, we would have to find a huge energy source for the bacteria to savage a large land area.<br />
<br />
====Bacteria with toggle switch====<br />
Oscillating system that can emanate light with alternating wavelengths. As this project involves a lot of modeling, it is naturally appreciated by people from physics major in our team. However, the project does not have as many potential applications on human health as do our other ideas. In fact, some of our instructors pointed out that in order to achieve an apparent oscillation, the experimenting conditions must be fine-tuned, which would consume a lot of time.<br />
<br />
====Bacteria calculator====<br />
Bacteria that contain molecular logic circuits that can count numbers.<br />
<br />
====Engineered Cell Memory====<br />
Cholera toxins can permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein, resulting constitutive cAMP production (Wikipedia). We wanted to engineer a mammalian cell that can express cholera toxin when given external stimuli (the information we want to store). As mentioned above, the expressed cholera can induce constitutive cAMP production, which is a rather common intermediate step that appears in many signal transduction pathways. This will enable us to exploit a variety of signaling mechanism originally in the cell to achieve the function of memory.<br />
<br />
====Methane-consuming bacteria====<br />
Bacteria that can survive in the stomachs of livestock and convert methane, which is a greenhouse gas, to other compounds with a higher boiling point. The largest methane emissions come from the decomposition of wastes in landfills, ruminant digestion and manure management associated with domestic livestock. We would like to engineer strains of bacteria that can convert the greenhouse gases produced in the rumen of livestock to non-gaseous compound. This requires that the bacteria can survive the acidic enteric environment and colonize in the rumen of livestock. However, this project, similar to the idea of mosquito-repelling bacteria, implicates the manipulation of bacteria’s metabolic pathway. It is rather challenging for us to finish it within 3 months.<br />
<br />
====Bacteria signalling chain====<br />
Construct a chain of bacteria that are conjugated with each other at the ends and use light as the signal. The signals will be produced by luciferase and received by bacteriorhodopsin. Light is produced by the oxidation of luciferin. If we confine this light-emanating protein to one end of the bacterium and install a light-sensing bacteriorhodopsin at the closely-apposed end of another bacterium, luminescence can function as a signal between these bacteria. We only have to couple the changes brought by the bacteriorhodopsin to the cell to the oxidation of luciferase.<br />
<br />
----<br />
When we decide our final goals from a long list of ideas, we took into account the following considerations:<br />
<br />
# The project has to be do-able within 3 months. We have to have some results to present in the Jamboree!<br />
# The project has to have far-reaching implications for the future society.<br />
# The project must sound interesting and attract viewer's attention.<br />
<br />
We finally chose 'Bactomotor' as our final project. This project, as described in our Wiki, can have great implications for our society in terms of energy utilization. Our Bactomotor can generate forces by metabolizing nutrition in its living environment with a high efficiency. The cost of obtaining clean mechanical energy is only a minuscule amount of glucose!<br />
<br />
The brainstorming process is a valuable experience for our team. As everyone has to find sufficient evidence to support his own idea, we got a lot to read and we learned a lot!<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-21T15:23:57Z<p>Utopian: /* Design */</p>
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=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up many possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capillaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''Escherichia coli'' or ''Salmonella typhimurium'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momentum and produces non-random movement. When the rotation is in the clockwise direction, the bactomotor will tumble in one place and stop'swimming' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1b.png | frame | center | '''Fig. 1''' Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of ''cheZ'' gene. The gene of CheZ plays the key role here as it controls the phosphorylation level of CheY. CheZ protein can dephosphorylate CheY. High levels of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to tumbling movement while low levels of phosphorylation switch the flagella to its non-tumbling mode and enable the bacteria to swim. Therefore, an increase in the expression level of CheZ gene allows us to reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering was applied to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)were placed inside the ''CheZ'' gene. The ''CheZ'' gene was substituted by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''cheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurrence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in an 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png| frame | center | '''Fig. 2''' Genetic circuit of control CheZ expression|400px]]<br />
<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''pTet''' as the regulator, which tetracycline(or aTc)-inducible. We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png| center |800px|]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T10:39:10Z<p>Utopian: /* Notes: Brooks is currently editing this page. He has a tutorial at 7:00 pm and will come back later. Plz do not re-edit.Thank you. */</p>
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='''Applications'''=<br />
<br />
<br />
== Notes: Brooks is currently editing this page. He has a tutorial at 7:00 pm and will come back later. Plz do not re-edit.Thank you. ==<br />
<br />
Our version of 'Bactomotor' is only a preliminary one. But the idea of using the mechanical forces generated by microorganisms to do useful work is thrilling and will have great implications in many fields of future applications. <br />
Although forces generated by a single bacterium counts little, the concentration of forces generated by a population of bacteria can actually make a great difference. Motors powered by living organisms can have numerous advantages over the conventional electronic devices that are powered by batteries. The advantages are concluded as follows:<br />
<br />
# The size of the motor can be reduced to a much smaller scale. The motor are available to many applications that involve microscale manipulation.<br />
# Without the presence of batteries that contain inorganic or organic chemicals, the bacteria-driven motor will cause no threat to both environment and human health. <br />
# The bacteria-powered motor is genetically manipulated. <br />
<br />
The key is to develop a better interface between the microorganisms and the non-living device that can concentrate and forces and serves as a motion rectifier.<br />
<br />
==Clinical medicine and surgery==<br />
<br />
Genetically-engineered microorganism-powering'Bactomotor' <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T10:37:02Z<p>Utopian: /* Notes: Brooks is currently editing this page. Plz do not re-edit.Thank you. */</p>
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='''Applications'''=<br />
<br />
<br />
== Notes: Brooks is currently editing this page. He has a tutorial at 7:00 pm and will come back later. Plz do not re-edit.Thank you. ==<br />
<br />
Our version of 'Bactomotor' is only a preliminary one. But the idea of using the mechanical forces generated by microorganisms to do useful work is thrilling and will have great implications in many fields of future applications. <br />
Although forces generated by a single bacterium counts little, the concentration of forces generated by a population of bacteria can actually make a great difference. Motors powered by living organisms can have numerous advantages over the conventional electronic devices that are powered by batteries. The advantages are concluded as follows:<br />
<br />
# The size of the motor can be reduced to a much smaller scale. The motor are available to many applications that involve microscale manipulation.<br />
# Without the presence of batteries that contain inorganic or organic chemicals, the bacteria-driven motor will cause no threat to both environment and human health. <br />
# The bacteria-powered motor is genetically manipulated. <br />
<br />
The key to successful utilization is the<br />
<br />
==Clinical medicine and surgery==<br />
<br />
Genetically-engineered microorganism-powering'Bactomotor' <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T10:29:09Z<p>Utopian: /* Applications */</p>
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{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
='''Applications'''=<br />
<br />
<br />
== Notes: Brooks is currently editing this page. Plz do not re-edit.Thank you. ==<br />
<br />
Our version of 'Bactomotor' is only a preliminary one. But the idea of using the mechanical forces generated by microorganisms to do useful work is thrilling and will have great implications in many fields of future applications. <br />
Although forces generated by a single bacterium counts little, the concentration of forces generated by a population of bacteria can actually make a great difference. Motors powered by living organisms can have numerous advantages over the conventional electronic devices that are powered by batteries. The advantages are concluded as follows:<br />
<br />
# The size of the motor can be reduced to a much smaller scale. The motor are available to many applications that involve microscale manipulation.<br />
# Without the presence of batteries that contain inorganic or organic chemicals, the bacteria-driven motor will cause no threat to both environment and human health. <br />
# The using <br />
<br />
The key to successful control of <br />
<br />
==Clinical medicine and surgery==<br />
<br />
Genetically-engineered microorganism-powering'Bactomotor' <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T10:27:38Z<p>Utopian: /* Applications */</p>
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<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
='''Applications'''=<br />
<br />
<br />
== Notes: Brooks is currently editing this page. Plz do not re-edit.Thank you. ==<br />
<br />
Our version of 'Bactomotor' is only a preliminary one. But the idea of using the mechanical forces generated by microorganisms to do useful work is thrilling and will have great implications in many fields of future applications. <br />
Although forces generated by a single bacterium counts little, the concentration of forces generated by a population of bacteria can actually make a great difference. Motors powered by living organisms can have numerous advantages over the conventional electronic devices that are powered by batteries. The advantages are concluded as follows:<br />
<br />
# The size of the motor can be reduced to a much smaller scale. The motor are available to many applications that involve microscale manipulation.<br />
# Without the presence of batteries that contain inorganic or organic chemicals, the bacteria-driven motor will cause no threat to both environment and human health. <br />
# The using <br />
<br />
The key to successful control of <br />
<br />
==Clinical medicine and surgery==<br />
<br />
Genetically-engineered microorganism-powering'Bactomotor' <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T10:17:49Z<p>Utopian: /* Application */</p>
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{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
='''Applications'''=<br />
<br />
<br />
== Notes: Brooks is currently editing this page. Plz do not re-edit.Thank you. ==<br />
<br />
Our version of 'Bactomotor' is only a preliminary one. But the idea of using the mechanical forces generated by microorganisms to do useful work is thrilling and will have great implications in many fields of future applications. <br />
Although forces generated by a single bacterium counts little, the concentration of forces generated by a population of bacteria can actually make a great difference. The key is how to incorporate these forces into df<br />
<br />
==Clinical medicine and surgery==<br />
<br />
Genetically-engineered microorganism-powering'Bactomotor' <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ApplicationTeam:HKU-HKBU/Application2009-10-21T09:57:15Z<p>Utopian: /* Application */</p>
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<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
='''Application'''=<br />
<br />
Notes: Brooks is currently editing this page. Plz do not re-edit.Thank you.<br />
<br />
==Clinical medicine and surgery==<br />
<br />
Our version of genetically-engineered Bactomotor opens up a variety of possibilities. <br />
<br />
<br />
<br />
== Zero-pollution energy source ==<br />
<br />
<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ModelingTeam:HKU-HKBU/Modeling2009-10-21T04:25:06Z<p>Utopian: /* Assumptions */</p>
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=Modeling=<br />
Theoretical analysis of the process gives us a quantitative insight into the process. We consider a motor having a simplest shape, i.e. a single lamina with a vertical axis in the middle.<br />
<br />
[[Image:HKU-HKBU_modeling_figure | center]]<br />
<br />
==Assumptions==<br />
An analytical solution can be derived on the basis of the following assumptions:<br />
# power of a bacteria is kept a constant;<br />
# friction coefficient of a small object undergoing slow motion is proportional to the cross sectional area;<br />
<br />
Let us take a look at the validity of the above assumptions.<br />
<br />
E.coli is used as the propeller in our project. Glucose is consumed in the mitochondria to generate ATP, which is then used to drive the rotation of flagella. As the number of mitochondria in a E.coli bacterium is kept relatively constant, thus the rate of ATP generation is also constant when the bacteria are provided with excess amount of glucose. This justifies our first assumption that the power of bacteria is a constant.<br />
<br />
A bacterium can be thought of as a truck travelling along an expressway. If it is free of loading and the power is kept constant, the truck will experience relatively small frictional force and will be moving at a relatively high speed. On the other hand, if the truck is loaded with heavy weights, the frictional force will increase significantly,impeding the movement of the truck. As a result, the truck will have a much lower maximum speed. Same thing happens for bacteria. The power supplied by the motor of the flagella is kept a constant, regardless of the “working condition”, namely whether pushing a motor or not. <br />
<br />
The second assumption is based on principles of fluid-dynamics.It is stated that friction is proportional to the cross sectional area of small objects moving at a low speed. The sizes of the motor and the driving bacteria are[[Image:HKU-HKBU_modeling_f1.png]] and [[Image:HKU-HKBU_modeling_f2.png]] respectively, both can be saftely regarded as 'small objects'. The low speed of bacteria, which is estimated to be[[Image:HKU-HKBU_modeling_f3.png]], also satisfies the “slow motion” condition required by the principle mentioned above. Therefore, the second assumption is justified.<br />
