Single Cell Analytics: An Overview

Chapter
Part of the Advances in Biochemical Engineering / Biotechnology book series (ABE, volume 124)

Abstract

The research field of single cell analysis is rapidly expanding, driven by developments in flow cytometry, microscopy, lab-on-a-chip devices, and many other fields. The promises of these developments include deciphering cellular mechanisms and the quantification of cell-to-cell differences, ideally with spatio-temporal resolution. However, these promises are challenging as the analytical techniques have to cope with minute analyte amounts and concentrations. We formulate first these challenges and then present state-of-the-art analytical techniques available to investigate the different cellular hierarchies—from the genome to the phenome, i.e., the sum of all phenotypes.

Graphical Abstract

Keywords

Cell population heterogeneity Envirostat Omics technologies Single cell analysis 

References

  1. 1.
    Kreiner T, Kirk MD, Scheller RH (1987) Cellular and synaptic morphology of a feeding motor circuit in Aplysia californica. J Comp Neurol 264(3):311–325Google Scholar
  2. 2.
    Wang Y, Hammes F, Duggelin M, Egli T (2008) Influence of size, shape, and flexibility on bacterial passage through micropore membrane filters. Environ Sci Technol 42(17):6749–6754Google Scholar
  3. 3.
    Schmid A, Kortmann H, Dittrich PS, Blank LM (2010) Chemical and biological single cell analysis. Curr Opin Biotechnol 21(1):12–20Google Scholar
  4. 4.
    Lange BM (2005) Single-cell genomics. Curr Opin Plant Biol 8(3):236–241Google Scholar
  5. 5.
    Jiang Z, Zhang X, Deka R, Jin L (2005) Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res 33(10):e91Google Scholar
  6. 6.
    Bengtsson M, Stahlberg A, Rorsman P, Kubista M (2005) Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 15(10):1388–1392Google Scholar
  7. 7.
    Bengtsson M, Hemberg M, Rorsman P, Stahlberg A (2008) Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. BMC Mol Biol 9:11Google Scholar
  8. 8.
    Hu S, Michels DA, Fazal MA, Ratisoontorn C, Cunningham ML, Dovichi NJ (2004) Capillary sieving electrophoresis/micellar electrokinetic capillary chromatography for two-dimensional protein fingerprinting of single mammalian cells. Anal Chem 76(14):4044–4049Google Scholar
  9. 9.
    Huang B, Wu H, Bhaya D, Grossman A, Granier S, Kobilka BK, Zare RN (2007) Counting low-copy number proteins in a single cell. Science 315(5808):81–84Google Scholar
  10. 10.
    Greif D, Galla L, Ros A, Anselmetti D (2008) Single cell analysis in full body quartz glass chips with native UV laser-induced fluorescence detection. J Chromatogr A 1206(1):83–88Google Scholar
  11. 11.
    Mapelli V, Olsson L, Nielsen J (2008) Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. Trends Biotechnol 26(9):490–497Google Scholar
  12. 12.
    van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T (2007) Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem 370(1):17–25Google Scholar
  13. 13.
    Ruestow EG (1983) Images and ideas: Leeuwenhoek’s perception of the spermatozoa. J Hist Biol 16(2):185–224Google Scholar
  14. 14.
    Smit P, Heniger J (1975) Antoni van Leeuwenhoek (1632–1723) and the discovery of bacteria. Antonie van Leeuwenhoek 41(3):219–228Google Scholar
  15. 15.
    Siesser WG (1981) Christian Gottfried Ehrenberg: founder of micropaleontology. Centaurus 25(3):166–188Google Scholar
  16. 16.
    Hoepfner D, Brachat A, Philippsen P (2000) Time-lapse video microscopy analysis reveals astral microtubule detachment in the yeast spindle pole mutant cnm67. Mol Biol Cell 11(4):1197–1211Google Scholar
  17. 17.
    Kortmann H, Chasanis P, Blank LM, Franzke J, Kenig EY, Schmid A (2009) The Envirostat—a new bioreactor concept. Lab Chip 9(4):576–585Google Scholar
  18. 18.
