Difference between revisions of "Team:TAS Taipei/Experimental Summary"

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                                     The first step of our project was to simulate the formation of cataracts, so that we can test our products in the future. We set up the model by extracting soluble proteins from the lens of Priacanthus macracanthus, a common freshwater fish that we purchased from a market (figure 2.1, left). There are two distinct parts of the lens: an outer soft layer called the cortex and an inner layer called the nucleus (figure 2.1, right). We used the lens nucleus, because it contains older cells and is more prone to cataract formation (Cvekl & Ashery-Padan, 2014). In order to isolate the lens protein, we shook the lens nucleus in Tris buffer overnight and centrifuged the samples (Mello et al., 2012). The supernatant contains dissolved proteins from the lens nucleus. We then added  hydrogen peroxide (H2O2), the main factor that oxidizes lens proteins and induces cataract formation.  
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                                     Through literature research, we found that glutathione (GSH) and 25-hydroxycholesterol (25HC) should prevent and treat cataracts, respectively. We wanted to first see if we could simulate cataract formation and reproduce the effects of GSH and 25HC seen by other researchers. If successful, then we can later test our own constructs using the same cataract model.
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                                <p>
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                                    We set up the model by extracting soluble proteins from the lens of Priacanthus macracanthus, a common freshwater fish that we purchased from a market (Figure 01 left). There are two distinct parts to the lens: an outer soft layer called the cortex and an inner layer called the nucleus (Figure 01 right). We focused on the lens nucleus, because that part contains older cells and is more prone to cataract formation. The lens nucleus was placed into Tris Buffer and gently shaken overnight. After centrifuging, the supernatant contains dissolved protein from the lens nucleus. We then incubated the lens solution with hydrogen peroxide (H2O2), since H2O2 is the main reactive oxygen species that oxidizes lens proteins and induces cataracts.  
 
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        <img src="https://static.igem.org/mediawiki/2016/8/86/T--TAS_Taipei--Fish_Lens_Picture.jpg" style="align:center">
 
        <img src="https://static.igem.org/mediawiki/2016/8/86/T--TAS_Taipei--Fish_Lens_Picture.jpg" style="align:center">
                                     <figcaption class='darkblue'> <b>Figure 1: Left</b> Our cataract model was set up using fish lens. Left: Priacanthus macracanthus purchased from the market. <b>Right:</b> the two spheres on the left are entire lenses and the two smaller spheres on the right are lens nuclei. </figcaption>
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                                     <figcaption class='darkblue'> <b>Figure 1 (left).</b> Priacanthus macracanthus purchased from the market. <b>(right)</b> The two spheres on the left are lens with cortex and nucleus and the two smaller spheres on the right are nucleus. </figcaption>
 
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                                     To quantify the severity of cataracts in our model, we used spectrophotometer to measure absorbance of the protein solution (Figure 03). As lens proteins get oxidized, absorbance should increase because protein clumps that form will scatter the emitted light. To find a wavelength of light for data collection, we compared the absorbance of an untreated proteins, H2O2-treated proteins, and heat-denatured proteins as a positive control. We observed an absorbance peak at 397.5 nm for insoluble lens proteins, and chose to collect all future absorbance values at that wavelength.
                                     To quantify the severity of cataracts in our model, we used a spectrophotometer to measure absorbance values of the lens solution (figure 2.2). As lens proteins become oxidized, absorbance should increase because as proteins aggregate, they fall out of solution, which will scatter incoming light. To find a wavelength of light for data collection, we compared the absorbance of lens solution alone (negative control), H2O2-treated lens solution, and heat-denatured lens solution (positive control). We observed an absorbance peak at 397.5 nm for both H2O2-treated and heat-denatured solutions, and chose to collect all future absorbance values at that wavelength.  
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        <img src="https://static.igem.org/mediawiki/2016/f/f5/T--TAS_Taipei--Spectrophotometer_Experimental.png">
 
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                                     <figcaption class='darkblue'><b>Figure 2.2:</b> CT-2400 Spectrophotometer was used to measure absorbance and determine severity of cataracts. </figcaption>
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                                     <figcaption class='darkblue'><b>Figure 3.</b> CT-2400 Spectrophotometer used to measure absorbance value </figcaption>
 
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                                     After adding different concentrations of H2O2, our results show that increasing concentrations of H2O2 lead to more severe cataracts (figure 2.3). We also ran a protein gel to compare the sizes of untreated and H2O2-treated proteins. After treatment with H2O2, there was an increase in higher bands, which is consistent with the idea that proteins are clumping and aggregating (figure 2.4). Together, the protein gel and our absorbance data suggest that our model accurately represents cataract development.
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                                     We tested different concentrations of H2O2 on this protein solution to see if cataracts form. Our results show that increasing concentrations of H2O2 lead to more severe cataracts (Figure 04). We also ran a protein gel to compare the sizes of untreated and H2O2-treated proteins. After treatment with H2O2, there was an increase in higher bands, which is consistent with the idea that proteins are clumping and aggregating (Figure 05). Together, the protein gel and our lens cataract model suggest that our model accurately represents cataract development.  
 
