Team:USTC-China/openday

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<p>We conducted the visiting activity in our Synthetic Biology Lab as part of the “Open Day of Biox ” program during the Week of Science of USTC(from 19th May to 20th May), which is an annual event aimed at promoting the spread of science. It is an unusual chance for the public to get to know what science really is. During these days many labs in our school will be accessible for people outside our campus and volunteers majoring in certain fields will be there as instructors. Our institute served moe than 6000 people in two days this year.</p>
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<p>We conducted the visiting activity in our Synthetic Biology Lab as part of the “Open Day of Biox ” program during the Week of Science of USTC(from 19th May to 20th May), which is an annual event aimed at promoting the spread of science. It is an unusual chance for the public to get to know what science really is. During these days many labs in our school will be accessible for people outside our campus and volunteers majoring in certain fields will be there Sequence_of_toggle_switchas instructors. Our institute served moe than 6000 people in two days this year.</p>
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<p>The phage widely lives in the nature, especially in the air around the manufacturing shops of the fermentation factory and the drainage system. The phage can spread by air and can sneak into nearly every procedure of the fermentation. Main reasons for the pollution of one single fermentation tank contains: remaining blind sides both in the tank and its assistant pipes and the misoperation during inoculating. Main sources of the mass invasion of phages including air filtration system, importation of new strains, lysogen and unthoroughly autoclaved media. All these reasons and sources can lead to continuous pollution among tanks and massive infection.</p>
 
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<p>In fermentation production, the loss results from the bacteria's being infected by the phage is striking. Because the phage infect intensely and spread rapidly, once the bacteria are infected, it is very difficult to eradicate the phages and the lysogens thoroughly. For this reason, it is quite important to prevent the invasion of the phages. If large tanks of fermentation broth are only polluted slightly, the period of the fermentation will be extended, the broth will become clear gradually and the synthesis of the fermented products will be much more difficult. However, if the fermentation broth is unluckily polluted severely, the factory will have to stop production totally, and massive loss in profit happens afterward. This kind of catastrophe occurs commonly in the fermentation of glutamic acid, amylase, protease, acetone and many kinds of antibiotics. For example, in the fermentation of lactic acid, the seed culture of the lactobacillus will stop production in 30 minutes once the bacteria are infected severely by phages.</p>
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<h2><a name="1">Who come to Open Day?</a></h2>
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<p>This "Week of Science" program is annually held in USTC under the instruction of the Ministry of Science and Technology of the People's Republic of China. With no limitations to our campus and part of our labs, people from outside our school can enjoy their journey of science freely. Thus a great range of people, from kids to the elderly are involved in our program. Especially, students from primary schools and high schools in Anhui province of China were well organized by their teachers. Many of them traveled a lot to get to our campus.</p>
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<div class="imgholder1" align="left"  style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/9/97/Openday_1.jpg"><img src="https://static.igem.org/mediawiki/2012/9/97/Openday_1.jpg" alt="Openday_1" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member JinXin Wang is introducing PCR for students from Lujiang Middle School Anhui Province.(picture from Lujiang Middle School)</small>
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<div class="imgholder1" align="center"  style="float:right;width:350px;height:auto;margin-bottom:55px;">
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<a href="https://static.igem.org/mediawiki/2012/6/6f/Openday_2.JPG"><img src="https://static.igem.org/mediawiki/2012/6/6f/Openday_2.JPG" alt="Openday_2" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Children are listening to the instructors.</small>
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<div class="imgholder1" align="center" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/3/37/Openday_3.JPG"><img src="https://static.igem.org/mediawiki/2012/3/37/Openday_3.JPG" alt="Openday_3" style="clear:both;width:350px;height:252px;"></a><br><small align="center">People at work come to our lab!</small>
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<div class="imgholder1" align="center" style="float:right;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/8/81/Openday_4.JPG"><img src="https://static.igem.org/mediawiki/2012/8/81/Openday_4.JPG" alt="Openday_4" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Team member Yangmin Yue is playing with kids.</small>
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<p>Some common phenomena that will occur if the fermentation broth is polluted by the phages are listed below:</p>
 
