Team:ZJU-China/Perspective

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        <li><b>Gene Socket</b>
 
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        <h3>Project Description</h3>
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        <p>The assembly of genetic circuits is a huge obstacle between designs and achievements in synthetic biology. Many well-known methods, from traditional restriction digestion &amp; ligation, 3A assembly to Gibson assembly, aim to overcome the difficulties but unfortunately get respective defects. This year, ZJU-CHINA seeks to build a gene-insertion system in bacterial chromosome, "GeneSocket". Clearly different from the in vitro constructing methods mentioned before, GeneSocket, which can be easily combined with existing in vitro methods, makes gene expression more accurate, stable and controllable by assembling genetic elements in chromosome directly.</p>
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        <p>Two core methods, lambda red recombination and recombinase-based bistable switch are applied to build our Gene Socket. Lambda red recombination is a widely used, efficient recombination system in prokaryotes. Recombinase-based bistable switch is relatively more stable and easier than transcription factor regulated bistable switch modules. Both the two are the best choices for achieving the characteristics of Gene Socket.</p>
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        <p>We hope that by using GeneSocket, synthetic biologists can turn their theoretical design into reality faster and better. We want to lead to the revolution in techniques of synthetic biology!</p>
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        <h3>Most important: Our gene sockets relieve lots of work of scientists.</h3>
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        <p>As shown before, via the methods of lambda-red homologous recombination and new-designed bistable switch, we perfectly achieved our goal to make constructing vectors on chromosomes easier. If we can change the chromosomes as we planned, just through some simple steps, would it sound marvelous?</p>
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        <h4>The prominent advantages of gene sockets.</h4>
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        <p>Our gene sockets have a lot of prominent advantages and it is superb and unique. The advantages can be divided into three parts, CEO.</p>
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         <h3>Gene Socket</h3>
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         <h5>Convenience</h5>
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         <p>The assembly of genetic circuits is a huge obstacle between designs and achievements in synthetic biology. Many well-known methods, from traditional restriction digestion &amp; ligation, 3A assembly to Gibson assembly, aim to overcome the difficulties but unfortunately get respective defects. This year, ZJU-CHINA seeks to build a gene-insertion system in bacterial chromosome, "GeneSocket". Clearly different from the in vitro constructing methods mentioned before, GeneSocket, which can be easily combined with existing in vitro methods, makes gene expression more accurate, stable and controllable by assembling genetic elements in chromosome directly.</p>
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         <p>First of all, as you can see, our gene sockets provide large convenience for adding specific group of genes into specific vectors. It is just like plugging into the power sockets which is what we do in every day life, can be so easy. For example, we have a blueprint in the future, that given a group of genes, maybe 4 or 5, and given metabolic pathways, which decide the logistic relationship among these proteins coded by these genes (even though these genes code promoters and terminators). And our super gene sockets can handle it right away, with little difficulty or effort. What we do is that we just need to standardize every gene, adding standardized ends to them to change them into parts, and put them into cells one by one. Also because of using standardized ends, we try to create a database and software that can help us standardize the given genes into available parts that can be used in our gene sockets (address of the software). We’re really glad to invite you to try our software and give us suggestions. What’s more, the workflow of gene sockets will given on the next section.</p>
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         <p>Two core methods, lambda red recombination and recombinase-based bistable switch, are applied. Both are the best choices for achieving the characteristics of GeneSocket.</p>
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        <h5>Efficiency</h5>
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        <p>We hope that by using GeneSocket, synthetic biologists can turn their theoretical design into reality faster and better. We want to lead to the revolution in techniques of synthetic biology!
+
         <p>Secondly, our gene sockets have high accuracy and high efficiency for constructing a vector. The high speed depends on the high efficiency of the homologous recombination we’ve chosen. Also, the high accuracy results from high accuracy of this homologous recombination. We chose lambda red dependent homologous recombination as our tools to build gene sockets, and it is one of the most efficient and mature ways to insert genes in prokaryotes. As we came up with this idea, we thought about the process that we could inset one gene by one day. Maybe, as the efficiency of lambda red could be high, we can insert genes faster than we expected. </p>
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        <h5>Originality</h5>
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        <p>Thirdly, we have an exquisite and original design without resistance screening. We add green and red light (sounds like traffic light) into this system to detect and verify whether the given gene has inserted into the specific spot. In this part, we use a new but great bistable switch to achieve this signal system. Our novel bistable switch is totally different from the traditional bistable switch we’ve seen for many times. It’s more stable and accurate. Through this signal system, do it step by step, we can confirm that every gene has been integrated successfully through every change between red and green light. What’s more, compared to the traditional restriction enzyme digestion and ligation ways, our gene sockets provide a chance to make a no gap linkage and sometimes it helps a lot.</p>
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        <h4>The workflow of using gene sockets. (Fantastic guide)</h4>
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        <h4>The circuits we can build.</h4>
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         <h3>Can be used in different species.</h3>
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        <p>Our gene sockets idea provides a wide application in all kinds of creatures. Except for prokaryotic cells, it can also outreached to eukaryotic cells. We’ve learned another ways of homologous recombination depending on CRISPR, and it is really possible to build gene sockets in eukaryotic cells instead of lambda red recombination. </p>
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        <h4>Prokaryotic cells</h4>
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        <p>As shown before, our gene sockets can be perfectly used in prokaryotic cells via lambda-red homologous recombination and tyrosine recombinase bistable switch methods. The workflow and software are available in the former section.</p>
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        <h4>Eukaryotic cells</h4>
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        <p>You can use these subtopics to further explain your project</p>
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            <li>Overall project summary</li>
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            <li>Project Details</li>
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            It's important for teams to describe all the creativity that goes into an iGEM project, along with all the great ideas your team will come up with over the course of your work.
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            It's also important to clearly describe your achievements so that judges will know what you tried to do and where you succeeded. Please write your project page such that what you achieved is easy to distinguish from what you attempted.
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            iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
 
