1
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He H, Wu C, Saqib M, Hao R. Single-molecule fluorescence methods for protein biomarker analysis. Anal Bioanal Chem 2023:10.1007/s00216-022-04502-9. [PMID: 36609860 DOI: 10.1007/s00216-022-04502-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Proteins have been considered key building blocks of life. In particular, the protein content of an organism and a cell offers significant information for the in-depth understanding of the disease and biological processes. Single-molecule protein detection/sequencing tools will revolutionize clinical (proteomics) research, offering ultrasensitivity for low-abundance biomarker (protein) detection, which is important for the realization of early-stage disease diagnosis and single-cell proteomics. This improved detection/measurement capability delivers new sets of techniques to explore new frontiers and address important challenges in various interdisciplinary areas including nanostructured materials, molecular medicine, molecular biology, and chemistry. Importantly, fluorescence-based methods have emerged as indispensable tools for single protein detection/sequencing studies, providing a higher signal-to-noise ratio (SNR). Improvements in fluorescent dyes/probes and detector capabilities coupled with advanced (image) analysis strategies have fueled current developments for single protein biomarker detections. For example, in comparison to conventional ELISA (i.e., based on ensembled measurements), single-molecule fluorescence detection is more sensitive, faster, and more accurate with reduced background, high-throughput, and so on. In comparison to MS sequencing, fluorescence-based single-molecule protein sequencing can achieve the sequencing of peptides themselves with higher sensitivity. This review summarizes various typical single-molecule detection technologies including their methodology (modes of operation), detection limits, advantages and drawbacks, and current challenges with recent examples. We describe the fluorescence-based single-molecule protein sequencing/detection based on five kinds of technologies such as fluorosequencing, N-terminal amino acid binder, nanopore light sensing, and DNA nanotechnology. Finally, we present our perspective for developing high-performance fluorescence-based sequencing/detection techniques.
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Affiliation(s)
- Haihan He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuhong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Muhammad Saqib
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.,Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China. .,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
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2
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Onyeaka H, Anumudu CK, Okpe C, Okafor A, Ihenetu F, Miri T, Odeyemi OA, Anyogu A. Single Cell Protein for Foods and Feeds: A Review of Trends. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2206160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Introduction:
Predictions on the world’s population in the next few decades suggest that the global demand for animal-derived proteins may not be met if current conventional agriculture approaches are used. One promising solution to this complex crisis lies in the use of single-cell proteins (SCP). SCP refers to the edible biomass of unicellular microorganisms and can be developed as animal feeds or human foods. This paper provides a detailed overview on research towards the production and utilisation of SCPs and trends within the field.
Study Design:
A bibliometric based study was conducted on 425 SCP research articles collected from the Web of Science database, analysing the most cited papers using VOSviewer software, and contributing authors, affiliations and country of origin. Research publications on SCP started in 1961 and has grown steadily over the years.
Discussion:
Emerging research topics within SCP production focused on the use of improved fungal strains, the composition and characteristics of SCPs based on the type of substrates used, industrial production processes and the use of waste for SCP production, which serves the dual purpose of mitigating the cost associated with waste disposal and production of a valuable product.
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3
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Yu Z, Jin J, Shui L, Chen H, Zhu Y. Recent advances in microdroplet techniques for single-cell protein analysis. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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4
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Lv S, Chu Y, Zhang P, Ma S, Zhao M, Wang Z, Gu Y, Sun X. Improved efficiency of urine cell image segmentation using droplet microfluidics technology. Cytometry A 2020; 99:722-731. [PMID: 33342063 DOI: 10.1002/cyto.a.24296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Recent advances in the recognition of biological samples using machine vision have made this technology increasingly important in research and detection. Image segmentation is an important step in this process. This study focuses on how to reduce the interference factors such as the overlap between different types (or within the same type) of urine cells according to microfluidics and improve the machine vision segmentation accuracy for cell images. In this study, we demonstrate that the platform can realize this hypothesis using urine cell image segmentation as an example application. We first discuss the reported urine cell droplet microfluidic chip system, which can realize the test conditions in which urine cells are encapsulated in the droplet and isolated from salt crystallization and/or bacteria and other urine-formed elements. Then, based on the analysis conditions set in the aforementioned experiment, the proportions of red blood cells, white blood cells, and squamous epithelial cells covered by various formed elements in the total urine cells in the same urine sample are measured. We simultaneously analyze the percentage of urine cells covered by salt crystallization and the incidence of overlapping between urine cells. Finally, the Otsu algorithm is used to segment the urine cell images encapsulated by the droplet and the urine cell images not encapsulated by the droplet, and the Dice, Jaccard, precision, and recall values are calculated. The results suggest that the method of encapsulating single cells based on droplets can improve the image segmentation effect without optimizing the algorithm.
