Difference between revisions of "Team:NCTU Formosa/Description"

 
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<ul>
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            <li><a class="active" data-scroll-nav='0'>The APOllO E.Cotector</a></li>
 +
            <li><a data-scroll-nav="1">Single Chain Variable Fragment (scFv)</a></li>
 +
            <li><a data-scroll-nav="2">Targeted drugs</a>
 +
                <ul>
 +
                <li><a data-scroll-nav="3">Pre-diagnosis of targeted drugs treatment</a>
 +
                <li><a data-scroll-nav="4">The concept of combination therapy</a></li>
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                </ul>
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            </li>
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            <li><a data-scroll-nav="5">Contribution to existing Biobrick</a></li>
 +
            </li>
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            </ul>
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    </div>
 
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<div class="p01">
 
<div class="p01">
 
<div class="background1"></div>
 
<div class="background1"></div>
<div class="title">Background</div>
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<div class="title">Description</div>
 
</div>
 
</div>
 
<div class="p02">
 
<div class="p02">
<div class="content"><h1>APPOllO E.Cotector</h1>
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<div class="content" data-scroll-index="0"><h1>The APOllO E.Cotector</h1>
<p>To enhance the efficiency of diagnosis and provide reference for proper usage of targeted drugs and combination therapy, we come up with the idea of detecting multimarker at the same time and this was how our marvelous E.Cotector was born. This year, NCTU_Formosa commits to creating a multimarker diagnosis platform via scFv as probes for helping physicians to determine and prescribe the usage of targeted drugs in cancer patients, especially the monoclonal-antibody-targeted drugs.</p></div>
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<p>This year, APOllO introduced a new customized detecting platform - The APOllO E.Cotector.</p>
 +
<p> Our customers can spontaneously choose plasmids from our biobrick libraries and match various plasmids for <font color="#AC1F4A">co-transformation</font>. This procedure helps tailor our product to the wishes of our customers and gives our company a major advantage in the manufacturing process. The simple process of co-transformation can create a dual display system that replaces the process of ligating several insertion genes into one single lengthy plasmid, which tremendously increases our manufacturing efficiency. </p>  
 +
<p>Our biobrick libraries consist of three kinds of plasmids: (1) scFv probes detect the target we want,
 +
(2) color signals are for observation, and (3) GBP can connect to gold. Customers can detect what they need just by randomly selecting up to two plasmids.</p>
 +
</div>
  
<div class="content"><h1>Customized Detection Platform</h1>
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<div class="content" data-scroll-index="1"><h1>Single Chain Variable Fragment (scFv)</h1>
<p>This year, APOllO, introduce a revolution customized detecting platform. We call it the E.Cotector.</p>
+
    <p>ScFv is a fusion protein of the variable regions of heavy chain (VH) and light chain (VL) of immunoglobulins, and the heavy chain and light chain are connected with a short linker peptide of about 15 to 20 amino acids. Even with addition of a linker, scFv can still <font color="#AC1F4A">retain the complete function</font> of antigen-binding site and specificity of the original immunoglobulin. </p>
<p>We built three individual biobrick libraries of scFv probes, color signals and Gold Binding Polypeptide (GBP) for the customized detection platform. Probes detect the target we want. Fluorescence protein or chromoprotein expresses signal for observation. GBP acts as a bridge to connect our product to gold, which enables our product to be applied to biosensors. Our customers can spontaneously choose from our libraries, pair up any biobricks. Next, comes the most crucial part of our project. Our team will then co-transform the plasmids into <i>E. coli</i>. Our customized detection platform, The APOllO E.Cotector, is therefore born.  By co-transforming plasmids, it not only helps us customize our product every which way for our customers but also brings us a major advantage in our manufacturing procedure. We no longer have to build lengthy biobricks, which tremendously increases our manufacturing efficiency.</P>  
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<div class="image">
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<img src="https://static.igem.org/mediawiki/2015/6/62/Design_Figure_2-2.png" height="200px"><br><br>
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Figure 1. ScFv is a fusion protein of the variable regions of heavy chain (VH) and light chain (VL) of a monoclonal antibody.
 
