http://2009.igem.org/wiki/index.php?title=Special:Contributions/Samitwatve&feed=atom&limit=50&target=Samitwatve&year=&month=2009.igem.org - User contributions [en]2024-03-29T11:58:01ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:IBB_Pune/safetyTeam:IBB Pune/safety2009-10-22T03:16:48Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{team:IBB_Pune/menu}}<br />
<br><br />
'''Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?'''<br />
<br />
No, our project does not raise any such safety issues.<br />
While formulating our project idea and the relevant experimental designs, we took special care that no safety problems would arise, public or environmental.<br />
We followed the GLPs established in our labs to ensure researcher safety. We were supervised in our observance of these GLPs by our instructors.<br />
<br />
<br />
'''Is there a local biosafety group, committee, or review board at your institution?'''<br />
<br />
No. To overcome this glitch while handling sensitive material like BioBricks, we made sure an experienced Instructor was involved and took stringent measures so that no mistakes were made.<br />
<br />
The reason for this lack of awareness in our University is due to the lack of ongoing Synthetic Biology research here. We have taken the initiative and talked to the relevant authorities including the Vice Chancellor, to set into motion the machinery to ensure such biosafety measures are put into place.<br />
<br />
<br />
'''What does your local biosafety group think about your project?'''<br />
<br />
-<br />
<br />
<br />
'''Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
'''<br />
<br />
No. We have a project plan that ensures no breach of biosafety.<br />
<br />
<br />
<br />
'''If yes, did you document these issues in the Registry?'''<br />
<br />
-</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/sponsorsTeam:IBB Pune/sponsors2009-10-22T03:13:55Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br><br><br><br />
We urge all the interested sponsors to contact us at<br />
<br />
Professor B.A.Chopade, Advisor, Team IBB_Pune: directoribb@unipune.ernet.in '''Tel: +91-20-25690442'''<br />
<br />
Praveen Kishore Sahu, Advisor, Team IBB_Pune: praveenkishore.sahu@gmail.com ''' Tel: +91-9373-258824'''<br />
<br />
Mandar Dilip Phatak, Team Leader, Team IBB_Pune: mandardilipphatak@gmail.com '''Tel: +91-9970-068048'''<br />
<br />
<br />
Cheques and Demand Drafts should be in favor of<br />
<br />
'''"Registrar, University of Pune"''' and <br />
<br />
Addressed to <br />
'''Director, IBB, University of Pune, Ganeshkhind, Pune-411 007, INDIA'''<br />
<br><br><br />
::::::::::<p><span style="font-weight:bold; font-size:150%; color:#009999;">We would like to thank our sponsors for their kind support! :-) </span></p><br />
<br><br />
<br />
{{Team:IBB_Pune/footer}}</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-22T03:13:17Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">The Simplified Construct</span></p><br><br />
[[Image:Turing1.GIF|center|800px]]<br />
[[Image:Simplified.png|center|800px]]<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">Working</span></p><br />
<br />
[[Image:tapstrt.png|center|450px]]<br />
<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|450px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
<br />
[[Image:tape22.png|center|450px]]<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
<br />
[[Image:Tapes.png|center|450px]]<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
<br />
[[Image:Tapend.png|center|450px]]<br />
<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">How does Simplification Help?</span></p><br />
By reducing the number of proteins required to 2 LuxI and LuxR, we drastically reduce the complexity of the system design. Our simplified constructs enable us to phenotypically mimic the behaviour of a Turing Machine Unary Adder.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/NotebookTeam:IBB Pune/Notebook2009-10-22T03:12:01Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<span style="font-weight:bold; font-size:200%; color:#000000;">Calendar</span><br />
<br />
<br />
Click on any day below to see what wet-lab procedures were conducted.<br />
<br />
<table><br />
<html><br />
<style type="text/css"><br />
table.calendar { margin: 0; padding: 2px; }<br />
table.calendar td { margin: 0; padding: 1px; vertical-align: top; }<br />
table.month .heading td { padding:1px; background-color: black; color: white; text-align:center; font-size:140%; font-weight:bold; }<br />
table.month .dow td { color:#000000; text-align:center; font-size:100%; }<br />
table.month td.today { background-color:#cd0000; }<br />
table.month td {<br />
border: none;<br />
margin: 0;<br />
padding: 0pt 0.5pt;<br />
font-weight: bold;<br />
font-size: 9pt;<br />
text-align: right;<br />
background-color: white;<br />
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#bodyContent table.month a { background:none; padding:0 }<br />
.day-active { color:#cd0000 }<br />
.day-empty { color:#000000 }<br />
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{|style="font color="#ffffff"; "background-color:"#cd0000"; cellpadding="0" cellspacing="4" border="4" bordercolor="#000"; border-spacing:0px; text-align:center" width="250px"<br />
</table><br />
<br />
{| align="center"<br />
|-valign="top"<br />
<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=05}}<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=06}}<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=07}}<br />
|}<br />
<table><br />
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<style type="text/css"><br />
table.calendar { margin: 0; padding: 2px; }<br />
table.calendar td { margin: 0; padding: 1px; vertical-align: top; }<br />
table.month .heading td { padding:1px; background-color: black; color: white; text-align:center; font-size:140%; font-weight:bold; }<br />
table.month .dow td { color:#000000; text-align:center; font-size:100%; }<br />
table.month td.today { background-color:#cd0000; }<br />
table.month td {<br />
border: none;<br />
margin: 0;<br />
padding: 0pt 0.5pt;<br />
font-weight: bold;<br />
font-size: 9pt;<br />
text-align: right;<br />
background-color: white;<br />
}<br />
#bodyContent table.month a { background:none; padding:0 }<br />
.day-active { color:#cd0000 }<br />
.day-empty { color:#000000 }<br />
<br />
</style> <br />
</html><br />
<br />
<br />
{|style="font color="#ffffff"; "background-color:"#cd0000"; cellpadding="0" cellspacing="4" border="4" bordercolor="#000"; border-spacing:0px; text-align:center" width="250px"<br />
</table><br />
<br />
{| align="center"<br />
|-valign="top"<br />
<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=08}}<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=09}}<br />
|align="center" width="250pt"|{{#calendar: title=IBB_Pune |year=2009 | month=10}}<br />
<br />
|}</div>Samitwatvehttp://2009.igem.org/Template:Team:IBB_Pune/headerTemplate:Team:IBB Pune/header2009-10-22T02:57:15Z<p>Samitwatve: </p>
<hr />
<div><html><br />
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body {<br />
color: #61553d;<br />
}<br />
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.s1 {font-family: Verdana, Arial, Helvetica, sans-serif; font-weight: bold; color: #6C96D5;}<br />
body {background-color:#336633;}<br />
.grid_1,.grid_2,.grid_3,.grid_4,.grid_5,.grid_6,.grid_7,.grid_8,.grid_9,.grid_10,.grid_11,.grid_12,.grid_13,.grid_14,.grid_15,.grid_16 {text-align:left; display:inline;float: left;position: relative; padding-right:10px; padding-left:10px; overflow:hidden;}<br />
#globalWrapper {<br />
margin: 0px;<br />
padding: 0px;<br />
}<br />
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div.color {<br />
background: rgb(51,153,153);<br />
padding: 0.5em;<br />
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</style><br />
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</head><br />
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<body background= "https://static.igem.org/mediawiki/2009/6/6d/Texture.gif"><br />
<p><br />
<img src="https://static.igem.org/mediawiki/2009/6/6e/Igem_banner_italics.jpg" width="968" height="160"/><br />
</p><br />
<br />
</body><br />
<br />
<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-22T02:56:36Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br />
<br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">The Simplified Construct</span></p><br><br />
[[Image:Turing1.GIF|center|800px]]<br />
[[Image:Simplified.png|center|800px]]<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">Working</span></p><br />
<br />
[[Image:tapstrt.png|center|450px]]<br />
<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|450px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
<br />
[[Image:tape22.png|center|450px]]<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
<br />
[[Image:Tapes.png|center|450px]]<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
<br />
[[Image:Tapend.png|center|450px]]<br />
<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">How does Simplification Help?</span></p><br />
By reducing the number of proteins required to 2 LuxI and LuxR, we drastically reduce the complexity of the system design. Our simplified constructs enable us to phenotypically mimic the behaviour of a Turing Machine Unary Adder.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-22T02:54:52Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br><br />
<br />
[[Image:Turing1.GIF|center|800px]]<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">The Simplified Construct</span></p><br><br />
[[Image:Simplified.png|center|800px]]<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">Working</span></p><br />
<br />
[[Image:tapstrt.png|center|450px]]<br />
<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|450px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
<br />
[[Image:tape22.png|center|450px]]<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
<br />
[[Image:Tapes.png|center|450px]]<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
<br />
[[Image:Tapend.png|center|450px]]<br />
<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.<br><br />
<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">How does Simplification Help?</span></p><br />
By reducing the number of proteins required to 2 LuxI and LuxR, we drastically reduce the complexity of the system design. Our simplified constructs enable us to phenotypically mimic the behaviour of a Turing Machine Unary Adder.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T02:44:34Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">Characterization of And Gates:</span></p><br><br />
Even as the wiki freezes we are characterizing Const.Prom-LacO-mRFP for its expression. We hope we get positive results.<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">We carried out the following transformations successfully:</span></p><br><br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">OUR PARTS</span></p><br />
<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Assembly</span></p><br />
<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:175%; color:#FF6600;">Failed Transformations</span></p><br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Backbones</span></p><br />
<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">GEL PICTURES</span></p><br />
<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
<br />
[[Image:14octgel.jpg|center|500px]]<br />
<html><br />
<table border="0" align="center"><br />
<tr><td>Lane1</td><td>Lane2</td><td>Lane3</td> <td>Lane4</td><td>Lane5</td><td>Lane6</td><td>Lane7</td></tr><br />
<tr><td>TorA</td><td>YcdB</td><td>YcdB</td><td>LacO</td><td>LacO</td><td>pSB1AK3</td><td>pSB1AK3</td></tr></table></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T02:43:42Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">Characterization of And Gates:</span></p><br><br />
Even as the wiki freezes we are characterizing Const.Prom-LacO-mRFP for its expression.<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">We carried out the following transformations successfully:</span></p><br><br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">OUR PARTS</span></p><br />
<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Assembly</span></p><br />
<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:175%; color:#FF6600;">Failed Transformations</span></p><br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Backbones</span></p><br />
<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">GEL PICTURES</span></p><br />
<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
<br />
[[Image:14octgel.jpg|center|500px]]<br />
<html><br />
<table border="0" align="center"><br />
<tr><td>Lane1</td><td>Lane2</td><td>Lane3</td> <td>Lane4</td><td>Lane5</td><td>Lane6</td><td>Lane7</td></tr><br />
<tr><td>TorA</td><td>YcdB</td><td>YcdB</td><td>LacO</td><td>LacO</td><td>pSB1AK3</td><td>pSB1AK3</td></tr></table></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T02:43:23Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">Characterization of And Gates:</span></p><br><br />
<br />
Even as the wiki freezes we are characterizing Const.Prom-LacO-mRFP for its expression.<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">We carried out the following transformations successfully:</span></p><br><br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">OUR PARTS</span></p><br />
<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Assembly</span></p><br />
<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:175%; color:#FF6600;">Failed Transformations</span></p><br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Backbones</span></p><br />
<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">GEL PICTURES</span></p><br />
<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
<br />
[[Image:14octgel.jpg|center|500px]]<br />
<html><br />
<table border="0" align="center"><br />
<tr><td>Lane1</td><td>Lane2</td><td>Lane3</td> <td>Lane4</td><td>Lane5</td><td>Lane6</td><td>Lane7</td></tr><br />
<tr><td>TorA</td><td>YcdB</td><td>YcdB</td><td>LacO</td><td>LacO</td><td>pSB1AK3</td><td>pSB1AK3</td></tr></table></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T02:42:42Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">Characterization of And Gates:</span></p><br><br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#0000cc;">We carried out the following transformations successfully:</span></p><br><br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">OUR PARTS</span></p><br />
<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150%; color:#FF6600;">Assembly</span></p><br />
<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:175%; color:#FF6600;">Failed Transformations</span></p><br />
<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Backbones</span></p><br />
<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">Native Biobricks</span></p><br />