<br />
==Calculation of Rotational Velocity==<br />
<br />
We start out by calculating the power of a single bacterium first. Under freely swimming condition, a bacterium can move at a maximum speed of [[Image:HKU-HKBU_modeling_f4.png]] ([[Image:HKU-HKBU_modeling_f5.png]]). If the friction coefficient is [[Image:HKU-HKBU_modeling_f6.png]], then the friction is given by<br />
<br />
[[Image:HKU-HKBU_modeling_f7.png]].<br />
<br />
Here, [[Image:HKU-HKBU_modeling_f8.png]] is a function of expression level of CheZ: if CheZ is fully expressed, the bacteria speed should be maximized, correspondingly[[Image:HKU-HKBU_modeling_f9.png]]. On the other hand, if CheZ is completely knocked out, bacteria should lose the swimming ability. Thus, [[Image:HKU-HKBU_modeling_f10.png]] corresponds to this case.<br />
<br />
Hence, the power is <br />
<br />
[[Image:HKU-HKBU_modeling_f11.png]].<br />
<br />
Next, we estimate the power consumed by the motor, rotating at an angular velocity [[Image:HKU-HKBU_modeling_f12.png]], due to friction. Consider a small element on the motor from r to r+dr, namely the red part in Fig 2. Let [[Image:HKU-HKBU_modeling_f13.png]] be the friction coefficient of the motor. Hence, from the 2nd assumption, the friction coefficient for the small element is [[Image:HKU-HKBU_modeling_f14.png]], l here is the width of the motor. Thus, the friction force on this element, proportional to its velocity [[Image:HKU-HKBU_modeling_f15.png]], is <br />
<br />
[[Image:HKU-HKBU_modeling_f16.png]]<br />
<br />
Power consumed by this element is<br />
<br />
[[Image:HKU-HKBU_modeling_f17.png]]<br />
<br />
The total power consumed on the motor is then the sum, or integration in other words, of all the [[Image:HKU-HKBU_modeling_f18.png]],<br />
<br />
[[Image:HKU-HKBU_modeling_f19.png]]<br />
<br />
The power supplied by the bacteria is completely consumed by the motor frictional force. With the conservation of energy, we have<br />
<br />
[[Image:HKU-HKBU_modeling_f20.png]]<br />
<br />
Here, h is the height of the motor along the axis direction and n is the number of bacteria per unit area on the motor.<br />
<br />
==Resutls and Discussion==<br />
According to assumption 2, we can further reduce the above equation. Let [[Image:HKU-HKBU_modeling_f21.png]],<br />
[[Image:HKU-HKBU_modeling_f22.png]],<br />
<br />
C and [[Image:HKU-HKBU_modeling_f23.png]] are the friction coefficient per unit area of bacteria and motor respectively. a is the cross section area of a bacteria. Substitute them into the above equation gives<br />
<br />
[[Image:HKU-HKBU_modeling_f24.png]]<br />
<br />
[[Image:HKU-HKBU_modeling_f25.png]] here, is just a constant of order [[Image:HKU-HKBU_modeling_f26.png]]. <br />
<br />
The model predicts the followings:<br />
<br />
# Angular velocity is independent of height h of the motor;<br />
# Angular velocity is linearly proportional to the width l of motor and the velocity of bacteria. As a consequence, the expression level of CheZ monotonically affects the rotational velocity. In other words, higher expression level of CheZ results in faster rotation.<br />
<br />
This model is only applicable for small objects. So, despite independence of h, the height of the motor still can’t be too large. In other words, it should be confined within [[Image:HKU-HKBU_modeling_f27.png]]. What’s more, even the rotational velocity is inversely proportional to l, the length of the motor can’t be too small because narrow motor would result in too few bacteria attached, which leads to too much noise and fails to fit into this model. To be more precious, a suggested length of motor should be of the order of [[Image:HKU-HKBU_modeling_f28.png]]. Thus, with a motor having a width of [[Image:HKU-HKBU_modeling_f29.png]], the angular velocity will be about [[Image:HKU-HKBU_modeling_f30.png]].<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ModelingTeam:HKU-HKBU/Modeling2009-10-21T04:21:26Z<p>Utopian: /* Assumptions */</p>
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{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Modeling=<br />
Theoretical analysis of the process gives us a quantitative insight into the process. We consider a motor having a simplest shape, i.e. a single lamina with a vertical axis in the middle.<br />
<br />
[[Image:HKU-HKBU_modeling_figure | center]]<br />
<br />
==Assumptions==<br />
An analytical solution can be derived on the basis of the following assumptions:<br />
# power of a bacteria is kept a constant;<br />
# friction coefficient of a small object undergoing slow motion is proportional to the cross sectional area;<br />
<br />
Let us take a look at the validity of the above assumptions.<br />
<br />
E.coli is used as the propeller in our project. Glucose is consumed in the mitochondria to generate ATP, which is then used to drive the rotation of flagella. As the number of mitochondria in a E.coli bacterium is kept relatively constant, thus the rate of ATP generation is also constant when the bacteria are provided with excess amount of glucose. This justifies our first assumption that the power of bacteria is a constant.<br />
<br />
A bacterium can be thought of as a truck travelling along an expressway. If it is free of loading and the power is kept constant, the truck will experience relatively small frictional force and will be moving at a relatively high speed. On the other hand, if the truck is loaded with heavy weights, the frictional force will increase significantly,impeding the movement of the truck. As a result, the truck will have a much lower maximum speed. Same thing happens for bacteria. The power supplied by the motor of the flagella is kept a constant, regardless of the “working condition”, namely whether pushing a motor or not. <br />
<br />
The second assumption is based on principles of fluid-dynamics.It is stated that friction is proportional to the cross sectional area of small objects moving at a low speed. The sizes of the motor and the driving bacteria are[[Image:HKU-HKBU_modeling_f1.png]] and [[Image:HKU-HKBU_modeling_f2.png]] respectively, both can be saftely regarded as 'small objects'. The low speed of bacteria, [[Image:HKU-HKBU_modeling_f3.png]], also satisfies the “slow motion” condition required by the principle mentioned above. Therefore, the second assumption is justified.<br />
<br />
==Calculation of Rotational Velocity==<br />
<br />
We start out by calculating the power of a single bacterium first. Under freely swimming condition, a bacterium can move at a maximum speed of [[Image:HKU-HKBU_modeling_f4.png]] ([[Image:HKU-HKBU_modeling_f5.png]]). If the friction coefficient is [[Image:HKU-HKBU_modeling_f6.png]], then the friction is given by<br />
<br />
[[Image:HKU-HKBU_modeling_f7.png]].<br />
<br />
Here, [[Image:HKU-HKBU_modeling_f8.png]] is a function of expression level of CheZ: if CheZ is fully expressed, the bacteria speed should be maximized, correspondingly[[Image:HKU-HKBU_modeling_f9.png]]. On the other hand, if CheZ is completely knocked out, bacteria should lose the swimming ability. Thus, [[Image:HKU-HKBU_modeling_f10.png]] corresponds to this case.<br />
<br />
Hence, the power is <br />
<br />
[[Image:HKU-HKBU_modeling_f11.png]].<br />
<br />
Next, we estimate the power consumed by the motor, rotating at an angular velocity [[Image:HKU-HKBU_modeling_f12.png]], due to friction. Consider a small element on the motor from r to r+dr, namely the red part in Fig 2. Let [[Image:HKU-HKBU_modeling_f13.png]] be the friction coefficient of the motor. Hence, from the 2nd assumption, the friction coefficient for the small element is [[Image:HKU-HKBU_modeling_f14.png]], l here is the width of the motor. Thus, the friction force on this element, proportional to its velocity [[Image:HKU-HKBU_modeling_f15.png]], is <br />
<br />
[[Image:HKU-HKBU_modeling_f16.png]]<br />
<br />
Power consumed by this element is<br />
<br />
[[Image:HKU-HKBU_modeling_f17.png]]<br />
<br />
The total power consumed on the motor is then the sum, or integration in other words, of all the [[Image:HKU-HKBU_modeling_f18.png]],<br />
<br />
[[Image:HKU-HKBU_modeling_f19.png]]<br />
<br />
The power supplied by the bacteria is completely consumed by the motor frictional force. With the conservation of energy, we have<br />
<br />
[[Image:HKU-HKBU_modeling_f20.png]]<br />
<br />
Here, h is the height of the motor along the axis direction and n is the number of bacteria per unit area on the motor.<br />
<br />
==Resutls and Discussion==<br />
According to assumption 2, we can further reduce the above equation. Let [[Image:HKU-HKBU_modeling_f21.png]],<br />
[[Image:HKU-HKBU_modeling_f22.png]],<br />
<br />
C and [[Image:HKU-HKBU_modeling_f23.png]] are the friction coefficient per unit area of bacteria and motor respectively. a is the cross section area of a bacteria. Substitute them into the above equation gives<br />
<br />
[[Image:HKU-HKBU_modeling_f24.png]]<br />
<br />
[[Image:HKU-HKBU_modeling_f25.png]] here, is just a constant of order [[Image:HKU-HKBU_modeling_f26.png]]. <br />
<br />
The model predicts the followings:<br />
<br />
# Angular velocity is independent of height h of the motor;<br />
# Angular velocity is linearly proportional to the width l of motor and the velocity of bacteria. As a consequence, the expression level of CheZ monotonically affects the rotational velocity. In other words, higher expression level of CheZ results in faster rotation.<br />
<br />
This model is only applicable for small objects. So, despite independence of h, the height of the motor still can’t be too large. In other words, it should be confined within [[Image:HKU-HKBU_modeling_f27.png]]. What’s more, even the rotational velocity is inversely proportional to l, the length of the motor can’t be too small because narrow motor would result in too few bacteria attached, which leads to too much noise and fails to fit into this model. To be more precious, a suggested length of motor should be of the order of [[Image:HKU-HKBU_modeling_f28.png]]. Thus, with a motor having a width of [[Image:HKU-HKBU_modeling_f29.png]], the angular velocity will be about [[Image:HKU-HKBU_modeling_f30.png]].<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_Preliminary_TrialsTeam:HKU-HKBU/Motor Preliminary Trials2009-10-20T18:37:53Z<p>Utopian: /* Preliminary test using a Membrane */</p>
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==Binding performance test using a membrane==<br />
<br />
We used Immobilon-P transfer membrane to evaluate the performance of streptavidin-biotin binding of bacteria onto a surface. Before cutting apart the membrane into small pieces, pre-activation should be applied to it first [Link 1]. After the pre-activation, the membrane was first sheared into strings manually by using scissors, with the width and thickness being approximately 100μm. We then used Leica-crytomicrotome to cut the “threads” into even smaller fragments, with the length of which being 60μm. A binding performance testing device demension was aproximately 100μm×60μm×100μm. Since the surface of membrane had already been activated, the polar-expression bacteria could bind onto such biotin-coated motors. <br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_Preliminary_TrialsTeam:HKU-HKBU/Motor Preliminary Trials2009-10-20T18:31:13Z<p>Utopian: /* Membrane Version */</p>
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==Preliminary test using a Membrane==<br />
<br />
We used Immobilon-P transfer membrane to evaluate the performance of streptavidin-biotin binding of bacteria onto a surface. Before cutting down the membrane into small pieces, pre-activation should be applied to it first [Link 1]. After the pre-activation, the membrane was first sheared into strings manually by using scissors, with the width and thickness both around 100μm. Then, we used Leica-crytomicrotome to cut the “threads” into small fragments, with the length of 60μm. Thus, we got the motors, whose demention was aproximately 100μm×60μm×100μm. Since the surface of membrane had already been activated, the polar-expression bacteria could bind onto such biotin-coated motors. <br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/BrainstormingTeam:HKU-HKBU/Brainstorming2009-10-20T18:15:17Z<p>Utopian: /* Bactomotor */</p>
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=Brainstorming=<br />
The brainstorming for our team started at the beginning of June. All the team members racked their brains and we have come up with a heap of exciting ideas during this process. We mainly focused on developing engineered bacteria that can better our society and promote human health. <br />
A list of ideas that we came up with during our brainstorming sessions is provided below.<br />
<br />
====Mosquito-repelling bacteria====<br />
Bacteria that can ward off mosquitoes by releasing some 'anti-mosquito' chemicals and thus can be used to reduce malaria. The engineered bacteria can be distributed to malaria-afflicted area and control the population of the malaria-bearing mosquitoes. We need to manipulate the existing metabolic pathway of E.coli to make the bacteria produce organic repellent such as DEET. Alternatively, we can also introduce metabolic pathways that can generate mosquito repelling chemical into the bacteria. However, we found out that this project is a quite involved one and we only have 3 months! We decided to follow this project after the iGEM.<br />
<br />
====Bacteria radio====<br />
Bacteria conjugated with nanotubes that can sense the electromagnetic waves and thus wirelessly-controllable. How awesome it is to be able to wirelessly control a bacterium! We can implant these wireless 'robots' into the human body and let them do the cleaning work and even release therapeutic agents according to our will. Researchers at Berkeley(http://www.physics.berkeley.edu/research/zettl/projects/nanoradio/radio.html)have successfully developed a nanotube radio using carbon nanotube as the antenna. We want to incorporate a nanotube used by Berkeley researchers into our bacteria by conjugating it with a surface protein. When electromagnetic wave arrives at the nanotube, it will produce high frequency mechanical vibration on the nanotube and the vibration is conducted to the linking protein, causing changes in its conformation. A signal-transduction pathway can be constructed to achieve intracellular amplification of the signal and the bacterium will produce further biochemical response. It is an amazing idea; but owing to the time limit and the difficulty , we have to give up and move on to a more do-able idea.<br />
<br />
====Bacteria chain====<br />
Bacteria connected at ends to form a chain so that their locomotion is synchronized. Single-cell bacteria like E.coli swim on their own. It will be great if we can tie up a bunch of bacteria into a chain and synchronize their locomotion to generate large enough forces to power other devices. Also, the function of this bacteria chain is also implicated in our ‘bacteria signaling chain’ mentioned below.<br />
<br />
====Desalinating bacteria====<br />
Bacteria that can neutralize acidic soil or convert soluble salts in the soil to insoluble precipitation by releasing ions. This will be extremely helpful as China is suffering sever loss of arable soil due to salinization.<br />
<br />
====Bacteria with toggle switch====<br />
