Team:ZJU-China/Next Generation

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     <h1><b>Safety</b></h1>
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     <h1><b>Bach 2011</b></h1>
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    <h2>1. Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?</h2>
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     <p>&nbsp;&nbsp;&nbsp;&nbsp;The next generation of our software, Bach 2011, will continue its endeavor in the freedom and mystery of gene sequence composition, but with more proficiency, versatility and craziness. Bach 2011 will hopefully supersede Bach 2010 in the following aspects:
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     <p>&nbsp;&nbsp;&nbsp;&nbsp;No. As a gene composer software, Bach targets at synchronizing and optimizing coding sequence of biobricks by different methods of optimization. The mathematical model construction process is independent and which is also alienated from the wet lab research. As our approach of sequence alteration doesn't change the amino acid sequence at all, the protein produced would be exactly the same only with different translation rate theoretically. Thus, the adoption of our software in wet lab research is highly unlikely to cause any safety issues. Additionally, all our wet lab research and experiments are carefully complying with biosafety regulation in Zhejiang University.  
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    <p><b>1. </b>The estimation of RiPS in Bach 2010 is limited in the choice of host organism, since the parameters required by the model for RiPS output are organism specific and only those in Escherichia coli are detected and known at the moment. Bach 2011 intends to enlarge the choice to include organisms commonly adopted as chassis for biobricks, such as Saccharomyces cerevisiae. Published research results have to be looked through in order to gather more data. In the worst case, new experiments will also have to be made for the determination of such values. </p>
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     <h2>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</h2>
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     <p><b>2. </b>While Bach 2010 can interpret the input sequence in terms of RiPS to denote its translation behavior, Bach 2011 hopes to reverse the interpretation other way around. To fully utilize the insight in translation behavior based on our mathematical model, Bach 2011 will realize one of the original goals of the whole Bach program: quantitative alteration of gene sequence, which is to alter coding sequences according to the desired RiPS value. A simpler approach would be to proved users with certain levels of RiPS (such as to assign levels from fastest to slowest with numbers from 1-5 to denote its state), so that ordinary users can obtain the rewritten sequence without knowledge in the true value of RiPS. But for more advanced users who have a special need for the sequence translational behavior, Bach 2011 will keep substituting codons and rewriting sequences until finally produce the new sequence that has the same value of RiPS as the user intended. </p>
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    <p>&nbsp;&nbsp;&nbsp;&nbsp;No. BioBrick constructed by iGEM 2010 ZJU-China team would raise any safety issues. The BioBricks we used and made in the research process only encode non-hazardous genes.</p>
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     <h2>3. Is there a local biosafety group, committee, or review board at your institution?</h2>
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     <p><b>3. </b>The scope of sequence alteration will also be broadened in Bach 2011. Besides coding sequences of biobricks, certain parts of non-coding sequences (such as RBS, promoter etc.) will also be considered and incorporated into the new generation. RBS especially would be our focus, for the short sequence of RBS determines the strength of ribosome attachment and greatly influence the translation initiation rate (the parameter of walpha in our model). Thus the initiation process will be drawn into detail and the sequence of RBS can be recomposed for the initiation rate and also the RiPS of desire. </p>
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    <p>&nbsp;&nbsp;&nbsp;&nbsp;Yes. Our project is supported by Department of Life Science, Zhejiang University. Hence the project is also under their regulation. During the project making process, Department of Life Science reminds and promotes the ZJU-China team to put the safety issues of the highest priority. Concerned with the safety issue, ZJU-China team has also invited several professors and research assistants to regulate the wet lab experiment process, evaluating project proposal in terms of safety. </p>
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     <h2>4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? </h2>
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     <p><b>4. </b>More factors, playing roles in the elongation process, would also to be taken into consideration in Bach 2011, including mRNA secondary structures. As many factors in the life process are hard to be quantified, such intended improvements will remain as one of the greatest challenges for our new generation of Bach.</p>
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     <p>&nbsp;&nbsp;&nbsp;&nbsp;Standardization has been proved essential in assembling versatile biobricks and constructing novel biomachines. However, to step further, we believe that a universal standard based on xeno-nucleic acid will improve the safety of bioengineering by alienating the wild and synthetic species. Thus, our project of the gene composer is only an initiative step towards this goal. Based on the learning of existing organisms' sequences, gene composer's ability of recomposing is still limited. As Philippe Marliere once put it, the confrontational need to oppose dogmas and consecrated knowledge in order to achieve momentous discoveries did not always originate from improved hypotheses about the natural world. Xenobiotics could be a precious resource to discover and research, and hence it's also a valuable workspace for future gene composers to learn and test. The universal standard in synthetic biology will then be set up to protect natural habitats and human health.  </li>
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    <p><b>&nbsp;&nbsp;&nbsp;&nbsp;WAIT TO BE ROCKED BY BACH 2011 BY ZJU-CHINA IGEM TEAM! </b></p>
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Latest revision as of 03:58, 27 October 2010

Bach 2011

    The next generation of our software, Bach 2011, will continue its endeavor in the freedom and mystery of gene sequence composition, but with more proficiency, versatility and craziness. Bach 2011 will hopefully supersede Bach 2010 in the following aspects:

    1. The estimation of RiPS in Bach 2010 is limited in the choice of host organism, since the parameters required by the model for RiPS output are organism specific and only those in Escherichia coli are detected and known at the moment. Bach 2011 intends to enlarge the choice to include organisms commonly adopted as chassis for biobricks, such as Saccharomyces cerevisiae. Published research results have to be looked through in order to gather more data. In the worst case, new experiments will also have to be made for the determination of such values.


    2. While Bach 2010 can interpret the input sequence in terms of RiPS to denote its translation behavior, Bach 2011 hopes to reverse the interpretation other way around. To fully utilize the insight in translation behavior based on our mathematical model, Bach 2011 will realize one of the original goals of the whole Bach program: quantitative alteration of gene sequence, which is to alter coding sequences according to the desired RiPS value. A simpler approach would be to proved users with certain levels of RiPS (such as to assign levels from fastest to slowest with numbers from 1-5 to denote its state), so that ordinary users can obtain the rewritten sequence without knowledge in the true value of RiPS. But for more advanced users who have a special need for the sequence translational behavior, Bach 2011 will keep substituting codons and rewriting sequences until finally produce the new sequence that has the same value of RiPS as the user intended.


    3. The scope of sequence alteration will also be broadened in Bach 2011. Besides coding sequences of biobricks, certain parts of non-coding sequences (such as RBS, promoter etc.) will also be considered and incorporated into the new generation. RBS especially would be our focus, for the short sequence of RBS determines the strength of ribosome attachment and greatly influence the translation initiation rate (the parameter of walpha in our model). Thus the initiation process will be drawn into detail and the sequence of RBS can be recomposed for the initiation rate and also the RiPS of desire.


    4. More factors, playing roles in the elongation process, would also to be taken into consideration in Bach 2011, including mRNA secondary structures. As many factors in the life process are hard to be quantified, such intended improvements will remain as one of the greatest challenges for our new generation of Bach.


    WAIT TO BE ROCKED BY BACH 2011 BY ZJU-CHINA IGEM TEAM!



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