IGEM:Peking/2007: Difference between revisions

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| rowspan=2 | [[Image:Peking_University_BoYaTower.jpg|left|300px]] '''Hop count with conjugation'''
[[Image:PKU bear logo.gif|180px]]
Hop counting is a cell-cell communication system in which the signals transfered among the cells record the number of times of transfer.
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As a prerequisite for hop counting, cell-cell communication should be made on a one to one basis to ensure differential control over neighboring cells.
The two possible mechanism of signal transfer are bacterial conjugation and phage.
Although a hop count system can be implemented with some modifications to either of the natural systems, we tend to focus on conjugation while doing some basic work on phage.
With the conjugation, independent tandem oriT (<bbick) pairs can be inserted into the same plasmids, losing one tandem region at each single conjugation event.
Sequential conjugation and deletion of the different oriT pairs can be achieved by fine control of the expression of the cis-acting elements of the independent conjugation systems.
Besides intellectual interests, these systems are the core parts of controllable and encoded local cell-cell communication, which can be used in potential pattern formation and material weaving applications.


'''Push-on-push-off Switch'''
<div style="font: normal 1.6em georgia, serif">Towards Self-differentiated Bacterial Assembly Line</div>
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Our projects concern with the ability for bacterial cells to '''differentiate''' out of homogeneous conditions into populations with the '''division of labor'''. We aim at devices conferring host cells with the ability to form cooperating groups spontaneously and to take consecutive steps sequentially even when the genetic background and environmental inputs are identical. To break the mirror in such homogeneous condition, we need two devices respectively responsible for '''temporal''' and '''spatial''' differentiation. The implementation and application of such devices will lead to a picture of future bioengineering where complex programs consisted of sequential steps (structure oriented programs) and cooperating agencies (forked instances of a single class, object and event oriented) can be embedded in a single genome.
 
<br>
About the name of projects, the two devices are named after their respective functions: hop count and push-on-push-off switch, but they are common for breaking symmetry, which is interesting and ubiquitous in science. Although this "differentiation" process resemble the development of multicellular organism, we tend to use a more bioengineering style analogy: assembly line. Or maybe after some years from now, this will not be just an analogy. <br>
'''Also visit:''' [http://parts.mit.edu/igem07/index.php/Peking '''IGEM2007 Peking''']
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![http://parts.mit.edu/igem07/index.php/Peking IGEM 2007 Peking]
![http://parts.mit.edu/igem07/index.php/Peking_The_Projects Peking The Projects]
![http://parts.mit.edu/igem07/index.php/Peking_The_Community Peking The Team]
![http://parts.mit.edu/igem07/index.php/Peking_The_Fun Peking's Misc & Fun]
![http://parts.mit.edu/igem07/index.php/Peking_Thanks Acknowledgement]
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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Project">
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'''Hop Count with Conjugation'''<br>
[ftp://igem:igem2007@162.105.160.5/OurFiles/CountGroup/Documents/proposal.pdf Project Proposal]<br>
[ftp://igem:igem2007@162.105.160.5/OurFiles/CountGroup/Documents/presentation.pdf Project Presentation]<br>
[[iGEM:Peking/2007/Count-Road-Map| Road Map ]]<br>
[[iGEM:Peking/2007/Count-References | Related Articles ]]<br>
 
'''Push-on-push-off Switch'''<br>
[ftp://igem:igem2007@162.105.160.5/OurFiles/SwitchGroup/proposal_switch_revision2.doc Project proposal]<br>
Project presentation<br>
[[iGEM:Peking/2007/Switch-Road-Map | Road Map ]]<br>
[[iGEM:Peking/2007/Switch-References | Related Articles ]]<br>
 
'''Meetings'''
* [[iGEM:Peking/2007/iGEM-Promotion-Meeting|iGEM promotion meeting]]
* [[iGEM:Peking/2007/iGEM-Beijing-Preparation-Meeting|iGEM PKU prep meeting]]
* Journal Club [[iGEM:Peking/2007/JC01|01]] | [[iGEM:Peking/2007/JC02|02]] | [[iGEM:Peking/2007/JC03|03]] | [[iGEM:Peking/2007/JC04|04]] | [[iGEM:Peking/2007/JC05|05]] | [[iGEM:Peking/2007/JC06|06]] | [[iGEM:Peking/2007/JC07|07]] | [[iGEM:Peking/2007/JC08|08]] | [[iGEM:Peking/2007/JC09|09]] | [[iGEM:Peking/2007/JC10|10]] | [[iGEM:Peking/2007/JC11|11]] | [[iGEM:Peking/2007/JC12|12]] | [[iGEM:Peking/2007/JC13|13]] | [[iGEM:Peking/2007/JC17|17]]
 
