Microfluidic Systems for Marine Biotechnology References 525
Part C | 20
20.8
C.L. Hansen, E. Skordalakes, J.M. Berger,
S.R. Quake: A robust and scalable microfluidic metering method that allows protein crystal
growth by free interface diffusion, Proc. Natl.
Acad. Sci. USA 99(26), 16531–16536 (2002)
20.9
J.W. Hong, V. Studer, G. Hang, W.F. Anderson,
S.R. Quake: A nanoliter-scale nucleic acid processor with parallel architecture, Nat. Biotechnol.
22(4), 435–439 (2004)
20.10
L. Warren, D. Bryder, I.L. Weissman, S.R. Quake:
Transcription factor profiling in individual
hematopoietic progenitors by digital RT-PCR,
Proc. Natl. Acad. Sci. USA 103(47), 17807–17812
(2006)
20.11
R. Gomez-Sjoberg, A.A. Leyrat, D.M. Pirone,
C.S. Chen, S.R. Quake: Versatile, fully automated,
microfluidic cell culture system, Anal. Chem.
79(22), 8557–8563 (2007)
20.12
F.K. Balagaddé, H. Song, J. Ozaki, C.H. Collins,
M. Barnet, F.H. Arnold, S.R. Quake, L. You: A synthetic Escherichia coli predator–prey ecosystem,
Mol. Syst. Biol. 4, 1–8 (2008)
20.13
S. Jambovane, E. Duin, S. Kim, J. Hong: Determination of kinetic parameters, K m and k cat , with a
single experiment on a chip, Anal. Chem. 81(9),
3239–3245 (2009)
20.14
J.Y. Yun, S. Jambovane, S.-K. Kim, S.-H. Cho,
E.C. Duin, J.W. Hong: Log-scale dose response of
inhibitors on a chip, Anal. Chem. 83(16), 6148–
6153 (2011)
20.15
S. Jambovane, D.J. Kim, E.C. Duin, S.-K. Kim,
J.W. Hong: Creation of stepwise concentration
gradient in picoliter droplets for parallel reactions
of matrix metalloproteinase II and IX, Anal. Chem.
83(9), 3358–3364 (2011)
20.16
M. Hamon, S. Jambovane, L. Bradley, A. Khademhosseini, J.W. Hong: Cell-based dose responses
from open-well microchambers, Anal. Chem.
85(10), 5249–5254 (2013)
20.17
H.P. Chou, M.A. Unger, S.R. Quake: A microfabricated rotary pump, Biomed. Microdevices 3(4),
323–330 (2001)
20.18
N. Nguyen, Z. Wu: Micromixers – A review, J. Micromech. and Microen. 15(2), R1–R16 (2005)
20.19
A. Stroock, S. Dertinger, A. Ajdari, I. Mezic,
H. Stone, G. Whitesides: Chaotic mixer for microchannels, Science 295(5555), 647–651 (2002)
20.20
M. Oddy, J. Santiago, J. Mikkelsen: Electrokinetic instability micromixing, Anal. Chem. 73(24),
5822–5832 (2001)
20.21
C.H. Tai, R.J. Yang, M.Z. Huang, C.W. Liu,
C.H. Tsai, L.M. Fu: Micromixer utilizing electrokinetic instability-induced shedding effect, Electrophoresis 27(24), 4982–4990 (2006)
20.22
C.R. Woese, G.E. Fox: Phylogenetic structure of the
prokaryotic domain: The primary kingdoms, Proc.
Natl. Acad. Sci. USA 74(11), 5088–5090 (1977)
20.23
D.J. Lane, B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin, N.R. Pace: Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc. Natl. Acad. Sci. USA 82(20), 6955–6959
(1985)
20.24
J.L. Stein, T.L. Marsh, K.Y. Wu, H. Shizuya, E.F. DeLong: Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobasepair genome fragment from a planktonic marine archaeon, J. Bacteriol. 178(3), 591–599
(1996)
20.25
G. Dick, A. Andersson, B. Baker, S. Simmons,
B. Thomas, A.P. Yelton, J. Banfield: Communitywide analysis of microbial genome sequence signatures, Genome Biol. 10(8), R85 (2009)
20.26
Y. Marcy, C. Ouverney, E.M. Bik, T. Lösekann,
N. Ivanova, H.G. Martin, E. Szeto, D. Platt,
P. Hugenholtz, D.A. Relman, S.R. Quake: Dissecting biological “dark matter” with single-cell
genetic analysis of rare and uncultivated TM7 microbes from the human mouth, Proc. Natl. Acad.
