Team:ETH Zurich/Decoder

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== Principle ==
== Principle ==
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Our decoder aims to distinguish between the most common indoor and outdoor lightsources. These include for example sunlight (with UV), outdoor shade, room light and darkness. All of them have a unique footprint of both intensity and the ratio of blue to red light. This might facilitate the reliable detection of UV by combining only two outputs.  
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Our decoder aims to distinguish between the most common indoor and outdoor lightsources. These include for example sunlight (with UV), outdoor shade, room light and darkness. All of them have a unique footprint of both intensity and the ratio of blue to red light. This might facilitate the reliable detection of sunlight with UV by combining only two inputs, the light receptors [[Team:ETH_Zurich/LovTAP|LovTAP]] and [[Team:ETH_Zurich/Cph8|Cph8]].  
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| 0 || 1 || 1 || 0 || Green Pigment
| 0 || 1 || 1 || 0 || Green Pigment
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| 1 || 1 || 0 || 0 || pABA and Violet Pigment
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| 1 || 1 || 0 || 0 || PABA and Violet Pigment
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* ''pABA and Violet'' = '''NOR'''(''LacI'', ''TetR'') = '''NOT'''(''LacI'') '''AND NOT'''(''TetR'') = ''Blue'' '''AND''' ''Red''
* ''pABA and Violet'' = '''NOR'''(''LacI'', ''TetR'') = '''NOT'''(''LacI'') '''AND NOT'''(''TetR'') = ''Blue'' '''AND''' ''Red''
** Note that simultaneously to the production of pABA and the violet pigment also cI, a third repressor, is produced. cI is integrated in the other gates.  
** Note that simultaneously to the production of pABA and the violet pigment also cI, a third repressor, is produced. cI is integrated in the other gates.  
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* ''Red pigment'' = '''NOT'''(''pABA and Violet'') '''AND NOT'''(''TetR'') = '''NOR'''(''cI'', ''TetR'') = '''NOT'''(''cI'') '''AND NOT'''(''TetR'') = ''LacI'' '''AND NOT'''(''TetR'') = '''NOT'''(''Blue'') '''AND''' ''Red''
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* ''Red pigment'' = '''NOT'''(''PABA and Violet'') '''AND NOT'''(''TetR'') = '''NOR'''(''cI'', ''TetR'') = '''NOT'''(''cI'') '''AND NOT'''(''TetR'') = ''LacI'' '''AND NOT'''(''TetR'') = '''NOT'''(''Blue'') '''AND''' ''Red''
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* ''Green pigment'' = '''NOT'''(''pABA and Violet'') '''AND NOT'''(''LacI'') = '''NOR'''(''cI'', ''LacI'') = '''NOT'''(''cI'') '''AND NOT'''(''LacI'') = '''NOT'''(''LacI'') '''AND''' ''TetR'' = ''Blue'' '''AND NOT'''(''Red'')
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* ''Green pigment'' = '''NOT'''(''PABA and Violet'') '''AND NOT'''(''LacI'') = '''NOR'''(''cI'', ''LacI'') = '''NOT'''(''cI'') '''AND NOT'''(''LacI'') = '''NOT'''(''LacI'') '''AND''' ''TetR'' = ''Blue'' '''AND NOT'''(''Red'')
A detailed overview of the logic gates can be found [http://en.wikipedia.org/wiki/Logic_gate#Symbols here].
A detailed overview of the logic gates can be found [http://en.wikipedia.org/wiki/Logic_gate#Symbols here].
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By using the NOR-gate our decoder can be represented as follows:
By using the NOR-gate our decoder can be represented as follows:
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[[File:Design.jpg|frameless|700px|center|thumb|Figure: Boolean logic of Decoder.  ]]
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[[File:Design.jpg|frameless|700px|center|thumb|Figure 1: Boolean logic of Decoder.  ]]
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Latest revision as of 19:43, 26 October 2012

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Navigate through Overview, Design and Results
Schirm.png

Principle

Our decoder aims to distinguish between the most common indoor and outdoor lightsources. These include for example sunlight (with UV), outdoor shade, room light and darkness. All of them have a unique footprint of both intensity and the ratio of blue to red light. This might facilitate the reliable detection of sunlight with UV by combining only two inputs, the light receptors LovTAP and Cph8.


