Difference between revisions of "Team:Mingdao/InterLab"

 
(132 intermediate revisions by 5 users not shown)
Line 1: Line 1:
{{:Team:Mingdao/test}}
+
{{:Team:Mingdao/test9}}
 
<html>
 
<html>
  
Line 32: Line 32:
 
   }
 
   }
 
.bg-container {
 
.bg-container {
 +
  background-attachment: fixed;
 +
  background-color: #ccc;
 
   overflow: hidden;
 
   overflow: hidden;
 
   position: relative;
 
   position: relative;
   background-image: url(https://static.igem.org/mediawiki/2017/3/34/T--CSMU_NCHU_Taiwan--long-model.png);
+
   background-image: url(https://static.igem.org/mediawiki/2018/5/56/T--Mingdao--InterLabBackground2.jpg);
   background-repeat: repeat-y;
+
   background-repeat: no-repeat;
 
   background-size: 100%;
 
   background-size: 100%;
 
}
 
}
Line 45: Line 47:
  
 
.main-content {
 
.main-content {
   background-color: white;
+
   background-color: rgba(255, 255, 255,.8);
   width: 80%;
+
   width: 90%;
   margin-left: 10%;
+
   margin-left: 5%;
 +
  margin-top:600px;
 
   padding: 50px;
 
   padding: 50px;
 
   min-height: 180vh;
 
   min-height: 180vh;
Line 131: Line 134:
 
.path-tags{
 
.path-tags{
 
   position: fixed;
 
   position: fixed;
   left: 15%;
+
   left: 11%;
   top: 200px;
+
   top: 240px;
 
}
 
}
 
.path-tags ul{
 
.path-tags ul{
Line 170: Line 173:
 
     margin-top: 1rem;
 
     margin-top: 1rem;
 
     color: #385e66 !important; }
 
     color: #385e66 !important; }
 +
 
.m-text-area p2 {
 
.m-text-area p2 {
 
     font-size: 15px;
 
     font-size: 15px;
Line 203: Line 207:
 
   color:#385e66 !important;
 
   color:#385e66 !important;
 
   font-family: 'Ubuntu' !important;
 
   font-family: 'Ubuntu' !important;
 +
}
 +
 +
.top-picture{
 +
  position:absolute;
 +
  z-index:1
 
}
 
}
  
Line 209: Line 218:
 
<body>
 
<body>
 
     <div class="bg-container" style="max-height:none;">
 
     <div class="bg-container" style="max-height:none;">
       <!-- <img src="https://static.igem.org/mediawiki/2017/1/1b/T--CSMU_NCHU_Taiwan--modeling.png"> -->
+
       <img class="top-picture" src="https://static.igem.org/mediawiki/2018/4/45/T--Mingdao--Phil13-8.png" style="width:100%">
 
       <div class="my-main-container">
 
       <div class="my-main-container">
 
         <div class="main-content">
 
         <div class="main-content">
Line 215: Line 224:
 
             <h1>Interlab Study</h1>
 
             <h1>Interlab Study</h1>
 
             <div id="model-intro" class="m-block" >
 
             <div id="model-intro" class="m-block" >
                <h2 class="m-subtitle">Introduction</h2>
+
 
                <img src="https://static.igem.org/mediawiki/2017/f/f8/T--CSMU_NCHU_Taiwan--green.png" style="width: 60%; transform: translate(35%, -150%);">
+
<h3>Note</h3>
 +
<p>Description: the goal and main contents were quoted from iGEM International InterLab Measurement Study <p>
 +
Methods: the protocol was provided by iGEM InterLab Committee and described briefly in here <p>
 +
Results: the experiment and data presented here were all made by members of team Mingdao <p>
 +
Reference: <a href="https://2018.igem.org/Measurement/InterLab">Fifth International InterLab Measurement Study@iGEM</a>
 +
 +
</br></br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2018/8/8b/T--Mingdao--Interlablastday1.jpeg" alt="" style="width:49%">
 +
<img src="https://static.igem.org/mediawiki/2018/9/9f/T--Mingdao--Interlablastday2.jpeg" alt="" style="width:49%"></center><br />
 +
<center><img src="https://static.igem.org/mediawiki/2018/7/75/T--Mingdao--Interlablastday3.jpeg" alt="" style="width:49%">
 +
<img src="https://static.igem.org/mediawiki/2018/e/ef/T--Mingdao--Interlablastday4.jpeg" alt="" style="width:49%">
 +
</center></br>
 +
 
 +
<h3>Instrument</h3>
 +
<p>The machine in the Biolab of Mingdao High School: Synergy H1 Hybrid Multi-Mode Microplate Reader
 +
<p><img class="center" src="https://static.igem.org/mediawiki/2018/e/e6/T--Mingdao--Interlab0.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
</br></br>
 +
 
 +
 
 
                 <h3>Introduction</h3>
 
                 <h3>Introduction</h3>
                 <p>Reliable and repeatable measurement is a key component to all engineering disciplines. The same
+
                 <p>"Reliable and repeatable measurement is a key component to all engineering disciplines. The same
 
holds true for synthetic biology, which has also been called engineering biology. However, the
 
holds true for synthetic biology, which has also been called engineering biology. However, the
 
ability to repeat measurements in different labs has been difficult. The Measurement Committee,
 
ability to repeat measurements in different labs has been difficult. The Measurement Committee,
Line 224: Line 254:
 
fluorescent protein (GFP) over the last several years. We chose GFP as the measurement marker
 
fluorescent protein (GFP) over the last several years. We chose GFP as the measurement marker
 
for this study since it's one of the most used markers in synthetic biology and, as a result, most
 
for this study since it's one of the most used markers in synthetic biology and, as a result, most
laboratories are equipped to measure this protein.  
+
laboratories are equipped to measure this protein."
 