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Affiliation(s)
- Shuxing Lv
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Yuying Chu
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Panpan Zhang
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Sike Ma
- Engineering Research Center of Learning-Based Intelligent System, Ministry of Education of China, Tianjin University of Technology, Tianjin, China
| | - Meng Zhao
- Engineering Research Center of Learning-Based Intelligent System, Ministry of Education of China, Tianjin University of Technology, Tianjin, China
| | - Zhexiang Wang
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Yajun Gu
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Xuguo Sun
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
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5
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Cohen L, Cui N, Cai Y, Garden PM, Li X, Weitz DA, Walt DR. Single Molecule Protein Detection with Attomolar Sensitivity Using Droplet Digital Enzyme-Linked Immunosorbent Assay. ACS NANO 2020; 14:9491-9501. [PMID: 32589401 DOI: 10.1021/acsnano.0c02378] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Many proteins are present at low concentrations in biological samples, and therefore, techniques for ultrasensitive protein detection are necessary. To overcome challenges with sensitivity, the digital enzyme-linked immunosorbent assay (ELISA) was developed, which is 1000× more sensitive than conventional ELISA and allows sub-femtomolar protein detection. However, this sensitivity is still not sufficient to measure many proteins in various biological samples, thereby limiting our ability to detect and discover biomarkers. To overcome this limitation, we developed droplet digital ELISA (ddELISA), a simple approach for detecting low protein levels using digital ELISA and droplet microfluidics. ddELISA achieves maximal sensitivity by improving the sampling efficiency and counting more target molecules. ddELISA can detect proteins in the low attomolar range and is up to 25-fold more sensitive than digital ELISA using Single Molecule Arrays (Simoa), the current gold standard tool for ultrasensitive protein detection. Using ddELISA, we measured the LINE1/ORF1 protein, a potential cancer biomarker that has not been previously measured in serum. Additionally, due to the simplicity of our device design, ddELISA is promising for point-of-care applications. Thus, ddELISA will facilitate the discovery of biomarkers that have never been measured before for various clinical applications.
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Affiliation(s)
- Limor Cohen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yamei Cai
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Padric M Garden
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
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6
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Single-cell assays using integrated continuous-flow microfluidics. Methods Enzymol 2019. [PMID: 31668236 DOI: 10.1016/bs.mie.2019.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The recent maturation of continuous-flow microfluidic technologies has coincided with transformative new methods to profile single cells, including their genetic types, protein expression and enzyme activities. Continuous-flow high-throughput single-cell screening and sorting can reveal relationships across cellular phenotypes (e.g., enzyme activity and secretion) and genetic fingerprints. This technology provides unique opportunities, as well as experimental and computational challenges, for integrative approaches that can process large amounts of single-cell data. In this chapter, we discuss recent advances in integrated continuous-flow microfluidic approaches with a focus on measurements and statistical analysis of single-cell enzyme activity and their applications in quantitative biology, synthetic biology, and diagnosis.
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7
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Abstract
Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine.
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Affiliation(s)
- Kalliopi Trachana
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Rhishikesh Bargaje
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Gustavo Glusman
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Nathan D Price
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Sui Huang
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.).,Department of Biological Sciences, University of Calgary, Alberta, Canada (S.H.)
| | - Leroy E Hood
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
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8
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Wang C, Ren L, Liu W, Wei Q, Tan M, Yu Y. Fluorescence quantification of intracellular materials at the single-cell level by an integrated dual-well array microfluidic device. Analyst 2019; 144:2811-2819. [PMID: 30882810 DOI: 10.1039/c9an00153k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an integrated microfluidic device for quantifying intracellular materials at the single-cell level. This device combines a dual-well structure and a microfluidic control system. The dual-well structure includes capture wells (20 μm in diameter) for trapping a single cell and reaction wells (200 μm in diameter) for confining reagents. The control system enables a programmable procedure for single-cell analysis. This device achieves highly efficient trapping of single cells, overcoming the Poisson distribution, while affording sufficient biochemical reagents for each isolated reactor. We successfully utilized the presented device to monitor the catalytic interaction between intracellular alkaline phosphatase enzyme and a fluorogenic substrate and to quantify the intracellular glucose concentration of a single K562 cell based on an external standard method. The results demonstrate the feasibility and convenience of our dual-well array microfluidic device as a practical single-cell research tool.
