Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria

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References

  1. Zhang, J., Campbell, R. E., Ting, A. Y. & Tsien, R. Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906–918 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  2. Yagi, K. Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl. Microbiol. Biotechnol. 73, 1251–1258 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  3. Rodrigo-Navarro, A., Sankaran, S., Dalby, M. J., del Campo, A. & Salmeron-Sanchez, M. Engineered living biomaterials. Nat. Rev. Mater. 6, 1175–1190 (2021).

    Article 

    Google Scholar
     

  4. Kang, J. H. & Chung, J.-K. Molecular-genetic imaging based on reporter gene expression. J. Nucl. Med. 49, 164S–179S (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  5. Ghim, C. M., Lee, S. K., Takayama, S. & Mitchell, R. J. The art of reporter proteins in science: past, present and future applications. BMB Rep. 43, 451–460 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  6. Hall, C. V., Jacob, P. E., Ringold, G. M. & Lee, F. Expression and regulation of Escherichia coli lacZ gene fusions in mammalian cells. J. Mol. Appl. Genet. 2, 101–109 (1983).

    CAS 
    PubMed 

    Google Scholar
     

  7. Nielsen, D. A., Chou, J., MacKrell, A. J., Casadaban, M. J. & Steiner, D. F. Expression of a preproinsulin-β-galactosidase gene fusion in mammalian cells. Proc. Natl Acad. Sci. USA 80, 5198–5202 (1983).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  8. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W. & Prasher, D. C. Green fluorescent protein as a marker for gene expression. Science 263, 802–805 (1994).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  9. Shepherd, E. S., DeLoache, W. C., Pruss, K. M., Whitaker, W. R. & Sonnenburg, J. L. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature 557, 434–438 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  10. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  11. Geddes, B. A. et al. Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nat. Commun. 10, 3430 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  12. Heidecker, G. & Müller-Hill, B. Synthetic multifunctional proteins. Mol. Gen. Genet. 155, 301–307 (1977).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  13. Sharma, S. K., Poudel Sharma, S. & Leblanc, R. M. Methods of detection of β-galactosidase enzyme in living cells. Enzyme Microb. Technol. 150, 109885 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  14. Miller, J. H. Experiments in Molecular Genetics (Cold Spring Habour Laboratory, 1972).

  15. Hui, C.-y et al. Genetic control of violacein biosynthesis to enable a pigment-based whole-cell lead biosensor. RSC Adv. 10, 28106–28113 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  16. Hui, C.-y, Guo, Y., Li, H., Gao, C.-x & Yi, J. Detection of environmental pollutant cadmium in water using a visual bacterial biosensor. Sci. Rep. 12, 6898 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  17. Hui, C.-y et al. Indigoidine biosynthesis triggered by the heavy metal-responsive transcription regulator: a visual whole-cell biosensor. Appl. Microbiol. Biotechnol. 105, 6087–6102 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  18. Yoshida, K. et al. Novel carotenoid-based biosensor for simple visual detection of arsenite: characterization and preliminary evaluation for environmental application. Appl. Environ. Microbiol. 74, 6730–6738 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  19. Hui, C.-y et al. Metabolic engineering of the carotenoid biosynthetic pathway toward a specific and sensitive inorganic mercury biosensor. RSC Adv. 12, 36142–36148 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  20. He, Y., Zhang, T., Sun, H., Zhan, H. & Zhao, Y. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic. Res. 7, 152 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  21. Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–350 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  22. Sandell, J. L. & Zhu, T. C. A review of in-vivo optical properties of human tissues and its impact on PDT. J. Biophotonics 4, 773–787 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  23. McKinnon, K. M. Flow cytometry: an overview. Curr. Protoc. Immunol. 120, 5.1.1–5.1.11 (2018).

    Article 
    PubMed 

    Google Scholar
     

  24. Dietrich, J. A., McKee, A. E. & Keasling, J. D. High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu. Rev. Biochem. 79, 563–590 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  25. Prabowo, C. P. S. et al. Production of natural colorants by metabolically engineered microorganisms. Trends Chem. 4, 608–626 (2022).

