Single-cell microfluidics: Opportunity for bioprocess development

Current Opinion in Biotechnology

Volumn 29, Issue 1, 2014, Pages 15-23

  Grünberger, Alexander ^a   Wiechert, Wolfgang ^a   Kohlheyer, Dietrich ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCONVERSION; CELLS; CYTOLOGY; MICROANALYSIS; PRODUCTIVITY;

BIOPROCESS DEVELOPMENT; BIOTECHNOLOGICAL PROCESS; ENVIRONMENTAL CONDITIONS; MICRO FLUIDIC SYSTEM; MICROFABRICATED SYSTEMS; POPULATION HETEROGENEITY; SPATIOTEMPORAL ANALYSIS; STRAIN CHARACTERIZATION;

MICROFLUIDICS;

PROTOCATECHUIC ACID;

BIOREACTOR; BIOTECHNOLOGY; CORYNEBACTERIUM GLUTAMICUM; EQUIPMENT DESIGN; IMAGING SYSTEM; MICROBIAL COMMUNITY; MICROBIAL GROWTH; MICROBIAL IDENTIFICATION; MICROBIAL MORPHOLOGY; MICROFLUIDICS; MOLECULAR DYNAMICS; MOLECULAR IMAGING; NANOFABRICATION; NONHUMAN; PARTICLE SIZE; PERFORMANCE MEASUREMENT SYSTEM; PICHIA ANGUSTA; PICHIA PASTORIS; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS TECHNOLOGY; REVIEW; SACCHAROMYCES CEREVISIAE; SINGLE CELL ANALYSIS; SPATIOTEMPORAL ANALYSIS; STRAIN IDENTIFICATION; DEVICES;

BIOREACTORS; BIOTECHNOLOGY; MICROFLUIDICS; SINGLE-CELL ANALYSIS;

EID: 84896115265     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.02.008     Document Type: Review

References (60)