    Soejima T, Iida K, Qin T, Taniai H, Yoshida S (2009) Discrimination of live, anti-tuberculosis agent-injured, and dead Mycobacterium tuberculosis using flow cytometry. FEMS Microbiol Lett 294(1):74–81Google Scholar
  19. 19.
    Strauber H, Muller S (2010) Viability states of bacteria-specific mechanisms of selected probes. Cytom A 77(7):623–634Google Scholar
  20. 20.
    Shim J-u, Olguin LF, Whyte G, Scott D, Babtie A, Abell C, Huck WTS, Hollfelder F (2009) Simultaneous determination of gene expression and enzymatic activity in individual bacterial cells in microdroplet compartments. J Am Chem Soc 131(42):15251–15256Google Scholar
  21. 21.
    Li PC, de Camprieu L, Cai J, Sangar M (2004) Transport, retention and fluorescent measurement of single biological cells studied in microfluidic chips. Lab Chip 4(3):174–180Google Scholar
  22. 22.
    Schumann CA, Dorrenhaus A, Franzke J, Lampen P, Dittrich PS, Manz A, Roos PH (2008) Concomitant detection of CYP1A1 enzymatic activity and CYP1A1 protein in individual cells of a human urothelial cell line using a bilayer microfluidic device. Anal Bioanal Chem 392(6):1159–1166Google Scholar
  23. 23.
    Nyfeler B, Hauri HP (2007) Visualization of protein interactions inside the secretory pathway. Biochem Soc Trans 35(Pt 5):970–973Google Scholar
  24. 24.
    Drepper T, Eggert T, Circolone F, Heck A, Krauss U, Guterl JK, Wendorff M, Losi A, Gartner W, Jaeger KE (2007) Reporter proteins for in vivo fluorescence without oxygen. Nat Biotechnol 25(4):443–445Google Scholar
  25. 25.
    Shaner NC, Patterson GH, Davidson MW (2007) Advances in fluorescent protein technology. J Cell Sci 120(Pt 24):4247–4260Google Scholar
  26. 26.
    Golding I, Paulsson J, Zawilski SM, Cox EC (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123(6):1025–1036Google Scholar
  27. 27.
    Greeson JN, Organ LE, Pereira FA, Raphael RM (2006) Assessment of prestin self-association using fluorescence resonance energy transfer. Brain Res 1091(1):140–150Google Scholar
  28. 28.
    Ibrahim SF, van den Engh G (2007) Flow cytometry and cell sorting. Adv Biochem Eng Biotechnol 106:19–39Google Scholar
  29. 29.
    Duhamel S, Gerardi G (2009) Detection of extracellular phosphatase activity at the single-cell level by enzyme-labeled fluorescence and flow cytometry: the importance of time kinetics in ELFA labeling. Cytom A 75A(2):163–168Google Scholar
  30. 30.
    Muller S, Nebe-von-Caron G (2010) Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol Rev 34(4):554–587Google Scholar
  31. 31.
    Bergen AW, Haque KA, Qi Y, Beerman MB, Garcia-Closas M, Rothman N, Chanock SJ (2005) Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Hum Mutat 26(3):262–270Google Scholar
  32. 32.
    Hong JW, Studer V, Hang G, Anderson WF, Quake SR (2004) A nanoliter-scale nucleic acid processor with parallel architecture. Nat Biotechnol 22(4):435–439Google Scholar
  33. 33.
    Hanson EK, Ballantyne J (2005) Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA. Anal Biochem 346(2):246–257Google Scholar
  34. 34.
    Handyside AH, Pattinson JK, Penketh RJ, Delhanty JD, Winston RM, Tuddenham EG (1989) Biopsy of human preimplantation embryos and sexing by DNA amplification. Lancet 1(8634):347–349Google Scholar
  35. 35.