<p>
 
<p>
The aim to improve the measurement tools available to both the iGEM community and the synthetic
 
biology community as a whole. One of the big challenges in synthetic biology measurement has
 
been that fluorescence data usually cannot be compared because it has been reported in different
 
units or because different groups process data in different ways. Many have tried to work around
 
this using “relative expression” comparisons; however, being unable to directly compare
 
measurements makes it harder to debug engineered biological constructs, harder to effectively
 
share constructs between labs, and harder even to just interpret your experimental controls.
 
<p>
 
The InterLab protocol aims to address these issues by providing researchers with a detailed
 
protocol and data analysis form that yields absolute units for measurements of GFP in a plate
 
reader.
 
  
  
 
+
</ br>
 
+
</ br></ br></p>
<br></p>
+
  
 
                
 
                
 
            
 
            
             <div id="model-protein" class="m-block" >
+
             <div id="model-goal" class="m-block" >
                 <h2 class="m-subtitle">Goal for the Fifth InterLab</h2>
+
                 <h3>Goal for the Fifth InterLab</h3>
                <img src="https://static.igem.org/mediawiki/2017/f/f8/T--CSMU_NCHU_Taiwan--green.png" style="width: 60%; transform: translate(35%, -150%);">
+
  
               
+
                 <p>"The goal of the iGEM InterLab Study is to identify and correct the sources of systematic variability
 
+
                 <p>The goal of the iGEM InterLab Study is to identify and correct the sources of systematic variability
+
 
in synthetic biology measurements, so that eventually, measurements that are taken in different
 
in synthetic biology measurements, so that eventually, measurements that are taken in different
 
labs will be no more variable than measurements taken within the same lab. Until we reach this
 
labs will be no more variable than measurements taken within the same lab. Until we reach this
 
point, synthetic biology will not be able to achieve its full potential as an engineering discipline, as
 
point, synthetic biology will not be able to achieve its full potential as an engineering discipline, as
labs will not be able to reliably build upon others’ work.
+
labs will not be able to reliably build upon others’ work."
 
<p>
 
<p>
In the previous interlab studies, it was shown that by measuring GFP expression in absolute
+
 
fluorescence units calibrated against a known concentration of fluorescent molecule can greatly
+
"This year, teams participating in the interlab study helped iGEM to answer the following
reduce the variability in measurements between labs. However, when taking bulk measurements of
+
a population of cells (such as with a plate reader), there is still a large source of variability in these
+
measurements: the number of cells in the sample.
+
<p>
+
Because the fluorescence value measured by a plate reader is an aggregate measurement of an
+
entire population of cells, we need to divide the total fluorescence by the number of cells in order to
+
determine the mean expression level of GFP per cell. Usually this is done by measuring the
+
absorbance of light at 600nm, from which the “optical density (OD)” of the sample is computed as
+
an approximation of the number of cells. OD measurements are subject to high variability between
+
labs, however, and it is unclear how good of an approximation an OD measurement actually is. If a
+
more direct method is used to determine the cell count in each sample, then potentially another
+
source of variability can be removed from the measurements.
+
<p>
+
This year, teams participating in the interlab study helped iGEM to answer the following
+
 
question: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to
 
question: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to
absolute cell count or colony-forming units (CFUs) instead of OD?
+
absolute cell count or colony-forming units (CFUs) instead of OD?"
 
<p>
 
<p>
In order to compute the cell count in the different teams samples, two orthogonal approaches were
+
 
be used:
+
 
 +
           
 +
            </div>
 +
                <h3>Calibration Reference</h3>
 +
               
 +
                <div id="model-calibration1" class="m-block" >
 +
                <h2 class="m-subtitle">Calibration 1:OD600 Reference point - LUDOX Protocol</h2>
 +
               
 +
<p><span style="background-color: #ccffff;"><strong>Materials</strong></span></p>
 
<p>
 
<p>
1. Converting between absorbance of cells to absorbance of a known concentration of beads.
+
<P>1ml LUDOX CL-X
 
<p>
 
<p>
Absorbance measurements use the way that a sample of cells in liquid scatter light in order
 
to approximate the concentration of cells in the sample. In this year’s Measurement Kit,
 
teams were provided with a sample containing silica beads that are roughly the same size
 
and shape as a typical E. coli cell, so that it should scatter light in a similar way. Because the
 
concentration of the beads is known, each lab’s absorbance measurements can be
 
converted into a universal, standard “equivalent concentration of beads” measurement.
 
 
<p>
 
<p>
2. Counting colony-forming units (CFUs) from the sample.
+
ddH2O
 
<p>
 
<p>
A simple way to determine the number of cells in a sample of liquid media is to pour some out
 
on a plate and see how many colonies grow on the plate. Since each colony begins as a
 
single cell (for cells that do not stick together), we can determine how many live cells were in
 
the volume of media that we plated out and obtain a cell concentration for our sample as a
 
whole. Each team will have to determine the number of CFUs in positive and negative control
 
samples in order to compute a conversion factor from absorbance to CFU.
 