'''Brainstorming'''<br>
Some of our ideas are listed [[iGEM:Peking/2007/Ideas | here]]


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'''Rap up'''<br>
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Collections of the experiences.
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* A [[IGEM:Peking/2007/Experience-colletcion | response]] to Goodman. In English.
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* Collections of [[IGEM:Peking/2007/Things_we_want_to_say |chinese sentiments]].
<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
</html>Resources</h3>
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Interested in being a learning more about iGEM 2007?  Explore below for an example of what's possible.


For more info on this year's iGEM please see [http://www.igem2007.com www.igem2007.com] and the [http://parts.mit.edu/igem07 official iGEM 2007 wiki]
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<a href="http://www3.clustrmaps.com/counter/maps.php?url=http://www.openwetware.org/wiki/IGEM:Peking/2007"><img src="http://www3.clustrmaps.com/stats/maps-no_clusters/www.openwetware.org-wiki-IGEM-Peking-2007-thumb.jpg" />
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Many more valuable links and helpful tidbits are available at the [http://parts.mit.edu/wiki/index.php/Resources iGEM Resources page]
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What will be this year's project for the 2007 MIT team?  We're busy brainstorming ideas as you read this!
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===External links===
==<html>
*[[iGEM|iGEM on OpenWetWare]]
<img src="http://openwetware.org/images/e/e2/Icon_info.png" alt="News" border="0">
*[http://parts.mit.edu/registry Parts registry]
</html>Lab==
*[http://parts.mit.edu/igem official iGEM 2006 wiki]
*[http://parts.mit.edu/wiki/index.php/MIT_2006 MIT page on iGEM 2006 wiki]
*Our Parts:
**[http://parts.mit.edu/registry/index.php/Part:BBa_I728005 OmpC Surface Display]
**[http://parts.mit.edu/registry/index.php/Part:BBa_I728004 CPX Surface Display]


===For visitors===
'''Products and Parts'''
*Read more about [[Synthetic Biology|engineering biology]].
*[[../2006|2006 MIT iGEM wiki]]
*[[../2005/|2005 MIT iGEM wiki]]
*[[Synthetic_Biology:Polka_Dots|Polka Dots]]: The MIT IAP class, a precursor to iGEM


===Internal links===
'''Procedures'''<br>
*'''[[../2007/Notebook|Team Notebook]]'''
[[iGEM:Peking/2007/Count-Conjugation-Procedure |Hop-count with Conjugation]]<br>
*'''[[/Red_Team|Red Team]]'''
[[iGEM:Peking/2007/Switch-Procedure |Push-on-push-off Switch]]<br>
*'''[[/Contacts|Contact Numbers]]'''
*'''[[BE.109:DNA_engineering|DNA engineering from BE.109]]'''
*'''[[/Protocols|Protocols]]'''
*'''[[/Nomenclature|Nomenclature and Abbreviations]]'''
*'''[[/Codes|Test Tube Codes]]'''
*'''[[/OrderInfo|Order Information]]'''


'''Protocols'''<br>
[[iGEM:Peking/2007/Count:Agarose Gel Electrophoresis| Count:Agarose Gel Electrophoresis]]<br>
[[iGEM:Peking/2007/Count:Gel-Extraction | Count:DNA Gel Extraction]]<br>
[[iGEM:Peking/2007/Count:PCR product purifcation| Count:PCR product purifcation]]<br>
[[iGEM:Peking/2007/Count:Preparation of Competent Cells | Count:Preparation of Competent Cells]]<br>
[[iGEM:Peking/2007/Digestion | Enzymatic DNA Digestion]]<br>
[[iGEM:Peking/2007/Count:Ligation | Count:Ligation]]<br>
[[iGEM:Peking/2007/Count:Transformation | Count:Transformation]]<br>
[[iGEM:Peking/2007/Count:Sequencing | Count:Sequencing]]<br>
[[iGEM:Peking/2007/Count:Miniprep | Count: Miniprep]]<br>
[[iGEM:Peking/2007/Count:Conjugation| Count: Conjugation test]]<br>
[[iGEM:Peking/2007/Count:Knockout| Count: Gene Knock Out]]<br>
[[iGEM:Peking/2007/Switch:Miller | Switch: Miller Method]]<br>
[[iGEM:Peking/2007/Oligos | Oligonucleotides]]<br>
[[iGEM:Peking/2007/Switch: PCR | Switch: PCR]]<br>
[[iGEM:Peking/2007/Switch: DNA electrophoresis | Switch: DNA electrophoresis]]<br>
[[iGEM:Peking/2007/Switch: DNA ligation | Switch: DNA ligation]]<br>
[[iGEM:Peking/2007/Switch: DNA digestion | Switch: DNA digestion]]<br>
[[iGEM:Peking/2007/Switch: transformation | Switch: transformation]]<br>
[[iGEM:Peking/2007/Switch: DNA rescue by precipitation | Switch: DNA rescue by precipitation]]<br>
[[iGEM:Peking/2007/Switch: Plasmid mini prep| Switch: Plasmid mini prep]]<br>