    Fassihi H, Renwick PJ, Black C, McGrath JA (2006) Single cell PCR amplification of microsatellites flanking the COL7A1 gene and suitability for preimplantation genetic diagnosis of Hallopeau-Siemens recessive dystrophic epidermolysis bullosa. J Dermatol Sci 42(3):241–248Google Scholar
  36. 36.
    Lagally ET, Medintz I, Mathies RA (2001) Single-molecule DNA amplification and analysis in an integrated microfluidic device. Anal Chem 73(3):565–570Google Scholar
  37. 37.
    Rungpragayphan S, Kawarasaki Y, Imaeda T, Kohda K, Nakano H, Yamane T (2002) High-throughput, cloning-independent protein library construction by combining single-molecule DNA amplification with in vitro expression. J Mol Biol 318(2):395–405Google Scholar
  38. 38.
    Li H, Yeung ES (2002) Selective genotyping of individual cells by capillary polymerase chain reaction. Electrophoresis 23(19):3372–3380Google Scholar
  39. 39.
    Peng W, Takabayashi H, Ikawa K (2007) Whole genome amplification from single cells in preimplantation genetic diagnosis and prenatal diagnosis. Eur J Obstet Gynecol Reprod Biol 131(1):13–20Google Scholar
  40. 40.
    Cheung VG, Nelson SF (1996) Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci USA 93(25):14676–14679Google Scholar
  41. 41.
    Dietmaier W, Hartmann A, Wallinger S, Heinmoller E, Kerner T, Endl E, Jauch KW, Hofstadter F, Ruschoff J (1999) Multiple mutation analyses in single tumor cells with improved whole genome amplification. Am J Pathol 154(1):83–95Google Scholar
  42. 42.
    Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR, Riethmuller G (1999) Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci USA 96(8):4494–4499Google Scholar
  43. 43.
    Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99(8):5261–5266Google Scholar
  44. 44.
    Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, Du J, Kingsmore SF, Egholm M, Lasken RS (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res 13(5):954–964Google Scholar
  45. 45.
    Lasken RS, Egholm M (2003) Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol 21(12):531–535Google Scholar
  46. 46.
    Lasken RS (2007) Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol 10(5):510–516Google Scholar
  47. 47.
    Hawkins TL, Detter JC, Richardson PM (2002) Whole genome amplification–applications and advances. Curr Opin Biotechnol 13(1):65–67Google Scholar
  48. 48.
    Panelli S, Damiani G, Espen L, Micheli G, Sgaramella V (2006) Towards the analysis of the genomes of single cells: further characterisation of the multiple displacement amplification. Gene 372:1–7Google Scholar
  49. 49.
    Ren Z, Zeng HT, Xu YW, Zhuang GL, Deng J, Zhang C, Zhou CQ (2009) Preimplantation genetic diagnosis for Duchenne muscular dystrophy by multiple displacement amplification. Fertil Steril 91(2):359–364Google Scholar
  50. 50.
    Lasken RS (2009) Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 37:450–453Google Scholar
  51. 51.
    Chang HW, Sung Y, Kim KH, Nam YD, Roh SW, Kim MS, Jeon CO, Bae JW (2008) Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ Sci Technol 42(16):6058–6064Google Scholar
  52. 52.
    Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71(6):3342–3347Google Scholar
  53. 53.
    Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP, Speicher MR (2007) High resolution array-CGH analysis of single cells. Nucleic Acids Res 35(3):e15Google Scholar
  54. 54.
    Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, Rechavi G, Shapiro E (2008) Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol 8:17Google Scholar
  55. 55.
    Church GM (2006) Genomes for all. Sci Am 294(1):46–54Google Scholar
  56. 56.
    Wang TH, Peng Y, Zhang C, Wong PK, Ho CM (2005) Single-molecule tracing on a fluidic microchip for quantitative detection of low-abundance nucleic acids. J Am Chem Soc 127(15):5354–5359Google Scholar
  57. 57.
    Zhang CY, Yeh HC, Kuroki MT, Wang TH (2005) Single-quantum-dot-based DNA nanosensor. Nat Mater 4(11):826–831Google Scholar
  58. 58.