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        <img src="https://static.igem.org/mediawiki/2016/7/7c/T--TAS_Taipei--H2O2_Lens_Graph.jpg">
 
        <img src="https://static.igem.org/mediawiki/2016/7/7c/T--TAS_Taipei--H2O2_Lens_Graph.jpg">
                                     <figcaption class='darkblue'><b>Figure 2.3:</b> Increasing the amount of H2O2 leads to a greater      increase in lens solution absorbance. </figcaption>
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                                     <figcaption class='darkblue'><b>Figure 4.</b> Percent change in absorbance of lens solutions treated with H2O2</figcaption>
 
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        <img src="https://static.igem.org/mediawiki/2016/7/7c/T--TAS_Taipei--DegradedProtein_Experimental.jpg">
 
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                                     <br> <figcaption class='darkblue'><b>Figure 2.4</b> H2O2 causes protein aggregation. We ran a protein gel with our fish lens solutions, with or without H2O2. Compared to the untreated solution, treatment with H2O2 resulted in higher bands (red asterisk). The right lane is the molecular ladder (showing protein sizes in kDa). </figcaption>
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                                     <br> <figcaption class='darkblue'><b>Figure 5.</b> SDS Page. The left lane is lens protein solution seated in room temperature for two days. The middle lane is lens protein solution treated with 10mM of H2O2 for two days. The right lane is the molecular ladder. </figcaption>
 
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                                    <p>Through literature research, we learned that glutathione (GSH) and 25-hydroxycholesterol (25HC) are potential candidates for the prevention and treatment of cataracts, respectively (Ottonelloa et al., 2000; Makley et al., 2015). Using our cataract model, we wanted to test the effects of these compounds.</p>
 
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                         <h3>Prevention of Cataracts with GSH</h3>
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                         <h3>Testing Prevention of Cataracts with GSH</h3>
 
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                                 <p>
 
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                                     GSH is the main antioxidant in the lens and prevents H2O2 from oxidizing crystallin proteins. Glutathione reductase (GSR) is the enzyme responsible for making GSH. Older cells in the lens nucleus carry less GSR (Michael & Bron, 2011), which in turn decreases the amount of GSH. This makes the lens nucleus more prone to cataract formation. In order to restore GSH levels, we want to deliver more GSR into the lens.
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                                     GSH is the main antioxidant in the lens and prevents H2O2 from oxidizing crystallin proteins. After GSH converts H2O2 into water, it becomes GSSG, which will be recycled back to GSH with the help of glutathione reductase (GSR) (figure 06). Older cells in the nucleus are unable to produce GSR efficiently, so over time GSSG builds up. Our project is to deliver the GSR into the lens in order to facilitate the conversion of GSSG to GSH. We purchased GSH from Sigma Aldrich. 8 mg of GSH was added to the protein solution prior to the addition of H2O2 .
                                </p>
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                                <p>We found the concentration of GSH in healthy lenses (Kamei, 1993), and used that to determine how much GSH to use in our cataract model. We prepared two samples: one with GSH (from Sigma Aldrich) and H2O2, and the other with H2O2 alone. GSH-treated solutions showed lower absorbance values compared to the untreated control, which indicates less protein aggregation (figure 2.5). These results suggest that GSH has a preventative effect on cataract formation.
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        <img src="https://static.igem.org/mediawiki/2016/2/2a/T--TAS_Taipei--GSH_Lens_Graph.jpg">
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        <img src="https://static.igem.org/mediawiki/2016/4/43/T--TAS_Taipei--GSH_Pathway_Experimental.png">
                                     <figcaption class='darkblue'><b>Figure 2.5:</b> Addition of GSH results in a smaller increase in lens solution absorbance. Lens solutions were treated with H2O2 only, or with H2O2 and GSH together. Graph shows percent change in absorbance after 48 hours. </figcaption>
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                                     <figcaption class='darkblue' style="font-color:red"><b>Figure 6.</b> Glutathione and Reduced Glutathione recycling pathway</figcaption>
 
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                           <h3>Treatment of Cataracts with 25HC</h3>
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                           <h3>Testing Treatment of Cataracts with CH25H</h3>
 
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                                     We selected 25HC to be our treatment because it reverses aggregation and can restore the solubility of lens crystallin proteins (Makley et al., 2015). In order to test this, we bought 25HC from Sigma Aldrich and used this in our cataract model. From veterinarians, we learned that commercial eye drops are available for use in pets (OcluVet; figure 2.6), so we wanted to test the effects of 25HC against these eye drops.
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                                     We select 25 HC (25 hydroxycholesterol) to be our treatment because it reverses aggregation and restores solubility of the lens crystallin protein by stabilizing the natural state of the proteins.  
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                                    In order to verify our research, we use commercially bought 25 HC from Sigma Aldrich to treat the cataracts model. Commercial 25HC came in powder form, and was dissolved in 95% ethanol; thus, for our negative control, we added both H2O2 and ethanol into the protein solution. We also bought vet eyedrops for cataracts from OcluVet to be the positive control (Figure 1). Figure 2 shows the setup of the experiment.  
 