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<img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Resources">
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'''Addressable Cell-to-Cell Communication'''


*[[Media:071906-JCAGroupMeeting.ppt| 071906 JCA Group Meeting]]
[[Image:Peking_2007_Notebook_icon.jpg‎|20px]]'''Notebooks'''<br>
*[[Media:060506-Meeting.ppt| 060506 Meeting]]
[[iGEM:Peking/2007/Count-Conjugation-Notebook |Hop-count with Conjugation]]<br>
*[[Media:Berkeley 2005 Jamboree.ppt| Berkeley 2005 'Jamboree']]
[[iGEM:Peking/2007/Switch_Notebook|Push-on-push-off Switch]]<br>
*[http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005 2005 Project]
[[iGEM:Peking/2007/Turtle_Diary|Turtle Diary]]<br>
*[http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Berkeley '''2006 Parts List''']
'''Useful Links'''


*[[IGEM|iGEM]]
<br>
*[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 UC Berkeley iGEM wiki]
*[http://parts2.mit.edu/wiki/index.php/Main_Page iGEM wiki]
*[http://parts.mit.edu/registry/index.php/Main_Page Registry of Standard Biological Parts]
*[http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Berkeley 2005 Biobricks]
*[[Image:iGEM2006Distribution.xls|iGEM2006 Distribution compiled list]]
*[http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006 | iGEM site]




'''Subgroup Strategies, Overview'''
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*[[Powerpoint presentations, drafts]]
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==<html>
<!-- PEOPLE HEADER with edit link-->
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<img src="http://openwetware.org/images/3/39/Icon_groups.png" alt="People">
<img src="http://openwetware.org/images/3/39/Icon_groups.png" alt="People">
</html>People</h3>
</html>People==
<hr/>
<!-- END PEOPLE HEADER with edit link-->


'''New: [[Special:Chat/IGEM:Peking/2007| iGEM chat room!]]'''
The iGEM 2007 PKU Team now consists of about 20 students and several faculty members from School of Life Science and Center of Theoretical Biology.


===Students===
=== Students ===
*[[iGEM:Peking/2007/Anting Xu | Anting Xu]]
*[[iGEM:Peking/2007/Chang Liu | Chang Liu]]
*[[iGEM:Peking/2007/Chongyi Chen | Chongyi Chen]]
*[[iGEM:Peking/2007/Chunbo Lou | Chunbo Lou]]
*[[User:Chen Daizhuo | Chen Daizhuo, Henry]]
*[[iGEM:Peking/2007/Dan Lu | Dan Lu]]
*[[iGEM:Peking/2007/Haisu Ma | Haisu Ma]]
*[[iGEM:Peking/2007/Lingli Jiang | Lingli Jiang]]
*[[iGEM:Peking/2007/Ming Ni | Ming Ni]]
*[[iGEM:Peking/2007/Mingcong Wang | Mingcong Wang]]
*[[Peking_Mingzhi Qu | Mingzhi Qu]]
*[[iGEM:Peking/2007/Qinsi Zheng | Qinsi Zheng]]
*[[iGEM:Peking/2007/Tao Ma | Tao Ma]]
*[[iGEM:Peking/2007/Tao Yu | Tao Yu ]]
*[[iGEM:Peking/2007/Ting Liu | Ting Liu]]
*[[iGEM:Peking/2007/Xili Liu | Xili Liu]]
*[[User:YangYifan | Yifan Yang]]
*[[iGEM:Peking/2007/Zhe Ren | Zhe Ren]]


