1
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Lu B, Lunn J, Nightingale AM, Niu X. Highly sensitive absorbance measurement using droplet microfluidics integrated with an oil extraction and long pathlength detection flow cell. Front Chem 2024; 12:1394388. [PMID: 38803381 PMCID: PMC11129082 DOI: 10.3389/fchem.2024.1394388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
In droplet microfluidics, UV-Vis absorption spectroscopy along with colorimetric assays have been widely used for chemical and biochemical analysis. However, the sensitivity of the measurement can be limited by the short optical pathlength. Here we report a novel design to enhance the sensitivity by removing oil and converting the droplets into a single-phase aqueous flow, which can be measured within a U-shape channel with long optical pathlength. The flow cells were fabricated via 3D printing. The calibration results have demonstrated complete oil removal and effective optical pathlengths similar to the designed channel lengths (from 5 to 20 mm). The flow cell was further employed in a droplet microfluidic-based phosphate sensing system. The measured phosphate levels displayed excellent consistency with data obtained from traditional UV spectroscopy analysis. This flow cell design overcomes the limitations of short optical pathlengths in droplet microfluidics and has the potential to be used for in situ and continuous monitoring.
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Affiliation(s)
| | | | | | - Xize Niu
- Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
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2
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Lathia R, Nagpal S, Modak CD, Mishra S, Sharma D, Reddy BS, Nukala P, Bhat R, Sen P. Tunable encapsulation of sessile droplets with solid and liquid shells. Nat Commun 2023; 14:6445. [PMID: 37833273 PMCID: PMC10575970 DOI: 10.1038/s41467-023-41977-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Droplet encapsulations using liquid or solid shells are of significant interest in microreactors, drug delivery, crystallization, and cell growth applications. Despite progress in droplet-related technologies, tuning micron-scale shell thickness over a large range of droplet sizes is still a major challenge. In this work, we report capillary force assisted cloaking using hydrophobic colloidal particles and liquid-infused surfaces. The technique produces uniform solid and liquid shell encapsulations over a broad range (5-200 μm shell thickness for droplet volume spanning over four orders of magnitude). Tunable liquid encapsulation is shown to reduce the evaporation rate of droplets by up to 200 times with a wide tunability in lifetime (1.5 h to 12 days). Further, we propose using the technique for single crystals and cell/spheroid culture platforms. Stimuli-responsive solid shells show hermetic encapsulation with tunable strength and dissolution time. Moreover, scalability, and versatility of the technique is demonstrated for on-chip applications.
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Affiliation(s)
- Rutvik Lathia
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Satchit Nagpal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandantaru Dey Modak
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Satyarthi Mishra
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Deepak Sharma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Bheema Sankar Reddy
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Pavan Nukala
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Ramray Bhat
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
- Department of BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Prosenjit Sen
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Department of BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
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4
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Song Z, Lin ES, Uddin MH, Abid HA, Ong JW, Ng TW. Graphene Oxide Paper Manipulation of Micro-Reactor Drops. MICROMACHINES 2023; 14:1306. [PMID: 37512618 PMCID: PMC10384384 DOI: 10.3390/mi14071306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023]
Abstract
Digital microfluidics, which relies on the movement of drops, is relatively immune to clogging problems, making it suited for micro-reactor applications. Here, graphene oxide paper of 100 μm thickness, fabricated by blade coating sedimented dispersions onto roughened substrates, followed by drying and mechanical exfoliation, was found to be relatively free of cracks and curling. It also exhibited high wettability and elasto-capillary characteristics. Possessing low enough stiffness, it could rapidly and totally self-wrap water drops of 20 μL volume placed 2 mm from its edge when oriented between 0 and 60° to the horizontal. This complete wrapping behavior allowed drops to be translated via movement of the paper over long distances without dislodgement notwithstanding accelerations and decelerations. An amount of 2 drops that were wrapped with separate papers, when collided with each other at speeds up to 0.64 m/s, were found to eschew coalescence. This portends the development of robust digital microfluidic approaches for micro-reactors.
