New Parts Submission
Device 1 was submitted as a composite part under the name BBa_K3670001. Its function is to serve as a biodetector, which underwent several adjustments for improvement. First, regulatory factors for the algD promoter were added as a level of regulation for RDX detection. Following this, we noticed that our promoter lacked important codons that were essential for its optimal function. Based on the genome of P. putida, we optimized and included the missing segments into the genetic sequence. Additionally, due to Dr. Fausto’s recommendation, we decided to add the mCherry (BBa_J176005) reporter gene to this device to be able to quantitatively and qualitatively measure the transcription of the genes and to be able to measure RDX fluorescence intensity versus concentration, which would provide the necessary data to prove our device’s effectiveness.
Device 2 was submitted as BBa_K38570003. This part confers the ability of a cell to biodegrade the nitro-explosive 1,3,5-Trinitro-1,3,5 triazine, colloquially known as RDX. It contains the luxpr promoter, which can be activated in presence of luxR in complex with HSL. When activated, the RDX-metabolising cytochrome P450, XplA, and accompanying reductase, XplB will be produced. amilGFP will serve as the reporter gene for this device.
➜The xplB and xplA gene
Last year, we submitted the fusion gene xplA/B as a biobrick in iGEM’s part registry. This year, after doing research, this part was modified and resubmitted as a new, separate biobricks. xplA gene (BBa_K3670004) encodes for a flavodoxin domain fused at the N-terminus of a P450 cytochrome, while the xplB gene (BBa_K3857002) encodes for a partner flavodoxin reductase.
The algD promoter can now be found as a biobrick under this denotation (BBa_K3857000). It is an inducible promoter that is functioned to activate under the presence of RDX. This sequence was codon-optimized for E. coli Dh5 alpha and utilized in Device 1.
As stated in the previous year, there are not a lot of parts that work for the detection and biodegradation of RDX. Our goal is to continue optimizing our genetic parts to provide functional parts to iGEM teams so that continued research is dedicated to creating this system for the purpose of environmental cleanliness and to diminish health conditions in populations exposed to high concentrations of contaminants.
As a team, one of our primary goals is to bring to awareness the situations that Vieques is in, as well as our possible solution to it. Thus, we provided various conferences, such as the CROEM seminar, in which we presented the project as a whole, providing a brief overview of the situation in Vieques, and how synthetic biology can be utilized to bring a cost-effective solution to the problem. Furthermore, various workshops such as the ßßß Zeta Alpha Chapter Synthetic Biology Workshops series were held to teach students about learning techniques regarding synthetic biology concepts.
Past experiences in iGEM have taught us the importance of bringing science education to the forefront of the general public. This year we decided to bring the experience much closer to the people, especially high school students. With the implementation of the iGEM RUM-UPRM science fair, we gave the necessary tools and knowledge to students to create their very own hypothetical solution. From public speaking workshops to a crash course in research and development, we gave each student the opportunity to enhance their academic and social skills to enable them to present their findings regarding their hypothesis. In addition, the winners of the science fair were chosen for a chance to participate in our High School Internship Program where they would rotate in each branch of the team for eight weeks to understand the work done and the objectives implemented.
Our SynBio summer camp was celebrated for the third consecutive year with more than 90 participants. The summer camp was created so that students from all over Puerto Rico had an opportunity to learn about synthetic biology, and other science-related subjects, to create a group research project. The science project is one of the most essential activities of this camp because it gives these students the ability and knowledge to give formal presentations regarding their hypothetical solutions for a local problem in their area using synthetic biology. To capacite students for this presentation, we set out to give various activities that would enhance their knowledge towards synthetic biology and the fundamentals of doing a formal research project. For a whole week, we organized different activities for high school students, which included presentations about synthetic biology and its concepts; how synthetic biology might solve the situation in Vieques, and various workshops that emphasize research and presentation skills. For the duration of one week, this summer camp brought students from different regions of the island together to form solutions to different problems that are affecting Puerto Rico.
For this cycle, as one of our endeavors to continue providing educational activities to the public, we offered the SynBio week at our university. Here, we provided various activities such as synthetic biology fundamentals seminar given by mentor: Dr. Carlos Ríos-Velázquez; the American Sign Language workshop given by the American Sign Language Student Organization (ASLSO) from the University of Puerto Rico in Aguadilla to promote the inclusion of sign language; a special event denoted as “10 years with iGEM” given by iGEM’s very own Heber Torres, the LATAM ambassador; the “Vieques: an Environmental and Social Crisis'' conference given by Lic. Adrián González Costa to promote awareness of the situation in Vieques; and, as a conclusion to the SynBio week, a presentation of our team’s journey: from its foundation to present day.
Last, but not least, the interest to learn synthetic biology continues to grow. For this reason, a course, as well as a laboratory that specializes in synthetic biology was accepted in the Biology department of the University of Puerto Rico - Mayaguez precinct. This course is expected to be given by our mentor Dr. Carlos Ríos-Velázquez. We hope that this course will inspire students to pursue a degree in synthetic biology to find solutions to different problems from around the world.
BBa_J176005. (n.d.). Retrieved from http://parts.igem.org/Part:BBa_J176005