Difference between revisions of "Team:NCKU Tainan/Design"

Line 251: Line 251:
 
         <section class="resume-section">
 
         <section class="resume-section">
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="pbackground">
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="pbackground">
                 <h2 class="mb-3">Project Background</h2>
+
                 <h2 class="mb-3">Overview</h2>
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
+
                    <span>
+
                    <div class="flex-grow-1 row">
+
                      <div class="col-lg-7">
+
                        <p>    Glaucoma is an ocular disease that progressively damages the optic nerves. It is characterized by the loss of the peripheral visual field.  According to WHO, glaucoma is the first leading cause of irreversible blindness, affecting over 80 million people worldwide<sup>[<a href="#ref1" class="linklink">1</a>]</sup>. In terms of social security benefits, lost income tax revenues, and health care expenditures, the annual cost of glaucoma treatment to the US government alone is estimated to exceed US$2.9 billion<sup>[<a href="#ref2" class="linklink">2</a>]</sup>.</p>                       
+
                      </div>
+
                      <div class="col-lg-5 d-flex justify-content-center align-items-center">
+
                        <img src="https://static.igem.org/mediawiki/2020/d/d2/T--NCKU_Tainan--narrow_eye_field.gif" alt="Narrow_eye_field" class="narrow_eye_field">
+
                      </div>
+
                    </div>
+
                       
+
                    </span>
+
                      <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
+
                </div>
+
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">
 
                     <div class="flex-grow-1">
                         <p>    A major risk factor of glaucoma is the elevation of the intraocular pressure (IOP)<sup>[<a href="#ref3" class="linklink">3</a>]</sup>, which is caused by a buildup of aqueous humor inside the eye. Aqueous humor is the circulating fluid within the anterior chamber of the eye, which is secreted by the ciliary body and drained through the trabecular meshwork. However, if there is an imbalance between the rate of secretion and drainage, the aqueous humor will build up and increase IOP. The increase in IOP will damage the optic nerves, leading to blindness that cannot be reversed.</p>
+
                         <p>    In our mission to address glaucoma comprehensively, we decided to provide an even more effective treatment for the disease. Inspired by existing treatments using the nitric-oxide (NO) signaling pathway to target the trabecular meshwork and reduce intraocular pressure<sup>[<a href="#ref1" class="linklink">1</a>]</sup>, we came up with a novel treatment based on gaseous nitric oxide. However, since NO has a short half-life of 400 seconds [reference please], we are unable to use the gaseous form NO directly in our treatment.</p>
 
                     </div>     
 
                     </div>     
 
                 </div>               
 
                 </div>               
Line 277: Line 263:
 
         <section class="resume-section">
 
         <section class="resume-section">
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="papproaches">
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="papproaches">
                 <h2 class="mb-5" >Approaches</h2>
+
                 <h2 class="mb-3">Contact lens</h2>
                <h3 class="mb-0">Eye kNOw</h3>
+
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>    Despite the various types of glaucoma, including Open-Angle Glaucoma, Closed-Angle Glaucoma, or Normal-Tension Glaucoma, reducing intraocular pressure is the only proven method to treat the disease. Therefore, controlling the inflow and outflow of aqueous humor from the ciliary body into the trabecular meshwork is a rational strategy to lower the IOP. One of the most common treatments for glaucoma is the eye drops, which contain drugs such as beta blockers or nitric oxide prodrugs to lower the intraocular pressure of the patient. However, as we do not know when our intraocular pressure will spike, we are unable to apply eye drops effectively, thus reducing the drug’s efficacy. Therefore, this year, iGEM NCKU Tainan proposes a synthetic biology approach to provide a more effective treatment for glaucoma.</p>
+
                         <p>    Literature research stated that the increase in patients’ IOP will result in the deformation of cornea, further leading to a structural change in contact lens[1]. We utilized this phenomenon to design a pair of contact lenses that structurally change in response to fluctuations in intraocular pressure.</p>
 
                     </div>
 
                     </div>
 
                    
 
                    
Line 287: Line 272:
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>    <b>Eye kNOw</b> is a pair of contact lenses that is able to structurally change in response to the fluctuations in IOP. Inside the contact lens is our engineered bacteria, <i>E. coli</i> WM3064, to induce the production of nitric oxide in response to conformational changes of our contact lens.</p>
+
                         <p>    Our contact lens will be fitted with a tubular semipermeable chamber that is filled with our engineered bacteria, IPTG, NO precursor - L-arginine, and DAP. The volume change of the chamber will cause water to flow out thus increasing the IPTG concentration inside the chamber. The increase in IPTG will induce the bacteria to produce more Nitric Oxide Synthase, which can then convert L-arginine into nitric oxide to lower the intraocular pressure (IOP). This structural change is then able to induce dynamic drug delivery.</p>
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
                 <h3 class="mb-0">Eye Screen</h3>
+
                 <h3 class="mb-0">IOP simulation experiment</h3>
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">
 
