151
|
Zenhausern R, Chen CH, Yoon JY. Microfluidic sample preparation for respiratory virus detection: A review. BIOMICROFLUIDICS 2021; 15:011503. [PMID: 33643510 PMCID: PMC7889292 DOI: 10.1063/5.0041089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/28/2021] [Indexed: 05/05/2023]
Abstract
Techniques used to prepare clinical samples have been perfected for use in diagnostic testing in a variety of clinical situations, e.g., to extract, concentrate, and purify respiratory virus particles. These techniques offer a high level of purity and concentration of target samples but require significant equipment and highly trained personnel to conduct, which is difficult to achieve in resource-limited environments where rapid testing and diagnostics are crucial for proper handling of respiratory viruses. Microfluidics has popularly been utilized toward rapid virus detection in resource-limited environments, where most devices focused on detection rather than sample preparation. Initial microfluidic prototypes have been hindered by their reliance on several off-chip preprocessing steps and external laboratory equipment. Recently, sample preparation methods have also been incorporated into microfluidics to conduct the virus detection in an all-in-one, automated manner. Extraction, concentration, and purification of viruses have been demonstrated in smaller volumes of samples and reagents, with no need for specialized training or complex machinery. Recent devices show the ability to function independently and efficiently to provide rapid, automated sample preparation as well as the detection of viral samples with high efficiency. In this review, methods of microfluidic sample preparation for the isolation and purification of viral samples are discussed, limitations of current systems are summarized, and potential advances are identified.
Collapse
Affiliation(s)
- Ryan Zenhausern
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| |
Collapse
|
152
|
Jiang T, Jia Y, Sun H, Deng X, Tang D, Ren Y. Dielectrophoresis Response of Water-in-Oil-in-Water Double Emulsion Droplets with Singular or Dual Cores. MICROMACHINES 2020; 11:mi11121121. [PMID: 33348930 PMCID: PMC7766960 DOI: 10.3390/mi11121121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/16/2022]
Abstract
Microfluidic technologies have enabled generation of exquisite multiple emulsion droplets, which have been used in many fields, including single-cell assays, micro-sized chemical reactions, and material syntheses. Electrical controlling is an important technique for droplet manipulation in microfluidic systems, but the dielectrophoretic behaviors of multiple emulsion droplets in electrical fields are rarely studied. Here, we report on the dielectrophoresis response of double emulsion droplets in AC electric fields in microfluidic channel. A core-shell model is utilized for analyzing the polarization of droplet interfaces and the overall dielectrophoresis (DEP) force. The water-in-oil-in-water droplets, generated by glass capillary devices, experience negative DEP at low field frequency. At high frequency, however, the polarity of DEP is tunable by adjusting droplet shell thickness or core conductivity. Then, the behavior of droplets with two inner cores is investigated, where the droplets undergo rotation before being repelled or attracted by the strong field area. This work should benefit a wide range of applications that require manipulation of double emulsion droplets by electric fields.
Collapse
Affiliation(s)
- Tianyi Jiang
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
| | - Yankai Jia
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
| | - Haizhen Sun
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
| | - Xiaokang Deng
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
| | - Dewei Tang
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; (T.J.); (Y.J.); (H.S.); (X.D.); (D.T.)
- State Key Laboratory of Robotics and System, Harbin Institute of Technology, West Da-Zhi Street 92, Harbin 150001, Heilongjiang, China
- Correspondence: ; Tel.: +86-0451-86418028; Fax: +86-0451-86402658
| |
Collapse
|
153
|
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: 23] [Impact Index Per Article: 5.8] [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.
Collapse
|
154
|
Guo L, Zeng W, Xu S, Zhou J. Fluorescence-activated droplet sorting for enhanced pyruvic acid accumulation by Candida glabrata. BIORESOURCE TECHNOLOGY 2020; 318:124258. [PMID: 33099100 DOI: 10.1016/j.biortech.2020.124258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
One of the goals of metabolic engineering is to engineer strains that can optimally produce target metabolites. However, the current workflow for rational engineering of the metabolic pathway is sometimes time-consuming and labor-intensive. Here, we have established a cost-effective approach for screening for variants secreting metabolites. Different surface display systems were adopted and verified, which anchored pHluorin to the Candida glabrata cell surface to associate pyruvic acid detection with the read out of this reporter. A generalizable simulation approach based on computational fluid dynamics and regularity of generated droplet dimension was presented, which was found to be an efficient design tool to explore microfluidic characteristics or optimization. Finally, a microfluidic platform based on simulation coupled with surface display system was constructed. A mutant exhibiting a 73.6% increase in pyruvic acid production was identified. This ultrahigh-throughput screening pattern offers a practical guide for identifying microbial strains with many traits of interest.
