Difference between revisions of "Team:IIT Delhi/standardpage introduction"

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<h1 style="font-size:20px;"><b>Blueprint of our project</b></h1></br>
 
<h1 style="font-size:20px;"><b>Blueprint of our project</b></h1></br>
  
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If people want to drive a system to work for them, even if the system is a simple one, simply keep pushing the system toward the goal may not be the best shoot. For example, if a professor is too pushing, his students may, on the contrary, unable to perform their best; if a farmer adding too much fertilizer, the land may be damaged in the long run, etc.</br></br>
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In today’s modern world, greenhouse gases such as NOx and SOx pose a major global issue that needs to be addressed. These oxides also increase the oxidizing capacity of the atmosphere which are responsible for the photochemical production of ozone in the lower layers of the atmosphere which has detrimental effects. Sulfur Oxides (SOx) are the main precursors of air pollution which is a deteriorating problem as well. Producing acid rain and acidified soils, Sulfur Oxides not only result in respiratory problems such as asthma and pneumonia, but also destroy farm crops, buildings and environment, causing loss of millions of dollars every year.
  
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Biological systems are extremely complex, and the components in the system are intensely interconnected. So in order to exploit the maximum potentiality of a biological system, we'll have to keep the protein or metabolic product production in a desired range. Not too high, as it may hurt the cell or inhibit its growth; either not too low, as it will be economically inefficient. </br></br>
 
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So how can we reach a desired range of expression? We need to properly combine the transcription and translation initiation elements, just as an recent published Nature article suggested[1]. But that paper just used the throughly studied E.coli expression elements in E.coli. What if we are doing engineering in a non-model organism that we just have data about a handful of expression elements, can we create the elements we need? </br></br>
 
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Our project proposed a way to employ a limited set of promoters to reach any desired expression level, or even switch between several expression level. </br></br>
 
 
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<img src="https://static.igem.org/mediawiki/2013/9/95/WHUIntro1.png" /></br></br>
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<img src="https://static.igem.org/mediawiki/2014/2/25/Igem-iitd-pollution1.jpg" /></br></br>
 
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<center><em>Fig.1 Tandem promoter</em></br></center>
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<center><em>Fig.1 Pollution</em></br></center>
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First, we combined the known promoter into tandem promoter system. We've done experiments and modeling to show how can we use a 0.1 promoter and a 0.3 promoter to reach expression level from 0.1 to the maximum. Please check experiment here and modeling here. </br></br>
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Both these gases also have detrimental effects on the environment and our team plans to combat this catastrophic effect by reducing the amount of the NOx and SOx gases ejected through the exhaust vents. For this we have engineered nrfA gene (codes for nitrite reductase) in E.Coli to convert NOx to NH3 (Clarke et al;2008) and for SOx reduction we will incorporate cysI(sulfite reductase) that converts SO2 to H2S (Growth Yields and Growth Rates of. Desulfovibrio vulgaris (Marburg) growing on Hydrogen plus Sulfate and Hydrogen plus Thiosulfate as the Sole Energy Sources, Arch. Microbiol. 117, 209-214 [1978]) and sqr (sulfide quinone reductase) to convert H2S to S. In order to realize the whole sulfur metabolism pathway, we use several bioinformatics web sites such as KEGG and NCBI. We anticipate that the use of genetically engineered bacterium would subside the efficiency of existing chemical methods. </br></br>
 
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<img src="https://static.igem.org/mediawiki/2013/6/6f/WHUIntro2.png" /></br>
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<img src="https://static.igem.org/mediawiki/2014/3/34/Igem-iitd-pollution-3.jpg" /></br>
 
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<center><em>Fig.2 Cas9 regulated multistage promoter</em></br></center>
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<img src="https://static.igem.org/mediawiki/2013/4/4e/WHUSliderR.png" /></br>
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<center><em>Fig 3. An analog to slide rheostat</em></br></center>
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Then, we made the tandem promoter a “slide rheostat” by using d/aCas9 to regulate it. This enable the tandem promoter to switch between several designable expression level, and become a multistage promoter. This is different from the normal regulated promoter that usually has only two stage: on and off (Fig.4). To see our experiment about this multistage promoter, please <a href="https://2013.igem.org/Team:WHU-China/modules#tandem_promoter">click here</a>. It's also important to ensure the orthogonality of this multistage promoter. So the off-target tendency of Cas9 is modeled and analyzed by combining the data of six paper about Cas9 off-target. For the modeling result, please <a href="https://2013.igem.org/Team:WHU-China/modelingintro">click here</a>. </br></br>
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<img src="https://static.igem.org/mediawiki/2013/a/a8/WHUSwitches.png" /></br>
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<center><em>Fig 4. Bi-stage promoter and multistage promoter</em></br></center>
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<h1><b>Reference</b></h1>
 
<h1><b>Reference</b></h1>
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<em>[1]Mutalik, Vivek K., et al. "Precise and reliable gene expression via standard transcription and translation initiation elements." Nature methods 10.4 (2013): 354-360.</em>
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<em>[1]ABC....</em>
 
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Revision as of 16:36, 7 September 2015

Blueprint of our project


In today’s modern world, greenhouse gases such as NOx and SOx pose a major global issue that needs to be addressed. These oxides also increase the oxidizing capacity of the atmosphere which are responsible for the photochemical production of ozone in the lower layers of the atmosphere which has detrimental effects. Sulfur Oxides (SOx) are the main precursors of air pollution which is a deteriorating problem as well. Producing acid rain and acidified soils, Sulfur Oxides not only result in respiratory problems such as asthma and pneumonia, but also destroy farm crops, buildings and environment, causing loss of millions of dollars every year.


Fig.1 Pollution
Both these gases also have detrimental effects on the environment and our team plans to combat this catastrophic effect by reducing the amount of the NOx and SOx gases ejected through the exhaust vents. For this we have engineered nrfA gene (codes for nitrite reductase) in E.Coli to convert NOx to NH3 (Clarke et al;2008) and for SOx reduction we will incorporate cysI(sulfite reductase) that converts SO2 to H2S (Growth Yields and Growth Rates of. Desulfovibrio vulgaris (Marburg) growing on Hydrogen plus Sulfate and Hydrogen plus Thiosulfate as the Sole Energy Sources, Arch. Microbiol. 117, 209-214 [1978]) and sqr (sulfide quinone reductase) to convert H2S to S. In order to realize the whole sulfur metabolism pathway, we use several bioinformatics web sites such as KEGG and NCBI. We anticipate that the use of genetically engineered bacterium would subside the efficiency of existing chemical methods.


Reference

[1]ABC....