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Affiliation(s)
- Zhixiong Song
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Eric Shen Lin
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Md Hemayet Uddin
- Melbourne Centre for Nanofabrication, 151 Wellington Rd., Clayton, VIC 3168, Australia
| | - Hassan Ali Abid
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jian Wern Ong
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Tuck Wah Ng
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
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5
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Cai D, Wang Y, Zou J, Li Z, Huang E, Ouyang X, Que Z, Luo Y, Chen Z, Jiang Y, Zhang G, Wu H, Liu D. Droplet Encoding-Pairing Enabled Multiplexed Digital Loop-Mediated Isothermal Amplification for Simultaneous Quantitative Detection of Multiple Pathogens. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205863. [PMID: 36646503 PMCID: PMC9982564 DOI: 10.1002/advs.202205863] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/06/2022] [Indexed: 06/01/2023]
Abstract
Despite the advantages of digital nucleic acid analysis (DNAA) in terms of sensitivity, precision, and resolution, current DNAA methods commonly suffer a limitation in multiplexing capacity. To address this issue, a droplet encoding-pairing enabled DNAA multiplexing strategy is developed, wherein unique tricolor combinations are deployed to index individual primer droplets. The template droplets and primer droplets are sequentially introduced into a microfluidic chip with a calabash-shaped microwell array and are pairwise trapped and merged in the microwells. Pre-merging and post-amplification image analysis with a machine learning algorithm is used to identify, enumerate, and address the droplets. By incorporating the amplification signals with droplet encoding information, simultaneous quantitative detection of multiple targets is achieved. This strategy allows for the establishment of flexible multiplexed DNAA by simply adjusting the primer droplet library. Its flexibility is demonstrated by establishing two multiplexed (8-plex) droplet digital loop-mediated isothermal amplification (mddLAMP) assays for individually detecting lower respiratory tract infection and urinary tract infection causative pathogens. Clinical sample analysis shows that the microbial detection outcomes of the mddLAMP assays are consistent with those of the conventional assay. This DNAA multiplexing strategy can achieve flexible high-order multiplexing on demand, making it a desirable tool for high-content pathogen detection.
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Affiliation(s)
- Dongyang Cai
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Yu Wang
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Jingjing Zou
- College of Food Science and EngineeringSouth China University of TechnologyGuangzhou510640China
| | - Zhujun Li
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Enqi Huang
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Xiuyun Ouyang
- College of Food Science and EngineeringSouth China University of TechnologyGuangzhou510640China
| | - Zhiquan Que
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Yanzhang Luo
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Zhenhua Chen
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
| | - Yanqing Jiang
- Beijing Baicare Biotechnology Co., LtdBeijing102206China
| | - Guohao Zhang
- Beijing Baicare Biotechnology Co., LtdBeijing102206China
| | - Hongkai Wu
- Department of ChemistryHong Kong University of Science and TechnologyHong KongChina
| | - Dayu Liu
- Department of Laboratory Medicinethe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhou510180China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical DiagnosisGuangzhou510180China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong ProvinceGuangzhou510180China
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6
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Rondelez Y, Gines G. Programmable Ultrasensitive Molecular Amplifier for Digital and Multiplex MicroRNA Quantification. Methods Mol Biol 2023; 2630:89-102. [PMID: 36689178 DOI: 10.1007/978-1-0716-2982-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Digital bioassays, popularized by digital PCR, provide some of the most robust and accurate methods for nucleic acid quantification. In this chapter, we detail a protocol for digital, isothermal, and multiplex detection of microRNAs, which relies on a recently developed amplification method. Our approach uses programmable ultrasensitive molecular amplifiers (PUMAs) to reveal the presence of target microRNAs randomly isolated in picoliter-size microfluidic droplets. Nonspecific amplification in droplets that do not contain a target is eliminated by an active threshold mechanism. Multiple circuits can be assembled for the multiplex digital detection of up to three targets. We finally present the option of using fluorescent dropcodes to streamline the assay and analyze more than a dozen samples in parallel.
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Affiliation(s)
- Yannick Rondelez
- Gulliver Laboratory, ESPCI Paris - Université PSL, Paris, France
| | - Guillaume Gines
- Gulliver Laboratory, ESPCI Paris - Université PSL, Paris, France.