<br />
<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
<p><span style="font-weight:bold; font-size:150; color:#FF6600;">GEL PICTURES</span></p><br />
<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
<br />
[[Image:14octgel.jpg|center|500px]]<br />
<html><br />
<table border="0" align="center"><br />
<tr><td>Lane1</td><td>Lane2</td><td>Lane3</td> <td>Lane4</td><td>Lane5</td><td>Lane6</td><td>Lane7</td></tr><br />
<tr><td>TorA</td><td>YcdB</td><td>YcdB</td><td>LacO</td><td>LacO</td><td>pSB1AK3</td><td>pSB1AK3</td></tr></table></div>Samitwatvehttp://2009.igem.org/Template:Team:IBB_Pune/footerTemplate:Team:IBB Pune/footer2009-10-22T02:37:30Z<p>Samitwatve: </p>
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opacity: 1.0; /* purpose: opacity already 0.8 by #nav div */<br />
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}<br />
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}<br />
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}<br />
</style><br />
<br />
<script type="text/javascript" src="http://www.kuleuven.be/bioscenter/igem/js/jquery.js"></script><br />
<br />
<script type="text/javascript"><br />
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var myLayer = document.getElementById(layer);<br />
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<script type="text/javascript"><br />
<br />
function ddmsie() {<br />
$("#nav ul").css('display', 'inline-block');<br />
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<br />
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}<br />
<br />
function ddnav() {<br />
$("#nav li").hover(<br />
function () {<br />
$(this).find("div:first").css('display', 'inline');},<br />
function () {<br />
$(this).find("div:first").css('display', 'none');}<br />
);<br />
<br />
$("#nav span > a").toggle(<br />
function () {<br />
$(this).removeClass("#nav expand").addClass("#nav collapse");<br />
$(this).css('background-color', '#99AAFF');<br />
$(this).parent().find("div:first").css('display', 'block');},<br />
function () {<br />
$(this).removeClass("#nav collapse").addClass("#nav expand");<br />
$(this).hover(<br />
function () {<br />
$(this).css('background-color', '#d4e2ef');},<br />
function () {<br />
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);<br />
$(this).parent().find("div:first").css('display', 'none');<br />
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).addClass("#nav expand");<br />
}<br />
<br />
$(function () {<br />
if(jQuery.browser.msie) ddmsie();<br />
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ddnav();<br />
});<br />
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<div align="center" id="nav"><br />
<ul><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune">Home</a></li><br />
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<li><a href="https://2009.igem.org/Team:IBB_Pune/Team">Team</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Team">Meet the Team</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/press">Press Articles</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/whyarewedifferent">Why Are We Different?</a><br />
</div><br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Project</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Project">Summary</a><br />
<span><a>Details</a><br />
<div><br />
<a href="https://2009.igem.org/SNOWDRIFT">Project1</a><br />
<a href="https://2009.igem.org/Turing_machines"> Project2</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/project3">Project3</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/systems together">Master Plan</a><br />
<br />
</div><br />
</span><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Results">Results</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Modeling">Modeling</a></li><br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Related</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Applications">Applications</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/brainstorming">Brainstorming</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/reference lit">Reading</a><br />
</div><br />
<br />
<br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">Bioethics</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">BioEthics</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Protocols">Protocols</a><br />
</div><br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Parts">Parts</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Notebook">Notebook</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/sponsors">Sponsors</a><br />
</li><br />
</ul><br />
</div><br />
</html></div>Samitwatvehttp://2009.igem.org/Template:Team:IBB_Pune/menuTemplate:Team:IBB Pune/menu2009-10-22T02:20:31Z<p>Samitwatve: </p>
<hr />
<div><html><br />
<style type="text/css"><br />
#nav, #nav ul {<br />
position: relative;<br />
margin: 0 auto; /* purpose: allow centering ul table */<br />
padding: 0;<br />
display: table /* purpose: ul doesn't stretch width 100% */<br />
}<br />
<br />
#nav li {<br />
display: table-cell; /* purpose: li behaves like table-cell */<br />
position: relative; /* purpose: non-overlap li elements in ul */<br />
list-style: none; /* purpose: remove default html list-style */<br />
}<br />
<br />
#nav li a {<br />
display: block; /* purpose: non-overlap div on a */<br />
margin: 0 1px 0 0; /* purpose: spacing main menu items */<br />
padding: 4px 35px;<br />
background-color: #000066;<br />
color: #FFF;<br />
text-align: right;<br />
text-decoration: none; /* purpose: remove underline from a */<br />
font: bold 13px arial;<br />
}<br />
<br />
#nav li a:hover {<br />
background-color: #00CC33;<br />
color: black;<br />
}<br />
<br />
#nav div {<br />
position: absolute; /* purpose: li of div doesn't spread out */<br />
display: none;<br />
width: 10em;<br />
opacity: 0.8;<br />
filter: alpha(opacity=80);<br />
border: 1px solid #28B095;<br />
background: #EAEBD8;<br />
}<br />
<br />
#nav span a, #nav div a {<br />
position: relative;<br />
display: block; /* purpose: a's in div have same width */<br />
margin: 0;<br />
padding: 5px 10px;<br />
text-align: left;<br />
font: 11px arial;<br />
}<br />
<br />
#nav span a:hover, #nav div a:hover {<br />
background-color: #00CC33;<br />
color: #000;<br />
}<br />
<br />
#nav span div {<br />
position: relative;<br />
margin: 0;<br />
border: none; /* purpose: reset border to none */<br />
border-top: 1px solid #5970B2; /* purpose: add a seperator */<br />
border-bottom: 1px solid #5970B2; /* purpose: add a seperator */<br />
opacity: 1.0; /* purpose: opacity already 0.8 by #nav div */<br />
filter: alpha(opacity=100); /* purpose: opacity already 80 by #nav div */<br />
}<br />
<br />
#nav span div a {<br />
text-indent: 10px;<br />
}<br />
<br />
#nav span div span div a {<br />
text-indent: 20px;<br />
}<br />
<br />
#nav .expand {<br />
background-image: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png');<br />
background-repeat: no-repeat;<br />
background-position: 95% 50%;<br />
}<br />
<br />
#nav .collapse {<br />
background-image: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png');<br />
background-repeat: no-repeat;<br />
background-position: 95% 50%;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://www.kuleuven.be/bioscenter/igem/js/jquery.js"></script><br />
<br />
<script type="text/javascript"><br />
function toggleElement(layer){<br />
var myLayer = document.getElementById(layer);<br />
if(myLayer.style.display=="none"){<br />
myLayer.style.display="block";<br />
myLayer.backgroundPosition="top";<br />
} else {<br />
myLayer.style.display="none";<br />
}<br />
}<br />
</script><br />
<br />
<script type="text/javascript"><br />
<br />
function ddmsie() {<br />
$("#nav ul").css('display', 'inline-block');<br />
$("#nav li").css('display', 'inline');<br />
$("#nav a").css('display', 'inline-block');<br />
$("#nav a").hover(function () {$(this).css('background-color', '#252025')},<br />
function () {$(this).css('background-color', '#649cd7')});<br />
$("#nav div a").css('display', 'block');<br />
$("#nav div").css('left', '0');<br />
$("#nav div").css('top', '100%');<br />
$("#nav span div").css('top', '0');<br />
}<br />
<br />
function ddmozilla() {<br />
<br />
}<br />
<br />
function ddnav() {<br />
$("#nav li").hover(<br />
function () {<br />
$(this).find("div:first").css('display', 'inline');},<br />
function () {<br />
$(this).find("div:first").css('display', 'none');}<br />
);<br />
<br />
$("#nav span > a").toggle(<br />
function () {<br />
$(this).removeClass("#nav expand").addClass("#nav collapse");<br />
$(this).css('background-color', '#99AAFF');<br />
$(this).parent().find("div:first").css('display', 'block');},<br />
function () {<br />
$(this).removeClass("#nav collapse").addClass("#nav expand");<br />
$(this).hover(<br />
function () {<br />
$(this).css('background-color', '#d4e2ef');},<br />
function () {<br />
$(this).css('background-color', '#649cd7');}<br />
);<br />
$(this).parent().find("div:first").css('display', 'none');<br />
}<br />
).addClass("#nav expand");<br />
}<br />
<br />
$(function () {<br />
if(jQuery.browser.msie) ddmsie();<br />
if(jQuery.browser.mozilla) ddmozilla();<br />
ddnav();<br />
});<br />
</script><br />
<div align="center" id="nav"><br />
<ul><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune">Home</a></li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Team">Team</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Team">Meet the Team</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/press">Press Articles</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/whyarewedifferent">Why Are We Different?</a><br />
</div><br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Project</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Project">Summary</a><br />
<span><a>Details</a><br />
<div><br />
<a href="https://2009.igem.org/SNOWDRIFT">Project1</a><br />
<a href="https://2009.igem.org/Turing_machines"> Project2</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/Project3">project3</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/systems together">Master Plan</a><br />
<br />
</div><br />
</span><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Results">Results</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Modeling">Modeling</a></li><br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Related</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Applications">Applications</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/brainstorming">Brainstorming</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/reference lit">Reading</a><br />
</div><br />
<br />
<br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">Bioethics</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">BioEthics</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Protocols">Protocols</a><br />
</div><br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Parts">Parts</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Notebook">Notebook</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/sponsors">Sponsors</a><br />
</li><br />
</ul><br />
</div><br />
</html></div>Samitwatvehttp://2009.igem.org/Template:Team:IBB_Pune/menuTemplate:Team:IBB Pune/menu2009-10-22T02:09:26Z<p>Samitwatve: </p>
<hr />
<div><html><br />
<style type="text/css"><br />
#nav, #nav ul {<br />
position: relative;<br />
margin: 0 auto; /* purpose: allow centering ul table */<br />
padding: 0;<br />
display: table /* purpose: ul doesn't stretch width 100% */<br />
}<br />
<br />
#nav li {<br />
display: table-cell; /* purpose: li behaves like table-cell */<br />
position: relative; /* purpose: non-overlap li elements in ul */<br />
list-style: none; /* purpose: remove default html list-style */<br />
}<br />
<br />
#nav li a {<br />
display: block; /* purpose: non-overlap div on a */<br />
margin: 0 1px 0 0; /* purpose: spacing main menu items */<br />
padding: 4px 35px;<br />
background-color: #000066;<br />
color: #FFF;<br />
text-align: right;<br />
text-decoration: none; /* purpose: remove underline from a */<br />
font: bold 13px arial;<br />
}<br />
<br />
#nav li a:hover {<br />
background-color: #00CC33;<br />
color: black;<br />
}<br />
<br />
#nav div {<br />
position: absolute; /* purpose: li of div doesn't spread out */<br />
display: none;<br />
width: 10em;<br />
opacity: 0.8;<br />
filter: alpha(opacity=80);<br />
border: 1px solid #28B095;<br />
background: #EAEBD8;<br />
}<br />
<br />
#nav span a, #nav div a {<br />
position: relative;<br />
display: block; /* purpose: a's in div have same width */<br />
margin: 0;<br />
padding: 5px 10px;<br />
text-align: left;<br />
font: 11px arial;<br />
}<br />
<br />
#nav span a:hover, #nav div a:hover {<br />
background-color: #00CC33;<br />
color: #000;<br />
}<br />
<br />
#nav span div {<br />
position: relative;<br />
margin: 0;<br />
border: none; /* purpose: reset border to none */<br />
border-top: 1px solid #5970B2; /* purpose: add a seperator */<br />
border-bottom: 1px solid #5970B2; /* purpose: add a seperator */<br />
opacity: 1.0; /* purpose: opacity already 0.8 by #nav div */<br />
filter: alpha(opacity=100); /* purpose: opacity already 80 by #nav div */<br />
}<br />
<br />
#nav span div a {<br />
text-indent: 10px;<br />
}<br />
<br />
#nav span div span div a {<br />
text-indent: 20px;<br />
}<br />
<br />
#nav .expand {<br />
background-image: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png');<br />
background-repeat: no-repeat;<br />
background-position: 95% 50%;<br />
}<br />
<br />
#nav .collapse {<br />
background-image: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png');<br />
background-repeat: no-repeat;<br />
background-position: 95% 50%;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://www.kuleuven.be/bioscenter/igem/js/jquery.js"></script><br />
<br />
<script type="text/javascript"><br />
function toggleElement(layer){<br />
var myLayer = document.getElementById(layer);<br />
if(myLayer.style.display=="none"){<br />
myLayer.style.display="block";<br />
myLayer.backgroundPosition="top";<br />
} else {<br />
myLayer.style.display="none";<br />
}<br />
}<br />
</script><br />
<br />
<script type="text/javascript"><br />
<br />
function ddmsie() {<br />
$("#nav ul").css('display', 'inline-block');<br />
$("#nav li").css('display', 'inline');<br />
$("#nav a").css('display', 'inline-block');<br />
$("#nav a").hover(function () {$(this).css('background-color', '#252025')},<br />
function () {$(this).css('background-color', '#649cd7')});<br />
$("#nav div a").css('display', 'block');<br />
$("#nav div").css('left', '0');<br />
$("#nav div").css('top', '100%');<br />
$("#nav span div").css('top', '0');<br />
}<br />
<br />
function ddmozilla() {<br />
<br />
}<br />
<br />
function ddnav() {<br />
$("#nav li").hover(<br />
function () {<br />
$(this).find("div:first").css('display', 'inline');},<br />
function () {<br />