Oscillating system that can emanate light with alternating wavelengths. As this project involves a lot of modeling, it is naturally appreciated by physics majors in our team. However, the project serves mainly as an experimental demonstration of some beautiful differential equations; it doesn’t have as many implications of human health as do our other ideas. In fact, some of our instructors pointed out that in order to achieve an apparent oscillation, the experimenting conditions must be finely tuned and consumes a lot of time.<br />
<br />
====Bacteria calculator====<br />
Bacteria that contains molecular logic circuits that can count numbers.<br />
<br />
====Engineered Cell Memory====<br />
Cholera toxin can permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein, resulting constitutive cAMP production (Wikipedia). We originally wanted to engineer a mammalian cell that can express cholera toxin when given external stimuli (the information we want to store). As mentioned above, the expressed cholera can induce constitutive cAMP production, which is a rather common intermediate step that appears in many signal transduction pathways. This enables us to exploit a variety of signaling mechanism originally in the cell to achieve the function of memory.<br />
<br />
====Methane-consuming bacteria====<br />
Bacteria that can survive in the stomachs of livestock and convert methane, which is a greenhouse gas, to other compounds with a higher boiling point. It is reported by Lerner et al. in 1998 that the largest methane emissions come from the decomposition of wastes in landfills, ruminant digestion and manure management associated with domestic livestock, natural gas and oil systems, and coal mining. We would like to engineer a strain of bacteria that can convert the greenhouse gases produced in the rumen of livestock during digestion to non-gaseous compound. This requires that the bacteria can survive the acidic enteric environment. However, this project, similar to the idea of mosquito-repelling bacteria, implicates the manipulation of bacteria’s metabolic pathway. It is rather challenging for us to finish it within 3 months.<br />
<br />
<br />
<br />
====Bacteria signalling chain====<br />
Construct a chain of bacteria that are conjugated with each other at ends and use light as the signal. The signal is produced by luciferase and received by bacteriorhodopsin. Light is produced by the oxidation of luciferin. If we confine this light-emanating protein to one end of the bacterium and install a light-sensing bacteriorhodopsin at the closely-apposed end of another bacterium, luminescence can function as a signal between these bacteria. We only have to couple the changes brought by the bacteriorhodopsin to the cell to the oxidation of luciferase.<br />
<br />
<br />
----<br />
When we decide our final goals from a long list of ideas, we took into account the following considerations:<br />
<br />
# The project has to be do-able within 3 months. We have to have some results to demonstrate on the Jamborree!<br />
# The project has to have far-reaching implications for the future society.<br />
# The project must sound interesting and attract viewer's attention.<br />
<br />
We finally chose 'Bactomotor' as our final project. This project,as described in our wiki, can have great implications for our soceity in terms of energy utilization. Our Bactomotor can generage forces by metabolizing nutrition in its living environment with a high efficiency. The cost of obtaining clean mechanical energy is only a minuscule amount of glucose!<br />
<br />
The brainstorming process is a valuable experience for our team. As everyone has to find sufficient evidence to support his own idea, we got a lot to read and we learned a lot!<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/TeamTeam:HKU-HKBU/Team2009-10-20T17:48:44Z<p>Utopian: /* FU Zhong Zheng Brooks */</p>
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__NOTOC__<br />
=Student Members (in alphabetical order)=<br />
<br />
===CHU Tsz Long Nelson===<br />
[[Image:HKU-HKBU_Nelson_120_150.jpg | right]]<br />
<br />
I am entering my second year of biochemistry at HKU and i have a special interest in bio-gerontology. I join the igem2009 because i want to understand more about synthetic biology and to get some practical research experience. In my spare time i enjoy table tennis, archery and chess games. I hope to pursue my PhD program in the US after i graduate.<br />
<br />
In this competition, I am responsible for biobrick construction and speed control. I learnt a lot of useful skills and hand-on experience of practical research. Though there were many failures, i managed to provide some possible explanations for the failures and discuss it with other teamates. I found myself addicted to scientific research after this competition. I hope I can be a successful scientist and contribute a lot to mankind in the future.<br />
<br />
===FU Zhong Zheng Brooks===<br />
[[Image:HKU-HKBU_Brooks_120_150.JPG | left]]<br />
<br />
Brooks Fu Zhongzheng is a second year undergraduate student studying at the University of Hong Kong. Aspiring to be a successful researcher, he decided to choose biochemistry and physics as majors to train himself in reasoning skills and the ability of gleaning useful information from books as heavy as two bags of potatoes. He personally thinks knowledge of physics is indispensable for him to make sense of the abstruseness and intricacy of life. It is quite challenging to deal with these two majors that require different thinking patterns and learning methods, but his brain manages to develop an ability of quickly switching between 'biology mode' and 'physics mode'. He really enjoys himself when learning and attains satisfactory academic results. In the spare time, he usually plays the piano to get relaxed. He is a big fan of Bach and Prokofiev.<br />
<br />
It occurs to him that 'all textbooks no experiments will make Brooks a dull boy'. Only will an opportunity of self-motivated scientific 'DIY' enable him to internalize what he learn from the textbook. When first introduced to the iGEM competition by Dr.Huang, he was totally fascinated by the idea of assembling ‘biological machines’ using standardized biological parts. He thinks it is time to exploit the intricate principles discovered by so many talented scientists after centuries of dutiful research to engineer man-made organisms that can ‘change the world’ and help people. He was thus motivated to join the HKU-HKBU team. In the team, he devotes a lot of time to generating ideas,designing the project,editing the wiki and manufacturing Biobricks. With enthusiasm and diligence, he succeeded in collaborating with his talented teammates to create a bacteria-powered motor. The argument that our future world will heavily rely on the motors we've built may seem ridiculous to some. It may or may not happen, but who knows? Nothing is impossible. iGEM is for people with imagination.<br />
<br />
iGEM proves to be an invaluable learning experience for him. Thanks to the competition, he not only masters the necessary research skills, but more importantly, the spirit of teamwork and the importance of taking up responsibility.<br />
<br />
===JIANG Qin Qin===<br />
[[Image:HKU-HKBU_QQ_120_150.JPG | right]]<br />
<br />
I’m a second year student studying Biochemistry and Chemistry at the University of Hong Kong. I have a strong interest in doing research and enjoy the process of trying new ideas. On the team I spent most of my time doing wet lab. Although I have been defeated for many trials, once I had positive results, a great sense of accomplishments made all the efforts worthy. Meanwhile, the variable possibilities in experiments display the fascination of synthetic biology. Another great thing is that I have met lots of like-minded friends in this IGEM competition. We exchanged our ideas, experienced failure and success together, which made us like a big family. Outside the lab, I’m an easy-going person with lots of interests. I usually do sports and go travelling in my spare time to relax myself.<br />
<br />
===LI Wei Han James===<br />
[[Image:HKU-HKBU_James_120_150.png | left]]<br />
<br />
My name is Weihan Li, and I am a year 2 undergraduate student from the physics department of Hong Kong Baptist University. I have been an undergraduate research assistant, under the supervision of Prof Leihan Tang, in Condenced Matter Theory and Biophysics Lab for over 1 year and a half. My research mainly aimed at quantatively understanding biological processes, especially metabolism. Attending different conferences and symposiums on synthetic biology, system biology and physics also opened my eyes. I also had the honor to give a 20-minute academic repeort, titled Biological Network Analysis: on oscillation and synchronization, on the International Conference on Complexity and Disciplinary Sciences, which is an encouragement and also a good start for me. In this iGEM project, we worked as a team to realize our dreams to engineer something we always long for with the help of bacteria. I am glad to be a part of the team where I gained not only the knowledge and the valuable wet lab experience, but also the precious friendship. I believe this iGEM project will be a great treasure through out my life!<br />
<br />
===LI Yan Lin Jubi===<br />
[[Image:HKU-HKBU_Jubi_120_150.JPG | right]]<br />
<br />
hailing from Hong Kong, is a second-year undergraduate reading medicine and surgery. He joined the iGEM team primarily because he sees synthetic biology as a powerful tool for inventing novel therapeutic strategies.<br />
<br />
He has thus far taken up three roles in the competition: firstly as fund-raising manager, then as group leader of the Che-Z knockout (2443ompT) team, and now as leader of the Human Practices Advance team. Moreover, as one of the only two clinicians around (alas!), he is also responsible for imagining – and developing – the potential clinical applications of the Bacto-Motor.<br />
<br />
Outside medicine, his other academic interests include philosophy, politics and economics and he has represented both Hong Kong and HKU at international debating competitions, advancing to the Octo-Finals of the Worlds Schools Washington DC in 2008. He is also editor-in-chief of Caduceus, the official journal of the Undergraduate Medical Society. While not preoccupied by other tasks, he enjoys classical music, jogging, table tennis and banter – where everybody gets a good laugh :)<br />
<br />
===SHENG Zi Wei Amy===<br />
[[Image:HKU-HKBU_Amy_120_150.JPG | left]]<br />
<br />
I am senior biology student of Hong Kong Baptist University. Mainly working on wet lab, I, together with teammates, take responsibility of measuring the swimming speed and categorizing the trait of polar expression after bacteria being modified. When James, one of our members, introduced me to this group, I had zero knowledge of what synthetic biology means or what we suppose to do. However, had gone through papers and handled wet lab work, I have started to understand the significance of this subject and its bright future and moreover exhibit great interest to it. I attained from this experience not only practical laboratory skills and knowledge of synthetic biology but also friendship and teamwork spirit. Other interests of mine include traveling, reading, growing vegetables and eating them.<br />
<br />
===SIN Sheung Man Alexander===<br />
[[Image:HKU-HKBU_Alex_120_150.jpg | right]]<br />
<br />
When I first heard about iGEM and the idea of synthetic biology, it really caught my interest. This is a chance where I can combine other’s work and findings and make the best out of them. This is what I have learnt recently from object-orientated programming – breaking ideas down into objects, manipulating and assembling them into one working machine.<br />
<br />
Being in the second year of the Bioinformatics Programme, I am in the middle of learning how the knowledge of computer science can be applied on biochemistry. By participating in the iGEM competition, one would be able to gain hands-on experience on what biochemistry research is like, how the knowledge learnt from lectures can be applied to practical laboratory work, and the wisdom to work as a team – sharing results, joys as well as deadlines and pressure. I am glad and honoured to be a part of the team HKU-HKBU, and it is a wonderful opportunity to be able to work with students from another university in Hong Kong.<br />
<br />
===TSE Kwong To Paul===<br />
[[Image:HKU-HKBU_Paul_120_150.jpg | left]]<br />
<br />
I'm a second year student studying Chemistry at the University of Hong Kong. It is my first time to take part in an international competition about synthetic biology. After acquiring information from my other iGEM members, my strong interest drives me to participate into iGEM in summer. At the very beginning, I think this is just another means to kill my time in summer. However, after attending several meeting and assisting others to do different kinds of laboratory work, I find myself immersed in this competition. Some of the laboratory work like western blotting, PCR, electrophoresis and the like are very new to me and I never come across this stuff from Chemistry laboratory. Though repeated failure in the genes knockout, I never felt frustrated since I could learn new things from each failed experiment. Indeed, with the help of other iGEM members and supervisors, I acquire tremendous knowledge about the synthetic biology as well as biochemistry in this competition. My part of work in this iGEM competition is mainly dry lab, which include wikis work, human practice, some search for experiment stuff. Hoping our effort in this competition can pay off and earn the glory and reputation of HKU and HKBU.<br />
<br />
===WEI Ling===<br />
[[Image:HKU-HKBU_WEI_Ling_120_150.jpg | right]]<br />
<br />
Hi, I’m WEI Ling, a student member of iGEM09 HKU-HKBU team. I come from Department of Physics, Hong Kong Baptist University, majoring in biophysics. I graduated from Beijing Normal University this summer. As a physics student, biology is totally new for me. Frankly speaking, it is the first time that I hear so many biology terminologies and deal with some simple manipulations. Fortunately, with the help of friendly and amusing team members, I have learnt a lot in the lab. <br />
<br />
Thanks to all the pretty girls and handsome boys in our team. They bring so much fun during the little bit boring lab life. No matter what the final result of this competition is, I enjoy the course and cherish our friendship. I have to say that I LOVE YOU ALL!!!<br />
<br />
Oh, by the way, although I’m interested in many things, songs of Westlife, movies of Leung Chiuwai, and also show of Lakers are my most favorite. If you are also their fans, please share your feelings and opinions with me. Thank you!<br />
<br />
===WONG Chi Kin Felix===<br />
[[Image:HKU-HKBU_Felix_120_150.jpg | left]]<br />
<br />
I am an MBBS student with immense interest in research. By research I would like to find solutions for healthcare and make the world better. Seems my aspiration is a bit far away from the contents of our project? In fact, I am still trying to learn experimental technique. I believe doing any kinds of biological experiment can enrich my understanding in research routines and insights. Meanwhile, I am responsible for the Human Practices Project. By letting people know about synthetic biology, they understand how it can contribute to the advancement of quality of life.<br />