  26. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H. & Miyawaki, A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl Acad. Sci. USA 99, 12651–12656 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  27. Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567–1572 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  28. Shcherbakova, D. M. & Verkhusha, V. V. Near-infrared fluorescent proteins for multicolor in vivo imaging. Nat. Methods 10, 751–754 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  29. Drepper, T. et al. Reporter proteins for in vivo fluorescence without oxygen. Nat. Biotechnol. 25, 443–445 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  30. Belkin, S. et al. Remote detection of buried landmines using a bacterial sensor. Nat. Biotechnol. 35, 308–310 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  31. Rigoulot, S. B. et al. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. Plant Biotechnol. J. 19, 830–843 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  32. Shcherbakova, D. M., Stepanenko, O. V., Turoverov, K. K. & Verkhusha, V. V. Near-infrared fluorescent proteins: multiplexing and optogenetics across scales. Trends Biotechnol. 36, 1230–1243 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  33. Liu, P., Mu, X., Zhang, X.-D. & Ming, D. The near-infrared-II fluorophores and advanced microscopy technologies development and application in bioimaging. Bioconjug. Chem. 31, 260–275 (2019).

    Article 
    PubMed 

    Google Scholar
     

  34. Shu, X. et al. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 324, 804–807 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  35. Piatkevich, K. D. et al. Near-infrared fluorescent proteins engineered from bacterial phytochromes in neuroimaging. Biophys. J. 113, 2299–2309 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  36. Rodriguez, E. A. et al. A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein. Nat. Methods 13, 763–769 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  37. Ow, D. W. et al. Transient and stable expression of the firefly luciferase gene in plant cells and transgenic plants. Science 234, 856–859 (1986).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  38. Millar, A. J., Short, S. R., Chua, N. H. & Kay, S. A. A novel circadian phenotype based on firefly luciferase expression in transgenic plants. Plant Cell 4, 1075–1087 (1992).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  39. Liu, Y., Golden, S. S., Kondo, T., Ishiura, M. & Johnson, C. H. Bacterial luciferase as a reporter of circadian gene expression in cyanobacteria. J. Bacteriol. 177, 2080–2086 (1995).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  40. McElroy, W. D. The energy source for bioluminescence in an isolated system. Proc. Natl Acad. Sci. USA 33, 342–345 (1947).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  41. Love, A. C. & Prescher, J. A. Seeing (and using) the light: recent developments in bioluminescence technology. Cell Chem. Biol. 27, 904–920 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  42. Cheng, H.-Y., Masiello, C. A., Bennett, G. N. & Silberg, J. J. Volatile gas production by methyl halide transferase: an in situ reporter of microbial gene expression in soil. Environ. Sci. Technol. 50, 8750–8759 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  43. Cheng, H.-Y. et al. Ratiometric gas reporting: a nondisruptive approach to monitor gene expression in soils. ACS Synth. Biol. 7, 903–911 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  44. Shu, X. et al. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 9, e1001041 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  45. Shapiro, M. G. et al. Biogenic gas nanostructures as ultrasonic molecular reporters. Nat. Nanotechnol. 9, 311–316 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  46. Farhadi, A., Ho, G. H., Sawyer, D. P., Bourdeau, R. W. & Shapiro, M. G. Ultrasound imaging of gene expression in mammalian cells. Science 365, 1469–1475 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  47. Wang, L. V. & Yao, J. A practical guide to photoacoustic tomography in the life sciences. Nat. Methods 13, 627–638 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  48. Genove, G., DeMarco, U., Xu, H., Goins, W. F. & Ahrens, E. T. A new transgene reporter for in vivo magnetic resonance imaging. Nat. Med. 11, 450–454 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  49. Luker, G. D. et al. Noninvasive imaging of protein–protein interactions in living animals. Proc. Natl Acad. Sci. USA 99, 6961–6966 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  50. Daeffler, K. N. M. et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol. Syst. Biol. 13, 923 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  51. Del Valle, I. et al. Translating new synthetic biology advances for biosensing into the earth and environmental sciences. Front. Microbiol. 11, 618373 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  52. McNerney, M. P., Doiron, K. E., Ng, T. L., Chang, T. Z. & Silver, P. A. Theranostic cells: emerging clinical applications of synthetic biology. Nat. Rev. Genet. 22, 730–746 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  53. Voigt, C. A. Genetic parts to program bacteria. Curr. Opin. Biotechnol. 17, 548–557 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  54. Lazar, J. T. & Tabor, J. J. Bacterial two-component systems as sensors for synthetic biology applications. Curr. Opin. Syst. Biol. 28, 100398 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  55. Nielsen, A. A. et al. Genetic circuit design automation. Science 352, aac7341 (2016).

