Difference between revisions of "Team:DLUT China/Safety"

 
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        <li><a href="#A3">Safety of lab</a></li>
 
        <li><a href="#A3">Safety of lab</a></li>
 
        <li><a href="#A4">Safety of transporting DNA</a></li>
 
        <li><a href="#A4">Safety of transporting DNA</a></li>
 +
              <li><a href="#A5">Insecticide safety</a></li>
 
                
 
                
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  <iimg src="https://static.igem.org/mediawiki/2018/b/b0/T--DLUT_China--safety.png" />
 
 
   <header id="top" class="responsive-fonts">
 
   <header id="top" class="responsive-fonts">
 
<h1 style="font-size:40px;font-family: 'Cinzel', serif;">Safety</h1>
 
<h1 style="font-size:40px;font-family: 'Cinzel', serif;">Safety</h1>
 
 
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  </header> 
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  <img src="https://static.igem.org/mediawiki/2018/b/b0/T--DLUT_China--safety.png" style="position:absolute;z-index:-1;width:300px;height:300px;left:300px;top:300px;" />
  
  
 
   <main>
 
   <main>
 
  <section id="food">
 
  <section id="food">
<article id="A1"><span style="font-size:30px;font-family: 'Cinzel', serif;">Safety of chassis:</span><br><br><div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">We use Escherichia coli as our chassis,the names of all strains are:Escherichia coli strain Nissle, BL21 Competent E. coli, DH5-Alpha Escherichia coli strain.Our chassis organisms are all widely-used E.coli strains.So they're all very safe, and even if they get out of the lab, the risk can be effectively controlled. </div></article>
+
<article id="A1"><span style="font-size:30px;font-family: 'Cinzel', serif;color:purple;">Safety of chassis:</span><br><br><div style="font-size:20px;text-align:justify;width:800px;font-family: 'Quicksand', sans-serif;line-height:30px;">We use Escherichia coli as our chassis,the names of all strains are:Escherichia coli strain Nissle, BL21 Competent E. coli, DH5-Alpha Escherichia coli strain.Our chassis organisms are all widely-used E.coli strains.So they're all very safe, and even if they get out of the lab, the risk can be effectively controlled. </div></article>
<article id="A2"><span style="font-size:30px;font-family: 'Cinzel', serif;">Safety of parts:</span><br><br>
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<article id="A2"><span style="font-size:30px;font-family: 'Cinzel', serif;color:purple;">Safety of parts:</span><br><br>
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">Fluorescence is widely used as a representative of promoter activity. Although this is an indirect measurement, fluorescent proteins such as green fluorescent protein (GFP) provide useful insights into expression levels and can be continuously monitored without destroying the cells.<br><br>
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;line-height:30px;">
 +
We add lethal sequences to our plasmids, and there are two ways to do that.<br>
 +
<img src="https://static.igem.org/mediawiki/2018/a/ab/T--DLUT_China--safetydeath1.png" style="width:624px;height:377px;"/><br>
 +
<center><span style="font-size:15px;">Figure 1 &nbsp;  Conditional lethal system 1, composed of two plasmids. Plasmid 1 is composed of
 +
the promoter hucO, hypothetical uricase regulator which called HucR, uric acid transporter which called ygfU, sRNA and lysis protein. Plasmid 2 is composed of the sRNA and lysis protein.
 +
</span></center><br>
 +
SRNA in plasmid 1 is an inhibitory element of lysis2 in plasmid 2, which inhibits lysis2 expression. SRNA in plasmid 2 is an inhibiting element of lysis1 in plasmid 1, which inhibits lysis1 expression. When one of the plasmids is lost, the lytic protein of the other plasmids will not be inhibited, that is, the bacteria will express the lytic protein and cause the bacteria to lyse, thus killing the bacteria that lose the plasmids, so as to prevent the loss of plasmids.<br>
  