<br />
I was a late comer in this team, since I joined in September. In these two months, I have become good friends with all my teammates. May I grasp this opportunity to say thank you to all of them.<br />
<br />
===WONG Ho Yin Bosco===<br />
[[Image:HKU-HKBU_Bosco_120_150.jpg | right]]<br />
<br />
Hi, my name is Bosco and i am a year 2 student at HKU reading biochemistry and chemistry. During these days working as a member in the HKU_HKBU team, i have learnt a lot about synthetic biology and yet made invaluable friendship from the other members. <br />
<br />
I joined this competition not only for learning more about biochemistry, but also the essential lab skills that i need for my studies. Through these months conducting experiments in the lab and holding numerous meetings late, i am very surprised i have survived from all these. <br />
<br />
Especially when some of the members went home and there were only few people here in hong kong, we have encountered a very great crisis in human resources. Yet, with all our keen devotion, we have resolved and learnt from problems to problems. I love the days being in the team and the days spent with my teammates, making fun of each other, hard working together without sleeping. Now i just wanna finish our current and can't wait to see us beating up the other teams at MIT (if we were able = =). <br />
<br />
To be honest, actually i never emphasized i am the leader of the compeition. As i am a person who don;t want to make the other people shoulder a lot of pressure and i don't want think i am the person with good leading skills. <br />
<br />
I just think of myself being a normal member and try to do my best. I know i am not a good leader at all but anyway i feel very grateful for those who gave me support and forgave my wrongdoings during the hard times. <br />
I know i have said a chunk of stuff and i know it is clumsy. The last thing i wanna say is that i am very proud that i have spent time with my friends pursuing a dream during my most busy summer, pursuing a goal that to undergraduate students seems so far away and demanding yet it is the sweetest ,remarkable and memorable dream i have ever had in my life time. <br />
<br />
I just love you all!<br />
<br />
===YIP Ka Ho Raymond===<br />
[[Image:HKU-HKBU_Raymond_120_150.jpg | left]]<br />
<br />
2nd Year biochemistry and microbiology student. Was studying in UK for several years before coming back to the homeland and join the big HKU family. After spending a year doing nothing, skipping lectures (switched onto the “sleep” mood even do appear) and resting, I finally picked myself up to get some work done by registering to the iGEM team. Being the one who is responsible for the BIG fund-raising job, human practices activities and others wet lab experiments for our team. I must say that was the busiest summer I have ever had but also the one which I truly enjoyed. <br />
<br />
It was an honor for me to work with many hilarious, “hard-working” fellow geniuses. Especially those weekly meetings that end at mid-night, meals time which we make fun out of each other and when the swine flu suddenly hit our lab. Many and many more memorable moments that we shared together throughout the past few months were totally awesome and enjoyable. Hope we shall get some good results this year and ROCK THEM!<br />
<br />
===ZHANG Yi Nan===<br />
[[Image:HKU-HKBU_ZhangYiNan_120_150.JPG | right]]<br />
<br />
I am a second-year undergraduate at the University of Hong Kong majoring in bioinformatics, which is really a combination of two majors - in biochemistry and computer science. Being one of the earliest members of our team, I was responsible for writing and presenting our project proposal at the beginning, some wet lab experiments in the middle, and at last, perhaps the one I enjoyed most, our wiki's build-up work. Specifically, I converted our first two framework designs into code, though not the final one. It seemed to be quite a hard job for me at first since I started out as a complete newbie, even without knowing any HTML tags but only some <code>if</code> and <code>while</code> statements in programming languages such as C. However, driven by a burning curiosity in the field of web coding, I decided to give it a try and studied some HTML, CSS, and JavaScript online tutorials myself, and then embarked on an exciting journey of constructing my very first website. And I found it never less amazing than working with those traditional programming languages!<br />
<br />
Besides coding, I also enjoyed undergoing the entire process of a scientific project as well as learning a bunch of basic wet lab techniques. And yet the thing I treasure most is the friendship with other team mates I have harvested. It has been a really nice experience to work with people with different backgrounds and distinct characters, from both HKU and HKBU. We had such a great time together in the past couple of months. We strived together, laughed together, and faced challenges together. I will never forget the time we spent together.<br />
<br />
===ZHONG Xing Xin Nova===<br />
[[Image:HKU-HKBU_Nova_120_150.png | left]]<br />
<br />
I am a year 2 student from the Department of Mathematics of the University of Hong Kong. I joined the iGEM team of HKU-BU at the beginning of this summer, and feel great honored to join in the jamboree representing HKU. As a mathematics students, I have never entered a Biochemistry lab before but the experience this time has enlighten me a lot. Actually, iGEM is the first time for me to touch the concept of synthetic biology. <br />
<br />
Working together with the whole team, under the guidance of instructors, I am able to see my progress day after day. Those creative ideas in the brainstorm, rigorous spirit of setting controlling, and the ingenious designing of experiment have impressed me and changed my mind significantly. <br />
<br />
During the summer, I mainly worked on controlling the speed of our bacteria-motor, and on measuring the expressing level related to a concentration gradient of the IPTG inducer, by the method of Western Blotting. Besides, I have tried on knocking out cheZ fragment of E.coli 2443 and spent some time in making bio-brick. <br />
<br />
Generally, I have learned a lot in the iGEM and really enjoyed the project.<br />
<br />
=Student Helper=<br />
<br />
===XUE Yuan Soso===<br />
[[Image:HKU-HKBU_Soso_120_150.png | right]]<br />
<br />
Yuan Xue is a senior high school student (graduating in 2010) currently pursuing study in La Salle Catholic College Preparatory located in Portland, Oregon. He developed an interest in the field of biology and chemistry after studying the corresponding courses at high school that soon attracted him to iGEM. After approximately two weeks of volunteering in a former iGEM project of iHKU team over the summer of 2008, he had an honor to pledge to working with university students as a HKU-HKBU team member this year in 2009. This precious opportunity gave him an insight into the application of principles of synthetic biology to contributing human welfare; furthermore, it inspired him to pursue further studies in the corresponding field of study as he found it to be intellectually provocative and intriguing. <br />
<br />
He was assigned as a wet lab researcher tasked with activating the polar expression on Escherichia coli 2443 OMPT. His primary approach to tackling this task was transforming plasmids into 2443 OMPT. He learned a tremendous amounts of knowledge on regards to research techniques, data analysis, setting for experiments, and the mindset of research – to be both innovative and steadfast.<br />
<br />
=Instructors (in alphabetical order)=<br />
[http://www.hku.hk/biochem/research/jdhuang/pi_jdhuang.html Dr. HUANG Jiang Dong]<br />
<br />
[http://www.hku.hk/biochem/research/yqsong/pi_yqsong.html Dr. SONG You Qiang]<br />
<br />
[http://physics.hkbu.edu.hk/home/lhtang.html Professor TANG Lei Han]<br />
<br />
[http://www.hku.hk/biochem/research/jjwang/pi_jjwang.html Dr. WANG Jun Wen John]<br />
<br />
=Advisors (in alphabetical order)=<br />
FU Xiong Fei<br />
<br />
LI Xue Fei<br />
<br />
LIU Chen Li<br />
<br />
SHI Lei<br />
<br />
XIANG Lu<br />
<br />
YU Bin<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/ModelingTeam:HKU-HKBU/Modeling2009-10-20T17:01:25Z<p>Utopian: /* Modeling */</p>
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{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
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=Modeling=<br />
Theoretical analysis of the process gives us a quantitative insight into the process. We consider a motor having a simplest shape, i.e. a single lamina with a vertical axis in the middle.<br />
<br />
[[Image:HKU-HKBU_modeling_figure | center]]<br />
<br />
==Assumptions==<br />
An analytical solution can be derived on the basis of the following assumptions:<br />
# power of a bacteria is kept a constant;<br />
# friction coefficient of a small object undergoing slow motion is proportional to the cross sectional area;<br />
<br />
Let us take a look at the validity of the above assumptions.<br />
<br />
A bacterium can be thought of as a truck travelling along an expressway. If it is free of loading and the power is kept constant, the truck will experiences relatively small frictional force and will be moving at a relatively high speed. On the other hand, if the truck is loaded with heavy weights, the frictional force will increase significantly. As a result, the truck will have a much lower maximum speed. However, in both situations, the power of the truck remains the same because of the property of the engine. Same thing happens for bacteria. The power supplied by the motor of the flagella is kept a constant, regardless of the “working condition”, namely whether pushing a motor or not. Thus, the first assumption seems to be reasonable. <br />
<br />
The second assumption is taken from the fluid-dynamics, saying that friction is proportional to the cross sectional area for small objects with slow motion. The motor and the bacteria have a size of [[Image:HKU-HKBU_modeling_f1.png]] and [[Image:HKU-HKBU_modeling_f2.png]] respectively, both falling into the region of “small objects”. The low speed of a bacteria, [[Image:HKU-HKBU_modeling_f3.png]], also fits into the “slow motion” condition. Therefore, the 2nd assumption is believed to be suitable in our case.<br />
<br />
==Calculation of Rotational Velocity==<br />
<br />
We start out by calculating the power of a single bacterium first. Under freely swimming condition, a bacterium can move at a maximum speed of [[Image:HKU-HKBU_modeling_f4.png]] ([[Image:HKU-HKBU_modeling_f5.png]]). If the friction coefficient is [[Image:HKU-HKBU_modeling_f6.png]], then the friction is given by<br />
<br />
[[Image:HKU-HKBU_modeling_f7.png]].<br />
<br />
Here, [[Image:HKU-HKBU_modeling_f8.png]] is a function of expression level of CheZ: if CheZ is fully expressed, the bacteria speed should be maximized, correspondingly[[Image:HKU-HKBU_modeling_f9.png]]. On the other hand, if CheZ is completely knocked out, bacteria should lose the swimming ability. Thus, [[Image:HKU-HKBU_modeling_f10.png]] corresponds to this case.<br />
<br />
Hence, the power is <br />
<br />
[[Image:HKU-HKBU_modeling_f11.png]].<br />
<br />
Next, we estimate the power consumed by the motor, rotating at an angular velocity [[Image:HKU-HKBU_modeling_f12.png]], due to friction. Consider a small element on the motor from r to r+dr, namely the red part in Fig 2. Let [[Image:HKU-HKBU_modeling_f13.png]] be the friction coefficient of the motor. Hence, from the 2nd assumption, the friction coefficient for the small element is [[Image:HKU-HKBU_modeling_f14.png]], l here is the width of the motor. Thus, the friction force on this element, proportional to its velocity [[Image:HKU-HKBU_modeling_f15.png]], is <br />
<br />
[[Image:HKU-HKBU_modeling_f16.png]]<br />
<br />
Power consumed by this element is<br />
<br />
[[Image:HKU-HKBU_modeling_f17.png]]<br />
<br />
The total power consumed on the motor is then the sum, or integration in other words, of all the [[Image:HKU-HKBU_modeling_f18.png]],<br />
<br />
[[Image:HKU-HKBU_modeling_f19.png]]<br />
<br />
The power supplied by the bacteria is completely consumed by the motor frictional force. With the conservation of energy, we have<br />
<br />
[[Image:HKU-HKBU_modeling_f20.png]]<br />
<br />
Here, h is the height of the motor along the axis direction and n is the number of bacteria per unit area on the motor.<br />
<br />
==Resutls and Discussion==<br />
According to assumption 2, we can further reduce the above equation. Let [[Image:HKU-HKBU_modeling_f21.png]],<br />
[[Image:HKU-HKBU_modeling_f22.png]],<br />
<br />
C and [[Image:HKU-HKBU_modeling_f23.png]] are the friction coefficient per unit area of bacteria and motor respectively. a is the cross section area of a bacteria. Substitute them into the above equation gives<br />
<br />
[[Image:HKU-HKBU_modeling_f24.png]]<br />
<br />
[[Image:HKU-HKBU_modeling_f25.png]] here, is just a constant of order [[Image:HKU-HKBU_modeling_f26.png]]. <br />
<br />
The model predicts the followings:<br />
<br />
# Angular velocity is independent of height h of the motor;<br />
# Angular velocity is linearly proportional to the width l of motor and the velocity of bacteria. As a consequence, the expression level of CheZ monotonically affects the rotational velocity. In other words, higher expression level of CheZ results in faster rotation.<br />
<br />
This model is only applicable for small objects. So, despite independence of h, the height of the motor still can’t be too large. In other words, it should be confined within [[Image:HKU-HKBU_modeling_f27.png]]. What’s more, even the rotational velocity is inversely proportional to l, the length of the motor can’t be too small because narrow motor would result in too few bacteria attached, which leads to too much noise and fails to fit into this model. To be more precious, a suggested length of motor should be of the order of [[Image:HKU-HKBU_modeling_f28.png]]. Thus, with a motor having a width of [[Image:HKU-HKBU_modeling_f29.png]], the angular velocity will be about [[Image:HKU-HKBU_modeling_f30.png]].<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:52:42Z<p>Utopian: /* Design */</p>
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{{Team:HKU-HKBU/script.js}}<br />
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=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of CheZ gene. The gene of CheZ plays the key role here as it controls the phosphorylation level of CheY. CheZ protein can dephophorylate CheY. High levels of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to tumbling movement while low levels of phosphorylation switch the flagella to its non-tumbling mode and enable the bacteria to swim. Therefore, an increase in the expression level of CheZ gene allows us to reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is applied to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is substituted by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which tetracycline(or aTc)-inducible. We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:45:43Z<p>Utopian: /* Step 3: Dry Etch */</p>
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{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# In this project, we use chemically reactive gases to consume silicon.<br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:45:02Z<p>Utopian: /* Step 3: Dry Etch */</p>