Collapse
Affiliation(s)
- Likun Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
155
|
Zhang P, Abate AR. High-Definition Single-Cell Printing: Cell-by-Cell Fabrication of Biological Structures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2005346. [PMID: 33206435 PMCID: PMC7987217 DOI: 10.1002/adma.202005346] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/10/2020] [Indexed: 05/17/2023]
Abstract
Bioprinting is a powerful technology with the potential to transform medical device manufacturing, organ replacement, and the treatment of diseases and physiologic malformations. However, current bioprinters are unable to reliably print the fundamental unit of all living things, single cells. A high-definition single-cell printing, a novel microfluidic technology, is presented here that can accurately print single cells from a mixture of multiple candidates. The bioprinter employs a highly miniaturized microfluidic sorter to deterministically select single cells of interest for printing, achieving an accuracy of ≈10 µm and speed of ≈100 Hz. This approach is demonstrated by fabricating intricate cell patterns with pre-defined features through selective single-cell printing. The approach is used to synthesize well-defined spheroids with controlled composition and morphology. The speed, accuracy, and flexibility of the approach will advance bioprinting to enable new studies in organoid science, tissue engineering, and spatially targeted cell therapies.
Collapse
Affiliation(s)
- Pengfei Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| |
Collapse
|
156
|
Ortseifen V, Viefhues M, Wobbe L, Grünberger A. Microfluidics for Biotechnology: Bridging Gaps to Foster Microfluidic Applications. Front Bioeng Biotechnol 2020; 8:589074. [PMID: 33282849 PMCID: PMC7691494 DOI: 10.3389/fbioe.2020.589074] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Microfluidics and novel lab-on-a-chip applications have the potential to boost biotechnological research in ways that are not possible using traditional methods. Although microfluidic tools were increasingly used for different applications within biotechnology in recent years, a systematic and routine use in academic and industrial labs is still not established. For many years, absent innovative, ground-breaking and “out-of-the-box” applications have been made responsible for the missing drive to integrate microfluidic technologies into fundamental and applied biotechnological research. In this review, we highlight microfluidics’ offers and compare them to the most important demands of the biotechnologists. Furthermore, a detailed analysis in the state-of-the-art use of microfluidics within biotechnology was conducted exemplarily for four emerging biotechnological fields that can substantially benefit from the application of microfluidic systems, namely the phenotypic screening of cells, the analysis of microbial population heterogeneity, organ-on-a-chip approaches and the characterisation of synthetic co-cultures. The analysis resulted in a discussion of potential “gaps” that can be responsible for the rare integration of microfluidics into biotechnological studies. Our analysis revealed six major gaps, concerning the lack of interdisciplinary communication, mutual knowledge and motivation, methodological compatibility, technological readiness and missing commercialisation, which need to be bridged in the future. We conclude that connecting microfluidics and biotechnology is not an impossible challenge and made seven suggestions to bridge the gaps between those disciplines. This lays the foundation for routine integration of microfluidic systems into biotechnology research procedures.
