When phase contrast fails: ChainTracer and NucTracer, two ImageJ methods for semi-automated single cell analysis using membrane or DNA staining

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Syvertsson, Simon ^a   Vischer, Norbert O E ^b   Gao, Yongqiang ^b   Hamoen, Leendert W ^a,b  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; DNA; GREEN FLUORESCENT PROTEIN;

ANALYTIC METHOD; ARTICLE; AUTOANALYSIS; BACILLUS SUBTILIS; BACTERIAL CELL; CELL MEMBRANE; CELL SIZE; CHAINTRACER; IMAGE CYTOMETRY; INTERMETHOD COMPARISON; LACTOCOCCUS LACTIS; MEASUREMENT ACCURACY; NONHUMAN; NUCTRACER; PHASE CONTRAST MICROSCOPY; PROTEIN EXPRESSION; SINGLE CELL ANALYSIS; STAINING; AUTOMATION; FLUORESCENCE MICROSCOPY; METABOLISM;

AUTOMATION; DNA; MICROSCOPY, FLUORESCENCE; SINGLE-CELL ANALYSIS;

EID: 84962089345     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0151267     Document Type: Article

References (20)

1. Lopez D, Vlamakis H, Kolter R. Generation of multiple cell types in Bacillus subtilis. FEMS Microbiol Rev. 2009;33:152-163. doi: 10.1111/j.1574-6976.2008.00148.x PMID: 19054118
2. Vlamakis H, Aguilar C, Losick R, Kolter R. Control of cell fate by the formation of an architecturally complex bacterial community. Genes Dev. 2008;22:945-953. doi: 10.1101/gad.1645008 PMID: 18381896
3. Veening JW, Stewart EJ, Berngruber TW, Taddei F, Kuipers OP, Hamoen LW. Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci USA. 2008;105:4393-4398. doi: 10.1073/pnas.0700463105 PMID: 18326026
4. Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 2006;6:53. PMID: 16768798
5. Robert L, Paul G, Chen Y, Taddei F, Baigl D, Lindner AB. Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch. Mol Syst Biol. 2010;6:357. doi: 10.1038/msb. 2010.12 PMID: 20393577
6. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7:R100. PMID: 17076895
7. Sliusarenko O, Heinritz J, Emonet T, Jacobs-Wagner C. High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics. Mol Microbiol. 2011;80:612-627. doi: 10.1111/j.1365-2958.2011.07579.x PMID: 21414037
8. Piersma S, Denham EL, Drulhe S, Tonk RH, Schwikowski B, van Dijl JM. TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells. PLoSOne. 2013;8:e68696. doi: 10.1371/journal.pone.0068696 PMID: 23874729
9. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9:671-675. PMID: 22930834
10. Kearns DB, Losick R. Cell population heterogeneity during growth of Bacillus subtilis. Genes Dev. 2005;19:3083-3094. PMID: 16357223
11. Smits WK, Eschevins CC, Susanna KA, Bron S, Kuipers OP, Hamoen LW. Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development. Mol Microbiol. 2005;56:604-614. PMID: 15819618
12. Maamar H, Dubnau D. Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol. 2005;56:615-624. PMID: 15819619
13. Marquez-Magana LM, Chamberlin MJ. Characterization of the sigD transcription unit of Bacillus subtilis. J Bacteriol. 1994;176:2427-2434. PMID: 8157612
14. Cozy LM, Kearns DB. Gene position in a long operon governs motility development in Bacillus subtilis. Mol Microbiol. 2010;76:273-285. doi: 10.1111/j.1365-2958.2010.07112.x PMID: 20233303
15. Chen R, Guttenplan SB, Blair KM, Kearns DB. Role of thesigmaD-dependentautolysins in Bacillus subtilis population heterogeneity. J Bacteriol. 2009;191:5775-5784. doi: 10.1128/JB.00521-09 PMID: 19542270
16. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997;390:249-256. PMID: 9384377
17. Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol. 1961;81:741-746. PMID: 16561900
18. Harwood CR, Cutting SM, editors Molecular biological methods for Bacillus. 1990 Chichester: John Wiley & Sons Ltd.
19. Solopova A, van Gestel J, Weissing FJ, Bachmann H, Teusink B, Kok J, et al. Bet-hedging during bacterial diauxic shift. Proc Natl Acad Sci USA. 2014;111:7427-7432. doi: 10.1073/pnas.1320063111 PMID: 24799698
20. Pandey R, Ter Beek A, Vischer NO, Smelt JP, Brul S, Manders EM. Live cell imaging of germination and outgrowth of individual Bacillus subtilis spores; the effect of heat stress quantitatively analyzed with SporeTracker. PLoS One. 2013;8:e58972. doi: 10.1371/journal.pone.0058972 PMID: 23536843