651
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Abolhasani M, Singh M, Kumacheva E, Günther A. Cruise control for segmented flow. LAB ON A CHIP 2012; 12:4787-4795. [PMID: 22992756 DOI: 10.1039/c2lc40513j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Capitalizing on the benefits of microscale segmented flows, e.g., enhanced mixing and reduced sample dispersion, so far requires specialist training and accommodating a few experimental inconveniences. For instance, microscale gas-liquid flows in many current setups take at least 10 min to stabilize and iterative manual adjustments are needed to achieve or maintain desired mixing or residence times. Here, we report a cruise control strategy that overcomes these limitations and allows microscale gas-liquid (bubble) and liquid-liquid (droplet) flow conditions to be rapidly "adjusted" and maintained. Using this strategy we consistently establish bubble and droplet flows with dispersed phase (plug) velocities of 5-300 mm s(-1), plug lengths of 0.6-5 mm and continuous phase (slug) lengths of 0.5-3 mm. The mixing times (1-5 s), mass transfer times (33-250 ms) and residence times (3-300 s) can therefore be directly imposed by dynamically controlling the supply of the dispersed and the continuous liquids either from external pumps or from local pressurized reservoirs. In the latter case, no chip-external pumps, liquid-perfused tubes or valves are necessary while unwanted dead volumes are significantly reduced.
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Affiliation(s)
- Milad Abolhasani
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
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652
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Ruff AJ, Dennig A, Wirtz G, Blanusa M, Schwaneberg U. Flow Cytometer-Based High-Throughput Screening System for Accelerated Directed Evolution of P450 Monooxygenases. ACS Catal 2012. [DOI: 10.1021/cs300115d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Alexander Dennig
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Georgette Wirtz
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
| | - Milan Blanusa
- School of Engineering
and Science, Jacobs University Bremen,
Campus Ring 1, 28759 Bremen,
Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 1, 52074 Aachen,
Germany
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653
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Kaminski TS, Jakiela S, Czekalska MA, Postek W, Garstecki P. Automated generation of libraries of nL droplets. LAB ON A CHIP 2012; 12:3995-4002. [PMID: 22968539 DOI: 10.1039/c2lc40540g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate an integrated system for rapid and automated generation of multiple, chemically distinct populations of ~10(3)-10(4) sub-nanoliter droplets. Generation of these 'libraries of droplets' proceeds in the following automated steps: i) generation of a sequence of micro-liter droplets of individually predetermined composition, ii) injection of these 'parental' droplets onto a chip, iii) transition from a mm- to a μm-scale of the channels and splitting each of the parental drops with a flow-focusing module into thousands of tightly monodisperse daughter drops and iv) separation of such formed homogeneous populations with plugs of a third immiscible fluid. This method is compatible both with aspiration of microliter portions of liquid from a 96-well plate with a robotic station and with automated microfluidic systems that generate (~μL) droplets of preprogrammed compositions. The system that we present bridges the techniques that provide elasticity of protocols executed on microliter droplets with the techniques for high-throughput screening of small (~pL, ~nL) droplet libraries. The method that we describe can be useful in exploiting the synergy between the ability to rapidly screen distinct chemical environments and to perform high-throughput studies of single cells or molecules and in digital droplet PCR systems.
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Affiliation(s)
- Tomasz S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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654
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Ali-Cherif A, Begolo S, Descroix S, Viovy JL, Malaquin L. Programmable magnetic tweezers and droplet microfluidic device for high-throughput nanoliter multi-step assays. Angew Chem Int Ed Engl 2012; 51:10765-9. [PMID: 23011819 DOI: 10.1002/anie.201203862] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/04/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Anaïs Ali-Cherif
- Institut Curie UMR 168, Research Center, CNRS, UMR168, 11 rue Pierre et Marie Curie, 75005 Paris (France)
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655
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Ali-Cherif A, Begolo S, Descroix S, Viovy JL, Malaquin L. Programmable Magnetic Tweezers and Droplet Microfluidic Device for High-Throughput Nanoliter Multi-Step Assays. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203862] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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656
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Okano T, Matsuura T, Kazuta Y, Suzuki H, Yomo T. Cell-free protein synthesis from a single copy of DNA in a glass microchamber. LAB ON A CHIP 2012; 12:2704-2711. [PMID: 22622196 DOI: 10.1039/c2lc40098g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To achieve a cell-mimetic reaction environment, we fabricated and tested quartz microchambers for conducting protein synthesis using an in vitro transcription and translation system, the PURE system. By introducing a glass microchamber and blocking the surface of the chamber with amino acids, the concentration of the synthesized marker protein (green fluorescent protein, GFP) was significantly improved compared to that in the poly(dimethylsiloxane) (PDMS) microchamber. The concentration was below the detection limit in the PDMS microchambers, whereas the glass microchambers yielded 700 nM GFP, representing 41% of the bulk reaction. There was no detectable difference when the GFP synthesis was performed in microchambers with sizes ranging from 40 fL to 7 pL, indicating that the present microchamber system can serve as a cell-sized test tube with a variable reaction volume. Finally, we demonstrated that two different proteins, GFP and β-galactosidase, can be expressed from single genes in our experimental setup. Quantized and distinctive signals from proteins synthesized from 0, 1, or 2 copies of genes were obtained. The microchamber presented here can be utilized not only to study the effects of compartment volume on protein synthesis but also for the comprehensive analysis of complex biochemical reactions in cell-mimetic environments.
