Difference between revisions of "Team:AHUT China/design"

Line 93: Line 93:
 
             <div class="container">
 
             <div class="container">
 
               <div class="section_title ">
 
               <div class="section_title ">
                <div align="center"> <h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Introduction</h2></div>
+
             
                   <p>We took part in the Fifth International InterLab Measurement Study which ains to achieve the purpose of comparative measurement. The goal of this study is to obtain large amounts of data from labs across the world,to develop absolute units for measurements GFP in a plate reader to eliminate variation between labs.</p><br>
+
                   <p>As we have described in the background, traditional carbon dioxide collection techniques are still in its early stages, characterized by high consumption and low efficiency. We want low-energy, large-scale, efficient collection of carbon dioxide, in order to achieve this goal, we by the carbon anhydride enzyme gene into E. coli.</p><br>
<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Materials</h2></div>
+
                   <p>To ensure that E. coli-producing carbonic anhydride (CA-II) normally absorbs carbon dioxide in an industrialized environment, we first simulate the protein molecule expressed by a computer to obtain a thermally stable carbonic anhydride (CA-II), which produces a thermally stable carbonic anhydride (CA-II), so that it can normally absorb carbon dioxide in a factory-like environment.
                   <p>Plate reader: Synergy H1 (Biotek)<br>
+
Plate reader plates: Corning 3603 96-Well Microplates (black plates with clear flat bottom)<br>
+
Cell culture shaker: ZWYR-200D<br><br>
+
Devices:<br>
+
Negative control :BBa_R0040 <br>
+
Positive control :BBa_I20270 <br>
+
Device 1: BBa_J364000  <br>
+
Device 2: BBa_J364001  <br>
+
Device 3: BBa_J364002  <br>
+
Device 4: BBa_J364007  <br>
+
Device 5: BBa_J364008  <br>
+
Device 6: BBa_J364009  <br>
+
Note: for Device 5, we have not transformed it into DH5⍺ competent cells successfully for many times, therefore, we thank IGEM team of Nanjing University for providing the Device 5.<br>
+
Calibration material: Provided in the 2018 IGEM distribution kit <br>
+
Microorganism: Escherichia coli DH5⍺ strains<br>
+
 
</p><br>
 
</p><br>
<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Methods</h2></div>
+
                   <p>E. Coli's carbonic anhydride enzyme (CA-II) promotes CO2 hydration to produce co32-, which binds to the free ca2+ in the environment to form calcium carbonate deposits, thereby achieving the purpose of absorbing carbon dioxide, and producing inorganic products that can be used.</p><br>
                   <p>Following iGEM requirements, Team AHUT_China performed measurements according to these 2018 InterLab Protocols <a href="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf">https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf</a> </p><br>
+
<p>
<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Results</h2></div>
+
Selection of carbonic anhydride enzymes:<br>
                  <h4>1.OD 600 reference point</h4><p>
+
Our team acquired a sequence of the human Body's carbonic anhydride, and contacted biotech companies to help us synthesize the carbonic anhydride gene in full sequence. The Carbon-anhydride (CA-II) activity of the human being used by our team is more active than that of other mammals, plants, algae, and bacteria-producing carbonic anhydride (CA-II). The carbon anhydride (CA-II) extracted in the human body at 37 ℃ the fastest reaction rate, 50 ℃ conditions, But its maximum reaction rate can reach 106 s-1, the fastest catalytic rate of carbonic anhydride (CA-II).
Using OD 600 and H2O to generate the conversion factor for the transformation later. The average of OD600 is 0.063; the correction factor (OD600/ABS600) is 3.500
+
 
