Nano-Enabled Approaches to Chemical Imaging in Biosystems

Literature Cited

1. 1.  Thorn K 2017. Genetically encoded fluorescent tags. Mol. Biol. Cell 28:848–57
   [Google Scholar]
2. 2.  Dunn WB, Ellis DI 2005. Metabolomics: current analytical platforms and methodologies. Trends Anal. Chem. 24:285–94
   [Google Scholar]
3. 3.  Meyer E, Hug HJ, Bennewitz R 2004. Scanning Probe Microscopy: The Lab on a Tip Berlin/Heidelberg: Springer-Verlag
4. 4.  Lyra da Cunha MM, Trepout S, Messaoudi C, Wu T-D, Ortega R et al. 2016. Overview of chemical imaging methods to address biological questions. Micron 84:23–36
   [Google Scholar]
5. 5.  Watrous JD, Dorrestein PC 2011. Imaging mass spectrometry in microbiology. Nat. Rev. Microbiol. 9:683–94
   [Google Scholar]
6. 6.  Lanni EJ, Rubakhin SS, Sweedler JV 2012. Mass spectrometry imaging and profiling of single cells. J. Proteom. 75:5036–51
   [Google Scholar]
7. 7.  Watrous JD, Dorrestein PC 2011. Imaging mass spectrometry in microbiology. Nat. Rev. Microbiol. 9:683–94
   [Google Scholar]
8. 8.  Allison DP, Mortensen NP, Sullivan CJ, Doktycz MJ 2010. Atomic force microscopy of biological samples. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 2:618–34
   [Google Scholar]
9. 9.  Müller DJ, Dufrêne YF 2011. Atomic force microscopy: a nanoscopic window on the cell surface. Trends Cell Biol 21:461–69
   [Google Scholar]
10. 10.  Sydor AM, Czymmek KJ, Puchner EM, Mennella V 2015. Super-resolution microscopy: from single molecules to supramolecular assemblies. Trends Cell Biol 25:730–48
    [Google Scholar]
11. 11.  Lereu AL, Passian A, Dumas P 2012. Near field optical microscopy: a brief review. Int. J. Nanotechnol. 9:488
    [Google Scholar]
12. 12.  Lewis A, Taha H, Strinkovski A, Manevitch A, Khatchatouriants A et al. 2003. Near-field optics: from subwavelength illumination to nanometric shadowing. Nat. Biotechnol. 21:1378–86
    [Google Scholar]
13. 13.  Richards D 2003. Near-field microscopy: throwing light on the nanoworld. Philos. Trans. R. Soc. A 361:2843–57
    [Google Scholar]
14. 14.  Mauser N, Hartschuh A 2014. Tip-enhanced near-field optical microscopy. Chem. Soc. Rev. 43:1248–62
    [Google Scholar]
15. 15.  Schmid T, Opilik L, Blum C, Zenobi R 2013. Nanoscale chemical imaging using tip-enhanced Raman spectroscopy: a critical review. Angew. Chem. Int. Ed. 52:5940–54
    [Google Scholar]
16. 16.  Shalaev VM 2008. Transforming light. Science 322:384–86
    [Google Scholar]
17. 17.  Khorasaninejad M, Chen WT, Devlin RC, Oh J, Zhu AY, Capasso F 2016. Metalenses at visible wavelengths: diffraction-limited focusing and subwavelength resolution imaging. Science 352:1190–94
    [Google Scholar]
18. 18.  Simovski CR, Belov PA, Atrashchenko AV, Kivshar YS 2012. Wire metamaterials: physics and applications. Adv. Mater. 24:4229–48
    [Google Scholar]
19. 19.  Valentine J, Zhang S, Zentgraf T, Ulin-Avila E, Genov DA et al. 2008. Three-dimensional optical metamaterial with a negative refractive index. Nature 455:376–79
    [Google Scholar]
20. 20.  Pendry JB 2000. Negative refraction makes a perfect lens. Phys. Rev. Lett. 85:3966–69
    [Google Scholar]
21. 21.  Liu Z, Lee H, Xiong Y, Sun C, Zhang X 2007. Far-field optical hyperlens magnifying sub-diffraction-limited objects. Science 315:1686
    [Google Scholar]
22. 22.  Smolyaninov II, Hung YJ, Davis CC 2007. Magnifying superlens in the visible frequency range. Science 315:1699–701
    [Google Scholar]
23. 23.  Ono A, Kato J, Kawata S 2005. Subwavelength optical imaging through a metallic nanorod array. Phys. Rev. Lett. 95:267407
    [Google Scholar]
24. 24.  Kawata S, Ono A, Verma P 2008. Subwavelength colour imaging with a metallic nanolens. Nat. Photonics 2:438–42
    [Google Scholar]
25. 25.  Casse BDF, Lu WT, Huang YJ, Gultepe E, Menon L, Sridhar S 2010. Super-resolution imaging using a three-dimensional metamaterials nanolens. Appl. Phys. Lett. 96:023114
    [Google Scholar]
26. 26.  Mansfield SM, Kino GS 1990. Solid immersion microscope. Appl. Phys. Lett. 57:2615–16
    [Google Scholar]
27. 27.  Lee JY, Hong BH, Kim WY, Min SK, Kim Y et al. 2009. Near-field focusing and magnification through self-assembled nanoscale spherical lenses. Nature 460:498–501
