In vitro microbial culture models and their application in drug development

Advanced Drug Delivery Reviews

Volumn 69-70, Issue , 2014, Pages 217-224

  Vyawahare, Saurabh ^a   Zhang, Qiucen ^b   Lau, Alexandra ^c   Austin, Robert H ^d  

^a Princeton University   (United States)

^b United States of America   (United States)

^c MOUNT HOLYOKE COLLEGE   (United States)

^d PRINCETON UNIVERSITY   (United States)

Author keywords

Antibiotics; Evolution; Microbes; Microfluidics; Resistance

Indexed keywords

CHEMOTHERAPY; DRUG DOSAGE; ELECTRIC RESISTANCE; MICROFLUIDICS; TISSUE;

BACTERIAL RESISTANCE; DESIGN PRINCIPLES; EVOLUTION; HETEROGENEOUS TISSUES; MICRO-FLUIDIC DEVICES; MICROBES; MICROBIAL CULTURE; NATURAL SELECTION;

ANTIBIOTICS;

BACTERIAL DNA; CHLORAMPHENICOL; CIPROFLOXACIN; GENOMIC DNA; KANAMYCIN; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; BACTERIUM CULTURE; BIOTECHNOLOGY; CELL CULTURE; CELL MOTILITY; CELL POPULATION; CELL STRESS; CULTURE TECHNIQUE; DNA REPLICATION; DRUG RESEARCH; DRUG SCREENING; DRUG SYNTHESIS; ESCHERICHIA COLI; EUKARYOTIC CELL; IN VITRO STUDY; MICROBIAL ACTIVITY; MICROFLUIDICS; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; POPULATION SIZE; PRIORITY JOURNAL; REVIEW; ANIMAL; BIOLOGICAL MODEL; DRUG DEVELOPMENT; HUMAN; MICROFLUIDIC ANALYSIS; PROCEDURES; TRENDS;

ANIMALS; ANTI-INFECTIVE AGENTS; CELL CULTURE TECHNIQUES; DRUG DISCOVERY; HUMANS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MODELS, BIOLOGICAL;

EID: 84899953825     PISSN: 0169409X     EISSN: 18728294     Source Type: Journal    
DOI: 10.1016/j.addr.2014.02.005     Document Type: Review

References (57)