  </p><br>
 
  </p><br>
  <div align="center"><img src="https://static.igem.org/mediawiki/2018/c/cb/T--AHUT_China--_LUDOX_correct_result.jpg" width="317" height="234" alt=""/></div><br><div align="center">Fig. 1 LUDOX correct value
+
  <h4>Carbonic anhydride Enzyme structure:</h4>
  </div>
+
                <div align="center"><img src="https://static.igem.org/mediawiki/2018/2/24/T--AHUT_China--_Fig._4_Fluorescein_Standard_Curve.jpg" width="701" height="440" alt=""/></div><br>
  <h4>2.Particle standard curve</h4>
+
                  <div align="center"> Fig. 4 Fluorescein Standard Curve </div>
 
                   <p>
 
                   <p>
We obtained the two Particle Standard Curve (normal and log scale).
+
CHRISTOPHERKS,JAMESJL.Biotechnologyfor theaccelerationofcarbondioxidecaptureandseques- tration[J].ScienceDirect,2011,22:818-823.
 
  </p><br>
 
  </p><br>
  <div align="center"><img src="https://static.igem.org/mediawiki/2018/6/65/T--AHUT_China--_Fig._2_Particle_Standard_Curve.jpg" width="701" height="440" alt=""/></div><br><div align="center">Fig. 2 Particle Standard Curve
+
  </div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2018/7/7e/T--AHUT_China--_Fig._3_Particle_Standard_Curve_%28log_scale%29.jpg" width="701" height="440" alt=""/></div><br><div align="center">
+
  Fig. 3 Particle Standard Curve (log scale)
+
</div>
+
<h4>3.Fluorescein standard curve</h4><p>
+
Dilution serious of fluorescein were prepared and measured in a 96 well plate. A standard curve is generated to correct the cell based readings to an equivalent fluorescein concentration.<br>
+
We obtained the two Fluorescein Standard Curve (normal and log scale).
+
</p><br>
+
 
+
<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/24/T--AHUT_China--_Fig._4_Fluorescein_Standard_Curve.jpg" width="701" height="440" alt=""/></div><br><div align="center">
+
  Fig. 4 Fluorescein Standard Curve
+
</div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2018/a/a9/T--AHUT_China--_Fig._5_Fluorescein_Standard_Curve_%28log_scale%29.jpg" width="701" height="440" alt=""/></div><br><div align="center">
+
  <div align="center" >Fig. 5 Fluorescein Standard Curve (log scale) </div>
+
</div>
+
 
 
  <h4>4.Cell measurements</h4>
+
<h6>Increased thermal stability of carbonic anhydride (CA-II):</h6>
  </ol>
+
<p>In order to make the carbonic anhydride enzyme (CA-II) suitable for the industrial environment to absorb carbon dioxide, later we use molecular simulation technology, the amino acid as the basic unit, the residual radical mutation on the two-stage structure of carbon anhydride, and the influence of molecular conformation, to obtain the best amino acid mutation sites, The thermal stability of enzymes was improved without affecting the enzyme Activity.<br>
<p>&nbsp;</p><br>
+
Note: This part also the experimental data of the thermal stability of the carbon anhydride enzyme and the three-dimensional map of the fixed-point mutant base of the carbonic anhydride gene have not been added and referenced
 
+
<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/21/T--AHUT_China--_Fig._6_Fluorescence_Measurements_Curve_.jpg" width="732" height="492" alt=""/></div><br><div align="center">
+
  <div align="center">Fig. 6 Fluorescence Measurements Curve</div>
+
</div>
+
    <p>Test devices 1 and 4 show high fluorescence intensity. Test devices 2 show a modest fluorescence intensity alone with positive control group, while devices3,5,6 barely show low fluorescence intensity alone with the negative control group.
+
 
  </p><br>
 
  </p><br>
 
+
<p>The mechanism of hydration of carbon dioxide catalyzed by carbonic anhydride enzyme (CA-II:</p>
 +
 
<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/36/T--AHUT_China--_Fig._7_Raw_OD600_Curve_.jpg" width="724" height="484" alt=""/></div><br><div align="center">
 
<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/36/T--AHUT_China--_Fig._7_Raw_OD600_Curve_.jpg" width="724" height="484" alt=""/></div><br><div align="center">
 