 
<p>
 
<p>
By using these two approaches, Interlab Measurement Study will be able to determine how much
+
96 well Black Clear Bottom Plate
they agree with each other, and whether using one (or both) can help to reduce lab-to-lab variability
+
in measurements. If it can, then together we will have brought synthetic biology one step closer to
+
becoming a true, reliable engineering discipline.</p>
+
             
+
 
<p>
 
<p>
 +
<p>
 +
</P>
 
<p>
 
<p>
  
 
+
<p><span style="background-color: #ccffff;"><strong>Method</strong></span></p>
            <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Results#enzyme_function_results" target="_blank">
+
              <img class="right" src="https://static.igem.org/mediawiki/2017/6/66/T--CSMU_NCHU_Taiwan--see_more.png" style="width: 15%" alt=""></a>
+
            </div>
+
            <div id="model-docking" class="m-block" >
+
                <h2 class="m-subtitle">Calibration Reference</h2>
+
                <img src="https://static.igem.org/mediawiki/2017/f/f8/T--CSMU_NCHU_Taiwan--green.png" style="width: 60%; transform: translate(22%, -150%);">
+
                <h3>Calibration 1:OD600 Reference point - LUDOX Protocol</h3>
+
                <p>LUDOX CL-X (45% colloidal silica suspension) was used as a single point reference to
+
obtain a conversion factor to transform our absorbance (Abs600) data from our plate reader
+
into a comparable OD600 measurement as would be obtained in a spectrophotometer. Such
+
conversion is necessary because plate reader measurements of absorbance are volume
+
dependent; the depth of the fluid in the well defines the path length of the light passing
+
through the sample, which can vary slightly from well to well. In a standard
+
spectrophotometer, the path length is fixed and is defined by the width of the cuvette, which
+
is constant. Therefore this conversion calculation can transform Abs600 measurements from
+
a plate reader (i.e., absorbance at 600nm, the basic output of most instruments) into
+
comparable OD600 measurements. The LUDOX solution is only weakly scattering and so
+
will give a low absorbance value.
+
 
<p>
 
<p>
[ IMPORTANT NOTE : many plate readers have an automatic path length correction feature. This adjustment compromises the accuracy of measurement in highly light scattering
+
<P>
solutions, such as dense cultures of cells. YOU MUST THEREFORE TURN OFF
+
&#8595; Add 100 μl LUDOX into wells A1, B1, C1, D1
PATHLENGTH CORRECTION if it can be disabled on your instrument . Our Instrument did
+
not have any pathlength correction].
+
 
<p>
 
<p>
</p>
 
 
<p><span style="background-color: #ccffff;"><strong>Materials</strong></span></p>
 
 
<p>
 
<p>
<P>1ml LUDOX CL-X (provided in kit)
+
&#8595; Add 100 μl of ddH2 O into wells A2,B2,C2,D2
 
<p>
 
<p>
ddH2 0 (provided by team)
 
 
<p>
 
<p>
96 well plate, black with clear flat bottom preferred (provided by team)
+
&#8595; Measure absorbance at 600 nm
 
<p>
 
<p>
</P>
+
<p>
 +
&#8595; Record the data <p>
 +
<p>
 +
</p>
  
 +
<p>
  
 +
<p><span style="background-color: #ccffff;"><strong>Result</strong></span></p>
 +
<P>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/9/9a/T--Mingdao--Modeling--Chart%28img45%29.jpg"alt=""
 +
style="width:80%">
 +
<p>
  
 +
<p>The table shows the OD600 measured by a spectrophotometer (see table above) and plate
 +
reader data for H2O and LUDOX corresponding to the expected results. The corrected
 +
Abs600 is calculated by subtracting the mean H2O reading. The reference OD600 is defined
 +
as that measured by the reference spectrophotometer. The correction factor to convert
 +
measured Abs600 to OD600 is thus the reference OD600 divided by Abs600. All cell density
 +
readings using this instrument with the same settings and volume can be converted to
 +
OD600 by multiplying by 4.200.</p>
 +
<p>
  
  
 +
<div id="model-calibration2" class="m-block" >
 +
<h2 class="m-subtitle">Calibration 2: Particle Standard Curve - Microsphere Protocol</h2>
 +
<p>
  
 
+
<p><span style="background-color: #ccffff;"><strong>Materials</strong></span></p>
 