Sci. USA 104(29), 1889–11894 (2007)
20.27
T. Woyke, D. Tighe, K. Mavromatis, A. Clum,
A. Copeland, W. Schackwitz, A. Lapidus, D. Wu,
J.P. McCutcheon, B.R. McDonald, N.A. Moran,
J. Bristow, J.F. Cheng: One bacterial cell, one
complete genome, PLoS ONE 5(4)(29), e10314
(2010)
20.28
E.K. Binga, R.S. Lasken, J.D. Neufeld: Something
from (almost) nothing: The impact of multiple
displacement amplification on microbial ecology,
ISME Journal 2(3), 233–241 (2008)
20.29
T. Ishoey, T. Woyke, R. Stepanauskas, M. Novotny,
R.S. Lasken: Genomic sequencing of single microbial cells from environmental samples, Curr. Opin.
Microbiol. 11(3), 198–204 (2008)
20.30
R.S. Lasken: Single-cell genomic sequencing using Multiple Displacement Amplification, Curr.
Opin. Microbiol. 10(5), 510–516 (2007)
20.31
R.S. Lasken: Genomic sequencing of uncultured
microorganisms from single cells, Nat. Rev. Microbiol. 10(9), 631–640 (2012)
20.32
V. de Jager, R.J. Siezen: Single-cell genomics: Unravelling the genomes of unculturable microorganisms, Microb. Biotechnol. 4(4), 431–437 (2011)
20.33
T. Kalisky, P. Blainey, S.R. Quake: Genomic analysis
at the single-cell level, Annu. Rev. Genet. 45, 431–
445 (2011)
20.34
T. Kalisky, S.R. Quake: Single-cell genomics, Nat.
Methods 8(4), 311–314 (2011)
20.35
Y. Marcy, T. Ishoey, R.S. Lasken, T.B. Stockwell,
B.P. Walenz, A.L. Halpern, K.Y. Beeson, S.M. Goldberg, S.R. Quake: Nanoliter reactors improve
multiple displacement amplification of genomes
from single cells, PLoS Genetics 3(9), 1702–1708
(2007)
20.36
A.K. White, M. VanInsberghe, O.I. Petriv, M. Ha
midi, D. Sikorski, M.A. Marra, J. Piret, S. Aparicio, C.L. Hansen: High-throughput microfluidic
single-cell RT-qPCR, Proc. Natl. Acad. Sci. USA
108(34), 13999–14004 (2011)
Part C | 20
20.8
C.L. Hansen, E. Skordalakes, J.M. Berger,
S.R. Quake: A robust and scalable microfluidic metering method that allows protein crystal
growth by free interface diffusion, Proc. Natl.
Acad. Sci. USA 99(26), 16531–16536 (2002)
20.9
J.W. Hong, V. Studer, G. Hang, W.F. Anderson,
S.R. Quake: A nanoliter-scale nucleic acid processor with parallel architecture, Nat. Biotechnol.
22(4), 435–439 (2004)
20.10
L. Warren, D. Bryder, I.L. Weissman, S.R. Quake:
Transcription factor profiling in individual
hematopoietic progenitors by digital RT-PCR,
Proc. Natl. Acad. Sci. USA 103(47), 17807–17812
(2006)
20.11
R. Gomez-Sjoberg, A.A. Leyrat, D.M. Pirone,
C.S. Chen, S.R. Quake: Versatile, fully automated,
microfluidic cell culture system, Anal. Chem.
79(22), 8557–8563 (2007)
20.12
F.K. Balagaddé, H. Song, J. Ozaki, C.H. Collins,
M. Barnet, F.H. Arnold, S.R. Quake, L. You: A synthetic Escherichia coli predator–prey ecosystem,
Mol. Syst. Biol. 4, 1–8 (2008)
20.13
S. Jambovane, E. Duin, S. Kim, J. Hong: Determination of kinetic parameters, K m and k cat , with a
single experiment on a chip, Anal. Chem. 81(9),
3239–3245 (2009)
20.14
J.Y. Yun, S. Jambovane, S.-K. Kim, S.-H. Cho,
E.C. Duin, J.W. Hong: Log-scale dose response of
inhibitors on a chip, Anal. Chem. 83(16), 6148–
6153 (2011)
20.15
S. Jambovane, D.J. Kim, E.C. Duin, S.-K. Kim,
J.W. Hong: Creation of stepwise concentration
gradient in picoliter droplets for parallel reactions
of matrix metalloproteinase II and IX, Anal. Chem.
83(9), 3358–3364 (2011)
20.16
M. Hamon, S. Jambovane, L. Bradley, A. Khademhosseini, J.W. Hong: Cell-based dose responses
from open-well microchambers, Anal. Chem.