    [Google Scholar]
28. 28.  Fan W, Yan B, Wang ZB, Wu LM 2016. Three-dimensional all-dielectric metamaterial solid immersion lens for subwavelength imaging at visible frequencies. Sci. Adv. 2:8e1600901
    [Google Scholar]
29. 29.  Kim MS, Scharf T, Haq MT, Nakagawa W, Herzig HP 2011. Subwavelength-size solid immersion lens. Opt. Lett. 36:3930–32
    [Google Scholar]
30. 30.  Jang J-W, Zheng Z, Lee O-S, Shim W, Zheng G et al. 2010. Arrays of nanoscale lenses for subwavelength optical lithography. Nano Lett 10:4399–404
    [Google Scholar]
31. 31.  Kang D, Pang C, Kim SM, Cho HS, Um HS et al. 2012. Shape-controllable microlens arrays via direct transfer of photocurable polymer droplets. Adv. Mater. 24:1709–15
    [Google Scholar]
32. 32.  Liau ZL, Liau AA, Porter JM, Salmon WC, Sheu SS, Chen JJ 2015. Solid-immersion fluorescence microscopy with increased emission and super resolution. J. Appl. Phys. 117:014502
    [Google Scholar]
33. 33.  Wang Z, Guo W, Li L, Luk'yanchuk B, Khan A et al. 2011. Optical virtual imaging at 50 nm lateral resolution with a white-light nanoscope. Nat. Commun. 2:218
    [Google Scholar]
34. 34.  Darafsheh A, Walsh GF, Dal Negro L, Astratov VN 2012. Optical super-resolution by high-index liquid-immersed microspheres. Appl. Phys. Lett. 101:141128
    [Google Scholar]
35. 35.  Monks JN, Yan B, Hawkins N, Vollrath F, Wang Z 2016. Spider silk: mother nature's bio-superlens. Nano Lett 16:5842–45
    [Google Scholar]
36. 36.  Darafsheh A, Wu GX, Yang S, Finlay JC 2016. Super-resolution optical microscopy by using dielectric microwires. Proc. SPIE Three-Dimens. Multidimens. Microsc. Image Acquis. Process., 9713. https://doi.org/10.1117/12.2211431
    [Crossref]
37. 37.  Heifetz A, Kong SC, Sahakian AV, Taflove A, Backman V 2009. Photonic nanojets. J. Comput. Theor. Nanosci. 6:1979–92
    [Google Scholar]
38. 38.  Allen KW, Farahi N, Li Y, Limberopoulos NI, Walker DE et al. 2015. Super-resolution microscopy by movable thin-films with embedded microspheres: resolution analysis. Ann. Phys. 527:513–22
    [Google Scholar]
39. 39.  Li PY, Tsao Y, Liu YJ, Lou ZX, Lee WL et al. 2016. Unusual imaging properties of superresolution microspheres. Opt. Express 24:16479–86
    [Google Scholar]
40. 40.  Yan YZ, Li L, Feng C, Guo W, Lee S, Hong MH 2014. Microsphere-coupled scanning laser confocal nanoscope for sub-diffraction-limited imaging at 25 nm lateral resolution in the visible spectrum. ACS Nano 8:1809–16
    [Google Scholar]
41. 41.  Darafsheh A, Guardiola C, Palovcak A, Finlay JC, Cárabe A 2015. Optical super-resolution imaging by high-index microspheres embedded in elastomers. Opt. Lett. 40:5–8
    [Google Scholar]
42. 42.  Du B, Ye Y-H, Hou J, Guo M, Wang T 2015. Sub-wavelength image stitching with removable microsphere-embedded thin film. Appl. Phys. A 122:15
    [Google Scholar]
43. 43.  Krivitsky LA, Wang JJ, Wang Z, Luk'yanchuk B 2013. Locomotion of microspheres for super-resolution imaging. Sci. Rep. 3:3501
    [Google Scholar]
44. 44.  Wang F, Liu L, Yu H, Wen Y, Yu P et al. 2016. Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging. Nat. Commun. 7:13748
    [Google Scholar]
45. 45.  Wang S, Zhang D, Zhang H, Han X, Xu R 2015. Super-resolution optical microscopy based on scannable cantilever-combined microsphere. Microsc. Res. Tech. 78:1128–32
    [Google Scholar]
46. 46.  Li J, Liu W, Li T, Rozen I, Zhao J et al. 2016. Swimming microrobot optical nanoscopy. Nano Lett 16:6604–9
    [Google Scholar]
47. 47.  Miklyaev YV, Asselborn SA, Zaytsev KA, Darscht MY 2014. Superresolution microscopy in far-field by near-field optical random mapping nanoscopy. Appl. Phys. Lett. 105:113103
    [Google Scholar]
48. 48.  Li L, Guo W, Yan Y, Lee S, Wang T 2013. Label-free super-resolution imaging of adenoviruses by submerged microsphere optical nanoscopy. Light Sci. Appl. 2:e104
    [Google Scholar]
49. 49.  Yang H, Moullan N, Auwerx J, Gijs MAM 2014. Super-resolution biological microscopy using virtual imaging by a microsphere nanoscope. Small 10:1712–18
    [Google Scholar]
50. 50.  Rogers ET, Lindberg J, Roy T, Savo S, Chad JE et al. 2012. A super-oscillatory lens optical microscope for subwavelength imaging. Nat. Mater. 11:432–35
