Bangalore

From 2007.igem.org

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|On June 1st 2007, a group of undergraduates of various disciplines and from around the country assembled at NCBS, to attempt a 'proof of principle' demonstration. Their mission: to assemble and test a 'genetically engineered machine', a complex network assembled from simple biological parts. You will be amazed how much they managed to achieve in just six weeks!
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''The National Centre for Biological Sciences is a research institute located in Bangalore, India. In 2006, a team of graduate students from NCBS was the first from India to participate in iGEM. This year, we are very excited to compete as an all-undergraduate team of six students, from six different colleges located in four cities around India. Now that the summer is over, we hope to take the excitement of iGEM back to our home institutions, and create new teams across India who will participate in future iGEMs.''
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|align="center"|[http://www.ncbs.res.in/ National Centre for Biological Sciences, Bangalore]
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== '''The Company''' ==
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<!--- The Mission, Experiments --->
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*Mukund:    Chief Mentor, Consultant and The Godfather
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{| style="color:#294e9c;background-color:#e1e0db;" cellpadding="3" cellspacing="1" border="1" bordercolor="#1100ff" width="62%" align="center"
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*Sugat:     Right-hand Man and Manager of Operations
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!align="center"|[[Bangalore|Home]]
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*Nilesh:     The Man for all Seasons 
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!align="center"|[[The Team|The Team]]
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*Vivek:     Chief Troubleshooter, often his role is confused with one of a Troublemaker
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!align="center"|[[The Goal|The Goal]]
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*Krishna:    The Sharpshooter
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!align="center"|[[Parts Data Sheets|Parts Data Sheets]]
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*Senthil:    The Wikiman, also fondly referred to as the "Bio Info God"
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!align="center"|[[Mathematical Models|Mathematical Models]]
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*Varun:      The Voice of Reason and Anti-Reason
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!align="center"|[[e-Notebook|e-Notebook]]
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*K12Z1:      The Workhorse
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== '''The Mission''' ==
 
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To investigate multistability and hysteresis in combinatorially constructed synthetic ''Vibrio'' quorum sensing circuits
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[[Image:timeline.png|center|]]
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== '''The Target - Vibrio Quorum Sensing System''' ==
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== ==
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Quorum sensing is a phenomenon by which bacteria sense a critical cell density before turning on the expression of certain genes. It involves the gradual build-up of a chemical termed the 'autoinducer' in the cell. The autoinducer freely diffuses across the cell membrane and hence, its concentration is population density dependent. When the concentration crosses a threshold, the bacteria switch to a different physiological state such as bioluminescence, virulent gene expression, and bio-film formation.
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<font size="2">
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[[Image:vibrio_qs.jpg|thumb|200px|Fig. 1:  Quorum sensing in Vibrio fischeri - a LuxI-R signalling circuit. Red triangles indicate the autoinducer that is produced by LuxI. OM, outer membrane; IM, inner membrane.]]
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In Vibrio fischeri, when the population density (and hence the concentration of autoinducer) crosses a certain threshold, the expression of a set of genes that is required for bioluminescence is turned on. The production of the autoinducer is under the control of a gene, the expression of which involves positive feedback. Figure 1 shows the various components of this system (Ref. 1).
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[[Image:igem_bangalore_07.jpg|thumb|550px|center|<font color="green">'''Top to Bottom''':</font><font color="black"> Navneet, Nilesh, Vivek, Vini, Krishna, Varun, E.coli, Shashanka, Mukund, Senthil and Sushant at the NCBS Amphitheatre.</font>]]
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</font>
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==='''Why did we pick this system?'''===
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The Vibrio quorum sensing system involves a well-defined set of genes and a promoter, and has a degree of complexity that offers wide scope for exploration. Additionally, the concentration of the active transcriptional regulator, LuxR* is dependent on 3 factors:
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i) The concentration of LuxI
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ii) The population density 
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iii) The concentration of LuxR
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All these factors can be experimentally controlled. Thus, the nature of the system offers one an extremely good handle on the feedback strength of the genetic circuit.
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=='''A note on Multistability and Hysteresis'''==
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[[Image:Break_feedback_loop.jpg|thumb|200px|left|Fig. 2: Schematic view of a feedback system before (Left) and after (Right) breaking the feedback loop. ‘ω’ is the input of the open-loop system and ‘η’ is the output.]]
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In the recent past, multistability has been an important recurring theme in studies on cell signalling. Angeli et al (Ref. 2) have shown that for a class of feedback systems of arbitrary order, the stability properties and bifurcation diagram of the system can be deduced mathematically from how the system behaves when feedback is blocked. The system is guaranteed to be bistable for some range of feedback strengths provided the feedback-blocked system is monotone and shows a sigmoidal characteristic.
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A simple graphical method can be used to deduce the stability behaviour of such systems (Ref. 2). The key feature of this approach is to view the positive feedback system as a feedback closure of its corresponding 'open loop' system. This open loop system is obtained by breaking the feedback loop at the point of feedback (Fig. 2).
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Now, one can experimentally manipulate the amount of input (ω) and monitor the output (η) as a function of ω. The fixed points of the corresponding closed loop system are then obtained by intersecting η = f (ω) with the straight line, η = (1/ν) ω, where ' ν ' is the feedback strength. At these points of intersection, the open loop system exactly mimics the closed loop system.
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Latest revision as of 07:20, 24 October 2007

On June 1st 2007, a group of undergraduates of various disciplines and from around the country assembled at NCBS, to attempt a 'proof of principle' demonstration. Their mission: to assemble and test a 'genetically engineered machine', a complex network assembled from simple biological parts. You will be amazed how much they managed to achieve in just six weeks!
Ncbs Logo.jpg

The National Centre for Biological Sciences is a research institute located in Bangalore, India. In 2006, a team of graduate students from NCBS was the first from India to participate in iGEM. This year, we are very excited to compete as an all-undergraduate team of six students, from six different colleges located in four cities around India. Now that the summer is over, we hope to take the excitement of iGEM back to our home institutions, and create new teams across India who will participate in future iGEMs.

Ncbs.jpg
[http://www.ncbs.res.in/ National Centre for Biological Sciences, Bangalore]


Home The Team The Goal Parts Data Sheets Mathematical Models e-Notebook


Timeline.png

Top to Bottom: Navneet, Nilesh, Vivek, Vini, Krishna, Varun, E.coli, Shashanka, Mukund, Senthil and Sushant at the NCBS Amphitheatre.

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