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7
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Okumura S, Gines G, Lobato-Dauzier N, Baccouche A, Deteix R, Fujii T, Rondelez Y, Genot AJ. Nonlinear decision-making with enzymatic neural networks. Nature 2022; 610:496-501. [PMID: 36261553 DOI: 10.1038/s41586-022-05218-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/09/2022] [Indexed: 12/22/2022]
Abstract
Artificial neural networks have revolutionized electronic computing. Similarly, molecular networks with neuromorphic architectures may enable molecular decision-making on a level comparable to gene regulatory networks1,2. Non-enzymatic networks could in principle support neuromorphic architectures, and seminal proofs-of-principle have been reported3,4. However, leakages (that is, the unwanted release of species), as well as issues with sensitivity, speed, preparation and the lack of strong nonlinear responses, make the composition of layers delicate, and molecular classifications equivalent to a multilayer neural network remain elusive (for example, the partitioning of a concentration space into regions that cannot be linearly separated). Here we introduce DNA-encoded enzymatic neurons with tuneable weights and biases, and which are assembled in multilayer architectures to classify nonlinearly separable regions. We first leverage the sharp decision margin of a neuron to compute various majority functions on 10 bits. We then compose neurons into a two-layer network and synthetize a parametric family of rectangular functions on a microRNA input. Finally, we connect neural and logical computations into a hybrid circuit that recursively partitions a concentration plane according to a decision tree in cell-sized droplets. This computational power and extreme miniaturization open avenues to query and manage molecular systems with complex contents, such as liquid biopsies or DNA databases.
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Affiliation(s)
- S Okumura
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - G Gines
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - N Lobato-Dauzier
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - A Baccouche
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - R Deteix
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - T Fujii
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Y Rondelez
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - A J Genot
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan.
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8
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Sanka I, Bartkova S, Pata P, Smolander OP, Scheler O. Investigation of Different Free Image Analysis Software for High-Throughput Droplet Detection. ACS OMEGA 2021; 6:22625-22634. [PMID: 34514234 PMCID: PMC8427638 DOI: 10.1021/acsomega.1c02664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Droplet microfluidics has revealed innovative strategies in biology and chemistry. This advancement has delivered novel quantification methods, such as droplet digital polymerase chain reaction (ddPCR) and an antibiotic heteroresistance analysis tool. For droplet analysis, researchers often use image-based detection techniques. Unfortunately, the analysis of images may require specific tools or programming skills to produce the expected results. In order to address the issue, we explore the potential use of standalone freely available software to perform image-based droplet detection. We select the four most popular software and classify them into rule-based and machine learning-based types after assessing the software's modules. We test and evaluate the software's (i) ability to detect droplets, (ii) accuracy and precision, and (iii) overall components and supporting material. In our experimental setting, we find that the rule-based type of software is better suited for image-based droplet detection. The rule-based type of software also has a simpler workflow or pipeline, especially aimed for non-experienced users. In our case, CellProfiler (CP) offers the most user-friendly experience for both single image and batch processing analyses.
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9
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Okumura S, Hapsianto BN, Lobato-Dauzier N, Ohno Y, Benner S, Torii Y, Tanabe Y, Takada K, Baccouche A, Shinohara M, Kim SH, Fujii T, Genot A. Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:293. [PMID: 33499417 PMCID: PMC7912653 DOI: 10.3390/nano11020293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022]
Abstract
Hydrogels are essential in many fields ranging from tissue engineering and drug delivery to food sciences or cosmetics. Hydrogels that respond to specific biomolecular stimuli such as DNA, mRNA, miRNA and small molecules are highly desirable from the perspective of medical applications, however interfacing classical hydrogels with nucleic acids is still challenging. Here were demonstrate the generation of microbeads of DNA hydrogels with droplet microfluidic, and their morphological actuation with DNA strands. Using strand displacement and the specificity of DNA base pairing, we selectively dissolved gel beads, and reversibly changed their size on-the-fly with controlled swelling and shrinking. Lastly, we performed a complex computing primitive-A Winner-Takes-All competition between two populations of gel beads. Overall, these results show that strand responsive DNA gels have tantalizing potentials to enhance and expand traditional hydrogels, in particular for applications in sequencing and drug delivery.