</div>
 
</div>
  
<div class="content">
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<p>Moreover, scFv can be easily produced and displayed by bacteria as it is only 20 percent of the size of most normal antibodies<sup>[1]</sup>. In addition, scFv can be envisaged to be <font color="#AC1F4A">applied in the non-pharmaceutical sector</font>, such as in food, cosmetic or environmental industries. The unique and highly specific antigen-binding ability of biosensors might, for example, be exploited to block enzymes that cause food spoilage or to detect environmental factors present in very low concentrations<sup>[2]</sup>.</p>
<h1>Single chain variable fragment as probe</h1>
+
 
<p> In our product, we chose Single chain variable fragment (scFv) Abs as probes to detect. ScFv are one of the recombinant antibody (rAb) fragments, which are popular therapeutic alternatives to full length monoclonal Abs. Compared to generating whole Abs from animal cell culture, scFv are smaller and can be expressed rapidly, economically and in large quantities in a bacterial host, such as <i>E. coli</i>. A scFv possesses the complete antigen binding site, which contains the variable heavy (VH) and variable light domain of an antibody. The VH domain is linked to a VL domain by an introduced flexible polypeptide linker. A scFv is capable of binding to the target antigens with an affinity similar to that of the parent mAb. Since scFv fragments contain specific antigen binding units, scFv fragments show tremendous versatility and importance in human therapeutics and diagnostics. <sup>[1]</sup> In addition, scFv fragments can be envisaged to be applied in the non-pharmaceutical sector, such as in food, cosmetic or environmental industries. The unique and highly specific antigen-binding ability might, for example, be exploited to block specific enzymes (e.g. enzymes that cause food spoilage), bacteria (e.g. in toothpaste or mouthwashes) or to detect environmental factors present in very low concentrations (as biosensors).<sup>[2]</sup></p>
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<img src="https://static.igem.org/mediawiki/2015/thumb/c/c8/Background_Figure1.png/706px-Background_Figure1.png" height="400px"><br><br>
Figure 1.
+
Figure 2. With scFv probes, E.Cotector could be applied to various fields. For example, in health & medicine, food, agriculture, and environment industries.
 +
</div>
 
</div>
 
</div>
  
<div class="content"><h1>Health and Medical Detection Platform</h1>
+
<div class="content" data-scroll-index="2"><h1>Targeted drugs</h1>
  <p>With our hit product, E.Cotector, we can focus on health and medical dimension. We want to provide a convenient and efficient diagnosis for prescribing personalized targeted drug therapy via tissue biopsies. Therefore, we chose single chain variable fragments (scFv), which are directly from monoclonal antibody targeted drugs to act as our probe to detect specific biomarkers. Our customer can pair up any scFv with any color signal. By changing various kinds of scFv on the surfaces of E.Cotector, it can identify multimarkers and suggest appropriate different kinds of targeted drugs.</P>
+
<p> We focus on health and medicine, leading us to realize the significance of the targeted drug's market. According to statistics, the usage rate of targeted drug therapy in cancer treatment has increased in less than ten years. In Figure 3, it was shown that the targeted drug is not commonly used, accounting for only 11% usage in 2003. Over one decade, it is estimated that the usage of targeted drug will dramatically increase to 46%. However, targeted drugs have been shown to have a more accurate attack on cancer cells and cause <font color="#AC1F4A">less harmful damage</font> to normal tissues via specific binding to target molecules<sup>[3]</sup>. Targeted therapy is alleged to be a "personalized medicine" because health care professionals can use clinical test results from a patient to select a specific drug that has a higher likelihood of being effective for that particular person. This indicates that detection for targeted drugs is a growing field and will become a prevalent pre-diagnosis for cancer treatment in the near future.</p>
  <p> Our E.Cotector can consequently bind to various targeted antigen also simultaneously express color as signal for instant observation. We provide another plasmid of Gold Binding Polypeptide for customers to pair up. By pairing up scFv and GBP, we can achieve quantitative detection through biosensors. In conclusion, the customized APOllO E.Cotector will bring a brand new era for pre-diagnosis target drugs treatment.</P>
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<div class="image">
 
+
<img src="https://static.igem.org/mediawiki/2015/1/1e/NCTU_Formosa_Dis_1.png" height="350px"><br><br>
 +
Figure 3. The usage of targeted drugs in cancer treatment.
 