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Affiliation(s)
- Taiji Okano
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Suita, Osaka, Japan
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657
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Robinson JP, Rajwa B, Patsekin V, Davisson VJ. Computational analysis of high-throughput flow cytometry data. Expert Opin Drug Discov 2012; 7:679-93. [PMID: 22708834 PMCID: PMC4389283 DOI: 10.1517/17460441.2012.693475] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Flow cytometry has been around for over 40 years, but only recently has the opportunity arisen to move into the high-throughput domain. The technology is now available and is highly competitive with imaging tools under the right conditions. Flow cytometry has, however, been a technology that has focused on its unique ability to study single cells and appropriate analytical tools are readily available to handle this traditional role of the technology. AREAS COVERED Expansion of flow cytometry to a high-throughput (HT) and high-content technology requires both advances in hardware and analytical tools. The historical perspective of flow cytometry operation as well as how the field has changed and what the key changes have been discussed. The authors provide a background and compelling arguments for moving toward HT flow, where there are many innovative opportunities. With alternative approaches now available for flow cytometry, there will be a considerable number of new applications. These opportunities show strong capability for drug screening and functional studies with cells in suspension. EXPERT OPINION There is no doubt that HT flow is a rich technology awaiting acceptance by the pharmaceutical community. It can provide a powerful phenotypic analytical toolset that has the capacity to change many current approaches to HT screening. The previous restrictions on the technology, based on its reduced capacity for sample throughput, are no longer a major issue. Overcoming this barrier has transformed a mature technology into one that can focus on systems biology questions not previously considered possible.
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Affiliation(s)
- J Paul Robinson
- Purdue University Cytometry Laboratories, Purdue University, West Lafayette, IN 47907, USA.
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658
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Goldsmith M, Tawfik DS. Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 2012; 22:406-12. [DOI: 10.1016/j.sbi.2012.03.010] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 12/26/2022]
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659
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Abstract
In the present paper, we review and discuss current developments and challenges in the field of droplet-based microfluidics. This discussion includes an assessment of the basic fluid dynamics of segmented flows, material requirements, fundamental unit operations and how integration of functional components can be applied to specific biological problems.
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660
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Wang M, Si T, Zhao H. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY 2012; 115:117-25. [PMID: 22310212 PMCID: PMC3351540 DOI: 10.1016/j.biortech.2012.01.054] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 05/13/2023]
Abstract
Biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. To overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. Recent advances in mutant library creation and high-throughput screening have greatly facilitated the engineering of novel and improved biocatalysts. This review provides an update of the recent developments in the use of directed evolution to engineer biocatalysts for practical applications.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tong Si
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Departments of Chemistry, Biochemistry, and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- To whom correspondence should be addressed. Phone: (217) 333-2631. Fax: (217) 333-5052.
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661
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MA FQ, FENG Y, YANG GY. Ultrahigh-throughput Enzymatic Screening Method Based on Fluorescence-activated Cell Sorting and Its Applications*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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662
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Guo MT, Rotem A, Heyman JA, Weitz DA. Droplet microfluidics for high-throughput biological assays. LAB ON A CHIP 2012; 12:2146-55. [PMID: 22318506 DOI: 10.1039/c2lc21147e] [Citation(s) in RCA: 631] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics offers significant advantages for performing high-throughput screens and sensitive assays. Droplets allow sample volumes to be significantly reduced, leading to concomitant reductions in cost. Manipulation and measurement at kilohertz speeds enable up to 10(8) samples to be screened in one day. Compartmentalization in droplets increases assay sensitivity by increasing the effective concentration of rare species and decreasing the time required to reach detection thresholds. Droplet microfluidics combines these powerful features to enable currently inaccessible high-throughput screening applications, including single-cell and single-molecule assays.
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Affiliation(s)
- Mira T Guo
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
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663
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Sun S, Slaney TR, Kennedy RT. Label free screening of enzyme inhibitors at femtomole scale using segmented flow electrospray ionization mass spectrometry. Anal Chem 2012; 84:5794-800. [PMID: 22656268 DOI: 10.1021/ac3011389] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Droplet-based microfluidics is an attractive platform for screening and optimizing chemical reactions. Using this approach, it is possible to reliably manipulate nanoliter volume samples and perform operations such as reagent addition with high precision, automation, and throughput. Most studies using droplet microfluidics have relied on optical techniques to detect the reaction; however, this requires engineering color or fluorescence change into the reaction being studied. In this work, we couple electrospray ionization mass spectrometry (ESI-MS) to nanoliter scale segmented flow reactions to enable direct (label-free) analysis of reaction products. The system is applied to a screen of inhibitors for cathepsin B. In this approach, solutions of test compounds (including three known inhibitors) are arranged as an array of nanoliter droplets in a tube segmented by perfluorodecalin. The samples are pumped through a series of tees to add enzyme, substrate (peptides), and quenchant. The resulting reaction mixtures are then infused into a metal-coated, fused silica ESI emitter for MS analysis. The system has potential for high-throughput as reagent addition steps are performed at 0.7 s per sample and ESI-MS at up to 1.2 s per sample. Carryover is inconsequential in the ESI emitter and between 2 and 9% per reagent addition depending on the tee utilized. The assay was reliable with a Z-factor of ~0.8. The method required 0.8 pmol of test compound, 1.6 pmol of substrate, and 5 fmol of enzyme per reaction. Segmented flow ESI-MS allows direct, label free screening of reactions at good throughput and ultralow sample consumption.
