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Team:ZJU-China/Project
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| - | + | <li href="#Description"><b>Project Description</b> | |
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<h3>Project Description</h3> | <h3>Project Description</h3> | ||
<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 & 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> | <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 & 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> | ||
| - | <p>Two core methods, lambda red recombination and recombinase-based bistable switch are applied to build our | + | <p>Two core methods, lambda red recombination and recombinase-based bistable switch are applied to build our GeneSocket. 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 GeneSocket.</p> |
<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> | <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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| - | < | + | <center><big><big><big><b>What is GeneSocket？</b></big></big></big></center> |
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<li><a class="active" href="#tab1">A Design</a></li> | <li><a class="active" href="#tab1">A Design</a></li> | ||
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| - | <p>We accomplish DNA recombination by Lambda red. | + | <p>We accomplish DNA recombination by Lambda red.<br /> |
| - | We accomplish accurate selection by bistable switch. | + | We accomplish accurate selection by bistable switch.<br /> |
| - | The socket is an integrated system, which can solve the two problems together. | + | The socket is an integrated system, which can solve the two problems together.<br /> |
| - | The omnibus design concentrates all the elements into one plasmid and one circuit. The highest simplicity can greatly save your time and work. | + | The omnibus design concentrates all the elements into one plasmid and one circuit. The highest simplicity can greatly save your time and work.<br /> |
| - | Bistable switching makes continuous operation much easier to come true; our accompanying tools (GS-BOX) and the wonderful design of its solution is qualified enough to deal with different kinds of circuits. | + | Bistable switching makes continuous operation much easier to come true; our accompanying tools (GS-BOX) and the wonderful design of its solution is qualified enough to deal with different kinds of circuits.<br /> |
Simple but powerful, Gene Socket can catch up your endless imagination. | Simple but powerful, Gene Socket can catch up your endless imagination. | ||
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| - | <p>Taking different situations into account, the accompanying software could give you the strategy of constructing the entire circuit, leaving simple and repetitive work for you: PCR, ligation, electrotransformation, selection, induction, re-selection, and next round | + | <p>Taking different situations into account, the accompanying software could give you the strategy of constructing the entire circuit, leaving simple and repetitive work for you: PCR, ligation, electrotransformation, selection, induction, re-selection, and next round! |
All you need to do is to give the design of your circuit. Gene Socket will help you do the others. | All you need to do is to give the design of your circuit. Gene Socket will help you do the others. | ||
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<div style="display: none;" id="tab3" class="tabs"> | <div style="display: none;" id="tab3" class="tabs"> | ||
| - | <p>The core of | + | <p>The core of GeneSocket is simplicity, which gives the product the best generalization. |
| - | With | + | With GeneSocket, you will need no complicated kits or solution any more. All you need is a strain of E.coli, which is the carrier, the object and even the production of GeneSocket! |
| - | With only a bottle of LB medium, exponential growth of | + | With only a bottle of LB medium, exponential growth of GeneSocket and the circuit inside can be accomplished, and the distance between theories and reality will decrease exponential, too! |
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| + | <center><big><big><big><b>Our main purpose</big></big></big></b></center><br /> | ||
| + | <center><big><big><big><big><b>Circuit construction on chromosome</big></big></big></big></b></center> | ||
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<h3>Why circuit construction?</h3> | <h3>Why circuit construction?</h3> | ||
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<p>With more and more complicated genetic circuits designed, more efficient, time-saving and inexpensive methods are needed to bring the design into reality. Many well-known methods like traditional restriction digestion and ligation, 3A assembly and Gibson assembly all aim to overcome the difficulties of gene assembly while problems like cumbersome steps, low cost performance, lots of time consuming do not receive quite effective solutions. The new gene-insertion method we build, which we call GeneSocket, is able to assembly genetic elements in vivo efficiently, with reporters easy to be identified, and simple isolation methods. We hope that it can become another choice for researchers in future.</p> | <p>With more and more complicated genetic circuits designed, more efficient, time-saving and inexpensive methods are needed to bring the design into reality. Many well-known methods like traditional restriction digestion and ligation, 3A assembly and Gibson assembly all aim to overcome the difficulties of gene assembly while problems like cumbersome steps, low cost performance, lots of time consuming do not receive quite effective solutions. The new gene-insertion method we build, which we call GeneSocket, is able to assembly genetic elements in vivo efficiently, with reporters easy to be identified, and simple isolation methods. We hope that it can become another choice for researchers in future.</p> | ||