$(this).find("div:first").css('display', 'none');}<br />
);<br />
<br />
$("#nav span > a").toggle(<br />
function () {<br />
$(this).removeClass("#nav expand").addClass("#nav collapse");<br />
$(this).css('background-color', '#99AAFF');<br />
$(this).parent().find("div:first").css('display', 'block');},<br />
function () {<br />
$(this).removeClass("#nav collapse").addClass("#nav expand");<br />
$(this).hover(<br />
function () {<br />
$(this).css('background-color', '#d4e2ef');},<br />
function () {<br />
$(this).css('background-color', '#649cd7');}<br />
);<br />
$(this).parent().find("div:first").css('display', 'none');<br />
}<br />
).addClass("#nav expand");<br />
}<br />
<br />
$(function () {<br />
if(jQuery.browser.msie) ddmsie();<br />
if(jQuery.browser.mozilla) ddmozilla();<br />
ddnav();<br />
});<br />
</script><br />
<div align="center" id="nav"><br />
<ul><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune">Home</a></li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Team">Team</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Team">Meet the Team</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/press">Press Articles</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/whyarewedifferent">Why Are We Different?</a><br />
</div><br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Project</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Project">Summary</a><br />
<span><a>Details</a><br />
<div><br />
<a href="https://2009.igem.org/SNOWDRIFT">Project1</a><br />
<a href="https://2009.igem.org/Turing_machines"> Project2</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/Project3">project3</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/systems together">Master Plan</a><br />
<br />
</div><br />
</span><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Results">Results</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Modeling">Modeling</a></li><br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Related</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Applications">Applications</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/brainstorming">Brainstorming</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/reference lit">Reading</a><br />
</div><br />
<br />
<br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">Bioethics</a><br />
<div><br />
<a href="">BioEthics</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Protocols">Protocols</a><br />
</div><br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Parts">Parts</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Notebook">Notebook</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/sponsors">Sponsors</a><br />
</li><br />
</ul><br />
</div><br />
</html></div>Samitwatvehttp://2009.igem.org/Template:Team:IBB_Pune/menuTemplate:Team:IBB Pune/menu2009-10-22T01:53:35Z<p>Samitwatve: </p>
<hr />
<div><html><br />
<style type="text/css"><br />
#nav, #nav ul {<br />
position: relative;<br />
margin: 0 auto; /* purpose: allow centering ul table */<br />
padding: 0;<br />
display: table /* purpose: ul doesn't stretch width 100% */<br />
}<br />
<br />
#nav li {<br />
display: table-cell; /* purpose: li behaves like table-cell */<br />
position: relative; /* purpose: non-overlap li elements in ul */<br />
list-style: none; /* purpose: remove default html list-style */<br />
}<br />
<br />
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<ul><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune">Home</a></li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Team">Team</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Team">Meet the Team</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/press">Press Articles</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/whyarewedifferent">Why Are We Different?</a><br />
</div><br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Project</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Project">Summary</a><br />
<span><a>Details</a><br />
<div><br />
<a href="https://2009.igem.org/SNOWDRIFT">Project1</a><br />
<a href="https://2009.igem.org/Turing_machines"> Project2</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/Project3">project3</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/systems together">Master Plan</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/project/Results">Results</a><br />
</div><br />
</span><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Modeling">Modeling</a></li><br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Project">Related</a><br />
<div><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Applications">Applications</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/brainstorming">Brainstorming</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/reference lit">Reading</a><br />
</div><br />
<br />
<br />
</li><br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/BIOETHICS">Bioethics</a><br />
<div><br />
<a href="">BioEthics</a><br />
<a href="https://2009.igem.org/Team:IBB_Pune/Protocols">Protocols</a><br />
</div><br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Parts">Parts</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/Notebook">Notebook</a><br />
<br />
</li><br />
<br />
<br />
<li><a href="https://2009.igem.org/Team:IBB_Pune/sponsors">Sponsors</a><br />
</li><br />
</ul><br />
</div><br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/ProjectTeam:IBB Pune/Project2009-10-22T01:46:39Z<p>Samitwatve: </p>
<hr />
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<P>We are a team initiated by students. This is our first year at iGEM and we are excited to be a part of the whole iGEM experience. We are proud to be the first student representatives of IBB at any international level competition.</p><br />
<p> We are a group of 7 undergrads currently studying biotechnology in the third, fourth and fifth years of the Integrated Master's course at IBB, University Pune. We are a bunch of creative, hardworking and enthusiastic students. The team members know each others strengths and weaknesses very well and that makes us work as a team.<br />
We hope to succeed this year in iGEM and make a mark in the field of synthetic biology at the international level.</p><br />
<br />
</p><br />
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</font><br />
</td><br />
</table><br />
<br />
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<html><p><span style="font-weight:bold; font-size:150%; color:#6600FF;">Overall project</span></p><br />
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<p><br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">1. Export tag synthesis and inducible export of desired proteins for in vivo simulation of the <a href="https://2009.igem.org/SNOWDRIFT"><u>SNOWDRIFT</u></a> game:</span></a></p><br />
<br />
<p>In this project, Firstly, we are planning to get the Wisconsin iGEM2008 export tag bio-bricks synthesized and standardize the induced export of proteins like beta galactosidase.The export of beta galactosidase can be used to make an in vivo simulation of the snow drift game.this system will be a great way to calculate the equilibrium concentrations of cooperators and defectors by controlling the cost and benefit ratio.The most peculiar characteristic of this system is that the cost and benefit ratio here is PROGRAMMABLE and can be measured in terms of PoPs.</p><br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">2. Bacterial <a href="https://2009.igem.org/Turing_machines"><u>Turing Machines</u></a>. We are trying to make <a href="https://2009.igem.org/Small_two-state"><u>Small two-state</u></a> Turing machines like unary adder<br />
and attempting to build an AND gate.</span></p><br />
<br />
<p>Can bacteria be used as mini computational devices?We are going to find this out by testing a system made entirely out of available bio-bricks from the registry with the introduction of two AND gates.<br />
Our primary goal is to make simple two state Turing machine like a unary adder.We will also be working on the more complicated Turing machines and also on the ways by which we could connect different two state Turing machines in combination. </P><br />
</p><br />
</font><br />
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<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">3. Inducible <a href="https://2009.igem.org/Team:IBB_Pune/project/project3"><u>Natural Competence</u></a></span></p><br />
<br />
<p> This project bears the primary goal of introducing new competence inducing genes (com) to the registry. Competence genes enhance the automated uptake of surrounding genes and further expression.These genes are derived from naturally competent bacteria. The biobricks produced can be used to form competent bacteria which do not have to be induced to take up foreign DNA by chemical means and hence can become permanently competent. Competent bacteria can simply be grown. In addition, bacterial competence coded by a biobrick can be used as a crucial component in cell to cell signalling systems and can even be used to facilitate RNA based signalling between two cells.</p><br />
</p><br />
<br />
</font><br />
</td><br />
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<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/ProjectTeam:IBB Pune/Project2009-10-22T01:43:15Z<p>Samitwatve: </p>
<hr />
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<p><br />
<P>We are a team initiated by students. This is our first year at iGEM and we are excited to be a part of the whole iGEM experience. We are proud to be the first student representatives of IBB at any international level competition.</p><br />
<p> We are a group of 7 undergrads currently studying biotechnology in the third, fourth and fifth years of the Integrated Master's course at IBB, University Pune. We are a bunch of creative, hardworking and enthusiastic students. The team members know each others strengths and weaknesses very well and that makes us work as a team.<br />
We hope to succeed this year in iGEM and make a mark in the field of synthetic biology at the international level.</p><br />
<br />
</p><br />
<br />
</font><br />
</td><br />
</table><br />
<br />
</html><br />
<br />
<br />
<br />
<html><p><span style="font-weight:bold; font-size:150%; color:#6600FF;">Overall project</span></p><br />
<br />
<html><br />
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<p><br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">1. Export tag synthesis and inducible export of desired proteins for in vivo simulation of the <a href="https://2009.igem.org/SNOWDRIFT"><u>SNOWDRIFT</u></a> game:</span></a></p><br />
<br />
<p>In this project, Firstly, we are planning to get the Wisconsin iGEM2008 export tag bio-bricks synthesized and standardize the induced export of proteins like beta galactosidase.The export of beta galactosidase can be used to make an in vivo simulation of the snow drift game.this system will be a great way to calculate the equilibrium concentrations of cooperators and defectors by controlling the cost and benefit ratio.The most peculiar characteristic of this system is that the cost and benefit ratio here is PROGRAMMABLE and can be measured in terms of PoPs.</p><br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">2. Bacterial <a href="https://2009.igem.org/Turing_machines"><u>Turing Machines</u></a>. We are trying to make <a href="https://2009.igem.org/Small_two-state"><u>Small two-state</u></a> Turing machines like unary adder<br />
and attempting to build an AND gate.</span></p><br />
<br />
<p>Can bacteria be used as mini computational devices?We are going to find this out by testing a system made entirely out of available bio-bricks from the registry with the introduction of two AND gates.<br />
Our primary goal is to make simple two state Turing machine like a unary adder.We will also be working on the more complicated Turing machines and also on the ways by which we could connect different two state Turing machines in combination. </P><br />
</p><br />
<br />
</font><br />
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<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">3. Inducible <a href="https://2009.igem.org/Team:IBB_Pune/project/project3"><u>Natural Competence</u></a></span></p><br />
<br />
<p><br />
This project bears the primary goal of introducing new competence inducing genes (com) to the registry. Competence genes enhance the automated uptake of surrounding genes and further expression.These genes are derived from naturally competent bacteria. The biobricks produced can be used to form competent bacteria which do not have to be induced to take up foreign DNA by chemical means and hence can become permanently competent. Competent bacteria can simply be grown. In addition, bacterial competence coded by a biobrick can be used as a crucial component in cell to cell signalling systems and can even be used to facilitate RNA based signalling between two cells.</p><br />
</p><br />
<br />
</font><br />
</td><br />
</table><br />
<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/ProjectTeam:IBB Pune/Project2009-10-22T01:38:52Z<p>Samitwatve: </p>
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<P>We are a team initiated by students. This is our first year at iGEM and we are excited to be a part of the whole iGEM experience. We are proud to be the first student representatives of IBB at any international level competition.</p><br />
<p> We are a group of 7 undergrads currently studying biotechnology in the third, fourth and fifth years of the Integrated Master's course at IBB, University Pune. We are a bunch of creative, hardworking and enthusiastic students. The team members know each others strengths and weaknesses very well and that makes us work as a team.<br />
We hope to succeed this year in iGEM and make a mark in the field of synthetic biology at the international level.</p><br />
<br />
</p><br />
<br />
</font><br />
</td><br />
</table><br />
<br />
</html><br />
<br />
<br />
<br />
<html><p><span style="font-weight:bold; font-size:150%; color:#6600FF;">Overall project</span></p><br />
<br />
<html><br />
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<p><br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">1. Export tag synthesis and inducible export of desired proteins for in vivo simulation of the <a href="https://2009.igem.org/SNOWDRIFT"><u>SNOWDRIFT</u></a> game:</span></a></p><br />
<br />
<p>In this project, Firstly, we are planning to get the Wisconsin iGEM2008 export tag bio-bricks synthesized and standardize the induced export of proteins like beta galactosidase.The export of beta galactosidase can be used to make an in vivo simulation of the snow drift game.this system will be a great way to calculate the equilibrium concentrations of cooperators and defectors by controlling the cost and benefit ratio.The most peculiar characteristic of this system is that the cost and benefit ratio here is PROGRAMMABLE and can be measured in terms of PoPs.</p><br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">2. Bacterial <a href="https://2009.igem.org/Turing_machines"><u>Turing Machines</u></a>. We are trying to make <a href="https://2009.igem.org/Small_two-state"><u>Small two-state</u></a> Turing machines like unary adder<br />