</div>
 
</div>
  
 +
<h2 data-scroll-index="3">Pre-diagnosis of targeted drugs treatment</h2>
 +
  <p>To create the new era of tailored targeted drugs, doctors must aim at appropriate target molecules for patients with particular diseases. In 2014, the U.S. Food and Drug Administration (FDA) issued a guideline to facilitate the development and review of <font color="#AC1F4A">diagnostic tests</font>. The diagnostic tests are a crucial step to identifying the abnormal cancer biomarkers as they can help medical practitioners <font color="#AC1F4A">determine</font> which patients could benefit from the <font color="#AC1F4A">certain drugs</font> as opposed to those who should not receive the medication. Treatment decisions must be optimal as to not cause bodily damage and waste time, money, and medical resources. FDA encourages the joint of targeted drugs therapies and precise diagnostics tests as they are essential in the safety and effectiveness of targeted drugs<sup>[4]</sup>.</p>
  
<div class="content"><h1>Properties and development of targeted drugs</h1>
+
  <h2 data-scroll-index="4">The concept of combination therapy</h2>
  <p>This year, we decided to utilize the scFv as probes to detect cancer markers and aid in the prescription of targeted drugs in cancer treatments. Targeted drugs therapy utilize compounds that are capable of inhibiting target molecules, the cancer markers which send messages along signaling pathways in cell growth, cell division or cell death.<sup>[3]</sup> Via specific binding to target molecules, targeted drugs show more accurate attack to cancer cells and less harmful damage to normal tissues. <sup>[4]</sup> The precision of targeting the cancer cells has enhanced the efficiency of treatment by a large margin. Targeted therapy is a major step forward for many cancers, especially advanced cancers, and physicians and researchers are now focusing on the development of targeted drugs, creating a new era of personalized cancer treatment. <sup>[5]</sup>Targeted therapy are so-called "personalized medicine" because health care professionals can use clinical test results from a patient to select a specific drug that has a higher likelihood of being effective for that particular person.</p>
+
<p>Although targeted drugs treatments can lead to the dramatic regressions of solid tumors, the responses are often short-lived as the resistant cancer cells will arise after the period of treatment. The major strategy proposed for <font color="#AC1F4A">overcoming the resistance</font> is combination therapy<sup>[5]</sup>. The clinical and preclinical researches further indicates that targeted drug therapy combined with other types of therapies to treat cancers may <font color="#AC1F4A">attain greater effects</font> than using only one therapy. With the concept of combination therapy, the doctor can improve the treating effect and reduce the occurrence of cancer cell resistance toward the targeted drugs. This lessens the probability that a single mutation will cause cross-resistance to both drugs<sup>[6]</sup>.</p>
 
+
<h2>Pre-diagnosis of targeted drugs treatment</h2>
+
  <p>To create the new era of tailored targeted drugs, doctors must aim at appropriate target molecules for patients with particular diseases. In 2014, the U.S. Food and Drug Administration (FDA) issued a guidance to facilitate the development and review of diagnostics tests. The diagnostics tests are the steps to identify the abnormal cancer biomarkers. Moreover, the purpose of diagnostics tests are to help medical practitioners determine which patients could benefit from the certain drugs, conversely, those who should not receive the medication. If the treatment decisions is not optimal, it would not only cause the fatal body damage, but also lead to the waste of time, money and medical resources. FDA encourages the joint of targeted drugs therapies and precise diagnostics tests which are essential for the safe and effective use of targeted drugs.<sup>[6]</sup></p>
+
 
+
  
 
</div>
 
</div>
  
    <p>According to the statistics, the usage rate of targeted drug therapy has increased within ten years. In Figure 2, in 2003, targeted drug therapy is not commonly used compared with other therapies, accounting for only 11% usage. Over one decade, it is estimated that the usage of targeted drug therapy dramatically increases to 46%. It indicates targeted drugs therapy is a potential growing field and will become the commonly used therapy in cancer treatments in the near future.</p>
+
<div class="content" data-scroll-index="5">
 
