Difference between revisions of "Team:CSU Fort Collins/Description"

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<h1> Human Practices </h1>
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<h2> Building with Biology - Larimer County Farmer’s Market</h2>
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<h2> Project Description - Cyanobacteria AND Gate (BioLogic Gate) </h2>
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<p>Boolean logic is largely used in computer science but can be applied to various other disciplines. It regulates the occurrence of desired outcomes by stipulating necessary inputs. One operation from this system is AND. In its simplest form, an AND gate requires two simultaneous inputs in order for an output to be produced. An example of this operation is a driver moving a car forward. For this situation, the engine must be on AND the gearbox must be in drive before pushing the gas pedal will allow the car to move forward. Adhering to Boolean logic, our goal is to create a modular genetic circuit in the cyanobacterium <i> Synechocystis </i> sp. PCC 6803 to optimize expression of a desired product. Additionally, we want to eliminate the need for expensive induction molecules such as IPTG. To accomplish these goals, we selected two conditions to implement in an AND gate and regulate gene expression: light and a quorum of cells. These conditions make use of natural mechanisms of <i> Synechocystis </i> sp. PCC 6803 (herein referred to as <i> Synechocystis </i>) and the quorum sensing mechanism from <i> Vibrio fischeri </i>. </p>
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<p> <i> Synechocystis </i> is a photosynthetic bacterium which has the ability to react diurnally (Labiosa 2006, Beck 2014), suggesting that it is able to change central metabolic flux following a circadian clock. In fact, studies using constant light found that about 2% to 9% of the organism's genes change following a circadian rhythm (Kucho 2005). Using data collected by Beck et al. about the relative abundance of transcripts during light-dark cycles, we identified two loci in the genome of <i> Synechocystis </i> that show peak abundance during the dark cycle. From these two loci, we aim to extract the promoter region and compare them to a known dark induced promoter called <i> LrtA </i>
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as well as a green light induced promoter called <i> cpcG2 </i>. Both <i> LrtA </i> and <i> cpcG2 </i> promoters are found in the genome of <i> Synechocystis </i>. After characterizing the four promoter regions, we will chose the one that expresses best during a dark cycle for further use in our AND gate.
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<p> According to Merriam-Webster, a quorum is defined as ”the smallest number of people who must be present at a meeting in order for decisions to be made.” For our project, we are construing a quorum as the lowest density cell culture at which a product can be optimally produced. Quorum sensing is a communication mechanism bacteria may use to assess population density before allowing gene expression to occur. The bacterium <i> Vibrio fischeri </i> uses quorum sensing to provide bioluminescence for the bobtail squid. Bioluminosity isn’t easily visible until the <i> V. fischeri </i> population reaches a certain density, so to conserve resources, the population will act as a group and drive gene expression only when a quorum is met (Waters and Bassler 2005). Similarly, we want to optimize production in <i> Synechocystis </i>. We chose to implement the <i> luxR-luxI </i> intergenic region from <i> V. fischeri </i> strain MJ1S because its promoters and RBS result in considerably high expression of bioluminescence (Bose et al. 2011). </p>
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<p> This year we decided to approach human practices in a different manner. We decided that we wanted to get more involved with the public and see how we could use our project to address stigmas about synthetic biology. While attending the 2015 iGEM Jamboree, we learned about an interesting opportunity to apply for a Building with Biology kit. Developed by the Museum of Science, the Building with Biology kit is a part of the Building with Biology public engagement with science endeavor, where scientists and the public communicate about science and engage in mutual learning. Building with Biology is funded by a National Science Foundation grant. </p>
  
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<p> The first portion of our AND gate will consist of a dark induced promoter driving expression of an antisense RNA (asRNA) that is complementary to our desired product. The asRNA interferes with translation of the product if light is not present. In the second portion, we have the <i> luxR-luxI </i> quorum sensing system allowing product expression only at a threshold population density. </p>
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<p>We were fortunate to receive a Building with Biology kit and we brought this educational tool to the Larimer County farmer’s market. We engaged people of all ages and walks of life, and introduced them to synthetic biology concepts through hands on activities. These hands on activities provided an ideal method for demonstration that segued smoothly into explanations and discussion about the scientific principles behind the activities. The DNA extraction activity seemed to have the greatest impact on fairgoers. Watching people experience revelations about cells, their membrane structure, and how DNA fits into it all was an amazing experience for us all.   </p>
  