and attempting to build an AND gate.</span></p><br />
<br />
<p>Can bacteria be used as mini computational devices?We are going to find this out by testing a system made entirely out of available bio-bricks from the registry with the introduction of two AND gates.<br />
Our primary goal is to make simple two state Turing machine like a unary adder.We will also be working on the more complicated Turing machines and also on the ways by which we could connect different two state Turing machines in combination. </P><br />
</p><br />
<br />
</font><br />
</td><br />
</table><br />
<br />
</html><br />
<br />
<br><br />
<br />
<br />
<br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">3. Inducible <a href="https://2009.igem.org/Team:IBB_Pune/project/project3"><u>Natural Competence</u></a></span></p><br />
<br />
<p><br />
This project bears the primary goal of introducing new competence inducing genes (com) to the registry. Competence genes enhance the automated uptake of surrounding genes and further expression.These genes are derived from naturally competent bacteria. The biobricks produced can be used to form competent bacteria which do not have to be induced to take up foreign DNA by chemical means and hence can become permanently competent. Competent bacteria can simply be grown. In addition, bacterial competence coded by a biobrick can be used as a crucial component in cell to cell signalling systems and can even be used to facilitate RNA based signalling between two cells.</p><br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/ProjectTeam:IBB Pune/Project2009-10-22T01:35:41Z<p>Samitwatve: </p>
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<P>We are a team initiated by students. This is our first year at iGEM and we are excited to be a part of the whole iGEM experience. We are proud to be the first student representatives of IBB at any international level competition.</p><br />
<p> We are a group of 7 undergrads currently studying biotechnology in the third, fourth and fifth years of the Integrated Master's course at IBB, University Pune. We are a bunch of creative, hardworking and enthusiastic students. The team members know each others strengths and weaknesses very well and that makes us work as a team.<br />
We hope to succeed this year in iGEM and make a mark in the field of synthetic biology at the international level.</p><br />
<br />
</p><br />
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</font><br />
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</table><br />
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<br />
<br />
<br />
<html><p><span style="font-weight:bold; font-size:150%; color:#6600FF;">Overall project</span></p><br />
<br />
<br><br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">1. Export tag synthesis and inducible export of desired proteins for in vivo simulation of the <a href="https://2009.igem.org/SNOWDRIFT"><u>SNOWDRIFT</u></a> game:</span></a></p><br />
<br />
<p>In this project, Firstly, we are planning to get the Wisconsin iGEM2008 export tag bio-bricks synthesized and standardize the induced export of proteins like beta galactosidase.The export of beta galactosidase can be used to make an in vivo simulation of the snow drift game.this system will be a great way to calculate the equilibrium concentrations of cooperators and defectors by controlling the cost and benefit ratio.The most peculiar characteristic of this system is that the cost and benefit ratio here is PROGRAMMABLE and can be measured in terms of PoPs.</p><br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">2. Bacterial <a href="https://2009.igem.org/Turing_machines"><u>Turing Machines</u></a>. We are trying to make <a href="https://2009.igem.org/Small_two-state"><u>Small two-state</u></a> Turing machines like unary adder<br />
and attempting to build an AND gate.</span></p><br />
<br />
<p>Can bacteria be used as mini computational devices?We are going to find this out by testing a system made entirely out of available bio-bricks from the registry with the introduction of two AND gates.<br />
Our primary goal is to make simple two state Turing machine like a unary adder.We will also be working on the more complicated Turing machines and also on the ways by which we could connect different two state Turing machines in combination. </P><br />
<br />
<br />
<br><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">3. Inducible <a href="https://2009.igem.org/Team:IBB_Pune/project/project3"><u>Natural Competence</u></a></span></p><br />
<br />
<p><br />
This project bears the primary goal of introducing new competence inducing genes (com) to the registry. Competence genes enhance the automated uptake of surrounding genes and further expression.These genes are derived from naturally competent bacteria. The biobricks produced can be used to form competent bacteria which do not have to be induced to take up foreign DNA by chemical means and hence can become permanently competent. Competent bacteria can simply be grown. In addition, bacterial competence coded by a biobrick can be used as a crucial component in cell to cell signalling systems and can even be used to facilitate RNA based signalling between two cells.</p><br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/PartsTeam:IBB Pune/Parts2009-10-22T01:29:53Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br><br><br />
<p><span style="font-weight:bold; font-size:200%; color:#000000;">Parts shipped to the registry</span></p><br />
[[Image:Truck.jpg|center| "width: 1400 px"]]<br />
{|class="wikitable sortable" border="1"<br />
|- style="background: #339933; text-align: center;"<br />
|width=15| '''Sr No.'''<br />
|width=85| '''BioBrick Name'''<br />
|width=160| '''Part Name'''<br />
|width=85| '''TYPE'''<br />
|width=980| '''Description'''<br />
|width=95| '''Backbone'''<br />
|width=50| '''LENGTH (bp)'''<br />
|width=1| '''SEQUENCED'''<br />
|- style="background:#66ffcc; color:black; text-align: center" <br />
| 1<br />
| [http://partsregistry.org/Part:BBa_K233306 BBa_K233306] <br />
| YcdB<br />
| Signalling<br />
| YcdB - This part is a export tag that utilizes the Twin Arginine Transport pathway(TAT)<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 123<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 2<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233004 BBa_K233004] <br />
| lac operator<br />
| regulatory<br />
| Lac operator.<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 30<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 3<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233307 BBa_K233307] <br />
| TorA<br />
| Signalling<br />
| TorA- This part is a export tag that utilizes the Twin Arginine Transport pathway(TAT)<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 139<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 4<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233008 BBa_K233008] <br />
| TorA-GFP<br />
| Signalling<br />
| This construct is an intermediate in the production of an exportable GFP.<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 865<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 5<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233309 BBa_K233309] <br />
| YcdB-GFP<br />
| Signalling<br />
| This is an intermediate which can be used for constructing a module which can be used to produce an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 849<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 6<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233310 BBa_K233310] <br />
| constitutive GFP device<br />
| Reporter<br />
| Promoter-RBS-GFP- constitutive green fluorescent protein device<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 800<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 7<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233311 BBa_K233311] <br />
| Protein(GFP) secretion device<br />
| Device<br />
| This device codes for an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 945<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 8<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233312 BBa_K233312] <br />
| GFP secretion device using Ycdb<br />
| Device<br />
| This device codes for an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 929<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 9<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233313 BBa_K233313] <br />
| ahl induced ahl producer<br />
| Composite<br />
| construct designed to produce AHL (a quorum sensing molecule) in response to environmental AHL<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 725<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 10<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233314 BBa_K233314] <br />
| constitutive luxR production device<br />
| Generator<br />
| This part allows constitutive production of the LuxR protein which binds to AHL and the LuxR-AHL complex activates the pLuxR promoter.<br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
| 881<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 11<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233315 BBa_K233315] <br />
| constitutive LuxR generating device<br />
| Generator<br />
|This part allows constitutive production of the LuxR protein <br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
| 824<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|12<br />
|[http://partsregistry.org/wiki/index.php?title=Part:BBa_K233316 BBa_K233316]<br />
|Constitutive promoter lac operator<br />
|Device<br />
|This part can be used to calibrate the working of the lac operator<br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
|73<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|13<br />
|[http://partsregistry.org/wiki/index.php?title=Part:BBa_K233317 BBa_K233317]<br />
|rfp measurement device<br />
|measurement<br />
|This part can be used to calibrate the working of BBa_J13002<br />
|[http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
|912<br />
| - <br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
| 14<br />
| [http://partsregistry.org/Part:BBa_K233003 BBa_K233003] <br />
| AND Gate 1<br />
| Regulatory<br />
| This is an AND Gate, responsive to two external inputs, Lactose and AHL.<br />
| [http://partsregistry.org/Part:pSB1C3 pSB1C3]<br />
| 94<br />
| -<br />
|}<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#000000;">Parts designed by us</span></p><br><br />
{|class="wikitable sortable" border="1"<br />
|- style="background: #339933; Align: center;"<br />
|width=100| '''Sr No.'''<br />
|width=200| '''BioBrick Name'''<br />
|width=400| '''Part Name'''<br />
|WIDTH=400|'''Description'''<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|1<br />
|<html> <a href="http://partsregistry.org/Part:BBa_K233002"> Part: BBa_K233002</a> </html> <br />
|Snowdrift 2 , using YcdB. <br />
|A module to secrete B-galactosidase using the TAT-export Pathway<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|2<br />
|<html> <a href="http://partsregistry.org/Part:BBa_K233001"> Part: BBa_K233001</a><br />
</html><br />
|Snowdrift 1 , using TorA<br />
| A module to secrete B-galactosidase using the TAT-export Pathway<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|3<br />
| <html><br />
<a href="http://partsregistry.org/Part:BBa_K233005"> Part: BBa_K233005</a><br />
</html><br />
|AND gate 2<br />
| phage protein ogr regulated AND GATE<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|4<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233006"> Part: BBa_K233006</a><br />
</html> <br />
|AND Gate 3<br />
|Phage T7 polymerase regulated And Gate<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|5<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233318"> Part: BBa_K233318</a><br />
</html> <br />
|Gfp exporter 1<br />
|A tester for Snowdrift 1<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|6<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233319"> Part: BBa_K233319</a><br />
</html> <br />
|Gfp exporter 2<br />
|A tester for Snowdrift 2<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|7<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233320"> Part: BBa_K233320</a><br />
</html> <br />
|Turing Machine- Unary Adder<br />
|The simplified construct for the Turing machine<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|8<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233321"> Part: BBa_K233321</a><br />
</html> <br />
|Turing Machine- Unary Adder 2<br />
|The simplified construct for the Turing Machine 2<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|9<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233322"> Part: BBa_K233322</a><br />
</html> <br />
|Turing machine cassette 2<br />
|AHL and Lactose Modulated Cell Lysis <br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|10<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233323"> Part: BBa_K233323</a><br />
</html> <br />
|Turing machine cassette 2<br />
|AHL and Lactose modulated Gfp production<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|11<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233324"> Part: BBa_K233324</a><br />
</html> <br />
|pIDTSmart-KAN Vector<br />
|The Backbone of our favorite parts<br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
|12<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233325"> Part: BBa_K233325</a><br />
</html> <br />
|The Complete Turing Machine Construct<br />
|The Complete Turing Machine Construct<br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
|}</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/PartsTeam:IBB Pune/Parts2009-10-22T01:29:20Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br><br><br />
<p><span style="font-weight:bold; font-size:200%; color:#000000;">Parts shipped to the registry</span></p><br />
[[Image:Truck.jpg|center| "width: 1400 px"]]<br />
{|class="wikitable sortable" border="1"<br />
|- style="background: #339933; text-align: center;"<br />
|width=15| '''Sr No.'''<br />
|width=85| '''BioBrick Name'''<br />
|width=160| '''Part Name'''<br />
|width=85| '''TYPE'''<br />
|width=980| '''Description'''<br />
|width=95| '''Backbone'''<br />
|width=50| '''LENGTH (bp)'''<br />
|width=1| '''SEQUENCED'''<br />
|- style="background:#66ffcc; color:black; text-align: center" <br />
| 1<br />
| [http://partsregistry.org/Part:BBa_K233306 BBa_K233306] <br />
| YcdB<br />
| Signalling<br />
| YcdB - This part is a export tag that utilizes the Twin Arginine Transport pathway(TAT)<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 123<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 2<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233004 BBa_K233004] <br />
