Team:Fudan Lux/biowave

From 2012.igem.org

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             <h1><a name="Introduction">Introduction</a></h1>
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             <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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             <p>Recently, there has been increased interest in visible light controlled system. Optogenetics, a seven-year-old field branching out from molecular biology and neuroscience, is leading the trend of creating novel synthesized proteins as “tools” </p><img src="" style="width:50%;float:right"><p>helping people understand the brain mechanism. These “opsins”, which light-activated domain borrowed from microbes or plants, were transferred into model animal organisms. These controllers are acting in the center part of light system. Unlike the drug treatment, light can be delivered by lasers with extremely high spatial precision; therefore, one can manipulate only target cells. </p><p>Our Biowave project is more than performing light control. By establishing the light depending feedback system within the cell we have realized a light communication system. This is the very first time that putting the intracellular and intercellular light communication in the biological system. Using the fundamental gene circuit and brand new parts we created, each cell becomes a communication node. </p><img src="" style="width:50%;float:left"><p>The first Biowave circuit we have created is the Negative Feedback Biowave. The circuit comprising light sensor and light generator established the negative feedback between them. The properties of time delay, caused by gene expression or the accumulation of the element’s concentration, and negative feedback could form an oscillation of light output within a single cell or the neighbouring cells. By placing the bacteria on a Petri dish and letting them evenly distributed, each cell could sense the light of others equally. With the certain condition and observation analysis, the whole dish could form a detectable synchronized oscillation. In a macroscopic view, this kind of synchronization could be distracted by the attenuation of light. So we could expect a wave like pattern on this level.</p><p>The Positive Feedback Biowave is another attempt for the intracellular and intercellular light communication. Thus the positive feedback under this situation makes the system a bistable circuit; each cell can remain in either a light state or a dark state. But the light irradiation across the colony makes things different. The bacteria would form a static strip or other bistable system caused patterns within or beyond our expected.</p>
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            <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames, Pellentesque habitant morbi tristique senectus et netus et malesuada fames Pellentesque habitant morbi tristique senectus et netus et malesuada fames.</p>
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  <td height="14" width="100" style="height:14.0pt;width:100pt"></td>
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  <td class="xl67" width="208" style="width:208pt">LIGHT</td>
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  <td class="xl67" width="184" style="width:184pt">CHEMICAL</td>
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  <td width="53" style="width:53pt"></td>
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  <td width="53" style="width:53pt"></td>
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  <td width="53" style="width:53pt"></td>
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</tr>
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<tr height="14" style="height:14.0pt">
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  <td height="14" class="xl67" width="100" style="height:14.0pt;width:100pt">manipulate&nbsp;</td>
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  <td class="xl67" width="208" style="width:208pt">controllable</td>
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  <td class="xl67" width="184" style="width:184pt">Hard to control</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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<tr height="14" style="height:14.0pt">
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  <td height="14" class="xl67" width="100" style="height:14.0pt;width:100pt">elimination</td>
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  <td class="xl68" width="208" style="width:208pt">light induction could be changed
 +
  or erased<span style="mso-spacerun:yes">&nbsp;</span></td>
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  <td class="xl67" width="184" style="width:184pt"><span style="mso-spacerun:yes">&nbsp;</span>hard to wipe out</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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<tr height="28" style="height:28.0pt">
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  <td height="28" class="xl67" width="100" style="height:28.0pt;width:100pt">transfer
 +
  speed</td>
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  <td class="xl68" width="208" style="width:208pt">Signal travels fast(as a speed
 +
  of light)<br>
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  Non-time-delay</td>
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  <td class="xl67" width="184" style="width:184pt">Speed is limited by chemical
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  diffusion System has a minimum delay</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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<tr height="28" style="height:28.0pt">
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  <td height="28" class="xl67" width="100" style="height:28.0pt;width:100pt">crosstalk</td>
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  <td class="xl68" width="208" style="width:208pt">never has the crosstalk with
 +
  constitutive pathway</td>
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  <td class="xl67" width="184" style="width:184pt">may cross the constitutive
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  pathway</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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<tr height="28" style="height:28.0pt">
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  <td height="28" class="xl67" width="100" style="height:28.0pt;width:100pt">measurement</td>
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  <td class="xl68" width="208" style="width:208pt">Visible and detectable<br>
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  easy to measure</td>
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  <td class="xl67" width="184" style="width:184pt">hard to detect or measure</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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<tr height="42" style="height:42.0pt">
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  <td height="42" class="xl67" width="100" style="height:42.0pt;width:100pt">noise
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  immunity<span style="mso-spacerun:yes">&nbsp;</span></td>
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  <td class="xl67" width="208" style="width:208pt">sensitive <br>
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  could be easily disturbed by the nature light</td>
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  <td class="xl67" width="184" style="width:184pt">only the same molecule or the
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  analogue could disturb the signal pathway</td>
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  <td colspan="2" style="mso-ignore:colspan"></td>
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  <td class="xl69"></td>
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</tr>
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<tr height="28" style="height:28.0pt">
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  <td height="28" class="xl67" width="100" style="height:28.0pt;width:100pt">channel</td>
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  <td class="xl67" width="208" style="width:208pt">has limited channels(only 390nm
 +
  to 700nm)</td>
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  <td class="xl67" width="184" style="width:184pt">countless channels(each kind of
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  chemical analogues group is a channel)</td>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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</tr>
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  <td colspan="3" style="mso-ignore:colspan"></td>
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  <td class="xl66" width="184" style="width:184pt"></td>
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Revision as of 15:00, 26 September 2012

NOVA

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Project Biowave You have never seen something like this.