Boolean logic

The input (red and blue light) is converted into TetR and LacI using a NOT-gate. The truth table demonstrate our aim of the decoder.

Truth table of our Decoder
Red Light Blue Light TetR LacI Output
0 0 1 1 No Output
1 0 0 1 Red Pigment
0 1 1 0 Green Pigment
1 1 0 0 PABA and Violet Pigment

This can be simplified to the following logics:

  • pABA and Violet = NOR(LacI, TetR) = NOT(LacI) AND NOT(TetR) = Blue AND Red
    • Note that simultaneously to the production of pABA and the violet pigment also cI, a third repressor, is produced. cI is integrated in the other gates.
  • Red pigment = NOT(PABA and Violet) AND NOT(TetR) = NOR(cI, TetR) = NOT(cI) AND NOT(TetR) = LacI AND NOT(TetR) = NOT(Blue) AND Red
  • Green pigment = NOT(PABA and Violet) AND NOT(LacI) = NOR(cI, LacI) = NOT(cI) AND NOT(LacI) = NOT(LacI) AND TetR = Blue AND NOT(Red)

A detailed overview of the logic gates can be found [http://en.wikipedia.org/wiki/Logic_gate#Symbols here].


By using the NOR-gate our decoder can be represented as follows:

Figure 1: Boolean logic of Decoder.