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Affiliation(s)
- Chenyu Wang
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
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9
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Azizi M, Zaferani M, Cheong SH, Abbaspourrad A. Pathogenic Bacteria Detection Using RNA-Based Loop-Mediated Isothermal-Amplification-Assisted Nucleic Acid Amplification via Droplet Microfluidics. ACS Sens 2019; 4:841-848. [PMID: 30908029 DOI: 10.1021/acssensors.8b01206] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acid amplifications, such as polymerase chain reaction (PCR), are very beneficial for diagnostic applications, especially in the context of bacterial or viral outbreaks due to their high specificity and sensitivity. However, the need for bulky instrumentation and complicated protocols makes these methods expensive and slow, particularly for low numbers of RNA or DNA templates. In addition, implementing conventional nucleic acid amplification in a high-throughput manner is both reagent- and time-consuming. We bring droplet-based microfluidics and loop-mediated isothermal amplification (LAMP) together in an optimized operational condition to provide a sensitive biosensor for amplifying extracted RNA templates for the detection of Salmonella typhimurium (targeting the invA gene). By simultaneously performing ∼106 LAMP-assisted amplification reactions in picoliter-sized droplets and applying a new mathematical model for the number of droplets necessary to screen for the first positive droplet, we study the detection limit of our platform with pure culture and real samples (bacterial contaminated milk samples). Our LAMP-assisted droplet-based microfluidic technique was simple in operation, sensitive, specific, and rapid for the detection of pathogenic bacteria Salmonella typhimurium in comparison with well-established conventional methods. More importantly, the high-throughput nature of this technique makes it suitable for many applications in biological assays.
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Affiliation(s)
- Morteza Azizi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Meisam Zaferani
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Soon Hon Cheong
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
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10
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Azizi M, Zaferani M, Dogan B, Zhang S, Simpson KW, Abbaspourrad A. Nanoliter-Sized Microchamber/Microarray Microfluidic Platform for Antibiotic Susceptibility Testing. Anal Chem 2018; 90:14137-14144. [DOI: 10.1021/acs.analchem.8b03817] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Morteza Azizi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Meisam Zaferani
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Kenneth W. Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York 14853, United States
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11
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Ng EX, Sun G, Wei SC, Miller MA, DasGupta R, Lam PYP, Chen CH. Ultrafast Single-Cell Level Enzymatic Tumor Profiling. Anal Chem 2018; 91:1277-1285. [DOI: 10.1021/acs.analchem.8b02576] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ee Xien Ng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
| | - Guoyun Sun
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
| | - Shih-Chung Wei
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
- Biomedical Institute for Global Health Research and Technology, Singapore, Singapore
| | - Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Paula Yeng Po Lam
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
- Biomedical Institute for Global Health Research and Technology, Singapore, Singapore
- Singapore Institute for Neurotechnology, 28 Medical Dr. 05-COR, Singapore, Singapore
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12
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Saxena A, Dagur PK, Desai A, McCoy JP. Ultrasensitive Quantification of Cytokine Proteins in Single Lymphocytes From Human Blood Following ex-vivo Stimulation. Front Immunol 2018; 9:2462. [PMID: 30405640 PMCID: PMC6206239 DOI: 10.3389/fimmu.2018.02462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022] Open
Abstract
In this study we demonstrate the feasibility of direct, quantitative measurement of cytokine proteins in single human CD8 lymphocytes from fresh peripheral blood of healthy donors following a brief ex vivo stimulation. Cytokine-secreting cells were identified using cell surface “catch” reagents and single cell data were obtained by sorting of individual cytokine-secreting cells into 96 well plates containing lysis buffer followed by analysis using ultrasensitive immunoassays for interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). CD8 cells negative for cytokine production, as determined by the cell surface catch reagents were used as negative controls. Furthermore, studies were undertaken to compare the mean fluorescence intensity (MFI) values of cytokine staining by flow cytometry with the quantification of cytokines using the current method. This study demonstrates that it is feasible to quantify cytokines from individual primary cells. A shift from qualitative to quantitative determinations of cytokine protein levels in single cells will permit more precise and reproducible studies of heterogeneity in the immune system and can be accomplished with readily available instrumentation.
