Pitfalls in optical on-line monitoring for high-throughput screening of microbial systems

Microbial Cell Factories

Volumn 13, Issue 1, 2014, Pages

  Kunze, Martin ^a   Roth, Simon ^a   Gartz, Esther ^a,b   Büchs, Jochen ^a  

^a RWTH AACHEN UNIVERSITY   (Germany)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

Fluorescent protein; High throughput screening; Microtiter plate; On line monitoring; Optical measurement

Indexed keywords

DISSOLVED OXYGEN; GREEN FLUORESCENT PROTEIN; YELLOW FLUORESCENT PROTEIN;

ARTICLE; BIOMASS; BIOTECHNOLOGY; ESCHERICHIA COLI; HIGH THROUGHPUT SCREENING; KLUYVEROMYCES LACTIS; MICROBIAL GROWTH; MICROBIAL SYSTEM; MICROTITER PLATE ASSAY; NONHUMAN; ONLINE MONITORING; OPTICS; OXYGEN TENSION; PH MEASUREMENT; PROTEIN EXPRESSION;

BACTERIA (MICROORGANISMS);

BATCH CELL CULTURE TECHNIQUES; BIOMASS; BIOREACTORS; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; INDUSTRIAL MICROBIOLOGY; KINETICS; KLUYVEROMYCES; LUMINESCENT PROTEINS; RECOMBINANT PROTEINS;

EID: 84899907188     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-13-53     Document Type: Article

References (52)

