High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 368, Issue 1611, 2013, Pages

  Ullman, G ^a   Wallden, M ^a   Marklund, E G ^a   Mahmutovic, A ^a   Razinkov, Ivan ^b   Elf, J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Cell tracking; Gene expression; Growth; Image analysis; Microfluidics; Single molecule

Indexed keywords

AUTOMATION; CHROMOSOME; FECAL COLIFORM; GENE EXPRESSION; GENERATION TIME; IMAGE ANALYSIS; PROTEIN;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

BACTERIAL DNA; BACTERIAL PROTEIN; COTRANSPORTER; ESCHERICHIA COLI PROTEIN; GLUCOSE TRANSPORTER; LAC REPRESSOR; LACI PROTEIN, E COLI; LACY PROTEIN, E COLI; MEMBRANE PROTEIN; METHYL ACCEPTING CHEMOTAXIS PROTEINS; METHYL-ACCEPTING CHEMOTAXIS PROTEINS; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL GENE; CELL CYCLE; CELL TRACKING; CHEMISTRY; CHROMOSOME; EQUIPMENT; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SCREENING; IMAGE PROCESSING; METHODOLOGY; MICROFLUIDIC ANALYSIS; MICROFLUIDICS; PHOTOMETRY; STATISTICAL MODEL; TIME LAPSE IMAGING;

BACTERIAL PROTEINS; CELL CYCLE; CELL TRACKING; CHROMOSOMES; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; HIGH-THROUGHPUT SCREENING ASSAYS; IMAGE PROCESSING, COMPUTER-ASSISTED; LAC REPRESSORS; LIKELIHOOD FUNCTIONS; MEMBRANE PROTEINS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MICROFLUIDICS; MONOSACCHARIDE TRANSPORT PROTEINS; NEPHELOMETRY AND TURBIDIMETRY; SYMPORTERS; TIME-LAPSE IMAGING; TRANSCRIPTION FACTORS;

EID: 84871682744     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0025     Document Type: Article

References (18)

1. Elowitz MB, Levine AJ, Siggia ED, Swain PS. (2002). Stochastic gene expression in a single cell. Science 297, 1183-1186. (doi:10.1126/science. 1070919)
2. Xie XS, Choi PJ, Li GW, Lee NK, Lia G. (2008). Single-molecule approach to molecular biology in living bacterial cells. Annu. Rev. Biophys. 37, 417-444. (doi:10.1146/annurev.biophys.37. 092607.174640)
3. Yu J, Xiao J, Ren X, Lao K, Xie XS. (2006). Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600-1603. (doi:10.1126/science.1119623)
4. Nagai T, Ibata K, Park ES, Kubota M, Mikoshiba K, Miyawaki A. (2002). A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 20, 87-90. (doi:10.1038/nbt0102-87)
5. Elf J, Li GW, Xie XS. (2007). Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191-1194. (doi:10.1126/science.1141967)
6. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533-538. (doi:10.1126/science.1188308)
7. Wang P, Robert L, Pelletier J, Dang WL, Taddei F, Wright A, Jun S. (2010). Robust growth of Escherichia coli. Curr. Biol. 20, 1099-1103. (doi:10.1016/j.cub. 2010.04.045)
8. Danino T, Mondragon-Palomino O, Tsimring L, Hasty J. (2010). A synchronized quorum of genetic clocks. Nature 463, 326-330. (doi:10.1038/nature08753)
9. Young JW, Locke JCW, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB. (2012). Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat. Protoc. 7, 80-88. (doi:10.1038/nprot.2011.432)
10. Sliusarenko O, Heinritz J, Emonet T, Jacobs-Wagner C. (2011). High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatiotemporal dynamics. Mol. Microbiol. 80, 612-627. (doi:10.1111/j.1365-2958.2011.07579.x)
11. Mather W, Mondragon-Palomino O, Danino T, Hasty J, Tsimring LS. (2010). Streaming instability in growing cell populations. Phys. Rev. Lett. 104, 208101. (doi:10.1103/PhysRevLett.104.208101)
12. Datsenko KA, Wanner BL. (2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640-6645. (doi:10.1073/pnas. 120163297)
13. Choi PJ, Cai L, Frieda K, Xie XS. (2008). A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 442-446. (doi:10. 1126/science.1161427).
14. Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J. (2012). The lac repressor displays facilitated diffusion in living cells. Science 336, 1595-1598. (doi:10.1126/science.1221648)
15. Kass M, Witkin A, Terzopoulos D. (1988). Snakes: active contour models. Int. J. Comput. Vis. 1, 321-331. (doi:10.1007/bf00133570)
16. Bishop CM. (2006). Pattern recognition and machine learning. Berlin, Germany: Springer.
17. Ronneberger O, Raffel M, Kompenhans J. (1998). Advanced evaluation algorithms for standard and dual plane particle image velocimetry. Proc. 9th Int. Symp. Applications of Laser Techniques to Fluid Mechanics, Lisbon, Portugal, 13-16 July 1998, paper 10.1.
18. Moré J. (1978). The Levenberg-Marquardt algorithm: implementation and theory, chapter 10. In Numerical Analysis (ed. GA Watson), Lecture Notes in Mathematics, pp. 105-116. Berlin, Germany: Springer.