Latest revision as of 20:21, 25 June 2013

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

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
Bucher, J. R. (2009). ACTION :, 74(227), 38–46.
Framework, S. (2011). correspondence Strengths and limitations of the federal guidance on synthetic DNA, 29(3), 1–3. doi:10.1038/nbt0311-208
HHS AND USDA SELECT AGENTS AND TOXINS 7 CFR Part 331 , 9 CFR Part 121 , and 42 CFR Part 73. (n.d.)., 331.
No Title. (n.d.)., 45–49.
Preventing the misuse of gene synthesis Commercialized GM crops and yield. (2009)., 27(9), 800–801.
Schmidt, M., & Giersch, G. (2011). Dna s s, 1–15.
Select, F., & Program, A. (n.d.). Restricted Experiment Guidance Document, (Cdc).
Federal Register/Vol. 74, No. 227/Friday, November 27, 2009/Notices
IGSC-Harmonized-Screening-Protocol

@@ Line 11: / Line 11: @@
 	<li class="biosecurity"><a href="/Team:Greensboro-Austin/Biosecurity" class="selected" title="biosecurity"><span class="displace">Biosecurity</span></a></li>
 	<li class="human_practices"><a href="/Team:Greensboro-Austin/Human_Practices" title="Human Practices"><span class="displace">Human Practices</span></a></li>
+        <li class="Standard_Proposal"><a href="/Team:Greensboro-Austin/Standard_Proposal" title="Standard_Proposal"><span class="displace">Standard_Proposal</span></a></li>
 	<li class="safety"><a href="/Team:Greensboro-Austin/Safety" title="safety"><span class="displace">Safety</span></a></li>
 	<li class="parts_submitted"><a href="/Team:Greensboro-Austin/Parts" title="parts_submitted"><span class="displace">Parts Submitted</span></a></li>
@@ Line 20: / Line 21: @@
 </html>
-=hello world=
+=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=
+# 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
+# Bucher, J. R. (2009). ACTION :, 74(227), 38–46.
+# Framework, S. (2011). correspondence Strengths and limitations of the federal guidance on synthetic DNA, 29(3), 1–3. doi:10.1038/nbt0311-208
+# HHS AND USDA SELECT AGENTS AND TOXINS 7 CFR Part 331 , 9 CFR Part 121 , and 42 CFR Part 73. (n.d.)., 331.
+# No Title. (n.d.)., 45–49.
+# Preventing the misuse of gene synthesis Commercialized GM crops and yield. (2009)., 27(9), 800–801.
+# Schmidt, M., & Giersch, G. (2011). Dna s s, 1–15.
+# Select, F., & Program, A. (n.d.). Restricted Experiment Guidance Document, (Cdc).
+# Federal Register/Vol. 74, No. 227/Friday, November 27, 2009/Notices
+# IGSC-Harmonized-Screening-Protocol