| - | <h3> | + | <h3 name="References" id="References">References</h3> |
<p>[1]Santos, C. N. S. & Yoshikuni, Y. Engineering complex biological systems in bacteria through recombinase-assisted genome engineering. Nature Protocols 9, 1320-1336, doi:10.1038/nprot.2014.084 (2014).</p> | <p>[1]Santos, C. N. S. & Yoshikuni, Y. Engineering complex biological systems in bacteria through recombinase-assisted genome engineering. Nature Protocols 9, 1320-1336, doi:10.1038/nprot.2014.084 (2014).</p> | ||
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<p>[4]Paulsson, J. & Ehrenberg, M. Noise in a minimal regulatory network: plasmid copy number control. Q. Rev. Biophys. 34, 1–59 (2001).</p> | <p>[4]Paulsson, J. & Ehrenberg, M. Noise in a minimal regulatory network: plasmid copy number control. Q. Rev. Biophys. 34, 1–59 (2001).</p> | ||
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| + | <td><img src="https://static.igem.org/mediawiki/2014/4/47/ZJU_left_arow.png"> </img></td><td> <a href="https://2014.igem.org/Team:ZJU-China/Team">Previous: Team</a></td> | ||
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Latest revision as of 03:30, 18 October 2014
Project Description
The assembly of genetic circuits is a huge obstacle between designs and achievements in synthetic biology. Many well-known methods, from traditional restriction digestion & 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.
Two core methods, lambda red recombination and recombinase-based bistable switch are applied to build our GeneSocket. 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 GeneSocket.
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!
We accomplish DNA recombination by Lambda red.
We accomplish accurate selection by bistable switch.
The socket is an integrated system, which can solve the two problems together.
The omnibus design concentrates all the elements into one plasmid and one circuit. The highest simplicity can greatly save your time and work.
Bistable switching makes continuous operation much easier to come true; our accompanying tools (GS-BOX) and the wonderful design of its solution is qualified enough to deal with different kinds of circuits.
Simple but powerful, Gene Socket can catch up your endless imagination.
Why circuit construction?
Genetic regulatory circuits are artificially-designed gene clusters constructed by disparate genetic elements, which can produce novel genetic function according to people’s desire. Able to be modeled and simulated in silico, genetic regulatory circuits can be either qualitatively or quantitatively examined, with its function even able to be predicted. Sound construction of circuits has been one of the crucial parts of synthetic biology, which has been taking people great efforts to perfect.
Why on chromosome?
Nowadays, modern techniques have enabled the construction of more complicated and large-capacity genetic systems. However, most of the genetic circuits are constructed on plasmids, which, with the increasing of complexity, has brought about incremental uncertainty and unpredictability. This indeterminacy is mainly generated by plasmid loss, allele inactivation, copy number variability or plasmid-associated metabolic burden[1]-[4]. To obtain optimal performance in certain microbial host, rounds of examination and troubleshooting may be needed. Nevertheless, with genetic regulatory circuits constructed on microbial chromosome or on bacterial artificial chromosome (BAC), more robust systems can be obtained.
Why GeneSocket?
With more and more complicated genetic circuits designed, more efficient, time-saving and inexpensive methods are needed to bring the design into reality. Many well-known methods like traditional restriction digestion and ligation, 3A assembly and Gibson assembly all aim to overcome the difficulties of gene assembly while problems like cumbersome steps, low cost performance, lots of time consuming do not receive quite effective solutions. The new gene-insertion method we build, which we call GeneSocket, is able to assembly genetic elements in vivo efficiently, with reporters easy to be identified, and simple isolation methods. We hope that it can become another choice for researchers in future.
References
[1]Santos, C. N. S. & Yoshikuni, Y. Engineering complex biological systems in bacteria through recombinase-assisted genome engineering. Nature Protocols 9, 1320-1336, doi:10.1038/nprot.2014.084 (2014).
[2]Tyo, K.E., Ajikumar, P.K. & Stephanopoulos, G. Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat. Biotechnol. 27, 760–765 (2009).
[3]Bentley, W.E. & Quiroga, O.E. Investigation of subpopulation heterogeneity and plasmid stability in recombinant Escherichia colivia a simple segregated model. Biotechnol. Bioeng. 42, 222–234 (1993).
[4]Paulsson, J. & Ehrenberg, M. Noise in a minimal regulatory network: plasmid copy number control. Q. Rev. Biophys. 34, 1–59 (2001).
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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 |
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