Team:Penn State/Other

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     <h2 class="hide">Sample navigation menu:</h2>
     <h2 class="hide">Sample navigation menu:</h2>
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<a class="activenavitab" href="http://2012.igem.org/Team:Penn_State">Home</a><span class="hide"> | </span>
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<a class="navitab" href="http://2012.igem.org/Team:Penn_State">Home</a><span class="hide"> | </span>
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<a class="navitab" href="http://2012.igem.org/Team:Penn_State/Project">Projects</a><span class="hide"> | </span>
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<a class="navitab" href="http://2012.igem.org/Team:Penn_State/Modeling
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">Main Results</a><span class="hide"> | </span>
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<a class="navitab" href="http://2012.igem.org/Team:Penn_State/Safety">Other</a>
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<h2>Safety, Attribution, and More!</h2>
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<h3>Safety, Attribution, and More!</h3></br>
<p>This page is for safety questions, attributions, collaboration, and contact information. Check out the menu below to jump to our completed Safety Questions, Collaboration with other iGEM teams, and Attributions to our generous sponsors and supporters. If you have any questions, please shoot us an email or give us a call!</p>
<p>This page is for safety questions, attributions, collaboration, and contact information. Check out the menu below to jump to our completed Safety Questions, Collaboration with other iGEM teams, and Attributions to our generous sponsors and supporters. If you have any questions, please shoot us an email or give us a call!</p>
<p class="right"><a href="#">Contact Information</a> &raquo;</p>
<p class="right"><a href="#">Contact Information</a> &raquo;</p>
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     <p>Using vectors from the Salis lab, both the multiple start codon and bidirectional promoter projects were assembled. </p>
     <p>Using vectors from the Salis lab, both the multiple start codon and bidirectional promoter projects were assembled. </p>
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<p>In addition to using plasmid vectors and equipment, the Salis lab provides a <a href="https://salis.psu.edu/software">RBS Library Calculator</a> software program to the public, which both forward- and reverse-engineers RBS sequences and translation initiation rates. This software was used heavily in the design of the multiple start codon project in synthesizing varying RBS lengths and strengths for the construct.
     <p>The codon optimization portion of the project was a side project of one of the Richard lab's graduate students, Michael Speer. His partially-assembled construct was the basis testing codon bias.</p>
     <p>The codon optimization portion of the project was a side project of one of the Richard lab's graduate students, Michael Speer. His partially-assembled construct was the basis testing codon bias.</p>
     <p>IDT, or <a href="http://www.idtdna.com/site">Integrated DNA Technologies</a>, synthesized the majority of small oligonucleotides for the Penn State iGEM team. The codon optimization repeat-sequences and varying RBS length and strength sequence variations were annealed from IDT's ssDNA oligos.</p>
     <p>IDT, or <a href="http://www.idtdna.com/site">Integrated DNA Technologies</a>, synthesized the majority of small oligonucleotides for the Penn State iGEM team. The codon optimization repeat-sequences and varying RBS length and strength sequence variations were annealed from IDT's ssDNA oligos.</p>
     <p>Since Penn State did not extensively collaborate with other iGEM teams this year, most parts were locally obtained, or synthesized off-campus.</p>
     <p>Since Penn State did not extensively collaborate with other iGEM teams this year, most parts were locally obtained, or synthesized off-campus.</p>
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    <h2>Sponsors</h2>
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<p><strong>&copy; Hannah Jepsen-Burger<a href="#"></a></strong> | Follow us on Twitter<a href="#"></a></p>
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<p><strong>&copy; Hannah Jepsen-Burger</strong> | Follow us on Twitter<a href="#"></a></p>
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Latest revision as of 03:03, 27 October 2012

Index

Safety, Attribution, and More!


This page is for safety questions, attributions, collaboration, and contact information. Check out the menu below to jump to our completed Safety Questions, Collaboration with other iGEM teams, and Attributions to our generous sponsors and supporters. If you have any questions, please shoot us an email or give us a call!

Contact Information »

Safety Questions

Would any of your project ideas raise safety issues in terms of research safety, public safety, or environmental safety?


There are potential safety concerns with our project, but they do not exceed the normal caution exercised when working with antibiotic-resistant organisms. Although the team is working with a lab strain of E. coli that must be provided with the proper nutrients to survive, we are also working with a variety of antibiotic-resistant plasmids. While we follow proper sterile protocol in our work in the lab, there is still a chance that a wild pathogenic bacteria may enter reactions. In this event, a wild bacteria may have the chance to acquire an antibiotic resistant plasmid. If it were to be removed from the lab, this bacteria could exchange this resistance factor with other bacteria.

We do not work with virulent or potentially hazardous strains of bacteria in the lab, and thus would not risk infection or illness from these antibiotic-resistant bacteria. The only hazard is in allowing these antibiotic-resistant bacteria to transfer their plasmids to pathogenic bacteria outside the lab. Here there is the possibility of danger to the public or the environment depending on the strain of bacteria.

Since some of our project ideas require the use of specific antibiotics, their use and disposal must be taken into consideration. Some of these compounds are toxic or even carcinogenic to humans and must be handled appropriately. These compounds may also be toxic to the environment or public if they were to not be disposed of properly.



Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?


None of our BioBrick components raise any safety issues other than the antibiotic resistance they carry. Steps must be taken to ensure the antibiotic resistance is not accidentally imparted to a pathogen bacterial strain. Otherwise all of the BioBricks created by the team are for analytical purposes only and can only produce fluorescent proteins when correctly used.



Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project?


Yes, there is a biological safety review board at Penn State University. The Institutional Biosafety Committee (IBC) records, reviews, and approves laboratory research based on the NIH Guidelines for Research Involving Recombinant DNA Molecules. They have approved the research conducted in our lab, and we are in full compliance with the biosafety regulations imposed on our work by the IBC.



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?


Another way to ensure safety could be to create a new lab strain of E.coli that has more auxotrophic requirements. This would make it more difficult for a modified bacteria to escape and possibly spread a Resistance factor or Virulence factor.

Parts could be made safer by introducing more regulation components. By making the bacteria require cofactors to function or to live in an antibiotic containing environment would help to ensure containment of the strain being studied. You could also make it more difficult for the new BioBricks to be transmitted in an active form to an undesired bacterial strain.



Collaboration

This year, the Penn State iGEM team completed a survey for the Macquarie Australia team, commenting on the open source nature of the iGEM competition wikis. We were able to provide detailed responses to questions about collaboration practices and open source material.



Attributions

Due to the foundational nature of this year's project objectives, the Penn State iGEM team used several BioBrick promoter pieces its constructs. Therefore, all the non-synthesized genetic material was obtained from the Salis and Richard labs at Penn State.

Using vectors from the Salis lab, both the multiple start codon and bidirectional promoter projects were assembled.

In addition to using plasmid vectors and equipment, the Salis lab provides a RBS Library Calculator software program to the public, which both forward- and reverse-engineers RBS sequences and translation initiation rates. This software was used heavily in the design of the multiple start codon project in synthesizing varying RBS lengths and strengths for the construct.

The codon optimization portion of the project was a side project of one of the Richard lab's graduate students, Michael Speer. His partially-assembled construct was the basis testing codon bias.

IDT, or Integrated DNA Technologies, synthesized the majority of small oligonucleotides for the Penn State iGEM team. The codon optimization repeat-sequences and varying RBS length and strength sequence variations were annealed from IDT's ssDNA oligos.

Since Penn State did not extensively collaborate with other iGEM teams this year, most parts were locally obtained, or synthesized off-campus.

Sponsors