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                                     <figcaption class='darkblue' style="font-color:red"><b>Figure 2.6:</b> OcluVet eye drops are prescribed for pets with cataracts.</figcaption>
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                                     <figcaption class='darkblue' style="font-color:red"><b>Figure 1.</b> The Ocluvet vet eyedrop contains antioxidants that can treat cataracts. We used this eyedrop as our positive control for cataracts treatment.</figcaption>
 
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                                    <figcaption class='darkblue' style="font-color:red"><b>Figure 2.</b> Lens Treatment Experiment after 48hrs. (left) Control, Vet eyedrop treated cataracts solution, 50uM 25HC treated cataracts solution, 20uM 25HC treated cataracts solution. Each treatment is added after adding H2O2 for 24 hours. </figcaption>
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                                <p>
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                                    Two sets of experiments were conducted to prove that 25 HC treats cataracts. For the first set, we added H2O2 into fresh fish lens protein solution, and waited for 24 hours before adding the treatment. After adding 25HC into the cataracts model, we measured the absorbance of the treated protein solutions with a UV spectrophotometer in 24 hours increments (F3). We used Tris buffer to blank the UV spectrophotometer before measuring the absorbances for the 25HC treated tubes, and since the vet eyedrop is yellow, we blanked the spectrophotometer with Tris buffer containing vet eyedrop before measuring vet eyedrop treated cataracts solution. Absorbance increases due to increase of opaqueness of the protein solution. Thus, we assume that, the higher the absorbance, the more cataracts is formed due to protein aggregation.
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        <img src="https://static.igem.org/mediawiki/2016/3/35/T--TAS_Taipei--25HCLensGraph_Experimental.jpg">
 
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                                     <figcaption class='darkblue' style="font-color:red"><b>Figure 2.7:</b> 25HC is more effective at treating cataracts compared to pet eye drops. Increasing the concentration of 25HC increases effectiveness. Two trials were conducted and the error bars showed a significant difference between untreated and 25HC-treated samples. </figcaption>
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                                     <figcaption class='darkblue' style="font-color:red"><b>Figure 4.</b> Percent change in absorbance of the treated cataracts lens protein solution after 48 hours</figcaption>
 
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                                     Lens solutions were first incubated with H2O2, then treatments were added. As shown in figure 2.7, absorbance values increased when lens proteins were incubated with H2O2. Adding pet eye drops did not lower the absorbance as much as treatment with 25HC, suggesting that 25HC is more effective at reducing cataracts. In addition, a higher concentration of 25HC lowered the absorbance even further (50 μM compared to 20 μM).  
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                                     As shown in Figure 4, absorbance values increased when lens proteins were incubated with H2O2 for 48 hours. Adding vet eyedrops did not lower the absorbance as much as treatment with 25HC, suggesting that 25HC is more effective at reducing cataracts. In addition, a higher concentration of 25HC lowered the absorbance even further (50 μM compared to 20 μM). Two trials were conducted and the error bars show that the difference between untreated and 25HC-treated proteins is significant.  
 
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+
                   
 
                      
 
                      
 
                      
 
                      
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                                 <h3>Prevention: GSR-HIS</h3>
 
                                 <h3>Prevention: GSR-HIS</h3>
 
                                 <p>
 
                                 <p>
                                     WGSR catalyzes the formation of GSH, the main antioxidant in the lens. This will prevent crystallin proteins from being oxidized by H2O2. Since people oppose putting bacteria in their bodies, we included a polyhistidine-tag (his-tag) to purify the desired proteins.  
+
                                     We want to express glutathione reductase (GSR) to catalyze the reduction of GSSG to GSH, the main antioxidant in the lens. This will prevent crystallin proteins from being oxidized by H2O2 . We also want to extract the proteins produced by E. coli so that no bacteria is used in our final delivery prototype. Thus, we include a histidine tag behind the gene we want to express. Proteins with a histidine tag can be detected and purified.
                                </p>
+
                                <p>
+
                                    The final construct (figure 2.10) includes a strong promoter, strong ribosome binding site, GSR (mutated to remove internal restriction sites), 10x his-tag, and a double terminator. We acquired a strong promoter + strong ribosome binding site part (BBa_K880005) from the iGEM distribution kit to maximize protein production. We ordered the cDNA of GSR from Origene and used the 10x histidine-tag part from the distribution kit (BBa_K844000). A double terminator (BBa_B0015) was added at the end to stop transcription.  
+
 
                                 </p>
 
                                 </p>
 
                                 </div>
 
                                 </div>
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                                 <figure class = "col-sm-6">
 
                                 <figure class = "col-sm-6">
 
        <img src="https://static.igem.org/mediawiki/2016/6/67/T--TAS_Taipei--GSR_Construct_Experimental.jpg">
 
        <img src="https://static.igem.org/mediawiki/2016/6/67/T--TAS_Taipei--GSR_Construct_Experimental.jpg">
                                     <figcaption class='darkblue'><b>Figure 2.8: </b>Our construct includes a strong promoter, strong ribosome binding site, GSR, his-tag, and double terminator.</figcaption>
+
                                     <figcaption class='darkblue'><b>Figure X. </b>Full Construct.</figcaption>
 