Collapse
Affiliation(s)
- Vera Ortseifen
- Proteome and Metabolome Research, Faculty of Biology, Center for Biotechnology/CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Martina Viefhues
- Experimental Biophysics and Applied Nanosciences, Faculty of Physics, Bielefeld University, Bielefeld, Germany
| | - Lutz Wobbe
- Algae Biotechnology and Bioenergy Group, Faculty of Biology, Center for Biotechnology/CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
157
|
Cavett V, Paegel BM. Multiplexed Enzyme Activity-Based Probe Display via Hybridization. ACS COMBINATORIAL SCIENCE 2020; 22:579-585. [PMID: 32803953 DOI: 10.1021/acscombsci.0c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Emulsions offer the means to miniaturize and parallelize high-throughput screening but require a robust method to localize activity-based fluorescent probes in each droplet. Multiplexing probes in droplets is impractical, though highly desirable for identifying library members that possess very specific activity. Here, we present multiplexed probe immobilization on library beads for emulsion screening. During library bead preparation, we quantitated ∼106 primers per bead by fluorescence in situ hybridization, however emulsion PCR yielded only ∼103 gene copies per bead. We leveraged the unextended bead-bound primers to hybridize complementary probe-oligonucleotide heteroconjugates to the library beads. The probe-hybridized bead libraries were then used to program emulsion in vitro transcription/translation reactions and analyzed by FACS to perform multiplexed activity-based screening of trypsin and chymotrypsin mutant libraries for novel proteolytic specificity. The approach's modularity should permit a high degree of probe multiplexing and appears extensible to other enzyme classes and library types.
Collapse
Affiliation(s)
- Valerie Cavett
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Brian M. Paegel
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
- Departments of Chemistry & Biomedical Engineering, University of California, Irvine, California 92617, United States
| |
Collapse
|
158
|
Clark IC, Delley CL, Sun C, Thakur R, Stott SL, Thaploo S, Li Z, Quintana FJ, Abate AR. Targeted Single-Cell RNA and DNA Sequencing With Fluorescence-Activated Droplet Merger. Anal Chem 2020; 92:14616-14623. [PMID: 33049138 PMCID: PMC8182774 DOI: 10.1021/acs.analchem.0c03059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analyzing every cell in a diverse sample provides insight into population-level heterogeneity, but abundant cell types dominate the analysis and rarer populations are scarcely represented in the data. To focus on specific cell types, the current paradigm is to physically isolate subsets of interest prior to analysis; however, it remains difficult to isolate and then single-cell sequence such populations because of compounding losses. Here, we describe an alternative approach that selectively merges cells with reagents to achieve enzymatic reactions without having to physically isolate cells. We apply this technique to perform single-cell transcriptome and genome sequencing of specific cell subsets. Our method for analyzing heterogeneous populations obviates the need for pre- or post-enrichment and simplifies single-cell workflows, making it useful for other applications in single-cell biology, combinatorial chemical synthesis, and drug screening.
Collapse
Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Rohan Thakur
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shannon L Stott
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
159
|
Gerlt MS, Haidas D, Ratschat A, Suter P, Dittrich PS, Dual J. Manipulation of single cells inside nanoliter water droplets using acoustic forces. BIOMICROFLUIDICS 2020; 14:064112. [PMID: 33381252 PMCID: PMC7749759 DOI: 10.1063/5.0036407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/08/2020] [Indexed: 05/10/2023]
Abstract
Droplet microfluidics enables high-throughput screening of single cells and is particularly valuable for applications, where the secreted compounds are analyzed. Typically, optical methods are employed for analysis, which are limited in their applicability as labeling protocols are required. Alternative label-free methods such as mass spectrometry would broaden the range of assays but are harmful to the cells, which is detrimental for some applications such as directed evolution. In this context, separation of cells from supernatant is beneficial prior to the analysis to retain viable cells. In this work, we propose an in-droplet separation method based on contactless and label-free acoustic particle manipulation. In a microfluidic chip, nanoliter droplets containing particles are produced at a T-junction. The particles are trapped in the tip of the droplet by the interplay of acoustic forces in two dimensions and internal flow fields. The droplets are subsequently split at a second T-junction into two daughter droplets-one containing the supernatant and the other containing the corresponding particles. The separation efficiency is measured in detail for polystyrene (PS) beads as a function of droplet speed, size, split ratio, and particle concentration. Further, single-bead (PS) and single-cell (yeast) experiments were carried out. At a throughput of 114 droplets/min, a separation efficiency of 100% ± 0% was achieved for more than 150 droplets. Finally, mammalian cells and bacteria were introduced into the system to test its versatility. This work demonstrates a robust, non-invasive strategy to perform single yeast cell-supernatant sampling in nanoliter volumes.