                     <div class="flex-grow-1">
                         <p>    Glaucoma is considered a difficult disease to treat due to the absence of early signs or symptoms. Without early warnings, people are unaware of its presence and slowly, but silently lose their vision - earning glaucoma the moniker “the silent killer of vision.” Thus, having accessible and accurate diagnostic methods is vital in dealing with glaucoma. In order to address glaucoma comprehensively, besides providing a more effective treatment, improving diagnostic methods is also needed.</p>
+
                         <p>    To prove the concept of our contact lens and our device, we designed an IOP simulation experiment with porcine eye.By changing the drip bag’s height, water pressure will directly increase IOP in the porcine eye, enabling precise control of IOP for experiments[2][3].</p>
 
                     </div>     
 
                     </div>     
 
                 </div>
 
                 </div>
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">
 
                     <div class="flex-grow-1">
                         <p>    Thus we designed <b>Eye Screen</b> - an affordable and portable detection device that uses ultrasound to improve patient’s experience. </p>
+
                         <p>    For more details, please visit proof of concept (a link to “proof of concept”) and <a href="https://2020.igem.org/Team:NCKU_Tainan/Hardware" class="linktohard">hardware.</a></p>
 
                     </div>     
 
                     </div>     
 
                 </div>   
 
                 </div>   
Line 307: Line 292:
 
         <section class="resume-section" >
 
         <section class="resume-section" >
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="pinspiration">
 
             <div class="resume-section-content" data-aos="fade-up" data-aos-duration="2000" id="pinspiration">
                 <h2 class="mb-3">Inspiration</h2>
+
                 <h2 class="mb-3">Gene Design</h2>
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>    Our sense of vision plays a significant role in our daily life. According to research, the visual senses process 80% information at the same time as compared to our other senses<sup>[<a href="#ref4" class="linklink">4</a>]</sup>. Yet, in this modern society, extensive use of electronic devices has become a common phenomenon. Not only does it place severe strain on our eyes, but also increases the risk of ocular diseases<sup>[<a href="#ref5" class="linklink">5</a>]</sup>, including glaucoma, myopia, astigmatism, etc. In particular, glaucoma is ranked as the leading cause of irreversible blindness globally. Since there are no early signs or symptoms, it is hard to detect the disease in its earlier stages. This leads to patients being diagnosed only when their vision has deteriorated to the point of no return. Not only that, current treatments do not show satisfying results due to its low efficacy. </p>
+
                         <p>    In order for our bacteria to reduce intraocular pressure, we planned to engineer our bacteria to have the ability to produce Nitric Oxide Synthase (NOS) [3], an enzyme that can convert L-arginine into NO.</p>
 
                     </div>
 
                     </div>
 
                     <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 
                     <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
Line 316: Line 301:
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">
 
                     <div class="flex-grow-1">
                         <p>    Therefore, iGEM NCKU Tainan 2020 aims to provide a comprehensive solution for glaucoma treatment.</p>
+
                         <p>    For biosafety, we engineered our bacteria to overexpress csgD and csgA for securing bacteria onto the contact lens by increasing binding affinity between bacteria and lens.</p>
 
                     </div>     
 
                     </div>     
                 </div>
+
                 </div>
 +
                <h3 class="mb-0">Gene Design</h3>
 +
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p>    During literature research, we found out that Bacillus subtilis carries Nitric Oxide Synthases and has the ability to produce NO. So we cloned Bacillus subtilis' NOS gene under the control of an inducible promoter, pLacI, into a plasmid and transformed it into E. coli.</p>
 +
                    </div>
 +
                    <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 +
                </div>
 +
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p>    In order to induce our target gene, NOS, with IPTG, we put a LacI and T7 promoter in front of NOS and LacO after it. We chose WM3064 as our bacteria strand strain because it contains T7 RNA polymerase.</p>
 +
                    </div>
 +
                    <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 +
                </div>
 +
                <h4 class="mb-0">Functional Test</h4>
 +
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p>    We tested the kinetics of the enzyme using a NOS assay kit, which utilizes Griess reagents to react with NO and generate colormertic readouts by measuring O.D.540 value. For the purpose of controlling the production of NOS, we induce bacteria with different concentrations of IPTG and induce them for different times.</p>
 +
                    </div>
 +
                    <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 +
                </div>
 +
                <h3 class="mb-0">Biosafety</h3>
 +
                <h4 class="mb-0">DAP-deficient strain</h4>
 +
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p>    We chose E. coli WM3064 as our chassis, which lacks the essential gene dapA. This gene encodes for 4-hydroxy-tetrahydrodipicolinate synthase that is critical to the production of lysine through the DAP pathway.[4] Lysine is an essential amino acid in animals, including humans, but can be synthesised de novo in bacteria, lower eukaryotes and plants for utilisation in protein and peptidoglycan cell wall synthesis.[5] Without this gene, the bacteria will have to depend on exogenous diaminopimelate (DAP) to survive.</p>
 +
                    </div>
 +
                    <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 +
                </div>
 +
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p>    However, in our design, the expression of nos is controlled by the T7-lacI promoter which requires T7 RNA polymerase, which WM3064 doesn't have. Therefore, we transformed a plasmid carrying T7 RNA polymerase into WM3064 to meet our purpose.</p>
 +
                    </div>
 +
                    <!--<div class="flex-shrink-0"><span class="text-primary">March 2013 - Present</span></div> 可以置左藍線-->
 +
                </div>
 +
                <h4 class="mb-0">Functional Test</h4>
 