                                 </figure>
 
                                 </figure>
 
                                 <div class="col-sm-3"></div>
 
                                 <div class="col-sm-3"></div>
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                             <div class="row">
 
                                  
 
                                  
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+
                                 <div class="col-sm-8">
 
                                  
 
                                  
 
                                 <p>
 
                                 <p>
                                     The purchased GSR cDNA had two internal PstI and three EcoRI cutting sites. After making silent mutations to the sequence, we sent the cDNA to Mission Biotech for mutagenesis to remove these cutting sites. Once we had the correct sequence of GSR (with 5 point mutations), we designed primers to add the BioBrick prefix and suffix in order to clone GSR into a BioBrick backbone. The primer designs were sent to Tri-I Biotech for oligo synthesis, and polymerase chain reaction (PCR) was set up. We first cloned GSR behind BBa_K880005 (strong promoter + strong ribosome binding site; Figure 2.9), then front-inserted this before a new plasmid (Figure 2.10) containing 10x his-tag (BBa_K844000) and double terminator (BBa_B0015). Sequencing results from Tri-I Biotech show that our final construct was correct.  
+
                                     The purchased GSR cDNA has two internal PstI and three EcoRI cutting sites. After making silent mutations to the sequence, we sent the cDNA to MissionBiotech for mutagenesis to remove these cutting sites. Once we had the correct sequence of GSR (with 5 point mutations), we designed primers to add the BioBrick prefix and suffix in order to clone GSR into a BioBrick backbone. The primer designs were sent to Tri-I Biotech for oligo synthesis, and polymerase chain reaction (PCR) was set up. We first cloned GSR behind BBa_K880005 (strong promoter + strong ribosome binding site; Figure AA), then front-inserted this before a new plasmid (Figure BB) containing 10x Histidine tag (BBa_K844000) and double terminator (BBa_B0015). The sequence of the full construct was confirmed by sequencing (Tri-I Biotech).  
 
                                 </p>
 
                                 </p>
 
                                 </div>
 
                                 </div>
                                  
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                                 <figure class = "col-sm-4">
 +
        <img src="https://static.igem.org/mediawiki/2016/9/97/T--TAS_Taipei--HisTermCloning_Experimental.jpg">
 +
                                    <figcaption class='darkblue'><b>Figure BB. </b>His + term cloning</figcaption>
 +
                                </figure>
 
                                  
 
                                  
 
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                                 <figure class = "col-sm-8">
 
                                 <figure class = "col-sm-8">
 
        <img src="https://static.igem.org/mediawiki/2016/3/35/T--TAS_Taipei--GSR_PCR_Check_Experimental.jpg">
 
        <img src="https://static.igem.org/mediawiki/2016/3/35/T--TAS_Taipei--GSR_PCR_Check_Experimental.jpg">
                                     <figcaption class='darkblue'><b>Figure 2.9: </b>PCR check for BBa_K880005 + GSR. After inserting GSR (pink box, 1.7kb) behind a strong promoter and strong RBS (BBa_K880005), the expected ligation size is around 2kb (blue box). </figcaption>
+
                                     <figcaption class='darkblue'><b>Figure AA. </b>1kb ladder, GSR alone, samples after are K880005 + GSR PCR checks. Boxed bands are correct (slightly higher than GSR alone)</figcaption>
                                </figure>
+
                                <figure class = "col-sm-4">
+
        <img src="https://static.igem.org/mediawiki/2016/9/97/T--TAS_Taipei--HisTermCloning_Experimental.jpg">
+
                                    <figcaption class='darkblue'><b>Figure 2.10: </b>PCR check for his-tag (BBa_K844000) + double terminator (BBa_B0015). The double terminator (~130 bps; or ~400 bps after PCR check, pink box) was inserted behind 10x his-tag (~30 bps). After PCR, the expected ligation size is ~450 bps (blue box).</figcaption>
+
 
                                 </figure>
 
                                 </figure>
  
 +
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                                 <figure class = "col-sm-6">
 
                                 <figure class = "col-sm-6">
 
        <img src="https://static.igem.org/mediawiki/2016/a/a1/T--TAS_Taipei--CH25H_Construct_Experimental.jpg">
 
        <img src="https://static.igem.org/mediawiki/2016/a/a1/T--TAS_Taipei--CH25H_Construct_Experimental.jpg">
                                     <figcaption class='darkblue'><b>Figure 2.11 </b>Our construct includes a strong promoter, strong ribosome binding site, CH25H, his-tag, and double terminator. </figcaption>
+
                                     <figcaption class='darkblue'><b>Figure ???. </b>Caption not provided!!!</figcaption>
 
                                 </figure>
 
                                 </figure>
 
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                                 <p>
 
                                 <p>
                                     CH25H is the enzyme that converts lens cholesterol into 25HC, which reverses protein aggregation (Makley et al., 2015). The final construct contains similar components as the prevention construct, except the first part of the open reading frame is replaced by CH25H. CH25H was also mutated (by Mission Biotech) to remove internal cutting sites and put into a Biobrick backbone to make a new basic part. The sequence of the final construct was sent to Integrated DNA Technologies (IDT) for synthesis and cloned into a Biobrick backbone.  
+
                                     We want to extract alpha crystallin B protein, one of the main proteins in the lens, to see if we can create the same aggregation as cataracts lenses.The construct here contains similar components, except the open reading is replaced by CRYAB and 10x Histidine tag. We wanted to express CRYAB, one of the two main crystallin proteins in the lens, to test if h2o2 can aggregate crystallin proteins. CRYAB cDNA was ordered from Origene. We designed primers that were synthesized by Tri-I biotech to move CRYAB into iGEM backbone. The full construct is shown in figure #.  
 