Collapse
Affiliation(s)
- Michael S. Gerlt
- Department of Mechanical and Process Engineering, ETH Zurich, Institute for Mechanical Systems (IMES), Tannenstrasse 3, CH-8092 Zurich, Switzerland
| | - Dominik Haidas
- Department of Biosystems Science and Engineering, ETH Zurich, Bioanalytics Group, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Alexandre Ratschat
- Department of Mechanical and Process Engineering, ETH Zurich, Institute for Mechanical Systems (IMES), Tannenstrasse 3, CH-8092 Zurich, Switzerland
| | - Philipp Suter
- Department of Mechanical and Process Engineering, ETH Zurich, Institute for Mechanical Systems (IMES), Tannenstrasse 3, CH-8092 Zurich, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Bioanalytics Group, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Jürg Dual
- Department of Mechanical and Process Engineering, ETH Zurich, Institute for Mechanical Systems (IMES), Tannenstrasse 3, CH-8092 Zurich, Switzerland
| |
Collapse
|
160
|
Ling SD, Geng Y, Chen A, Du Y, Xu J. Enhanced single-cell encapsulation in microfluidic devices: From droplet generation to single-cell analysis. BIOMICROFLUIDICS 2020; 14:061508. [PMID: 33381250 PMCID: PMC7758092 DOI: 10.1063/5.0018785] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
Abstract
Single-cell analysis to investigate cellular heterogeneity and cell-to-cell interactions is a crucial compartment to answer key questions in important biological mechanisms. Droplet-based microfluidics appears to be the ideal platform for such a purpose because the compartmentalization of single cells into microdroplets offers unique advantages of enhancing assay sensitivity, protecting cells against external stresses, allowing versatile and precise manipulations over tested samples, and providing a stable microenvironment for long-term cell proliferation and observation. The present Review aims to give a preliminary guidance for researchers from different backgrounds to explore the field of single-cell encapsulation and analysis. A comprehensive and introductory overview of the droplet formation mechanism, fabrication methods of microchips, and a myriad of passive and active encapsulation techniques to enhance single-cell encapsulation efficiency were presented. Meanwhile, common methods for single-cell analysis, especially for long-term cell proliferation, differentiation, and observation inside microcapsules, are briefly introduced. Finally, the major challenges faced in the field are illustrated, and potential prospects for future work are discussed.
Collapse
Affiliation(s)
- Si Da Ling
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuhao Geng
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - An Chen
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yanan Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianhong Xu
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| |
Collapse
|
161
|
Shimko TC, Fordyce PM, Orenstein Y. DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinformatics 2020; 36:3357-3364. [PMID: 32176271 DOI: 10.1093/bioinformatics/btaa162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/13/2020] [Accepted: 03/13/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High-throughput protein screening is a critical technique for dissecting and designing protein function. Libraries for these assays can be created through a number of means, including targeted or random mutagenesis of a template protein sequence or direct DNA synthesis. However, mutagenic library construction methods often yield vastly more nonfunctional than functional variants and, despite advances in large-scale DNA synthesis, individual synthesis of each desired DNA template is often prohibitively expensive. Consequently, many protein-screening libraries rely on the use of degenerate codons (DCs), mixtures of DNA bases incorporated at specific positions during DNA synthesis, to generate highly diverse protein-variant pools from only a few low-cost synthesis reactions. However, selecting DCs for sets of sequences that covary at multiple positions dramatically increases the difficulty of designing a DC library and leads to the creation of many undesired variants that can quickly outstrip screening capacity. RESULTS We introduce a novel algorithm for total DC library optimization, degenerate codon design (DeCoDe), based on integer linear programming. DeCoDe significantly outperforms state-of-the-art DC optimization algorithms and scales well to more than a hundred proteins sharing complex patterns of covariation (e.g. the lab-derived avGFP lineage). Moreover, DeCoDe is, to our knowledge, the first DC design algorithm with the capability to encode mixed-length protein libraries. We anticipate DeCoDe to be broadly useful for a variety of library generation problems, ranging from protein engineering attempts that leverage mutual information to the reconstruction of ancestral protein states. AVAILABILITY AND IMPLEMENTATION github.com/OrensteinLab/DeCoDe. CONTACT yaronore@bgu.ac.il. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Polly M Fordyce
- Department of Genetics
- Department of Bioengineering
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| |
Collapse
|
162
|
Method for Passive Droplet Sorting after Photo-Tagging. MICROMACHINES 2020; 11:mi11110964. [PMID: 33126559 PMCID: PMC7692103 DOI: 10.3390/mi11110964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
We present a method to photo-tag individual microfluidic droplets for latter selection by passive sorting. The use of a specific surfactant leads to the interfacial tension to be very sensitive to droplet pH. The photoexcitation of droplets containing a photoacid, pyranine, leads to a decrease in droplet pH. The concurrent increase in droplet interfacial tension enables the passive selection of irradiated droplets. The technique is used to select individual droplets within a droplet array as illuminated droplets remain in the wells while other droplets are eluted by the flow of the external oil. This method was used to select droplets in an array containing cells at a specific stage of apoptosis. The technique is also adaptable to continuous-flow sorting. By passing confined droplets over a microfabricated trench positioned diagonally in relation to the direction of flow, photo-tagged droplets were directed toward a different chip exit based on their lateral movement. The technique can be performed on a conventional fluorescence microscope and uncouples the observation and selection of droplets, thus enabling the selection on a large variety of signals, or based on qualitative user-defined features.