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Affiliation(s)
- Shuwen Sun
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
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664
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Dammann C, Nöding B, Köster S. Vimentin networks at tunable ion-concentration in microfluidic drops. BIOMICROFLUIDICS 2012; 6:22009-2200910. [PMID: 22655012 PMCID: PMC3360716 DOI: 10.1063/1.4705103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/04/2012] [Indexed: 05/11/2023]
Abstract
The structure and function of biological systems, for example, cells and proteins, depend strongly on their chemical environment. To investigate such dependence, we design a polydimethylsiloxane-based microfluidic device to encapsulate biological systems in picoliter-sized drops. The content of each individual drop is tuned in a defined manner. As a key feature of our method, the individual chemical composition is determined and related to the drop content. In our case, the drop content is imaged using microscopy methods, while the drops are immobilized to allow for long-time studies. As an application of our device, we study the influence of divalent ions on vimentin intermediate filament networks in a quantitative way by tuning the magnesium concentration from drop to drop. This way we are able to directly image the effect of magnesium on the fluorescently tagged protein in a few hundreds of drops. Our study shows that with increasing magnesium concentration in the drops, the compaction of the networks becomes more pronounced. The degree of compaction is characterized by different morphologies; freely fluctuating networks are observed at comparatively low magnesium concentrations of 5-10 mM, while with increasing magnesium concentration reaching 16 mM they develop into fully aggregated networks. Our approach demonstrates how a systematic study of interactions in biological systems can benefit from the exceptional controllability of microfluidic methods.
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Affiliation(s)
- Christian Dammann
- Institute for X-Ray Physics and Courant Research Centre "Nano-Spectroscopy and X-Ray Imaging," Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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665
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Nishimura K, Suzuki H, Toyota T, Yomo T. Size control of giant unilamellar vesicles prepared from inverted emulsion droplets. J Colloid Interface Sci 2012; 376:119-25. [DOI: 10.1016/j.jcis.2012.02.029] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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666
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Translational research in infectious disease: current paradigms and challenges ahead. Transl Res 2012; 159:430-53. [PMID: 22633095 PMCID: PMC3361696 DOI: 10.1016/j.trsl.2011.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/23/2011] [Accepted: 12/24/2012] [Indexed: 12/25/2022]
Abstract
In recent years, the biomedical community has witnessed a rapid scientific and technologic evolution after the development and refinement of high-throughput methodologies. Concurrently and consequentially, the scientific perspective has changed from the reductionist approach of meticulously analyzing the fine details of a single component of biology to the "holistic" approach of broadmindedly examining the globally interacting elements of biological systems. The emergence of this new way of thinking has brought about a scientific revolution in which genomics, proteomics, metabolomics, and other "omics" have become the predominant tools by which large amounts of data are amassed, analyzed, and applied to complex questions of biology that were previously unsolvable. This enormous transformation of basic science research and the ensuing plethora of promising data, especially in the realm of human health and disease, have unfortunately not been followed by a parallel increase in the clinical application of this information. On the contrary, the number of new potential drugs in development has been decreasing steadily, suggesting the existence of roadblocks that prevent the translation of promising research into medically relevant therapeutic or diagnostic application. In this article, we will review, in a noninclusive fashion, several recent scientific advancements in the field of translational research, with a specific focus on how they relate to infectious disease. We will also present a current picture of the limitations and challenges that exist for translational research, as well as ways that have been proposed by the National Institutes of Health to improve the state of this field.
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Key Words
- 2-de, 2-dimensional electrophoresis
- 2-d dige, 2-dimensional differential in-gel electrophoresis
- cf, cystic fibrosis
- ctsa, clinical and translational science awards program
- ebv, epstein-barr virus
- fda, u.s. food and drug administration
- gwas, genome-wide association studies
- hcv, hepatitis c virus
- hmp, human microbiome project
- hplc, high-pressure liquid chromatography
- lc, liquid chromatography
- lsb, laboratory of systems biology
- mab, monoclonal antibody
- mrm/srm, multiple reaction monitoring/selective reaction monitoring
- ms, mass spectrometry
- ms/ms, tandem mass spectrometry
- ncats, national center for advancing translational sciences
- ncrr, national center of research resources
- niaid, national institute of allergy and infectious disease
- nih, national institutes of health
- nme, new molecular entity
- nmr, nuclear magnetic resonance
- pbmc, peripheral blood mononuclear cell
- pcr, polymerase chain reaction
- prr, pathogen recognition receptor
- qqq, triple quadrupole mass spectrometry
- sars-cov, coronavirus associated with severe acute respiratory syndrome
- snp, single nucleotide polymorphism
- tb, tuberculosis
- uti, urinary tract infection
- yfv, yellow fever virus
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667
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Sander JS, Erb RM, Denier C, Studart AR. Magnetic transport, mixing and release of cargo with tailored nanoliter droplets. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:2582-2510. [PMID: 22451154 DOI: 10.1002/adma.201200263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Indexed: 05/31/2023]
Affiliation(s)
- Jonathan S Sander
- Complex Materials, Department of Materials, ETH Zurich, 8093 Zurich, Switzerland
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668
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Balls M, Combes RD, Bhogal N. The use of integrated and intelligent testing strategies in the prediction of toxic hazard and in risk assessment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 745:221-53. [PMID: 22437821 PMCID: PMC7122993 DOI: 10.1007/978-1-4614-3055-1_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
There is increasing concern that insurmountable differences between humans and laboratory animals limit the relevance and reliability for hazard identification and risk assessment purposes of animal data produced by traditional toxicity test procedures. A way forward is offered by the emerging new technologies, which can be directly applied to human material or even to human beings themselves. This promises to revolutionise the evaluation of the safety of chemicals and chemical products of various kinds and, in particular, pharmaceuticals. The available and developing technologies are summarised and it is emphasised that they will need to be used selectively, in integrated and intelligent testing strategies, which, in addition to being scientifically sound, must be manageable and affordable. Examples are given of proposed testing strategies for general chemicals, cosmetic ingredients, candidate pharmaceuticals, inhaled substances, nanoparticles and neurotoxicity.
