Difference between revisions of "Team:William and Mary/Human Practices"

 
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<h1 style="color: black;text-align:center;">Integrated Human Practices</h1>
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<div style = 'padding-left: 8%; padding-bottom: 10px;font-size: 25px' ><b>Motivation</b></div>
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This year, our team had the opportunity to share our project with several diverse groups of people: a group of middle school medical explorers, our high school summer interns, and the general public who attended our Building with Biology Public Forum. When connecting with each of these groups we shared the basics behind our project and asked for feedback on our idea as well as general opinions about the work.  
 
This year, our team had the opportunity to share our project with several diverse groups of people: a group of middle school medical explorers, our high school summer interns, and the general public who attended our Building with Biology Public Forum. When connecting with each of these groups we shared the basics behind our project and asked for feedback on our idea as well as general opinions about the work.  
 
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<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Medical Explorers</b></div>
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The other topic that dominated our conversation were the potential applications. The students wanted to know if we could put our edited bacteria into their bodies and still use the same measurements.
 
The other topic that dominated our conversation were the potential applications. The students wanted to know if we could put our edited bacteria into their bodies and still use the same measurements.
 
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Figure 1: Overview of 3G workflow
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Team member Stephanie Do explaining our project to the Medical Explores during their tour of lab
 
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<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Summer Interns</b></div>
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In Golden-Gate Assembly, type IIS restriction enzymes are used to cut DNA. Type IIS restriction enzymes are useful in that they cut outside their recognition sites, creating fragments of DNA with no unwanted base pair scars. We use the restriction enzyme BsaI, which recognizes specific DNA sequences (BsaI sites) and cuts outside of these sites, leaving sticky ends that can be ligated together with T4 DNA ligase.
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In this stage of assembly, 3G takes advantage of the Cidar MoClo system, in which specific part types are distinguished by their sticky ends. After being cut, each type of part reveals a distinct sticky end on either side. The standard parts used in most synthetic circuits are promoters, 5’ untranslated regions, coding sequences, and terminators. Their MoClo sticky ends are shown in the image below:
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The high school students working in our lab for the month of July were more deeply involved with our project than any other groups. One of these students in particular, Davis, committed a lot of time to learning about our project, even attending our lab meetings outside of normal wet lab hours. Davis is hoping to study biomedical engineering in college and as a result was very interested in the potential medical applications of our project. His questions pushed us to think about making a system compatible with animals systems.
 
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Figure 2: Schematic of MoClo Sticky Ends of promoters, 5' UTRs, CDSs and terminators
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Team member Stephanie Do discussing potential for our project with our summer intern, Davis
 
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The unique sticky ends allow for the parts to line up in the correct sequence before being ligated together. In this way, a full transcriptional unit can be created. To prepare for the Gibson step of 3G, unique nucleotide sequences (UNS) are attached to both ends of the transcriptional unit. The UNS on the 5’ end of the transcriptional unit must have a sticky end A so that it can anneal to the promoter’s sticky end. The UNS on the 3’ end has a sticky end E so that it can anneal to the terminator’s sticky end. These sequences serve as a landing pad for primers in the next stage of PCR. They will also be used when combining the transcriptional units on to a backbone in the final stage of 3G assembly.  
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One of our earliest adult outreach programs was our <a href = 'https://2018.igem.org/Team:William_and_Mary/Human_Practices/Continuing_the_Conversation
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' style = "color:green;">Building with Biology Public Forum</a>. Many adults stayed after the event to hear more about our work as an iGEM team and we were happy to share our project. The Building with Biology Forum had a strong human genome editing theme so many of the participants were primed to think about medical uses for synthetic biology. They were especially interested in the potential for our project to help measure the signals in cancer cells and the ultimate goal of not just interpreting signals but interacting with them.
 