1. Lara A.R., Galindo E., Ramirez O.T., Palomares L.A. Living with heterogeneities in bioreactors. Mol Biotechnol 2006, 34:355-381.
2. Lidstrom M.E., Konopka M.C. The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol 2010, 6:705-712.
3. Carlquist M., Fernandes R.L., Helmark S., Heins A.L., Lundin L., Sorensen S.J., Gernaey K.V., Lantz A.E. Physiological heterogeneities in microbial populations and implications for physical stress tolerance. Microb Cell Fact 2012, 11:94.
4. Delvigne F., Goffin P. Microbial heterogeneity affects bioprocess robustness: dynamic single-cell analysis contributes to understanding of microbial populations. Biotechnol J 2014, 9:61-72.
5. Fernandes R.L., Nierychlo M., Lundin L., Pedersen A.E., Tellez P.E.P., Dutta A., Carlquist M., Bolic A., Schapper D., Brunetti A.C., et al. Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnol Adv 2011, 29:575-599.
6. Takors R. Scale-up of microbial processes: impacts, tools and open questions. J Biotech 2012, 160:3-9.
7. Fernandes P., Carvalho F.,P.C., Marques M. Miniaturization in biotechnology: speeding up the development of bioprocesses. Recent Pat Biotechnol 2011, 5:160-173.
8. Marques M.P.C., Fernandes P. Microfluidic devices: useful tools for bioprocess intensification. Molecules 2011, 16:8368-8401.
9. Tracy B.P., Gaida S.M., Papoutsakis E.T. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotech 2010, 21:85-99.
10. Schneider T., Kreutz J., Chiu D.T. The potential impact of droplet microfluidics in biology. Anal Chem 2013, 85:3476-3482.
11. Klepárník K., Foret F. Recent advances in the development of single cell analysis-a review. Anal Chim Acta 2013, 800:12-21.
12. Okumus B., Yildiz S., Toprak E. Fluidic and microfluidic tools for quantitative systems biology. Curr Opin Biotechnol 2014, 25:30-38.
13. Love K.R., Bagh S., Choi J., Love J.C. Microtools for single-cell analysis in biopharmaceutical development and manufacturing. Trends Biotechnol 2013, 31:16-22.
14. Lecault V., White A.K., Singhal A., Hansen C.L. Microfluidic single cell analysis: from promise to practice 2012, 16:381-390.
15. Nilsson J., Evander M., Hammarström B., Laurell T. Review of cell and particle trapping in microfluidic systems. Anal Chim Acta 2009, 649:141-157.
16. Bakstad D., Adamson A., Spiller D.G., White M.R.H. Quantitative measurement of single cell dynamics. Curr Opin Biotechnol 2012, 23:103-109.
17. Okumoto S., Jones A., Frommer W.B. Quantitative imaging with fluorescent biosensors. Annu Rev Plant Biol 2012, 63:663-706.
18. Ren K., Chen Y., Wu H. New materials for microfluidics in biology. Curr Opin Biotechnol 2014, 25:78-85.
19. Moolman M.C., Huang Z.X., Krishnan S.T., Kerssemakers J.W.J., Dekker N.H. Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria. J Nanobiotechnol 2013, 11:12.
20. Kim M.C., Lam R.H.W., Thorsen T., Asada H.H. Mathematical analysis of oxygen transfer through polydimethylsiloxane membrane between double layers of cell culture channel and gas chamber in microfluidic oxygenator. Microfluid Nanofluid 2013, 15:285-296.
21. Coutu D.L., Schroeder T. Probing cellular processes by long-term live imaging-historic problems and current solutions. J Cell Sci 2013, 126:3805-3815.
22. Nienhaus K., Ulrich Nienhaus G. Fluorescent proteins for live-cell imaging with super-resolution. Chem Soc Rev 2014, 43:1088-1106.
23. van Teeffelen S., Shaevitz J.W., Gitai Z. Image analysis in fluorescence microscopy: bacterial dynamics as a case study. BioEssays 2012, 34:427-436.
24. Young J.W., Locke J.C.W., Altinok A., Rosenfeld N., Bacarian T., Swain P.S., Mjolsness E., Elowitz M.B. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat Protoc 2012, 7:80-88.
25. Groisman A., Lobo C., Cho H.J., Campbell J.K., Dufour Y.S., Stevens A.M., Levchenko A. A microfluidic chemostat for experiments with bacterial and yeast cells. Nat Methods 2005, 2:685-689.
26. Mather W., Mondragon-Palomino O., Danino T., Hasty J., Tsimring L.S. Streaming instability in growing cell populations. Phys Rev Lett 2010, 104:208101.
27. Ullman G., Wallden M., Marklund E.G., Mahmutovic A., Razinkov I., Elf J. High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking. Philos T R Soc B 2013, 368:20120025.
28. Grünberger A., Paczia N., Probst C., Schendzielorz G., Eggeling L., Noack S., Wiechert W., Kohlheyer D. A disposable picolitre bioreactor for cultivation and investigation of industrially relevant bacteria on the single cell level. Lab Chip 2012, 12:2060-2068.
29. Lee S.S., Avalos Vizcarra I., Huberts D.H.E.W., Lee L.P., Heinemann M. Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform. Proc Natl Acad Sci USA 2012, 109:4916-4920.
30. Wang P., Robert L., Pelletier J., Dang W.L., Taddei F., Wright A., Jun S. Robust growth of Escherichia coli. Curr Biol 2010, 20:1099-1103.
31. Norman T.M., Lord N.D., Paulsson J., Losick R. Memory and modularity in cell-fate decision making. 2013, 503:481-486.
