Team:Nanjing-China/project

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Revision as of 06:04, 27 October 2013

Overall Project: (Here is an interesting cartoon we made, showing the general idea of our project.)

Atrazine is one of the most heavily used herbicides and it is used to control the growth of weeds. Atrazine is also a persistent environmental pollutant, it can cause problems like suppressing the growth of some other plants, inducing complete feminization and chemical castration in male frogs, and disrupting the human body's internal systems. Widespread contamination of groundwater has been reported in the United States. As such, there are increasing concerns over the toxicity of atazine in the environment ^{[1, 2]}.

Considering the fact that atrazine can hardly be degraded naturally in soil and water, we designed and constructed a system in E.coli to make them move towards atrazine simultaneously and absorb it, degrade it into a harmless chemical substance.

For a start, to equip the bacteria with the ability to recognize atrazine, we utilized a smart ribosome switch to recognize the presence of atrazine. In the absence of atrazine, the secondary structure of the ribosome switch forms a pseudoknot, sequestering the ribosome-binding site. In this way, the expression of downstream genes is inhibited. However, in the presence of atrazine, the conformation of the switch changes, the ribosome-binding site is therefore exposed, so the genes downstream can be expressed ^[1].

When our bacteria could detect the presence of atrazine, we improved their performance by inserting quorum sensing (QS) system into the circuits. When our bacteria smell the signal of atrazine, they send out acyl-homoserine lactone (AHL) to recruit more team members to gather around the atrazine center ^[3].

Once enough atrazine gathers around the atrazine center, the density of bacteria pulls the trigger of Plsr, and the genes at the downstream of Plsr start to express and the bacteria are therefore able to secrete the super degrading enzyme, TrzN.

However, the low transportation efficiency of atrazine from outside the membrane to the inside of the bacteria posed a problem to us. Luckily, an amazing transporter TRM provided us with an answer. With the help of HPLC (high performance liquid chromatography), we surprisingly found that TRM can distinctively transport atrazine into our bacteria so our entire system can work more sensitively.

What's more, in order to acquire a better performance, we modified some of our parts, such as TrzN and CI, to make them function even better.

At the same time, we also used the computer calculation to simulate the system we constructed, hoping to endow our system with high stability.

For the last two months, we have completed some great achievements. A happy and united team was formed and we have successfully constructed 7 brilliant biobrick parts. Hoping to do better, we improved some of the parts function by scientific modification. Our human practice work has spread the concept and notion of synthetic biology as well as our project to many advanced teenagersacross the nation.

We know exactly that our work still has a long way to go to get near to industrialization and commercialization, but we do believe that this hope can be eventually realized. Just think about the fascinating progress from the first computer to the PC, iPad and iPhone today, our research perhaps is still lingering in the "old times", but we have enough confidence that it will shock the world one day, providing us with a final answer to the pollution of atrazine.

Reference
[1] Sinha J, et al. Reprogramming bacteria to seek and destroy a herbicide. Nature chemical biology, 2010, 6 (6): 464-470.
[2] Hayes TB, et al. Atrazine induces complete feminization and chemical castration in male African clawed frogs (Xenopus laevis). Proceedings of the National Academy of Sciences, 2010, 107 (10): 4612-4617.
[3] Carter KK, et al. Pathway engineering via quorum sensing and sRNA riboregulators-Interconnected networks and controllers. Metabolic Engineering, 2012, 14 (3): 281-288.

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              <dd class="dd_1">
 (Here is an interesting <a href="https://2013.igem.org/Team:Nanjing-China/mp4"><strong>cartoon</strong></a> we made, showing the general idea of our project.)<br><br>
-Atrazine is one of the most heavily used herbicides and it is used to control the growth of weeds. Atrazine is also a persistent environmental pollutant, it can cause problems like suppressing the growth of some other plants, inducing complete feminization and chemical castration in male frogs, and disrupting the human body's internal systems. Widespread contamination of groundwater has been reported in the United States. As such, there are increasing concerns over the toxicity of atazine in the environment<sup>[1, 2]</sup>.<br/><br/>
+Atrazine is one of the most heavily used herbicides and it is used to control the growth of weeds. Atrazine is also a persistent environmental pollutant, it can cause problems like suppressing the growth of some other plants, inducing complete feminization and chemical castration in male frogs, and disrupting the human body's internal systems. Widespread contamination of groundwater has been reported in the United States. As such, there are increasing concerns over the toxicity of atazine in the environment <sup>[1, 2]</sup>.<br/><br/>
-Considering the fact that atrazine can hardly be degraded naturally in soil and water, we designed and constructed a system in Escherichia coli to make them move towards atrazine simultaneously up to the gradient and absorb it, degrade it into a harmless chemical substance.<br/><br/>
+Considering the fact that atrazine can hardly be degraded naturally in soil and water, we designed and constructed a system in E.coli to make them move towards atrazine simultaneously and absorb it, degrade it into a harmless chemical substance.<br/><br/>
-For a start, to equip the bacteria with the ability to recognize atrazine, we utilized a smart ribosome switch to recognize the presence of atrazine. In the absence of atrazine, the secondary structure of the ribosome switch forms a pseudoknot, sequestering the ribosome-binding site. In this way, the expression of downstream genes is inhibited. However, in the presence of atrazine, the conformation of the switch changes, the ribosome-binding site is therefore exposed, so the genes downstream can be expressed.<br/><br/>
+For a start, to equip the bacteria with the ability to recognize atrazine, we utilized a smart ribosome switch to recognize the presence of atrazine. In the absence of atrazine, the secondary structure of the ribosome switch forms a pseudoknot, sequestering the ribosome-binding site. In this way, the expression of downstream genes is inhibited. However, in the presence of atrazine, the conformation of the switch changes, the ribosome-binding site is therefore exposed, so the genes downstream can be expressed <sup>[1]</sup>.<br/><br/>
 When our bacteria could detect the presence of atrazine, we improved their performance by inserting quorum sensing (QS) system into the circuits. When our bacteria smell the signal of atrazine, they send out acyl-homoserine lactone (AHL) to recruit more team members to gather around the atrazine center <sup>[3]</sup>.<br/><br/>
 Once enough atrazine gathers around the atrazine center, the density of bacteria pulls the trigger of Plsr, and the genes at the downstream of Plsr start to express and the bacteria are therefore able to secrete the super degrading enzyme, TrzN.<br/><br/>