  <div align="center">Fig. 7 Raw OD600 Curve</div>
 
  <div align="center">Fig. 7 Raw OD600 Curve</div>
 
</div>
 
</div>
    <h4>5.We obtained the Colony Forming Units per 0.1 OD600 E. coli cultures</h4>  
+
<div align="center"><img src="https://static.igem.org/mediawiki/2018/f/f1/T--AHUT_China--_Fig._8_CFU_Result.jpg" width="724" height="420" alt=""/></div><br>
+
                <p>Duda D, Tu C , Qian M, et al , 2001.Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic an- hydrase Ⅱ [ J] .Biochemistry , 40 (6):1741—1748 <br><br>
    <div align="center"><img src="https://static.igem.org/mediawiki/2018/e/e5/T--AHUT_China--_Fig._8_CFU_Result1.jpg" width="732" height="492" alt=""/></div><br>
+
Elder I , Han S , Tu C , et al , 2004.Activation of carbonic anhydrase Ⅱ by active-site incorporation of histidine analogs [ J] .Arc Bioch Biophys, 421:283—289
    <div align="center">
+
  <div align="center" >Fig. 8 CFU Result</div>
+
  <p >&nbsp;</p>
+
<div align="center"><h2 class="title_color">Discussion</h2></div>
+
                <p>For Figure 3, the log graph isn’t a straight line but not 1:1 slope. In figure 6, highest fluorescence was obtained from device 4, closely followed by test device 1. Test device 2 and positive control group show a modest fluorescence intensity and device 5,6 show low fluorescence intensity, while test devices 3 barely have any fluorescence signal as well as the negative group.
+
 
  </p>             
 
  </p>             
<div align="center"><h2 class="title_color">Conclusion</h2></div>
+
                 <p>It was certainly a technical challenge to Participate in the InterLab Study. Performing the prescribed protocols with adherence to all the InterLab guidelines yielded parts of expected results, and with the completed InterLab Google Forms, confirms our team participation in this InterLab Study.
+
                 <p>Application of carbonic anhydride enzyme (ca-ii) in carbon dioxide concentration
 
  </p>
 
  </p>
 +
                <p>There are two kinds of enzymatic trapping techniques: non-immobilized carbon anhydride trapping technology and immobilized carbon anhydride trapping technology. Non-immobilized Carbon anhydride trapping technology is the first carbon anhydride capture technology, This method directly using free carbon anhydride enzyme CO2 capture, at this time the activity of carbonic anhydride enzyme is low, about 30% of the activity, and this method is not conducive to the re-use of enzymes; in order to compensate for the deficiency of non-immobilized carbonic anhydride enzyme technology, Some people will silica and other inorganic compounds as a carrier of the carbon anhydride enzyme, thereby curing the carbon anhydride enzyme, it is found that the activity of carbon anhydride at this time to maintain about 60%, and the easy recovery of carbonic anhydride enzyme, so our team is using immobilized carbon anhydride enzyme capture technology. </p>
 
                  
 
                  
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/36/T--AHUT_China--_Fig._7_Raw_OD600_Curve_.jpg" width="724" height="484" alt=""/></div><br><div align="center">
 +
  <div align="center">Fig. 7 Raw OD600 Curve</div>
 +
</div>
 +
          <p>Reference documentation<br>
 +
S L. Structure and mechanism of carbonic anhydrase [J]. Pharmacology & Therapeutics, 1997, 74(1): 1.
 +
Supuran C T, Conroy C W, Maren T H. Is cyanate a carbonic anhydrase substrate? [J]. Proteins-structure Function & Bioinformatics, 2015, 27(2): 272-8.</p>
 
                  
 
                  
 
             </div>
 
             </div>

Revision as of 10:08, 8 October 2018

Royal Hotel Royal Hotel







As we have described in the background, traditional carbon dioxide collection techniques are still in its early stages, characterized by high consumption and low efficiency. We want low-energy, large-scale, efficient collection of carbon dioxide, in order to achieve this goal, we by the carbon anhydride enzyme gene into E. coli.