                                 </p>
 
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                           <br><br>
                          <h3 id="ConstructTreatment"></h3>
 
                          <br>
 
                          <h3>Crystallin Protein: Alpha-crystallin B (CRYAB)-HIS</h3>
 
 
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        <img src="https://static.igem.org/mediawiki/2016/c/ce/T--TAS_Taipei--ProteinGelFiona_Experimental.png">
                                     <figcaption class='darkblue'><b>Figure 2.12 </b> CHECK! Our construct includes a strong promoter, strong ribosome binding site, CRYAB, his-tag, and double terminator.  </figcaption>
+
                                     <figcaption class='darkblue'><b>Figure ???. </b>Caption not provided!!!</figcaption>
 
                                 </figure>
 
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                                    <br>
                          <br><br>
+
        <img src="https://static.igem.org/mediawiki/2016/f/f7/T--TAS_Taipei--CRYAB-HIS-Gel-1.png">
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                                     <figcaption class='darkblue'><b>Figure ???. </b>Caption not provided!!!</figcaption>
                               
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                                <p>
+
                                    CRYAB is one of the main proteins in the human lens that aggregates to form cataracts. In our fish lens model, we observed protein aggregation after adding H2O2. However, we also wanted to make sure that the fish model results represent what happens with human crystallin proteins, so we designed a CRYAB construct (figure 2.12).
+
                                    </p>
+
                                <p>
+
                                    The final CRYAB construct contains similar components, except the first part of the open reading frame is replaced by CRYAB. CRYAB cDNA was ordered from Origene. We designed primers that were synthesized by Tri-I biotech to clone CRYAB into a Biobrick backbone, similar to how the GSR construct was made. Sequencing results (Tri-I Biotech) show that the construct was correct, and we confirmed protein expression of both CRYAB (without a poly-his tag; yellow asterisk in (figure 2.13) and CRYAB-HIS (blue asterisk in figure 2.13).
+
                                     </p>
+
                                <p>
+
                                    To test that CRYAB aggregates in response to H2O2, we cultured bacteria expressing CRYAB and CRYAB-HIS. Liquid cultures were grown overnight and detergent was added to lyse the bacteria cultures. Different concentrations of H2O2 were added to the lysates and a protein gel was prepared (figure 2.13). With increasing concentration of H2O2, the original band for CRYAB-HIS (blue asterisk) becomes lighter as higher bands (indicated by the blue bracket) increase in concentration. This shows that H2O2 has the same effect on human crystallin proteins, causing them to aggregate and clump.
+
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        <img src="https://static.igem.org/mediawiki/2016/3/33/T--TAS_Taipei--2.13.jpg">
+
                                    <figcaption class='darkblue'><b>Figure 2.13 </b> CHECK! Our construct includes a strong promoter, strong ribosome binding site, CRYAB, his-tag, and double terminator.  </figcaption>
+
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Revision as of 03:20, 16 October 2016

Experimental Summary - TAS Taipei iGEM Wiki





Experimental Summary

Setting Up a Cataract Model

Through literature research, we found that glutathione (GSH) and 25-hydroxycholesterol (25HC) should prevent and treat cataracts, respectively. We wanted to first see if we could simulate cataract formation and reproduce the effects of GSH and 25HC seen by other researchers. If successful, then we can later test our own constructs using the same cataract model.

We set up the model by extracting soluble proteins from the lens of Priacanthus macracanthus, a common freshwater fish that we purchased from a market (Figure 01 left). There are two distinct parts to the lens: an outer soft layer called the cortex and an inner layer called the nucleus (Figure 01 right). We focused on the lens nucleus, because that part contains older cells and is more prone to cataract formation. The lens nucleus was placed into Tris Buffer and gently shaken overnight. After centrifuging, the supernatant contains dissolved protein from the lens nucleus. We then incubated the lens solution with hydrogen peroxide (H2O2), since H2O2 is the main reactive oxygen species that oxidizes lens proteins and induces cataracts.

Figure 1 (left). Priacanthus macracanthus purchased from the market. (right) The two spheres on the left are lens with cortex and nucleus and the two smaller spheres on the right are nucleus.


To quantify the severity of cataracts in our model, we used spectrophotometer to measure absorbance of the protein solution (Figure 03). As lens proteins get oxidized, absorbance should increase because protein clumps that form will scatter the emitted light. To find a wavelength of light for data collection, we compared the absorbance of an untreated proteins, H2O2-treated proteins, and heat-denatured proteins as a positive control. We observed an absorbance peak at 397.5 nm for insoluble lens proteins, and chose to collect all future absorbance values at that wavelength.