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Affiliation(s)
- Shu Okumura
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
- Department of Bioengineering, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (B.N.H.); (M.S.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Benediktus Nixon Hapsianto
- Department of Bioengineering, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (B.N.H.); (M.S.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Nicolas Lobato-Dauzier
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Yuto Ohno
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (Y.O.); (S.B.); (Y.T.)
| | - Seiju Benner
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (Y.O.); (S.B.); (Y.T.)
| | - Yosuke Torii
- Faculty of Agriculture, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan;
| | - Yuuka Tanabe
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (Y.O.); (S.B.); (Y.T.)
| | - Kazuki Takada
- Faculty of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan;
| | - Alexandre Baccouche
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
| | - Marie Shinohara
- Department of Bioengineering, The University of Tokyo 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan; (B.N.H.); (M.S.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Soo Hyeon Kim
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Teruo Fujii
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Anthony Genot
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, Tokyo 153-8505, Japan; (S.O.); (N.L.-D.); (A.B.); (S.H.K.); (T.F.)
- Institute of Industrial Science, The University of Tokyo 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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10
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Zoupanou S, Chiriacò MS, Tarantini I, Ferrara F. Innovative 3D Microfluidic Tools for On-Chip Fluids and Particles Manipulation: From Design to Experimental Validation. MICROMACHINES 2021; 12:mi12020104. [PMID: 33494413 PMCID: PMC7912382 DOI: 10.3390/mi12020104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/23/2022]
Abstract
Micromixers are essential components in lab-on-a-chip devices, of which the low efficiency can limit many bio-application studies. Effective mixing with automation capabilities is still a crucial requirement. In this paper, we present a method to fabricate a three-dimensional (3D) poly(methyl methacrylate) (PMMA) fluidic mixer by combining computer-aided design (CAD), micromilling technology, and experimental application via manipulating fluids and nanoparticles. The entire platform consists of three microfabricated layers with a bottom reservoir-shaped microchannel, a central serpentine channel, and a through-hole for interconnection and an upper layer containing inlets and outlet. The sealing process of the three layers and the high-precision and customizable methods used for fabrication ensure the realization of the monolithic 3D architecture. This provides buried running channels able to perform passive chaotic mixing and dilution functions, thanks to a portion of the pathway in common between the reservoir and serpentine layers. The possibility to plug-and-play micropumping systems allows us to easily demonstrate the feasibility and working features of our device for tracking the mixing and dilution performances of the micromixer by using colored fluids and fluorescent nanoparticles as the proof of concept. Exploiting the good transparency of the PMMA, spatial liquid composition and better control over reaction variables are possible, and the real-time monitoring of experiments under a fluorescence microscope is also allowed. The tools shown in this paper are easily integrable in more complex lab-on-chip platforms.
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Affiliation(s)
- Sofia Zoupanou
- CNR NANOTEC—Institute of Nanotechnology, via per Monteroni, 73100 Lecce, Italy;
- Department of Mathematics & Physics E. de Giorgi, via Arnesano, University of Salento, 73100 Lecce, Italy;
| | - Maria Serena Chiriacò
- CNR NANOTEC—Institute of Nanotechnology, via per Monteroni, 73100 Lecce, Italy;
- Correspondence: (M.S.C.); (F.F.)
| | - Iolena Tarantini
- Department of Mathematics & Physics E. de Giorgi, via Arnesano, University of Salento, 73100 Lecce, Italy;
| | - Francesco Ferrara
- CNR NANOTEC—Institute of Nanotechnology, via per Monteroni, 73100 Lecce, Italy;
- STMicroelectronics S.R.L., via per Monteroni, 73100 Lecce, Italy
- Correspondence: (M.S.C.); (F.F.)
