Team:NYMU-Taipei/Project

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== Project overview by animation ==
== Project overview by animation ==
== Motivation ==
== Motivation ==
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The Biobrick Parts Registry is beginning to overflow with parts. At last count, there are over 14000 parts in the registry. With this many parts, the registry has made it a very easy to design experiments, but for its complexness it has made it very hard to complete experiments. We design experients, order the parts, receive the parts, and ligate them together, only to find failed results. Even if we follow the correct arrangement of parts (i.e. regulator-RBS-coding sequence-terminator), some parts still don't fit together in a circuit; and we can't tell without spending time finding out through experimentation.  
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The biobrick parts registry is beginning to overflow with parts. However, every team that has used to parts registry knows how complex it is. Even we follow the correct arrangement of parts (i.e. regulator-RBS-coding sequence-terminator), some parts just won’t work together in a big circuit design. Current iGEM teams are favor to do a big project which has a complex circuit design. However, these excellent projects almost turn out to be just design ultimately. So much time is wasted trying to guess blindly at which parts can interact together, and which parts cannot. We need some detail rules for “big circuit” design, for improve the development of synthetic biology.
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Yet, the current iGEM trend is to create larger and larger circuits, circuits that have less and less chance of working together. We've seen iGEM teams get more creative with bacteria, with more ideas that can enhance synthetic biology. But it often ends as ideas and designs. Rather than spending time hoping that the parts we want will fit together, we need to find out how parts interact so that we know which parts work with each other.  
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With this in mind, we are interested in more specific design rules of a genetic circuit. We want to look closely at the central dogma, and more specifically, mRNA.
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Just like we know how IC components work with each other to create a working circuit, we need to find similar design rules in synthetic biology. The lack of these rules creates limitations in the development of synthetic biology. However, another problem arises when we try to find these rules. With current technology, it takes to much to culture cells, much less be able to discover the intricacies of a cell, even one as simple as bacteria
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Modern research is focused on using genes as a reporter, but we want to quantitative description of gene expression in both space and time. Base on the more detail information of gene expression, we can know the interaction between parts in ''vivo''. However, studying the gene expression mechanism by traditional methods takes too much time. To reduce the times of dealing this problem we have come up with our project: SpeedyBac.
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Current research focuses on using genes as reporters to find out the inner workings of transcription control: “What will happen when a promoter is turned on?” In our case, rather than focusing on transcription, we wish to concentrate on gene expression with regards to space and time. With more detail and information on gene expression, we can explore the interaction between parts in vivo.
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So with these problems in mind, we created '''SpeedyBac'''.
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== Overview ==
== Overview ==

Revision as of 11:41, 27 October 2010

Contents

Project overview by animation

Motivation

The biobrick parts registry is beginning to overflow with parts. However, every team that has used to parts registry knows how complex it is. Even we follow the correct arrangement of parts (i.e. regulator-RBS-coding sequence-terminator), some parts just won’t work together in a big circuit design. Current iGEM teams are favor to do a big project which has a complex circuit design. However, these excellent projects almost turn out to be just design ultimately. So much time is wasted trying to guess blindly at which parts can interact together, and which parts cannot. We need some detail rules for “big circuit” design, for improve the development of synthetic biology.

With this in mind, we are interested in more specific design rules of a genetic circuit. We want to look closely at the central dogma, and more specifically, mRNA.

Modern research is focused on using genes as a reporter, but we want to quantitative description of gene expression in both space and time. Base on the more detail information of gene expression, we can know the interaction between parts in vivo. However, studying the gene expression mechanism by traditional methods takes too much time. To reduce the times of dealing this problem we have come up with our project: SpeedyBac.

Overview

For iGEM2010, the NYMU-Taipei team has created a novel assay that can speed up the expression cycle of a gene. Furthermore, the assay also reveals the location and quantity of both mRNA and Proteins. Between the mRNA level and protein level of our gene expression cycle, we have integrated a riboswitch that allows us to stop, start and control the translation of protein. Using this switch, we can study mRNA and protein in one cycle without the interference of one on the other. Lastly, we have built a speedy degradation system that stops the gene expression quickly, and cleanly.

Design

To achieve our goals, our design can split into three parts:

  • Speedy switch
    • Controls and speends up protein translation via a riboswitch between mRNA and protein level of gene expression.
  • Speedy reporter
    • Using mRNA aptamers and split GFP-eIF4A reporter systems to quickly promoter activity.
  • Speedy protein degrader
    • Fast, specific, and constitutive proteolysis achieved by engineering fluorescent proteins with LVA tags.

Acknowledgements

[http://www.southampton.ac.uk/biosci/about/staff/cgp1x07.page Dr. Chris Proud], for providing us pGEX-eIF4A for experiment.


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