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<li>1. The bacteria will die and lyse in a short time and only the fragments of bacteria will remain afterward.</li>
 
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<li>2. OD at 600nm of the fermentation broth can be found quite low.</li>
 
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<li>3. Under the microscope, you can see the number of the bacteria is extremely decreased and the bacteria in a colony are abnormally arranged. What's worse, there are no complete bacteria can be found.</li>
 
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<li>4. The physicochemical properties are changing. The pH is increasing, the temperature stop climbing and start to decrease gradually. The amount of CO2 emitted is dropping rapidly.</li>
 
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<li>5. The metabolism of the bacteria becomes abnormal and the production of the fermentation products stops.</li>
 
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<li>6. Plenty of bubbles emerge and the broth appears red and grey. Sometimes the broth can be even sticky.</li>
 
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<li>7. Plaques can be seen when using double-layer media to test the bacteria.</li>
 
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<h2><a name="2">What do we do?</a></h3>
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<p>After applying to the School of Life Sciences, we are part of the Week of Science of USTC activity. Since our lab is open to the public, we have the chance to reach people from different backgrounds and ages. That is, we gain a wonderful opportunity to make synthetic biology known by more people. Various of sections are designed for people from different ages to better understand what synthetic biology is. The whole process consists of videos&explanations, forums&lectures, panels&presentations, introductions of equipments and games&interactions.</p>
 +
<p>Movies about the central dogma and genetic engineering are played on a continuous loop during the opening time, providing the visitors a vivid image of synthetic biology. Lectures concerning on biobricks and iGEM are given when adults and students from high schools enter, they are considered to be able to further understand the details of synthetic biology. Panels are placed aside the passage way, and when the visitors come by, USTC iGEMers will be there instructing. The characters and usages of equipments such as the PCR instrument, the centrifuge, the micropette plus and the Gel Image System which are available in our lab are explained by our team members. Taken the safety of the visitors into consideration, we keep warning them to stay away from our equipments. For kids who may have difficulty in understanding the lecture and movies, we set up a game zone where building blocks and paper DNA models are used to make it easier to understand the basic idea of synthetic biology.</p>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/8/85/Openday_5.JPG"><img src="https://static.igem.org/mediawiki/2012/8/85/Openday_5.JPG" alt="Openday_5" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member Xuexuan Zhen is demonstrating the usage of the centrifuge.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/8/87/Openday_6.JPG"><img src="https://static.igem.org/mediawiki/2012/8/87/Openday_6.JPG" alt="Openday_6" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member Zhaoxiong Chen is explaining the panels.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/d/d6/Openday_7.JPG"><img src="https://static.igem.org/mediawiki/2012/d/d6/Openday_7.JPG" alt="Openday_7" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member Qian Li is introducing the Gel Image System.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/1/15/Openday_8.jpg"><img src="https://static.igem.org/mediawiki/2012/1/15/Openday_8.jpg" alt="Openday_8" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member Wuyang Chen is demonstrating the usage of the micropette plus.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/7/7b/Openday_9.JPG"><img src="https://static.igem.org/mediawiki/2012/7/7b/Openday_9.JPG" alt="Openday_9" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Children are playing with their moms behind.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/4/46/Openday_10.JPG"><img src="https://static.igem.org/mediawiki/2012/4/46/Openday_10.JPG" alt="Openday_10" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team members are playing too!</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;">
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<a href="https://static.igem.org/mediawiki/2012/1/17/Openday_11.JPG"><img src="https://static.igem.org/mediawiki/2012/1/17/Openday_11.JPG" alt="Openday_11" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Our team member Ting Fu is giving a lecture to students from high school.</small></div>
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<div class="imgholder1" align="left" style="float:left;width:350px;height:auto;margin-bottom:40px;">
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<a href="https://static.igem.org/mediawiki/2012/7/78/Openday_12.JPG"><img src="https://static.igem.org/mediawiki/2012/7/78/Openday_12.JPG" alt="Openday_12" style="clear:both;width:350px;height:252px;"></a><br><small align="center">Kids are watching movies about the central dogma!</small></div>
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<h2><a name="2">Introduction to lambda phage</a></h2>
 