Collapse
|
163
|
Liu H, Xu X, Peng K, Zhang Y, Jiang L, Williams TC, Paulsen IT, Piper JA, Li M. Microdroplet enabled cultivation of single yeast cells correlates with bulk growth and reveals subpopulation phenomena. Biotechnol Bioeng 2020; 118:647-658. [PMID: 33022743 DOI: 10.1002/bit.27591] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/18/2020] [Accepted: 10/04/2020] [Indexed: 12/18/2022]
Abstract
Yeast has been engineered for cost-effective organic acid production through metabolic engineering and synthetic biology techniques. However, cell growth assays in these processes were performed in bulk at the population level, thus obscuring the dynamics of rare single cells exhibiting beneficial traits. Here, we introduce the use of monodisperse picolitre droplets as bioreactors to cultivate yeast at the single-cell level. We investigated the effect of acid stress on growth and the effect of potassium ions on propionic acid tolerance for single yeast cells of different species, genotypes, and phenotypes. The results showed that the average growth of single yeast cells in microdroplets experiences the same trend to those of yeast populations grown in bulk, and microdroplet compartments do not significantly affect cell viability. This approach offers the prospect of detecting cell-to-cell variations in growth and physiology and is expected to be applied for the engineering of yeast to produce value-added bioproducts.
Collapse
Affiliation(s)
- Hangrui Liu
- ARC Centre of Excellence for Nanoscale BioPhotonics, NSW, Australia.,Department of Physics and Astronomy, Macquarie University, Sydney, NSW, Australia
| | - Xin Xu
- ARC Centre of Excellence in Synthetic Biology, NSW, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kai Peng
- ARC Centre of Excellence in Synthetic Biology, NSW, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Yuxin Zhang
- School of Engineering, Macquarie University, Sydney, NSW, Australia
| | - Lianmei Jiang
- ARC Centre of Excellence for Nanoscale BioPhotonics, NSW, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Thomas C Williams
- ARC Centre of Excellence in Synthetic Biology, NSW, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, NSW, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - James A Piper
- ARC Centre of Excellence for Nanoscale BioPhotonics, NSW, Australia.,Department of Physics and Astronomy, Macquarie University, Sydney, NSW, Australia
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
164
|
McIntyre D, Lashkaripour A, Densmore D. Rapid and inexpensive microfluidic electrode integration with conductive ink. LAB ON A CHIP 2020; 20:3690-3695. [PMID: 32895672 DOI: 10.1039/d0lc00763c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Electrode integration significantly increases the versatility of droplet microfluidics, enabling label-free sensing and manipulation at a single-droplet (single-cell) resolution. However, common fabrication techniques for integrating electronics into microfluidics are expensive, time-consuming, and can require cleanroom facilities. Here, we present a simple and cost-effective method for integrating electrodes into thermoplastic microfluidic chips using an off-the-shelf conductive ink. The developed conductive ink electrodes cost less than $10 for an entire chip, have been shown here in channel geometries as small as 75 μm by 50 μm, and can go from fabrication to testing within a day without a cleanroom. The geometric fabrication limits of this technique were explored over time, and proof-of-concept microfluidic devices for capacitance sensing, droplet merging, and droplet sorting were developed. This novel method complements existing rapid prototyping systems for microfluidics such as micromilling, laser cutting, and 3D printing, enabling their wider use and application.