             </div>
 
             </div>
 
         </section>
 
         </section>

Revision as of 11:15, 21 October 2020


Design

Intrinsic details about Eye kNow and Eye Screen


Overview

In our mission to address glaucoma comprehensively, we decided to provide an even more effective treatment for the disease. Inspired by existing treatments using the nitric-oxide (NO) signaling pathway to target the trabecular meshwork and reduce intraocular pressure[1], we came up with a novel treatment based on gaseous nitric oxide. However, since NO has a short half-life of 400 seconds [reference please], we are unable to use the gaseous form NO directly in our treatment.


Contact lens

Literature research stated that the increase in patients’ IOP will result in the deformation of cornea, further leading to a structural change in contact lens[1]. We utilized this phenomenon to design a pair of contact lenses that structurally change in response to fluctuations in intraocular pressure.

Our contact lens will be fitted with a tubular semipermeable chamber that is filled with our engineered bacteria, IPTG, NO precursor - L-arginine, and DAP. The volume change of the chamber will cause water to flow out thus increasing the IPTG concentration inside the chamber. The increase in IPTG will induce the bacteria to produce more Nitric Oxide Synthase, which can then convert L-arginine into nitric oxide to lower the intraocular pressure (IOP). This structural change is then able to induce dynamic drug delivery.

IOP simulation experiment

To prove the concept of our contact lens and our device, we designed an IOP simulation experiment with porcine eye.By changing the drip bag’s height, water pressure will directly increase IOP in the porcine eye, enabling precise control of IOP for experiments[2][3].

For more details, please visit proof of concept (a link to “proof of concept”) and hardware.


Gene Design

In order for our bacteria to reduce intraocular pressure, we planned to engineer our bacteria to have the ability to produce Nitric Oxide Synthase (NOS) [3], an enzyme that can convert L-arginine into NO.

For biosafety, we engineered our bacteria to overexpress csgD and csgA for securing bacteria onto the contact lens by increasing binding affinity between bacteria and lens.

Gene Design

During literature research, we found out that Bacillus subtilis carries Nitric Oxide Synthases and has the ability to produce NO. So we cloned Bacillus subtilis' NOS gene under the control of an inducible promoter, pLacI, into a plasmid and transformed it into E. coli.

In order to induce our target gene, NOS, with IPTG, we put a LacI and T7 promoter in front of NOS and LacO after it. We chose WM3064 as our bacteria strand strain because it contains T7 RNA polymerase.

Functional Test

We tested the kinetics of the enzyme using a NOS assay kit, which utilizes Griess reagents to react with NO and generate colormertic readouts by measuring O.D.540 value. For the purpose of controlling the production of NOS, we induce bacteria with different concentrations of IPTG and induce them for different times.

Biosafety

DAP-deficient strain

We chose E. coli WM3064 as our chassis, which lacks the essential gene dapA. This gene encodes for 4-hydroxy-tetrahydrodipicolinate synthase that is critical to the production of lysine through the DAP pathway.[4] Lysine is an essential amino acid in animals, including humans, but can be synthesised de novo in bacteria, lower eukaryotes and plants for utilisation in protein and peptidoglycan cell wall synthesis.[5] Without this gene, the bacteria will have to depend on exogenous diaminopimelate (DAP) to survive.

However, in our design, the expression of nos is controlled by the T7-lacI promoter which requires T7 RNA polymerase, which WM3064 doesn't have. Therefore, we transformed a plasmid carrying T7 RNA polymerase into WM3064 to meet our purpose.

Functional Test


References

  1. Varma R, Lee PP, Goldberg I, Kotak S. An Assessment of the Health and Economic Burdens of Glaucoma. American Journal of Ophthalmology. 2011;152(4):515-522.
  2. Rein DB. The Economic Burden of Major Adult Visual Disorders in the United States. Archives of Ophthalmology. 2006;124(12):1754.
  3. Weinreb RN, Aung T, Medeiros FA. The Pathophysiology and Treatment of Glaucoma. JAMA. 2014;311(18):1901.
  4. Hurt J. Your Senses Are Your Raw Information Learning Portals. 2012; Retrieved from https://velvetchainsaw.com/2012/05/23/your-senses-your-raw-information-learning-portals/
  5. Ha A, Kim YK, Park YJ, Jeoung JW, Park KH. Intraocular pressure change during reading or writing on smartphone. Bhattacharya S, ed. PLOS ONE. 2018;13(10):e0206061.