Difference between revisions of "Team:IIT Kanpur/InterLab"

 
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<h1>InterLab<br></h1>
 
<h1>InterLab<br></h1>
 
<p style="font-size:120%;">Complying with the trend of InterLab Study, iGEM conducts every year, to achieve the full potential of synthetic biology, invariably making every lab on earth build upon others’ work. <br>
 
<p style="font-size:120%;">Complying with the trend of InterLab Study, iGEM conducts every year, to achieve the full potential of synthetic biology, invariably making every lab on earth build upon others’ work. <br>
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The question of iGEM 2018 InterLab Study was, ‘Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?’<br>
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The question of iGEM 2018 InterLab Study was, ‘Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?’<br><br>
 
Approach 1:<br>
 
Approach 1:<br>
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Converting absorbance of cells to absorbance of a known concentration of beads.<br><br>
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Converting absorbance of cells to absorbance of a known concentration of beads.<br>
 
Approach 2:<br>
 
Approach 2:<br>
 
Counting colony-forming units (CFUs) from the sample.<br><br>
 
Counting colony-forming units (CFUs) from the sample.<br><br>
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<embed src="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf" width="40%" height="300px" style="float:left"
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<button class="collapsible">The Protocol</button>
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<embed src="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf" width="100%" height="400px" style="float:left"
 
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<h3>Here are the summarised results of our interlab:<br></h3>
 
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<button class="collapsible">Visiting Unique Agencies Sewage Treatment Plant</button>
 
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  <p style="font-size:120%;">Naturally human waste takes around 4-5 days to completely decompose. Nowadays sewage is treated in plants where it takes about 4-5 hours to degrade. To understand better how water from households is cleaned, we organized an industry visit to Unique water industries in Kanpur. <br>
 
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After an in depth conversation with the company official, it became clear that biological processes are at the heart of almost every sewage treatment process. The industry which we visited uses a technique called RBC (Rotating biological contactor)<br>
 
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This plant uses a 3-Rotor model for RBC. The first rotor introduces the bacteria into the sewage and aerates the sewage. Thereafter, the sewage is fed to a second chamber where the second rotor carries out the main aerobic reaction, where bacteria degrades . Maximum time is spent in the second chamber where the majority of the cleaning takes place. Eventually the third rotor removes dead bacteria from the water, after which the treated water is collected based on laminar flow. This water is fit for use in basic horticulture.<br>
 
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Other methods include sequential batch reactor, MBBR(Moving bed biofilm reactor) etc. There are issues regarding the complex procedure and huge amount of energy required to mix semi solid sludge. RBC is the simple to install and has low maintenance costs. <br>
 
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From our experiments we  found out that the presence of (%) SDS reduces growth of E.Coli. Treating water for SDS before feeding to the RBC may improve the efficiency of the water that the RBC currently provides. <br>
 
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One more chamber can be connected where the first rotor is coated with the SDS-a protein obtained by the extracellular expression which will degrade the SDS in the primary discharge. Such subtle changes can bring out a drastic improvement in the water purification techniques, especially when dealing with SDS-Rich discharges from Hotel and Hospital discharges. The SDS concentration in such discharges reaches 8-9% which is difficult to neutralize even using chemical processes. Such an improvement can lead to a more efficient way of dealing high SDS content discharges using the RBC technique.<br>
 
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<button class="collapsible">Meeting with Dr. Purnendu Bose</button>
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<h3>Here are the summarised results of our interlab:<br></h3>
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<button class="collapsible">Particle standard curve (Microsphere protocol)
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  <p style="font-size:120%;">As an academic venture, our team felt that discussing our ideas with fellow academicians would contribute to the growth of our project and also help us from pursue new lines of thought that we had not yet explored. To address this we felt that experts with knowledge on both environmental engineering and experience in practical implementations would be of great value.<br>
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<img src = "https://static.igem.org/mediawiki/2018/f/f6/T--IIT_Kanpur--Interlab01.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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We met with Dr. Purnendu Bose who is a Professor at the Dept. of Civil Engineering at IIT Kanpur and he specializes in environmental engineering. Our discussion was a fruitful exchange where we introduced our project about how we plan to clean detergent-laden water. We were unclear of any useful implementations.<br>
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<img src = "https://static.igem.org/mediawiki/2018/3/3a/T--IIT_Kanpur--Interlab02.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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He told us about the current problem faced by companies making Washing machines. People who are the target customers for these companies have the money to afford washing machines, but they still do not get personal washing machines due to lack of availability of clean water. He then suggested that we can model our product along the lines of this problem. It proved to be a crucial piece of information, and the whole conversation proceeded to ideate a washing machine add-on that recycles the water that it uses, and hence the water requirement for the washing machine decreases a lot. This model could be used generally to cut water wastage at a significant rate.
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<button class="collapsible">Meeting with Dr. Rajiv Sinha</button>
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<button class="collapsible">Fluorescein Standard Curve</button>
 
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  <p style="font-size:120%;">We met Dr. Rajiv Sinha who is also a Professor at the Dept. of Civil Engg. His expertise lies in Bioremediation, and his advice and suggestions were very helpful to us. Our problem was that though we had some idea of how our bacteria would work in the controlled settings of our lab, we did not know what challenges we would face when applying the same to water samples from the real world. One particular problem we had was that our enzyme might not work in the pH conditions, the presence of other ions etc. and so to understand real-world challenges we shared this problem with him.<br>
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<img src = "https://static.igem.org/mediawiki/2018/3/39/T--IIT_Kanpur--Interlab03.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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He suggested that we test our protein’s function on SDS in the presence of major ions in water and see the concentration's effect on protein function. He guided us to check protein functionality with each of the major ions separately, to better assess the effects of each ion individually. We could then see the level of these prominent ions in water bodies in different places and formulate our strategy for implementing our device in the future.
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<img src = "https://static.igem.org/mediawiki/2018/c/ca/T--IIT_Kanpur--Interlab04.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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Another important point he reiterated was, that instead of targeting the affected water bodies, it would be more efficient if we could tackle the problem right at the source itself. He explained to us how that model would not only bring down cost, but help avoid the unpredictability of the composition of water being cleansed.<br>
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<button class="collapsible">AutoCAD Model - Our Design</button>
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<button class="collapsible">Cell measurement protocol</button>
 
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   <p style="font-size:120%;">To be soon uploaded...
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The first column represents the fluorescence reading of two replicates for every device
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The second column represents the OD reading of two replicates for every device.</p><br>
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<img src = "https://static.igem.org/mediawiki/2018/6/65/T--IIT_Kanpur--Interlab05.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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<img src = "https://static.igem.org/mediawiki/2018/8/8e/T--IIT_Kanpur--Interlab06.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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<img src = "https://static.igem.org/mediawiki/2018/3/34/T--IIT_Kanpur--Interlab07.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
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<img src = "https://static.igem.org/mediawiki/2018/6/66/T--IIT_Kanpur--Interlab08.png" width="48%" style = "margin-left: auto;margin-right: auto;padding:0% 0% 0% 0%;border:5px solid black"></img>
 
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Latest revision as of 22:45, 17 October 2018

InterLab

Complying with the trend of InterLab Study, iGEM conducts every year, to achieve the full potential of synthetic biology, invariably making every lab on earth build upon others’ work.
The question of iGEM 2018 InterLab Study was, ‘Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?’

Approach 1:
Converting absorbance of cells to absorbance of a known concentration of beads.
Approach 2:
Counting colony-forming units (CFUs) from the sample.

Here are the summarised results of our interlab:

The first column represents the fluorescence reading of two replicates for every device The second column represents the OD reading of two replicates for every device.