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669
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A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc Natl Acad Sci U S A 2012; 109:7665-70. [PMID: 22547789 DOI: 10.1073/pnas.1106752109] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.
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670
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Abate AR, Mary P, van Steijn V, Weitz DA. Experimental validation of plugging during drop formation in a T-junction. LAB ON A CHIP 2012; 12:1516-21. [PMID: 22402628 DOI: 10.1039/c2lc21263c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
At low capillary number, drop formation in a T-junction is dominated by interfacial effects: as the dispersed fluid flows into the drop maker nozzle, it blocks the path of the continuous fluid; this leads to a pressure rise in the continuous fluid that, in turn, squeezes on the dispersed fluid, inducing pinch-off of a drop. While the resulting drop volume predicted by this "squeezing" mechanism has been validated for a range of systems, as of yet, the pressure rise responsible for the actual pinch-off has not been observed experimentally. This is due to the challenge of measuring the pressures in a T-junction with the requisite speed, accuracy, and localization. Here, we present an empirical study of the pressures in a T-junction during drop formation. Using Laplace sensors, pressure probes we have developed, we confirm the central ideas of the squeezing mechanism; however, we also uncover other findings, including that the pressure of the dispersed fluid is not constant but rather oscillates in anti-phase with that of the continuous fluid. In addition, even at the highest capillary number for which monodisperse drops can be formed, pressure oscillations persist, indicating that drop formation in confined geometries does not transition to an entirely shear-driven mechanism, but to a mechanism combining squeezing and shearing.
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Affiliation(s)
- Adam R Abate
- School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, Massachusetts, USA.
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671
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Theberge AB, Mayot E, El Harrak A, Kleinschmidt F, Huck WTS, Griffiths AD. Microfluidic platform for combinatorial synthesis in picolitre droplets. LAB ON A CHIP 2012; 12:1320-6. [PMID: 22344399 DOI: 10.1039/c2lc21019c] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This paper presents a droplet-based microfluidic platform for miniaturized combinatorial synthesis. As a proof of concept, a library of small molecules for early stage drug screening was produced. We present an efficient strategy for producing a 7 × 3 library of potential thrombin inhibitors that can be utilized for other combinatorial synthesis applications. Picolitre droplets containing the first type of reagent (reagents A(1), A(2), …, A(m)) were formed individually in identical microfluidic chips and then stored off chip with the aid of stabilizing surfactants. These droplets were then mixed to form a library of droplets containing reagents A(1-m), each individually compartmentalized, which was reinjected into a second microfluidic chip and combinatorially fused with picolitre droplets containing the second reagent (reagents B(1), B(2), …, B(n)) that were formed on chip. The concept was demonstrated with a three-component Ugi-type reaction involving an amine (reagents A(1-3)), an aldehyde (reagents B(1-7)), and an isocyanide (held constant), to synthesize a library of small molecules with potential thrombin inhibitory activity. Our technique produced 10(6) droplets of each reaction at a rate of 2.3 kHz. Each droplet had a reaction volume of 3.1 pL, at least six orders of magnitude lower than conventional techniques. The droplets can then be divided into aliquots for different downstream screening applications. In addition to medicinal chemistry applications, this combinatorial droplet-based approach holds great potential for other applications that involve sampling large areas of chemical parameter space with minimal reagent consumption; such an approach could be beneficial when optimizing reaction conditions or performing combinatorial reactions aimed at producing novel materials.
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Affiliation(s)
- Ashleigh B Theberge
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 Allée Gaspard Monge, 67083 Strasbourg Cedex, France
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672
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Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MKL, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Compound prioritization methods increase rates of chemical probe discovery in model organisms. ACTA ACUST UNITED AC 2012; 18:1273-83. [PMID: 22035796 DOI: 10.1016/j.chembiol.2011.07.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 06/29/2011] [Accepted: 07/15/2011] [Indexed: 11/30/2022]
Abstract
Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.