| lac operator<br />
| regulatory<br />
| Lac operator.<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 30<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 3<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233307 BBa_K233307] <br />
| TorA<br />
| Signalling<br />
| TorA- This part is a export tag that utilizes the Twin Arginine Transport pathway(TAT)<br />
| [http://partsregistry.org/Part:BBa_K233324 BBa_K233324]<br />
| 139<br />
| Yes<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 4<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233008 BBa_K233008] <br />
| TorA-GFP<br />
| Signalling<br />
| This construct is an intermediate in the production of an exportable GFP.<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 865<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 5<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233309 BBa_K233309] <br />
| YcdB-GFP<br />
| Signalling<br />
| This is an intermediate which can be used for constructing a module which can be used to produce an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 849<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 6<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233310 BBa_K233310] <br />
| constitutive GFP device<br />
| Reporter<br />
| Promoter-RBS-GFP- constitutive green fluorescent protein device<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 800<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 7<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233311 BBa_K233311] <br />
| Protein(GFP) secretion device<br />
| Device<br />
| This device codes for an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 945<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 8<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233312 BBa_K233312] <br />
| GFP secretion device using Ycdb<br />
| Device<br />
| This device codes for an exportable GFP<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 929<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 9<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233313 BBa_K233313] <br />
| ahl induced ahl producer<br />
| Composite<br />
| construct designed to produce AHL (a quorum sensing molecule) in response to environmental AHL<br />
| [http://partsregistry.org/Part:pSB1AK3 pSB1AK3]<br />
| 725<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 10<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233314 BBa_K233314] <br />
| constitutive luxR production device<br />
| Generator<br />
| This part allows constitutive production of the LuxR protein which binds to AHL and the LuxR-AHL complex activates the pLuxR promoter.<br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
| 881<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
| 11<br />
| [http://partsregistry.org/wiki/index.php?title=Part:BBa_K233315 BBa_K233315] <br />
| constitutive LuxR generating device<br />
| Generator<br />
|This part allows constitutive production of the LuxR protein <br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
| 824<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|12<br />
|[http://partsregistry.org/wiki/index.php?title=Part:BBa_K233316 BBa_K233316]<br />
|Constitutive promoter lac operator<br />
|Device<br />
|This part can be used to calibrate the working of the lac operator<br />
| [http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
|73<br />
| -<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|13<br />
|[http://partsregistry.org/wiki/index.php?title=Part:BBa_K233317 BBa_K233317]<br />
|rfp measurement device<br />
|measurement<br />
|This part can be used to calibrate the working of BBa_J13002<br />
|[http://partsregistry.org/Part:pSB1A2 pSB1A2]<br />
|912<br />
| - <br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
| 14<br />
| [http://partsregistry.org/Part:BBa_K233003 BBa_K233003] <br />
| AND Gate 1<br />
| Regulatory<br />
| This is an AND Gate, responsive to two external inputs, Lactose and AHL.<br />
| [http://partsregistry.org/Part:pSB1C3 pSB1C3]<br />
| 94<br />
| -<br />
|}<br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">Parts designed by us</span></p><br><br />
{|class="wikitable sortable" border="1"<br />
|- style="background: #339933; Align: center;"<br />
|width=100| '''Sr No.'''<br />
|width=200| '''BioBrick Name'''<br />
|width=400| '''Part Name'''<br />
|WIDTH=400|'''Description'''<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|1<br />
|<html> <a href="http://partsregistry.org/Part:BBa_K233002"> Part: BBa_K233002</a> </html> <br />
|Snowdrift 2 , using YcdB. <br />
|A module to secrete B-galactosidase using the TAT-export Pathway<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|2<br />
|<html> <a href="http://partsregistry.org/Part:BBa_K233001"> Part: BBa_K233001</a><br />
</html><br />
|Snowdrift 1 , using TorA<br />
| A module to secrete B-galactosidase using the TAT-export Pathway<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|3<br />
| <html><br />
<a href="http://partsregistry.org/Part:BBa_K233005"> Part: BBa_K233005</a><br />
</html><br />
|AND gate 2<br />
| phage protein ogr regulated AND GATE<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|4<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233006"> Part: BBa_K233006</a><br />
</html> <br />
|AND Gate 3<br />
|Phage T7 polymerase regulated And Gate<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|5<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233318"> Part: BBa_K233318</a><br />
</html> <br />
|Gfp exporter 1<br />
|A tester for Snowdrift 1<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|6<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233319"> Part: BBa_K233319</a><br />
</html> <br />
|Gfp exporter 2<br />
|A tester for Snowdrift 2<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|7<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233320"> Part: BBa_K233320</a><br />
</html> <br />
|Turing Machine- Unary Adder<br />
|The simplified construct for the Turing machine<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|8<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233321"> Part: BBa_K233321</a><br />
</html> <br />
|Turing Machine- Unary Adder 2<br />
|The simplified construct for the Turing Machine 2<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|9<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233322"> Part: BBa_K233322</a><br />
</html> <br />
|Turing machine cassette 2<br />
|AHL and Lactose Modulated Cell Lysis <br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|10<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233323"> Part: BBa_K233323</a><br />
</html> <br />
|Turing machine cassette 2<br />
|AHL and Lactose modulated Gfp production<br />
|-<br />
|- style="background:#66ffcc; color:black; text-align: center"<br />
|11<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233324"> Part: BBa_K233324</a><br />
</html> <br />
|pIDTSmart-KAN Vector<br />
|The Backbone of our favorite parts<br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
|12<br />
|<html><br />
<a href="http://partsregistry.org/Part:BBa_K233325"> Part: BBa_K233325</a><br />
</html> <br />
|The Complete Turing Machine Construct<br />
|The Complete Turing Machine Construct<br />
|-style="background:#66ffcc; color:black; text-align: center" <br />
|}</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/whyarewedifferentTeam:IBB Pune/whyarewedifferent2009-10-22T01:24:59Z<p>Samitwatve: /* WHY ARE WE DIFFERENT? */</p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{team:IBB_Pune/menu}}<br />
<br />
<br />
==WHY ARE WE DIFFERENT?==<br />
<br />
<br />
*'''Student Initiative'''<br />
::* The one thing that separates us from other teams in iGEM'09 is that we are a completely student initiated team. From looking for ideas, getting advisors, getting the requisite permissions from the university, getting funding etc was done by students.<br />
<br />
<br />
*'''Intellectual Resources'''<br />
::* One of our initial problems we faced was that not only did we lack a course in Synthetic Biology available to us, but also that there is no researcher working in Synthetic Biology from amongst the many biology institutes in our city. We overcame this problem by figuring out many things on our own (making lots of mistakes along the way :P) helped in no small amount by our advisor Praveen Sahu, an expert in things MolBio.<br />
<br />
<br />
*'''Academic Background'''<br />
::* Unlike most other teams, all the 6 student members of our team have the same academic background. We are all undergraduates studying Biotechnology.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:19:40Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
=We carried out the following transformations successfully:=<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
[[Image:14octgel.jpg|center|500px]]</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:08:14Z<p>Samitwatve: /* GEL PICTURES */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==<br />
[[Image:10sepgel.jpg|center|500px]]<br />
<br><br><br />
[[Image:14octgel.jpg|center|500px]]</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:07:38Z<p>Samitwatve: /* GEL PICTURES */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==<br />
[[Image:10sepgel.jpg|center]]<br />
[[Image:14octgel.jpg|center|500px]]</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:07:22Z<p>Samitwatve: /* GEL PICTURES */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==<br />
[[Image:10sepgel.jpg]]<br />
[[Image:14octgel.jpg|center|500px]]</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:06:16Z<p>Samitwatve: /* GEL PICTURES */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==<br />
[[Image:10sepgel.jpg]]</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T01:05:07Z<p>Samitwatve: /* Native Biobricks */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP<br />
<br />
==GEL PICTURES==</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/nucleic-acid-based-signallingTeam:IBB Pune/nucleic-acid-based-signalling2009-10-22T01:01:11Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
=Riboswitches=<br />
<br />
A riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, depending on the presence or absence of its target molecule.<br />
<br />
They are metabolite-binding domains within certain messenger RNAs that act as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression.<br />
<br />
==The idea==<br />
<br />
Similar to the concept of protein-based signalling, we propose a nucleic acid based signaling system based on riboswitches. This system will consist of different strains that encode riboswitches and they will interact by means of exported riboswitches. <br />
<br />
The Riboswitches will have a an export tag fused to it at the 5' end of the switch. These switches will be placed under regulatable promoters like the pLuxR (responsive to LuxR and AHL), pLL(responsive to ogr), or pLac( responsive to lactose/IPTG)<br />
<br />
A second strain will then take this secreted riboswitch up and thus regulate the activity of the genes present within the control of this riboswitch. Thus this can lead to a signaling cascade and efficient cell-cell communication.<br />
<br />
<br />
==Why riboswitches?==<br />
<br />
This system involves the use of riboswitches which are small RNA molecules. The energy required for a cell to produce a riboswitch is far lesser than that required to produce a protein. Also, since this approach works at the mRNA level, it eliminates the need to use protein responsive promoters like pLL. Thus we can regulate the expression level of any gene within a cell using such a system.<br />
<br />
==How do we plan to implement this plan==<br />
<br />
<br />
<html><br />
<p><a href="https://2009.igem.org/Team:IBB_Pune/project/project3<br />
"><span style="font-weight:bold; font-size:150%; color:#6600FF;"><u>Find out</u></span></a></p><br />
<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/protein-based-signallingTeam:IBB Pune/protein-based-signalling2009-10-22T01:00:05Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
=The Complete Turing Machine=<br />
<br />
[[Image: BBa_K233325.JPG|center|900px]]<br />
<br />
The above image is a representation of the complete turing machine including inter state regulation. This model is true to Alan Turing's vision of multi-mutually exclusive states and the states being regulated by one another through outputs.<br />
<br />
==Working of the Construct==<br />
[[Image:Complicated.png|center|800px]]<br />
In the above construct, there are three independent modules that function<br />
* A constitutively working module which produces LuxR protein and LacI and Cassette 1 (encodes ogr and activates state 'B')<br />
*A State-'B' which is activated by State' A' and which in turn represses the working of the default state<br />
*An AND gate regulated activation of the turing machine function (it could be lysis, expression of a fluorescent protein or the synthesis of vanillin or methyl salicylate)<br />
<br />
The default state of the turing machine is 'A'.<br />
In this state it encounters a '0' (represented by Lactose) first.However there are no Lactose responsive elements in either the first or the second module.<br />
The third Module which has such a module however also requires the presence of the phage protein 'ogr '<br />
. Hence the first 0 is unable to produce any effect and the machine moves on to the next cell in the tape while remaining in state A.<br />
<br />
The machine now encounters a 1 in this default state 'A' (represented by AHL). This results in the activation of the second module which in turn produces more of ogr. This acts like a positive feedback loop and hence state 'B' is switched on and can remain active without intervention from cassette 1.<br />
<br />
Cassette 2 also encodes for the phage lambda cI repressor protein which represses cassette 1. Thus we have a system in which the two states are mutually exclusive. In state 'B', when the machine encounters a '1', it keeps the '1' unchanged and transits to the next cell. <br />
<br />
Now in this state, when the machine encounters a '0' the AND gate obtains both its inputs viz. ogr and lactose which results in the production of Homoserine Lactone Synthase (enzyme producing AHL). This results in the conversion of the '0' to a '1'. Therefore this construct behaves like a unary adder as per Turing's specification.<br />
<br />
=Problems Associated with such an Approach=<br />
*At 6.5kb the construct too darn BIG!<br />
<br />
*It is a metabolic load on the cell. <br />
<br />
*Assembling these many parts together is extremely challenging by using even the most advanced molecular biology techniques.<br />
<br />
*Transformation of such a large construct is difficult. <br />
<br />