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<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
<br />
3. In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:44:40Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
3. In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:44:22Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
3. In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:44:10Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
3. In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:43:47Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>* Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>* Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>* Combination of both physical and chemical removal method</nowiki><br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:43:16Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>(1) Chemical reactions using chemically reactive gases or plasma to consume the material </nowiki> <br />
<nowiki>(2) Physical removal of the material, usually by momentum transfer </nowiki> <br />
<nowiki>(3) Combination of both physical and chemical removal method</nowiki><br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:41:22Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices:<br />
<nowiki>Insert non-formatted text here</nowiki>(1) Chemical reactions using chemically reactive gases or plasma to consume the material <br />
<nowiki>Insert non-formatted text here</nowiki>(2) Physical removal of the material, usually by momentum transfer <br />
<nowiki>Insert non-formatted text here</nowiki>(3) Combination of both physical and chemical removal method<br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:40:16Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices: <br />
(1) Chemical reactions using chemically reactive gases or plasma to consume the material<br />
(2) Physical removal of the material, usually by momentum transfer<br />
(3) Combination of both physical and chemical removal method<br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:39:53Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices: <br />
1) Chemical reactions using chemically reactive gases or plasma to consume the material<br />
2) Physical removal of the material, usually by momentum transfer<br />
3) Combination of both physical and chemical removal method<br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:39:15Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following choices: <br />
1) Chemical reactions using chemically reactive gases or plasma to consume the material<br />
2) Physical removal of the material, usually by momentum transfer<br />
3) Combination of both physical and chemical removal method<br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:36:36Z<p>Utopian: /* Step 7: Photoresist Removal (Stripping) */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following methods: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to eliminate photoresist(SU-8) .<br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, but it cannot react with silver (Ag). We thus coat one side of the motor with silver and leave the other side uncoated. At the same time, the substrate SiO2 has also been removed.<br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:31:55Z<p>Utopian: /* Step 8: Biotin Binding */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following methods: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to remove the photoresist and any of its residues. <br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, while, it cannot react with silver (Ag). Thus, we get the motor with one side coated with Ag, while the other side is not. At the same time, the substrate SiO2 has also been removed, only remaining the motors. <br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
Our final design is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The force exerted by bacteria on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3.The smaller size allows a larger angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:28:03Z<p>Utopian: /* Step 3: Dry Etch */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer.Only volatile byproducts are generated in the process. <br />
# Dry etching may be accomplished by any of the following methods: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume silicon.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to remove the photoresist and any of its residues. <br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, while, it cannot react with silver (Ag). Thus, we get the motor with one side coated with Ag, while the other side is not. At the same time, the substrate SiO2 has also been removed, only remaining the motors. <br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
<br />
In this project, we are going to use the final design which is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The Force that the bacteria act on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3. The smaller size can offer a fast angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:26:49Z<p>Utopian: /* Step 2: Alignment and Exposure */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Remarks:<br />
# For simple contact, proximity, and projection systems, the mask is the same in size and scale as those of the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Adjusting to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source.<br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer, generating only volatile byproducts in the process. <br />
# Dry etching may be accomplished by any of the following: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume Si.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to remove the photoresist and any of its residues. <br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, while, it cannot react with silver (Ag). Thus, we get the motor with one side coated with Ag, while the other side is not. At the same time, the substrate SiO2 has also been removed, only remaining the motors. <br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
<br />
In this project, we are going to use the final design which is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The Force that the bacteria act on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3. The smaller size can offer a fast angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:24:43Z<p>Utopian: /* Step 1--CheZ knockout */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of cheZ gene. The gene of cheZ plays the key role here as it controls the phosphorylation level of cheY as cheZ protein can dephophorylate cheY. High levels of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to tumbling movement while low levels of phosphorylation switch the flagella to its non-tumbling mode and enable the bacteria to swim. Therefore, an increase in the expression level of CheZ gene allows us to reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is applied to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is substituted by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:24:29Z<p>Utopian: /* Step 1--CheZ knockout */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of cheZ gene. The gene of cheZ plays the key role here as it controls the phosphorylation level of cheY as cheZ protein can dephophorylate cheY. High levels of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to tumbling movement while low levels of phosphorylation switch the flagella to its non-tumbling mode and enable the bacteria to swim. Therefore, an increase in the expression level of CheZ gene allows us to reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is substituted by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:22:55Z<p>Utopian: /* Design */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of cheZ gene. The gene of cheZ plays the key role here as it controls the phosphorylation level of cheY as cheZ protein can dephophorylate cheY. High levels of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to tumbling movement while low levels of phosphorylation switch the flagella to its non-tumbling mode and enable the bacteria to swim. Therefore, an increase in the expression level of CheZ gene allows us to reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T16:16:23Z<p>Utopian: /* Step 1: Photoresist (SU-8) Spin Coating */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Remarks: <br />
# Typical contaminants must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist-coating. <br />
# Ideally, no water is allowed on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum. Resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm.<br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Note:<br />
# For simple contact, proximity, and projection systems, the mask is the same size and scale as the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Going to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source. <br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer, generating only volatile byproducts in the process. <br />
# Dry etching may be accomplished by any of the following: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume Si.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to remove the photoresist and any of its residues. <br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, while, it cannot react with silver (Ag). Thus, we get the motor with one side coated with Ag, while the other side is not. At the same time, the substrate SiO2 has also been removed, only remaining the motors. <br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
<br />
In this project, we are going to use the final design which is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The Force that the bacteria act on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3. The smaller size can offer a fast angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:13:42Z<p>Utopian: /* Design */</p>
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=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the collaborative change in the swimming behavior of a population of bacteria that are attached onto the silicon nano-scale motor via biotin-streptavidin interaction. The aim is achieved by regulation of the expression level of cheZ gene. The gene of cheZ plays the key role here as it influences the expression level of cheY. A high level phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to the majority of bacteria tumbling movement, while a low level of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' is found in non-tumbling bacteria and cheZ can dephophorylate cheY. Therefore, when increasing the expression level of CheZ gene, we can reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve the manipulation of speed.<br />
<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T16:10:53Z<p>Utopian: /* Design */</p>
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=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations. But the capacity of tweaking the swimming speed greatly promotes its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded Bactomotor to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor in time to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
To control the speed of our Bactomotor, we aim at the direct swimming of bacteria for propelling the motor and the adjustable speed of swimming within a certain range. The aim is achieved by regulation of the expression level of cheZ gene. The gene of cheZ plays the key role here as it influences the expression level of cheY. A high level phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to the majority of bacteria tumbling movement, while a low level of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' is found in non-tumbling bacteria and cheZ can dephophorylate cheY. Therefore, when increasing the expression level of CheZ gene, we can reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve the manipulation of speed.<br />
<br />
Speed control is not achieved by a single bacterium; On the contrary, it is the result of the change of behavior <br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/AssemblyTeam:HKU-HKBU/Assembly2009-10-20T16:00:52Z<p>Utopian: /* Assembly of BactoMotor */</p>
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='''Assembly of BactoMotor'''=<br />
<br />
<br />
==Introduction==<br />
Our BactoMotor is comprised of three parts – the Micro-Motor; the Directional Controller and the Speed Controller.<br />
<br />
As their names indicate, the Micro-Motor is the core part of the Motor, and it is small (micrometer scale). The Directional Controller ensures directional propelling force generated by the bacteria, and therefore directional rotation of the motor. The Speed Controller is used to implement a speed control over the motor.<br />
<br />
Each module is designed, engineered and tested seperately, and are functional on their own. After testing and fine-tuning, the parts are brought together to form the final BactoMotor. After final assembly, we would have a micrometer-scale BactoMotor which has unidirectional rotation and speed adjustment controls.<br />
<br />
==Prodecures==<br />
<br />
==='''Step 1. Installation of Micro-Motor'''===<br />
The Micro-Motor will be installed into a microchip container (Fig.1a, 1b) with separated chambers. Only one side of the arms of the motor is coated with Biotin (for the Directional Controller Module).[[Image:HKU-HKBU_ass_f1a_s2.png|frame|center|600px|'''Fig.1a:''' Photos of the microchips for micro-motor installation; '''A:''' A photo showing the chambers and the valve systems; '''B:''' Valve 3 closed; '''C:''' Valves 4, 5, 6 and 7 are closed while water is injected into the channel; '''D:''' Valve 1 and 7 closed, enclosing the crystal violet solution in the lower 4 chambers; '''E:''' The photo of the chamber system]][[Image:HKU-HKBU ass f1b.PNG|thumb|300px|center|'''Fig.1b:''' A diagram showing the Micro-Motor Module installed into a chamber inside the microchip.]]<br />
<br />
==='''Step 2. Introduction of Bacteria'''===<br />
The Bacteria with both Directional Controller and Speed Controller Modules implemented will be introduced to the Micro-Motor (Fig.2). [[Image:HKU-HKBU ass f2.PNG|thumb|300px|center|'''Fig.2:''' Introduction of Bacteria into the Micro-Motor]]<br />
<br />
==='''Step 3. Action of Directional Controller'''===<br />
Under the effect of the Directional Controller, the Bacteria will bind onto the Micro-Motor directionally. (Fig.3a, 3b)[[Image:HKU-HKBU ass f3a.PNG|thumb|300px|center|'''Fig.3a:''' The bacteria bounded to the Micro-Motor through action of the Directional Controller Module (Plan View)]][[Image:HKU-HKBU ass f3b.PNG|thumb|300px|center|'''Fig.3b:''' A zoomed view of the Directional Controller Module at work.]]<br />
<br />
==='''Step 4. Removing Excessive Bacteria'''===<br />
The extra bacterial cells will be removed by medium flush. (Fig. 4)[[Image:HKU-HKBU ass f3s.PNG|thumb|300px|center|'''Fig.4:''' Bacteria not binding to the Micro-Motor will be flushed away by medium flush.]]<br />
<br />
==='''Step 5. BactoMotor in Action'''===<br />
As the Bacteria swims, they will push the motor into rotation. (clockwise as demonstrated in Fig. 5a, 5b)[[Image:HKU-HKBU ass f4a.PNG|thumb|300px|center|'''Fig.5a:''' The Directional Rotation of the Micro-Motor achieved by the Directional Controller Module]][[Image:HKU-HKBU ass f4b.gif|thumb|300px|center|'''Fig.5b:''' An animation showing the BactoMotor in action.]]<br />