    [Google Scholar]
51. 51.  Wong AM, Eleftheriades GV 2013. An optical super-microscope for far-field, real-time imaging beyond the diffraction limit. Sci. Rep. 3:1715
    [Google Scholar]
52. 52.  Qin F, Huang K, Wu J, Teng J, Qiu CW, Hong M 2017. A supercritical lens optical label-free microscopy: sub-diffraction resolution and ultra-long working distance. Adv. Mater. 29:1602721
    [Google Scholar]
53. 53.  Brus LE 1984. Electron–electron and electron–hole interactions in small semiconductor crystallites: the size dependence of the lowest excited electronic state. J. Chem. Phys. 80:4403–9
    [Google Scholar]
54. 54.  Åkerman ME, Chan WCW, Laakkonen P, Bhatia SN, Ruoslahti E 2002. Nanocrystal targeting in vivo. . PNAS 99:12617–21
    [Google Scholar]
55. 55.  Dubertret B, Skourides P, Norris DJ, Noireaux V, Brivanlou AH, Libchaber A 2002. In vivo imaging of quantum dots encapsulated in phospholipid micelles. Science 298:1759–62
    [Google Scholar]
56. 56.  Jaiswal JK, Mattoussi H, Mauro JM, Simon SM 2003. Long-term multiple color imaging of live cells using quantum dot bioconjugates. Nat. Biotech. 21:47–51
    [Google Scholar]
57. 57.  Wu X, Liu H, Liu J, Haley KN, Treadway JA et al. 2003. Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots. Nat. Biotech. 21:41–46
    [Google Scholar]
58. 58.  De M Ghosh PS, Rotello VM 2008. Applications of nanoparticles in biology. Adv. Mater. 20:4225–41
    [Google Scholar]
59. 59.  Wang EC, Wang AZ 2014. Nanoparticles and their applications in cell and molecular biology. Integr. Biol. 6:9–26
    [Google Scholar]
60. 60.  Sun Y-P, Zhou B, Lin Y, Wang W, Fernando KAS et al. 2006. Quantum-sized carbon dots for bright and colorful photoluminescence. J. Am. Chem. Soc. 128:7756–57
    [Google Scholar]
61. 61.  Yang S-T, Cao L, Luo PG, Lu F, Wang X et al. 2009. Carbon dots for optical imaging in vivo. J. Am. Chem. Soc. 131:11308–9
    [Google Scholar]
62. 62.  Wang W, Nallathamby PD, Foster CM, Morrell-Falvey JL, Mortensen NP et al. 2013. Volume labeling with Alexa Fluor dyes and surface functionalization of highly sensitive fluorescent silica (SiO₂) nanoparticles. Nanoscale 5:10369–75
    [Google Scholar]
63. 63.  Nallathamby PD, Mortensen NP, Palko HA, Malfatti M, Smith C et al. 2015. New surface radiolabeling schemes of super paramagnetic iron oxide nanoparticles (SPIONs) for biodistribution studies. Nanoscale 7:6545–55
    [Google Scholar]
64. 64.  Mortensen NP, Hurst GB, Wang W, Foster CM, Nallathamby PD, Retterer ST 2013. Dynamic development of the protein corona on silica nanoparticles: composition and role in toxicity. Nanoscale 5:6372–80
    [Google Scholar]
65. 65.  Zhang Y, Guo S, Cheng S, Ji X, He Z 2017. Label-free silicon nanodots featured ratiometric fluorescent aptasensor for lysosomal imaging and pH measurement. Biosens. Bioelectron. 94:478–84
    [Google Scholar]
66. 66.  Wang L, Hu C, Shao L 2017. The antimicrobial activity of nanoparticles: present situation and prospects for the future. Int. J. Nanomed. 12:1227–49
    [Google Scholar]
67. 67.  Sanvicens N, Pastells C, Pascual N, Marco MP 2009. Nanoparticle-based biosensors for detection of pathogenic bacteria. Trends Anal. Chem. 28:1243–52
    [Google Scholar]
68. 68.  Kloepfer J, Mielke R, Nadeau J 2005. Uptake of CdSe and CdSe/ZnS quantum dots into bacteria via purine-dependent mechanisms. Appl. Environ. Microbiol. 71:2548–57
    [Google Scholar]
69. 69.  Baena JR, Lendl B 2004. Raman spectroscopy in chemical bioanalysis. Curr. Opin. Chem. Biol. 8:534–39
    [Google Scholar]
70. 70.  Abalde-Cela S, Carregal-Romero S, Coelho JP, Guerrero-Martínez A 2016. Recent progress on colloidal metal nanoparticles as signal enhancers in nanosensing. Adv. Colloid Interface Sci. 233:255–70
    [Google Scholar]
71. 71.  Liu L, Jin M, Shi Y, Lin J, Zhang Y et al. 2015. Optical integrated chips with micro and nanostructures for refractive index and SERS-based optical label-free sensing. Nanophotonics 4:419–36
    [Google Scholar]
72. 72.  Opilik L, Schmid T, Zenobi R 2013. Modern Raman imaging: vibrational spectroscopy on the micrometer and nanometer scales. Annu. Rev. Anal. Chem. 6:379–98
    [Google Scholar]