First, measure three calibration protocols: use LUDOX CL-X (45% colloidal silica suspension) as a single point reference to obtain conversion factor to convert absorbance (Abs600) to OD 600, use silica gel beads - microsphere suspension Obtain a particle standard curve,the fluorescein standard curve was measured with fluorescein at an excitation wavelength of 495 nm and an emission wavelength of this filter of 525 nm.
+
Due to the high concentration of uric acid in the intestines of hyperuricemia patients, we use uric acid as the response signal of the lethal system. When the uric acid concentration exceeds the threshold, HucR is inhibited by uric acid, and Phuco is in the open state. Subsequent genes can be transcribed and translated normally, but since lysis1 is inhibited by sRNA, the bacteria will not be cracked. When the uric acid concentration was lower than the threshold value, HucR inhibited Phuco, and Phuco was turned off. Subsequent genes could not be transcribed and translated, so that sRNA inhibiting lysis2 could not be expressed, while lysis2 could be normally expressed, resulting in death of bacteria. Due to the high concentration of uric acid in the intestinal tract of uric acid patients, the death rate of bacteria in the patient is not high. However, when the bacteria are lost to the external environment, the uric acid concentration in the external environment is lower than the threshold value, which activates the lethal system of the bacteria, leading to the death of bacteria cracking and reaching the purpose and effect of in vitro death.<br>
<br><br>
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<img src="https://static.igem.org/mediawiki/2018/6/6f/T--DLUT_China--safetydeath2.png" style="width:509px;height:168px;"/><br>
After making the standard curve, we successfully transformed the eight plasmids provided by the measurement committee and performed cell assays according to the protocol.
+
<center><span style="font-size:15px;">Figure 2 &nbsp;    Conditional lethal system 2, composed of one plasmid. Plasmid 3 is composed of
 +
the promoter pCold and lysis protein.
 +
 
 +
</span></center><br>
 +
Death in vitro was controlled by pCold to lysis3. PCold is cold shock plasmid in vitro in 16 ℃ under the condition of using IPTG induction of 3 h can activate lysis3, killed bacteria cracking, achieve the purpose of in vitro to death and effect. PCold came from the IGEM team of Northeastern University, and our two teams had a friendly interlab exchange.<br>
 
</div></article>
 
</div></article>
<article id="A3"><span style="font-size:30px;font-family: 'Cinzel', serif;">Safety of lab:</span><br><br>
+
<article id="A3"><span style="font-size:30px;font-family: 'Cinzel', serif;color:purple;">Safety of lab:</span><br><br>
  
<span style="font-size:25px;font-family: 'Cinzel', serif;">Plasmid Used<br></span>
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;line-height:30px;">
Negative control:BBa-R0040<br>
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We wear plastic gloves, white coats and goggles when performing the experiment. In addition, the experimental team of our team conducted safety training and had a clear understanding and deep understanding of how to ensure safety during the experiment. During the experiment, we will use the knowledge we received during safety training to ensure safety.<br>
Possitive control:BBa-I20270<br>
+
At the same time, we always guarantee the clean and orderly laboratory.<br><br>
Test device1:BBa-J364000<br>
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<center><img src="https://static.igem.org/mediawiki/2018/5/50/T--DLUT_china--Lab1.jpeg"   style="width:400px;height:380px;"/></center>
Test device2:BBa-J364001<br>
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Test device3:BBa-J364002<br>
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Test device4:BBa-J364007<br>
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Test device5:BBa-J364008<br>
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Test device6:BBa-J364009<br><br>
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</div>
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<span style="font-size:25px;font-family: 'Cinzel', serif;">Strain used<br></span>
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">
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Escherichia coli DH5a<br><br>
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</div>
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<span style="font-size:25px;font-family: 'Cinzel', serif;">Materials<br></span>
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">
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1ml LUDOX CL-X <br>
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ddH2O <br>
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96 well plate,black with clear flat bottom <br>
+
Clear plates<br>
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300 mL Silica beads - Microsphere suspension (provided in kit,4.7×10^8 microspheres)<br>
+
Fluorescein<br>
+
10ml 1×PBS pH 7.4-7.6<br>
+
LB (Luria Bertani)  liquid media<br>
+
LB (Luria Bertani) solid media<br>
+
Chloramphenicol (stock concentration 25 mg/ml dissolved in EtOH)<br>
+
50 ml Falcon tube<br>
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1.5 ml tube <br>
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Ice bucket with ice <br>
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Micropipettes and tips <br><br>
+
</div>
+
<span style="font-size:25px;font-family: 'Cinzel', serif;">Machines<br></span>
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<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">
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BD FACSCanto Flow cytometer<br>
+
SpectraMax M2 full wavelength microplate reader<br>
+
Medifuge™ Small Benchtop Centrifuge <br>
+
Eppendorf large Centrifuge<br>
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Constant temperature incubator<br>
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Constant temperature water bath<br>
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Vortex oscillator<br><br>
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</div>
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<span style="font-size:25px;font-family: 'Cinzel', serif;">Methods<br></span>
+
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;"><a href="https://static.igem.org/mediawiki/2018/e/ec/2018_InterLab_Flow_Cytometry_Protocol.pdf">2018_InterLab_Plate_Reader_Protocol  <br></a>
+
<a href=" https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf">2018_InterLab_Flow_Cytometry_Protocol<br></a>
+
 
