Difference between revisions of "Team:IIT Madras/Notebook"

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{{IIT_Madras}}
 
{{IIT_Madras}}
 
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<h2>Sept 17</h2>
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<ul>
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<li>First meeting of Team:IIT_Madras for iGEM 2015.</li>
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<li>Ideation begins.</li>
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</ul>
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<h2>May 18-24</h2>
 
<h2>May 18-24</h2>
 
<ul>
 
<ul>
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<li>Cleaned fridge and transferred materials.</li>
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<li></li>
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<li>Circuit finalised toggle switch/ mutual depressor switch using TAL repressor.</li>
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<li></li>
 
</ul>
 
</ul>
  
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<h3> June 1-7</h3>
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<h3>June 1-7</h3>
 
<ul>
 
<ul>
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<li> MoleculGROMACS simulations started
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<li>Molecul Dynamic Simulation started.</li>
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-> Made a catalog of all available materials
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<li>Made a catalog of all available materials.</li>
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-> Lacto Bacilus strains are available NZ9000 and MG1363
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<li>Lacto Bacilus strains, NZ9000 and MG1363, were collected from Prof. KBR's lab.</li>
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-> Simulations finished the proteins were found to interact favourably  
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<li>MD Simulations finished the proteins were found to interact favourably.</li>  
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-> Heidelberg 2008 Auto Inducer 2 produced by LuxS sensed by LuxQ
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</ul>
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-> Reference:Quorum Sensing AI@ in campylobacter Orla Cloak, Barbara Solow doi:10.1128
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Can we do the whole circuit using just Lux components??!!
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Week 4
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<h3>June 8-14</h3>
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<ul>
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->Circuit will be composed of purely Lux components.
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<li>Started working on the design of genetic circuit.</li>
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-> MD Simulations were done with ionic solution of protein complex. MD Simultions showed that naly  
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<li>One more MD Simulation was performed with the ionic solution of protein complex. MD Simultions showed that naly  
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interacts favorably with Alytesterin forming a cavity of hydrophobic residues
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interacts favorably with Alyteserin forming a cavity of hydrophobic residues.</li>
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-> Sender is finalised to be E.Coli DH5Alpha with LuxP-PFS gene  
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<li>Sender is finalised to be E.Coli DH5Alpha with LuxP-PFS gene.</li>
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Receiver is L.lactis NZ9000/MG1316 with LUXPQOU coupled with Lux R through sRNA's qrr1-5 and HFQ
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<li>Receiver is L.lactis NZ9000/MG1316 with LUXPQOU coupled with Lux R through sRNA's qrr1-5, HFQ and sigma54 gene.</li>
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</ul>
 
   
 
   
 
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Revision as of 15:27, 12 September 2015

Sept 17

  • First meeting of Team:IIT_Madras for iGEM 2015.
  • Ideation begins.

May 18-24



May 25-31

  • Inventory of all supplies is to be done.
  • Alyteserin-1a was chosen to test our model as the structural feature, mechanism of action and other relevent details of anit-microbial peptide Alyteserin-1c, which has two mutations (D4E, N23S), were available in the literature.
  • The pdb structure of Alyteserin-1a was generated in pymol, while introducing two mutations D4E and S23N in the pdb structure of Alyteserin-1c.
  • The structural features of Alyteserin-1a was analyzed carefully to design a novel peptide which could interact with it.
  • Pymol and Pepstr, an online tool, were used to generate a large number of peptide pdb structures of size 10-18 amino acid.
  • A software, ZDOCK, was used to assess the docking parameters of Alyteserin-1a and novel peptide.
  • Best peforming peptide was chosen to test it's functionality in molecular dynamic simulation.

June 1-7

  • Molecul Dynamic Simulation started.
  • Made a catalog of all available materials.
  • Lacto Bacilus strains, NZ9000 and MG1363, were collected from Prof. KBR's lab.
  • MD Simulations finished the proteins were found to interact favourably.

June 8-14

  • Started working on the design of genetic circuit.
  • One more MD Simulation was performed with the ionic solution of protein complex. MD Simultions showed that naly interacts favorably with Alyteserin forming a cavity of hydrophobic residues.
  • Sender is finalised to be E.Coli DH5Alpha with LuxP-PFS gene.
  • Receiver is L.lactis NZ9000/MG1316 with LUXPQOU coupled with Lux R through sRNA's qrr1-5, HFQ and sigma54 gene.
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