73. 73.  Zhou H, Yang D, Ivleva NP, Mircescu NE, Niessner R, Haisch C 2014. SERS detection of bacteria in water by in situ coating with Ag nanoparticles. Anal. Chem. 86:1525–33
    [Google Scholar]
74. 74.  Polisetti S, Baig NF, Morales-Soto N, Shrout JD, Bohn PW 2017. Spatial mapping of pyocyanin in Pseudomonas aeruginosa bacterial communities using surface enhanced Raman scattering. Appl. Spectrosc. 71:215–23
    [Google Scholar]
75. 75.  Polisetti S, Bible AN, Morrell-Falvey JL, Bohn PW 2016. Raman chemical imaging of the rhizosphere bacterium Pantoea sp. YR343 and its co-culture with Arabidopsis thaliana. Analyst 141:2175–82
    [Google Scholar]
76. 76.  Li JF, Huang YF, Ding Y, Yang ZL, Li SB et al. 2010. Shell-isolated nanoparticle-enhanced Raman spectroscopy. Nature 464:392–95
    [Google Scholar]
77. 77.  Li J-F, Zhang Y-J, Ding S-Y, Panneerselvam R, Tian Z-Q. 2017. Core–shell nanoparticle-enhanced Raman spectroscopy. Chem. Rev. 117:5002–69
    [Google Scholar]
78. 78.  Zhu A, Qu Q, Shao X, Kong B, Tian Y 2012. Carbon-dot-based dual-emission nanohybrid produces a ratiometric fluorescent sensor for invivo imaging of cellular copper ions. Angew. Chem. 124:7297–301
    [Google Scholar]
79. 79.  Yang R, Guo X, Jia L, Zhang Y 2017. A fluorescent “on-off-on” assay for selective recognition of Cu(II) and glutathione based on modified carbon nanodots, and its application to cellular imaging. Microchim. Acta 184:1143–50
    [Google Scholar]
80. 80.  Wang H, Zhang P, Chen J, Li Y, Yu M et al. 2017. Polymer nanoparticle-based ratiometric fluorescent probe for imaging Hg²⁺ ions in living cells. Sens. Actuators B 242:818–24
    [Google Scholar]
81. 81.  Yan F, Kong D, Luo Y, Ye Q, He J et al. 2016. Carbon dots serve as an effective probe for the quantitative determination and for intracellular imaging of mercury(II). Microchim. Acta 183:1611–18
    [Google Scholar]
82. 82.  Hidalgo G, Burns A, Herz E, Hay AG, Houston PL et al. 2009. Functional tomographic fluorescence imaging of pH microenvironments in microbial biofilms by use of silica nanoparticle sensors. Appl. Environ. Microbiol. 75:7426–35
    [Google Scholar]
83. 83.  Chen J, Tang Y, Wang H, Zhang P, Li Y, Jiang J 2016. Design and fabrication of fluorescence resonance energy transfer-mediated fluorescent polymer nanoparticles for ratiometric sensing of lysosomal pH. J. Colloid Interface Sci. 484:298–307
    [Google Scholar]
84. 84.  Jiang Y, Wang M, Hardie J, Tonga GY, Ray M et al. 2016. Chemically engineered nanoparticle-protein interface for real-time cellular oxidative stress monitoring. Small 12:3775–79
    [Google Scholar]
85. 85.  Vaishanav SK, Korram J, Nagwanshi R, Ghosh KK, Satnami ML 2017. Mn²⁺ doped-CdTe/ZnS modified fluorescence nanosensor for detection of glucose. Sens. Actuators B 245:196–204
    [Google Scholar]
86. 86.  Huang S, Wang L, Huang C, Su W, Xiao Q 2017. Label-free and ratiometric fluorescent nanosensor based on amino-functionalized graphene quantum dots coupling catalytic G-quadruplex/hemin DNAzyme for ultrasensitive recognition of human telomere DNA. Sens. Actuators B 245:648–55
    [Google Scholar]
87. 87.  Liang S-S, Qi L, Zhang R-L, Jin M, Zhang Z-Q 2017. Ratiometric fluorescence biosensor based on CdTe quantum and carbon dots for double strand DNA detection. Sens. Actuators B 244:585–90
    [Google Scholar]
88. 88.  Qian J, Wang K, Wang C, Ren C, Liu Q et al. 2017. Ratiometric fluorescence nanosensor for selective and visual detection of cadmium ions using quencher displacement-induced fluorescence recovery of CdTe quantum dots-based hybrid probe. Sens. Actuators B 241:1153–60
    [Google Scholar]
89. 89.  Fu H, Ji Z, Chen X, Cheng A, Liu S et al. 2017. A versatile ratiometric nanosensing approach for sensitive and accurate detection of Hg²⁺ and biological thiols based on new fluorescent carbon quantum dots. Anal. Bioanal. Chem. 409:2373–82
    [Google Scholar]
90. 90.  Xu H, Zhang K, Liu Q, Liu Y, Xie M 2017. Visual and fluorescent detection of mercury ions by using a dually emissive ratiometric nanohybrid containing carbon dots and CdTe quantum dots. Microchim. Acta 184:1199–206
    [Google Scholar]