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<p>Entcrobacteria phage λ (lambda phage, coliphage λ) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. This virus is temperate and may reside within the genome of its host through lysogeny or amplify its number and lyse the host through lytic life cycle.</p>
 
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<div class="imgholder1" align="left"  style="float:right;width:200px;height:auto;">
 
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<a href="https://static.igem.org/mediawiki/2012/2/25/593px-LambdaPlaques.jpg"><img src="https://static.igem.org/mediawiki/2012/2/25/593px-LambdaPlaques.jpg" alt="project image" style="clear:both;width:200px;height:200px;"></a><br><small align="center">Lysis plaques of lambda phage on E. coli bacteria lambda phage</small>
 
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</div>
 
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<p>Usually, a <a href="">"lytic cycle"</a> ensues, where the lambda DNA is replicated many times and the genes for head, tail and lysis proteins are expressed. This leads to assembly of multiple new phage particles within the cell and subsequent cell lysis, releasing the cell contents, including virions that have been assembled, into the environment</p>
 
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<p>However, under certain conditions the phage DNA may integrate itself into the host cell chromosome in the <a href="">lysogenic pathway</a>. In this state, the λ DNA is called a prophage and stays resident within the host's genome without apparent harm to the host. The host can be termed a lysogen when a prophage is present.</p><br>
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<h2><a name="3">In the end</a></h3>
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<h3><a name="2.1">Genome structure of the toggle switch in lambda phage</a></h3>
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<div class="imgholder1" align="right" style="float:right;width:400px;height:auto;margin-right:0px;">
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<div class="imgholder1" align="left" style="clear:both;width:289px;height:auto;margin-left:100px;">
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<a href="https://static.igem.org/mediawiki/2012/f/ff/Openday_13.JPG"><img src="https://static.igem.org/mediawiki/2012/f/ff/Openday_13.JPG" alt="Openday 13" style="clear:both;width:400px;height:267px;"></a><small align="left">Part of our team members volunteering in the activity.</small>
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<a href="https://static.igem.org/mediawiki/2012/6/6f/Bacteriophage_lambda_genome_total.jpg"><img src="https://static.igem.org/mediawiki/2012/6/6f/Bacteriophage_lambda_genome_total.jpg" alt="Bacteriophage_lambda_genome_total" style="clear:both;width:289px;height:254px;"></a><br><small align="center">Schematic representation of the genome of the bacteriophage lambda.</small>
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</div>
</div>
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<div class="imgholder1" align="left" style="float:right;width:235px;height:auto;">
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<p>During the Week of Science our team have served enormous number of people outside our campus. We believe that people who ever come to our lab will be impressed by the magic of synthetic biology. Visitors can get a picture of the basic principles of synthetic biology and pick up some tips for the equipments. We feel happy to find that people are curious about our lab and strongly interested when we are introducing. It is axiomatic that our work is of great significance to the outreach of Synthetic Biology. And we enjoy our volunteering very much! </p>
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<a href="https://static.igem.org/mediawiki/2012/f/f7/Sequence_of_toggle_switch_%E5%89%AF%E6%9C%AC.jpg"><img src="https://static.igem.org/mediawiki/2012/f/f7/Sequence_of_toggle_switch_%E5%89%AF%E6%9C%AC.jpg" alt="project image" style="clear:both;width:235px;height:109px;"></a><br><small align="center">Sequence_of_toggle_switch</small>
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<p><b>Promoter pR:</b>>Initializes the rightward transcription. If the pR is not repressed, these proteins will be expressed and the phage will transfer into lytic cycle and plenty of new phage particles will be assembled.</p>
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<p><b>Promoter pRM:</b>Initializes the transcription of repressor CI. It transcripts leftwards.
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OR1, OR2, OR3: Three protein binding regions on the genome of lambda phage. They can be bound by protein CI dimmers(CI2) and Cro dimmers(Cro2). The sites of these three regions on DNA are shown in the picture below.</p>
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<h3><a name="2.2">Function overview of the proteins involve in the toggle switch</a></h3>
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<p><span>Cro:<span> Transcription inhibitor. The protein Cro can automatically form diamer Cro2 and then binds OR3, OR2 and OR1 (affinity OR3 > OR2 = OR1, i.e. preferentially binds OR3) (<a href="">See the free energy of CI2 or Cro2 interacting with the three regions</a>)..At low concentrations the Cro2 blocks the pRM promoter, preventing cI production afterwards. At high concentrations the Cro2 downregulates its own production through OR2 and OR1 binding. No cooperative binding (c.f. below for cI binding)</p>
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<p><span>CI:<span> Transcription inhibitor. The protein CI can also automatically form diamer CI2(similar to Cro2) and then binds OR1, OR2 and OR3 (affinity OR1 > OR2 = OR3, i.e. preferentially binds OR1). At low concentrations the CI2 blocks the pR promoter, preventing cro production afterwards. At high concentrations the CI2 downregulates its own production through OR3 binding. N terminal domain of cI on OR2 tightens the binding of RNA polymerase holoenzyme complex to pRM and hence stimulate its own transcription. Repressor also inhibits transcription from the pL promoter.</p>
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<h3><a name="2.3">Maintenance of lysogeny</a></h3>
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<p>Lysogeny is maintained solely by cI. cI represses transcription from pL and pR while upregulating and controlling its own expression from pRM. It is therefore the only protein expressed by lysogenic phage.</p>
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<div class="imgholder1" align="right" style="float:right;width:800px;height:auto;margin-right:0px;">
 