+
<h1>Contribution to existing Biobrick: Lpp-OmpA BBa_K103006</h1>
 
<div class="image">
 
<div class="image">
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<img src="https://static.igem.org/mediawiki/2015/9/9a/NCTU_Formosa_001-1.png" width="40%">
Figure 2. The usage of targeted drugs.
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<img src="https://static.igem.org/mediawiki/2015/5/59/2015_NCTU_Parts_A.png" width="40%">
 +
<br>Figure 4. (Left) NCTU_Formosa's Lpp-OmpA sequence<br><br>
 +
Figure 5. (Right) Warsaw 2008 iGEM team's Lpp-OmpA sequence
 
</div>
 
</div>
 
+
<p>The original Lpp-OmpA sequence contains: a Ndel restriction site, one to twenty-nine amino acids of LPP_ECOLI P69776 from UniProtKB, forty-six to one hundred fifty-nine amino acids of outer membrane protein A fragment, Gly-Ser-Gly unstructuralized linker BBa_K103007, and SacI restriction site. We successfully exerted the function of Lpp-OmpA by the following steps. We removed the Ndel and SacI restriction .Furthermore, Gly-Ser-Gly unstructuralized linker BBa_K103007 is said to allow proper folding of both fusion partners[7]. However, Lpp-OmpA fusion protein can still retain its function without GGGSGGGS sequence[8]. Therefore, we are left with one to twenty-nine amino acids of LPP_ECOLI and forty-six to one hundred fifty-nine amino acids of outer membrane protein A fragment. To shorten the distance of scFv and the outer membrane, we adjusted the amino acids of OmpA from forty-six to twenty-five and one hundred fifty-nine to one hundred thirty-eight. Then, we added a NcoI restriction site to allow convenient fusions. By this improvement, we perfectly utilized Lpp-OmpA to bring scFv onto the outer membrane <i>E. coli</i> and are completely proved by our experiments. </p> In sum, we submitted a contributed redesigned biobrick to iGEM Giant Jamboree. 
  <h2>The concept of combination therapy</h2>
+
<p>Although targeted drugs treatments can lead to the dramatic regressions of solid tumors, the responses are often short-lived because resistant cancer cells arise after a period of treatment. The major strategy proposed for overcoming the resistance is combination therapy.<sup>[7]</sup> The clinical and preclinical researches further indicated that targeted drug therapy combined with another targeted drug therapy or other types of therapies to treat cancers simultaneously may attain greater effects than using only one therapy. With the concept of combination therapy, we can not only improve the treating effect but also reduce the occurrence of cancer cells resistance toward the targeted drugs as there are less probability that a single mutation will cause cross-resistance to both drugs.<sup>[8]</sup></p>
+
 
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<div class="reference">
 
<div class="reference">
 
<b>Reference<br></b>
 
<b>Reference<br></b>
[1] Applications of single-chain variable fragment antibodies in therapeutics and diagnostics, Nina E. Weisser 1, J. Christopher Hall (2009)<a href="http://www.sciencedirect.com/science/article/pii/S0734975009000548">http://www.sciencedirect.com/science/article/pii/S0734975009000548</a> <br>
+
[1] <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626261/">Single Chain Epidermal Growth Factor Receptor Antibody Conjugated Nanoparticles for in vivo Tumor Targeting and Imaging, Yang L, Mao H, Wang YA, Cao Z, Peng X, Wang X, Duan H, Ni C, Yuan Q, Adams G, Smith MQ, Wood WC, Gao X, Nie S (2009)</a> <br>
[2] Stability Engineering of Antibody Single-chain Fv Fragments, Arne WoÈ rn and Andreas PluÈ ckthun (2001)<a href="網址">這裡是超連結的字</a> <br>
+
[2] <a href="http://www.sciencedirect.com/science/article/pii/S0022283600942657">Stability Engineering of Antibody Single-chain Fv Fragments, Arne WoÈ rn and Andreas PluÈ ckthun (2001)</a> <br>
[3] From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage.
+
 