    Zhang CY, Chao SY, Wang TH (2005) Comparative quantification of nucleic acids using single-molecule detection and molecular beacons. Analyst 130(4):483–488Google Scholar
  59. 59.
    Sauer M, Angerer B, Ankenbauer W, Foldes-Papp Z, Gobel F, Han KT, Rigler R, Schulz A, Wolfrum J, Zander C (2001) Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. J Biotechnol 86(3):181–201Google Scholar
  60. 60.
    Braslavsky I, Hebert B, Kartalov E, Quake SR (2003) Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci USA 100(7):3960–3964Google Scholar
  61. 61.
    Astier Y, Braha O, Bayley H (2006) Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J Am Chem Soc 128(5):1705–1710Google Scholar
  62. 62.
    Irimia D, Tompkins RG, Toner M (2004) Single-cell chemical lysis in picoliter-scale closed volumes using a microfabricated device. Anal Chem 76(20):6137–6143Google Scholar
  63. 63.
    Cheng J, Sheldon EL, Wu L, Uribe A, Gerrue LO, Carrino J, Heller MJ, O’Connell JP (1998) Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips. Nat Biotechnol 16(6):541–546Google Scholar
  64. 64.
    Liu J, Enzelberger M, Quake S (2002) A nanoliter rotary device for polymerase chain reaction. Electrophoresis 23(10):1531–1536Google Scholar
  65. 65.
    He Y, Zhang YHH, Yeung ES (2001) Capillary-based fully integrated and automated system for nanoliter polymerase chain reaction analysis directly from cheek cells. J Chromatogr A 924(1–2):271–284Google Scholar
  66. 66.
    Hartshorn C, Rice JE, Wangh LJ (2003) Differential pattern of Xist RNA accumulation in single blastomeres isolated from 8-cell stage mouse embryos following laser zona drilling. Mol Reprod Dev 64(1):41–51Google Scholar
  67. 67.
    Stahlberg A, Bengtsson M (2010) Single-cell gene expression profiling using reverse transcription quantitative real-time PCR. Methods 50(4):282–288Google Scholar
  68. 68.
    Peixoto A, Monteiro M, Rocha B, Veiga-Fernandes H (2004) Quantification of multiple gene expression in individual cells. Genome Res 14(10A):1938–1947Google Scholar
  69. 69.
    Taniguchi K, Kajiyama T, Kambara H (2009) Quantitative analysis of gene expression in a single cell by qPCR. Nat Methods 6(7):503–506.Google Scholar
  70. 70.
    Diercks A, Kostner H, Ozinsky A (2009) Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS ONE 4(7):e6326Google Scholar
  71. 71.
    Toledo-Rodriguez M, Blumenfeld B, Wu C, Luo J, Attali B, Goodman P, Markram H (2004) Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cereb Cortex 14(12):1310–1327Google Scholar
  72. 72.
    Eberwine J, Kacharmina JE, Andrews C, Miyashiro K, McIntosh T, Becker K, Barrett T, Hinkle D, Dent G, Marciano P (2001) mRna expression analysis of tissue sections and single cells. J Neurosci 21(21):8310–8314Google Scholar
  73. 73.
    Xiang CC, Kozhich OA, Chen M, Inman JM, Phan QN, Chen Y, Brownstein MJ (2002) Amine-modified random primers to label probes for DNA microarrays. Nat Biotechnol 20(7):738–742Google Scholar
  74. 74.
    Zhou W, Abruzzese RV, Polejaeva I, Davis S, Davis S, Ji W (2005) Amplification of nanogram amounts of total RNA by the SMART-based PCR method for high-density oligonucleotide microarrays. Clin Chem 51(12):2354–2356Google Scholar
  75. 75.
    Jenson SD, Robetorye RS, Bohling SD, Schumacher JA, Morgan JW, Lim MS, Elenitoba-Johnson KS (2003) Validation of cDNA microarray gene expression data obtained from linearly amplified RNA. Mol Pathol 56(6):307–312Google Scholar
  76. 76.
