Difference between revisions of "Team:Virginia/Safety"

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                 All activities of the Virginia iGEM team were done in adherence to the safety regulations of the University of Virginia and the state of Virginia.
 
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              The development of the project began in-person in the spring semester but quickly shifted to solely virtual development in March, due to the COVID-19 pandemic progression. In order to maintain the health and safety of all team members and advisors, development remained entirely virtual throughout the summer and was predominantly virtual in the fall, with some access to a laboratory. See the “Safe Lab Work” section to learn more about how the UVA iGEM team was able to successfully work in the lab while following both COVID-19 and general lab regulations.
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                Over the summer, all work was effectively completed through various scheduled Zoom calls, including daily committee meetings, conversations with advisors, discussions with experts, and much more. In addition, this method of communication through Zoom was maintained throughout the fall.
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               The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified,  but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.
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               talk about safe project design here
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              <img src="https://static.igem.org/mediawiki/2019/3/31/T--NCKU_Tainan--CBMB-Amplification.png"/>
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used,  if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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              In the fall, the Virginia iGEM Team was fortunate enough to get access to a BSL-2 laboratory, following all iGEM, University of Virginia, and general laboratory specifications.
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              Students and advisors who entered the lab wore appropriate PPE, including a mask, goggles, a lab coat, and gloves. In addition, only two team members were allowed in the lab at once, adhering to both the general laboratory regulation of there needing to be more than one person in the lab and the UVA COVID-19 regulation of not having three or more people in the lab. This regulation was successfully adhered to through strategic planning and effective communication amongst team members and advisors, including, but not limited to, scheduling on a google calendar, individually swiping into the laboratory, and logging out once all work is completed. 
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              In addition, all team members that worked in the lab were required to complete 4 safety training before being allowed into the lab. These lab safety trainings were:“Bloodborne Pathogen and BioSafety Training for Research Personnel”,“Autoclaving Safely”, “Chemical Safety and Waste Training for Students”, and “Chemical Storage”. With these trainings,team members were prepared to address any issues that might arise while working in the lab.
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              As aforementioned, the chassis of our device was BL21 (DE3) Escherichia coli. Although this is a Risk Group 1 organism and, thus, required a BSL-1 Lab, Virginia iGEM students worked in a BSL-2 Lab.
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              More detailed safety precautions and information can be found here, on our iGEM Safety Form and additional part information.
 
                  
 
                  
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Revision as of 00:28, 25 October 2020

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Safety
Safe Project Development
All activities of the Virginia iGEM team were done in adherence to the safety regulations of the University of Virginia and the state of Virginia.
The development of the project began in-person in the spring semester but quickly shifted to solely virtual development in March, due to the COVID-19 pandemic progression. In order to maintain the health and safety of all team members and advisors, development remained entirely virtual throughout the summer and was predominantly virtual in the fall, with some access to a laboratory. See the “Safe Lab Work” section to learn more about how the UVA iGEM team was able to successfully work in the lab while following both COVID-19 and general lab regulations.
Over the summer, all work was effectively completed through various scheduled Zoom calls, including daily committee meetings, conversations with advisors, discussions with experts, and much more. In addition, this method of communication through Zoom was maintained throughout the fall.
Safe Project Design
talk about safe project design here
Safe Lab Work
In the fall, the Virginia iGEM Team was fortunate enough to get access to a BSL-2 laboratory, following all iGEM, University of Virginia, and general laboratory specifications.
Students and advisors who entered the lab wore appropriate PPE, including a mask, goggles, a lab coat, and gloves. In addition, only two team members were allowed in the lab at once, adhering to both the general laboratory regulation of there needing to be more than one person in the lab and the UVA COVID-19 regulation of not having three or more people in the lab. This regulation was successfully adhered to through strategic planning and effective communication amongst team members and advisors, including, but not limited to, scheduling on a google calendar, individually swiping into the laboratory, and logging out once all work is completed.
In addition, all team members that worked in the lab were required to complete 4 safety training before being allowed into the lab. These lab safety trainings were:“Bloodborne Pathogen and BioSafety Training for Research Personnel”,“Autoclaving Safely”, “Chemical Safety and Waste Training for Students”, and “Chemical Storage”. With these trainings,team members were prepared to address any issues that might arise while working in the lab.
As aforementioned, the chassis of our device was BL21 (DE3) Escherichia coli. Although this is a Risk Group 1 organism and, thus, required a BSL-1 Lab, Virginia iGEM students worked in a BSL-2 Lab.
More detailed safety precautions and information can be found here, on our iGEM Safety Form and additional part information.




References
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