+
<p>
 
+
300 μL silica beads Microsphere suspension
 
+
<p>
 
+
<p>
 
+
ddH2O
 
+
<p>
 
+
<p>
 
+
96 well Black Clear Bottom Plate
 
+
<p>
 
+
<p>
                <h3>The docking simulation of “Thioredoxin-Fusion protein”</h3>
+
                <p>1.&nbsp;&nbsp;Since the structure of Thioredoxin has been studied, we can lock down the active site of thioredoxin by use Uniprot. The team found that there are two active site , which are NO. 33 and NO.36 of the sequence.</p>
+
                <p>2.&nbsp;&nbsp;By using NCBI BLAST, the team compared the sequence of the fusion protein with Thioredoxin. The team confirmed that the active sites of fusion protein corresponding to the ones of Thioredoxin are No.33 and 36 , both are Cysteine, C.<br><br></p>
+
                <img src="https://static.igem.org/mediawiki/2017/7/72/T--CSMU_NCHU_Taiwan--m-4-thioredoxin.png" style="width: 100%">
+
                <br><br>
+
                <p>3.&nbsp;&nbsp;The team later constructed a fusion protein 3D model and then labelled the active sites by using PyMOL. By creating the model, the team could learn why thioredoxin is helpful toward protein folding since the active sites of Thioredoxin are not facing away from MSMEG5998.<br><br></p>
+
                <img src="https://static.igem.org/mediawiki/2017/7/7e/T--CSMU_NCHU_Taiwan--model08.png" style="width: 100%">
+
                <br><br>
+
                <p>This 3D model shows the surface of the fusion protein, which allows us to grasp the concept of what our protein looks like. The region labeled in red is the possible binding site of Thioredoxin, which maybe can assist the fusion protein itself or other proteins folding.<br></p>
+
                <h3>The structure of the fusion protein (MSMEG5998 part)</h3>
+
                <p>1.&nbsp;&nbsp;While the structure of MSMEG5998 remains unknown, the team still manage to predict the model by using similar protein to create a model, the software tool we used is Swiss Model<small><small>[3] [4]</small></small>.</p>
+
                <p>2.&nbsp;&nbsp;When deciding the model of MEMEG5998, the team used the Swiss Model by comparing the amino acid sequence among the database of protein sequence. There are two main factors lead to two different models, which are by coverage or by identity. The team choose the highest coverage protein sequence to be our model, named” MSMEG5998 Swiss model”.<br><br></p>
+
            <img src="https://static.igem.org/mediawiki/2017/b/b1/T--CSMU_NCHU_Taiwan--model09.png" style="width: 60%" class="center">
+
              <img src="https://static.igem.org/mediawiki/2017/0/02/T--CSMU_NCHU_Taiwan--swiss.png" style="width: 100%">
+
                <br><br>
+
              <p>3.&nbsp;&nbsp;The sequence of the MSMEG5998 by using Swiss model is compared with that of fusion protein by using Uniprot. The team then discovered three similar groups being labeled below, which are likely active sites.<br><br></p>
+
                <img src="https://static.igem.org/mediawiki/2017/0/02/T--CSMU_NCHU_Taiwan--m-8-uniprot.png" style="width: 100%">
+
                <br><br>
+
                <p>4.&nbsp;&nbsp;The three possible loci corresponding to the fusion protein sequence are:</p>
+
                <p>i.&nbsp;&nbsp;189,Arginine,R</p>
+
                <p>ii.&nbsp;&nbsp;214,Glutamine,Q</p>
+
                <p>iii.&nbsp;246,Alanine,A</p>
+
                <p>Since the pdb. files presented by raptorX were unable to visualize hydrogen bonds of the compound, thus the team used PMViewer v1.5.7 to add on hydrogen bonds and negative charge. (the following pictures are compounds before and after enhancements)<br><br></p>
+
                <h3>Further enhancements to the compound before docking simulation on MSMEG5998</h3>
+
                <img src="https://static.igem.org/mediawiki/2017/7/79/T--CSMU_NCHU_Taiwan--model121.png" style="width: 100%">
+
              <p><br>Under PMViewer, the appearance of the protein before enhancements.<br><br></p>
+
 
+
              <img src="https://static.igem.org/mediawiki/2017/9/9d/T--CSMU_NCHU_Taiwan--model131.png" style="width: 100%">
+
              <p><br>The fusion protein after enhancements, which adds hydrogen and charge to the protein. This process allows the structure and the binding process as real as possible.<br></p>
+
 
+
 
+
 
+
              <h3>Adding ligand to the docking simulation of MSMEG5998-Aflatoxin B2</h3>
+
              <p>Search PubChem to locate the ligand, which in this case is AflatoxinB2, and then download the SDF format.<br></p>
+
              <img src="https://static.igem.org/mediawiki/2017/1/1c/T--CSMU_NCHU_Taiwan--m-11-aflatoxin-3.png" style="width: 100%">
+
 
+
              <br><br>
+
              <h3>The docking of MSMEG5998 to Aflatoxin B2</h3>
+
 
+
              <p>1.&nbsp;&nbsp;The settings for Aflatoxin B2 before docking:
+
Minimize the energy, in order to acquire a stabilized compound which is easier to go through the docking simulation.
+
 