    Hinkle D, Glanzer J, Sarabi A, Pajunen T, Zielinski J, Belt B, Miyashiro K, McIntosh T, Eberwine J (2004) Single neurons as experimental systems in molecular biology. Prog Neurobiol 72(2):129–142Google Scholar
  77. 77.
    Chiang MK, Melton DA (2003) Single-cell transcript analysis of pancreas development. Dev Cell 4(3):383–393Google Scholar
  78. 78.
    Kralj JG, Player A, Sedrick H, Munson MS, Petersen D, Forry SP, Meltzer P, Kawasaki E, Locascio LE (2009) T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements. Lab Chip 9(7):917–924Google Scholar
  79. 79.
    Gong Y, Ogunniyi AO, Love JC (2010) Massively parallel detection of gene expression in single cells using subnanolitre wells. Lab Chip: Epub ahead of printGoogle Scholar
  80. 80.
    Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6(5):377–382Google Scholar
  81. 81.
    Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, Khrebtukova I, Yang Y, Thannhauser T, Butcher BG, Cartinhour S, Schneider DJ (2010) Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol 192(9):2359–2372Google Scholar
  82. 82.
    Isaacs FJ, Blake WJ, Collins JJ (2005) Molecular biology. Signal processing in single cells. Science 307(5717):1886–1888Google Scholar
  83. 83.
    Lidstrom ME, Meldrum DR (2003) Life-on-a-chip. Nat Rev Microbiol 1(2):158–164Google Scholar
  84. 84.
    Le TT, Harlepp S, Guet CC, Dittmar K, Emonet T, Pan T, Cluzel P (2005) Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci USA 102(26):9160–9164Google Scholar
  85. 85.
    Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH (2004) Dynamics of single mRNPs in nuclei of living cells. Science 304(5678):1797–1800Google Scholar
  86. 86.
    Paulsson J (2004) Summing up the noise in gene networks. Nature 427(6973):415–418Google Scholar
  87. 87.
    Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2(4):437–445Google Scholar
  88. 88.
    Golding I, Cox EC (2004) RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci USA 101(31):11310–11315Google Scholar
  89. 89.
    Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Hixson KK, Zhao R, Anderson GA, Smith RD (2004) Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal Chem 76(1):144–154Google Scholar
  90. 90.
    Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198–207Google Scholar
  91. 91.
    Hu S, Le Z, Krylov S, Dovichi NJ (2003) Cell cycle-dependent protein fingerprint from a single cancer cell: image cytometry coupled with single-cell capillary sieving electrophoresis. Anal Chem 75(14):3495–3501Google Scholar
  92. 92.
    Hu S, Le Z, Newitt R, Aebersold R, Kraly JR, Jones M, Dovichi NJ (2003) Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins. Anal Chem 75(14):3502–3505Google Scholar
  93. 93.
    Gao J, Yin XF, Fang ZL (2004) Integration of single cell injection, cell lysis, separation and detection of intracellular constituents on a microfluidic chip. Lab Chip 4(1):47–52Google Scholar
  94. 94.
    Han F, Wang Y, Sims CE, Bachman M, Chang R, Li GP, Allbritton NL (2003) Fast electrical lysis of cells for capillary electrophoresis. Anal Chem 75(15):3688–3696Google Scholar
  95. 95.
    Zhang Z, Krylov S, Arriaga EA, Polakowski R, Dovichi NJ (2000) One-dimensional protein analysis of an HT29 human colon adenocarcinoma cell. Anal Chem 72(2):318–322Google Scholar
  96. 96.
    Hellmich W, Pelargus C, Leffhalm K, Ros A, Anselmetti D (2005) Single cell manipulation, analytics, and label-free protein detection in microfluidic devices for systems nanobiology. Electrophoresis 26(19):3689–3696Google Scholar
  97. 97.
    Malek A, Khaledi MG (1999) Expression and analysis of green fluorescent proteins in human embryonic kidney cells by capillary electrophoresis. Anal Biochem 268(2):262–269Google Scholar
  98. 98.