Figure 3. CT-2400 Spectrophotometer used to measure absorbance value


We tested different concentrations of H2O2 on this protein solution to see if cataracts form. Our results show that increasing concentrations of H2O2 lead to more severe cataracts (Figure 04). We also ran a protein gel to compare the sizes of untreated and H2O2-treated proteins. After treatment with H2O2, there was an increase in higher bands, which is consistent with the idea that proteins are clumping and aggregating (Figure 05). Together, the protein gel and our lens cataract model suggest that our model accurately represents cataract development.



Figure 4. Percent change in absorbance of lens solutions treated with H2O2

Figure 5. SDS Page. The left lane is lens protein solution seated in room temperature for two days. The middle lane is lens protein solution treated with 10mM of H2O2 for two days. The right lane is the molecular ladder.


Testing Prevention of Cataracts with GSH

GSH is the main antioxidant in the lens and prevents H2O2 from oxidizing crystallin proteins. After GSH converts H2O2 into water, it becomes GSSG, which will be recycled back to GSH with the help of glutathione reductase (GSR) (figure 06). Older cells in the nucleus are unable to produce GSR efficiently, so over time GSSG builds up. Our project is to deliver the GSR into the lens in order to facilitate the conversion of GSSG to GSH. We purchased GSH from Sigma Aldrich. 8 mg of GSH was added to the protein solution prior to the addition of H2O2 .

Figure 6. Glutathione and Reduced Glutathione recycling pathway


Figure ???. Caption not provided!!!

Protein solutions with GSH and H2O2 have an absorbance value lesser than those with just protein solutions with H2O2 . The smaller absorbance value indicates smaller protein aggregation and shows GSH has preventative effect. (figure #)



Testing Treatment of Cataracts with CH25H

We select 25 HC (25 hydroxycholesterol) to be our treatment because it reverses aggregation and restores solubility of the lens crystallin protein by stabilizing the natural state of the proteins. In order to verify our research, we use commercially bought 25 HC from Sigma Aldrich to treat the cataracts model. Commercial 25HC came in powder form, and was dissolved in 95% ethanol; thus, for our negative control, we added both H2O2 and ethanol into the protein solution. We also bought vet eyedrops for cataracts from OcluVet to be the positive control (Figure 1). Figure 2 shows the setup of the experiment.

Figure 1. The Ocluvet vet eyedrop contains antioxidants that can treat cataracts. We used this eyedrop as our positive control for cataracts treatment.

Figure 2. Lens Treatment Experiment after 48hrs. (left) Control, Vet eyedrop treated cataracts solution, 50uM 25HC treated cataracts solution, 20uM 25HC treated cataracts solution. Each treatment is added after adding H2O2 for 24 hours.


Two sets of experiments were conducted to prove that 25 HC treats cataracts. For the first set, we added H2O2 into fresh fish lens protein solution, and waited for 24 hours before adding the treatment. After adding 25HC into the cataracts model, we measured the absorbance of the treated protein solutions with a UV spectrophotometer in 24 hours increments (F3). We used Tris buffer to blank the UV spectrophotometer before measuring the absorbances for the 25HC treated tubes, and since the vet eyedrop is yellow, we blanked the spectrophotometer with Tris buffer containing vet eyedrop before measuring vet eyedrop treated cataracts solution. Absorbance increases due to increase of opaqueness of the protein solution. Thus, we assume that, the higher the absorbance, the more cataracts is formed due to protein aggregation.



Figure 4. Percent change in absorbance of the treated cataracts lens protein solution after 48 hours

As shown in Figure 4, absorbance values increased when lens proteins were incubated with H2O2 for 48 hours. Adding vet eyedrops did not lower the absorbance as much as treatment with 25HC, suggesting that 25HC is more effective at reducing cataracts. In addition, a higher concentration of 25HC lowered the absorbance even further (50 μM compared to 20 μM). Two trials were conducted and the error bars show that the difference between untreated and 25HC-treated proteins is significant.

Construct Design


Prevention: GSR-HIS

We want to express glutathione reductase (GSR) to catalyze the reduction of GSSG to GSH, the main antioxidant in the lens. This will prevent crystallin proteins from being oxidized by H2O2 . We also want to extract the proteins produced by E. coli so that no bacteria is used in our final delivery prototype. Thus, we include a histidine tag behind the gene we want to express. Proteins with a histidine tag can be detected and purified.



Figure X. Full Construct.


The purchased GSR cDNA has two internal PstI and three EcoRI cutting sites. After making silent mutations to the sequence, we sent the cDNA to MissionBiotech for mutagenesis to remove these cutting sites. Once we had the correct sequence of GSR (with 5 point mutations), we designed primers to add the BioBrick prefix and suffix in order to clone GSR into a BioBrick backbone. The primer designs were sent to Tri-I Biotech for oligo synthesis, and polymerase chain reaction (PCR) was set up. We first cloned GSR behind BBa_K880005 (strong promoter + strong ribosome binding site; Figure AA), then front-inserted this before a new plasmid (Figure BB) containing 10x Histidine tag (BBa_K844000) and double terminator (BBa_B0015). The sequence of the full construct was confirmed by sequencing (Tri-I Biotech).