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Affiliation(s)
- Ankit Saxena
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Pradeep K Dagur
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Alisha Desai
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - John Philip McCoy
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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13
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Sinha N, Subedi N, Tel J. Integrating Immunology and Microfluidics for Single Immune Cell Analysis. Front Immunol 2018; 9:2373. [PMID: 30459757 PMCID: PMC6232771 DOI: 10.3389/fimmu.2018.02373] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022] Open
Abstract
The field of immunoengineering aims to develop novel therapies and modern vaccines to manipulate and modulate the immune system and applies innovative technologies toward improved understanding of the immune system in health and disease. Microfluidics has proven to be an excellent technology for analytics in biology and chemistry. From simple microsystem chips to complex microfluidic designs, these platforms have witnessed an immense growth over the last decades with frequent emergence of new designs. Microfluidics provides a highly robust and precise tool which led to its widespread application in single-cell analysis of immune cells. Single-cell analysis allows scientists to account for the heterogeneous behavior of immune cells which often gets overshadowed when conventional bulk study methods are used. Application of single-cell analysis using microfluidics has facilitated the identification of several novel functional immune cell subsets, quantification of signaling molecules, and understanding of cellular communication and signaling pathways. Single-cell analysis research in combination with microfluidics has paved the way for the development of novel therapies, point-of-care diagnostics, and even more complex microfluidic platforms that aid in creating in vitro cellular microenvironments for applications in drug and toxicity screening. In this review, we provide a comprehensive overview on the integration of microsystems and microfluidics with immunology and focus on different designs developed to decode single immune cell behavior and cellular communication. We have categorized the microfluidic designs in three specific categories: microfluidic chips with cell traps, valve-based microfluidics, and droplet microfluidics that have facilitated the ongoing research in the field of immunology at single-cell level.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nikita Subedi
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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14
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Campbell JM, Balhoff JB, Landwehr GM, Rahman SM, Vaithiyanathan M, Melvin AT. Microfluidic and Paper-Based Devices for Disease Detection and Diagnostic Research. Int J Mol Sci 2018; 19:E2731. [PMID: 30213089 PMCID: PMC6164778 DOI: 10.3390/ijms19092731] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/12/2022] Open
Abstract
Recent developments in microfluidic devices, nanoparticle chemistry, fluorescent microscopy, and biochemical techniques such as genetic identification and antibody capture have provided easier and more sensitive platforms for detecting and diagnosing diseases as well as providing new fundamental insight into disease progression. These advancements have led to the development of new technology and assays capable of easy and early detection of pathogenicity as well as the enhancement of the drug discovery and development pipeline. While some studies have focused on treatment, many of these technologies have found initial success in laboratories as a precursor for clinical applications. This review highlights the current and future progress of microfluidic techniques geared toward the timely and inexpensive diagnosis of disease including technologies aimed at high-throughput single cell analysis for drug development. It also summarizes novel microfluidic approaches to characterize fundamental cellular behavior and heterogeneity.
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Affiliation(s)
- Joshua M Campbell
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Joseph B Balhoff
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Grant M Landwehr
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Sharif M Rahman
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
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15
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Abstract
![]()
The compartmentalization of reactions
in monodispersed droplets
is valuable for applications across biology. However, the requirement
of microfluidics to partition the sample into monodispersed droplets
is a significant barrier that impedes implementation. Here, we introduce
particle-templated emulsification, a method to encapsulate samples
in monodispersed emulsions without microfluidics. By vortexing a mixture
of hydrogel particles and sample solution, we encapsulate the sample
in monodispersed emulsions that are useful for most droplet applications.
We illustrate the method with ddPCR and single cell culture. The ability
to encapsulate samples in monodispersed droplets without microfluidics
should facilitate the implementation of compartmentalized reactions
in biology.
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Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Samuel C Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
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16
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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17
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Bai Y, Gao M, Wen L, He C, Chen Y, Liu C, Fu X, Huang S. Applications of Microfluidics in Quantitative Biology. Biotechnol J 2017; 13:e1700170. [PMID: 28976637 DOI: 10.1002/biot.201700170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/03/2017] [Indexed: 01/15/2023]
Abstract
Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.
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Affiliation(s)
- Yang Bai
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Meng Gao
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Lingling Wen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Caiyun He
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yuan Chen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Chenli Liu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Xiongfei Fu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Shuqiang Huang
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
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18
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Huang L, Michael SA, Chen Y, Wu H. Current Advances in Highly Multiplexed Antibody-Based Single-Cell Proteomic Measurements. Chem Asian J 2017; 12:1680-1691. [PMID: 28493387 DOI: 10.1002/asia.201700404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Indexed: 12/29/2022]
Abstract
Single-cell measurements have played a critical role in revealing the complex signaling dynamics and heterogeneity present in cells, but there is still much to learn. Measuring samples from bulk populations of cells often masks the information and dynamics present in subsets of cells. Common single-cell protein studies rely on fluorescent microscopy and flow cytometry but are limited in multiplexing ability owing to spectral overlap. Recently, technology advancements in single-cell proteomics have allowed highly multiplexed measurement of multiple parameters simultaneously by using barcoded microfluidic enzyme-linked immunosorbent assays and mass cytometry techniques. In this review, we will describe recent work around multiparameter single-cell protein measurements and critically analyze the techniques.