    Article 
    PubMed 

    Google Scholar
     

  56. Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Escherichia coli ‘Marionette’ strains with 12 highly optimized small-molecule sensors. Nat. Chem. Biol. 15, 196–204 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  57. Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl Acad. Sci. USA 101, 6355–6360 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  58. Wilke, C. Remote sensing for crops spots pests and pathogens. ACS Cent. Sci. 9, 339–342 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  59. do Prado Ribeiro, L. et al. Hyperspectral imaging to characterize plant–plant communication in response to insect herbivory. Plant Methods 14, 54 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  60. Stuart, M. B., McGonigle, A. J. & Willmott, J. R. Hyperspectral imaging in environmental monitoring: a review of recent developments and technological advances in compact field deployable systems. Sensors 19, 3071 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  61. Silva, C. S. et al. Near infrared hyperspectral imaging for forensic analysis of document forgery. Analyst 139, 5176–5184 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  62. Chen, H.-W., McGurr, M. & Brickhouse, M. in Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XXI (eds Velez-Reyes, M. & Kruse, F. A.) 947202 (SPIE, 2015).

  63. Mahlein, A.-K., Kuska, M. T., Behmann, J., Polder, G. & Walter, A. Hyperspectral sensors and imaging technologies in phytopathology: state of the art. Annu. Rev. Phytopathol. 56, 535–558 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  64. Leblanc, G., Kalacska, M. & Soffer, R. Detection of single graves by airborne hyperspectral imaging. Forensic Sci. Int. 245, 17–23 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  65. Briechle, S., Molitor, N., Krzystek, P. & Vosselman, G. Detection of radioactive waste sites in the Chornobyl exclusion zone using UAV-based lidar data and multispectral imagery. ISPRS J. Photogramm. Remote Sens. 167, 345–362 (2020).

    Article 

    Google Scholar
     

  66. Lang, M., Stelzer, M. & Schomburg, D. BKM-react, an integrated biochemical reaction database. BMC Biochem. 12, 42 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  67. Bansal, P. et al. Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 50, D693–D700 (2021).

    Article 
    PubMed Central 

    Google Scholar
     

  68. Karp, P. D. et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief. Bioinform. 20, 1085–1093 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  69. Taniguchi, M. & Lindsey, J. S. Database of absorption and fluorescence spectra of >300 common compounds for use in PhotoChemCAD. Photochem. Photobiol. 94, 290–327 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  70. Noelle, A. et al. UV/Vis+ photochemistry database: structure, content and applications. J. Quant. Spectrosc. Radiat. Transf. 253, 107056 (2020).

    Article 
    CAS 

    Google Scholar
     

  71. Vokáčová, Z. & Burda, J. V. Computational study on spectral properties of the selected pigments from various photosystems: structure–transition energy relationship. J. Phys. Chem. A 111, 5864–5878 (2007).

    Article 
    PubMed 

    Google Scholar
     

  72. Phan, K., De Meester, S., Raes, K., De Clerck, K. & Van Speybroeck, V. A comparative study on the photophysical properties of anthocyanins and pyranoanthocyanins. Chemistry 27, 5956–5971 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  73. Jacquemin, D., Perpète, E. A., Ciofini, I. & Adamo, C. Accurate simulation of optical properties in dyes. Acc. Chem. Res. 42, 326–334 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  74. Charaf-Eddin, A., Planchat, A., Mennucci, B., Adamo, C. & Jacquemin, D. Choosing a functional for computing absorption and fluorescence band shapes with TD-DFT. J. Chem. Theory Comput. 9, 2749–2760 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  75. Conradie, J., Wamser, C. C. & Ghosh, A. Understanding hyperporphyrin spectra: TDDFT calculations on diprotonated tetrakis(p-aminophenyl)porphyrin. J. Phys. Chem. A 125, 9953–9961 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  76. Jacquemin, D., Wathelet, V., Perpète, E. A. & Adamo, C. Extensive TD-DFT benchmark: singlet-excited states of organic molecules. J. Chem. Theory Comput. 5, 2420–2435 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  77. Gritsenko, O. & Baerends, E. J. Asymptotic correction of the exchange–correlation kernel of time-dependent density functional theory for long-range charge-transfer excitations. J. Chem. Phys. 121, 655–660 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  78. Laurent, A. D. & Jacquemin, D. TD-DFT benchmarks: a review. Int. J. Quant. Chem. 113, 2019–2039 (2013).