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11
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Microfluidic droplet generation based on non-embedded co-flow-focusing using 3D printed nozzle. Sci Rep 2020; 10:21616. [PMID: 33303772 PMCID: PMC7729985 DOI: 10.1038/s41598-020-77836-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
Most commercial microfluidic droplet generators rely on the planar flow-focusing configuration implemented in polymer or glass chips. The planar geometry, however, suffers from many limitations and drawbacks, such as the need of specific coatings or the use of dedicated surfactants, depending on the fluids in play. On the contrary, and thanks to their axisymmetric geometry, glass capillary-based droplet generators are a priori not fluid-dependent. Nevertheless, they have never reached the market because their assembly requires fastidious and not scalable fabrication techniques. Here we present a new device, called Raydrop, based on the alignment of two capillaries immersed in a pressurized chamber containing the continuous phase. The dispersed phase exits one of the capillaries through a 3D-printed nozzle placed in front of the extraction capillary for collecting the droplets. This non-embedded implementation of an axisymmetric flow-focusing is referred to non-embedded co-flow-focusing configuration. Experimental results demonstrate the universality of the device in terms of the variety of fluids that can be emulsified, as well as the range of droplet radii that can be obtained, without neither the need of surfactant nor coating. Additionally, numerical computations of the Navier-Stokes equations based on the quasi-steadiness assumption allow to provide an explanation to the underlying mechanism behind the drop formation and the mechanism of the dripping to jetting transition. Excellent predictions were also obtained for the droplet radius, as well as for the dripping-jetting transition, when varying the geometrical and fluid parameters, showing the ability of this configuration to enventually enhance the dripping regime. The monodispersity ensured by the dripping regime, the robustness of the fabrication technique, the optimization capabilities from the numerical modelling and the universality of the configuration confer to the Raydrop technology a very high potential in the race towards high-throughput droplet generation processes.
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12
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Hlaváček A, Křivánková J, Pizúrová N, Václavek T, Foret F. Photon-upconversion barcode for monitoring an enzymatic reaction with a fluorescence reporter in droplet microfluidics. Analyst 2020; 145:7718-7723. [PMID: 32996917 DOI: 10.1039/d0an01667e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report luminescent photon-upconversion barcodes for indexing the chemical content of droplets. The barcode is compatible with the simultaneous detection of fluorescence. The encoding and decoding of the initial concentration of enzyme β-galactosidase and substrate 4-methylumbelliferyl β-d-galactopyranoside are described. The fluorescent product 4-methylumbelliferone is detected simultaneously with the barcode.
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Affiliation(s)
- Antonín Hlaváček
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic.
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13
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Accelerating the Finite-Element Method for Reaction-Diffusion Simulations on GPUs with CUDA. MICROMACHINES 2020; 11:mi11090881. [PMID: 32971889 PMCID: PMC7569852 DOI: 10.3390/mi11090881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate the physics of such systems where boundary conditions play a crucial role. However, a fine discretization in time and space is required for complex geometries (like sharp corners) and highly nonlinear chemistry. Graphical Processing Units (GPUs) are increasingly used to speed up scientific computing, but their application to accelerate simulations of reaction-diffusion in DNA nanotechnology has been little investigated. Here we study reaction-diffusion equations (a DNA-based predator-prey system) in a tortuous geometry (a maze), which was shown experimentally to generate subtle geometric effects. We solve the partial differential equations on a GPU, demonstrating a speedup of ∼100 over the same resolution on a 20 cores CPU.
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Payne EM, Holland-Moritz DA, Sun S, Kennedy RT. High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects. LAB ON A CHIP 2020; 20:2247-2262. [PMID: 32500896 DOI: 10.1039/d0lc00347f] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.
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Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Wippold JA, Wang H, Tingling J, Leibowitz J, de Figueiredo P, Han A. PRESCIENT: platform for the rapid evaluation of antibody success using integrated microfluidics enabled technology. LAB ON A CHIP 2020; 20:1628-1638. [PMID: 32196032 PMCID: PMC7269184 DOI: 10.1039/c9lc01165j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Identifying antibodies (Abs) that neutralize infectious agents is the first step for developing therapeutics, vaccines, and diagnostic tools for these infectious agents. However, current approaches for identifying neutralizing Abs (nAbs) typically rely on dilution-based assays that are costly, inefficient, and only survey a small subset of the entire repertoire. There are also intrinsic biases in many steps of conventional nAb identification processes. More importantly, conventional assays rely on simple Ab-antigen binding assays, which may not result in identifying the most potent nAbs, as the strongest binder may not be the most potent nAb. Droplet microfluidic systems have the capability to overcome such limitations by conducting complex multi-step assays with high reliability, resolution, and throughput in a pico-liter volume water-in-oil emulsion droplet format. Here, we describe the development of PRESCIENT (Platform for the Rapid Evaluation of antibody SucCess using Integrated microfluidics ENabled Technology), a droplet microfluidic system that can enable high-throughput single-cell resolution identification of nAb repertoires elicited in response to viral infection. We demonstrate PRESCIENT's ability to identify Abs that neutralize a model viral agent, Murine coronavirus (murine hepatitis virus), which causes high mortality rates in experimentally infected mice. In-droplet infection of host cells by the virus was first demonstrated, followed by demonstration of in-droplet neutralization by nAbs produced from a single Ab-producing hybridoma cell. Finally, fluorescence intensity analyses of two populations of hybridoma cell lines (nAb-producing and non-nAb-producing hybridoma cell lines) successfully discriminated between the two populations. The presented strategy and platform have the potential to identify and investigate neutralizing activities against a broad range of potential infectious agents for which nAbs have yet to be discovered, significantly advancing the nAb identification process as well as reinvigorating the field of Ab discovery, characterization, and development.