</p>
 
</p>
              <img src="https://static.igem.org/mediawiki/2017/4/4e/T--CSMU_NCHU_Taiwan--model15.png" style="width: 100%">
+
<p>
              <p><br>2.&nbsp;&nbsp;Select the docking function to proceed.</p>
+
<p><span style="background-color: #ccffff;"><strong>Method</strong></span></p>
              <h3>Autodocking area</h3>
+
<p>
              <p>The possible autodocking area are limited to the three active sites of MSMEG5998 mentioned earlier, which can increase the model’s accuracy. After autodocking, we visualize the result by using PyMOL to create a 3D docking model. The three active sites for docking are tested, and compared to one another. The team finally come up with one ideal active site, which is 214,glutamine,Q.<br></p>
+
<p><em><strong>Preparation of the Microsphere stock solution:</strong></em></p>
 +
<p>
 +
<p>
 +
&#8595; Obtain Silica Beads
 +
<p>
 +
&#8595; Pipet 96 μL beads into an eppendorf
 +
<p>
 +
<p>
 +
&#8595; Add 904 μL of ddH2O to the microspheres
 +
<p>
 +
<p>
 +
&#8595; Vortex well to obtain stock Microsphere Solution.
 +
</p>
 +
<p>
 +
&#8595; Preparation of microsphere serial dilutions as follows
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/b/b0/T--Mingdao--Modeling--SerialDelution%28img47%29.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
&#8595; Measure Abs 600
 +
<p>
 +
&#8595; Record the data
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Result</strong></span></p>
 +
<p>
 +
<p><em><strong>Raw Data</strong></em></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/5/56/T--Mingdao--Modeling--RawData%28img50%29.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><em><strong>Particle Standard Curve</strong></em></p>
 +
<p>
 +
<p>
 +
<img class="center"src="https://static.igem.org/mediawiki/2018/0/04/T--Mingdao--Interlab4.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><em><strong>Particle Standard Curve(log scale)</strong></em></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/a/ac/T--Mingdao--interlab5.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<div id="model-calibration3" class="m-block" >
 +
<h2 class="m-subtitle">Calibration 3: Fluorescence standard curve - Fluorescein Protocol</h2>
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Materials</strong></span></p>
 +
<p>
 +
<p>
 +
Fluorescein (provided in kit)
 +
<p>
 +
<p>
 +
10ml 1xPBS pH 7.4-7.6 (phosphate buffered saline; provided by team)
 +
<p>
 +
<p>
 +
96 well Black Clear Bottom Plate
 +
<p></p>
 +
<p>
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Method</strong></span></p>
 +
<p>
 +
&#8595; Spin down fluorescein kit tube to make sure pellet is at the bottom of tube.  
 +
&#8595; Prepare 10x fluorescein stock solution (100 μM) by resuspending fluorescein in 1 mL of 1xPBS.
 +
<p>
 +
&#8595; Dilute the 10x fluorescein stock solution with 1xPBS to make a 1x fluorescein solution with concentration of 10 μM
 +
<p>
 +
&#8595; Prepare the serial dilutions of fluorescein as follows:
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/0/0b/T--Mingdao--Interlab6.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
&#8595; Measure fluorescence of all samples in instrument
 +
<p>
 +
&#8595; Record the data
 +
<p>
  
              <img src="https://static.igem.org/mediawiki/2017/1/17/T--CSMU_NCHU_Taiwan--model16.png" style="width: 100%">
+
<p><span style="background-color: #ccffff;"><strong>Result</strong></span></p>
              <p><br>The docking was processed by Autodock (please visit our <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Software" target="_blank">software tools page</a>, the cube area is the area our team choose to process the docking stimulation, the results are in the picture below.<br></p>
+
<p>
              <img src="https://static.igem.org/mediawiki/2017/c/c9/T--CSMU_NCHU_Taiwan--m-12-214-2.png" style="width: 100%">
+
<p><em><strong>Raw Data</strong></em></p>
              <p><br><br>This is a side view of the protein macromolecule. The MSMEG5998 active site 214 is presented in red, while the blue compound represents Aflatoxin.<br><br></p>
+
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/3/3c/T--Mingdao--Interlab7.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><em><strong>Fluorescein Standard Curves</strong></em></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/f/f2/T--Mingdao--Interlab8.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><em><strong>Fluorescein Standard Curves(log scale)</strong></em></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/6/69/T--Mingdao--Interlab9.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<div id="model-cell" class="m-block" >
 +
<h3>Cell Measurement</h3>
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Materials</strong></span></p>
 +
<p> Competent cells ( Escherichia coli strain DH5 )
 +
<p>
 +
 LB (Luria Bertani) media
 +
<p>
 +
 Chloramphenicol (stock concentration 25 mg/mL dissolved in EtOH)
 +
<p>
 +
 50 ml Falcon tube (or equivalent, preferably amber or covered in foil to block light)
 +
<p>
 +
 Incubator at 37°C
 +
<p>
 +
 1.5 ml eppendorf tubes for sample storage
 +
<p>
 +
 Ice bucket with ice
 +
<p>
 +
 Micropipettes and tips
 +
<p>
 +
 96 well Black Clear Bottom Plate
 +
<p></p>
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Workflow</strong></span></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/2/22/T--Mingdao--Interlab10.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Method</strong></span></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/c/c6/T--Mingdao--Interlab11.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><em><strong>Day1</strong></em></p>
 +
<p>
 +
&#8595; Transform Escherichia coli DH5 with these plasmids
 +
<p>
 +
<p><em><strong>Day2</strong></em></p>
 +
<p>
 +
&#8595; Pick 2 colonies from each group
 +
<p>
 +
&#8595; Inoculate in 5-10 mL LB medium + Cm
 +
<p>
 +
&#8595; Grow the cells overnight (16-18 hours) at 37°C and shake at 220 rpm.
 +
<p>
 +
<p><em><strong>Day 3</strong></em></p>
 +
<p>
 +
&#8595; Make a 1:10 dilution of each overnight culture in LB + Cm by putting 0.5mL of culture into 4.5mL of LB + Cm
 +
<p>
 +
&#8595; Measure Abs 600 of these 1:10 diluted cultures
 +
<p>
 +
&#8595; Record the data
 +
<p>
 +
&#8595; Dilute the cultures further to a target Abs6 00 of 0.02 in a final volume of 12 ml LB medium + Cm in 50 mL tube
 +
<p>
 +
&#8595; Incubate the cultures at 37°C and shake at 220 rpm for 6 hours.  
 +
<p>
 +
&#8595; Measure your samples for Abs600 and fluorescence
 +
<p>
 +
&#8595; Record data in your notebook
 +
<p>
 +
<center> Layout for Abs 600 and fluorescence measurement </center>
 +
<p></p>
 +
<p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/1/1a/T--Mingdao--Interlab12.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<p><span style="background-color: #ccffff;"><strong>Result</strong></span></p>
 +
<p>
 +
<p><em><strong>Fluorescence Raw Reading</strong></em></p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/2/2b/T--Mingdao--Interlab13.jpg"alt=""
 +
style="width:80%">
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/6/60/T--Mingdao--Interlab14.jpg"alt=""
 +
style="width:80%">
 +
<p><em><strong>Abs600 Raw Reading</strong></em></p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/2/2d/T--Mingdao--Interlab15.jpg"
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/4/45/T--Mingdao--Interlab16.jpg">
 +
<div id="model-protocol" class="m-block" >
  