91. 91.  Donmez M, Yilmaz MD, Kilbas B 2017. Fluorescent detection of dipicolinic acid as a biomarker of bacterial spores using lanthanide-chelated gold nanoparticles. J. Hazard. Mater. 324:Pt. B593–98
    [Google Scholar]
92. 92.  Xiang G-Q, Ren Y, Xia Y, Mao W, Fan C et al. 2017. Carbon-dot-based dual-emission silica nanoparticles as a ratiometric fluorescent probe for Bisphenol A. Spectrochim. Acta A 177:153–57
    [Google Scholar]
93. 93.  Campos BB, Contreras-Cáceres R, Bandosz TJ, Jiménez-Jiménez J, Rodríguez-Castellón E et al. 2017. Carbon dots coated with vitamin B₁₂ as selective ratiometric nanosensor for phenolic carbofuran. Sens. Actuators B 239:553–61
    [Google Scholar]
94. 94.  Lu H, Koo LY, Wang WM, Lauffenburger DA, Griffith LG, Jensen KF 2004. Microfluidic shear devices for quantitative analysis of cell adhesion. Anal. Chem. 76:5257–64
    [Google Scholar]
95. 95.  Takayama S, Ostuni E, LeDuc P, Naruse K, Ingber DE 2001. Laminar flows: subcellular positioning of small molecules. Nature 411:1016
    [Google Scholar]
96. 96.  Takayama S, Ostuni E, LeDuc P, Naruse K, Ingber DE, Whitesides GM 2003. Selective chemical treatment of cellular microdomains using multiple laminar streams. Chem. Biol. 10:123–30
    [Google Scholar]
97. 97.  Lucchetta EM, Munson MS, Ismagilov RF 2006. Characterization of the local temperature in space and time around a developing Drosophila embryo in a microfluidic device. Lab Chip 6:185–90
    [Google Scholar]
98. 98.  Qin D, Xia Y, Whitesides GM 1997. Elastomeric light valves. Adv. Mater. 9:407–10
    [Google Scholar]
99. 99.  Duffy DC, McDonald JC, Schueller OJ, Whitesides GM 1998. Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal. Chem. 70:4974–84
    [Google Scholar]
100. 100.  McDonald JC, Duffy DC, Anderson JR, Chiu DT, Wu H et al. 2000. Fabrication of microfluidic systems in poly(dimethylsiloxane). Electrophoresis 2:27–40
     [Google Scholar]
101. 101.  Thorsen T, Maerkl SJ, Quake SR 2002. Microfluidic large-scale integration. Science 298:580–84
     [Google Scholar]
102. 102.  Khademhosseini A, Yeh J, Eng G, Karp J, Kaji H et al. 2005. Cell docking inside microwells within reversibly sealed microfluidic channels for fabricating multiphenotype cell arrays. Lab Chip 5:1380–86
     [Google Scholar]
103. 103.  Toh YC, Zhang C, Zhang J, Khong YM, Chang S et al. 2007. A novel 3D mammalian cell perfusion-culture system in microfluidic channels. Lab Chip 7:302–9
     [Google Scholar]
104. 104.  Tourovskaia A, Figueroa-Masot X, Folch A 2005. Differentiation-on-a-chip: a microfluidic platform for long-term cell culture studies. Lab Chip 5:14–19
     [Google Scholar]
105. 105.  Meyvantsson I, Beebe DJ 2008. Cell culture models in microfluidic systems. Annu. Rev. Anal. Chem. 1:423–49
     [Google Scholar]
106. 106.  Abaci HE, Shuler ML 2015. Human-on-a-chip design strategies and principles for physiologically based pharmacokinetics/pharmacodynamics modeling. Integr. Biol. 7:383–91
     [Google Scholar]
107. 107.  Huh D, Matthews BD, Mammato A, Montoya-Zavala M, Hsin HY, Ingber DE 2010. Reconstituting organ-level lung functions on a chip. Science 328:1662–68
     [Google Scholar]
108. 108.  Mahler GJ, Esch MB, Glahn RP, Shuler ML 2009. Characterization of a gastrointestinal tract microscale cell culture analog used to predict drug toxicity. Biotechnol. Bioeng. 104:193–205
     [Google Scholar]
109. 109.  Powers MJ, Domansky K, Kaazempur-Mofrad MR, Kalezi A, Capitano A et al. 2002. A microfabricated array bioreactor for perfused 3D liver culture. Biotechnol. Bioeng. 78:257–69
     [Google Scholar]
110. 110.  Grossmann G, Guo WJ, Ehrhardt DW, Frommer WB, Sit RV et al. 2011. The RootChip: an integrated microfluidic chip for plant science. Plant Cell 23:4234–40
     [Google Scholar]
111. 111.  Grossmann G, Meier M, Cartwright HN, Sosso D, Quake SR et al. 2012. Time-lapse fluorescence imaging of Arabidopsis root growth with rapid manipulation of the root environment using the RootChip. J. Vis. Exp. 65:4290
     [Google Scholar]
112. 112.  Jiang H, Xu Z, Aluru MR, Dong L 2014. Plant chip for high-throughput phenotyping of Arabidopsis. . Lab Chip 14:1281–93
     [Google Scholar]
113. 113.  Meier M, Lucchetta EM, Ismagilov RF 2010. Chemical stimulation of the Arabidopsis thaliana root using multi-laminar flow on a microfluidic chip. Lab Chip 10:2147