*It poses major complications with respect to quality control, sequencing and data validation.<br />
<br />
One of the methods of solving these problems is to [https://2009.igem.org/Team:IBB_Pune/construct simplify] the construct.<br />
<br />
=Modular Systems=<br />
We decided to use a modular approach to tackle the problems enlisted above.<br />
<br />
We therefore decided to divide the complicated construct into three separate interdependent strains which together combine to form the Unary Adder.<br />
<br />
[[Image:Asdasdasd.png|center|968px]]<br />
<br />
In this system the first module gets activated in the presence of AHL ( '1' ) and produces ogr attached to an export tag (YcdB or TorA) this results in the export of ogr protein which acts as an input for the second module.<br />
<br />
The second module gets activated by ogr and produces phage lambda repressor cI protein and more ogr protein in response. The cI protein serves to turn the first module 'off' and and keeps itself on by a positive feedback loop regulated by ogr.<br />
<br />
The third module gets activated in response to extracellular lactose and ogr and produces RFP. This indicates the conversion of a '0' to '1'.<br />
<br />
This functions as a unary adder<br />
9<br />
<br />
=Proof-of-concept=<br />
As a proof of concept of the export-based signalling machinery, we attempted to test the working of the export tags by fusing them upstream of Green Fluorescent Protein.<br />
<br />
<html><br />
<p><a href="https://2009.igem.org/SNOWDRIFT/Proof_of_concept<br />
"><span style="font-weight:bold; font-size:150%; color:#6600FF;"><u>NEXT</u></span></a></p><br />
<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/protein-based-signallingTeam:IBB Pune/protein-based-signalling2009-10-22T00:58:31Z<p>Samitwatve: /* Problems Associated with such an Approach */</p>
<hr />
<div>=The Complete Turing Machine=<br />
<br />
[[Image: BBa_K233325.JPG|center|900px]]<br />
<br />
The above image is a representation of the complete turing machine including inter state regulation. This model is true to Alan Turing's vision of multi-mutually exclusive states and the states being regulated by one another through outputs.<br />
<br />
==Working of the Construct==<br />
[[Image:Complicated.png|center|800px]]<br />
In the above construct, there are three independent modules that function<br />
* A constitutively working module which produces LuxR protein and LacI and Cassette 1 (encodes ogr and activates state 'B')<br />
*A State-'B' which is activated by State' A' and which in turn represses the working of the default state<br />
*An AND gate regulated activation of the turing machine function (it could be lysis, expression of a fluorescent protein or the synthesis of vanillin or methyl salicylate)<br />
<br />
The default state of the turing machine is 'A'.<br />
In this state it encounters a '0' (represented by Lactose) first.However there are no Lactose responsive elements in either the first or the second module.<br />
The third Module which has such a module however also requires the presence of the phage protein 'ogr '<br />
. Hence the first 0 is unable to produce any effect and the machine moves on to the next cell in the tape while remaining in state A.<br />
<br />
The machine now encounters a 1 in this default state 'A' (represented by AHL). This results in the activation of the second module which in turn produces more of ogr. This acts like a positive feedback loop and hence state 'B' is switched on and can remain active without intervention from cassette 1.<br />
<br />
Cassette 2 also encodes for the phage lambda cI repressor protein which represses cassette 1. Thus we have a system in which the two states are mutually exclusive. In state 'B', when the machine encounters a '1', it keeps the '1' unchanged and transits to the next cell. <br />
<br />
Now in this state, when the machine encounters a '0' the AND gate obtains both its inputs viz. ogr and lactose which results in the production of Homoserine Lactone Synthase (enzyme producing AHL). This results in the conversion of the '0' to a '1'. Therefore this construct behaves like a unary adder as per Turing's specification.<br />
<br />
=Problems Associated with such an Approach=<br />
*At 6.5kb the construct too darn BIG!<br />
<br />
*It is a metabolic load on the cell. <br />
<br />
*Assembling these many parts together is extremely challenging by using even the most advanced molecular biology techniques.<br />
<br />
*Transformation of such a large construct is difficult. <br />
<br />
*It poses major complications with respect to quality control, sequencing and data validation.<br />
<br />
One of the methods of solving these problems is to [https://2009.igem.org/Team:IBB_Pune/construct simplify] the construct.<br />
<br />
=Modular Systems=<br />
We decided to use a modular approach to tackle the problems enlisted above.<br />
<br />
We therefore decided to divide the complicated construct into three separate interdependent strains which together combine to form the Unary Adder.<br />
<br />
[[Image:Asdasdasd.png|center|968px]]<br />
<br />
In this system the first module gets activated in the presence of AHL ( '1' ) and produces ogr attached to an export tag (YcdB or TorA) this results in the export of ogr protein which acts as an input for the second module.<br />
<br />
The second module gets activated by ogr and produces phage lambda repressor cI protein and more ogr protein in response. The cI protein serves to turn the first module 'off' and and keeps itself on by a positive feedback loop regulated by ogr.<br />
<br />
The third module gets activated in response to extracellular lactose and ogr and produces RFP. This indicates the conversion of a '0' to '1'.<br />
<br />
This functions as a unary adder<br />
9<br />
<br />
=Proof-of-concept=<br />
As a proof of concept of the export-based signalling machinery, we attempted to test the working of the export tags by fusing them upstream of Green Fluorescent Protein.<br />
<br />
<html><br />
<p><a href="https://2009.igem.org/SNOWDRIFT/Proof_of_concept<br />
"><span style="font-weight:bold; font-size:150%; color:#6600FF;"><u>NEXT</u></span></a></p><br />
<br />
</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-22T00:55:35Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br><br />
<br />
[[Image:Turing1.GIF|center|800px]]<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">The Simplified Construct</span></p><br><br />
[[Image:Simplified.png|center|800px]]<br />
==Working==<br />
<br />
<br />
[[Image:tapstrt.png|center|450px]]<br />
<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|450px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
<br />
[[Image:tape22.png|center|450px]]<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
<br />
[[Image:Tapes.png|center|450px]]<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
<br />
[[Image:Tapend.png|center|450px]]<br />
<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.<br />
<br />
==How does Simplification Help?==<br />
<br />
By reducing the number of proteins required to 2 LuxI and LuxR, we drastically reduce the complexity of the system design. Our simplified constructs enable us to phenotypically mimic the behaviour of a Turing Machine Unary Adder.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T00:42:36Z<p>Samitwatve: /* Native Biobricks */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
# Lysis Cassette<br />
# Constitutive GFP<br />
# COnstitutive CFP</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T00:36:27Z<p>Samitwatve: /* Assembly */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
<br />
<br />
==Failed Transformations==<br />
<br />
===Backbones===<br />
# pSB1AK3 with CcdB gene<br />
# pSB1T3 with CcdB gene<br />
# pSB1C3 with CcdB gene<br />
# pSB1K3 with CcdB gene<br />
# pSB1A3 with CcdB gene<br />
# pSB1AC3 with CcdB gene<br />
# pSB1AK3 with mRFP<br />
# pSB1T3 with mRFP<br />
# pSB1C3 with mRFP<br />
# pSB1K3 with mRFP<br />
# pSB1A3 with mRFP<br />
# pSB1AC3 with mRFP<br />
<br />
===Native Biobricks===<br />
<br />
#</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T00:29:22Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
# pLL promoter - BBa_I746365<br />
# GFP coding sequence - BBa_E0040<br />
# RFP coding sequence <br />
# GFP Translational unit <br />
# RFP Translational unit <br />
# Enhanced CFP<br />
# Fast GFP<br />
# Constitutive promoter -BBa_J23102<br />
# Promoter + RBS<br />
# T7 promoter<br />
# pLuxR<br />
# Double terminator<br />
# RBS<br />
# Constitutive LuxI<br />
# LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
# YcdB<br />
# TorA<br />
# Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
# Const. Promoter-LacO<br />
# PluxR- LuxI<br />
# {Promoter + RBS}-GFP<br />
# {Promoter + RBS}-TorA<br />
# {Promoter + RBS}-Ycdb<br />
# luxR-PluxR-{RBS-LuxI}<br />
# Promoter + RBS <br />
# YcdB-GFP<br />
# TorA-GFP<br />
# {Promoter + RBS}-LuxR<br />
# {Promoter + RBS}-YcdB-GFP<br />
# {Promoter + RBS}-TorA-GFP<br />
# Const. Promoter-LuxR<br />
#</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T00:21:46Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
We carried out the following transformations successfully:<br />
<br />
==Native Biobricks==<br />
<br />
1) pLL promoter - BBa_I746365<br />
2) GFP coding sequence - BBa_E0040<br />
3) RFP coding sequence <br />
4) GFP Translational unit <br />
5) RFP Translational unit <br />
6) Enhanced CFP<br />
7) Fast GFP<br />
8) Constitutive promoter -BBa_J23102<br />
9) Promoter + RBS<br />
10) T7 promoter<br />
11) pLuxR<br />
12) Double terminator<br />
13) RBS<br />
14) Constitutive LuxI<br />
15) LuxR Translational unit<br />
<br />
==OUR PARTS==<br />
<br />
1) YcdB<br />
2) TorA<br />
3) Lac Operator<br />
<br />
<br />
==Assembly==<br />
<br />
1) Const. Promoter-LacO<br />
2) PluxR- LuxI<br />
3) {Promoter + RBS}-GFP<br />
4) {Promoter + RBS}-TorA<br />
5) {Promoter + RBS}-Ycdb<br />
6) luxR-PluxR-{RBS-LuxI}<br />
7) Promoter + RBS <br />
8) YcdB-GFP<br />
9) TorA-GFP<br />
10) {Promoter + RBS}-LuxR<br />
11) {Promoter + RBS}-YcdB-GFP<br />
12) {Promoter + RBS}-TorA-GFP<br />
13) Const. Promoter-LuxR<br />
14)</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/project/ResultsTeam:IBB Pune/project/Results2009-10-22T00:08:21Z<p>Samitwatve: /* Project 1 */</p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<br />
<br />
=Project 2 =</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/ModelingTeam:IBB Pune/Modeling2009-10-22T00:03:43Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br />
<br />
<html><br />
<br><br />
<p><span style="font-weight:bold; font-size:200%; color:#006600;">Modelling</span></p></html><br />
<p>The aim of the modelling aspect of our project is to develop simulations that would enable us to predict the behavior of the export tag with the Snowdrift Game as the backdrop. </p><br />
<br />
<html><br />
<p><span style="font-weight:bold; font-size:200%; color:#006600;"><br />
<br><br />
Project 1- A Model Of The Snowdrift Game</span><br />
</p></html><br />
<br />
<br><br><br />
[[Image:Modelling (1).JPG|center|800 px|thumbnail|Model]]<br />
<br />
<br><br />
<br />
<br />
<br />
<p>This is a Model of the Snowdrift game. This model assumes use of two different strains as '''co-operators''' and '''defectors'''.</p><br />
Co-operators constitutively secrete/produce b-gal. Defectors cannot secrete/produce B-gal.<br />
<br />
This model is for a Single iteration of the experiment i.e. the culture is initiated in shaker flask and allowed to grow. In order to find ESS or stable equilibria, we will have to repeatedly subculture the cells under similar conditions, by replacing the medium or supplying fresh medium. In such a setup, the input for the next cycle of experiments will be the output of the previous cycle of experiments. <br />
<br />
<span style="font-weight:bold; font-size:125%; color:#006600;"><p>Assumptions</p></span><br />
<br />
''At time t=0;''<br />
<br />
*There are ''''k'''' co-operators and ''''N-k'''' defectors<br />
<br />
*Medium contains ''''L'''' mg/ml of lactose, glucose conc. (g) = 0<br />
<br />
*Culture is well mixed. <br />
<br />
*Extracellular Enzyme conc ('''Ec''') = 0 units/ml<br />
<span style="font-weight:bold; font-size:150%; color:#006600;"><p>Artificial assumptions</p></span><br />
*<p>Glucose is consumed by all cells. Galactose is also consumed at the same rate Gc mg/cell/min/ml.<br />
*The metabolic benefit due to glucose and galactose is same.So effectively each lactose molecule gives rise to 2 glucose molecules</p><br />
<br />
*<p>There is no intracellular lactose metabolism (only extracellular). </p><br />
<br />
*<p>There is no lag in enzyme production and secretion.</p><br />
<br />
*<p>Rate of degradation of enzyme is zero</p><br />
<span style="font-weight:bold; font-size:125%; color:#006600;"><p>Model</p></span><br />
In this Model,<br />
<br />
1. Each co-operator secretes ''''B'''' units of enzyme/ min and pays cost of ''''c''''/min <br />
<br />
2. These molecules diffuse freely through the medium <br />
<br />
3. They convert Lactose to Glucose + Galactose given by <br />
<br />
<br />
g = (k2)*(Ec)*(L) mg/ml/min .... (1) <br />
<br />
4. Absorbed glucose confers growth rate advantage of '''r''' <br />
<br />
r = (R)*(g)*(Gc) .... (2)<br />
<br />
After each min, the population of co-operators and defectors is updated depending upon their respective growth rates. <br />
<br />
D(t) = D(t-1)+ r * D(t-1) .... (3) Defector population (t) <br />
k(t) = k(t-1) + (r-c) * k(t-1) .... (4) Co-operator population (t)<br />
<br />
<br />
<br />
<br />
The Lactose that remains at time ''''t'''' is given by:<br />
<br><br />
L = L - L * Ec * k2 .... (5)<br />
<br />
<br />
<br />
The net Glucose present in the medium at time ''''t'''' is given by:<br />
<br><br />
G = G +(( 2* L* Ec* k2)-( N * Gc) .... (6)<br />
<span style="font-weight:bold; font-size:125%; color:#006600;"><p>Results</p></span><br />
[[Image:Pic1.GIF |center|400px|thumbnail|Plot of lactose and glucose levels at k2=1, Gc = 0.0001 mg/cell/min, R=0.99, c=0.001 ]]<br />
<br><br />
<br />
[[Image:Pic2.GIF |center|400px|thumbnail|The population distribution at k2=1, Gc = 0.0001 mg/cell/min, R=0.99, c=0.001]]<br />
<br />
<br><br />
<br />
[[Image:Pic3.gif |center|400px|thumbnail|The Cooperator to defector ratio at k2=1, Gc = 0.0001 mg/cell/min, R=0.99, c=0.001 ]]</div>Samitwatvehttp://2009.igem.org/Turing_machinesTuring machines2009-10-21T23:10:11Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{team:IBB_Pune/menu}}<br />
<html><br />
<body bgcolor="blue"><br />
</html><br />
<br />
=Turing Machines=<br />
<html><br />
<p><p>Turing machines form an extremely exciting part of mathematics, yes; they are a piece of mathematics(!) which are elegant, simple and powerful. They form the basis of computer programming. They help us understand the nature of algorithms and how the mind works.<br />