<br />
==='''Step 6. Using the Speed Controller'''===<br />
To utilize the Speed Controller Module, an inducer is added to the Microchip containing the Micro-Motor. Increase in concentration of the inducer will lead to an overall increase in rotational speed of the Bacto-Motor. (Fig. 6a, 6b)[[Image:HKU-HKBU ass f5a.gif|thumb|300px|center|'''Fig.6a:''' On additional of 0.5 effective dose of inducer]][[Image:HKU-HKBU ass f5b.gif|thumb|300px|center|'''Fig.6b:''' On additional of 1.0 effective dose of inducer]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_DesignTeam:HKU-HKBU/Motor Design2009-10-20T15:57:10Z<p>Utopian: /* Silicon Version */</p>
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==Silicon Version==<br />
<br />
For Version 1, the size of motor is somewhat larger than we have expected. The size of an E. coli is about 0.8μm and consequently the motor should have a size of approximately 50μm in order to match with the bacteria in dimentions. However, the precision of Leica-crytomicrotome is around 50μm, which is just the size of motor. We need to search for more sophiscated methods to produce motor. <br />
<br />
We decide to choose silicon as the material for motor. The micro-fabrication means of photolithography [Link 2] is used to create the motor. The precision of photolithography is 2μm, which is adequate to serve our purpose. The main steps of motor production are listed as follows:<br />
<br />
===Step 1: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_1.png | centre|thumb|300px]]<br />
Note: <br />
# Typical contaminants that must be removed prior to photoresist (SU-8) coating. <br />
# Adhesion promoters are used to assist resist coating. <br />
# Ideally want no H2O on wafer surface. <br />
# Wafer is held on a spinner chuck by vacuum and resist is coated to uniform thickness by spin coating.<br />
# Resist thickness is 1-2 mm. <br />
<br />
===Step 2: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_2.png | centre |thumb| 300px]]<br />
Note:<br />
# For simple contact, proximity, and projection systems, the mask is the same size and scale as the printed wafer pattern.<br />
# Projection systems give the ability to change the reproduction ratio. Going to 10:1 reduction allows larger size patterns on the mask, which is more robust to mask defects. <br />
# Normally requires at least two alignment mark sets on opposite sides of wafer or stepped region.<br />
# We use "deep ultraviolet", which is produced by excimer lasers, as light source. <br />
<br />
===Step 3: Dry Etch===<br />
<br />
[[Image:HKU-HKBU_motor_production_3.png | centre |thumb| 300px]]<br />
Note:<br />
# Dry Etching is an etching process that does not utilize any liquid chemicals or etchants to remove materials from the wafer, generating only volatile byproducts in the process. <br />
# Dry etching may be accomplished by any of the following: 1) through chemical reactions that consume the material, using chemically reactive gases or plasma; 2) physical removal of the material, usually by momentum transfer; or 3) a combination of both physical removal and chemical reactions. <br />
# In this project, we use chemically reactive gases to consume Si.<br />
<br />
===Step 4: Photoresist (SU-8) Spin Coating===<br />
<br />
[[Image:HKU-HKBU_motor_production_4.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 1. <br />
<br />
===Step 5: Alignment and Exposure===<br />
<br />
[[Image:HKU-HKBU_motor_production_mask.png | centre |thumb| 300px]]<br />
[[Image:HKU-HKBU_motor_production_5.png | centre |thumb| 300px]]<br />
Note: <br />
Please refer to Step 2.<br />
<br />
===Step 6: Silver Plating===<br />
<br />
[[Image:HKU-HKBU_motor_production_6.png | centre |thumb| 300px]]<br />
Note:<br />
A silver coating is plated onto the “primary motor”, which is around 50μm thick.<br />
<br />
===Step 7: Photoresist Removal (Stripping)===<br />
<br />
[[Image:HKU-HKBU_motor_production_7.png | centre |thumb| 300px]]<br />
Note:<br />
# The aim is to remove the photoresist and any of its residues. <br />
# We use hydrofluoric acid to remove the photoresist (SU-8). While it is extremely corrosive and difficult to handle, it is technically a weak acid. It can react with SiO2 and SU-8 and dissolve them, while, it cannot react with silver (Ag). Thus, we get the motor with one side coated with Ag, while the other side is not. At the same time, the substrate SiO2 has also been removed, only remaining the motors. <br />
<br />
===Step 8: Biotin Binding===<br />
<br />
Biotin can only bind on the silver (Ag) side, while the other side (Si) will have no biotin. <br />
<br />
Previously, we have designed four kinds of motor with different shapes, which are shown in the figure below. The red lines in the figure represent the biotin binding sides.<br />
<br />
[[Image:HKU-HKBU_motor_production_8.png | centre |thumb| 300px]]<br />
<br />
In this project, we are going to use the final design which is shown below. The red lines in the figure represent the biotin binding sides. <br />
<br />
[[Image:HKU-HKBU_motor_production_9.png | centre |thumb| 300px]]<br />
<br />
The Force that the bacteria act on the motor is proportional to R. The rotational motility of the motor is proportional to 1/R3. The smaller size can offer a fast angular speed.<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/PartsTeam:HKU-HKBU/Parts2009-10-20T15:48:10Z<p>Utopian: /* Parts submitted to the registry */</p>
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=Parts submitted to the registry=<br />
<br />
We have submitted to the Registry Biobricks with code number from K283000 to K28300. Please click [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=HKU-HKBU here] to have a look. <br />
<br />
BBa_K283000 and BBa_K283002 are genetic circuits for polar expression and speed control. <br />
<br />
===Assembly method of BBa_K283002:===<br />
<br />
[[Image:Assembly of BBa K283002.jpg|center|caption]]<br />
<br />
<br />
===Assembly method of BBa_K283000:===<br />
<br />
[[Image:K283000.jpg|center|caption]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/PartsTeam:HKU-HKBU/Parts2009-10-20T15:47:58Z<p>Utopian: /* Parts submitted to the registry */</p>
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=Parts submitted to the registry=<br />
<br />
We have submitted to the Registry Biobricks with code number from K283000 to K28300. Please click [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=HKU-HKBU here]. to have a look. <br />
<br />
BBa_K283000 and BBa_K283002 are genetic circuits for polar expression and speed control. <br />
<br />
===Assembly method of BBa_K283002:===<br />
<br />
[[Image:Assembly of BBa K283002.jpg|center|caption]]<br />
<br />
<br />
===Assembly method of BBa_K283000:===<br />
<br />
[[Image:K283000.jpg|center|caption]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/PartsTeam:HKU-HKBU/Parts2009-10-20T15:47:08Z<p>Utopian: /* Parts submitted to the registry */</p>
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=Parts submitted to the registry=<br />
<br />
We have submitted to the Registry Biobricks with code number from K283000 to K28300. Please check the following link. [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=HKU-HKBU here].<br />
<br />
BBa_K283000 and BBa_K283002 are genetic circuits for polar expression and speed control. <br />
<br />
===Assembly method of BBa_K283002:===<br />
<br />
[[Image:Assembly of BBa K283002.jpg|center|caption]]<br />
<br />
<br />
===Assembly method of BBa_K283000:===<br />
<br />
[[Image:K283000.jpg|center|caption]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/TeamTeam:HKU-HKBU/Team2009-10-20T15:43:17Z<p>Utopian: /* FU Zhong Zheng Brooks */</p>
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__NOTOC__<br />
=Student Members (in alphabetical order)=<br />
<br />
===CHU Tsz Long Nelson===<br />
[[Image:HKU-HKBU_Nelson_120_150.jpg | right]]<br />
<br />
I am entering my second year of biochemistry at HKU and i have a special interest in bio-gerontology. I join the igem2009 because i want to understand more about synthetic biology and to get some practical research experience. In my spare time i enjoy table tennis, archery and chess games. I hope to pursue my PhD program in the US after i graduate.<br />
<br />
In this competition, I am responsible for biobrick construction and speed control. I learnt a lot of useful skills and hand-on experience of practical research. Though there were many failures, i managed to provide some possible explanations for the failures and discuss it with other teamates. I found myself addicted to scientific research after this competition. I hope I can be a successful scientist and contribute a lot to mankind in the future.<br />
<br />
===FU Zhong Zheng Brooks===<br />
[[Image:HKU-HKBU_Brooks_120_150.JPG | left]]<br />
<br />
Brooks Fu Zhongzheng is a second year undergraduate student studying at the University of Hong Kong. Aspiring to be a successful researcher, he decided to choose biochemistry and physics as majors to train himself in reasoning skills and the ability of gleaning useful information from books as heavy as two bags of potatoes. He personally thinks knowledge of physics is indispensable for him to make sense of the abstruseness and intricacy of life. It is quite challenging to deal with these two majors that require different thinking patterns and learning methods, but his brain manages to develop an ability of quickly switching between 'biology mode' and 'physics mode'. He really enjoys himself when learning and attains satisfactory academic results. In the spare time, he usually plays the piano to get relaxed. He is a big fan of Bach and Prokofiev.<br />
<br />
It occurs to him that 'all textbooks no experiments will make Brooks a dull boy'. Only will an opportunity of self-motivated scientific 'DIY' enable him to internalize what he learn from the textbook. When first introduced to the iGEM competition by Dr.Huang, he was totally fascinated by the idea of assembling ‘biological machines’ using standardized biological parts. He thinks it is time to exploit the intricate principles discovered by so many talented scientists after centuries of dutiful research to engineer man-made organisms that can ‘change the world’ and help people. He was thus motivated to join the HKU-HKBU team. In the team, he devotes a lot of time to generating ideas,designing the project and manufacturing Biobricks. With enthusiasm and diligence, he succeeded in collaborating with his talented teammates to create a bacteria-powered motor. The argument that our future world will heavily rely on the motors we've built may seem ridiculous to some. It may or may not happen, but who knows? Nothing is impossible. iGEM is for people with imagination.<br />
<br />
iGEM proves to be an invaluable learning experience for him. Thanks to the competition, he not only masters the necessary research skills, but more importantly, the spirit of teamwork and the importance of taking up responsibility.<br />
<br />
===JIANG Qin Qin===<br />
[[Image:HKU-HKBU_QQ_120_150.JPG | right]]<br />
<br />
I’m a second year student studying Biochemistry and Chemistry at the University of Hong Kong. I have a strong interest in doing research and enjoy the process of trying new ideas. On the team I spent most of my time doing wet lab. Although I have been defeated for many trials, once I had positive results, a great sense of accomplishments made all the efforts worthy. Meanwhile, the variable possibilities in experiments display the fascination of synthetic biology. Another great thing is that I have met lots of like-minded friends in this IGEM competition. We exchanged our ideas, experienced failure and success together, which made us like a big family. Outside the lab, I’m an easy-going person with lots of interests. I usually do sports and go travelling in my spare time to relax myself.<br />
<br />
===LI Wei Han James===<br />
[[Image:HKU-HKBU_James_120_150.png | left]]<br />
<br />
My name is Weihan Li, and I am a year 2 undergraduate student from the physics department of Hong Kong Baptist University. I have been an undergraduate research assistant, under the supervision of Prof Leihan Tang, in Condenced Matter Theory and Biophysics Lab for over 1 year and a half. My research mainly aimed at quantatively understanding biological processes, especially metabolism. Attending different conferences and symposiums on synthetic biology, system biology and physics also opened my eyes. I also had the honor to give a 20-minute academic repeort, titled Biological Network Analysis: on oscillation and synchronization, on the International Conference on Complexity and Disciplinary Sciences, which is an encouragement and also a good start for me. In this iGEM project, we worked as a team to realize our dreams to engineer something we always long for with the help of bacteria. I am glad to be a part of the team where I gained not only the knowledge and the valuable wet lab experience, but also the precious friendship. I believe this iGEM project will be a great treasure through out my life!<br />
<br />
===LI Yan Lin Jubi===<br />
[[Image:HKU-HKBU_Jubi_120_150.JPG | right]]<br />
<br />
hailing from Hong Kong, is a second-year undergraduate reading medicine and surgery. He joined the iGEM team primarily because he sees synthetic biology as a powerful tool for inventing novel therapeutic strategies.<br />
<br />
He has thus far taken up three roles in the competition: firstly as fund-raising manager, then as group leader of the Che-Z knockout (2443ompT) team, and now as leader of the Human Practices Advance team. Moreover, as one of the only two clinicians around (alas!), he is also responsible for imagining – and developing – the potential clinical applications of the Bacto-Motor.<br />
<br />
Outside medicine, his other academic interests include philosophy, politics and economics and he has represented both Hong Kong and HKU at international debating competitions, advancing to the Octo-Finals of the Worlds Schools Washington DC in 2008. He is also editor-in-chief of Caduceus, the official journal of the Undergraduate Medical Society. While not preoccupied by other tasks, he enjoys classical music, jogging, table tennis and banter – where everybody gets a good laugh :)<br />
<br />
===SHENG Zi Wei Amy===<br />
[[Image:HKU-HKBU_Amy_120_150.JPG | left]]<br />
<br />
I am senior biology student of Hong Kong Baptist University. Mainly working on wet lab, I, together with teammates, take responsibility of measuring the swimming speed and categorizing the trait of polar expression after bacteria being modified. When James, one of our members, introduced me to this group, I had zero knowledge of what synthetic biology means or what we suppose to do. However, had gone through papers and handled wet lab work, I have started to understand the significance of this subject and its bright future and moreover exhibit great interest to it. I attained from this experience not only practical laboratory skills and knowledge of synthetic biology but also friendship and teamwork spirit. Other interests of mine include traveling, reading, growing vegetables and eating them.<br />
<br />
===SIN Sheung Man Alexander===<br />
[[Image:HKU-HKBU_Alex_120_150.jpg | right]]<br />
<br />
When I first heard about iGEM and the idea of synthetic biology, it really caught my interest. This is a chance where I can combine other’s work and findings and make the best out of them. This is what I have learnt recently from object-orientated programming – breaking ideas down into objects, manipulating and assembling them into one working machine.<br />