    Article 
    CAS 

    Google Scholar
     

  79. Duan, C., Nandy, A., Meyer, R., Arunachalam, N. & Kulik, H. J. A transferable recommender approach for selecting the best density functional approximations in chemical discovery. Nat. Comput. Sci. 3, 38–47 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  80. Shao, Y., Mei, Y., Sundholm, D. & Kaila, V. R. I. Benchmarking the performance of time-dependent density functional theory methods on biochromophores. J. Chem. Theory Comput. 16, 587–600 (2020).

    Article 
    PubMed 

    Google Scholar
     

  81. Weimer, A., Kohlstedt, M., Volke, D. C., Nikel, P. I. & Wittmann, C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl. Microbiol. Biotechnol. 104, 7745–7766 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  82. Steunou, A.-S., Astier, C. & Ouchane, S. Regulation of photosynthesis genes in Rubrivivax gelatinosus: transcription factor PpsR is involved in both negative and positive control. J. Bacteriol. 186, 3133–3142 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  83. Lachaud, F. et al. Ground and excited state properties of new porphyrin based dyads: a combined theoretical and experimental study. J. Phys. Chem. A 116, 10736–10744 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  84. Kantorovich, L. V. Mathematical methods of organizing and planning production. Manag. Sci. 6, 366–422 (1960).

    Article 

    Google Scholar
     

  85. Ramdas, A., García Trillos, N. & Cuturi, M. On Wasserstein two-sample testing and related families of nonparametric tests. Entropy 19, 47 (2017).

    Article 

    Google Scholar
     

  86. Kotlobay, A. A. et al. Genetically encodable bioluminescent system from fungi. Proc. Natl Acad. Sci. USA 115, 12728–12732 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  87. Gallo, G., Longo, G., Pallottino, S. & Nguyen, S. Directed hypergraphs and applications. Discret. Appl. Math. 42, 177–201 (1993).

    Article 

    Google Scholar
     

  88. Chen, G. E. et al. Complete enzyme set for chlorophyll biosynthesis in Escherichia coli. Sci. Adv. 4, eaaq1407 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  89. Bioucas-Dias, J. M. et al. Hyperspectral unmixing overview: geometrical, statistical, and sparse regression-based approaches. IEEE J. Sel. Top. Appl. Earth Obs. Remote Sens. 5, 354–379 (2012).

    Article 

    Google Scholar
     

  90. Xu, L., Li, J., Wong, A. & Peng, J. K-P-Means: a clustering algorithm of K ‘purified’ means for hyperspectral endmember estimation. IEEE Geosci. Remote Sens. Lett. 11, 1787–1791 (2014).

    Article 

    Google Scholar
     

  91. Prades, J., Safont, G., Salazar, A. & Vergara, L. Estimation of the number of endmembers in hyperspectral images using agglomerative clustering. Remote Sensing 12, 3585 (2020).

    Article 

    Google Scholar
     

  92. Wegele, R., Tasler, R., Zeng, Y., Rivera, M. & Frankenberg-Dinkel, N. The heme oxygenase (s)-phytochrome system of Pseudomonas aeruginosa. J. Biol. Chem. 279, 45791–45802 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  93. Maiti, A. et al. Structural and photophysical characterization of the small ultra-red fluorescent protein. Nat. Commun. 14, 4155 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  94. Boo, A. et al. Synthetic microbe-to-plant communication channels. Nat. Commun. 15, 1817 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  95. Chen, G. E. & Hunter, C. N. Engineering chlorophyll, bacteriochlorophyll, and carotenoid biosynthetic pathways in Escherichia coli. ACS Synth. Biol. 12, 2236–2244 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  96. Saga, Y. et al. Selective oxidation of B800 bacteriochlorophyll a in photosynthetic light-harvesting protein LH2. Sci. Rep. 9, 3636 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  97. Becker, M., Nagarajan, V. & Parson, W. W. Properties of the excited singlet states of bacteriochlorophyll a and bacteriopheophytin a in polar solvents. J. Am. Chem. Soc. 113, 6840–6848 (1991).

    Article 
    CAS 

    Google Scholar
     

  98. Yokobayashi, Y., Weiss, R. & Arnold, F. H. Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  99. Tabor, J. J., Levskaya, A. & Voigt, C. A. Multichromatic control of gene expression in Escherichia coli. J. Mol. Biol. 405, 315–324 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  100. Fernandez-Rodriguez, J., Moser, F., Song, M. & Voigt, C. A. Engineering RGB color vision into Escherichia coli. Nat. Chem. Biol. 13, 706–708 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  101. Bradley, A. P. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognit. 30, 1145–1159 (1997).