85(10), 5249–5254 (2013)
20.17
H.P. Chou, M.A. Unger, S.R. Quake: A microfabricated rotary pump, Biomed. Microdevices 3(4),
323–330 (2001)
20.18
N. Nguyen, Z. Wu: Micromixers – A review, J. Micromech. and Microen. 15(2), R1–R16 (2005)
20.19
A. Stroock, S. Dertinger, A. Ajdari, I. Mezic,
H. Stone, G. Whitesides: Chaotic mixer for microchannels, Science 295(5555), 647–651 (2002)
20.20
M. Oddy, J. Santiago, J. Mikkelsen: Electrokinetic instability micromixing, Anal. Chem. 73(24),
5822–5832 (2001)
20.21
C.H. Tai, R.J. Yang, M.Z. Huang, C.W. Liu,
C.H. Tsai, L.M. Fu: Micromixer utilizing electrokinetic instability-induced shedding effect, Electrophoresis 27(24), 4982–4990 (2006)
20.22
C.R. Woese, G.E. Fox: Phylogenetic structure of the
prokaryotic domain: The primary kingdoms, Proc.
Natl. Acad. Sci. USA 74(11), 5088–5090 (1977)
20.23
D.J. Lane, B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin, N.R. Pace: Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc. Natl. Acad. Sci. USA 82(20), 6955–6959
(1985)
20.24
J.L. Stein, T.L. Marsh, K.Y. Wu, H. Shizuya, E.F. DeLong: Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobasepair genome fragment from a planktonic marine archaeon, J. Bacteriol. 178(3), 591–599
(1996)
20.25
G. Dick, A. Andersson, B. Baker, S. Simmons,
B. Thomas, A.P. Yelton, J. Banfield: Communitywide analysis of microbial genome sequence signatures, Genome Biol. 10(8), R85 (2009)
20.26
Y. Marcy, C. Ouverney, E.M. Bik, T. Lösekann,
N. Ivanova, H.G. Martin, E. Szeto, D. Platt,
P. Hugenholtz, D.A. Relman, S.R. Quake: Dissecting biological “dark matter” with single-cell
genetic analysis of rare and uncultivated TM7 microbes from the human mouth, Proc. Natl. Acad.
Sci. USA 104(29), 1889–11894 (2007)
20.27
T. Woyke, D. Tighe, K. Mavromatis, A. Clum,
A. Copeland, W. Schackwitz, A. Lapidus, D. Wu,
J.P. McCutcheon, B.R. McDonald, N.A. Moran,
J. Bristow, J.F. Cheng: One bacterial cell, one
complete genome, PLoS ONE 5(4)(29), e10314
(2010)
20.28
E.K. Binga, R.S. Lasken, J.D. Neufeld: Something
from (almost) nothing: The impact of multiple
displacement amplification on microbial ecology,
ISME Journal 2(3), 233–241 (2008)
20.29
T. Ishoey, T. Woyke, R. Stepanauskas, M. Novotny,
R.S. Lasken: Genomic sequencing of single microbial cells from environmental samples, Curr. Opin.
Microbiol. 11(3), 198–204 (2008)
20.30
R.S. Lasken: Single-cell genomic sequencing using Multiple Displacement Amplification, Curr.
Opin. Microbiol. 10(5), 510–516 (2007)
20.31
R.S. Lasken: Genomic sequencing of uncultured
microorganisms from single cells, Nat. Rev. Microbiol. 10(9), 631–640 (2012)
20.32
V. de Jager, R.J. Siezen: Single-cell genomics: Unravelling the genomes of unculturable microorganisms, Microb. Biotechnol. 4(4), 431–437 (2011)
20.33
T. Kalisky, P. Blainey, S.R. Quake: Genomic analysis
at the single-cell level, Annu. Rev. Genet. 45, 431–
445 (2011)
20.34
T. Kalisky, S.R. Quake: Single-cell genomics, Nat.
Methods 8(4), 311–314 (2011)
20.35
Y. Marcy, T. Ishoey, R.S. Lasken, T.B. Stockwell,
B.P. Walenz, A.L. Halpern, K.Y. Beeson, S.M. Goldberg, S.R. Quake: Nanoliter reactors improve
multiple displacement amplification of genomes
from single cells, PLoS Genetics 3(9), 1702–1708
(2007)
20.36
A.K. White, M. VanInsberghe, O.I. Petriv, M. Ha
midi, D. Sikorski, M.A. Marra, J. Piret, S. Aparicio, C.L. Hansen: High-throughput microfluidic
single-cell RT-qPCR, Proc. Natl. Acad. Sci. USA
108(34), 13999–14004 (2011)