References

  • Brown, B. a, Headland, L. R., & Jenkins, G. I. (2009). UV-B action spectrum for UVR8-mediated HY5 transcript accumulation in Arabidopsis. Photochemistry and photobiology, 85(5), 1147–55.
  • Christie, J. M., Salomon, M., Nozue, K., Wada, M., & Briggs, W. R. (1999): LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proceedings of the National Academy of Sciences of the United States of America, 96(15), 8779–83.
  • Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O’Hara, A., Kelly, S. M., et al. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science (New York, N.Y.), 335(6075), 1492–6.
  • Cloix, C., & Jenkins, G. I. (2008). Interaction of the Arabidopsis UV-B-specific signaling component UVR8 with chromatin. Molecular plant, 1(1), 118–28.
  • Cox, R. S., Surette, M. G., & Elowitz, M. B. (2007). Programming gene expression with combinatorial promoters. Molecular systems biology, 3(145), 145. doi:10.1038/msb4100187
  • Drepper, T., Eggert, T., Circolone, F., Heck, A., Krauss, U., Guterl, J.-K., Wendorff, M., et al. (2007). Reporter proteins for in vivo fluorescence without oxygen. Nature biotechnology, 25(4), 443–5
  • Drepper, T., Krauss, U., & Berstenhorst, S. M. zu. (2011). Lights on and action! Controlling microbial gene expression by light. Applied microbiology, 23–40.
  • EuropeanCommission (2006). SCIENTIFIC COMMITTEE ON CONSUMER PRODUCTS SCCP Opinion on Biological effects of ultraviolet radiation relevant to health with particular reference to sunbeds for cosmetic purposes.
  • Elvidge, C. D., Keith, D. M., Tuttle, B. T., & Baugh, K. E. (2010). Spectral identification of lighting type and character. Sensors (Basel, Switzerland), 10(4), 3961–88.
  • GarciaOjalvo, J., Elowitz, M. B., & Strogatz, S. H. (2004). Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proceedings of the National Academy of Sciences of the United States of America, 101(30), 10955–60.
  • Gao Q, Garcia-Pichel F. (2011). Microbial ultraviolet sunscreens. Nat Rev Microbiol. 9(11):791-802.
  • Goosen N, Moolenaar GF. (2008) Repair of UV damage in bacteria. DNA Repair (Amst).7(3):353-79.
  • Heijde, M., & Ulm, R. (2012). UV-B photoreceptor-mediated signalling in plants. Trends in plant science, 17(4), 230–7.
  • Hirose, Y., Narikawa, R., Katayama, M., & Ikeuchi, M. (2010). Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8854–9.
  • Hirose, Y., Shimada, T., Narikawa, R., Katayama, M., & Ikeuchi, M. (2008). Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9528–33.
  • Kast, Asif-Ullah & Hilvert (1996) Tetrahedron Lett. 37, 2691 - 2694., Kast, Asif-Ullah, Jiang & Hilvert (1996) Proc. Natl. Acad. Sci. USA 93, 5043 - 5048
  • Kiefer, J., Ebel, N., Schlücker, E., & Leipertz, A. (2010). Characterization of Escherichia coli suspensions using UV/Vis/NIR absorption spectroscopy. Analytical Methods, 9660. doi:10.1039/b9ay00185a
  • Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes using synthetic promoter shuffling. PloS one, 3(4), e2030.
  • Krebs in Deutschland 2005/2006. Häufigkeiten und Trends. 7. Auflage, 2010, Robert Koch-Institut (Hrsg) und die Gesellschaft der epidemiologischen Krebsregister in Deutschland e. V. (Hrsg). Berlin.
  • Lamparter, T., Michael, N., Mittmann, F., & Esteban, B. (2002). Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11628–33.
  • Levskaya, A. et al (2005). Engineering Escherichia coli to see light. Nature, 438(7067), 442.
  • Mancinelli, A. (1986). Comparison of spectral properties of phytochromes from different preparations. Plant physiology, 82(4), 956–61.
  • Nakasone, Y., Ono, T., Ishii, A., Masuda, S., & Terazima, M. (2007). Transient dimerization and conformational change of a BLUF protein: YcgF. Journal of the American Chemical Society, 129(22), 7028–35.
  • Orth, P., & Schnappinger, D. (2000). Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nature structural biology, 215–219.
  • Parkin, D.M., et al., Global cancer statistics, 2002. CA: a cancer journal for clinicians, 2005. 55(2): p. 74-108.
  • Rajagopal, S., Key, J. M., Purcell, E. B., Boerema, D. J., & Moffat, K. (2004). Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli. Photochemistry and photobiology, 80(3), 542–7.
  • Rizzini, L., Favory, J.-J., Cloix, C., Faggionato, D., O’Hara, A., Kaiserli, E., Baumeister, R., et al. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science (New York, N.Y.), 332(6025), 103–6.
  • Roux, B., & Walsh, C. T. (1992). p-aminobenzoate synthesis in Escherichia coli: kinetic and mechanistic characterization of the amidotransferase PabA. Biochemistry, 31(30), 6904–10.
  • Strickland, D. (2008). Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10709–10714.
  • Sinha RP, Häder DP. UV-induced DNA damage and repair: a review. Photochem Photobiol Sci. (2002). 1(4):225-36
  • Sambandan DR, Ratner D. (2011). Sunscreens: an overview and update. J Am Acad Dermatol. 2011 Apr;64(4):748-58.
  • Tabor, J. J., Levskaya, A., & Voigt, C. A. (2011). Multichromatic Control of Gene Expression in Escherichia coli. Journal of Molecular Biology, 405(2), 315–324.
  • Thibodeaux, G., & Cowmeadow, R. (2009). A tetracycline repressor-based mammalian two-hybrid system to detect protein–protein interactions in vivo. Analytical biochemistry, 386(1), 129–131.
  • Tschowri, N., & Busse, S. (2009). The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes & development, 522–534.
  • Tschowri, N., Lindenberg, S., & Hengge, R. (2012). Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli. Molecular microbiology.
  • Tyagi, A. (2009). Photodynamics of a flavin based blue-light regulated phosphodiesterase protein and its photoreceptor BLUF domain.
  • Vainio, H. & Bianchini, F. (2001). IARC Handbooks of Cancer Prevention: Volume 5: Sunscreens. Oxford University Press, USA
  • Quinlivan, Eoin P & Roje, Sanja & Basset, Gilles & Shachar-Hill, Yair & Gregory, Jesse F & Hanson, Andrew D. (2003). The folate precursor p-aminobenzoate is reversibly converted to its glucose ester in the plant cytosol. The Journal of biological chemistry, 278.
  • van Thor, J. J., Borucki, B., Crielaard, W., Otto, H., Lamparter, T., Hughes, J., Hellingwerf, K. J., et al. (2001). Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1. Biochemistry, 40(38), 11460–71.
  • Wegkamp A, van Oorschot W, de Vos WM, Smid EJ. (2007 )Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol. Apr;73(8):2673-81.
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