    Turner EH, Lauterbach K, Pugsley HR, Palmer VR, Dovichi NJ (2007) Detection of green fluorescent protein in a single bacterium by capillary electrophoresis with laser-induced fluorescence. Anal Chem 79(2):778–781Google Scholar
  99. 99.
    Zhang H, Jin W (2004) Determination of different forms of human interferon-gamma in single natural killer cells by capillary electrophoresis with on-capillary immunoreaction and laser-induced fluorescence detection. Electrophoresis 25(7–8):1090–1095Google Scholar
  100. 100.
    Michels DA, Hu S, Schoenherr RM, Eggertson MJ, Dovichi NJ (2002) Fully automated two-dimensional capillary electrophoresis for high sensitivity protein analysis. Mol Cell Proteomics 1(1):69–74Google Scholar
  101. 101.
    Zhang H, Jin W (2006) Single-cell analysis by intracellular immuno-reaction and capillary electrophoresis with laser-induced fluorescence detection. J Chromatogr A 1104(1–2):346–351Google Scholar
  102. 102.
    Sun X, Jin W (2003) Catalysis-electrochemical determination of zeptomole enzyme and its application for single-cell analysis. Anal Chem 75(22):6050–6055Google Scholar
  103. 103.
    Li L, Garden RW, Romanova EV, Sweedler JV (1999) In situ sequencing of peptides from biological tissues and single cells using MALDI-PSD/CID analysis. Anal Chem 71(24):5451–5458Google Scholar
  104. 104.
    Rubakhin SS, Greenough WT, Sweedler JV (2003) Spatial profiling with MALDI MS: distribution of neuropeptides within single neurons. Anal Chem 75(20):5374–5380Google Scholar
  105. 105.
    Rubakhin SS, Sweedler JV (2008) Quantitative measurements of cell-cell signaling peptides with single-cell MALDI MS. Anal Chem 80(18):7128–7136Google Scholar
  106. 106.
    Rubakhin SS, Churchill JD, Greenough WT, Sweedler JV (2006) Profiling signaling peptides in single mammalian cells using mass spectrometry. Anal Chem 78(20):7267–7272Google Scholar
  107. 107.
    Rubakhin SS, Sweedler JV (2007) Characterizing peptides in individual mammalian cells using mass spectrometry. Nat Protoc 2(8):1987–1997Google Scholar
  108. 108.
    Jehmlich N, Hubschmann T, Salazar MG, Volker U, Benndorf D, Muller S, Bergen Mv, Schmidt F (2010) Advanced tool for characterization of microbial cultures by combining cytomics and proteomics. Appl Microbiol Biotechnol in press.Google Scholar
  109. 109.
    Hofstadler SA, Severs JC, Smith RD, Swanek FD, Ewing AG (1996) Analysis of single cells with capillary electrophoresis electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 10(8):919–922Google Scholar
  110. 110.
    Cao P, Moini M (1999) Separation and detection of the alpha- and beta-chains of hemoglobin of a single intact red blood cells using capillary electrophoresis/electrospray ionization time-of-flight mass spectrometry. J Am Soc Mass Spectrom 10(2):184–186Google Scholar
  111. 111.
    Moini M, Demars SM, Huang H (2002) Analysis of carbonic anhydrase in human red Blood cells using capillary electrophoresis/electrospray ionization-mass spectrometry. Anal Chem 74(15):3772–3776Google Scholar
  112. 112.
    Belov ME, Gorshkov MV, Udseth HR, Anderson GA, Smith RD (2000) Zeptomole-sensitivity electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry of proteins. Anal Chem 72(10):2271–2279Google Scholar
  113. 113.
    Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG 2nd, Lipton MS, Anderson GA, Smith RD (2004) Nanoscale proteomics. Anal Bioanal Chem 378(4):1037–1045Google Scholar
  114. 114.
    Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441(7095):840–846Google Scholar
  115. 115.
    Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322(5907):1511–1516Google Scholar
  116. 116.
    Yin H, Killeen K, Brennen R, Sobek D, Werlich M, van de Goor T (2005) Microfluidic chip for peptide analysis with an integrated HPLC column, sample enrichment column, and nanoelectrospray tip. Anal Chem 77(2):527–533Google Scholar
  117. 117.
    Fortier MH, Bonneil E, Goodley P, Thibault P (2005) Integrated microfluidic device for mass spectrometry-based proteomics and its application to biomarker discovery programs. Anal Chem 77(6):1631–1640Google Scholar
  118. 118.
    Jo K, Heien ML, Thompson LB, Zhong M, Nuzzo RG, Sweedler JV (2007) Mass spectrometric imaging of peptide release from neuronal cells within microfluidic devices. Lab Chip 7(11):1454–1460Google Scholar
  119. 119.
    Ryley J, Pereira-Smith OM (2006) Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae. Yeast 23(14–15):1065–1073Google Scholar
  120. 120.
    Yu J, Xiao J, Ren XJ, Lao KQ, Xie XS (2006) Probing gene expression in live cells, one protein molecule at a time. Science 311(5767):1600–1603Google Scholar
  121. 121.
    Gefen O, Gabay C, Mumcuoglu M, Engel G, Balaban NQ (2008) Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria. Proc Natl Acad Sci USA 105(16):6145–6149Google Scholar
  122. 122.
    Kortmann H, Kurth F, Blank LM, Dittrich P, Schmid A (2009) Towards real time analysis of protein secretion from single cells. Lab Chip 9(21):3047–3049Google Scholar
  123. 123.
    Amantonico A, Oh JY, Sobek J, Heinemann M, Zenobi R (2008) Mass spectrometric method for analyzing metabolites in yeast with single cell sensitivity. Angew Chem Int Ed Engl 47(29):5382–5385Google Scholar
  124. 124.
    Schrumpf B, Eggeling L, Sahm H (1992) Isolation and prominent characteristics of an L-lysine hyperproducing strain of Corynebacterium glutamicum. Appl Microbiol Biotechnol 37(5):566–571Google Scholar
  125. 125.
    Blank LM, Kuepfer L, Sauer U (2005) Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 6(6):R49Google Scholar
  126. 126.
    Krylov SN, Zhang Z, Chan NW, Arriaga E, Palcic MM, Dovichi NJ (1999) Correlating cell cycle with metabolism in single cells: combination of image and metabolic cytometry. Cytometry 37(1):14–20Google Scholar
  127. 127.
    Whitmore CD, Hindsgaul O, Palcic MM, Schnaar RL, Dovichi NJ (2007) Metabolic cytometry. Glycosphingolipid metabolism in single cells. Anal Chem 79(14):5139–5142Google Scholar
  128. 128.
    Zhang H, Jin W (2004) Analysis of amino acids in individual human erythrocytes by capillary electrophoresis with electroporation for intracellular derivatization and laser-induced fluorescence detection. Electrophoresis 25(3):480–486Google Scholar
  129. 129.
    Allen PB, Doepker BR, Chiu DT (2009) High-throughput capillary-electrophoresis analysis of the contents of a single mitochondria. Anal Chem 81(10):3784–3791Google Scholar
  130. 130.
    Wu H, Wheeler A, Zare RN (2004) Chemical cytometry on a picoliter-scale integrated microfluidic chip. Proc Natl Acad Sci USA 101(35):12809–12813Google Scholar
  131. 131.
    Lapainis T, Rubakhin SS, Sweedler JV (2009) Capillary electrophoresis with electrospray ionization mass spectrometric detection for single-cell metabolomics. Anal Chem 81(14):5858–5864Google Scholar
  132. 132.
    Mizuno H, Tsuyama N, Date S, Harada T, Masujima T (2008) Live single-cell metabolomics of tryptophan and histidine metabolites in a rat basophil leukemia cell. Anal Sci 24(12):1525–1527Google Scholar
  133. 133.