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Affiliation(s)
- Jose A. Wippold
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, CHINA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Joseph Tingling
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Julian Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
- Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Medicine, Texas A&M University, College Station, TX 77843
| | - Arum Han
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, CHINA
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Li J, Qiu Y, Zhang Z, Li C, Li S, Zhang W, Guo Z, Yao J, Zhou L. Heterogeneous modification of through-hole microwell chips for ultralow cross-contamination digital polymerase chain reaction. Analyst 2020; 145:3116-3124. [PMID: 32162628 DOI: 10.1039/d0an00220h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chip-based dPCR (cdPCR) with a physical boundary between micro-units allows for high parallelism, robustness and sensitivity. However, cross-contamination between micro-units is still a problem that affects the accuracy of results. To overcome this problem, we introduced a heterogeneous modification strategy by microcontact printing to prepare a through-hole microwell chip (TMC) with a hydrophobic exterior surface and hydrophilic interior surface. The modified TMC can reduce cross-contamination (sample residual rate (SRR) of (4.9 ± 1.5)%) by an efficient partitioning yield (unit filling rate (UFR) of (91.1 ± 2.2)%). The sample-residual properties of modified TMCs could be tuned by the reaction conditions. As the contact time increased, the surface CA of the TMC increased, which caused decreases of the SRR and UFR. However, prolonging the contact time to 25 s would cause a sharp reduction of the UFR. The modified TMCs with high UFRs were used for further dPCR studies. The fluorescence images of dPCR chips were collected by fluorescence microscopy and a self-developed optical system, followed by image processing and data statistics to obtain quantitative results. The copy number variation results of the surface hydrophobic TMC was closer to the true value compared to that of the hydrophilic TMC. The results indicated that the sample residue on the hydrophilic TMC would increase the number of positive points, which would cause false positives and clustering error. The absolute quantitative results of gradient dilution plasmid DNA of JAK2 gene using modified TMC also proved that heterogeneous modification made the quantitative results more accurate. The heterogeneous modified TMC is expected to be used for high-throughput, high-sensitivity and high-specificity biological analyses, such as circulating tumor DNA and cell analysis.
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Affiliation(s)
- Jinze Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Yajun Qiu
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Zhiqi Zhang
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and University of Science and Technology of China, Hefei 230026, China
| | - Chuanyu Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and University of Science and Technology of China, Hefei 230026, China
| | - Shuli Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and Shanghai University, Shanghai 200444, China
| | - Wei Zhang
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Zhen Guo
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Jia Yao
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and Soochow University, Suzhou 215163, China
| | - Lianqun Zhou
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
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Prangemeier T, Lehr FX, Schoeman RM, Koeppl H. Microfluidic platforms for the dynamic characterisation of synthetic circuitry. Curr Opin Biotechnol 2020; 63:167-176. [PMID: 32172160 DOI: 10.1016/j.copbio.2020.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/28/2023]
Abstract
Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically modulated and set in a dynamic fluctuating environment within a living cell. To build more complex circuits and to gain insight into context effects, intrinsic noise and transient performance, characterisation techniques that resolve both heterogeneity and dynamics are required. Here we review recent advances in both in vitro and in vivo microfluidic technologies that are suitable for the characterisation of synthetic circuitry, modules and parts.