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<a href="https://static.igem.org/mediawiki/2012/0/02/ThebacteriophagelCIproteinfindsanasymmetricsolution%28b%29.jpg"><img src="https://static.igem.org/mediawiki/2012/0/02/ThebacteriophagelCIproteinfindsanasymmetricsolution%28b%29.jpg" alt="project image" style="clear:both;width:800px;height:267px;"></a><br><p><small align="center">CI dimers bound cooperatively to adjacent operator sites in OR and OL. The CI dimers are shown in blue. Each subunit of the dimer consists of an N-terminal DNA-binding domain (N), a C-terminal oligomerization domain(C), and a linker region (black) connecting the two. The dimer pair bound cooperatively at OR1 and OR2 represses transcription from PR and the dimer bound at OR2 also activates transcription from PRM. The dimer pair bound cooperatively at OL1 and OL2 represses transcription from PL.</small></p>
 
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</div>
 
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<h3><a name="2.4">Transformation into Lytic life cycle</a></h3>
 
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<p>Cro is responsible for preventing the synthesis of the repressor CI and this action shuts off the possibility of establishing lysogeny. It has two effects:</p>
 
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<ul>
 
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<li>It prevents the synthesis of repressor via the maintenance circuit; that is, it prevents transcription via pRM .</li>
 
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<li>It also inhibits the expression of early genes from both pL and pR
 
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Cro achieves its function by binding to the same operators as (el) repressor protein. </li>
 
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</ul>
 
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<h3><a name="2.5">Lytic or lysogenic? </a></h3>
 
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<p>The gene regulatory circuitry of phage λ is among the best-understood circuits at the mechanistic level. This circuitry involves several interesting regulatory behaviors. An infected cell undergoes a decision between two alternative pathways, the lytic and lysogenic pathways, just like two states controlled by a toggle switch.</p>
 
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<p>Simplistically, in cells with sufficient nutrients, protease activity is high, which breaks down cI.[10] This leads to the lytic lifestyle. In cells with limited nutrients, protease activity is low, making cI stable. This leads to the lysogenic lifestyle. This means that a cell "in trouble", i.e. lacking in nutrients and in a more dormant state, is more likely to lysogenise. This would be selected for because the phage can now lie dormant in the bacterium until it falls on better times, and so the phage can create more copies of itself with the additional resources available and with the more likely proximity of further infectable cells.</p>
 