     [Google Scholar]
114. 114.  Deng J, Orner EP, Chau JF, Anderson EM, Kadilak AL et al. 2015. Synergistic effects of soil microstructure and bacterial EPS on drying rate in emulated soil micromodels. Soil Biol. Biochem. 83:116–24
     [Google Scholar]
115. 115.  Rubinstein RL, Kadilak AL, Cousens VC, Gage DJ, Shor LM 2015. Protist-facilitated particle transport using emulated soil micromodels. Environ. Sci. Technol. 49:1384–91
     [Google Scholar]
116. 116.  Stanley CE, Grossmann G, Cassadevall i Solvas X, deMello AJ 2016. Soil-on-a-Chip: microfluidic platforms for environmental organismal studies. Lab Chip 16:228–41
     [Google Scholar]
117. 117.  Massalha H, Korenblum E, Malitsky S, Shapiro OH, Aharoni A 2017. Live imaging of root-bacteria interactions in a microfluidics setup. PNAS 114:4549–54
     [Google Scholar]
118. 118.  Parashar A, Pandey S 2011. Plant-in-chip: microfluidic system for studying root growth and pathogenic interactions in Arabidopsis. . Appl. Phys. Lett. 98:263703
     [Google Scholar]
119. 119.  Craighead HG, Turner SW, Davis RC, James C, Kam L et al. 1998. Chemical and topographical surface modification for control of central nervous system cell adhesion. J. Biomed. Microdevices 1:49–64
     [Google Scholar]
120. 120.  James CD, Davis RC, Kam L, Craighead HG, Isaacson M et al. 1998. Patterned protein layers on solid substrates by thin stamp microcontact printing. Langmuir 14:741–44
     [Google Scholar]
121. 121.  Geng T, Bredeweg EL, Szymanski CJ, Liu B, Baker SE et al. 2015. Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics. Sci. Rep. 5:16111
     [Google Scholar]
122. 122.  Chen CS, Mrksich M, Huang S, Whitesides GM, Ingber DE 1997. Geometric control of cell life and death. Science 276:1425–28
     [Google Scholar]
123. 123.  Vargis E, Peterson CB, Morrell-Falvey JL, Retterer ST, Collier CP 2014. The effect of retinal pigment epithelial cell patch size on growth factor expression. Biomaterials 35:3999–4004
     [Google Scholar]
124. 124.  Hansen RR, Hinestrosa JP, Shubert KR, Morrell-Falvey JL, Pelletier DA et al. 2013. Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface scaffolds for high avidity microbial capture. Biomacromolecules 14:3742–48
     [Google Scholar]
125. 125.  Hansen RR, Shubert KR, Morrell-Falvey JL, Lokitz BS, Doktycz MJ, Retterer ST 2014. Microstructured block copolymer surfaces for control of microbe adhesion and aggregation. Biosensors 4:63–75
     [Google Scholar]
126. 126.  Bhatia SN, Yarmush ML, Toner M 1997. Controlling cell interactions by micropatterning in co-cultures: hepatocytes and 3T3 fibroblasts. J. Biomed. Mater. Res. 34:189–99
     [Google Scholar]
127. 127.  Timm CM, Hansen RR, Doktycz MJ, Retterer ST, Pelletier DA 2015. Microstencils to generate defined, multi-species patterns of bacteria. Biomicrofluidics 9:064103
     [Google Scholar]
128. 128.  Keymer JE, Galajda P, Muldoon C, Park S, Austin RH 2006. Bacterial metapopulations in nanofabricated landscapes. PNAS 103:17290–95
     [Google Scholar]
129. 129.  Keymer JE, Galajda P, Lambert G, Liao D, Austin RH 2008. Computation of mutual fitness by competing bacteria. PNAS 105:20269–73
     [Google Scholar]
130. 130.  Shankles PG, Timm AC, Doktycz MJ, Retterer ST 2015. Fabrication of nanoporous membranes for tuning microbial interactions and biochemical reactions. J. Vacuum Sci. Technol. B 33:06FM03
     [Google Scholar]
131. 131.  Beebe DJ, Moore JS, Bauer JM, Yu Q, Liu RH et al. 2000. Functional hydrogel structures for autonomous flow control inside microfluidic channels. Nature 404:588–90
     [Google Scholar]
132. 132.  Connell JL, Kim J, Shear JB, Bard AJ, Whiteley M 2014. Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy. PNAS 111:18255–60
     [Google Scholar]
133. 133.  Connell JL, Ritschdorff ET, Whiteley M, Shear JB 2013. 3D printing of microscopic bacterial communities. PNAS 110:18380–85
     [Google Scholar]
134. 134.  Dertinger SKW, Chiu DT, Jeon NL, Whitesides GM 2001. Generation of gradients having complex shapes using microfluidic networks. Anal. Chem. 73:1240–46
     [Google Scholar]