    Amantonico A, Urban PL, Oh JY, Zenobi R (2009) Interfacing microfluidics and laser desorption/Ionization mass spectrometry by continuous deposition for application in single cell analysis. Chimia (Aarau) 63(4):185–188Google Scholar
  134. 134.
    Deuschle K, Chaudhuri B, Okumoto S, Lager I, Lalonde S, Frommer WB (2006) Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants. Plant Cell 18(9):2314–2325Google Scholar
  135. 135.
    Niittylae T, Chaudhuri B, Sauer U, Frommer WB (2009) Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics. Methods Mol Biol 553:355–372Google Scholar
  136. 136.
    Cai L, Friedman N, Xie XS (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440(7082):358–362Google Scholar
  137. 137.
    Cai X, Klauke N, Glidle A, Cobbold P, Smith GL, Cooper JM (2002) Ultra-low-volume, real-time measurements of lactate from the single heart cell using microsystems technology. Anal Chem 74(4):908–914Google Scholar
  138. 138.
    Cheng W, Klauke N, Sedgwick H, Smith GL, Cooper JM (2006) Metabolic monitoring of the electrically stimulated single heart cell within a microfluidic platform. Lab Chip 6(11):1424–1431Google Scholar
  139. 139.
    Molter TW, Holl MR, Dragavon JM, McQuaide SC, Anderson JB, Young AC, Burgess LW, Lidstrom ME, Meldrum DR (2008) A new approach for measuring single-cell oxygen consumption rates. IEEE Trans Autom Sci Eng 5(1):32–42Google Scholar
  140. 140.
    Dragavon J, Molter T, Young C, Strovas T, McQuaide S, Holl M, Zhang M, Cookson B, Jen A, Lidstrom M, Meldrum D, Burgess L (2008) A cellular isolation system for real-time single-cell oxygen consumption monitoring. J R Soc Interface 5 Suppl 2:S151–S159Google Scholar
  141. 141.
    Molter TW, McQuaide SC, Suchorolski MT, Strovas TJ, Burgess LW, Meldrum DR, Lidstrom ME (2009) A microwell array device capable of measuring single-cell oxygen consumption rates. Sens Actuators B Chem 135(2):678–686Google Scholar
  142. 142.
    Diaz-Ruiz R, Uribe-Carvajal S, Devin A, Rigoulet M (2009) Tumor cell energy metabolism and its common features with yeast metabolism. Biochim Biophys Acta 1796(2):252–265Google Scholar
  143. 143.
    Chao TC, Ros A (2008) Microfluidic single-cell analysis of intracellular compounds. J R Soc Interface 5:S139–S150Google Scholar
  144. 144.
    Andersson H, van den Berg A (2004) Microtechnologies and nanotechnologies for single-cell analysis. Curr Opin Biotechnol 15(1):44–49Google Scholar
  145. 145.
    Sims CE, Allbritton NL (2007) Analysis of single mammalian cells on-chip. Lab Chip 7(4):423–440Google Scholar
  146. 146.
    Huang WH, Ai F, Wang ZL, Cheng JK (2008) Recent advances in single-cell analysis using capillary electrophoresis and microfluidic devices. J Chromatogr B Analyt Technol Biomed Life Sci 866(1–2):104–122Google Scholar
  147. 147.
    Borland LM, Kottegoda S, Phillips KS, Allbritton NL (2008) Chemical analysis of single cells. Annu Rev Anal Chem 1:191–227Google Scholar
  148. 148.
    Roman GT, Chen YL, Viberg P, Culbertson AH, Culbertson CT (2007) Single-cell manipulation and analysis using microfluidic devices. Anal Bioanal Chem 387(1):9–12Google Scholar
  149. 149.
    Schmid A, Blank LM (2010) Systems biology: hypothesis-driven omics integration. Nat Chem Biol 6(7):485–487Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical EngineeringTU Dortmund UniversityDortmundGermany
  2. 2.Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.DortmundGermany

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