</div>
 
</div>
 +
 
</article>
 
</article>
 
<article id="A4">
 
<article id="A4">
<span style="font-size:30px;font-family: 'Cinzel', serif;">Safety of transporting DNA:</span><br><br>
+
<span style="font-size:30px;font-family: 'Cinzel', serif;color:purple;">Safety of transporting DNA:</span><br><br>
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;"><a href="https://static.igem.org/mediawiki/2018/a/a0/T--DLUT_China--intresult.pdf">Details</a>
+
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;line-height:30px;">
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;"><a  href="https://static.igem.org/mediawiki/2018/e/ec/T--DLUT_China--liushixibaoyi.zip">Flow_Cytometry_Protocol  </a></div></article>
+
Miniprepped plasmid DNA (over 250ng) have been dried down. They are in 96 well plate format sealed with adhesive foil. We commissioned GenScript Biotech Corp. to carry the transportation components. Submission shipments have been declared and labeled as DNA (non-hazardous, non-regulated, non-infectious, for research purposes only).</div></article>
<article id="A5">
+
        <article id="A5">
<span style="font-size:30px;font-family: 'Cinzel', serif;">Discussion:</span><br><br><div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;">1. According to the Abs results at each time point 0 hours and 6 hours, the cell concentration of Device 1 is significantly lower than that of other devices.<br>
+
<span style="font-size:30px;font-family: 'Cinzel', serif;color:purple;">Insecticide safety:</span><br><br>
2. According to the fluorescence raw readings, the fluorescence of Device 3 is weakest, the fluorescence of Device 4 is strongest. And the fluorescence of each group increased from 0h to 6 h, abnormally, the fluorescence of the two bacteria of Device 5 was different.<br>
+
<div style="font-size:20px;text-align:justify;width:800px;font-family: 'Oxygen', sans-serif;line-height:30px;">
3. There is significant difference in plasmid conversion rate between negative control (device 1) and positive control (device 2).
+
We investigated the approval and management of probiotics in different countries.And find that in China, there is no separate regulation or management method for the safety and quality control of edible fungicides, and the quality of products on the market is also uneven.So after the team members’ discussion,we believe that in the future, we can improve relevant regulations in the following aspects:  <br> 
</div>
+
1)The safety evaluation of probiotics should consider the safety of people with low immunity;<br>
</article>
+
2)How to accurately quantify live probiotics entering and colonizing the intestines;<br>
 +
3)How to simplify laws and regulations to encourage industrial development under the premise of ensuring food safety;<br>
 +
4)How to develop probiotics, product development, and laws and regulations to form a systematic process, and then promote each other and develop together;<br>
 +
5)How to effectively communicate these standards and norms, and build a global system to adapt to the globalization of the probiotic industry.<br>
 +
 
 +
 
 +
 
 +
 
 +
<center><a href="https://static.igem.org/mediawiki/2018/c/c7/T--DLUT_China--hpInsecticide_safety.pdf" style="font-size:20px;">Insecticide safety of different countries </a></center></div></article>
 
  </section>   
 
  </section>   
 
     
 
     

Latest revision as of 14:00, 17 October 2018

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Safety

Safety of chassis:

We use Escherichia coli as our chassis,the names of all strains are:Escherichia coli strain Nissle, BL21 Competent E. coli, DH5-Alpha Escherichia coli strain.Our chassis organisms are all widely-used E.coli strains.So they're all very safe, and even if they get out of the lab, the risk can be effectively controlled.
Safety of parts:

We add lethal sequences to our plasmids, and there are two ways to do that.