            </div>
+
<h3>Colony Forming Units per E. coli cultures at OD600=0.1 </h3>
            <div id="model-conslusion" class="m-block" >
+
<p>
                <h2 class="m-subtitle">Discussion and Conclusion</h2>
+
&#8595; Measure the OD600 of your cell cultures
                <img src="https://static.igem.org/mediawiki/2017/f/f8/T--CSMU_NCHU_Taiwan--green.png" style="width: 60%; transform: translate(35%, -150%);">
+
<p>
 
+
&#8595; Dilute your overnight culture to OD600 = 0.1 in 1mL of LB + Cm media. Do this in triplicate.
                <p>1.&nbsp;&nbsp;By using protein modeling techniques, the team predicted a fusion protein with multifunction while one doesn’t inhibit the other, or creating structural failure. Which later on helped us in the wet lab experiment to proceed.<br></p>
+
<p>
                <p>2.&nbsp;&nbsp;With the software tools, the team is able to predict an enhanced fusion protein (MSMEG5998 combined with Thioredoxin) that performs better than the original protein (MSMEG5998).<br></p>
+
&#8595; Make the following serial dilutions for your triplicates
                <p>3.&nbsp;&nbsp;With the cooperation of the wet lab projects, the team is able to confirm the results of the prediction.(Click the button to visit our project’s result.)</p>
+
<p><p>
                <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Results#antidote" target="_blank">
+
<img class="center" src="https://static.igem.org/mediawiki/2018/8/8a/T--Mingdao--Interlab19.jpg"alt=""
              <img class="right" src="https://static.igem.org/mediawiki/2017/6/66/T--CSMU_NCHU_Taiwan--see_more.png" style="width: 15%" alt=""></a><br>
+
style="width:80%">
                <p>4.&nbsp;&nbsp;&nbsp;Future goals:</p>
+
<p>
 
+
<p>
                <p>i.&nbsp;&nbsp;unfortunately, there is a time limit to our project. However, the team would like to continue our modeling project and also put the theory into practice, trying to see whether active site 214 is the actually binding site with Aflatoxin. The team would conduct experiments of point mutation on site 214, to see if the binding affinity changes or not, in order to explain why this site 214 is crucial toward Aflatoxin degradation.</p>
+
&#8595; Aseptically spread plate with 100 μL of the dilutions
                <p>ii.&nbsp;&nbsp;After conducting the two main modeling project, our team successfully predicts the function of our fusion protein; however, the long term goal is that the team envisions our aflatoxin-degrading protein put in to massive and commercialized production. <font color="#1c869c"> Therefore, our team would want to measure the productivity of our protein, in order to seek for the ideal producing conditions and reach the maximum efficiency.</font>(Click the button to see some of the results from the experiment our team has conducted.)<br></p>
+
<p>
            <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Model/Parts" target="_blank">
+
&#8595; Incubate at 37°C overnight
              <img class="right" src="https://static.igem.org/mediawiki/2017/6/66/T--CSMU_NCHU_Taiwan--see_more.png" style="width: 15%" alt=""></a>
+
<p>
<br>
+
&#8595; Count colonies after 18-20 hours of growth.
 