1. Micheletti M, Lye GJ. Microscalle bioprocess optimisation. Curr Opin Biotech 2006, 17:611-618. 10.1016/j.copbio.2006.10.006, 17084609.
2. Tustian AD, Chhatre S. Speeding the design of bioprocesses. Chem Eng Prog 2008, 104:S8-S13.
3. Bareither R, Pollard D. A review of advanced small-scale parallel bioreactor technology for accelerated process development: current state and future need. Biotechnol Progr 2011, 27:2-14.
4. Gill NK, Appleton M, Baganz F, Lye GJ. Quantification of power consumption and oxygen transfer characteristics of a stirred miniature bioreactor for predictive fermentation scale-up. Biotechnol Bioeng 2008, 100:1144-1155. 10.1002/bit.21852, 18404769.
5. Gill NK, Appleton M, Baganz F, Lye GJ. Design and characterisation of a miniature stirred bioreactor system for parallel microbial fermentations. Biochem Eng J 2008, 39:164-176.
6. Lee HLT, Boccazzi P, Ram RJ, Sinskey AJ. Microbioreactor arrays with integrated mixers and fluid injectors for high-throughput experimentation with pH and dissolved oxygen control. Lab Chip 2006, 6:1229-1235. 10.1039/b608014f, 16929403.
7. Maharbiz MM, Holtz WJ, Howe RT, Keasling JD. Microbioreactor arrays with parametric control for high-throughput experimentation. Biotechnol Bioeng 2004, 85:376-381. 10.1002/bit.10835, 14755555.
8. Puskeiler R, Kaufmann K, Weuster-Botz D. Development, parallelization, and automation of a gas-inducing milliliter-scale bioreactor for high-throughput bioprocess design (HTBD). Biotechnol Bioeng 2005, 89:512-523. 10.1002/bit.20352, 15669089.
9. Weuster-Botz D, Puskeiler R, Kusterer A, Kaufmann K, John GT, Arnold M. Methods and milliliter scale devices for high-throughput bioprocess design. Bioproc Biosyst Eng 2005, 28:109-119.
10. Duetz WA. Microtiter plates as mini-bioreactors: miniaturization of fermentation methods. Trends Microbiol 2007, 15:469-475. 10.1016/j.tim.2007.09.004, 17920276.
11. Zhang H, Lamping SR, Pickering SCR, Lye GJ, Shamlou PA. Engineering characterisation of a single well from 24-well and 96-well microtitre plates. Biochem Eng J 2008, 40:138-149.
12. Duetz WA, Ruedi L, Hermann R, O'Connor K, Büchs J, Witholt B. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl Environ Microb 2000, 66:2641-2646.
13. Hermann R, Lehmann M, Büchs J. Characterization of gas-liquid mass transfer phenomena in microtiter plates. Biotechnol Bioeng 2003, 81:178-186. 10.1002/bit.10456, 12451554.
14. Kensy F, John GT, Hofmann B, Büchs J. Characterisation of operation conditions and online monitoring of physiological culture parameters in shaken 24-well microtiter plates. Bioproc Biosyst Eng 2005, 28:75-81.
15. Kensy F, Zimmermann HF, Knabben I, Anderlei T, Trauthwein H, Dingerdissen U, Büchs J. Oxygen transfer phenomena in 48-well microtiter plates: Determination by optical monitoring of sulfite oxidation and verification by real-time measurement during microbial growth. Biotechnol Bioeng 2005, 89:698-708. 10.1002/bit.20373, 15696519.
16. Duetz WA, Witholt B. Effectiveness of orbital shaking for the aeration of suspended bacterial cultures in square-deepwell microtiter plates. Biochem Eng J 2001, 7:113-115. 10.1016/S1369-703X(00)00109-1, 11173298.
17. Weiss S, John GT, Klimant I, Heinzle E. Modeling of mixing in 96-well microplates observed with fluorescence indicators. Biotechnol Progr 2002, 18:821-830.
18. Funke M, Diederichs S, Kensy F, Müller C, Büchs J. The baffled microtiter plate: increased oxygen transfer and improved online monitoring in small scale fermentations. Biotechnol Bioeng 2009, 103:1118-1128. 10.1002/bit.22341, 19449392.
19. Chudakov DM, Lukyanov S, Lukyanov KA. Fluorescent proteins as a toolkit for in vivo imaging. Trends Biotechnol 2005, 23:605-613. 10.1016/j.tibtech.2005.10.005, 16269193.
20. Crivat G, Taraska JW. Imaging proteins inside cells with fluorescent tags. Trends Biotechnol 2012, 30:8-16. 10.1016/j.tibtech.2011.08.002, 3246539, 21924508.
21. Day RN, Davidson MW. The fluorescent protein palette: tools for cellular imaging. Chem Soc Rev 2009, 38:2887-2921. 10.1039/b901966a, 2910338, 19771335.
22. Frommer WB, Davidson MW, Campbell RE. Genetically encoded biosensors based on engineered fluorescent proteins. Chem Soc Rev 2009, 38:2833-2841. 10.1039/b907749a, 3000468, 19771330.
23. Giepmans BNG, Adams SR, Ellisman MH, Tsien RY. Review - The fluorescent toolbox for assessing protein location and function. Science 2006, 312:217-224. 10.1126/science.1124618, 16614209.
24. Drepper T, Eggert T, Circolone F, Heck A, Krauss U, Guterl JK, Wendorff M, Losi A, Gartner W, Jäger KE. Reporter proteins for in vivo fluorescence without oxygen. Nat Biotechnol 2007, 25:443-445. 10.1038/nbt1293, 17351616.
25. Drepper T, Huber R, Heck A, Circolone F, Hillmer AK, Büchs J, Jäger KE. Flavin mononucleotide-based fluorescent reporter proteins outperform green fluorescent protein-like proteins as quantitative in vivo real-time reporters. Appl Environ Microb 2010, 76:5990-5994.
26. Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. A bilirubin-inducible fluorescent protein from eel muscle. Cell 2013, 153:1602-1611. 10.1016/j.cell.2013.05.038, 23768684.
27. Samorski M, Müller-Newen G, Büchs J. Quasi-continuous combined scattered light and fluorescence measurements: a novel measurement technique for shaken microtiter plates. Biotechnol Bioeng 2005, 92:61-68. 10.1002/bit.20573, 15988771.
28. Arain S, John GT, Krause C, Gerlach J, Wolfbeis OS, Klimant I. Characterization of microtiterplates with integrated optical sensors for oxygen and pH, and their applications to enzyme activity screening, respirometry, and toxicological assays. Sensor Actuat B-Chem 2006, 113:639-648.
