Difference between revisions of "Team:IIT Delhi/notebook2"

 
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       <h2  class="boogaloo_font "><span style="font-size:30px;cursor:pointer" ">April</span></h2>
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       <h2  class="boogaloo_font "><span style="font-size:30px;line-height:30px;cursor:pointer;display:block">We planned early on to document the work we did and efforts we put into our project, on a daily basis,hence, we were able to compile a comprehensive notebook accounting for all the events that took place.<br><br>April</span></h2>
<object data="https://static.igem.org/mediawiki/2017/5/52/T--IIT_Delhi--NoteApril.pdf" type="application/pdf" width="100%" height="900px">  
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<object data="https://static.igem.org/mediawiki/2017/5/52/T--IIT_Delhi--NoteApril.pdf" type="application/pdf" width="100%" height="500px">  
 
   <p>It appears you don't have a PDF plugin for this browser.
 
   <p>It appears you don't have a PDF plugin for this browser.
   No biggie... you can <a href="https://static.igem.org/mediawiki/2016/e/ec/T--Imperial_College--LabBook.pdf">click here to
+
   No probs... you can <a href="https://static.igem.org/mediawiki/2017/5/52/T--IIT_Delhi--NoteApril.pdf">click here to
 
   download the PDF file.</a></p>   
 
   download the PDF file.</a></p>   
 
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      <h2  class="boogaloo_font "><span style="font-size:30px;cursor:pointer">May</span></h2>
  <a href="javascript:void(0)" class="closebtn1" onclick="closeNav1()">&times;</a>
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<object data="https://static.igem.org/mediawiki/2017/d/d3/T--IIT_Delhi--NoteMay.pdf" type="application/pdf" width="100%" height="500px">  
  <div class="overlay1-content paddingleft" style="overflow:scroll; ">
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  <p>It appears you don't have a PDF plugin for this browser.
  <h2  class="boogaloo_font1 " style="overflow:scroll; ">  
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  No probs... you can <a href="https://static.igem.org/mediawiki/2017/d/d3/T--IIT_Delhi--NoteMay.pdf">click here to
<div style="overflow:scroll; ">
+
  download the PDF file.</a></p>
01/05<br>
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</object>
First lab visit of the team and instructions on how to handle the instruments and
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safety guidelines were presented<br>
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02/05<br>
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<ol>
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<li> Practicing inoculation, streaking and spreading of bacterial cultures of a biobrick used
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in previous year
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<li> LA plates and LB media preparation</ol><br>
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03/05<br>
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<ol>
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<li> Practicing plasmid isolation and transformation with the part inoculated yesterday
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<li> Inoculation of following parts from iGEM kit plate:-
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<ul>
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<li> RBS + GFP + T(without deg tag)
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<li> RBS + TetR + T
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<li>SYFP2
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<li> J23119 promoter
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<li> J23107 promoter</ul><br>
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<li> Plasmid isolation of :-<br>
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<ul>
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<li> RBS + GFP + T(without deg tag)
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<li> RBS + TetR + T
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<li> SYFP2
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<li> J23119 promoter
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<li> J23107 promoter</ul><br>
+
<li> Transformation of plasmids mentioned previously following iGEM protocol</ol><br>
+
04/05<br>
+
<ol>
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<li> Discussion on toggles switches and oscillators in relation to iGEM IITD project - 2016.
+
More detailed discussion on light activated self-repression and its effect on oscillator
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frequency.
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<li> Discussion on IITD 2015 project
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<li> Discussion on some iGEM projects of other countries.
+
<li> Received the colonies transformed yesterday</ol><br>
+
06/05<br>
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Further discussion on the research papers and different aspects of project<br>
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09/05<br>
+
Formation of a marketing and human practices team and discussion on marketing
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strategies used last year.<br>
+
11/05<br>
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<ol>
+
<li>Video and content for crowd-funding initiative
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<li>Mails and calls to potential sponsors</ol><br>
+
13/05<br>
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<ol><li>Discussion on gene regulation in prokaryotes and eukaryotes with special emphasis on
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prokaryotes.
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<li> Discussion on how we can modify the Lac system by keeping its switching on properties
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intact and replacing the gene part with, suppose, insulin such that presence Lactose
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molecules trigger the activation of insulin gene.
+
<li> Discussion on the different class of promoters.</ol><br>
+
15/05<br>
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<ol>
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<li> Discussion on PCR
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<li> Sample PCR product formed and ran on gel.</ol><br>
+
17/05
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 1. Logic Gates:
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a) AND GATE:
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 discussion on simple AND gate
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    </div>
 AND gate with modified tRNA (Discussion on tRNA that would read TAG as Serine)
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b) OR GATE
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c) NOR GATE
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d) XOR GATE: Using combination of different gates i.e. OR , AND , NOR, NAND, NOT and
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further discussion on other ways of XOR gate formation.
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 2. Steady state: Rate of accumulation=0
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 3. Discussion on different equations for rate of change of protein and rate of change of RNA
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(First and second order reactions) by discussing the journey from promoter to mRNA to
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protein to nothingness.
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 4. Enzyme Kinetics
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 S+E === ES ----> P+E
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 Differential equations of rate of change of ES and P discussed with equations of conservation
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of mass for the same.
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 Graphical analysis of ES/E0 vs S/S0 with discussion on quasi steady state.
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 Graphical discussion on Concentration vs Time of the reaction.
+
 5. Michaelis menten equation
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 6. Discussion on Degradation Tag and how it works in a bacterium where translation and
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transcription happen in the same compartment and there are no stop codons.
+
 7. Discussion on Cancer Cell about how it was thought to find a cure of cancer using
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these logic gates with inputs as miRNA(regulate genes) and output as apoptosis.
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 8. Example of virus that can be used as vectors for human cells. e.g. Vaccinia virus
+
18/05
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 Discussion on ways to generate different signal responses in bacterial gene regulatory
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circuits
+
22/05
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 Discussion on :-
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1) Chemotactic response in bacteria
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2) Temporal and spatial response in chemotaxis
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3) Mechanism of chemotaxis in bacteria flagellum
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4) Electrical model of chemotaxis
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5) Adaptation time of chemotaxis
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6) Finding electrical analogue of the biological system by varying frequency of the electrical circuit
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made
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7) Finding optimal frequency
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8) Biological Robustness and causes of it in a biological system
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9) System controls, bistability, modularity, buffering, bow-tie framework, decoupling
+
10) Robustness in signal transduction pathways and insect's segmental development
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11) Robustness trade-offs
+
24/05
+
 Discussion on :-
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1) Design principles of biochemical oscillators
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2) Time delay's relevance in oscillation
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3) Introduction of time delay with Intermediates
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4) Limit cycles, conservative cycles and circadian rhythms
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5) Time delay by positive feedback
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6) Different classes of feedback
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7) Linear and hyperbolic response
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8) Goldbeter Kosher Function
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9) Sniffers
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10) Toggle Switch
+
 