135. 135.  Mao H, Cremer PS, Manson MD 2003. A sensitive, versatile microfluidic assay for bacterial chemotaxis. PNAS 100:5449–54
     [Google Scholar]
136. 136.  Ahmed T, Stocker R 2008. Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics. Biophys. J. 95:4481–93
     [Google Scholar]
137. 137.  Kovarik ML, Brown PJB, Kysela DT, Berne C, Kinsella AC et al. 2010. Microchannel-nanopore device for bacterial chemotaxis assays. Anal. Chem. 82:9357–64
     [Google Scholar]
138. 138.  Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF 2008. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. PNAS 105:4209–14
     [Google Scholar]
139. 139.  Abhyankar VV, Lokuta MA, Huttenlocher A, Beebe DJ 2006. Characterization of a membrane-based gradient generator for use in cell-signaling studies. Lab Chip 6:389–93
     [Google Scholar]
140. 140.  Abhyankar VV, Toepke MW, Cortesio CL, Lokuta MA, Huttenlocher A, Beebe DJ 2008. A platform for assessing chemotactic migration within a spatiotemporally defined 3D microenvironment. Lab Chip 8:1507–15
     [Google Scholar]
141. 141.  Walker GM, Sai J, Richmond A, Stremler M, Chung CY, Wikswo JP 2005. Effects of flow and diffusion on chemotaxis studies in a microfabricated gradient generator. Lab Chip 5:611–18
     [Google Scholar]
142. 142.  Branchford BR, Ng CJ, Neeves KB, Di Paola J 2015. Microfluidic technology as an emerging clinical tool to evaluate thrombosis and hemostasis. Thromb. Res. 136:13–19
     [Google Scholar]
143. 143.  Neeves KB, Diamond SL 2008. A membrane-based microfluidic device for controlling the flux of platelet agonists into flowing blood. Lab Chip 8:701–9
     [Google Scholar]
144. 144.  Neeves KB, McCarty OJ, Reininger AJ, Sugimoto M, King MR et al. 2014. Flow-dependent thrombin and fibrin generation in vitro: opportunities for standardization: communication from SSC of the ISTH. J. Thromb. Haemost. 12:418–20
     [Google Scholar]
145. 145.  Schoeman RM, Rana K, Danes N, Lehmann M, Di Paola JA et al. 2017. A microfluidic model of hemostasis sensitive to platelet function and coagulation. Cell. Mol. Bioeng. 10:3–15
     [Google Scholar]
146. 146.  Biswas I, Ghosh R, Sadrzadeh M, Kumar A 2016. Nonlinear deformation and localized failure of bacterial streamers in creeping flows. Sci. Rep. 6:32204
     [Google Scholar]
147. 147.  Hassanpourfard M, Ghosh R, Thundat T, Kumar A 2016. Dynamics of bacterial streamers induced clogging in microfluidic devices. Lab Chip 16:4091–96
     [Google Scholar]
148. 148.  Marty A, Causserand C, Roques C, Bacchin P 2014. Impact of tortuous flow on bacteria streamer development in microfluidic system during filtration. Biomicrofluidics 8:014105
     [Google Scholar]
149. 149.  Yazdi S, Ardekani AM 2012. Bacterial aggregation and biofilm formation in a vortical flow. Biomicrofluidics 6:44114
     [Google Scholar]
150. 150.  Chen LJ, Ito S, Kai H, Nagamine K, Nagai N et al. 2017. Microfluidic co-cultures of retinal pigment epithelial cells and vascular endothelial cells to investigate choroidal angiogenesis. Sci. Rep. 7:3538
     [Google Scholar]
151. 151.  Retterer ST, Siuti P, Choi CK, Thomas DK, Doktycz MJ 2010. Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip. Lab Chip 10:1174–81
     [Google Scholar]
152. 152.  Siuti P, Retterer ST, Choi CK, Doktycz MJ 2012. Enzyme reactions in nanoporous, picoliter volume containers. Anal. Chem. 84:1092–97
     [Google Scholar]
153. 153.  Siuti P, Retterer ST, Doktycz MJ 2011. Continuous protein production in nanoporous, picolitre volume containers. Lab Chip 11:3523–29
     [Google Scholar]
154. 154.  Timm AC, Shankles PG, Foster CM, Doktycz MJ, Retterer ST 2015. Characterization of extended channel bioreactors for continuous-flow protein production. J. Vac. Sci. Technol. B 33:06FM02
     [Google Scholar]
155. 155.  Timm AC, Shankles PG, Foster CM, Doktycz MJ, Retterer ST 2016. Toward microfluidic reactors for cell-free protein synthesis at the point-of-care. Small 12:810–17
     [Google Scholar]
156. 156.  Hung PJ, Lee PJ, Sabounchi P, Lin R, Lee LP 2005. Continuous perfusion microfluidic cell culture array for high-throughput cell-based assays. Biotechnol. Bioeng. 89:1–8
     [Google Scholar]