32. Rowat A.C., Bird J.C., Agresti J.J., Rando O.J., Weitz D.A. Tracking lineages of single cells in lines using a microfluidic device. Proc Natl Acad Sci USA 2009, 106:18149-18154.
33. Long Z., Nugent E., Javer A., Cicuta P., Sclavi B., Lagomarsino M.C., Dorfman K.D. Microfluidic chemostat for measuring single cell dynamics in bacteria. Lab Chip 2013, 13:947-954.
34. Moffitt J.R., Lee J.B., Cluzel P. The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities. Lab Chip 2012, 12:1487-1494.
35. Schendzielorz G., Dippong M., Grünberger A., Kohlheyer D., Yoshida A., Binder S., Nishiyama C., Nishiyama M., Bott M., Eggeling L. Taking control over control: use of product sensing in single cells to remove flux control at key enzymes in biosynthesis pathways. ACS Synth Biol 2013, 3:21-29.
36. Di Carlo D., Wu L.Y., Lee L.P. Dynamic single cell culture array. Lab Chip 2006, 6:1445-1449.
37. Ryley J., Pereira-Smith O.M. Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae. Yeast 2006, 23:1065-1073.
38. Probst C., Grünberger A., Wiechert W., Kohlheyer D. Polydimethylsiloxane (PDMS) sub-micron traps for single-cell analysis of bacteria. Micromachines 2013, 4:357-369.
39. Rubakhin S.S., Lanni E.J., Sweedler J.V. Progress toward single cell metabolomics. Curr Opin Biotech 2013, 24:95-104.
40. Trouillon R., Passarelli M.K., Wang J., Kurczy M.E., Ewing A.G. Chemical analysis of single cells. Anal Chem 2012, 85:522-542.
41. Fornera S., Kuhn P., Lombardi D., Schluter A.D., Dittrich P.S., Walde P. Sequential immobilization of enzymes in microfluidic channels for cascade reactions. Chempluschem 2012, 77:98-101.
42. Wiedenmann J., Oswald F., Nienhaus G.U. Fluorescent proteins for live cell imaging: opportunities, limitations, and challenges. IUBMB Life 2009, 61:1029-1042.
43. Schallmey M., Frunzke J., Eggeling L., Marienhagen J. Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr Opin Biotechnol 2014, 26:148-154.
44. Mustafi N., Grünberger A., Mahr R., Helfrich S., Nöh K., Blombach B., Kohlheyer D., Frunzke J. Application of a genetically encoded biosensor for live cell imaging of L-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains. Plos One 2014, 9:e85731.
45. Huang Y., Cai D., Chen P. Micro- and nanotechnologies for study of cell secretion. Anal Chem 2011, 83:4393-4406.
46. Kortmann H., Kurth F., Blank L.M., Dittrich P.S., Schmid A. Towards real time analysis of protein secretion from single cells. Lab Chip 2009, 9:3047-3049.
47. Love K.R., Panagiotou V., Jiang B., Stadheim T.A., Love J.C. Integrated single-cell analysis shows pichia pastoris secretes protein stochastically. Biotechnol Bioeng 2010, 106:319-325.
48. Dusny C., Fritzsch F.S.O., Frick O., Schmid A. Isolated microbial single cells and resulting micropopulations are growing faster in controlled environments. Appl Environ Microbiol 2012, 78:7132-7136.
49. Grünberger A., van Ooyen J., Paczia N., Rohe P., Schiendzielorz G., Eggeling L., Wiechert W., Kohlheyer D., Noack S. Beyond growth rate 0.6: Corynebacterium glutamicum cultivated in highly diluted environments. Biotechnol Bioeng 2013, 110:220-228.
50. Unthan S., Grünberger A., van Ooyen J., Gätgens J., Heinrich J., Paczia N., Wiechert W., Kohlheyer D., Noack S. Beyond growth rate 0.6: what drives Corynebacterium glutamicum to higher growth rates in defined medium. Biotechnol Bioeng 2014, 111:359-371.
51. Jeon N.L., Dertinger S.K.W., Chiu D.T., Choi I.S., Stroock A.D., Whitesides G.M. Generation of solution and surface gradients using microfluidic systems. Langmuir 2000, 16:8311-8316.
52. Ahmed T., Shimizu T.S., Stocker R. Microfluidics for bacterial chemotaxis. Integr Biol-Uk 2010, 2:604-629.
53. Chung B.G., Choo J. Microfluidic gradient platforms for controlling cellular behavior. Electrophoresis 2010, 31:3014-3027.
54. Keenan T.M., Folch A. Biomolecular gradients in cell culture systems. Lab Chip 2008, 8:34-57.
55. Jin B.J., Ko E.A., Namkung W., Verkman A.S. Microfluidics platform for single-shot dose-response analysis of chloride channel-modulating compounds. Lab Chip 2013, 13:3862-3867.
56. Uhlendorf J., Miermont A., Delaveau T., Charvin G., Fages F., Bottani S., Batt G., Hersen P. Long-term model predictive control of gene expression at the population and single-cell levels. Proc Natl Acad Sci USA 2012, 109:14271-14276.
57. Dai J., Yoon S.H., Sim H.Y., Yang Y.S., Oh T.K., Kim J.F., Hong J.W. Charting microbial phenotypes in multiplex nanoliter batch bioreactors. Anal Chem 2013, 85:5892-5899.
58. Kensy F., Zang E., Faulhammer C., Tan R.K., Buchs J. Validation of a high-throughput fermentation system based on online monitoring of biomass and fluorescence in continuously shaken microtiter plates. Microb Cell Fact 2009, 8:31.
59. Araci I.E., Brisk P. Recent developments in microfluidic large scale integration. Curr Opin Biotechnol 2014, 25:60-68.
60. Dénervaud N., Becker J., Delgado-Gonzalo R., Damay P., Rajkumar A.S., Unser M., Shore D., Naef F., Maerkl S.J. A chemostat array enables the spatio-temporal analysis of the yeast proteome. Proc Natl Acad Sci USA 2013, 10.1073/pnas.1308265110.