<br />
Let us first try to see what a Turing machine actually is.<br />
The scientist and brilliant mathematician Alan Turing came up with this idea in an attempt to solve a problem in mathematics known as ''Entscheidungsproblem''. It translates to "a decision problem", and it was put forward by the German mathematician David Hilbert. Hilbert’s problem was- is there any general algorithmic procedure for resolving mathematical questions or whether in principle such a procedure might exist?.</p></p></body><br />
</html><br />
<br />
==Turing’s concept:==<br />
<br />
[[Image:Turing.jpg|center|thumbnail|500px]]<br />
<br />
<br />
Turing’s machine consisted of a box capable of performing the following actions on a ''tape'' supplied to it:<br />
It can ‘''read''’ the marks on the tape,<br />
It can erase the marks on the tape or can change the marks on the existing tape,<br />
It can move the tape towards the right or left, allowing it to ‘read’ further marks on the tape.<br />
<br />
[[Image:tape4.png|center|500px|thumbnail]]<br />
<br />
<br />
<br />
The above is a sample of such a ‘tape’ which is fed to the machine. <br />
For simplicity we label the tape in only two ways viz. 0 and 1. <br />
<br />
Turing allowed more complex markings but (heck) that shouldn’t bother us here.<br />
<br />
Coming back to the box, as we have seen that the box can move the tape, change its marks etc. but it should be noted that the machine does these operations in a ''non-random, deterministic'' way. That is, we can predict what the action of the Turing machine on the tape will be. The box has a set of finite internal states, but can work algorithmically on potentially infinite calculations using the tape.<br />
<br />
If you are wondering, "HOW??"<br />
<html><br />
<p><a href="https://2009.igem.org/Small_two-state"> <span style="font-weight:bold; font-size:125%; color:#6600FF;">Click Here</span></a></p><br />
</html><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">References</span></p><br />
<br />
1. http://en.wikipedia.org/wiki/Turing_machine<br />
<br />
2. http://plato.stanford.edu/entries/turing-machine/<br />
<br />
3. http://mathworld.wolfram.com/TuringMachine.html<br />
<br />
4. "The Emperor's New Mind", 2nd Edition, Roger Penrose, Martin Gardner (1999), Oxford University Press</div>Samitwatvehttp://2009.igem.org/Turing_machinesTuring machines2009-10-21T23:08:56Z<p>Samitwatve: </p>
<hr />
<div>{{Team:IBB_Pune/header}}<br />
{{team:IBB_Pune/menu}}<br />
<html><br />
<body bgcolor="blue"><br />
<br />
=Turing Machines=<br />
<br />
<br />
<br />
<p><p>Turing machines form an extremely exciting part of mathematics, yes; they are a piece of mathematics(!) which are elegant, simple and powerful. They form the basis of computer programming. They help us understand the nature of algorithms and how the mind works.<br />
<br />
Let us first try to see what a Turing machine actually is.<br />
The scientist and brilliant mathematician Alan Turing came up with this idea in an attempt to solve a problem in mathematics known as ''Entscheidungsproblem''. It translates to "a decision problem", and it was put forward by the German mathematician David Hilbert. Hilbert’s problem was- is there any general algorithmic procedure for resolving mathematical questions or whether in principle such a procedure might exist?.</p></p></body><br />
</html><br />
<br />
==Turing’s concept:==<br />
<br />
[[Image:Turing.jpg|center|thumbnail|500px]]<br />
<br />
<br />
Turing’s machine consisted of a box capable of performing the following actions on a ''tape'' supplied to it:<br />
It can ‘''read''’ the marks on the tape,<br />
It can erase the marks on the tape or can change the marks on the existing tape,<br />
It can move the tape towards the right or left, allowing it to ‘read’ further marks on the tape.<br />
<br />
[[Image:tape4.png|center|500px|thumbnail]]<br />
<br />
<br />
<br />
The above is a sample of such a ‘tape’ which is fed to the machine. <br />
For simplicity we label the tape in only two ways viz. 0 and 1. <br />
<br />
Turing allowed more complex markings but (heck) that shouldn’t bother us here.<br />
<br />
Coming back to the box, as we have seen that the box can move the tape, change its marks etc. but it should be noted that the machine does these operations in a ''non-random, deterministic'' way. That is, we can predict what the action of the Turing machine on the tape will be. The box has a set of finite internal states, but can work algorithmically on potentially infinite calculations using the tape.<br />
<br />
If you are wondering, "HOW??"<br />
<html><br />
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</html><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">References</span></p><br />
<br />
1. http://en.wikipedia.org/wiki/Turing_machine<br />
<br />
2. http://plato.stanford.edu/entries/turing-machine/<br />
<br />
3. http://mathworld.wolfram.com/TuringMachine.html<br />
<br />
4. "The Emperor's New Mind", 2nd Edition, Roger Penrose, Martin Gardner (1999), Oxford University Press</div>Samitwatvehttp://2009.igem.org/Turing_machinesTuring machines2009-10-21T23:07:58Z<p>Samitwatve: </p>
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<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">Turing Machines</span></p><br />
<br />
<br />
<br />
<p><p>Turing machines form an extremely exciting part of mathematics, yes; they are a piece of mathematics(!) which are elegant, simple and powerful. They form the basis of computer programming. They help us understand the nature of algorithms and how the mind works.<br />
<br />
Let us first try to see what a Turing machine actually is.<br />
The scientist and brilliant mathematician Alan Turing came up with this idea in an attempt to solve a problem in mathematics known as ''Entscheidungsproblem''. It translates to "a decision problem", and it was put forward by the German mathematician David Hilbert. Hilbert’s problem was- is there any general algorithmic procedure for resolving mathematical questions or whether in principle such a procedure might exist?.</p></p></body><br />
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<br />
==Turing’s concept:==<br />
<br />
[[Image:Turing.jpg|center|thumbnail|500px]]<br />
<br />
<br />
Turing’s machine consisted of a box capable of performing the following actions on a ''tape'' supplied to it:<br />
It can ‘''read''’ the marks on the tape,<br />
It can erase the marks on the tape or can change the marks on the existing tape,<br />
It can move the tape towards the right or left, allowing it to ‘read’ further marks on the tape.<br />
<br />
[[Image:tape4.png|center|500px|thumbnail]]<br />
<br />
<br />
<br />
The above is a sample of such a ‘tape’ which is fed to the machine. <br />
For simplicity we label the tape in only two ways viz. 0 and 1. <br />
<br />
Turing allowed more complex markings but (heck) that shouldn’t bother us here.<br />
<br />
Coming back to the box, as we have seen that the box can move the tape, change its marks etc. but it should be noted that the machine does these operations in a ''non-random, deterministic'' way. That is, we can predict what the action of the Turing machine on the tape will be. The box has a set of finite internal states, but can work algorithmically on potentially infinite calculations using the tape.<br />
<br />
If you are wondering, "HOW??"<br />
<html><br />
<p><a href="https://2009.igem.org/Small_two-state"> <span style="font-weight:bold; font-size:125%; color:#6600FF;">Click Here</span></a></p><br />
</html><br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#FF6600;">References</span></p><br />
<br />
1. http://en.wikipedia.org/wiki/Turing_machine<br />
<br />
2. http://plato.stanford.edu/entries/turing-machine/<br />
<br />
3. http://mathworld.wolfram.com/TuringMachine.html<br />
<br />
4. "The Emperor's New Mind", 2nd Edition, Roger Penrose, Martin Gardner (1999), Oxford University Press</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/safetyTeam:IBB Pune/safety2009-10-21T23:03:27Z<p>Samitwatve: </p>
<hr />
<div><br />
'''Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?'''<br />
<br />
No, our project does not raise any such safety issues.<br />
While formulating our project idea and the relevant experimental designs, we took special care that no safety problems would arise, public or environmental.<br />
We followed the GLPs established in our labs to ensure researcher safety. We were supervised in our observance of these GLPs by our instructors.<br />
<br />
<br />
'''Is there a local biosafety group, committee, or review board at your institution?'''<br />
<br />
No. To overcome this glitch while handling sensitive material like BioBricks, we made sure an experienced Instructor was involved and took stringent measures so that no mistakes were made.<br />
<br />
<br />
'''What does your local biosafety group think about your project?'''<br />
<br />
-<br />
<br />
<br />
'''Do any of the new BioBrick parts that you made this year raise any safety issues?<br />
'''<br />
<br />
No. We have a project plan that ensures no breach of biosafety.<br />
<br />
<br />
<br />
'''If yes, did you document these issues in the Registry?'''<br />
<br />
-</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/protein-based-signallingTeam:IBB Pune/protein-based-signalling2009-10-21T23:00:34Z<p>Samitwatve: /* Working of the Construct */</p>
<hr />
<div>=The Complete Turing Machine=<br />
<br />
[[Image: BBa_K233325.JPG|center|900px]]<br />
<br />
The above image is a representation of the complete turing machine including inter state regulation. This model is true to Alan Turing's vision of multi-mutually exclusive states and the states being regulated by one another through outputs.<br />
<br />
==Working of the Construct==<br />
[[Image:Complicated.png|center|800px]]<br />
In the above construct, there are three independent modules that function<br />
* A constitutively working module which produces LuxR protein and LacI and Cassette 1 (encodes ogr and activates state 'B')<br />
*A State-'B' which is activated by State' A' and which in turn represses the working of the default state<br />
*An AND gate regulated activation of the turing machine function (it could be lysis, expression of a fluorescent protein or the synthesis of vanillin or methyl salicylate)<br />
<br />
The default state of the turing machine is 'A'.<br />
In this state it encounters a '0' (represented by Lactose) first.However there are no Lactose responsive elements in either the first or the second module.<br />
The third Module which has such a module however also requires the presence of the phage protein 'ogr '<br />
. Hence the first 0 is unable to produce any effect and the machine moves on to the next cell in the tape while remaining in state A.<br />
<br />
The machine now encounters a 1 in this default state 'A' (represented by AHL). This results in the activation of the second module which in turn produces more of ogr. This acts like a positive feedback loop and hence state 'B' is switched on and can remain active without intervention from cassette 1.<br />
<br />
Cassette 2 also encodes for the phage lambda cI repressor protein which represses cassette 1. Thus we have a system in which the two states are mutually exclusive. In state 'B', when the machine encounters a '1', it keeps the '1' unchanged and transits to the next cell. <br />
<br />
Now in this state, when the machine encounters a '0' the AND gate obtains both its inputs viz. ogr and lactose which results in the production of Homoserine Lactone Synthase (enzyme producing AHL). This results in the conversion of the '0' to a '1'. Therefore this construct behaves like a unary adder as per Turing's specification.<br />
<br />
=Problems Associated with such an Approach=<br />
*At 6.5kb the construct too darn BIG!<br />
<br />
*It is a metabolic load on the cell. <br />
<br />
*Assembling these many parts together is extremely challenging by using even the most advanced molecular biology techniques.<br />
<br />
*Transformation of such a large construct is difficult. <br />
<br />
*It poses major complications with respect to quality control, sequencing and data validation.<br />
<br />
=Modular Systems=<br />
We decided to use a modular approach to tackle the problems enlisted above.<br />
<br />
We therefore decided to divide the complicated construct into three separate interdependent strains which together combine to form the Unary Adder.<br />
<br />
1) image 1<br />
2) Image 2<br />
3) image 3<br />
<br />
In this system the first module gets activated in the presence of AHL ( '1' ) and produces ogr attached to an export tag (YcdB or TorA) this results in the export of ogr protein which acts as an input for the second module.<br />
<br />
The second module gets activated by ogr and produces phage lambda repressor cI protein and more ogr protein in response. The cI protein serves to turn the first module 'off' and and keeps itself on by a positive feedback loop regulated by ogr.<br />
<br />
The third module gets activated in response to extracellular lactose and ogr and produces RFP. This indicates the conversion of a '0' to '1'.<br />
<br />
This functions as a unary adder<br />
<br />
=Proof-of-concept=<br />
As a proof of concept of the export-based signalling machinery, we attempted to test the working of the export tags by fusing them upstream of Green Fluorescent Protein.<br />
<br />
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<p><a href="https://2009.igem.org/SNOWDRIFT/Proof_of_concept<br />
"><span style="font-weight:bold; font-size:150%; color:#6600FF;"><u>NEXT</u></span></a></p><br />
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</html></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-21T22:59:06Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br><br />
<br />
[[Image:Turing1.GIF|center|800px]]<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">The Simplified Construct</span></p><br><br />
[[Image:Simplified.png|center|800px]]<br />
==Working==<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|450px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
[[Image:tape22.png|center|450px]]<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
[[Image:tapes.png|center|450px]]<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-21T22:37:50Z<p>Samitwatve: </p>
<hr />
<div>{{team:IBB_Pune/header}}<br />
{{Team:IBB_Pune/menu}}<br><br><br />
<br />
[[Image:Turing1.GIF|center|800px]]<br />
[[Image:Complicated.png|center|800px]]<br />
<br />
<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">The Simplified Construct</span></p><br><br />
[[Image:Simplified.png|center|800px]]<br />
==Working==<br />
<br />
The Turing Machine begins with the default state 'A'. <br />
[[Image:Tape1.png|center|400px]]<br />
In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
<br />
<br />