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There are multiple 5’ UNSs and multiple 3’ UNSs, denoted by numbers (ex: UNS 1, UNS 3, UNS 10). This allows us to combine multiple fragments in the Gibson step.
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Figure 3: UNSs attached to transcriptional unit at sticky end A and sticky end E
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Team captain Ethan Jones discussing applications of synthetic biology with community members
 
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<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Impact on Our Project</b></div>
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In all of these conversations there was the common thread of human uses. Our project is designed to interface with natural systems and after hearing the immense interest in implementing this work in humans in particular we began looking for a system which would be compatible with in vivo applications. Eventually we settled on exchanging our chemical sensitive system to a temperature sensitive systems. Temperature is a property that is easy to control dynamically, and has been shown to be important in the regulation of natural systems such as those involved in bacterial pathogenicity [1] and human immune cell function. Further, the system we chose has been demonstrated to be capable of controlling synthetic circuits in vivo [2]. 
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<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Education and Public Engagement</b></div>
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See <a href = 'https://2018.igem.org/Team:William_and_Mary/Public_Engagement' style = 'color:green;'</div> here</a> for our education and public engagement efforts.</div>
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<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>References</b></div>
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[1] Nandan Kumar Jana, Siddhartha Roy, Bhabatarak Bhattacharyya, Nitai Chandra Mandal; Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor, Protein Engineering, Design and Selection, Volume 12, Issue 3, 1 March 1999, Pages 225–233, https://doi.org/10.1093/protein/12.3.225
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[2] Piraner, D. I., Abedi, M. H., Moser, B. A., Lee-Gosselin, A., & Shapiro, M. G. (2016). Tunable thermal bioswitches for in vivo control of microbial therapeutics. Nature Chemical Biology, 13(1), 75-80. doi:10.1038/nchembio.2233
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Latest revision as of 01:22, 18 October 2018

Integrated Human Practices

Motivation
This year, our team had the opportunity to share our project with several diverse groups of people: a group of middle school medical explorers, our high school summer interns, and the general public who attended our Building with Biology Public Forum. When connecting with each of these groups we shared the basics behind our project and asked for feedback on our idea as well as general opinions about the work.
Medical Explorers
These students were incredibly excited about the idea of eavesdropping in on cellular conversations. During our discussion some students were interested in the precision of our measurements, equating our “listening in” to the dynamics of signals to a game of telephone where details are lost over time. This gave us the chance to talk about our measurement of florecens and our use of both a flow cytometer and a plate reader. Although a little challenging for the younger age group, several of the students were very excited about the way the machines worked.
The other topic that dominated our conversation were the potential applications. The students wanted to know if we could put our edited bacteria into their bodies and still use the same measurements.
Team member Stephanie Do explaining our project to the Medical Explores during their tour of lab
Summer Interns
The high school students working in our lab for the month of July were more deeply involved with our project than any other groups. One of these students in particular, Davis, committed a lot of time to learning about our project, even attending our lab meetings outside of normal wet lab hours. Davis is hoping to study biomedical engineering in college and as a result was very interested in the potential medical applications of our project. His questions pushed us to think about making a system compatible with animals systems.
Team member Stephanie Do discussing potential for our project with our summer intern, Davis
Building with Biology
One of our earliest adult outreach programs was our Building with Biology Public Forum. Many adults stayed after the event to hear more about our work as an iGEM team and we were happy to share our project. The Building with Biology Forum had a strong human genome editing theme so many of the participants were primed to think about medical uses for synthetic biology. They were especially interested in the potential for our project to help measure the signals in cancer cells and the ultimate goal of not just interpreting signals but interacting with them.
Team captain Ethan Jones discussing applications of synthetic biology with community members
Impact on Our Project
In all of these conversations there was the common thread of human uses. Our project is designed to interface with natural systems and after hearing the immense interest in implementing this work in humans in particular we began looking for a system which would be compatible with in vivo applications. Eventually we settled on exchanging our chemical sensitive system to a temperature sensitive systems. Temperature is a property that is easy to control dynamically, and has been shown to be important in the regulation of natural systems such as those involved in bacterial pathogenicity [1] and human immune cell function. Further, the system we chose has been demonstrated to be capable of controlling synthetic circuits in vivo [2].
Education and Public Engagement
See here for our education and public engagement efforts.
References
[1] Nandan Kumar Jana, Siddhartha Roy, Bhabatarak Bhattacharyya, Nitai Chandra Mandal; Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor, Protein Engineering, Design and Selection, Volume 12, Issue 3, 1 March 1999, Pages 225–233, https://doi.org/10.1093/protein/12.3.225
[2] Piraner, D. I., Abedi, M. H., Moser, B. A., Lee-Gosselin, A., & Shapiro, M. G. (2016). Tunable thermal bioswitches for in vivo control of microbial therapeutics. Nature Chemical Biology, 13(1), 75-80. doi:10.1038/nchembio.2233