+
<p>
 
+
<p>
            </div>
+
            <div id="model-references" class="m-block" >
+
                <h2 class="m-subtitle">References</h2>
+
                <img src="https://static.igem.org/mediawiki/2017/f/f8/T--CSMU_NCHU_Taiwan--green.png" style="width: 60%; transform: translate(35%, -150%);">
+
  
 +
<p><span style="background-color: #ccffff;"><strong>Result</strong></span></p>
 +
<p>
 +
<p>Colony Forming Units per o.1 OD600 E.coli cultures</p>
 +
<p>
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/0/06/T--Mingdao--Interlab20.jpg"alt=""
 +
style="width:80%">
 +
<img class="center" src="https://static.igem.org/mediawiki/2018/3/36/T--Mingdao--Interlab21.jpg"alt=""
 +
style="width:80%">
  
                <div class="pdf-area">
+
         
            <span  id="public-btn-1" class="pdfbtn">Click to expand content<i class="fa fa-caret-down" aria-hidden="true"></i></span>
+
 
             <div class="img-container" id="public-1">
 
             <div class="img-container" id="public-1">
              <img src="https://static.igem.org/mediawiki/2017/0/0b/T--CSMU_NCHU_Taiwan--modelfinal.png" alt="">
+
           
 
             </div>
 
             </div>
 
             </div>
 
             </div>
Line 451: Line 580:
 
       <div class="path-tags">
 
       <div class="path-tags">
 
         <ul>
 
         <ul>
           <p class="tag">Structure <br>  & Docking Model</p>
+
           <p class="tag">Interlab Study</p>
 
           <li id="intro-btn" class="tag-btn">- Introduction</li>
 
           <li id="intro-btn" class="tag-btn">- Introduction</li>
           <li id="protein-btn" class="tag-btn">- Protein Structure Modeling</li>
+
           <li id="goal-btn" class="tag-btn">- Goal </li>
           <li id="docking-btn" class="tag-btn">- Docking Modeling</li>
+
           <li id="calibration1-btn" class="tag-btn">- Calibration 1</li>
           <li id="conclusion-btn" class="tag-btn">- Discussion & Conclusion</li>
+
           <li id="calibration2-btn" class="tag-btn">- Calibration 2</li>
 +
          <li id="calibration3-btn" class="tag-btn">- Calibration 3</li>
 +
          <li id="cell-btn" class="tag-btn">- Cell Measurement</li>
 +
          <li id="protocol-btn" class="tag-btn">- Protocol</li>
  
 
           <br>
 
           <br>
           <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Model/Degradation"><p style="font-size:18px;font-family: 'Ubuntu'">Degradation Model</p></a>
+
            
          <a href="https://2017.igem.org/Team:CSMU_NCHU_Taiwan/Model/Parts"><p style="font-size:18px;font-family: 'Ubuntu'">Parts Model</p></a>
+
  
  
Line 466: Line 597:
 
     </div>
 
     </div>
 
     <div class="top">
 
     <div class="top">
       <img src="https://static.igem.org/mediawiki/2017/5/52/T--CSMU_NCHU_Taiwan--top.png" alt="">
+
       <img src="https://static.igem.org/mediawiki/2018/5/58/T--Mingdao--go_to_top.jpg" alt="">
 
     </div>
 
     </div>
 
   </body>
 
   </body>
Line 480: Line 611:
 
         }, 500);
 
         }, 500);
 
       });
 
       });
       $("#protein-btn").click(function() {
+
       $("#goal-btn").click(function() {
 
         $('html, body').animate({
 
         $('html, body').animate({
             scrollTop: $("#model-protein").offset().top
+
             scrollTop: $("#model-goal").offset().top
 
         }, 500);
 
         }, 500);
 
       });
 
       });
       $("#docking-btn").click(function() {
+
       $("#calibration1-btn").click(function() {
 
         $('html, body').animate({
 
         $('html, body').animate({
             scrollTop: $("#model-docking").offset().top
+
             scrollTop: $("#model-calibration1").offset().top
 
         }, 500);
 
         }, 500);
 
       });
 
       });
       $("#conclusion-btn").click(function() {
+
       $("#calibration2-btn").click(function() {
 
         $('html, body').animate({
 
         $('html, body').animate({
             scrollTop: $("#model-conslusion").offset().top
+
             scrollTop: $("#model-calibration2").offset().top
 
         }, 500);
 
         }, 500);
 
       });
 
       });
 +
            $("#calibration3-btn").click(function() {
 +
        $('html, body').animate({
 +
            scrollTop: $("#model-calibration3").offset().top
 +
        }, 500);
 +
      });  $("#cell-btn").click(function() {
 +
        $('html, body').animate({
 +
            scrollTop: $("#model-cell").offset().top
 +
        }, 500);
 +
      });
 +
          $("#protocol-btn").click(function() {
 +
        $('html, body').animate({
 +
            scrollTop: $("#model-protocol").offset().top
 +
        }, 500);
 +
      });
 +
 +
 +
 +
 +
 +
 +
 +
  
 
   });
 
   });
Line 524: Line 677:
 
   </script>
 
   </script>
  
 +
 +
 +
</div>
 +
</div>
 +
</div>
  
 
</html>
 
</html>
 +
 +
 +
{{:Team:Mingdao/test6}}

Latest revision as of 02:13, 18 October 2018

Model

Interlab Study

Note

Description: the goal and main contents were quoted from iGEM International InterLab Measurement Study

Methods: the protocol was provided by iGEM InterLab Committee and described briefly in here

Results: the experiment and data presented here were all made by members of team Mingdao

Reference: Fifth International InterLab Measurement Study@iGEM



Instrument

The machine in the Biolab of Mingdao High School: Synergy H1 Hybrid Multi-Mode Microplate Reader



Introduction

"Reliable and repeatable measurement is a key component to all engineering disciplines. The same holds true for synthetic biology, which has also been called engineering biology. However, the ability to repeat measurements in different labs has been difficult. The Measurement Committee, through the InterLab study, has been developing a robust measurement procedure for green fluorescent protein (GFP) over the last several years. We chose GFP as the measurement marker for this study since it's one of the most used markers in synthetic biology and, as a result, most laboratories are equipped to measure this protein."