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Affiliation(s)
- Iain M Wallace
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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673
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Fallah-Araghi A, Baret JC, Ryckelynck M, Griffiths AD. A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. LAB ON A CHIP 2012; 12:882-91. [PMID: 22277990 DOI: 10.1039/c2lc21035e] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In vitro screening systems based on the coupled transcription and translation of genes using cell-free systems have a number of attractive features for protein engineering and directed evolution. We present a completely in vitro ultrahigh-throughput screening platform using droplet-based microfluidics. Single genes are compartmentalized in aqueous droplets, dispersed in inert carrier oil, and amplified using the polymerase chain reaction (PCR). After amplification, the droplets, now containing 30,000 copies of each gene, are fused one-to-one with droplets containing a cell-free coupled transcription-translation (IVTT) system and the reagents for a fluorogenic assay. Fluorescence-activated electrocoalescence with an aqueous stream is then used to selectively recover genes from droplets containing the desired activity. We demonstrate, by selecting mixtures of lacZ genes encoding the enzyme β-galactosidase and lacZmut genes encoding an inactive variant, that this system can sort at 2000 droplets s(-1): lacZ genes were enriched 502-fold from a 1 : 100 molar ratio of lacZ : lacZmut genes. Indeed, the false positive and false negative error rates were both <0.004 and the results indicate that enrichment is not limited by the sorting efficiency, but by the co-encapsulation of multiple genes in droplets, which is described by the Poisson distribution. Compared to screening using microtiter plate-based systems, the volume and cost of PCR and IVTT reagents are reduced by almost 10(5)-fold, allowing the screening of 10(6) genes using only 150 μL of reagents.
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Affiliation(s)
- Ali Fallah-Araghi
- Institut de Science et d'Ingénierie Supramoleculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, Strasbourg, France
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674
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Hofmann TW, Hänselmann S, Janiesch JW, Rademacher A, Böhm CHJ. Applying microdroplets as sensors for label-free detection of chemical reactions. LAB ON A CHIP 2012; 12:916-22. [PMID: 22252585 DOI: 10.1039/c2lc20971c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Despite its tremendous high-throughput screening capabilities, widespread applications of droplet-based microfluidics are still limited by the poor availability of appropriate analytical assays. Here we report on a novel sensor method that exploits the osmosis-driven change in droplet size as a quantitative and label-free marker for reactions inside the droplets. We present an analysis of the underlying mechanism and apply the method for monitoring metabolic activity at a single-cell level.
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Affiliation(s)
- Tobias W Hofmann
- Max Planck Institute for Intelligent Systems, Department of New Materials and Biosystems, Stuttgart, Germany
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675
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Abstract
Surfactants are an essential part of the droplet-based microfluidic technology. They are involved in the stabilization of droplet interfaces, in the biocompatibility of the system and in the process of molecular exchange between droplets. The recent progress in the applications of droplet-based microfluidics has been made possible by the development of new molecules and their characterizations. In this review, the role of the surfactant in droplet-based microfluidics is discussed with an emphasis on the new molecules developed specifically to overcome the limitations of 'standard' surfactants. Emulsion properties and interfacial rheology of surfactant-laden layers strongly determine the overall capabilities of the technology. Dynamic properties of droplets, interfaces and emulsions are therefore very important to be characterized, understood and controlled. In this respect, microfluidic systems themselves appear to be very powerful tools for the study of surfactant dynamics at the time- and length-scale relevant to the corresponding microfluidic applications. More generally, microfluidic systems are becoming a new type of experimental platform for the study of the dynamics of interfaces in complex systems.
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Affiliation(s)
- Jean-Christophe Baret
- Droplets, Membranes and Interfaces, MPI for Dynamics and Self-organization, Am Fassberg 17, 37077 Goettingen, Germany.
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676
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Ng S, Jafari MR, Derda R. Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry. ACS Chem Biol 2012; 7:123-38. [PMID: 21988453 DOI: 10.1021/cb200342h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Display of polypeptide on the coat proteins of bacteriophages and viruses is a powerful tool for selection and amplification of libraries of great diversity. Chemical diversity of these libraries, however, is limited to libraries made of natural amino acid side chains. Bacteriophages and viruses can be modified chemically; peptide libraries presented on phage thus can be functionalized to yield moieties that cannot be encoded genetically. In this review, we summarize the possibilities for using bacteriophage and viral particles as support for the synthesis of diverse chemically modified peptide libraries. This review critically summarizes the key chemical considerations for on-phage syntheses such as selection of reactions compatible with protein of phage, modification of phage "support" that renders it more suitable for reactions, and characterization of reaction efficiency.