Background

  • A group of rough-toothed dolphins surfacing synchronously

    Origin Link
Feature image

One of the most interesting and complex types of group behaviors in animals is that in which several organisms simultaneously repeat the same activity at regular intervals of time.1 In ordinary usage, this kind of behavior is called “synchronous”. It has been observed in Thailand that male Pteroptyx malaccae fireflies, congregated in trees, flash in rhythmic synchrony with a period of about 560 ± 6 msec (at 28°C). Males of a China’s special species of firefly called Qiongyuying flash synchronously during mating season. And we also observed that bees crawling in the same small area display a synchrony of wings fluttering in order to scare off intruder，and we filmed a video clip to demonstrate this phenomenon. Moreover, synchrony has been described in a range of mammal groups, including odontocete cetaceans (a kind of toothed whale).2 The odontocete cetaceans behave synchronously when they breathe on the surface of water.

  • Synchronous fireflies (Pteroptyx Tener) flashing on the mangrove tree (Sonneratia Caseolaris) at Kuala Selangor, Malaysia (2008). Courtesy of Photo Researchers, Inc.

    Origin Link
Feature image

In the microcosm, a synthetic gene oscillator whose oscillatory cycle can be tuned by altering inducer levels, temperature and the media source has been designed by I and his cooperators to accomplish the synchronous oscillation. It uses both E.coli and yeast as component cells. In this oscillator system, chemicals (IPTG, arabinose) are used as a series of signals to initiate synchronous oscillations within single cells of the colony.3

  • Oscillations in the dual-feedback circuit.
    a, Network diagram of the dual-feedback oscillator.
    b, Single-cell fluorescence trajectories induced with 0.7% arabinose and 2mM IPTG.

    Origin Link
Feature image

Compared with chemical molecules, optical signal is more efficient for both the macrocosm and the microcosm. We wonder whether we can change the induced signal into light, which is visible and easy to control. It propagates much faster and has countless channels, for each wavelength is a different channel.

Introduction

Recently, there has been increased interest in visible light controlled system. Optogenetics, a seven-year-old field branching out from molecular biology and neuroscience, is leading the trend of creating novel synthesized proteins as “tools”

helping people understand the brain mechanism. These “opsins”, which light-activated domain borrowed from microbes or plants, were transferred into model animal organisms. These controllers are acting in the center part of light system. Unlike the drug treatment, light can be delivered by lasers with extremely high spatial precision; therefore, one can manipulate only target cells.

Our Biowave project is more than performing light control. By establishing the light depending feedback system within the cell we have realized a light communication system. This is the very first time that putting the intracellular and intercellular light communication in the biological system. Using the fundamental gene circuit and brand new parts we created, each cell becomes a communication node.

The first Biowave circuit we have created is the Negative Feedback Biowave. The circuit comprising light sensor and light generator established the negative feedback between them. The properties of time delay, caused by gene expression or the accumulation of the element’s concentration, and negative feedback could form an oscillation of light output within a single cell or the neighbouring cells. By placing the bacteria on a Petri dish and letting them evenly distributed, each cell could sense the light of others equally. With the certain condition and observation analysis, the whole dish could form a detectable synchronized oscillation. In a macroscopic view, this kind of synchronization could be distracted by the attenuation of light. So we could expect a wave like pattern on this level.

The Positive Feedback Biowave is another attempt for the intracellular and intercellular light communication. Thus the positive feedback under this situation makes the system a bistable circuit; each cell can remain in either a light state or a dark state. But the light irradiation across the colony makes things different. The bacteria would form a static strip or other bistable system caused patterns within or beyond our expected.

LIGHT CHEMICAL
manipulate  controllable Hard to control
elimination light induction could be changed or erased   hard to wipe out
transfer speed Signal travels fast(as a speed of light)
Non-time-delay		 Speed is limited by chemical diffusion System has a minimum delay
crosstalk never has the crosstalk with constitutive pathway may cross the constitutive pathway
measurement Visible and detectable
easy to measure		 hard to detect or measure
noise immunity  sensitive
could be easily disturbed by the nature light		 only the same molecule or the analogue could disturb the signal pathway
channel has limited channels(only 390nm to 700nm) countless channels(each kind of chemical analogues group is a channel)

Model Design

Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus

Pellentesque habitant morbi tristique senectus et netus et malesuada fames, Pellentesque habitant morbi tristique senectus et netus et malesuada fames Pellentesque habitant morbi tristique senectus et netus et malesuada fames.

Light Sensor

Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus

Pellentesque habitant morbi tristique senectus et netus et malesuada fames, Pellentesque habitant morbi tristique senectus et netus et malesuada fames Pellentesque habitant morbi tristique senectus et netus et malesuada fames.

Application

Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus

Pellentesque habitant morbi tristique senectus et netus et malesuada fames, Pellentesque habitant morbi tristique senectus et netus et malesuada fames Pellentesque habitant morbi tristique senectus et netus et malesuada fames.

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