Figure 1   Conditional lethal system 1, composed of two plasmids. Plasmid 1 is composed of the promoter hucO, hypothetical uricase regulator which called HucR, uric acid transporter which called ygfU, sRNA and lysis protein. Plasmid 2 is composed of the sRNA and lysis protein.

SRNA in plasmid 1 is an inhibitory element of lysis2 in plasmid 2, which inhibits lysis2 expression. SRNA in plasmid 2 is an inhibiting element of lysis1 in plasmid 1, which inhibits lysis1 expression. When one of the plasmids is lost, the lytic protein of the other plasmids will not be inhibited, that is, the bacteria will express the lytic protein and cause the bacteria to lyse, thus killing the bacteria that lose the plasmids, so as to prevent the loss of plasmids.
Due to the high concentration of uric acid in the intestines of hyperuricemia patients, we use uric acid as the response signal of the lethal system. When the uric acid concentration exceeds the threshold, HucR is inhibited by uric acid, and Phuco is in the open state. Subsequent genes can be transcribed and translated normally, but since lysis1 is inhibited by sRNA, the bacteria will not be cracked. When the uric acid concentration was lower than the threshold value, HucR inhibited Phuco, and Phuco was turned off. Subsequent genes could not be transcribed and translated, so that sRNA inhibiting lysis2 could not be expressed, while lysis2 could be normally expressed, resulting in death of bacteria. Due to the high concentration of uric acid in the intestinal tract of uric acid patients, the death rate of bacteria in the patient is not high. However, when the bacteria are lost to the external environment, the uric acid concentration in the external environment is lower than the threshold value, which activates the lethal system of the bacteria, leading to the death of bacteria cracking and reaching the purpose and effect of in vitro death.

Figure 2   Conditional lethal system 2, composed of one plasmid. Plasmid 3 is composed of the promoter pCold and lysis protein.

Death in vitro was controlled by pCold to lysis3. PCold is cold shock plasmid in vitro in 16 ℃ under the condition of using IPTG induction of 3 h can activate lysis3, killed bacteria cracking, achieve the purpose of in vitro to death and effect. PCold came from the IGEM team of Northeastern University, and our two teams had a friendly interlab exchange.
Safety of lab:

We wear plastic gloves, white coats and goggles when performing the experiment. In addition, the experimental team of our team conducted safety training and had a clear understanding and deep understanding of how to ensure safety during the experiment. During the experiment, we will use the knowledge we received during safety training to ensure safety.
At the same time, we always guarantee the clean and orderly laboratory.

Safety of transporting DNA:

Miniprepped plasmid DNA (over 250ng) have been dried down. They are in 96 well plate format sealed with adhesive foil. We commissioned GenScript Biotech Corp. to carry the transportation components. Submission shipments have been declared and labeled as DNA (non-hazardous, non-regulated, non-infectious, for research purposes only).
Insecticide safety:

We investigated the approval and management of probiotics in different countries.And find that in China, there is no separate regulation or management method for the safety and quality control of edible fungicides, and the quality of products on the market is also uneven.So after the team members’ discussion,we believe that in the future, we can improve relevant regulations in the following aspects:
1)The safety evaluation of probiotics should consider the safety of people with low immunity;
2)How to accurately quantify live probiotics entering and colonizing the intestines;
3)How to simplify laws and regulations to encourage industrial development under the premise of ensuring food safety;
4)How to develop probiotics, product development, and laws and regulations to form a systematic process, and then promote each other and develop together;
5)How to effectively communicate these standards and norms, and build a global system to adapt to the globalization of the probiotic industry.
Insecticide safety of different countries