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Contents 1 Collaboration between North Carolina A&T and The University of Texas at Austin 2 Biosecurity 2.1 Background 2.2 Project 2.3 References

Collaboration between North Carolina A&T and The University of Texas at Austin

Throughout the course of the spring and summer, our team has been pleased to work with the IGEM team at NCA&T University. Our goal has been to help guide NCA&T through the competition. By maintaining communication, we were able to explain some of the technicalities of the IGEM competition and provide advice on how to recruit team members, brainstorm project ideas, effectively develop and manage projects, maintain reasonable project timelines, make a wiki, etc.

During the summer, a few of our team members were fortunate enough to visit NCA&T. Workshops were held to teach NCA&T lab techniques such as PCR, sterile technique, gel electrophoresis, gel extraction, and plating technique. Other workshops included Geneious tutorials and research techniques. We were glad that NCA&T members were able to visit the UT campus as well. We held various workshops and showed them around our lab. One of the most important aspects of their visit was that they were able to see our team stucture and the way we function.

NCA&T now has the insight they need to create a solid team for next year’s IGEM competition. Working together has been a rewarding experience for the UT/NCA&T IGEM team and we are glad to say we now have friends in Greensboro, North Carolina.

Biosecurity

Background

With the growth and advancement of synthetic biology, bioterrorism has become a greater concern. Currently, the government does not mandate that DNA synthesizing companies take precautionary screening measures to lower the risk of bioterrorism. In stead, the government provides screening guidelines for potentially harmful oligonucleotides.[9]

Select Agents and Toxins is a documented composition of harmful bacteria, viruses, and toxins that the Department of Health and Safety is most concerned may be used as weapons for bioterrorism. [4] Various methods oligo screening methods have been developed such as Guidance, Top Homology, and Best Match. Best Match is the more popular screening method chosen by synthesizing companies. When an oligo is ordered, the sequence is screened for homology to any unique sequence of the Select Agents and Toxins. Best Match screens 200 base pairs at a time and screens using different reading frames. If the oligo is more homologous to a Select Agent or Toxin than any other sequence found in international sequence reference databanks, such as NCBI, the order is flagged. The owner of the account must disclose their purpose for ordering such an oligo and must be granted permission to have a dangerous oligo synthesized.

IGSC (International Gene Synthesis Consortium) companies screen ordered oligos as six different reading frames. The amino acid sequences are screened for protein similarity in a Regulated Pathogen Database. The Regulated Pathogen Database is currently being modified and will be a collaboration of the Select Agent list, the Australian Group list, and other regulated pathogens set by various countries.[10]

There are various inadequacies with Best Match. Best Match is not able to detect unrelated accounts conspiring to order harmful oligos. The Select Agents and Toxins list does not account for every harmful agent and toxin. Thus, harmful oligos that are not listed can be synthesized because they are not screened for. Forbidden oligos are distributed to government, university, non-profit, and industry researchers according to IGSC which may be a lenient list with access to these oligos.[10]

Bioterrorism is an unlikely form of terrorism because there are many more convenient and cheap methods of terrorism. The status for oligo screening is currently unsatisfactory and should be improved in the near future as synthetic biology expands. Although bioterrorism is not a great concern now, its imperative that sound methods of bioterrorist prevention be developed now.

Project

In this project, screening for the Ebola virus was imitated using the program Python. The program generates random sequences with 200 base pairs in length and blast searches them in NCBI to test for homology. The program also extracts random sequences from NCBI and screens them for homology to Ebola in 200 base pair segments testing each reading frame. The theoretical ordered sequences are only screened for the unique sequences that Ebola has to avoid false positives.

Ebola virus encodes seven polypeptides from its RNA genome of ca. 19.0 kb, including the glycoprotein (GP), nucleoprotein (NP), RNA-dependent RNA polymerase (L), VP35, VP30, VP40, and VP24.[1]

References

1. Han, Z., Boshra, H., Sunyer, J. O., Zwiers, S. H., Paragas, J., Harty, R. N., Han, Z., et al. (2003). Biochemical and Functional Characterization of the Ebola Virus VP24 Protein : Implications for a Role in Virus Assembly and Budding Biochemical and Functional Characterization of the Ebola Virus VP24 Protein : Implications for a Role in Virus Assembly and Budding. doi:10.1128/JVI.77.3.1793
2. Bucher, J. R. (2009). ACTION :, 74(227), 38–46.
3. Framework, S. (2011). correspondence Strengths and limitations of the federal guidance on synthetic DNA, 29(3), 1–3. doi:10.1038/nbt0311-208
4. HHS AND USDA SELECT AGENTS AND TOXINS 7 CFR Part 331 , 9 CFR Part 121 , and 42 CFR Part 73. (n.d.)., 331.
5. No Title. (n.d.)., 45–49.
6. Preventing the misuse of gene synthesis Commercialized GM crops and yield. (2009)., 27(9), 800–801.
7. Schmidt, M., & Giersch, G. (2011). Dna s s, 1–15.
8. Select, F., & Program, A. (n.d.). Restricted Experiment Guidance Document, (Cdc).
9. Federal Register/Vol. 74, No. 227/Friday, November 27, 2009/Notices
10. IGSC-Harmonized-Screening-Protocol