Difference between revisions of "Team:IIT Delhi/Model"

 
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     <div class="dropdown-content">
 
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       <a href="/Team:IIT_Delhi/Circuit_Design">Circuit design and construction</a>
 
       <a href="/Team:IIT_Delhi/Circuit_Design">Circuit design and construction</a>
       <a href="/Team:IIT_Delhi/Microfluidics">Microfluidics and Fluroscence</a>
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       <a href="/Team:IIT_Delhi/Microfluidics">Microfluidics and Fluorescence</a>
 
       <a href="/Team:IIT_Delhi/Photobleaching">Photobleaching</a>
 
       <a href="/Team:IIT_Delhi/Photobleaching">Photobleaching</a>
 
       <a href="/Team:IIT_Delhi/Promoter">Promoter strength</a>
 
       <a href="/Team:IIT_Delhi/Promoter">Promoter strength</a>
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             <h2 class="h2font">INTEGRATED HUMAN PRACTICES</h2>
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             <h2 class="h2font">Overview</h2>
  
 
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<h2 id="pfont">To get a better idea of how can we improve and move ahead with our project,we first set out to talk to some of the researchers and professors of various departments, both inside our institute and outside. Following is a summary of the talk that we had :
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          <button class="accordion back1" style="font-weight: bold;">Talk With Prof.Shaunak Sen</button>
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<h2 id="pfont1"><br> He is a Professor at our institute and does research in control Theory.Just when we had started Brainstorming for our Project,we reached out to him and talked to him about square wave oscillator that we were planning to make.It was him who suggested us about the idea of using an oscillator feeding into a toggle switch in order to generate Square Waves.He further also talked to us about the work Dr.Richard M Murray had done in this field oscillators with ring topologies. He also told us about trying out the relaxation oscillators in order to generate a better Square wave.
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A Mathematical model captures the essential dynamics of the system in the form of mathematical equations and helps to study and analyze the biological system before stepping into lab work. All of the chemical reactions in the system can essentially be written in the form of differential equations that capture the biological processes in the cell. These equations can then be simulated and the dynamics can be analyzed, in order to understand how a particular network is going to behave inside the cell. <br><br>
  
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The two molecular processes that are central to the functioning of a cell are transcription and translation. The cell consists of DNA, which contains all the genetic information of the cell. It contains information for synthesis of various proteins required for normal functioning of the cell. The process of transcription leads to creation of mRNA from DNA which contains the information for protein synthesis. This mRNA is then translated into protein with the help of ribosomes and tRNA. <br><br>
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Thus, the entire set of reactions happening inside a cell leading to the expression of a gene can be broken down into the following –<br><br>
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Here, the major processes occurring are as follows -
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<h3 id="pfont2"><u id="pfont2">mRNA</u> </h3>
  
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<li>mRNA is being produced from the plasmid DNA that has been introduced into the cell via transformation, by the process of transcription.
  
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<li>The mRNA produced is also being degraded, because it has a certain half life (just like radioactive elements decay, all chemicals have a half life, and so do DNA and RNA!).
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<h3 id="pfont2"><u id="pfont2">Protein</u> </h3><ol class="centered" id="pfont2"><left>
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<li>Protein is produced from the mRNA transcript by the process of translation.
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<li>Protein is also degraded since it has a half life, similar to the mRNA.
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</ol><br><br></left>
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<div id="pfont2">What needs to be noted before we start to write a model for this is that this is a very simplistic model that makes use of several assumptions and simplifications. This is because biological systems are extremely complex, and at a single instant of time, there are several hundred reactions happening. Thus, we need to simplify and lump certain intermediate reactions, in order to have some quantitative estimate of how our system will behave.
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<br><br>
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Some of the assumptions made here are - </div>
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<br><br>
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<li>mRNA is made directly from DNA, and all the other components and processes in between, such as pulling of RNA polymerase (RNAp) by the TATA box in the promoter, binding of RNAp to the promoter and initiation of transcription are sufficiently fast, so that the parameters can be lumped and variables (such as RNAp and Promoter) can be ignored.
 +
<li>Degradation of molecules such as mRNA and protein is spontaneous, and is not triggered or accelerated by certain components (such as ssrA).
 +
<li>The rates of production and degradation are constant.
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<li>mRNA is not degraded, damaged, or consumed in any way during translation or production (transcription).
 +
<li>Total DNA inside a cell is constant.
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<li>Mass action kinetics is valid for the reactions occurring above.
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</ol></left>
  
<h2 id="pfont1"><br> He is a Professor at the School of Biological Sciences,Delhi.His research is mainly focussed in the field  of Systems Biology.Once we had decided on the topology for our project.we discussed with him at length about our project and also got a lot of help from him in our Square wave Modelling.However,he wasn’t much impressed by our topology and rather suggested to us  about the use of  Build up and fire kind of oscillator for a better generation of Square Waves.
 