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Affiliation(s)
- Simon Ng
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mohammad R. Jafari
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
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677
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Kovarik ML, Gach PC, Ornoff DM, Wang Y, Balowski J, Farrag L, Allbritton NL. Micro total analysis systems for cell biology and biochemical assays. Anal Chem 2012; 84:516-40. [PMID: 21967743 PMCID: PMC3264799 DOI: 10.1021/ac202611x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Phillip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joseph Balowski
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lila Farrag
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
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678
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679
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Ostrovidov S, Annabi N, Seidi A, Ramalingam M, Dehghani F, Kaji H, Khademhosseini A. Controlled Release of Drugs from Gradient Hydrogels for High-Throughput Analysis of Cell–Drug Interactions. Anal Chem 2012; 84:1302-9. [DOI: 10.1021/ac202256c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Serge Ostrovidov
- World Premier International-Advanced
Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
| | - Nasim Annabi
- World Premier International-Advanced
Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
- School of Chemical and Biomolecular
Engineering, University of Sydney, Sydney,
New South Wales 2006, Australia
| | - Azadeh Seidi
- World Premier International-Advanced
Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
| | - Murugan Ramalingam
- World Premier International-Advanced
Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
- National Institute of Health and
Medical Research U977, Faculte de Medecine, Universite de Strasbourg, Strasbourg Cedex 67085, France
| | - Fariba Dehghani
- School of Chemical and Biomolecular
Engineering, University of Sydney, Sydney,
New South Wales 2006, Australia
| | - Hirokazu Kaji
- Department of Bioengineering and Robotics,
Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Ali Khademhosseini
- World Premier International-Advanced
Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
- Center for Biomedical Engineering,
Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139,
United States
- Harvard-MIT
Division of Health
Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Wyss Institute for Biologically
Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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680
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Joensson HN, Zhang C, Uhlén M, Andersson-Svahn H. A homogeneous assay for protein analysis in droplets by fluorescence polarization. Electrophoresis 2012; 33:436-9. [PMID: 22228311 DOI: 10.1002/elps.201100350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022]
Abstract
We present a novel homogeneous ("mix-incubate-read") droplet microfluidic assay for specific protein detection in picoliter volumes by fluorescence polarization (FP), for the first time demonstrating the use of FP in a droplet microfluidic assay. Using an FP-based assay we detect streptavidin concentrations as low as 500 nM and demonstrate that an FP assay allows us to distinguish droplets containing 5 μM rabbit IgG from droplets without IgG with an accuracy of 95%, levels relevant for hybridoma screening. This adds to the repertoire of droplet assay techniques a direct protein detection method which can be performed entirely inside droplets without the need for labeling of the analyte molecules.
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Affiliation(s)
- Haakan N Joensson
- Division of Nanobiotechnology, Royal Institute of Technology (KTH), Albanova University Center, Stockholm, Sweden.
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681
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Najah M, Griffiths AD, Ryckelynck M. Teaching single-cell digital analysis using droplet-based microfluidics. Anal Chem 2012; 84:1202-9. [PMID: 22229495 DOI: 10.1021/ac202645m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microfluidics allows the manipulation of small quantities of reagents in a high-throughput manner and is therefore highly amenable to single cell characterization and more generally to digital analysis, with applications in fields as varied as genomics, diagnostics, directed evolution, and drug screening. The growing place of microfluidics in biology laboratories encouraged us to develop a teaching method where advanced undergraduate or first-year graduate-level students are taught to fabricate droplet-based microfluidic devices, characterize them, and finally use them to perform a digital analysis of bacterial samples based on a phenotypic marker.
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Affiliation(s)
- Majdi Najah
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France
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682
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683
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Abstract
This book chapter aims at providing an overview of all the aspects and procedures needed to develop a droplet-based workflow for single-cell analysis (see Fig. 10.1). The surfactant system used to stabilize droplets is a critical component of droplet microfluidics; its properties define the type of droplet-based assays and workflows that can be developed. The scope of this book chapter is limited to fluorinated surfactant systems that have proved to generate extremely stable droplets and allow to easily retrieve the encapsulated material. The formulation section discusses how the experimental parameters influence the choice of the surfactant system to use. The circuit design section presents recipes to design and integrate different droplet modules into a whole assay. The fabrication section describes the manufacturing of microfluidic chip including the surface treatment which is pivotal in droplet microfluidics. Finally, the last section reviews the experimental setup for fluorescence detection with an emphasis on cell injection and incubation.
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Affiliation(s)
- Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
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684
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Abstract
Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist.
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Affiliation(s)
- Tore Dehli
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301/242, 2800, Lyngby, Denmark,
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685
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Analytical technologies for integrated single-cell analysis of human immune responses. Methods Mol Biol 2012; 853:211-35. [PMID: 22323150 DOI: 10.1007/978-1-61779-567-1_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The immune system is a network of cells in which the constitutive members interact through dense and sometimes overlapping connections. The extreme complexity of this network poses a significant challenge for monitoring pathological conditions (e.g., food allergies, autoimmunity, and other chronic inflammatory diseases) and for discovering robust signatures of immunological responses that correlate with or predict the efficacy of interventions. The diversity among immune cells found in clinical samples (variations in cellular functions, lineages, and clonotypic breadth) requires approaches for monitoring immune responses with single-cell resolution.In this chapter, we present an engineering approach for integrated single-cell analysis that uses interchangeable modular operations to provide a comprehensive characterization of the phenotypic, functional, and genetic variations for individual cells. We focus on the use of microfabricated devices to isolate and interrogate single cells, and on the analytical components that enable subsequent detection, correlation, and interpretation of multidimensional sets of data. We discuss specific challenges and opportunities in the realization of this concept, and review two examples where it has been implemented. The presented approach should provide a basis for the design and implementation of nonconventional bioanalytical processes for studying specific responses of an immune system.
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686
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Seemann R, Brinkmann M, Pfohl T, Herminghaus S. Droplet based microfluidics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:016601. [PMID: 22790308 DOI: 10.1088/0034-4885/75/1/016601] [Citation(s) in RCA: 488] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet based microfluidics is a rapidly growing interdisciplinary field of research combining soft matter physics, biochemistry and microsystems engineering. Its applications range from fast analytical systems or the synthesis of advanced materials to protein crystallization and biological assays for living cells. Precise control of droplet volumes and reliable manipulation of individual droplets such as coalescence, mixing of their contents, and sorting in combination with fast analysis tools allow us to perform chemical reactions inside the droplets under defined conditions. In this paper, we will review available drop generation and manipulation techniques. The main focus of this review is not to be comprehensive and explain all techniques in great detail but to identify and shed light on similarities and underlying physical principles. Since geometry and wetting properties of the microfluidic channels are crucial factors for droplet generation, we also briefly describe typical device fabrication methods in droplet based microfluidics. Examples of applications and reaction schemes which rely on the discussed manipulation techniques are also presented, such as the fabrication of special materials and biophysical experiments.