+
11) Mutual inhibition and mutual activation
+
26/05
+
 Discussion on :-
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1) A brief review of Sniffers, Buzzers and Toggle switch
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2) Negative feedback oscillations
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3) Positive feedback oscillations
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4) Neutral feedback oscillations
+
5) Sub-critical and Super-critical hop bit
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6) Study of mitosis
+
27/05
+
 Prepared lab supplies like LA, LB etc. to be used in the lab
+
29/05
+
1) Preparation of LuxI and PLux double digest using restriction enzymes EcoRI and PstI
+
2) Preparation of buffer and electrophoresis gel
+
3) Loading ladder, control and digest in the wells in gel
+
4) Electrophoresis and subsequent observation of gel to ensure digestion of plasmids
+
31/05
+
Discussion on:-
+
1) Plasmid isolation
+
2) Lysis solutions and their composition
+
3) Function of each component in the solutions
+
</div></h2>
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      <h2  class="boogaloo_font "><span style="font-size:30px;cursor:pointer" onclick="openNav1()">May</span></h2>
 
  
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To read...</p>
 
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    <div class="content1  boogaloo_font"><h2 class="boogaloo_font "><span style="font-size:30px;cursor:pointer" >June</span></h2>
 +
<object data="https://static.igem.org/mediawiki/2017/e/e3/T--IIT_Delhi--NoteJune.pdf" type="application/pdf" width="100%" height="500px">
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    <div class="content1  boogaloo_font"><h2 class="boogaloo_font "><span style="font-size:30px;cursor:pointer" >July</span></h2>
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Latest revision as of 17:49, 1 November 2017

iGEM IIT Delhi

We planned early on to document the work we did and efforts we put into our project, on a daily basis,hence, we were able to compile a comprehensive notebook accounting for all the events that took place.

April

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May

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June

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July

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August

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September

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October

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Contact Us Address

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