Team:UC Chile/Bactomithril

From 2012.igem.org

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== Results==
== Results==
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<big> Experiment 1 </big>
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You can see detailed informarion of our results in  [https://2012.igem.org/Team:UC_Chile/bactoresults this section]. Nevertheless, we can briefly summarize the following: we know that sfGFP expresses in our e. coli, but we don’t know if it is attached to the external side of the membrane, or if the HIV-1 protease works as expected. As this secretion system seems to be failing, we chose to try other alternatives.
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We transformed E. Coli with our GFP Reporter Plasmid (B2) and with the Protease Producer Plasmid (B3). We did a little experiment with those bacteria.
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== Future Prospects: The construction of the first spider silk biobrick ==
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The following samples were prepared:
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B2
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B2+
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B2+ & B3
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B2+ & supB3
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Nomenclature
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B2-  (coli transformed with GFP Reporter Plasmid)
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B2+ (coli transformed with GFP Reporter Plasmid, induced with Arabinose)
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B3+  (coli transformed with Protease Producer Plasmid, induced with Arabinose)
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supB3+ (supernatant of coli transformed with Protease Producer Plasmid induced with Arabinose)
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Then we observed each sample with an epifluorescence microscope. The results were promising. B2- did not express sfGFP, but B2+ did. Additionally, in both cases (B2+ & B3) and (B2+ & supB3) the fluorescence of sfGFP disappeared almost completely.
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[[File:UC_Chile_7_mayo_2012.jpg|center]]
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<big> Experiment 2 </big>
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We prepared for second time samples of B2+ & B3+ to observe in the epifluorescence microscope the effect of time in the samples.
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This time B2+ & B3+ presented much more fluorescence, and it persisted over time (at least 1 hour with no significant variation).
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[[File:UC_Chile-17_mayo_2012_-_B2_C_UV_1.jpg|center||962px]]
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<big> Experiment 3 </big>
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We did another experiment to investigate the interactions between our bacteria B2+ and B3, but this time with a serious protocol and recording the data for later analysis.
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We expected that our results were coherent with our theory. [https://static.igem.org/mediawiki/2012/3/3a/UC_Chile-Animacion-1-secrecion-1_v2(2).gif]. Both HIV protease and protease K should be able to cut the HIV cleavage site, releasing the sfGFP.
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The samples used this time were:
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B2+ :
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E. coli transformed with GFP Reporter Plasmid and induced with Arabinose
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B2+ / SN B3+ :
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E. coli transformed with GFP Reporter Plasmid and induced with Arabinose, and Supernatant of coli transformed with Protease Producer Plasmid induced with Arabinose
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B2+ / SN B3- :
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E. coli transformed with GFP Reporter Plasmid and induced with Arabinose, and Supernatant of coli transformed with Protease Producer Plasmid not induced with Arabinose
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B2+ / protease K :
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E. coli transformed with GFP Reporter Plasmid and induced with Arabinose, and protease K.
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Subsequently we proceeded to observe the samples in an epifluorescence microscope. In the following figure you can see one micrograph of each sample at 100x.
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[[File:UC_Chile2012-13_junio_bryon_2012.jpg|center]]
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Additionally, we analyzed 4 micrographs of each sample (n=4) with the software ImageJ to compare their fluorescence intensity.
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[[File:UC_Chile-Resultados_micrografias_Bryon2.png|center]]
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All the different treatments presented significant differences, except (B2+ & protease K) and (B2+). Remarkable is the difference between (B2+ / SN B3+) and (B2+ / NS B3-). Also, the direct application of protease K over the samples decreased even more the fluorescence. However, the low fluorescence of B2+ is very weird. We will have to repeat this experiment, but at least the major part of the results makes is what we expected.
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<big> Experiment 4 </big>
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We repeated the experiment to investigate the interactions between our bacteria B2+ and B3+ with a serious protocol and recording the data for later analysis. This time we added the control B2-.
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In the following figure you can see one micrograph of each sample at 100x obtained from a fluorescence microscope.
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[[File:UC_Chile15_junio_max_2012_UV%2C_light%2C_superpuestas%2C_4xlow.jpg|center|962px]]
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In the figure each row represents one sample. The first row contains the micragraphs with UV filter. The second row  contains the micrographs seen with light. The third row contains the previous micragraphs overlayed (the light image is in grayscale, and the UV image has its black background removed). The forth image is an amplification of the third image (1:4 ratio). Click over the image to open it in a higher resolution.
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Additionally, we analyzed 4 UV micrographs of each sample (n=4) with the software ImageJ
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[[File:UC_Chile-15_junio_max_2012_UV,_light,_superpuestas,_4xlow.jpg|center|962px]]
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The results were quite different compared to the ones of our previous experiment. Remarkable is that, as expected, B2- and B2+ present the lowest and highest fluorescence intensity. Additionally, (B2+ & B3+) and (B2+ & Protease K) present very similar fluorescence. However, for second time we obtained a weird result: (B2+ & B3+) and (B2+ & B3-) present the same amount of fluorescence.
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In conclusion, we know that sfGFP expresses in our e. coli. But we don’t know if it is attached to the external side of the membrane, or if the HIV-1 protease works as expected. As this secretion system seems to be failing, we chose to try other alternatives.
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== The construction of the first spider silk biobrick ==
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We tried with a lot of patience (in SEVERAL attempts with many different strategies) to make a biobrick with the spider silk monomer ADF-3 or the sequence of DNA corresponding to ADF-3 and tags necessary to identify and export the protein with the Type 3 Secretion System of Salmonella (SPI 2). The original sequences are described in  
We tried with a lot of patience (in SEVERAL attempts with many different strategies) to make a biobrick with the spider silk monomer ADF-3 or the sequence of DNA corresponding to ADF-3 and tags necessary to identify and export the protein with the Type 3 Secretion System of Salmonella (SPI 2). The original sequences are described in  

Latest revision as of 23:50, 23 October 2012

Project: Luxilla - Pontificia Universidad Católica de Chile, iGEM 2012