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<p class="level1"><a href="https://2012.igem.org/Team:USTC-China/methods">Methods</a></p>
<p class="level1"><a href="https://2012.igem.org/Team:USTC-China/methods">Methods</a></p>
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<p class="level0"><a href="https://2012.igem.org/Team:USTC-China/achievements">ACHIEVEMENTS</a></p>
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<p class="level0"><a href="https://2012.igem.org/Team:USTC-China/results">ACHIEVEMENTS</a></p>
<p class="level1"><a href="https://2012.igem.org/Team:USTC-China/results">Results</a></p>
<p class="level1"><a href="https://2012.igem.org/Team:USTC-China/results">Results</a></p>

Latest revision as of 09:09, 15 February 2013

OPEN DAY















We conducted the visiting activity in our Synthetic Biology Lab as part of the “Open Day of Biox ” program during the Week of Science of USTC(from 19th May to 20th May), which is an annual event aimed at promoting the spread of science. It is an unusual chance for the public to get to know what science really is. During these days many labs in our school will be accessible for people outside our campus and volunteers majoring in certain fields will be there Sequence_of_toggle_switchas instructors. Our institute served moe than 6000 people in two days this year.

Who come to Open Day?

This "Week of Science" program is annually held in USTC under the instruction of the Ministry of Science and Technology of the People's Republic of China. With no limitations to our campus and part of our labs, people from outside our school can enjoy their journey of science freely. Thus a great range of people, from kids to the elderly are involved in our program. Especially, students from primary schools and high schools in Anhui province of China were well organized by their teachers. Many of them traveled a lot to get to our campus.

Openday_1
Our team member JinXin Wang is introducing PCR for students from Lujiang Middle School Anhui Province.(picture from Lujiang Middle School)
Openday_2
Children are listening to the instructors.
Openday_3
People at work come to our lab!
Openday_4
Team member Yangmin Yue is playing with kids.

What do we do?

After applying to the School of Life Sciences, we are part of the Week of Science of USTC activity. Since our lab is open to the public, we have the chance to reach people from different backgrounds and ages. That is, we gain a wonderful opportunity to make synthetic biology known by more people. Various of sections are designed for people from different ages to better understand what synthetic biology is. The whole process consists of videos&explanations, forums&lectures, panels&presentations, introductions of equipments and games&interactions.

Movies about the central dogma and genetic engineering are played on a continuous loop during the opening time, providing the visitors a vivid image of synthetic biology. Lectures concerning on biobricks and iGEM are given when adults and students from high schools enter, they are considered to be able to further understand the details of synthetic biology. Panels are placed aside the passage way, and when the visitors come by, USTC iGEMers will be there instructing. The characters and usages of equipments such as the PCR instrument, the centrifuge, the micropette plus and the Gel Image System which are available in our lab are explained by our team members. Taken the safety of the visitors into consideration, we keep warning them to stay away from our equipments. For kids who may have difficulty in understanding the lecture and movies, we set up a game zone where building blocks and paper DNA models are used to make it easier to understand the basic idea of synthetic biology.


Openday_5
Our team member Xuexuan Zhen is demonstrating the usage of the centrifuge.
Openday_6
Our team member Zhaoxiong Chen is explaining the panels.
Openday_7
Our team member Qian Li is introducing the Gel Image System.
Openday_8
Our team member Wuyang Chen is demonstrating the usage of the micropette plus.
Openday_9
Children are playing with their moms behind.
Openday_10
Our team members are playing too!
Openday_11
Our team member Ting Fu is giving a lecture to students from high school.
Openday_12
Kids are watching movies about the central dogma!

In the end

Openday 13Part of our team members volunteering in the activity.

During the Week of Science our team have served enormous number of people outside our campus. We believe that people who ever come to our lab will be impressed by the magic of synthetic biology. Visitors can get a picture of the basic principles of synthetic biology and pick up some tips for the equipments. We feel happy to find that people are curious about our lab and strongly interested when we are introducing. It is axiomatic that our work is of great significance to the outreach of Synthetic Biology. And we enjoy our volunteering very much!