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Affiliation(s)
- Ralf Seemann
- Experimental Physics, Saarland University, D-66123 Saarbrücken, Germany.
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687
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Arayanarakool R, Shui L, van den Berg A, Eijkel JCT. A new method of UV-patternable hydrophobization of micro- and nanofluidic networks. LAB ON A CHIP 2011; 11:4260-4266. [PMID: 22064947 DOI: 10.1039/c1lc20716d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This work reports a new method to hydrophobize glass-based micro- and nanofluidic networks. Conventional methods of hydrophobizing glass surfaces often create particulate debris causing clogging especially in shallow nanochannels or require skilful handling. Our novel method employs oxygen plasma, silicone oil and ultraviolet (UV) light. The contact angle of the modified bare glass surface can reach 100° whilst the inner channels after treatment facilitate stable and durable water-in-oil droplet generation. This modified surface was found to be stable for more than three weeks. The use of UV in principle enables in-channel hydrophobic patterning.
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Affiliation(s)
- Rerngchai Arayanarakool
- BIOS/Lab-on-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
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688
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Joensson HN, Andersson-Svahn H. Droplet microfluidics--a tool for protein engineering and analysis. LAB ON A CHIP 2011; 11:4144-4147. [PMID: 21984065 DOI: 10.1039/c1lc90102h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Haakan N Joensson
- Albanova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden
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689
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Sun M, Bithi SS, Vanapalli SA. Microfluidic static droplet arrays with tuneable gradients in material composition. LAB ON A CHIP 2011; 11:3949-52. [PMID: 21993897 DOI: 10.1039/c1lc20709a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We describe a one-step passive strategy to create concentration gradients in static droplet arrays. The technique exploits controlled exchange of materials between moving plugs and stationary drops. The concentration of soluble reagents can be varied from drop-to-drop in the presence of other soluble reagents or insoluble materials (e.g. cells) at well-defined time points.
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Affiliation(s)
- Meng Sun
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409-3121, USA
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690
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Zeitoun RI, Goudie MJ, Zwier J, Mahawilli D, Burns MA. Active control of nanolitre droplet contents with convective concentration gradients across permeable walls. LAB ON A CHIP 2011; 11:4022-4028. [PMID: 21996980 DOI: 10.1039/c1lc20576e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nanolitre droplets in microfluidic devices can be used to perform thousands of independent chemical and biological experiments while minimizing reagents, cost and time. However, the absence of simple and versatile methods capable of controlling the contents of these nanolitre chemical systems limits their scientific potential. To address this, we have developed a method that is simple to fabricate and can continuously control nanolitre chemical systems by integrating a time-resolved convective flow signal across a permeable membrane wall. With this method, we can independently control the volume and concentration of nanolitre-sized drops without ever directly contacting the fluid. Transport occurring in these systems was also analyzed and thoroughly characterized. We achieved volumetric fluid introduction and removal rates ranging from 0.23 to 4.0 pL s(-1). Furthermore, we expanded this method to perform chemical processes. We precipitated silver chloride using a flow signal of sodium chloride and silver nitrate droplets. From there, we were able to separate sodium chloride reactants with a water flow signal, and dissolve silver chloride solids with an ammonia hydroxide flow signal. Finally, we demonstrate the potential to deliver large molecules and perform physical processes like crystallization and particle packing.
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Affiliation(s)
- Ramsey I Zeitoun
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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691
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Abstract
Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.
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Affiliation(s)
| | | | - David R. Liu
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute Harvard University, 12 Oxford Street, Cambridge, MA 02138
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692
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Cho SW, Kang DK, Choo JB, Demllo AJ, Chang SI. Recent advances in microfluidic technologies for biochemistry and molecular biology. BMB Rep 2011; 44:705-12. [DOI: 10.5483/bmbrep.2011.44.11.705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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693
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Uhlen M, Svahn HA. Lab on a chip technologies for bioenergy and biosustainability research. LAB ON A CHIP 2011; 11:3389-3393. [PMID: 21811717 DOI: 10.1039/c1lc90063c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Mathias Uhlen
- Albanova University Center and Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden
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694
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Chen F, Zhan Y, Geng T, Lian H, Xu P, Lu C. Chemical transfection of cells in picoliter aqueous droplets in fluorocarbon oil. Anal Chem 2011; 83:8816-20. [PMID: 21967571 DOI: 10.1021/ac2022794] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The manipulation of cells inside water-in-oil droplets is essential for high-throughput screening of cell-based assays using droplet microfluidics. Cell transfection inside droplets is a critical step involved in functional genomics studies that examine in situ functions of genes using the droplet platform. Conventional water-in-hydrocarbon oil droplets are not compatible with chemical transfection due to its damage to cell viability and extraction of organic transfection reagents from the aqueous phase. In this work, we studied chemical transfection of cells encapsulated in picoliter droplets in fluorocarbon oil. The use of fluorocarbon oil permitted high cell viability and little loss of the transfection reagent into the oil phase. We varied the incubation time inside droplets, the DNA concentration, and the droplet size. After optimization, we were able to achieve similar transfection efficiency in droplets to that in the bulk solution. Interestingly, the transfection efficiency increased with smaller droplets, suggesting effects from either the microscale confinement or the surface-to-volume ratio.