29. John GT, Klimant I, Wittmann C, Heinzle E. Integrated optical sensing of dissolved oxygen in microtiter plates: a novel tool for microbial cultivation. Biotechnol Bioeng 2003, 81:829-836. 10.1002/bit.10534, 12557316.
30. Boniello C, Mayr T, Bolivar JM, Nidetzky B. Dual-lifetime referencing (DLR): a powerful method for on-line measurement of internal pH in carrier-bound immobilized biocatalysts. BMC Biotechnol 2012, 12:11. 10.1186/1472-6750-12-11, 3359222, 22455624.
31. Kocincova AS, Borisov SM, Krause C, Wolfbeis OS. Fiber-optic microsensors for simultaneous sensing of oxygen and pH, and of oxygen and temperature. Anal Chem 2007, 79:8486-8493. 10.1021/ac070514h, 17948966.
32. Kocincova AS, Nagl S, Arain S, Krause C, Borisov SM, Arnold M, Wolfbeis OS. Multiplex bacterial growth monitoring in 24-well microplates using a dual optical sensor for dissolved oxygen and pH. Biotechnol Bioeng 2008, 100:430-438. 10.1002/bit.21793, 18383124.
33. Kensy F, Engelbrecht C, Büchs J. Scale-up from microtiter plate to laboratory fermenter: evaluation by online monitoring techniques of growth and protein expression in Escherichia coli and Hansenula polymorpha fermentations. Microb Cell Fact 2009, 8:68. 10.1186/1475-2859-8-68, 2806293, 20028556.
34. Huber R, Ritter D, Hering T, Hillmer AK, Kensy F, Müller C, Wang L, Büchs J. Robo-Lector - a novel platform for automated high-throughput cultivations in microtiter plates with high information content. Microb Cell Fact 2009, 8:42. 10.1186/1475-2859-8-42, 2731075, 19646274.
35. Scheidle M, Klinger J, Büchs J. Combination of on-line pH and oxygen transfer rate measurement in shake flasks by fiber optical technique and Respiration Activity Monitoring System (RAMOS). Sensors-Basel 2007, 7:3472-3480.
36. Wilms B, Hauck A, Reuss M, Syldatk C, Mattes R, Siemann M, Altenbuchner J. High-cell-density fermentation for production of L-N-carbamoylase using an expression system based on the Escherichia coli rhaBAD promoter. Biotechnol Bioeng 2001, 73:95-103. 10.1002/bit.1041, 11255157.
37. Hahn-Hagerdal B, Karhumaa K, Larsson CU, Gorwa-Grauslund M, Gorgens J, van Zyl WH. Role of cultivation media in the development of yeast strains for large scale industrial use. Microb Cell Fact 2005, 4:31. 10.1186/1475-2859-4-31, 1316877, 16283927.
38. Kunze M, Huber R, Gutjahr C, Müllner S, Büchs J. Predictive tool for recombinant protein production in Escherichia coli shake-flask cultures using an on-line monitoring system. Biotechnol Prog 2012, 28:103-113. 10.1002/btpr.719, 22012896.
39. Losen M, Frölich B, Pohl M, Büchs J. Effect of oxygen limitation and medium composition on Escherichia coli fermentation in shake-flask cultures. Biotechnol Prog 2004, 20:1062-1068. 10.1021/bp034282t, 15296430.
40. Funke M, Buchenauer A, Schnakenberg U, Mokwa W, Diederichs S, Mertens A, Müller C, Kensy F, Büchs J. Microfluidic BioLector-Microfluidic bioprocess control in microtiter plates. Biotechnol Bioeng 2010, 107:497-505. 10.1002/bit.22825, 20517981.
41. Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS. Plasmid-encoded protein - The principal factor in the metabolic burden associated with recombinant bacteria. Biotechnol Bioeng 1990, 35:668-681. 10.1002/bit.260350704, 18592563.
42. Bhattacharya SK, Dubey AK. Metabolic burden as reflected by maintenance coefficient of recombinant Escherichia coli overexpressing target gene. Biotechnol Lett 1995, 17:1155-1160.
43. Lee J, Ramirez WF. Mathematical-modeling of induced foreign protein-production by recombinant bacteria. Biotechnol Bioeng 1992, 39:635-646. 10.1002/bit.260390608, 18600993.
44. Jeude M, Dittrich B, Niederschulte H, Anderlei T, Knocke C, Klee D, Büchs J. Fed-batch mode in shake flasks by slow-release technique. Biotechnol Bioeng 2006, 95:433-445. 10.1002/bit.21012, 16736531.
45. Neubauer P, Siurkus J, Panula-Perala J, Neubauer A, Ukkonen K, Krause M, Meyer D, Pelzer S, Eck J, Tegel H, et al. EnBase (TM) - MTP based high-cell-density fermentation for high-throughput and high-content screening. New Biotechnol 2009, 25:S161-S161.
46. Brumberger H, Stein RS, Rowell R. Light scattering. Sci Technology 1968, 83:34-42.
47. Kottmeier K, Weber J, Muller C, Bley T, Büchs J. Asymmetric division of Hansenula polymorpha reflected by a drop of light scatter intensity measured in batch microtiter plate cultivations at phosphate limitation. Biotechnol Bioeng 2009, 104:554-561. 10.1002/bit.22410, 19517521.
48. Scheper T, Hoffmann H, Schügerl K. Flow cytometric studies during culture of Saccharomyces cerevisiae. Enzyme Microb Tech 1987, 9:399-405.
49. Siepert EM, Gartz E, Tur MK, Delbruck H, Barth S, Büchs J. Short-chain fluorescent tryptophan tags for on-line detection of functional recombinant proteins. BMC Biotechnol 2012, 12:65. 10.1186/1472-6750-12-65, 3544578, 22999206.
50. Shcherbakova DM, Verkhusha VV. Near-infrared fluorescent proteins for multicolor in vivo imaging. Nat Methods 2013, 10:751-754. 10.1038/nmeth.2521, 3737237, 23770755.
51. Aigner D, Borisov SM, Petritsch P, Klimant I. Novel near infra-red fluorescent pH sensors based on 1-aminoperylene bisimides covalently grafted onto poly(acryloylmorpholine). Chem Commun 2013, 49:2139-2141.
52. Borisov SM, Nuss G, Klimant I. Red light-excitable oxygen sensing materials based on platinum(II) and palladium(II) benzoporphyrins. Anal Chem 2008, 80:9435-9442. 10.1021/ac801521v, 19006407.