Goal for the Fifth InterLab

"The goal of the iGEM InterLab Study is to identify and correct the sources of systematic variability in synthetic biology measurements, so that eventually, measurements that are taken in different labs will be no more variable than measurements taken within the same lab. Until we reach this point, synthetic biology will not be able to achieve its full potential as an engineering discipline, as labs will not be able to reliably build upon others’ work."

"This year, teams participating in the interlab study helped iGEM to answer the following question: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?"

Calibration Reference

Calibration 1:OD600 Reference point - LUDOX Protocol

Materials

1ml LUDOX CL-X

ddH2O

96 well Black Clear Bottom Plate

Method

↓ Add 100 μl LUDOX into wells A1, B1, C1, D1

↓ Add 100 μl of ddH2 O into wells A2,B2,C2,D2

↓ Measure absorbance at 600 nm

↓ Record the data

Result

The table shows the OD600 measured by a spectrophotometer (see table above) and plate reader data for H2O and LUDOX corresponding to the expected results. The corrected Abs600 is calculated by subtracting the mean H2O reading. The reference OD600 is defined as that measured by the reference spectrophotometer. The correction factor to convert measured Abs600 to OD600 is thus the reference OD600 divided by Abs600. All cell density readings using this instrument with the same settings and volume can be converted to OD600 by multiplying by 4.200.

Calibration 2: Particle Standard Curve - Microsphere Protocol

Materials

300 μL silica beads Microsphere suspension

ddH2O

96 well Black Clear Bottom Plate

Method

Preparation of the Microsphere stock solution:

↓ Obtain Silica Beads

↓ Pipet 96 μL beads into an eppendorf

↓ Add 904 μL of ddH2O to the microspheres

↓ Vortex well to obtain stock Microsphere Solution.

↓ Preparation of microsphere serial dilutions as follows

↓ Measure Abs 600

↓ Record the data

Result

Raw Data

Particle Standard Curve

Particle Standard Curve(log scale)

Calibration 3: Fluorescence standard curve - Fluorescein Protocol

Materials

Fluorescein (provided in kit)

10ml 1xPBS pH 7.4-7.6 (phosphate buffered saline; provided by team)

96 well Black Clear Bottom Plate

Method

↓ Spin down fluorescein kit tube to make sure pellet is at the bottom of tube. ↓ Prepare 10x fluorescein stock solution (100 μM) by resuspending fluorescein in 1 mL of 1xPBS.

↓ Dilute the 10x fluorescein stock solution with 1xPBS to make a 1x fluorescein solution with concentration of 10 μM

↓ Prepare the serial dilutions of fluorescein as follows:

↓ Measure fluorescence of all samples in instrument

↓ Record the data

Result

Raw Data

Fluorescein Standard Curves

Fluorescein Standard Curves(log scale)

Cell Measurement

Materials

 Competent cells ( Escherichia coli strain DH5 )

 LB (Luria Bertani) media

 Chloramphenicol (stock concentration 25 mg/mL dissolved in EtOH)

 50 ml Falcon tube (or equivalent, preferably amber or covered in foil to block light)

 Incubator at 37°C

 1.5 ml eppendorf tubes for sample storage

 Ice bucket with ice

 Micropipettes and tips

 96 well Black Clear Bottom Plate

Workflow

Method

Day1

↓ Transform Escherichia coli DH5 with these plasmids

Day2

↓ Pick 2 colonies from each group

↓ Inoculate in 5-10 mL LB medium + Cm

↓ Grow the cells overnight (16-18 hours) at 37°C and shake at 220 rpm.

Day 3

↓ Make a 1:10 dilution of each overnight culture in LB + Cm by putting 0.5mL of culture into 4.5mL of LB + Cm

↓ Measure Abs 600 of these 1:10 diluted cultures

↓ Record the data

↓ Dilute the cultures further to a target Abs6 00 of 0.02 in a final volume of 12 ml LB medium + Cm in 50 mL tube

↓ Incubate the cultures at 37°C and shake at 220 rpm for 6 hours.

↓ Measure your samples for Abs600 and fluorescence

↓ Record data in your notebook

Layout for Abs 600 and fluorescence measurement

Result

Fluorescence Raw Reading

Abs600 Raw Reading

Colony Forming Units per E. coli cultures at OD600=0.1

↓ Measure the OD600 of your cell cultures

↓ Dilute your overnight culture to OD600 = 0.1 in 1mL of LB + Cm media. Do this in triplicate.

↓ Make the following serial dilutions for your triplicates

↓ Aseptically spread plate with 100 μL of the dilutions

↓ Incubate at 37°C overnight

↓ Count colonies after 18-20 hours of growth.

Result

Colony Forming Units per o.1 OD600 E.coli cultures

    Interlab Study

  • - Introduction
  • - Goal
  • - Calibration 1
  • - Calibration 2
  • - Calibration 3
  • - Cell Measurement
  • - Protocol