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Affiliation(s)
- Tim Prangemeier
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - François-Xavier Lehr
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Rogier M Schoeman
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany.
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18
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Droplet-Based Microfluidics Methods for Detecting Enzyme Inhibitors. Methods Mol Biol 2019. [PMID: 31773657 DOI: 10.1007/978-1-0716-0163-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Sub-nanoliter droplets produced in microfluidic devices have gained an enormous importance for performing all kinds of biochemical assays. One of the main reasons is that the amounts of reagents employed can be reduced in approximately five orders of magnitude compared to conventional microplate assays. In this chapter, we describe how to carry out the design, fabrication, and operation of a microfluidic device that allows performing enzyme kinetics and enzyme inhibition assays in droplets. This procedure can be used effectively to screen a small size library of compounds. Then, we describe how to use this droplet microfluidic setup to screen for potential inhibitor compounds eluted from a coupled high-performance liquid chromatography (HPLC) system that separates crude natural extracts.
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19
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Hlaváček A, Křivánková J, Přikryl J, Foret F. Photon-Upconversion Barcoding with Multiple Barcode Channels: Application for Droplet Microfluidics. Anal Chem 2019; 91:12630-12635. [PMID: 31514495 DOI: 10.1021/acs.analchem.9b03117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Barcoding facilitates high-throughput analytical methods in complex matrixes with a reduced volume of sample, reagents, time, and cost. Because of orthogonality to fluorescence, photon-upconversion barcodes attracted considerable attention in recent years. We constructed an epiluminescence detector, which, for the first time, demonstrated the reading of photon-upconversion spectra from microdroplets in a microfluidic chip with frequency up to 10 Hz. Non-negative least-squares deconvolution enabled the reading of an unprecedented number of photon-upconversion barcode channels (six) from emission spectra (excitation 980 nm, emission 430-875 nm). The standard deviation of barcode reading from microdroplets was ∼1%. Described barcoding can be, for example, used for multiparameter titrations, multiplexed biological and chemical assays, optimizations on a microfluidic platform, and preparation of barcoded concentration gradients and libraries.
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Affiliation(s)
- Antonín Hlaváček
- Institute of Analytical Chemistry of the Czech Academy of Sciences , Veveří 97 , 602 00 Brno , Czech Republic
| | - Jana Křivánková
- Institute of Analytical Chemistry of the Czech Academy of Sciences , Veveří 97 , 602 00 Brno , Czech Republic
| | - Jan Přikryl
- Institute of Analytical Chemistry of the Czech Academy of Sciences , Veveří 97 , 602 00 Brno , Czech Republic
| | - František Foret
- Institute of Analytical Chemistry of the Czech Academy of Sciences , Veveří 97 , 602 00 Brno , Czech Republic
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20
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Sun M, Li Z, Wang S, Maryu G, Yang Q. Building Dynamic Cellular Machineries in Droplet-Based Artificial Cells with Single-Droplet Tracking and Analysis. Anal Chem 2019; 91:9813-9818. [PMID: 31284720 PMCID: PMC7260773 DOI: 10.1021/acs.analchem.9b01481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the application of droplet microfluidics has grown exponentially in chemistry and biology over the past decades, robust universal platforms for the routine generation and comprehensive analysis of droplet-based artificial cells are still rare. Here we report using microfluidic droplets to reproduce a variety of types of cellular machinery in in vitro artificial cells. In combination with a unique image-based analysis method, the system enables full automation in tracking single droplets with high accuracy, high throughput, and high sensitivity. These powerful performances allow broad applicability evident in three representative droplet-based analytical prototypes that we develop for (i) droplet digital detection, (ii) in vitro transcription and translation reactions, and (iii) spatiotemporal dynamics of cell-cycle oscillations. The capacities of this platform to generate, incubate, track, and analyze individual microdroplets via real-time, long-term imaging unleash its great potential in accelerating cell-free synthetic biology. Moreover, the wide scope covering from digital to analog to morphological detections makes this droplet analysis technique adaptable for many other divergent types of droplet-based chemical and biological assays.