<br />
Being in the second year of the Bioinformatics Programme, I am in the middle of learning how the knowledge of computer science can be applied on biochemistry. By participating in the iGEM competition, one would be able to gain hands-on experience on what biochemistry research is like, how the knowledge learnt from lectures can be applied to practical laboratory work, and the wisdom to work as a team – sharing results, joys as well as deadlines and pressure. I am glad and honoured to be a part of the team HKU-HKBU, and it is a wonderful opportunity to be able to work with students from another university in Hong Kong.<br />
<br />
===TSE Kwong To Paul===<br />
[[Image:HKU-HKBU_Paul_120_150.jpg | left]]<br />
<br />
I'm a second year student studying Chemistry at the University of Hong Kong. It is my first time to take part in an international competition about synthetic biology. After acquiring information from my other iGEM members, my strong interest drives me to participate into iGEM in summer. At the very beginning, I think this is just another means to kill my time in summer. However, after attending several meeting and assisting others to do different kinds of laboratory work, I find myself immersed in this competition. Some of the laboratory work like western blotting, PCR, electrophoresis and the like are very new to me and I never come across this stuff from Chemistry laboratory. Though repeated failure in the genes knockout, I never felt frustrated since I could learn new things from each failed experiment. Indeed, with the help of other iGEM members and supervisors, I acquire tremendous knowledge about the synthetic biology as well as biochemistry in this competition. My part of work in this iGEM competition is mainly dry lab, which include wikis work, human practice, some search for experiment stuff. Hoping our effort in this competition can pay off and earn the glory and reputation of HKU and HKBU.<br />
<br />
===WEI Ling===<br />
[[Image:HKU-HKBU_WEI_Ling_120_150.jpg | right]]<br />
<br />
Hi, I’m WEI Ling, a student member of iGEM09 HKU-HKBU team. I come from Department of Physics, Hong Kong Baptist University, majoring in biophysics. I graduated from Beijing Normal University this summer. As a physics student, biology is totally new for me. Frankly speaking, it is the first time that I hear so many biology terminologies and deal with some simple manipulations. Fortunately, with the help of friendly and amusing team members, I have learnt a lot in the lab. <br />
<br />
Thanks to all the pretty girls and handsome boys in our team. They bring so much fun during the little bit boring lab life. No matter what the final result of this competition is, I enjoy the course and cherish our friendship. I have to say that I LOVE YOU ALL!!!<br />
<br />
Oh, by the way, although I’m interested in many things, songs of Westlife, movies of Leung Chiuwai, and also show of Lakers are my most favorite. If you are also their fans, please share your feelings and opinions with me. Thank you!<br />
<br />
===WONG Chi Kin Felix===<br />
[[Image:HKU-HKBU_Felix_120_150.jpg | left]]<br />
<br />
I am an MBBS student with immense interest in research. By research I would like to find solutions for healthcare and make the world better. Seems my aspiration is a bit far away from the contents of our project? In fact, I am still trying to learn experimental technique. I believe doing any kinds of biological experiment can enrich my understanding in research routines and insights. Meanwhile, I am responsible for the Human Practices Project. By letting people know about synthetic biology, they understand how it can contribute to the advancement of quality of life.<br />
<br />
I was a late comer in this team, since I joined in September. In these two months, I have become good friends with all my teammates. May I grasp this opportunity to say thank you to all of them.<br />
<br />
===WONG Ho Yin Bosco===<br />
[[Image:HKU-HKBU_Bosco_120_150.jpg | right]]<br />
<br />
Hi, my name is Bosco and i am a year 2 student at HKU reading biochemistry and chemistry. During these days working as a member in the HKU_HKBU team, i have learnt a lot about synthetic biology and yet made invaluable friendship from the other members. <br />
<br />
I joined this competition not only for learning more about biochemistry, but also the essential lab skills that i need for my studies. Through these months conducting experiments in the lab and holding numerous meetings late, i am very surprised i have survived from all these. <br />
<br />
Especially when some of the members went home and there were only few people here in hong kong, we have encountered a very great crisis in human resources. Yet, with all our keen devotion, we have resolved and learnt from problems to problems. I love the days being in the team and the days spent with my teammates, making fun of each other, hard working together without sleeping. Now i just wanna finish our current and can't wait to see us beating up the other teams at MIT (if we were able = =). <br />
<br />
To be honest, actually i never emphasized i am the leader of the compeition. As i am a person who don;t want to make the other people shoulder a lot of pressure and i don't want think i am the person with good leading skills. <br />
<br />
I just think of myself being a normal member and try to do my best. I know i am not a good leader at all but anyway i feel very grateful for those who gave me support and forgave my wrongdoings during the hard times. <br />
I know i have said a chunk of stuff and i know it is clumsy. The last thing i wanna say is that i am very proud that i have spent time with my friends pursuing a dream during my most busy summer, pursuing a goal that to undergraduate students seems so far away and demanding yet it is the sweetest ,remarkable and memorable dream i have ever had in my life time. <br />
<br />
I just love you all!<br />
<br />
===YIP Ka Ho Raymond===<br />
[[Image:HKU-HKBU_Raymond_120_150.jpg | left]]<br />
<br />
2nd Year biochemistry and microbiology student. Was studying in UK for several years before coming back to the homeland and join the big HKU family. After spending a year doing nothing, skipping lectures (switched onto the “sleep” mood even do appear) and resting, I finally picked myself up to get some work done by registering to the iGEM team. Being the one who is responsible for the BIG fund-raising job, human practices activities and others wet lab experiments for our team. I must say that was the busiest summer I have ever had but also the one which I truly enjoyed. <br />
<br />
It was an honor for me to work with many hilarious, “hard-working” fellow geniuses. Especially those weekly meetings that end at mid-night, meals time which we make fun out of each other and when the swine flu suddenly hit our lab. Many and many more memorable moments that we shared together throughout the past few months were totally awesome and enjoyable. Hope we shall get some good results this year and ROCK THEM!<br />
<br />
===ZHANG Yi Nan===<br />
[[Image:HKU-HKBU_ZhangYiNan_120_150.JPG | right]]<br />
<br />
I am a second-year undergraduate at the University of Hong Kong majoring in bioinformatics, which is really a combination of two majors - in biochemistry and computer science. Being one of the earliest members of our team, I was responsible for writing and presenting our project proposal at the beginning, some wet lab experiments in the middle, and at last, perhaps the one I enjoyed most, our wiki's build-up work. Specifically, I converted our first two framework designs into code, though not the final one. It seemed to be quite a hard job for me at first since I started out as a complete newbie, even without knowing any HTML tags but only some <code>if</code> and <code>while</code> statements in programming languages such as C. However, driven by a burning curiosity in the field of web coding, I decided to give it a try and studied some HTML, CSS, and JavaScript online tutorials myself, and then embarked on an exciting journey of constructing my very first website. And I found it never less amazing than working with those traditional programming languages!<br />
<br />
Besides coding, I also enjoyed undergoing the entire process of a scientific project as well as learning a bunch of basic wet lab techniques. And yet the thing I treasure most is the friendship with other team mates I have harvested. It has been a really nice experience to work with people with different backgrounds and distinct characters, from both HKU and HKBU. We had such a great time together in the past couple of months. We strived together, laughed together, and faced challenges together. I will never forget the time we spent together.<br />
<br />
===ZHONG Xing Xin Nova===<br />
[[Image:HKU-HKBU_Nova_120_150.png | left]]<br />
<br />
I am a year 2 student from the Department of Mathematics of the University of Hong Kong. I joined the iGEM team of HKU-BU at the beginning of this summer, and feel great honored to join in the jamboree representing HKU. As a mathematics students, I have never entered a Biochemistry lab before but the experience this time has enlighten me a lot. Actually, iGEM is the first time for me to touch the concept of synthetic biology. <br />
<br />
Working together with the whole team, under the guidance of instructors, I am able to see my progress day after day. Those creative ideas in the brainstorm, rigorous spirit of setting controlling, and the ingenious designing of experiment have impressed me and changed my mind significantly. <br />
<br />
During the summer, I mainly worked on controlling the speed of our bacteria-motor, and on measuring the expressing level related to a concentration gradient of the IPTG inducer, by the method of Western Blotting. Besides, I have tried on knocking out cheZ fragment of E.coli 2443 and spent some time in making bio-brick. <br />
<br />
Generally, I have learned a lot in the iGEM and really enjoyed the project.<br />
<br />
=Student Helper=<br />
<br />
===XUE Yuan Soso===<br />
[[Image:HKU-HKBU_Soso_120_150.png | right]]<br />
<br />
Yuan Xue is a senior high school student (graduating in 2010) currently pursuing study in La Salle Catholic College Preparatory located in Portland, Oregon. He developed an interest in the field of biology and chemistry after studying the corresponding courses at high school that soon attracted him to iGEM. After approximately two weeks of volunteering in a former iGEM project of iHKU team over the summer of 2008, he had an honor to pledge to working with university students as a HKU-HKBU team member this year in 2009. This precious opportunity gave him an insight into the application of principles of synthetic biology to contributing human welfare; furthermore, it inspired him to pursue further studies in the corresponding field of study as he found it to be intellectually provocative and intriguing. <br />
<br />
He was assigned as a wet lab researcher tasked with activating the polar expression on Escherichia coli 2443 OMPT. His primary approach to tackling this task was transforming plasmids into 2443 OMPT. He learned a tremendous amounts of knowledge on regards to research techniques, data analysis, setting for experiments, and the mindset of research – to be both innovative and steadfast.<br />
<br />
=Instructors (in alphabetical order)=<br />
[http://www.hku.hk/biochem/research/jdhuang/pi_jdhuang.html Dr. HUANG Jiang Dong]<br />
<br />
[http://www.hku.hk/biochem/research/yqsong/pi_yqsong.html Dr. SONG You Qiang]<br />
<br />
[http://physics.hkbu.edu.hk/home/lhtang.html Professor TANG Lei Han]<br />
<br />
[http://www.hku.hk/biochem/research/jjwang/pi_jjwang.html Dr. WANG Jun Wen John]<br />
<br />
=Advisors (in alphabetical order)=<br />
FU Xiong Fei<br />
<br />
LI Xue Fei<br />
<br />
LIU Chen Li<br />
<br />
SHI Lei<br />
<br />
XIANG Lu<br />
<br />
YU Bin<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T15:41:49Z<p>Utopian: /* Design */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations! But the capacity of speed control greatly increases its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area. Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
To control the speed of our Bactomotor, we aim at the direct swimming of bacteria for propelling the motor and the adjustable speed of swimming within a certain range. The aim is achieved by regulation of the expression level of cheZ gene. cheZ plays the key role here is due to its influence on the expression of cheY. A high level phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to the majority of bacteria tumbling movement, while a low level of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' is found in non-tumbling bacteria and cheZ can function to reduce the level of phophorylated cheY in the bacteria. Therefore, when increasing the expression level of CheZ gene, we can reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve the manipulation of speed.<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T15:41:00Z<p>Utopian: /* Design */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Design=<br />
<br />
Speed control is a crucial feature of our Bactomotor and is indispensable for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations! But the capacity of speed control greatly increases its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area.Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor to allow more accurate localization of drug. <br />
<br />
''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
<br />
<br />
[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
<br />
<br />
To control the speed of our Bactomotor, we aim at the direct swimming of bacteria for propelling the motor and the adjustable speed of swimming within a certain range. The aim is achieved by regulation of the expression level of cheZ gene. cheZ plays the key role here is due to its influence on the expression of cheY. A high level phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to the majority of bacteria tumbling movement, while a low level of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' is found in non-tumbling bacteria and cheZ can function to reduce the level of phophorylated cheY in the bacteria. Therefore, when increasing the expression level of CheZ gene, we can reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve the manipulation of speed.<br />
<br />
=='''Step 1--''CheZ'' knockout'''==<br />
<br />
By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
<br />
=='''Step 2--Controllable ''cheZ'' expression'''==<br />
<br />
An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
<br />
There are two designs for ''cheZ'' plasmid.<br />
<br />
===Original Design===<br />
<br />
The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
<br />
[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
<br />
===Back up Design===<br />
<br />
The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
<br />
<br />
[[Image:HKU-BU-pLAC-cheZ-tet.png|center|700px]]<br />
<br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_OverviewTeam:HKU-HKBU/Motor Overview2009-10-20T15:40:23Z<p>Utopian: /* Micro-Motor - Overview */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Micro-Motor - Overview=<br />
