1. Craig Venter has stated he will establish an IGEM style competition for the most innovative use of the JCVI minimal bacterial cell, JCVI-syn3.0. The JCVI built the organism to be used as a platform to investigate the first principles of cellular life. Rather than use the cell for a basic research question, imagine that you were head of R&D at a biotech and were trying to determine if a new biochemical pathway you had developed to fix carbon from CO2 had any industrial potential. You know the method works in cell free enzymatic reactions, but that is about all you are sure of other than the enzymes and pathway. Do not get stymied by technical details involving how you would genome engineer JCVI-syn3.0. Explain the concept and experimental rationale.
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After checking in the JCVI-syn3.0 the capacity of carbon fixation from CO2. We would have a type of autotrophic organism.
Industrial applications:
Climate change industry:
An alternative to sustainably remove excessive CO2 from the Earth's atmosphere is to make it useful. But only the autonomous conversion can be an efficient and fast elimination mechanism to use, therefore organisms with these capacities would be very interesting to have them in the main cities of the world to reduce the CO2 components, a convention among the 100 main mayors worldwide could be an alternative so that they can finance part of the implementation in their cities and the improvement of the organism.
Input: JCVI-syn3.0-CO2
Intermediate: Mayor, ONGs
Output: $100 millon x year.
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Climate to live on Mars, water and biocombustibles:
The planet Mars is one of the highest CO2 (95.32%). The recent animos for colonizing Mars, mechanisms that can reduce CO2, generate food components. Recently it has been reported that there is a significant release of water from Mars, so that mechanisms to stop it would be important to develop it, the minimum synthetic cell could help to stop that flow and also convert it into water next to the conversion of CO2. Biofuels on Mars are a very economically interesting alternative, the Elon Musk industry is at the forefront.
Input: JCVI-syn3.0-CO2
Intermediate: Elon Musk, NASA
Output: New colonies of millions of dollars.
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Biocombustibles:
Es referido a los B100 o cercano. Seria necesario convertir la JCVI-syn3.0-CO2-XX con una ruta especial para algun mono-alkyl ester (biodiesel), requiere mas inversion de tiempo y dinero para lograr el objetivo.
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2. In previous classes, George Church has talked about work done in his lab to do grand scale genome engineering of E. coli to alter its genetic code. While there are similarities with how his lab engineers E. coli with how the JCVI engineers mycoplasmas, what is the fundamental difference or differences?
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The phage lambda-derived Red recombination system is a powerful tool for making targeted genetic changes in E. coli, providing a simple and versatile method for generating insertion, deletion, and point mutations on chromosomal, plasmid, or BAC targets. And to rapidly optimize a metabolic pathway coding for the production of components.
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JCVI-syn3.0 (minimal cell) is controlled by a 531–kilobase pair (kbp) synthetic genome that encodes 438 proteins and 35 annotated RNAs. The JCVI group´s approach creates genome sequence from zero in order decrease the amount of genes in the cell and reorganizer of gene order in segments.
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a. Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases.
Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM.
PLoS One. 2012;7(9):e44638. doi: 10.1371/journal.pone.0044638. Epub 2012 Sep 5.
b. Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering.
Lajoie MJ, Gregg CJ, Mosberg JA, Washington GC, Church GM.
Nucleic Acids Res. 2012 Dec;40(22):e170. doi: 10.1093/nar/gks751. Epub 2012 Aug 16.
c.Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate.
Mosberg JA, Lajoie MJ, Church GM.
Genetics. 2010 Nov;186(3):791-9. doi: 10.1534/genetics.110.120782. Epub 2010 Sep 2.
d. Design and synthesis of a minimal bacterial genome.
Hutchison CA 3rd1, Chuang RY1, Noskov VN1, Assad-Garcia N1, Deerinck TJ2, Ellisman MH2, Gill J3, Kannan K3, Karas BJ1, Ma L1, Pelletier JF4, Qi ZQ3, Richter RA1, Strychalski EA4, Sun L1, Suzuki Y1, Tsvetanova B3, Wise KS1, Smith HO5, Glass JI1, Merryman C1, Gibson DG5, Venter JC5. Science. 2016 Mar 25;351(6280):aad6253. doi: 10.1126/science.aad6253.
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3. In the Science paper “Design and synthesis of a minimal bacterial genome,” the JCVI showed the figure below, which is the first step in an effort to rationally reorganize the minimal cell genome. As noted in the paper, when we reorganized the genome, which included separating genes in operons, as needed we placed genes behind transcriptional promoters that controlled expression of genes deleted to build minimized segment 2. We built a genome that had a reorganized segment 2, but with the other 7 segments in with their original gene order. As noted in the paper, that cell grew normally.
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I think the function is not known of some genes that may be related to promoters or be involved in gene activation processes, so they could have worked correctly.
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4. After reading the 2016 JCVI paper “Design and synthesis of a minimal bacterial genome” and Harold Morowitz’s 1984 essay “The completeness of molecular biology” list a few of your thoughts about how Morowitz’s thinking affects modern thinking about minimal cells and life. What did you like or not like about the Morowitz essay?
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Probably in 1984 Morowitz could not find suitable technologies to corroborate his experiments to develop minimum cells. The JCVI group used the great experimental technical information and previous genomic studies to determine what genetic information may be important for their minimal cell experiments, something that could only have happened with basic experimental studies.
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