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Affiliation(s)
- Meng Sun
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Gembu Maryu
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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21
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22
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23
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Wei Y, Zhu Y, Fang Q. Nanoliter Quantitative High-Throughput Screening with Large-Scale Tunable Gradients Based on a Microfluidic Droplet Robot under Unilateral Dispersion Mode. Anal Chem 2019; 91:4995-5003. [DOI: 10.1021/acs.analchem.8b04564] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yan Wei
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
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24
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Svensson CM, Shvydkiv O, Dietrich S, Mahler L, Weber T, Choudhary M, Tovar M, Figge MT, Roth M. Coding of Experimental Conditions in Microfluidic Droplet Assays Using Colored Beads and Machine Learning Supported Image Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1802384. [PMID: 30549235 DOI: 10.1002/smll.201802384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/16/2018] [Indexed: 06/09/2023]
Abstract
To efficiently exploit the potential of several millions of droplets that can be considered as individual bioreactors in microfluidic experiments, methods to encode different experimental conditions in droplets are needed. The approach presented here is based on coencapsulation of colored polystyrene beads with biological samples. The decoding of the droplets, as well as content quantification, are performed by automated analysis of triggered images of individual droplets in-flow using bright-field microscopy. The decoding strategy combines bead classification using a random forest classifier and Bayesian inference to identify different codes and thus experimental conditions. Antibiotic susceptibility testing of nine different antibiotics and the determination of the minimal inhibitory concentration of a specific antibiotic against a laboratory strain of Escherichia coli are presented as a proof-of-principle. It is demonstrated that this method allows successful encoding and decoding of 20 different experimental conditions within a large droplet population of more than 105 droplets per condition. The decoding strategy correctly assigns 99.6% of droplets to the correct condition and a method for the determination of minimal inhibitory concentration using droplet microfluidics is established. The current encoding and decoding pipeline can readily be extended to more codes by adding more bead colors or color combinations.
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Affiliation(s)
- Carl-Magnus Svensson
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Oksana Shvydkiv
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Stefanie Dietrich
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Lisa Mahler
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Thomas Weber
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Mahipal Choudhary
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
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Chang JC, Swank Z, Keiser O, Maerkl SJ, Amstad E. Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions. Sci Rep 2018; 8:8143. [PMID: 29802303 PMCID: PMC5970246 DOI: 10.1038/s41598-018-26542-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023] Open
Abstract
Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.
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Affiliation(s)
- Jui-Chia Chang
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Zoe Swank
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Oliver Keiser
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Esther Amstad
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Duan BK, Cavanagh PE, Li X, Walt DR. Ultrasensitive Single-Molecule Enzyme Detection and Analysis Using a Polymer Microarray. Anal Chem 2018; 90:3091-3098. [PMID: 29425025 DOI: 10.1021/acs.analchem.7b03980] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This report describes a novel method for isolating and detecting individual enzyme molecules using polymer arrays of picoliter microwells. A fluidic flow-cell device containing an array of microwells is fabricated in cyclic olefin polymer (COP). The use of COP microwell arrays simplifies experiments by eliminating extensive device preparation and surface functionalization that are common in other microwell array formats. Using a simple and robust loading method to introduce the reaction solution, individual enzyme molecules are trapped in picoliter microwells and subsequently isolated and sealed by fluorinated oil. The sealing is stable for hours in the COP device. The picoliter microwell device can measure enzyme concentrations in the low-femtomolar range by counting the number of active wells using a digital read-out. These picoliter microwell arrays can also easily be regenerated and reused.
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Affiliation(s)
- Barrett K Duan
- Department of Pathology , Harvard Medical School , Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering, Building for Transformative Medicine, 60 Fenwood Road , Boston , Massachusetts 02115 , United States
| | - Peter E Cavanagh
- Department of Pathology , Harvard Medical School , Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering, Building for Transformative Medicine, 60 Fenwood Road , Boston , Massachusetts 02115 , United States
| | - Xiang Li
- Department of Pathology , Harvard Medical School , Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering, Building for Transformative Medicine, 60 Fenwood Road , Boston , Massachusetts 02115 , United States
| | - David R Walt
- Department of Pathology , Harvard Medical School , Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering, Building for Transformative Medicine, 60 Fenwood Road , Boston , Massachusetts 02115 , United States
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