1Division of Molecular Oncology, Institute for Cancer Research and Treatment (IRCC), University of Turin Medical School (2008)<a href="網址">這裡是超連結的字</a> <br>
+
[3] <a href="http://www.eurekaselect.com/66364/article">From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage.
[4] From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage.
+
1Division of Molecular Oncology, Institute for Cancer Research and Treatment (IRCC), University of Turin Medical School (2008)</a> <br>
1Division of Molecular Oncology, Institute for Cancer Research and Treatment (IRCC), University of Turin Medical School (2008)<a href="網址">這裡是超連結的字</a> <br>
+
 
[5] Molecular-targeted agents combination therapy for cancer: Developments and potentials Feifei Li1,2,3, Changqi Zhao1,2 and Lili Wang3 Beijing Normal University, Beijing, China (2013)<a href="網址">這裡是超連結的字</a> <br>
+
[4] <a href="http://www.fda.gov/downloads/medicaldevices/deviceregulationandguidance/guidancedocuments/ucm262327.pdf">In vitro Companion Diagnostics Device, Guidance for Industry and Food and Drug Administration Staff document issued on: August 6, 2014</a><br>
[6] In vitro Companion Diagnostics Device, Guidance for Industry and Food and Drug Administration Staff document issued on: August 6, 2014<a href="網址">這裡是超連結的字</a><br>
+
[5] <a href="http://elifesciences.org/content/2/e00747">Evolutionary dynamics of cancer in response to targeted combination therapy
[7] Evolutionary dynamics of cancer in response to targeted combination therapy
+
Ivana Bozic, Johannes G Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee,Preya Shah, Yo Sup Moon, Amin Yaqubie, Nicole Kelly, Dung T Le, Evan J Lipson, Paul BChapman, Luis A Diaz Jr, Bert Vogelstein, Martin A Nowak (2013)</a> <br>
Ivana Bozic, Johannes G Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee,Preya Shah, Yo Sup Moon, Amin Yaqubie, Nicole Kelly, Dung T Le, Evan J Lipson, Paul BChapman, Luis A Diaz Jr, Bert Vogelstein, Martin A Nowak (2013)<a href="網址">這裡是超連結的字</a> <br>
+
[6] <a href="https://www.patientresource.com/Personalized_Treatment_Targeted_Therapy.aspx">Personalized Cancer Treatment, Patient Resource</a><br>
[8] Personalized Cancer Treatment, Patient Resource<a href="https://www.patientresource.com/Personalized_Treatment_Targeted_Therapy.aspx">https://www.patientresource.com/Personalized_Treatment_Targeted_Therapy.aspx</a><br>
+
[7] <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588912/">Linkers in the structural biology of protein–protein interactions</a><br>
 +
[8] <a href="http://www.nature.com/onc/journal/v29/n32/pdf/onc2010195a.pdf">Peptide mimotopes recognized by antibodies cetuximab and matuzumab induce a functionally equivalent anti-EGFR immune response</a><br>
  
 
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Latest revision as of 15:39, 31 October 2015

Description

The APOllO E.Cotector

This year, APOllO introduced a new customized detecting platform - The APOllO E.Cotector.

Our customers can spontaneously choose plasmids from our biobrick libraries and match various plasmids for co-transformation. This procedure helps tailor our product to the wishes of our customers and gives our company a major advantage in the manufacturing process. The simple process of co-transformation can create a dual display system that replaces the process of ligating several insertion genes into one single lengthy plasmid, which tremendously increases our manufacturing efficiency.

Our biobrick libraries consist of three kinds of plasmids: (1) scFv probes detect the target we want, (2) color signals are for observation, and (3) GBP can connect to gold. Customers can detect what they need just by randomly selecting up to two plasmids.

Single Chain Variable Fragment (scFv)

ScFv is a fusion protein of the variable regions of heavy chain (VH) and light chain (VL) of immunoglobulins, and the heavy chain and light chain are connected with a short linker peptide of about 15 to 20 amino acids. Even with addition of a linker, scFv can still retain the complete function of antigen-binding site and specificity of the original immunoglobulin.



Figure 1. ScFv is a fusion protein of the variable regions of heavy chain (VH) and light chain (VL) of a monoclonal antibody.