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<p>It’s important for scientific outreach to not only target those who already have an interest in science. How else will people find out if they have an interest in science? Our outreach will have been a success if even one of these events occurs because of our farmer’s market booth: someone discovers a lifelong love for science, someone develops an interest in scientific applications to their current work, someone develops an interest in scientific developments, someone has an interesting dinner conversation, or someone enters a career in science that leads to at least one person’s life being improved or saved. </p>
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<h2> Works Cited </h2>
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<p> Beck C, Hertel S, Rediger A, Lehmann R, Wiegard A, Kölsch A, Heilmann B, Georg J, Hess WR, Axmann IM. 2014. Daily expression pattern of protein-encoding genes and small noncoding RNAs in Synechocystis sp. strain PCC 6803. Appl Environ Microbiol 80:5195–5206. 10.1128/AEM.01086-14. </p>
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<p> Bose, J. L., Wollenberg, M. S., Colton, D. M., Mandel, M. J., Septer, A. N., Dunn, A. K., & Stabb, E. V. (2011). Contribution of Rapid Evolution of the luxR-luxI Intergenic Region to the Diverse Bioluminescence Outputs of Vibrio fischeri Strains Isolated from Different Environments. Applied and Environmental Microbiology, 77(7), 2445-2457. doi:10.1128/aem.02643-10 </p>
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<p> Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M,Ishiura M. 2005. Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 187:2190 –2199. http://dx.doi.org/10.1128/JB.187.6.2190-2199.2005. </p>
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<p> Labiosa, R. G., Arrigo, K. R., Tu, C. J., Bhaya, D., Bay, S., Grossman, A. R. and Shrager, J. (2006), EXAMINATION OF DIEL CHANGES IN GLOBAL TRANSCRIPT ACCUMULATION IN SYNECHOCYSTIS (CYANOBACTERIA). Journal of Phycology, 42: 622–636. doi: 10.1111/j.1529-8817.2006.00217.x </p>
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<p> Waters, C. M., & Bassler, B. L. (2005). QUORUM SENSING: Cell-to-Cell Communication in Bacteria. Annual Review of Cell and Developmental Biology Annu. Rev. Cell Dev. Biol., 21(1), 319-346. doi:10.1146/annurev.cellbio.21.012704.131001 </p>
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<p>Following the Larimer County farmer’s market, we used what we learned from our outreach to determine the aim and scope of our project. An activity called Tech Tokens invited participants to invest fake money in various synthetic biology industry ventures. These industries included biofuels, biomedicine, pest control, and the production of synthetic flavorings. An overwhelming majority of people chose to invest some of their fake money into biofuels, even people who were opposed to things like biomedicines and synthetic flavor production. This was a fascinating outcome, and we fully considered it while designing our project, which should improve biofuel production capacity. </p>
  
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<p> Following the farmer’s market, we were also made very aware of the importance of being able to communicate our ideas well with others. We would all like to discuss our research with the public and other scientists, but this can prove to be a lofty endeavor. It is important to consider various ways to communicate an idea to people of varying backgrounds. There are many ways to get an idea across to someone, but the best way is found only through trial and error in the form of repeated attempts at communication. It’s good practice! </p>
  
 
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Revision as of 02:42, 20 October 2016

Human Practices

Building with Biology - Larimer County Farmer’s Market

This year we decided to approach human practices in a different manner. We decided that we wanted to get more involved with the public and see how we could use our project to address stigmas about synthetic biology. While attending the 2015 iGEM Jamboree, we learned about an interesting opportunity to apply for a Building with Biology kit. Developed by the Museum of Science, the Building with Biology kit is a part of the Building with Biology public engagement with science endeavor, where scientists and the public communicate about science and engage in mutual learning. Building with Biology is funded by a National Science Foundation grant.

We were fortunate to receive a Building with Biology kit and we brought this educational tool to the Larimer County farmer’s market. We engaged people of all ages and walks of life, and introduced them to synthetic biology concepts through hands on activities. These hands on activities provided an ideal method for demonstration that segued smoothly into explanations and discussion about the scientific principles behind the activities. The DNA extraction activity seemed to have the greatest impact on fairgoers. Watching people experience revelations about cells, their membrane structure, and how DNA fits into it all was an amazing experience for us all.

It’s important for scientific outreach to not only target those who already have an interest in science. How else will people find out if they have an interest in science? Our outreach will have been a success if even one of these events occurs because of our farmer’s market booth: someone discovers a lifelong love for science, someone develops an interest in scientific applications to their current work, someone develops an interest in scientific developments, someone has an interesting dinner conversation, or someone enters a career in science that leads to at least one person’s life being improved or saved.

Following the Larimer County farmer’s market, we used what we learned from our outreach to determine the aim and scope of our project. An activity called Tech Tokens invited participants to invest fake money in various synthetic biology industry ventures. These industries included biofuels, biomedicine, pest control, and the production of synthetic flavorings. An overwhelming majority of people chose to invest some of their fake money into biofuels, even people who were opposed to things like biomedicines and synthetic flavor production. This was a fascinating outcome, and we fully considered it while designing our project, which should improve biofuel production capacity.

Following the farmer’s market, we were also made very aware of the importance of being able to communicate our ideas well with others. We would all like to discuss our research with the public and other scientists, but this can prove to be a lofty endeavor. It is important to consider various ways to communicate an idea to people of varying backgrounds. There are many ways to get an idea across to someone, but the best way is found only through trial and error in the form of repeated attempts at communication. It’s good practice!

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