To ensure that E. coli-producing carbonic anhydride (CA-II) normally absorbs carbon dioxide in an industrialized environment, we first simulate the protein molecule expressed by a computer to obtain a thermally stable carbonic anhydride (CA-II), which produces a thermally stable carbonic anhydride (CA-II), so that it can normally absorb carbon dioxide in a factory-like environment.


E. Coli's carbonic anhydride enzyme (CA-II) promotes CO2 hydration to produce co32-, which binds to the free ca2+ in the environment to form calcium carbonate deposits, thereby achieving the purpose of absorbing carbon dioxide, and producing inorganic products that can be used.


Selection of carbonic anhydride enzymes:
Our team acquired a sequence of the human Body's carbonic anhydride, and contacted biotech companies to help us synthesize the carbonic anhydride gene in full sequence. The Carbon-anhydride (CA-II) activity of the human being used by our team is more active than that of other mammals, plants, algae, and bacteria-producing carbonic anhydride (CA-II). The carbon anhydride (CA-II) extracted in the human body at 37 ℃ the fastest reaction rate, 50 ℃ conditions, But its maximum reaction rate can reach 106 s-1, the fastest catalytic rate of carbonic anhydride (CA-II).


Carbonic anhydride Enzyme structure:


Fig. 4 Fluorescein Standard Curve

CHRISTOPHERKS,JAMESJL.Biotechnologyfor theaccelerationofcarbondioxidecaptureandseques- tration[J].ScienceDirect,2011,22:818-823.


Increased thermal stability of carbonic anhydride (CA-II):

In order to make the carbonic anhydride enzyme (CA-II) suitable for the industrial environment to absorb carbon dioxide, later we use molecular simulation technology, the amino acid as the basic unit, the residual radical mutation on the two-stage structure of carbon anhydride, and the influence of molecular conformation, to obtain the best amino acid mutation sites, The thermal stability of enzymes was improved without affecting the enzyme Activity.
Note: This part also the experimental data of the thermal stability of the carbon anhydride enzyme and the three-dimensional map of the fixed-point mutant base of the carbonic anhydride gene have not been added and referenced


The mechanism of hydration of carbon dioxide catalyzed by carbonic anhydride enzyme (CA-II:


Fig. 7 Raw OD600 Curve

Duda D, Tu C , Qian M, et al , 2001.Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic an- hydrase Ⅱ [ J] .Biochemistry , 40 (6):1741—1748

Elder I , Han S , Tu C , et al , 2004.Activation of carbonic anhydrase Ⅱ by active-site incorporation of histidine analogs [ J] .Arc Bioch Biophys, 421:283—289

Application of carbonic anhydride enzyme (ca-ii) in carbon dioxide concentration

There are two kinds of enzymatic trapping techniques: non-immobilized carbon anhydride trapping technology and immobilized carbon anhydride trapping technology. Non-immobilized Carbon anhydride trapping technology is the first carbon anhydride capture technology, This method directly using free carbon anhydride enzyme CO2 capture, at this time the activity of carbonic anhydride enzyme is low, about 30% of the activity, and this method is not conducive to the re-use of enzymes; in order to compensate for the deficiency of non-immobilized carbonic anhydride enzyme technology, Some people will silica and other inorganic compounds as a carrier of the carbon anhydride enzyme, thereby curing the carbon anhydride enzyme, it is found that the activity of carbon anhydride at this time to maintain about 60%, and the easy recovery of carbonic anhydride enzyme, so our team is using immobilized carbon anhydride enzyme capture technology.


Fig. 7 Raw OD600 Curve

Reference documentation
S L. Structure and mechanism of carbonic anhydrase [J]. Pharmacology & Therapeutics, 1997, 74(1): 1. Supuran C T, Conroy C W, Maren T H. Is cyanate a carbonic anhydrase substrate? [J]. Proteins-structure Function & Bioinformatics, 2015, 27(2): 272-8.