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Revision as of 16:17, 16 October 2014

Team SponsorContact us

Zhejiang University ZJU International Education Fundation College of Life Sciences ZJU School of Medicine Zhejiang University

College of Agriculture & Biotechnology ZJU Faculty of Science Zhejiang University Undergraduate School of ZJU Department of Polymer Sciencce and Engneering Zhejiang University

International Relations Zhejiang University Vazyme Nanking ™ Co.

 Team Forum(BBS): ZJU-China 2014 Team Forum on www.zjubiolab.zju.edu.cn
Post Address: Biolab Center Room 413, ZJU Zijin'gang Campus,
Yuhang Tang Road No.866, Hangzhou, Zhejiang
Powered by . Zhejiang University. Email Address: zjuchina2014 @ 163.com

Most important: Our gene sockets relieve lots of work of scientists.

As shown before, via the methods of lambda-red homologous recombination and new-designed bistable switch, we perfectly achieved our goal to make constructing vectors on chromosomes easier. If we can change the chromosomes as we planned, just through some simple steps, would it sound marvelous?

The prominent advantages of gene sockets.

Our gene sockets have a lot of prominent advantages and it is superb and unique. The advantages can be divided into three parts, CEO.

Convenience

First of all, as you can see, our gene sockets provide large convenience for adding specific group of genes into specific vectors. It is just like plugging into the power sockets which is what we do in every day life, can be so easy. For example, we have a blueprint in the future, that given a group of genes, maybe 4 or 5, and given metabolic pathways, which decide the logistic relationship among these proteins coded by these genes (even though these genes code promoters and terminators). And our super gene sockets can handle it right away, with little difficulty or effort. What we do is that we just need to standardize every gene, adding standardized ends to them to change them into parts, and put them into cells one by one. Also because of using standardized ends, we try to create a database and software that can help us standardize the given genes into available parts that can be used in our gene sockets (address of the software). We’re really glad to invite you to try our software and give us suggestions. What’s more, the workflow of gene sockets will given on the next section.

Efficiency

Secondly, our gene sockets have high accuracy and high efficiency for constructing a vector. The high speed depends on the high efficiency of the homologous recombination we’ve chosen. Also, the high accuracy results from high accuracy of this homologous recombination. We chose lambda red dependent homologous recombination as our tools to build gene sockets, and it is one of the most efficient and mature ways to insert genes in prokaryotes. As we came up with this idea, we thought about the process that we could inset one gene by one day. Maybe, as the efficiency of lambda red could be high, we can insert genes faster than we expected.

Originality

Thirdly, we have an exquisite and original design without resistance screening. We add green and red light (sounds like traffic light) into this system to detect and verify whether the given gene has inserted into the specific spot. In this part, we use a new but great bistable switch to achieve this signal system. Our novel bistable switch is totally different from the traditional bistable switch we’ve seen for many times. It’s more stable and accurate. Through this signal system, do it step by step, we can confirm that every gene has been integrated successfully through every change between red and green light. What’s more, compared to the traditional restriction enzyme digestion and ligation ways, our gene sockets provide a chance to make a no gap linkage and sometimes it helps a lot.

The workflow of using gene sockets. (Fantastic guide)

The circuits we can build.

Can be used in different species.

Our gene sockets idea provides a wide application in all kinds of creatures. Except for prokaryotic cells, it can also outreached to eukaryotic cells. We’ve learned another ways of homologous recombination depending on CRISPR, and it is really possible to build gene sockets in eukaryotic cells instead of lambda red recombination.

Prokaryotic cells

As shown before, our gene sockets can be perfectly used in prokaryotic cells via lambda-red homologous recombination and tyrosine recombinase bistable switch methods. The workflow and software are available in the former section.

Eukaryotic cells

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