    Article 

    Google Scholar
     

  102. Gouterman, M. Study of the effects of substitution on the absorption spectra of porphin. J. Chem. Phys. 30, 1139–1161 (1959).

    Article 
    CAS 

    Google Scholar
     

  103. Taniguchi, M., Bocian, D. F., Holten, D. & Lindsey, J. S. Beyond green with synthetic chlorophylls—connecting structural features with spectral properties. J. Photoch. Photobio. C 52, 100513 (2022).

    Article 
    CAS 

    Google Scholar
     

  104. Gouterman, M. Spectra of porphyrins. J. Mol. Spectrosc. 6, 138–163 (1961).

    Article 
    CAS 

    Google Scholar
     

  105. Taniguchi, M. & Lindsey, J. S. Absorption and fluorescence spectral database of chlorophylls and analogues. Photochem. Photobiol. 97, 136–165 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  106. Lakomy, I. et al. C45– and C50-carotenoids. Part 8. Synthesis of (all-E,2S,2′S)-bacterioruberin, (all-E,2S,2′S)-monoanhydrobacterioruberin, (all-E,2S,2′S)-bisanhydrobacterioruberin, (all-E,2R,2′R)-3,4,3′,4′-tetrahydrobisanhydrobacterioruberin, and (all-E,S)-2-isopentenyl-3,4-dehydrorhodopin. Helvetica 80, 472–486 (2010).

  107. Levin, I., Liu, M., Voigt, C. A. & Coley, C. W. Merging enzymatic and synthetic chemistry with computational synthesis planning. Nat. Commun. 13, 7747 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  108. Sankaranarayanan, K. et al. Similarity based enzymatic retrosynthesis. Chem. Sci. 13, 6039–6053 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  109. Probst, D. et al. Biocatalysed synthesis planning using data-driven learning. Nat. Commun. 13, 964 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  110. Koch, M., Duigou, T. & Faulon, J.-L. Reinforcement learning for bioretrosynthesis. ACS Synth. Biol. 9, 157–168 (2019).

    Article 
    PubMed 

    Google Scholar
     

  111. Lin, G.-M., Warden-Rothman, R. & Voigt, C. A. Retrosynthetic design of metabolic pathways to chemicals not found in nature. Curr. Opin. Syst. Biol. 14, 82–107 (2019).

    Article 

    Google Scholar
     

  112. Koscher, B. A. et al. Autonomous, multiproperty-driven molecular discovery: from predictions to measurements and back. Science 382, eadi1407 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  113. Gómez-Bombarelli, R. et al. Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach. Nat. Mater. 15, 1120–1127 (2016).

    Article 
    PubMed 

    Google Scholar
     

  114. Chemla, Y., Sweeney, C. J., Wozniak, C. A. & Voigt, C. A. Design and regulation of engineered bacteria for environmental release. Nat. Microbiol. 10, 281–300 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  115. Bloch, S. E. et al. Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph. J. Exp. Bot. 71, 4591–4603 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  116. Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988).

    Article 
    CAS 

    Google Scholar
     

  117. Riniker, S. & Landrum, G. A. Better informed distance geometry: using what we know to improve conformation generation. J. Chem. Inf. Model. 55, 2562–2574 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  118. Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 17, 490–519 (1996).

    CAS 

    Google Scholar
     

  119. Bannwarth, C., Ehlert, S. & Grimme, S. GFN2-xTB—an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions. J. Chem. Theory Comput. 15, 1652–1671 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  120. Cossi, M. & Barone, V. Time-dependent density functional theory for molecules in liquid solutions. J. Chem. Phys. 115, 4708–4717 (2001).

    Article 
    CAS 

    Google Scholar
     

  121. Chemla, Y. et al. Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions. PLoS ONE 17, e0278471 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  122. Johnson, S. C. Hierarchical clustering schemes. Psychometrika 32, 241–254 (1967).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  123. Jiang, J., Liu, D., Gu, J. & Süsstrunk, S. What is the space of spectral sensitivity functions for digital color cameras? In Proc. 2013 IEEE Workshop on Applications of Computer Vision (WACV) 168–179 (IEEE, 2013).

  124. Chemla, Y. Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria. Zenodo https://doi.org/10.5281/zenodo.14756888 (2025).

  125. Levin, I. et al. VoigtLab/bioHSI: v.1.0.0. Zenodo https://doi.org/10.5281/zenodo.14827800 (2025).

  126. Levin, I. et al. VoigtLab/npspec-webapp: v1.0.0. Zenodo https://zenodo.org/records/14827805 (2025).

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