Figure BB. His + term cloning


Figure AA. 1kb ladder, GSR alone, samples after are K880005 + GSR PCR checks. Boxed bands are correct (slightly higher than GSR alone)



Treatment: CH25H-HIS

Figure ???. Caption not provided!!!


We want to extract alpha crystallin B protein, one of the main proteins in the lens, to see if we can create the same aggregation as cataracts lenses.The construct here contains similar components, except the open reading is replaced by CRYAB and 10x Histidine tag. We wanted to express CRYAB, one of the two main crystallin proteins in the lens, to test if h2o2 can aggregate crystallin proteins. CRYAB cDNA was ordered from Origene. We designed primers that were synthesized by Tri-I biotech to move CRYAB into iGEM backbone. The full construct is shown in figure #.



Figure ???. Caption not provided!!!

Figure ???. Caption not provided!!!


Prototype

The current method of treatment for cataracts is surgery, which is not only invasive and costly, but also unavailable in areas with limited medical facilities. Taking biosafety, cost, and delivery effectiveness into account, we designed and built a prototype with three distinct steps: Step 1) proteins must be purified and separated from bacteria, Step 2) proteins are packaged in nanoparticles that aid delivery through the cornea and into the lens, and Step 3) delivery of nanoparticles through eye drops or contact lenses.


STEP 1: POLYHISTIDINE-TAG PROTEIN PURIFICATION

Our survey results show that people are reluctant to put anything bacteria-related into their bodies, so we aimed to separate our protein products from the bacteria that produced them. As shown in figure 3.1, our constructs include a downstream 10x polyhistidine-tag (his-tag), which allows the protein to be purified.



Figure 3.1: His-tag allows the proteins to be purified. Both GSR and CH25H (in light blue) constructs include a downstream his-tag (in yellow) for protein purification.


The his-tag has 10 consecutive histidine amino acids that allow the protein to bind to nickel when it passes through a nickel column. In this way, the his-tagged proteins can be eluted to obtain purified proteins.

Since we confirmed the expression of CRYAB-HIS protein (figure 2.15), we used CRYAB and CRYAB-HIS to test a commercial kit (Capturem His-tagged Purification Miniprep Kit from Clontech). We lysed bacteria expressing GFP, CRYAB, and CRYAB-HIS and centrifuged the crude lysates to remove cell debris. Next, we passed the lysates through nickel columns to separate any his-tagged protein. To elute the his-tagged proteins, we added elution buffer with 500mM imidazole into the columns. We expected no protein in the GFP and CRYAB elutions and protein in the CRYAB-HIS elution. However, using the Nanodrop we found no protein in all three elutions.

Through literature research we learned that 6x his-tag are more commonly used and easier to elute off a column compared to a 10x his-tag (Carlsson et al., 2016). Thus, we hypothesized that our tags bound too strongly to the column. If this were the case, we should see a difference in protein concentration before and after passing his-tagged lysates through the column, whereas lysates containing untagged proteins should not change in protein concentration. After testing this hypothesis, we found that the protein concentration of CRYAB-HIS lysate decreased after passing through the column (figure 3.2), which shows that his-tagged proteins were indeed bound to the column. In contrast, the protein concentrations of CRYAB and GFP lysates remained similar.



Figure 3.2: CRYAB-HIS proteins bind to the nickel column. Nanodrop was used to measure protein concentrations. The protein concentration of the CRYAB-HIS lysate decreased after passing through the column, while the protein concentrations of GFP and CRYAB lysates remained almost the same.



Step 2: Packaging in Nanoparticles

The cornea is the outermost layer of the eye and protects the eye from foreign materials, but also prevents drugs from reaching the lens (Gaudana et al., 2010). Scientists have developed several methods to penetrate the cornea and deliver drugs to the lens, but many are invasive, such as implants (Patel et al., 2013). The most promising method is using nanoparticles as drug carriers (Cholkar et al., 2013). so we chose to use nanoparticles to deliver our proteins to the lens.

Nanoparticles can be made from a variety of materials, but we selected chitosan for several reasons. Researchers have used chitosan nanoparticles in the eye; its low toxicity to somatic cells makes it safe and it does not affect the anatomy of the eye (Enriquez de Salamanca et al., 2006). We also learned that chitosan nanoparticles can embed in the cornea, and its biodegradability allows the drug to be released continuously into the eye (figure 3.3) (Enriquez de Salamanca et al., 2006; Campos et al., 2005). Therefore, we want to load our purified proteins into chitosan nanoparticles (figure 3.4).





Figure 3.3: Nanoparticles containing our proteins embed into the cornea and degrade. The released proteins are then delivered within the eye.
Figure 3.4: Purified proteins can be encapsulated in chitosan nanoparticles.


Below is a video of our nanoparticle synthesis procedure.

Figure C. Video


Following the procedure of Quan and Wang (2007), we made nanoparticles and imaged them using scanning electron microscopy and atomic force microscopy (figure 3.5). This revealed our nanoparticles to be spherical and at the optimal size of 200-600 nm (figure 3.6 and 3.7).