Generating mechanical power to drive microdevices has great implications in future energy utilization as well as medical science. Fortunately, nature has provided us with numerous brilliant examples of nano-scale molecular machines. Some functional nanodevices derived from living organisms, such as motor proteins, can efficiently convert chemical energy into mechanical work. <br />
<br />
Using life-form power to propel micromotors has a number of unique advantages over conventional energy utilization process. This include efficient conversion of chemical energy into mechanical work and the potential of procedural control. The development of an appropriate interface between the bacteria and synthetic devices should enable us to realize useful hybrid micro-machines. <br />
<br />
In this project, we described some micromotors powered by bacteria. The motor is one of the most important parts in the whole design of Bactomotor. It provides a attaching surface for E. coli and serves to concentrate propelling forces generated by the bacteria. In order to achieve this design, the well-studied biotin-strepatavidin interaction was applied to bind the bacteria to the motor. <br />
<br />
The motor we need should have the following characteristics: <br />
<br />
# It should be symmetrical and small enough to match the size of bacteria, saying ~ 50μm.<br />
# Only one side of the motor has biotinteria so that the motor can only rotate in one direction,either clockwise or counterclockwise.<br />
<br />
Besides, it needs to be rigid and can undergo chemical modifications through which biotin can be coated on the surface. <br />
<br />
Taking into account the above considerations, we have designed two versions of motor using either Immobilon-P transfer membrane or the inorganic elemental silicon. <br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_OverviewTeam:HKU-HKBU/Motor Overview2009-10-20T15:38:47Z<p>Utopian: /* Micro-Motor - Overview */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Micro-Motor - Overview=<br />
Generating mechanical power to drive microdevices has great implications in future energy utilization as well as medical science. Fortunately, nature has provided us with numerous brilliant examples of nano-scale molecular machines. Some functional nanodevices derived from living organisms, such as motor proteins, can efficiently convert chemical energy into mechanical work. <br />
<br />
Using life-form power to propel micromotors has a number of unique advantages over conventional energy utilization process. This include efficient conversion of chemical energy into mechanical work and the potential of procedural control. The development of an appropriate interface between the bacteria and synthetic devices should enable us to realize useful hybrid micro-machines. <br />
<br />
In this project, we described some micromotors powered by bacteria. The motor is one of the most important parts in the whole design of Bactomotor. It provides a attaching surface for E. coli and serves to concentrate propelling forces generated by the bacteria. In order to achieve this design, the well-studied biotin-strepatavidin interaction was applied to bind the bacteria to the motor. <br />
<br />
The motor we need should have the following characteristics: <br />
<br />
# It should be symmetrical and small enough to match the size of bacteria, saying ~ 50μm.<br />
# Only one side of the motor has biotinteria so that the motor can only rotate in one direction,either clockwise or counterclockwise.<br />
<br />
Besides, it needs to be rigid and can undergo chemical modifications through which biotin can be coated on its surface. <br />
<br />
Taking into account the above considerations, we have designed two versions of motor using either Immobilon-P transfer membrane or the inorganic elemental silicon. <br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_OverviewTeam:HKU-HKBU/Motor Overview2009-10-20T15:38:02Z<p>Utopian: /* Micro-Motor - Overview */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Micro-Motor - Overview=<br />
Generating mechanical power to drive microdevices has great implications in future energy utilization as well as medical science. Fortunately, nature has provided us with numerous brilliant examples of nano-scale molecular machines. Some functional nanodevices derived from living systems, such as motor proteins, can efficiently convert chemical energy into mechanical work. <br />
<br />
Using life-form power to propel micromotors has a number of unique advantages over conventional energy utilization process. This include efficient conversion of chemical energy into mechanical work and the potential of procedural control. The development of an appropriate interface between the bacteria and synthetic devices should enable us to realize useful hybrid micro-machines. <br />
<br />
In this project, we described some micromotors powered by bacteria. The motor is one of the most important parts in the whole design of Bactomotor. It provides a attaching surface for E. coli and serves to concentrate propelling forces generated by the bacteria. In order to achieve this design, the well-studied biotin-strepatavidin interaction was applied to bind the bacteria to the motor. <br />
<br />
The motor we need should have the following characteristics: <br />
<br />
# It should be symmetrical and small enough to match the size of bacteria, saying ~ 50μm.<br />
# Only one side of the motor has biotinteria so that the motor can only rotate in one direction,either clockwise or counterclockwise.<br />
<br />
Besides, it needs to be rigid and can undergo chemical modifications through which biotin can be coated on its surface. <br />
<br />
Taking into account the above considerations, we have designed two versions of motor using either Immobilon-P transfer membrane or the inorganic elemental silicon. <br />
<br />
{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_OverviewTeam:HKU-HKBU/Motor Overview2009-10-20T15:35:57Z<p>Utopian: /* Micro-Motor - Overview */</p>
<hr />
<div>{{Team:HKU-HKBU/style.css}}<br />
{{Team:HKU-HKBU/script.js}}<br />
{{Team:HKU-HKBU/header}}<br />
<br />
=Micro-Motor - Overview=<br />
Generating mechanical power to drive microdevices has great implications in future energy utilization as well as medical science. Fortunately, nature has provided us with numerous brilliant examples of nano-scale molecular machines. Some functional nanodevices derived from living systems, such as motor proteins, can efficiently convert chemical energy into mechanical work. <br />
<br />
Using life-form power to propel micromotors has a number of unique advantages over conventional energy utilization process. This include efficient conversion of chemical energy into mechanical work and the potential of procedural control. The development of an appropriate interface between such biological materials and synthetic devices should enable us to realize useful hybrid micro-machines. <br />
<br />
In this project, we described some micromotors powered by bacteria. The motor is one of the most important parts in the whole design of Bactomotor. It provides a binding surface for E. coli and serves to concentrate propelling force generated by the bacteria. In order to achieve this design, the well-studied biotin-strepatavidin interaction was applied to bind the bacteria to the motor. <br />
<br />
The motor we need should have the following characteristics: <br />
<br />
# It should be symmetrical and small enough to match the size of bacteria, saying ~ 50μm.<br />
# It is feasible that only one side of the motor has biotin binding on it, which means that bacteria can push the motor to rotate in either clockwise or counterclockwise.<br />
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Besides, it needs to be rigid and can undergo chemical modifications through which biotin can be coated on its surface. <br />
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Taking into account the above considerations, we have designed two versions of motor using either Immobilon-P transfer membrane or the inorganic elemental silicon. <br />
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{{Team:HKU-HKBU/footer}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Motor_OverviewTeam:HKU-HKBU/Motor Overview2009-10-20T15:27:43Z<p>Utopian: </p>
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=Micro-Motor - Overview=<br />
Generating mechanical power to drive microdevices has great implications in future energy utilization as well as medical science. Fortunately, nature has provided us with numerous brilliant examples of nano-scale molecular machines. Some functional nanodevices derived from living systems, such as motor proteins, can efficiently convert chemical energy into mechanical work. <br />
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Using life-form power to propel micromotors has a number of unique advantages over conventional energy utilization process, including efficient conversion of chemical energy into mechanical work and the potential for procedure control. The development of an appropriate interface between such biological materials and synthetic devices should enable us to realize useful hybrid micro-machines. <br />
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In this project, we described some micromotors driven by bacteria. The motor is one of the most important parts of the bactomotor project. It provides a surface on which the E. coli cells can bind to and the swimming motion of them can be used to propel it. In order to achieve this design, the well-studied biotin-strepatavidin interaction was applied to bind the bacteria to the motor. <br />
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The motor we need should have the following two main characteristics: <br />
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# It should be symmetrical and small enough to match the size of bacteria, saying ~ 50μm.<br />
# It is feasible that only one side of the motor has biotin binding on it, which means that bacteria can push the motor to rotate in either clockwise or counterclockwise.<br />
<br />
Besides, it needs to be rigid and can undergo chemical modifications through which biotin can be coated on its surface. <br />
<br />
Taking into account the above considerations, we have designed two versions of motor using either Immobilon-P transfer membrane or the inorganic elemental silicon. <br />
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{{Team:HKU-HKBU/footer}}</div>Utopianhttp://2009.igem.org/Team:HKU-HKBU/Speed_Control_DesignTeam:HKU-HKBU/Speed Control Design2009-10-20T14:51:59Z<p>Utopian: /* Design */</p>
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=Design=<br />
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Speed control is a crucial feature of our Bactomotor and an indispensable feature for more advanced controllable applications. Devices equipped with the speed controllable Bactomotor open up possibilities of non-invasive micro-surgery. Obviously, we may not expect the bacteria motor to behave exactly according to our will. After all, our motor is alive! It is subjected to numerous physical and physiological limitations! But the capacity of speed control greatly increases its usefulness. In the case of micro-surgery, we can slow down the Bactomotor in order to locate the pathologic tissue. We can then increase the bacteria to its full speed to bring desirable mechanical changes to the target area.Another example that will illustrate the importance of speed control is in the case of drug delivery. On one hand, we may wish to make the drug-loaded to swim faster than it normally does to overcome the resistance it encounters with in the capilliaries during the process of delivery; on the other hand, we wish to slow down the Bactomotor to allow more accurate localization of drug. <br />
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''E. coli'' or ''Salmonella'' can swim around by rotating the flagella. When the flagella rotate in a counterclockwise fashion, the bactomotor gathers momemta and produce non-random locomotion. When the rotation is in the clockwise direction, the bactomotor will tumble in place and fail to 'swim' (Fig 1).<br />
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[[Image:HKU-HKBU_speed_control_1.png | frame | center | Fig. 1 Genetic circuit related to cell movement [https://2008.igem.org/Team:iHKU/modeling iHKU]]]<br />
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To control the speed of our Bactomotor, we aim at the direct swimming of bacteria for propelling the motor and the adjustable speed of swimming within a certain range. The aim is achieved by regulation of the expression level of cheZ gene. cheZ plays the key role here is due to its influence on the expression of cheY. A high level phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' leads to the majority of bacteria tumbling movement, while a low level of phosphorylation of cheY protein in ''E. coli'' or ''Salmonella'' is found in non-tumbling bacteria and cheZ can function to reduce the level of phophorylated cheY in the bacteria. Therefore, when increasing the expression level of CheZ gene, we can reduce the tumbling movement, which in turn can increase the swimming speed of the bacteria to achieve the manipulation of speed.<br />
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=='''Step 1--''CheZ'' knockout'''==<br />
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By using lamda red system, recombineering is utilized to knock out the ''CheZ'' gene in the chromosome of ''E. coli'' or ''Salmonella''. Homologous arms (about 50bp)are placed inside the ''CheZ'' gene. The ''CheZ'' gene is replaced by a chloramphenicol resistance gene after recombination.<br />
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=='''Step 2--Controllable ''cheZ'' expression'''==<br />
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An inducible ''cheZ'' plasmid was tranformed into ''CheZ'' knockout strains. Therefore, by controlling ''cheZ'' expression level, we can implement the adjustable control over the speed of the bacteria and hence the motor. <br />
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There are two designs for ''cheZ'' plasmid.<br />
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===Original Design===<br />
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The orinigal design is to use '''lacI''' as a repressor to prevent the occurence of leaky expression in the absence of the inducer, which in this case is IPTG(Isopropyl β-D-1-thiogalactopyranoside). We predict that the bacterium will swim at a lower speed when it is in a 'incomplete tumbling mode'. <br />
When the bacteria are treated with IPTG(switch on), the expression level of ''cheZ'' could be regulated according to inducer's concentration and hence swimming speed of the bacteria. <br />
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[[Image:HKU-BU-pLAC-cheZ.png|center|400px]]<br />
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===Back up Design===<br />
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The back up design is to use '''tetR''' as a repressor and '''ptet''' as the regulator, which can be induced by tetracycline(or aTc). We suppose that by changing the concentration of tetracycline, the expression amount of protein cheZ will be altered, resulting in the acceleration and deceleration.<br />
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[[Image:HKU-HKBU_speed_control_design_second.png|center|400px]]<br />
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