157. 157.  Flachsbart BR, Wong K, Iannacone JM, Abante EN, Vlach RL et al. 2006. Design and fabrication of a multilayered polymer microfluidic chip with nanofluidic interconnects via adhesive contact printing. Lab Chip 6:667–68
     [Google Scholar]
158. 158.  Gatimu EN, King TL, Sweedler JV, Bohn PW 2007. Three-dimensional integrated microfluidic architectures enabled through electrically switchable nanocapillary array membranes. Biomicrofluidics 1:21502
     [Google Scholar]
159. 159.  Li F, Guijt RM, Breadmore MC 2016. Nanoporous membranes for microfluidic concentration prior to electrophoretic separation of proteins in urine. Anal. Chem. 88:8257–63
     [Google Scholar]
160. 160.  Tan W, Desai TA 2005. Microscale multilayer cocultures for biomimetic blood vessels. J. Biomed. Mater. Res. A 72:146–60
     [Google Scholar]
161. 161.  Chen D, Du W, Liu Y, Liu W, Kuznetsov A et al. 2008. The chemistrode: a droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution. PNAS 105:16843–48
     [Google Scholar]
162. 162.  Walker BN, Antonakos C, Retterer ST, Vertes A 2013. Metabolic differences in microbial cell populations revealed by nanophotonic ionization. Angew. Chem. Int. Ed. 52:3650–53
     [Google Scholar]
163. 163.  Walker BN, Stolee JA, Pickel DL, Retterer ST, Vertes A 2010. Assessment of laser-induced thermal load on silicon nanostructures based on ion desorption yields. Appl. Phys. A 101:539–44
     [Google Scholar]
164. 164.  Polemi A, Wells SM, Lavrik NV, Sepaniak MJ, Shuford KL 2010. Local field enhancement of pillar nanosurfaces for SERS. J. Phys. Chem. C 114:18096–102
     [Google Scholar]
165. 165.  Wells SM, Retterer SD, Oran JM, Sepaniak MJ 2009. Controllable nanofabrication of aggregate-like nanoparticle substrates and evaluation for surface-enhanced Raman spectroscopy. ACS Nano 3:3845–53
     [Google Scholar]
166. 166.  Agapov RL, Srijanto B, Fowler C, Briggs D, Lavrik NV, Sepaniak MJ 2013. Lithography-free approach to highly efficient, scalable SERS substrates based on disordered clusters of disc-on-pillar structures. Nanotechnology 24:505302
     [Google Scholar]
167. 167.  Fu K, Han D, Ma C, Bohn PW 2017. Ion selective redox cycling in zero-dimensional nanopore electrode arrays at low ionic strength. Nanoscale 9:5164–71
     [Google Scholar]
168. 168.  Han D, Crouch G, Fu K, Zaino LP3rd, Bohn PW 2017. Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides. Chem. Sci. 8:5345–55
     [Google Scholar]
169. 169.  De Tommasi E, De Luca AC, Lavanga L, Dardano P, De Stefano M et al. 2014. Biologically enabled sub-diffractive focusing. Opt. Express 22:27214–27
     [Google Scholar]
170. 170.  Schuergers N, Lenn T, Kampmann R, Meissner MV, Esteves T et al. 2016. Cyanobacteria use micro-optics to sense light direction. eLife 5:e12620
     [Google Scholar]
171. 171.  Gashti MP, Asselin J, Barbeau J, Boudreau D, Greener J 2016. A microfluidic platform with pH imaging for chemical and hydrodynamic stimulation of intact oral biofilms. Lab Chip 16:1412–19
     [Google Scholar]
172. 172.  Gambin Y, Legrand O, Quake SR 2006. Microfabricated rubber microscope using soft solid immersion lenses. Appl. Phys. Lett. 88:174102
     [Google Scholar]
173. 173.  Psaltis D, Quake SR, Yang C 2006. Developing optofluidic technology through the fusion of microfluidics and optics. Nature 442:381–86
     [Google Scholar]
174. 174.  Lismont M, Páez CA, Dreesen L 2015. A one-step short-time synthesis of Ag@SiO₂ core–shell nanoparticles. J. Colloid Interface Sci. 447:40–49
     [Google Scholar]
175. 175.  Millet LJ, Doktycz MJ, Retterer ST 2015. Nanofluidic interfaces in microfluidic networks. J. Vac. Sci. Technol. B 33:06FM01
     [Google Scholar]
176. 176.  Walker BN, Stolee JA, Vertes A 2012. Nanophotonic ionization for ultratrace and single-cell analysis by mass spectrometry. Anal. Chem. 84:7756–62
     [Google Scholar]
177. 177.  Connell JL, Wessel AK, Parsek MR, Ellington AD, Whiteley M, Shear JB 2010. Probing prokaryotic social behaviors with bacterial lobster traps. mBio 1:e00202–10
     [Google Scholar]
178. 178.  Hatab NA, Hsueh C-H, Gaddis AL, Retterer ST, Li JH et al. 2010. Free-standing optical gold bowtie nanoantenna with variable gap size for enhanced Raman spectroscopy. Nano Lett 10:4952–55
     [Google Scholar]