Figure 3.5: Team members imaging nanoparticles on the scanning electron microscope and atomic force microscope.


Figure 3.6: Scanning electron microscope image of chitosan nanoparticles
Figure 3.7: We imaged chitosan nanoparticles using atomic force microscopy. On the left is the empty silica plate. On the right is an image of the chitosan nanoparticles, which were placed on the silica plate



Protein Encapsulation

Next, we wanted to load our purified proteins into the nanoparticles. We first used colored proteins to qualitatively test whether proteins could be successfully encapsulated. To do so, we lysed bacteria expressing green fluorescent protein (GFP), red fluorescent protein (RFP), and green pigment (from pGRN, Bba_K274003). We then add the proteins to the chitosan solution. After nanoparticles were made, our results showed that we successfully encapsulated the colored proteins. When we further viewed the nanoparticles under blue light, the GFP- and RFP-containing pellets glowed (figure 3.8), suggesting that the proteins remain functional. Thus, our nanoparticles can serve as protein carriers to enhance drug delivery.

Figure 3.8: Proteins were successfully encapsulated into nanoparticles. Figure shows nanoparticle pellets containing no protein, GFP, RFP, and pGRN (left to right) under white light (top) and blue light (bottom). Fluorescence of GFP and RFP-containing pellets shows that proteins are still functional.

In order to quantitatively determine encapsulation efficiency, we measured protein concentration in the supernatant before and after nanoparticle formation. We started with 1 mg/mL of bovine serum albumin (BSA). After nanoparticle formation, we performed a Bradford assay and found that the concentration decreased to 0.28 mg/mL. As shown in figure 3.9, the encapsulation efficiency was 72%.



Figure 3.9:The encapsulation efficiency is 72%. Using a Bradford assay, we created a standard curve of known BSA protein concentrations by measuring absorbance at 595 nm. Top: graph shows absorbance values of the supernatant after nanoparticle formation. Bottom: cuvettes containing standard solutions (left) and the sample solution (right).



Protein Release

Figure 3.10:BSA proteins are released from chitosan nanoparticles at 37℃, but almost no change occurred at 4℃.

After proteins are encapsulated, nanoparticles should embed in the cornea and release proteins as they degrade over time. To test whether nanoparticles degrade, we measured the release of proteins. After BSA-containing nanoparticles were made, they were spun down and the solution was replaced with phosphate buffered saline (PBS) (Wilson, 2014). Using a Bradford assay, we could then measure protein concentration in the PBS over a 72-hour period.

Trials were performed at two different temperatures: 4°C and 37°C. Our results show that proteins are released from nanoparticles at 37°C , but almost no change could be detected at 4°C (figure 3.10). This finding suggests that we can store a final functional product (e.g., eye drop) at 4°C without nanoparticle degradation, while the proteins can be released from nanoparticles when the eye drop is applied at body temperature.




Step 3: Application (EYE DROP OR CONTACT LENSES)

Our goal is to package GSR and CH25H in nanoparticles to deliver these proteins to the lens using a safe and non-invasive method. We have considered two drug delivery mechanisms to administer the nanoparticles: eye drops and contact lenses.


Eye drops

After packaging our proteins in nanoparticles, the nanoparticles can be spun down and resuspended in saline, since it is commonly used in eye drops (Falsini, 2016).


Contact Lenses

We found a method to make chitosan nanoparticle-embedded hydrogel contact lenses (Behl, 2016). Following their protocol, we created a polymer solution containing all the necessary components, and then transferred this solution into a 3D-printed mold (figure 3.11, left). After exposure to UV for 40 minutes, we successfully made hydrogel contact lenses (figure 3.11, right).

Figure 3.11:A 3D printed mold (left) used to make hydrogel lenses (right).

Final Proof of Concept

Figure 3.12:Experimental flowchart: using GSH or 25HC-packaged nanoparticles to test for prevention and treatment effects in our cataracts model.

In a final experiment, we wanted to test if our delivery prototype can actually be used to prevent and treat cataracts in our model. As shown in figure 3.12, we first solubilized fish lens proteins and treated these samples with H2O2 to simulate cataracts. Nanoparticles encapsulating the compounds GSH or 25HC were made. Next, we added the nanoparticles into our cataracts model to test for prevention and treatment effects. We compared the absorbance values after 48 hours.

After adding H2O2 to the lens solution, absorbance values increased. However, when GSH-containing nanoparticles were also added, the absorbance values remained unchanged (figure 3.13). Similarly, when 25HC-containing nanoparticles were added, the increase in absorbance was significantly lower than with only H2O2 (figure 3.14). These result show that, in our cataracts model, the compounds carried inside nanoparticles were released and effective at treating and preventing cataracts.

Figure 3.13:GSH-containing nanoparticles (blue) prevented an increase in lens solution absorbance after adding H2O2. In the control group (gray), empty nanoparticles were used.
Figure 3.14:25HC-containing nanoparticles (pink) showed a smaller increase in lens solution absorbance after adding H2O2. In the control group (gray), empty nanoparticles were used.


Citations












Prevention

GSR Eyedrop

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25HC Eyedrop

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