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Affiliation(s)
- Lu Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sean A Michael
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yangfan Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hongkai Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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19
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Che J, Yu V, Garon EB, Goldman JW, Di Carlo D. Biophysical isolation and identification of circulating tumor cells. LAB ON A CHIP 2017; 17:1452-1461. [PMID: 28352869 PMCID: PMC5507599 DOI: 10.1039/c7lc00038c] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Isolation and enumeration of circulating tumor cells (CTCs) from blood is important for determining patient prognosis and monitoring treatment. Methods based on affinity to cell surface markers have been applied to both purify (via immunoseparation) and identify (via immunofluorescence) CTCs. However, variability of cell biomarker expression associated with tumor heterogeneity and evolution and cross-reactivity of antibody probes have long complicated CTC enrichment and immunostaining. Here, we report a truly label-free high-throughput microfluidic approach to isolate, enumerate, and characterize the biophysical properties of CTCs using an integrated microfluidic device. Vortex-mediated deformability cytometry (VDC) consists of an initial vortex region which enriches large CTCs, followed by release into a downstream hydrodynamic stretching region which deforms the cells. Visualization and quantification of cell deformation with a high-speed camera revealed populations of large (>15 μm diameter) and deformable (aspect ratio >1.2) CTCs from 16 stage IV lung cancer samples, that are clearly distinguished by increased deformability compared to contaminating blood cells and rare large cells isolated from healthy patients. The VDC technology demonstrated a comparable positive detection rate of putative CTCs above healthy baseline (93.8%) with respect to standard immunofluorescence (71.4%). Automation allows full enumeration of CTCs from a 10 mL vial of blood within <1 h after sample acquisition, compared with 4+ hours with standard approaches. Moreover, cells are released into any collection vessel for further downstream analysis. VDC shows potential for accurate CTC enumeration without labels and confirms the unique highly deformable biophysical properties of large CTCs circulating in blood.
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Affiliation(s)
- James Che
- Department of Bioengineering, University of California, Los Angeles, 410 Westwood Plaza, Los Angeles, California 90095, USA.
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20
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Wen N, Zhao Z, Fan B, Chen D, Men D, Wang J, Chen J. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis. Molecules 2016; 21:E881. [PMID: 27399651 PMCID: PMC6272933 DOI: 10.3390/molecules21070881] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.
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Affiliation(s)
- Na Wen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhan Zhao
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Beiyuan Fan
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Deyong Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dong Men
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Junbo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
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21
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Single cell multiplexed assay for proteolytic activity using droplet microfluidics. Biosens Bioelectron 2016; 81:408-414. [PMID: 26995287 DOI: 10.1016/j.bios.2016.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
Abstract
Cellular enzymes interact in a post-translationally regulated fashion to govern individual cell behaviors, yet current platform technologies are limited in their ability to measure multiple enzyme activities simultaneously in single cells. Here, we developed multi-color Förster resonance energy transfer (FRET)-based enzymatic substrates and use them in a microfluidics platform to simultaneously measure multiple specific protease activities from water-in-oil droplets that contain single cells. By integrating the microfluidic platform with a computational analytical method, Proteolytic Activity Matrix Analysis (PrAMA), we are able to infer six different protease activity signals from individual cells in a high throughput manner (~100 cells/experimental run). We characterized protease activity profiles at single cell resolution for several cancer cell lines including breast cancer cell line MDA-MB-231, lung cancer cell line PC-9, and leukemia cell line K-562 using both live-cell and in-situ cell lysis assay formats, with special focus on metalloproteinases important in metastasis. The ability to measure multiple proteases secreted from or expressed in individual cells allows us to characterize cell heterogeneity and has potential applications including systems biology, pharmacology, cancer diagnosis and stem cell biology.
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22
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A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders. Sci Rep 2016; 6:22575. [PMID: 26940078 PMCID: PMC4778045 DOI: 10.1038/srep22575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 11/08/2022] Open
Abstract
Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution.
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