This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
<br />
This process keeps repeating until the Turing Machine reaches a zero again.<br />
<br />
In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
<br />
When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (RFP). This signals that the Turing machine has halted.<br />
<br />
The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/BIOETHICSTeam:IBB Pune/BIOETHICS2009-10-21T21:52:47Z<p>Samitwatve: </p>
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As scientists and citizens, we must address questions and controversies surrounding the use of biotechnology and make choices that will best serve humanity. We should be committed to the socially responsible use of biotechnology in health care, food and agriculture, industry and the environment. As biotechnology reaches toward such benefits as treatments for intractable diseases such as cancer, Alzheimer’s and Parkinson’s; abundant, nutritious food; industrial sustainability; and a cleaner world, we encourage public discussion of the ethical, legal and social implications of biotechnology research. Responsible and ethical testing of new technologies and believes that decisions regarding whether and how to use medical products and technologies always must be made with profound respect for the rights of patients. In our view, appropriate regulation of biotechnology is solidly rooted in values such as autonomy, privacy, beneficence, social justice and intellectual freedom.<br />
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<span style="font-weight:bold; font-size:125%; color:#0000cc;"><p>1. Synthetic Biology: How is it different from the ad-hoc molecular cloning / Genetic Engineering/RDT?</p></span><br />
<span style="font-weight:bold; font-size:100%; color:#0000cc;"><p> The scope has been widened and made simplified.</p></span><br />
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Synthetic biology is broadly defined as the area of intersection of biology and engineering, that is focused on: The design and fabrication of biological components and systems that do not already exist in the natural world and the redesign and fabrication of existing biological systems. A primary objective of this nascent research area is to create a programmable microorganism from scratch, as opposed to modifying components of living cells to achieve desired functionality. This distinguishes it from current genetic techniques that result in genetically modified organisms at the cellular level. How can we compare synthetic biology to other areas of biotechnology? Transgenic mice, bio-engineered plasmids, and other living forms are regularly created in the process of biomedical research. What would be the difference between these modified life forms and life forms created using a synthetic biology approach? In order to address these questions, the primary differentiators between synthetic biology and other techniques are outlined below. Synthetic biology systems would exhibit one or more of these attributes (first two are mandatory):<br />
Raw materials: Synthetic elements would be constructed from basic elements (synthetic or purified oligonucleotides in the case of synthetic DNA) in the lab (and not as part of a natural cellular process).<br />
<ul><br />
<br />
<li>''No natural counterpart:'' Synthetic elements or networks would not have an identical copy in natural cells. The caveat would be synthetically created whole genomes of existing organisms – although a minimal genome (critical genes for survival) organism would be more likely.<br />
<br />
<li>'' Programmable:'' Synthetic regulatory elements and networks engineered in cells would be controllable with external stimulus in a deterministic fashion.<br />
<br />
<li>''Synthetic whole genome:'' Starting with synthetic oligonucleotides as raw materials, the end product would be an artificially assembled genome or “minimal genome”. In order to distinguish between synthetic biological creations and other approaches like transgenic organisms, the key difference to be noted is that transgenic organisms are the result of introducing naturally occurring foreign or mutated DNA (genes) into the organism.<br />
<br />
<li>''Risks involved in synthetic biology practices''<br />
Some of the risks posed by products of synthetic biology are outlined below. As we move up the classification hierarchy of synthetic biology products, and thus on to higher levels of integration, the risks increase.<br />
<br />
<li>''Risk of negative environmental impact:'' <br />
This includes scenarios in which a synthetically created micro-organism designed for a particular task (e.g.: Environmental cleanup) could have a side effect of interacting with another environmental substance and impact the overall environment negatively.<br />
<br />
<li>'' Risk of natural genome pool contamination:'' Any genetic exchange between a synthetic biological entity and a naturally occurring biological entity would result in natural genome contamination. This is similar to the problem of “gene-flow” in the context of transgenic plants.<br />
<br />
<li>''Run-off risk (“Grey-goo” problem):'' This is similar to the problem often discussed in the context of nanotechnology. Synthetic biology products released into the environment to accomplish a specific task should have a controlled lifespan outside the lab. If this in not the case, one can envision unintended consequences of a system run amuck.<br />
<br />
<li>''Risk of creation of deadly pathogens for the purposes of bio-terrorism:'' The creation of the complete genome of Polio virus in the lab shows the potential of synthetic biology to engineer harmful pathogens. This technology, in rogue hands, could be used to engineer the genomes of deadly pathogens. The fact that the synthetic Polio virus was proven to be infectious shows the deadly potential of this technology.<br />
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<span style="font-weight:bold; font-size:125%; color:#0000cc;"><p>2. Bioethics in a broader sense: socio-scientific causes, IPR issues, controversies</p></span><br />
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For over 200 years, intellectual property laws have been the driving force for innovation and progress. The biotechnology industry as we know it did not exist prior to the landmark US Supreme Court decision of Diamond v. Chakrabarty of 1980. The court held that anything made by the hand of man was eligible for patenting. Since this decision, the biotechnology industry has flourished and continues to grow. The patent system fosters the development of new biotechnology products and discoveries, new uses for old products and employment opportunities for millions of Americans. Nowhere is this more apparent than in the biotechnology arena. Patents add value to laboratory discoveries, providing incentives for private sector investment into biotechnology development of new medicines and diagnostics for treatment and monitoring of intractable diseases, and agricultural and environmental products, to meet global needs. Patents facilitate academic research, because the release of information to the public is critical to the advancement of knowledge. The fact that an inventor can obtain patent protection on an invention encourages inventors not to withhold beneficial information from the public. In fact, the patent system provides strong incentive for sharing information. Not only can researchers use the information in a patent, but also by disclosing cutting-edge scientific information, the patent system helps prevent expensive duplication of efforts.<br />
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<p><span style="font-weight:bold; font-size:150%; color:#0000cc;">Our projects: Best Human practices in Synthetic Biology</span></p><br />
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<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Consideration of Ethical issues, conceptualization of projects in accordance with the Bioethics:</span></p><br />
<br />
Our project involves creation of synthetic constructs to be used for specific functions. We are attempting to construct a multi-state Turing machine which is a compound, modular computational system that has independent, interacting states which applies the above principle. This approach might overcome the shortcomings in building more complex and composite circuits. Our projects involves no inclusion of animal studies.<br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Host organism :</span></p><br />
<br />
For evaluation and further validation the gene circuits are inserted into control cell systems such as E.coli, which becomes genetically modified bacteria. ''E.coli'' is our organism of choice. It is generally a non-pathogenic bacteria and is a normal part of intestinal flora of warm-blooded animals. Neither the host strain nor the modifications introduced in them lead to any pathogenesis. <br />
<br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Good Lab Practices:</span></p><br />
<br />
All the undergrad students were provided with the standard GLP guidelines and biological lab ethics. Standardised precautions were taken to handle the strains only in a biosafety hood.<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Discrimination of the wild and genetically modified strains:</span></p><br />
<br />
Care was taken not to mix the synthetic organism gene pool with the naturally occurring gene pool. Decontamination before disposal, and disposal according to the prescribed GLP guidelines was carried out. <br />
<br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Opinion Exchange: BioEthics</span></p><br />
<br />
Throughout the course of iGEM projects, we have tried to criticize and review our methodologies ourselves as well as by others. A thorough revision and self retrospection on the same is something which is required for each Team in iGEM. We have discussed and reviewed our concepts,protocols, potential applications and risks, if any with Advisors, Faculties, research students from various biology departments in and around Pune University.<br />
<br />
<br />
<p><span style="font-weight:bold; font-size:125%; color:#0000cc;">Concluding Remarks</span></p><br />
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Synthetic biology holds immense promise as a beneficial technology. As with any other area of biotechnology, there are associated areas of concern and risk. The technology itself is in a nascent stage and some of these issues will no doubt evolve as the technology progresses.<br />
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We applaud the intellectual freedom of researchers to think and dream in the pursuit of greater understanding that could lead to a better life for all of us. We believe the public should fully participate in the introduction of these new products both through an open, accessible and accountable regulatory system and through the exercise of free choice via market mechanisms. We encourage increased awareness and understanding of how agricultural biotechnology is being applied, and its impact on agricultural practices, use of animals in research, the environment and biological diversity.<br />
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<div></div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-21T21:39:40Z<p>Samitwatve: </p>
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<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">The Simplified Construct</span></p><br><br />
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The Turing Machine begins with the default state 'A'. <br />
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In this state it encounters a '0' (represented by Lactose) first. In this state, the LuxR protein will be constitutively produced. The LacO (to which repressor protein remains bound in the normal state) becomes activated in presence of Lactose. However this does not lead to the expression of the reporter gene as this requires activation of the pLuxR promoter (requiring AHL). Thus the Turing Machine remains in state 'A', leaves the '0' unchanged and moves one step to the RIGHT.<br />
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This process is continues till the Turing Machine reaches the first '1' on the tape, (represented by 'AHL' (acyl homoserine lactone) ). This induces the pLuxR promoter to be switched 'on'. This occurs via the interaction of 'AHL-pLuxR' complex which activates the pLuxR promoter to express the LuxI gene. LuxI gene is responsible for the production of the enzyme Homoserine Lactone Synthase (an enzyme which produces AHL). This is regulated by a positive feedback loop. The AHL which is synthesized by the cells keeps the pLuxR active thus enabling the production of even more AHL. This also has the capacity to activate the other pLuxR promoter present in cassette 2. However in ABSENCE of Lactose, the LacO site has repressor protein bound to it. This prevents the transcription of the reporter gene.<br />
The overall effect of this module is that, the Turing Machine enters state 'B', it leaves the '1' unchanged and again moves RIGHT. <br />
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This process keeps repeating until the Turing Machine reaches a zero again.<br />
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In this case, the Turing Machine is in State 'B' and it encounters a '0'. According to the specification of the Turing machine, the machine changes this '0' to a '1' and HALTS. In physical terms, this is obtained by depletion of Lactose and the production of AHL. This is achieved in the following manner:<br />
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When the Turing Machine encounters Lactose ('0') the repressor protein is released from the LacO site. This enables the pLuxR promoter to be activated by the AHL-LuxR complex. This enables the expression of AHL (turning the state '0' into '1') and also enables the expression of the reporter gene (GFP). This signals that the Turing machine has halted.<br />
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The overall result of this process is that the Turing Machine adds +1 to a string of 11111's as is required by the specification of the Turing Machine.</div>Samitwatvehttp://2009.igem.org/Team:IBB_Pune/constructTeam:IBB Pune/construct2009-10-21T21:13:37Z<p>Samitwatve: </p>
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[[Image:Turing1.GIF|center|800px]]<br />
[[Image:Complicated.png|center|800px]]<br />
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<p><span style="font-weight:bold; font-size:200%; color:#6600FF;">The Simplified Construct</span></p><br><br />
[[Image:Simplified.png|center|800px]]<br />
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The Turing Machine begins with the default state 'A'. In this state when it encounters.</div>Samitwatve