Moreover, scFv can be easily produced and displayed by bacteria as it is only 20 percent of the size of most normal antibodies[1]. In addition, scFv can be envisaged to be applied in the non-pharmaceutical sector, such as in food, cosmetic or environmental industries. The unique and highly specific antigen-binding ability of biosensors might, for example, be exploited to block enzymes that cause food spoilage or to detect environmental factors present in very low concentrations[2].



Figure 2. With scFv probes, E.Cotector could be applied to various fields. For example, in health & medicine, food, agriculture, and environment industries.

Targeted drugs

We focus on health and medicine, leading us to realize the significance of the targeted drug's market. According to statistics, the usage rate of targeted drug therapy in cancer treatment has increased in less than ten years. In Figure 3, it was shown that the targeted drug is not commonly used, accounting for only 11% usage in 2003. Over one decade, it is estimated that the usage of targeted drug will dramatically increase to 46%. However, targeted drugs have been shown to have a more accurate attack on cancer cells and cause less harmful damage to normal tissues via specific binding to target molecules[3]. Targeted therapy is alleged to be a "personalized medicine" because health care professionals can use clinical test results from a patient to select a specific drug that has a higher likelihood of being effective for that particular person. This indicates that detection for targeted drugs is a growing field and will become a prevalent pre-diagnosis for cancer treatment in the near future.



Figure 3. The usage of targeted drugs in cancer treatment.

Pre-diagnosis of targeted drugs treatment

To create the new era of tailored targeted drugs, doctors must aim at appropriate target molecules for patients with particular diseases. In 2014, the U.S. Food and Drug Administration (FDA) issued a guideline to facilitate the development and review of diagnostic tests. The diagnostic tests are a crucial step to identifying the abnormal cancer biomarkers as they can help medical practitioners determine which patients could benefit from the certain drugs as opposed to those who should not receive the medication. Treatment decisions must be optimal as to not cause bodily damage and waste time, money, and medical resources. FDA encourages the joint of targeted drugs therapies and precise diagnostics tests as they are essential in the safety and effectiveness of targeted drugs[4].

The concept of combination therapy

Although targeted drugs treatments can lead to the dramatic regressions of solid tumors, the responses are often short-lived as the resistant cancer cells will arise after the period of treatment. The major strategy proposed for overcoming the resistance is combination therapy[5]. The clinical and preclinical researches further indicates that targeted drug therapy combined with other types of therapies to treat cancers may attain greater effects than using only one therapy. With the concept of combination therapy, the doctor can improve the treating effect and reduce the occurrence of cancer cell resistance toward the targeted drugs. This lessens the probability that a single mutation will cause cross-resistance to both drugs[6].

Contribution to existing Biobrick: Lpp-OmpA BBa_K103006


Figure 4. (Left) NCTU_Formosa's Lpp-OmpA sequence

Figure 5. (Right) Warsaw 2008 iGEM team's Lpp-OmpA sequence

The original Lpp-OmpA sequence contains: a Ndel restriction site, one to twenty-nine amino acids of LPP_ECOLI P69776 from UniProtKB, forty-six to one hundred fifty-nine amino acids of outer membrane protein A fragment, Gly-Ser-Gly unstructuralized linker BBa_K103007, and SacI restriction site. We successfully exerted the function of Lpp-OmpA by the following steps. We removed the Ndel and SacI restriction .Furthermore, Gly-Ser-Gly unstructuralized linker BBa_K103007 is said to allow proper folding of both fusion partners[7]. However, Lpp-OmpA fusion protein can still retain its function without GGGSGGGS sequence[8]. Therefore, we are left with one to twenty-nine amino acids of LPP_ECOLI and forty-six to one hundred fifty-nine amino acids of outer membrane protein A fragment. To shorten the distance of scFv and the outer membrane, we adjusted the amino acids of OmpA from forty-six to twenty-five and one hundred fifty-nine to one hundred thirty-eight. Then, we added a NcoI restriction site to allow convenient fusions. By this improvement, we perfectly utilized Lpp-OmpA to bring scFv onto the outer membrane E. coli and are completely proved by our experiments.

In sum, we submitted a contributed redesigned biobrick to iGEM Giant Jamboree.