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Affiliation(s)
- Fangyuan Chen
- Department of Chemistry, Nanjing University, Nanjing, PR China
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695
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Konry T, Bale SS, Bhushan A, Shen K, Seker E, Polyak B, Yarmush M. Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection. Mikrochim Acta 2011; 176:251-269. [PMID: 25378716 DOI: 10.1007/s00604-011-0705-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.
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Affiliation(s)
- Tania Konry
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Abhinav Bhushan
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Keyue Shen
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California, Davis, 3177 Kemper Hall, Davis, CA 95616, USA
| | - Boris Polyak
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Martin Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
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696
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Lee DH, Lee W, Um E, Park JK. Microbridge structures for uniform interval control of flowing droplets in microfluidic networks. BIOMICROFLUIDICS 2011; 5:34117-341179. [PMID: 22662043 PMCID: PMC3364831 DOI: 10.1063/1.3625604] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/26/2011] [Indexed: 05/10/2023]
Abstract
Precise temporal control of microfluidic droplets such as synchronization and combinatorial pairing of droplets is required to achieve a variety range of chemical and biochemical reactions inside microfluidic networks. Here, we present a facile and robust microfluidic platform enabling uniform interval control of flowing droplets for the precise temporal synchronization and pairing of picoliter droplets with a reagent. By incorporating microbridge structures interconnecting the droplet-carrying channel and the flow control channel, a fluidic pressure drop was derived between the two fluidic channels via the microbridge structures, reordering flowing droplets with a defined uniform interval. Through the adjustment of the control oil flow rate, the droplet intervals were flexibly and precisely adjustable. With this mechanism of droplet spacing, the gelation of the alginate droplets as well as control of the droplet interval was simultaneously achieved by additional control oil flow including calcified oleic acid. In addition, by parallel linking identical microfluidic modules with distinct sample inlet, controlled synchronization and pairing of two distinct droplets were demonstrated. This method is applicable to facilitate and develop many droplet-based microfluidic applications, including biological assay, combinatorial synthesis, and high-throughput screening.
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697
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Kojima T, Nagao N, Ando D, Ojima T, Kawarasaki Y, Kobayashi I, Nakajima M, Nakano H. Emulsion culture: A miniaturized library screening system based on micro-droplets in an emulsified medium. J Biosci Bioeng 2011; 112:299-303. [DOI: 10.1016/j.jbiosc.2011.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/06/2011] [Accepted: 05/31/2011] [Indexed: 10/18/2022]
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698
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Abate AR, Rotem A, Thiele J, Weitz DA. Efficient encapsulation with plug-triggered drop formation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031502. [PMID: 22060374 DOI: 10.1103/physreve.84.031502] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 06/14/2011] [Indexed: 05/31/2023]
Abstract
Monodisperse microscale drops formed with microfluidic devices are useful for encapsulating cells, microgel particles, or even additional drops. These techniques are thus useful for applications ranging from high-throughput biology to monodisperse particle and capsule synthesis, which require encapsulation of such objects. However, it is challenging to efficiently encapsulate the objects in all drops; often, the objects are encapsulated inefficiently, resulting in many improperly filled, unusable drops. Here, we describe a phenomenon that allows very efficient encapsulation. We use the inflow of the object to plug the drop maker nozzle; the continued injection of the outer phase pinches off a drop, thereby encapsulating the object; this yields precisely one object encapsulated per drop.
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Affiliation(s)
- Adam R Abate
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.
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699
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Hatch AC, Fisher JS, Pentoney SL, Yang DL, Lee AP. Tunable 3D droplet self-assembly for ultra-high-density digital micro-reactor arrays. LAB ON A CHIP 2011; 11:2509-17. [PMID: 21670837 DOI: 10.1039/c0lc00553c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present a tunable three-dimensional (3D) self-assembled droplet packing method to achieve high-density micro-reactor arrays for greater imaging efficiency and higher-throughput chemical and biological assays. We demonstrate the capability of this platform's high-density imaging method by performing single molecule quantification using digital polymerase chain reaction, or digital PCR, in multiple self-assembled colloid-like crystal lattice configurations. By controlling chamber height to droplet diameter ratios we predictively control three-dimensional packing configurations with varying degrees of droplet overlap to increase droplet density and imaging sensor area coverage efficiency. Fluorescence imaging of the densely packed 3D reactor arrays, up to three layers high, demonstrates high throughput quantitative analysis of single-molecule reactions. Now a greater number of microreactors can be observed and studied in a single picture frame without the need for confocal imaging, slide scanners, or complicated image processing techniques. Compared to 2D designs, tunable 3D reactor arrays yield up to a threefold increase in density and use 100% of the sensor's imaging area to enable simultaneous imaging a larger number of reactions without sacrificing digital quantification performance. This novel approach provides an important advancement for ultra-high-density reactor arrays.
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Affiliation(s)
- Andrew C Hatch
- Department of Biomedical Engineering, University of California-Irvine, 3120 Natural Sciences II, Irvine, CA 92697, USA
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700
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