Email us: '''igem-pku [AT] googlegroups.com'''
=== Advisors ===


===Advisors===
* [http://www.bio.pku.edu.cn/collegereview/scholarinfo.jsp?name=wangyp Wang Yiping]
* Li Fangting
* [http://ctb.pku.edu.cn/main/cn/graduation/graduation-daoshijianjie-ouyangqi.htm Ouyang Qi]
* [http://linux2.ipc.pku.edu.cn/ Lai Luhua]


=== Photo ===
[[iGEM:Peking/2007/Photo-Team | The Team]]
[[iGEM:Peking/2007/Photo-Campus | Our Campus]]
[[iGEM:Peking/2007/Photo-Lab | The Labs]]


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__NOTOC__
'''Email us''' at ''igem-pku AT googlegroups DOT com''
 
'''External links''' [http://parts.mit.edu/wiki/index.php/Main_Page iGEM] | [http://www.igem2006.com iGEM 2006] | [http://parts.mit.edu/ Registry of Standard Biological Parts] | [http://groups.google.com/group/igem-pku/topics?lnk=oa iGEM PKU Googlegroup] | [[iGEM|iGEM OWW Page]]

Latest revision as of 14:11, 21 November 2007
Towards Self-differentiated Bacterial Assembly Line

Our projects concern with the ability for bacterial cells to differentiate out of homogeneous conditions into populations with the division of labor. We aim at devices conferring host cells with the ability to form cooperating groups spontaneously and to take consecutive steps sequentially even when the genetic background and environmental inputs are identical. To break the mirror in such homogeneous condition, we need two devices respectively responsible for temporal and spatial differentiation. The implementation and application of such devices will lead to a picture of future bioengineering where complex programs consisted of sequential steps (structure oriented programs) and cooperating agencies (forked instances of a single class, object and event oriented) can be embedded in a single genome.


About the name of projects, the two devices are named after their respective functions: hop count and push-on-push-off switch, but they are common for breaking symmetry, which is interesting and ubiquitous in science. Although this "differentiation" process resemble the development of multicellular organism, we tend to use a more bioengineering style analogy: assembly line. Or maybe after some years from now, this will not be just an analogy.
Also visit: IGEM2007 Peking

IGEM 2007 Peking Peking The Projects Peking The Team Peking's Misc & Fun Acknowledgement

<html> <img src="http://openwetware.org/images/b/b9/Icon_board.png" alt="Project"> </html>Project

Hop Count with Conjugation
Project Proposal
Project Presentation
Road Map
Related Articles

Push-on-push-off Switch
Project proposal
Project presentation
Road Map
Related Articles

Meetings

Brainstorming
Some of our ideas are listed here

Rap up
Collections of the experiences.

<html> <a href="http://www3.clustrmaps.com/counter/maps.php?url=http://www.openwetware.org/wiki/IGEM:Peking/2007"><img src="http://www3.clustrmaps.com/stats/maps-no_clusters/www.openwetware.org-wiki-IGEM-Peking-2007-thumb.jpg" /> </a>

</html>

<html> <img src="http://openwetware.org/images/e/e2/Icon_info.png" alt="News" border="0"> </html>Lab

Products and Parts

Procedures
Hop-count with Conjugation
Push-on-push-off Switch

Protocols
Count:Agarose Gel Electrophoresis
Count:DNA Gel Extraction
Count:PCR product purifcation
Count:Preparation of Competent Cells
Enzymatic DNA Digestion
Count:Ligation
Count:Transformation
Count:Sequencing
Count: Miniprep
Count: Conjugation test
Count: Gene Knock Out
Switch: Miller Method
Oligonucleotides
Switch: PCR
Switch: DNA electrophoresis
Switch: DNA ligation
Switch: DNA digestion
Switch: transformation
Switch: DNA rescue by precipitation
Switch: Plasmid mini prep



Notebooks
Hop-count with Conjugation
Push-on-push-off Switch
Turtle Diary

<html> <img src="http://openwetware.org/images/3/39/Icon_groups.png" alt="People"> </html>People

The iGEM 2007 PKU Team now consists of about 20 students and several faculty members from School of Life Science and Center of Theoretical Biology.

Students

Advisors

Photo

The Team

Our Campus

The Labs

Email us at igem-pku AT googlegroups DOT com

External links iGEM | iGEM 2006 | Registry of Standard Biological Parts | iGEM PKU Googlegroup | iGEM OWW Page

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