1. Levy S., Marshall B. Antibacterial resistance worldwide: causes, challenges and responses. Nat. Med. 2004, 10:S122-S129.
2. Bjedov I., Tenaillon O., Gerard B., Souza V., Denamur E., Radman M., Taddei F., Matic I. Stress-induced mutagenesis in bacteria. Science 2003, 300:1404-1409.
3. D'Costa V.M., McGrann K.M., Hughes D.W., Wright G.D. Sampling the antibiotic resistome. Science 2006, 311:374-377.
4. Sommer M.O., Dantas G., Church G.M. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009, 325:1128-1131.
5. Whitesides G. The origins and the future of microfluidics. Nature 2006, 442:368-373.
6. Vyawahare S., Griffiths A.D., Merten C.A. Miniaturization and parallelization of biological and chemical assays in microfluidic devices. Chem. Biol. 2010, 17:1052-1065.
7. El-Ali J., Sorger P., Jensen K. Cells on chips. Nature 2006, 442:403-411.
8. Austin R., Tung C., Lambert G., Liao D., Gong X. An introduction to micro-ecology patches. Chem. Soc. Rev. 2010, 39:1049-1059.
9. Knight J., Vishwanath A., Brody J., Austin R. Hydrodynamic focusing on a silicon chip: mixing nanoliters in microseconds. Phys. Rev. Lett. 1998, 80:3863-3866.
10. Zhang Q., Lambert G., Liao D., Kim H., Robin K., Tung C.-K., Pourmand N., Austin R.H. Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments. Science 2011, 333:1764-1767.
11. Loutherback K., Puchalla J., Austin R., Sturm J. Deterministic microfluidic ratchet. Phys. Rev. Lett. 2009, 102:45301.
12. Lambert G., Liao D., Austin R. Collective escape of chemotactic swimmers through microscopic ratchets. Phys. Rev. Lett. 2010, 104:168102.
13. Zhang Q., Robin K., Liao D., Lambert G., Austin R.H. The Goldilocks principle and antibiotic resistance in bacteria. Mol. Pharm. 2011, 8:2063-2068.
14. Hong J., Quake S., et al. Integrated nanoliter systems. Nat. Biotechnol. 2003, 21:1179-1183.
15. Mark D., Weber P., Lutz S., Focke M., Zengerle R., von Stetten F. Aliquoting on the centrifugal microfluidic platform based on centrifugo-pneumatic valves. Microfluid. Nanofluid. 2011, 10:1279-1288.
16. Araci I., Quake S. Microfluidic very large scale integration (MVLSI) with integrated micromechanical valves. Lab Chip 2012, 12:2803-2806.
17. Tsai J., Lin L. Active microfluidic mixer and gas bubble filter driven by thermal bubble micropump. Sensors Actuators A Phys. 2002, 97:665-671.
18. Kannappan K., Bogle G., Travas-Sejdic J., Williams D. Computational design of mixers and pumps for microfluidic systems, based on electrochemically-active conducting polymers. Phys. Chem. Chem. Phys. 2011, 13:5450-5461.
19. Lee C., Chang C., Wang Y., Fu L. Microfluidic mixing: a review. Int. J. Mol. Sci. 2011, 12:3263-3287.
20. Graydon O. Microfluidics: laser-induced bubbles create valves and pumps. Nat. Photonics 2011, 5:256.
21. Kim J., Kang M., Jensen E., Mathies R. Lifting gate PDMS microvalves and pumps for microfluidic control. Anal. Chem. 2012, 84(4):2067-2071. 10.1021/ac202934x.
22. Gómez-Sjöberg R., Leyrat A.A., Pirone D.M., Chen C.S., Quake S.R. Versatile, fully automated, microfluidic cell culture system. Anal. Chem. 2007, 79:8557-8563.
23. Groisman A., Lobo C., Cho H., 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.
24. Young E.W., Beebe D.J. Fundamentals of microfluidic cell culture in controlled microenvironments. Chem. Soc. Rev. 2010, 39:1036-1048.
25. Lee P.J., Gaige T.A., Hung P.J. Dynamic cell culture: a microfluidic function generator for live cell microscopy. Lab Chip 2009, 9:164-166.
26. Zhang Q., Austin R.H. Applications of microfluidics in stem cell biology. BioNanoScience 2012, 2:277-286.
27. Huh D., Kim H.J., Fraser J.P., Shea D.E., Khan M., Bahinski A., Hamilton G.A., Ingber D.E. Microfabrication of human organs-on-chips. Nat. Protoc. 2013, 8:2135-2157.
28. Chan C.Y., Huang P.-H., Guo F., Ding X., Kapur V., Mai J.D., Yuen P.K., Huang T.J. Accelerating drug discovery via organs-on-chips. Lab Chip 2013, 13:4697-4710.
29. Barrick J.E., Lenski R.E. Genome dynamics during experimental evolution. Nat. Rev. Genet. 2013, 14:827-839.
30. Toprak E., Veres A., Michel J.-B., Chait R., Hartl D.L., Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 2011, 44:101-105.
31. Desai M.M., Fisher D.S., Murray A.W. The speed of evolution and maintenance of variation in asexual populations. Curr. Biol. 2007, 17:385-394.
32. Lang G.I., Rice D.P., Hickman M.J., Sodergren E., Weinstock G.M., Botstein D., Desai M.M. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 2013, 500:571-574.
33. Park S.-C., Krug J. Clonal interference in large populations. Proc. Natl. Acad. Sci. 2007, 104:18135-18140.
34. Kepler T.B., Perelson A.S. Drug concentration heterogeneity facilitates the evolution of drug resistance. Proc. Natl. Acad. Sci. 1998, 95:11514-11519.
35. Kaufmann B.B., Hung D.T. The fast track to multidrug resistance. Mol. Cell 2010, 37:297-298.
36. Dittrich P.S., Manz A. Lab-on-a-chip: microfluidics in drug discovery. Nat. Rev. Drug Discov. 2006, 5:210-218.
37. Lombardi D., Dittrich P.S. Advances in microfluidics for drug discovery. Expert Opin. Drug Discov. 2010, 5:1081-1094.
38. Agresti J.J., Antipov E., Abate A.R., Ahn K., Rowat A.C., Baret J.-C., Marquez M., Klibanov A.M., Griffiths A.D., Weitz D.A. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc. Natl. Acad. Sci. 2010, 107:4004-4009.
39. Ishida Y. Sewall Wright and Gustave Malecot on isolation by distance. Philos. Sci. 2009, 76:784-796.
40. Zhang Q., Austin R.H. Physics of cancer: the impact of heterogeneity. Ann. Rev. Condens. Matter Phys. 2012, 3:363-382.
41. Carlson E.A. HJ Muller's contributions to mutation research. Mutat. Res. Rev. Mutat. Res. 2013, 752:1-5.
42. Drlica K., Zhao X.L. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol. Mol. Biol. Rev. 1997, 61:377.
43. Rosenberg S.M. Evolving responsively: adaptive mutation. Nat. Rev. Genet. 2001, 2:504-515.
44. Cirz R.T., Chin J.K., Andes D.R., de Crcy-Lagard V., Craig W.A., Romesberg F.E. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 2005, 3:e176.
45. Khodursky A., Peter B., Schmid M., DeRisi J., Botstein D., Brown P., Cozzarelli N. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc. Natl. Acad. Sci. 2000, 97:9419.
46. Pestka S. The use of inhibitors in studies on protein synthesis. Methods Enzymol. 1974, 30:261-282.
47. Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science 1994, 264:375-382.
48. Krzywinski M., Schein J., Birol I., Connors J., Gascoyne R., Horsman D., Jones S., Marra M. Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19:1639-1645.
49. Hastings P., Lupski J., Rosenberg S., Ira G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 2009, 10:551-564.
50. Inoue K., Lupski J. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 2002, 3:199-242.
51. 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.
52. Sawai S., Guan X.J., Kuspa A., Cox E.C. High-throughput analysis of spatio-temporal dynamics in Dictyostelium. Genome Biol. 2007, 8.
53. Kim L., Toh Y.-C., Voldman J., Yu H. A practical guide to microfluidic perfusion culture of adherent mammalian cells. Lab Chip 2007, 7:681-694.
54. Meyvantsson I., Beebe D.J. Cell culture models in microfluidic systems. Annu. Rev. Anal. Chem. 2008, 1:423-449.
55. Wu A., Loutherback K., Lambert G., Estévez-Salmerón L., Tlsty T.D., Austin R.H., Sturm J.C. Cell motility and drug gradients in the emergence of resistance to chemotherapy. Proc. Natl. Acad. Sci. 2013, 110:16103-16108.
56. Kim H.J., Huh D., Hamilton G., Ingber D.E. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 2012, 12:2165-2174.
57. Lambert G., Estévez-Salmeron L., Oh S., Liao D., Emerson B.M., Tlsty T.D., Austin R.H. An analogy between the evolution of drug resistance in bacterial communities and malignant tissues. Nat. Rev. Cancer 2011, 11:375-382.