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<h2 id="pfont1"><br>He is a molecular Biologist at the Department of Biological Sciences,IIT Delhi.
 
Our talk with him was truly very helpful for us in the execution of our project. It was him who suggested us about the Streptomyces griseus (Orf2) whose biosafety facilities were available at our lab.
 
  
 
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<h2 id="pfont1"><br>A PhD student, Mr. Mahendra Sahare, doing a humanities project under a Supreme Court lawyer, Dr. Naveen Thayyil, has been in collaboration with iGEM IIT Delhi for the past two years. Together, we have worked on the aspect of ‘Ethical Scientific Practices’. Also, on his recent visit to IISER Mohali, he came back with a collaborative offer for iGEM IIT Delhi to mentor IISER Mohali and help in the establishment of iGEM club there. On our return from the Giant Jamboree 2016, our team members gave a presentation scheduled there, and thereafter our
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team mentored the iGEM Mohali team.
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<h2 id="pfont"><br><br>We also talked to many researchers pursuing their Ph.D here in IIT Delhi,to get to know about various possible uses of Biological Oscillators,before we started our project.
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Here are the their views on how Biological Oscillators can be used further.<br><br>
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          <h2 id="pfont1"><br> He is researcher in the field of System biology/oscillators.In our talk with him,he told us that Biological Oscillators can be used as a clock reference analogous to electrical engineering for signal processing,as a bridge between network of them.synchronisation and as a modem “MODEM” carrying Information .
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          <h2 id="pfont1"><br> He is a researcher in synchronisation non linear linear oscillators.According to him,Biological Oscillators can be used in the Field of repressilator or vanderpol oscillator and  in the field of cancer cells.
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            <h2 id="pfont1"><br>He does Research in field of convergent systems.He told us about how Biological oscillators can be linked up to his field of research.According to him,If the oscillator is tuned to be convergent,then many interesting phenomenon like time-scale,synchronisation can be analysed better.
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Latest revision as of 23:29, 1 November 2017

iGEM IIT Delhi


Overview

                                                                                                                                                                                                                 

A Mathematical model captures the essential dynamics of the system in the form of mathematical equations and helps to study and analyze the biological system before stepping into lab work. All of the chemical reactions in the system can essentially be written in the form of differential equations that capture the biological processes in the cell. These equations can then be simulated and the dynamics can be analyzed, in order to understand how a particular network is going to behave inside the cell.

The two molecular processes that are central to the functioning of a cell are transcription and translation. The cell consists of DNA, which contains all the genetic information of the cell. It contains information for synthesis of various proteins required for normal functioning of the cell. The process of transcription leads to creation of mRNA from DNA which contains the information for protein synthesis. This mRNA is then translated into protein with the help of ribosomes and tRNA.



Thus, the entire set of reactions happening inside a cell leading to the expression of a gene can be broken down into the following –



Here, the major processes occurring are as follows -

mRNA

  1. mRNA is being produced from the plasmid DNA that has been introduced into the cell via transformation, by the process of transcription.
  2. The mRNA produced is also being degraded, because it has a certain half life (just like radioactive elements decay, all chemicals have a half life, and so do DNA and RNA!).

Protein

  1. Protein is produced from the mRNA transcript by the process of translation.
  2. Protein is also degraded since it has a half life, similar to the mRNA.


What needs to be noted before we start to write a model for this is that this is a very simplistic model that makes use of several assumptions and simplifications. This is because biological systems are extremely complex, and at a single instant of time, there are several hundred reactions happening. Thus, we need to simplify and lump certain intermediate reactions, in order to have some quantitative estimate of how our system will behave.

Some of the assumptions made here are -


  1. mRNA is made directly from DNA, and all the other components and processes in between, such as pulling of RNA polymerase (RNAp) by the TATA box in the promoter, binding of RNAp to the promoter and initiation of transcription are sufficiently fast, so that the parameters can be lumped and variables (such as RNAp and Promoter) can be ignored.
  2. Degradation of molecules such as mRNA and protein is spontaneous, and is not triggered or accelerated by certain components (such as ssrA).
  3. The rates of production and degradation are constant.
  4. mRNA is not degraded, damaged, or consumed in any way during translation or production (transcription).
  5. Total DNA inside a cell is constant.
  6. Mass action kinetics is valid for the reactions occurring above.



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E-mail: iitd.igem@gmail.com
Undergraduate Laboratory
Department of Biotechnology and Biochemical Engineering, IIT Delhi