Collapse
Affiliation(s)
- David McIntyre
- Boston University Biomedical Engineering Department, 44 Cummington Mall, Boston, USA and Biological Design Center, 610 Commonwealth Ave, Boston, USA
| | - Ali Lashkaripour
- Boston University Biomedical Engineering Department, 44 Cummington Mall, Boston, USA and Biological Design Center, 610 Commonwealth Ave, Boston, USA
| | - Douglas Densmore
- Biological Design Center, 610 Commonwealth Ave, Boston, USA and Boston University Electrical and Computer Engineering Department, 8 Saint Mary's St., Boston, USA.
| |
Collapse
|
165
|
Ma F, Guo T, Zhang Y, Bai X, Li C, Lu Z, Deng X, Li D, Kurabayashi K, Yang GY. An ultrahigh-throughput screening platform based on flow cytometric droplet sorting for mining novel enzymes from metagenomic libraries. Environ Microbiol 2020; 23:996-1008. [PMID: 32985743 DOI: 10.1111/1462-2920.15257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/26/2020] [Indexed: 11/27/2022]
Abstract
Uncultivable microbial communities provide enormous reservoirs of enzymes, but their experimental identification by functional metagenomics is challenging, mainly due to the difficulty of screening enormous metagenomic libraries. Here, we propose a reliable and convenient ultrahigh-throughput screening platform based on flow cytometric droplet sorting (FCDS). The FCDS platform employs water-in-oil-in-water double emulsion droplets serving as single-cell enzymatic micro-reactors and a commercially available flow cytometer, and it can efficiently isolate novel biocatalysts from metagenomic libraries by processing single cells as many as 108 per day. We demonstrated the power of this platform by screening a metagenomic library constructed from domestic running water samples. The FCDS assay screened 30 million micro-reactors in only 1 h, yielding a collection of esterase genes. Among these positive hits, Est WY was identified as a novel esterase with high catalytic efficiency and distinct evolutionary origin from other lipolytic enzymes. Our study manifests that the FCDS platform is a robust tool for functional metagenomics, with the potential to significantly improve the efficiency of exploring novel enzymes from nature.
Collapse
Affiliation(s)
- Fuqiang Ma
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Tianjie Guo
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Yifan Zhang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Xue Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Changlong Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Zelin Lu
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Xi Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daixi Li
- Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Katsuo Kurabayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
166
|
High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
Collapse
|
167
|
Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. MICROBIOME 2020; 8:141. [PMID: 33004077 PMCID: PMC7531118 DOI: 10.1186/s40168-020-00911-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/23/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. RESULTS Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. CONCLUSION By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.
Collapse
Affiliation(s)
- Alexandra S Tauzin
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- CAPES Foundation, Ministry of Education of Brazil, BrasÍlia, DF, 70040-020, Brazil
| | - Liisa D Van Vliet
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Drop-Tech, Canterbury Court, Cambridge, CB4 3QU, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Sandrine Laguerre
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Terrapon
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Marion Leclerc
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
- Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| | | |
Collapse
|
168
|
Alavi A, Bar-Joseph Z. Iterative point set registration for aligning scRNA-seq data. PLoS Comput Biol 2020; 16:e1007939. [PMID: 33108369 PMCID: PMC7647120 DOI: 10.1371/journal.pcbi.1007939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/06/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022] Open
Abstract
Several studies profile similar single cell RNA-Seq (scRNA-Seq) data using different technologies and platforms. A number of alignment methods have been developed to enable the integration and comparison of scRNA-Seq data from such studies. While each performs well on some of the datasets, to date no method was able to both perform the alignment using the original expression space and generalize to new data. To enable such analysis we developed Single Cell Iterative Point set Registration (SCIPR) which extends methods that were successfully applied to align image data to scRNA-Seq. We discuss the required changes needed, the resulting optimization function, and algorithms for learning a transformation function for aligning data. We tested SCIPR on several scRNA-Seq datasets. As we show it successfully aligns data from several different cell types, improving upon prior methods proposed for this task. In addition, we show the parameters learned by SCIPR can be used to align data not used in the training and to identify key cell type-specific genes.
Collapse
Affiliation(s)
- Amir Alavi
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|
169
|
Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
Collapse
Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
| |
Collapse
|
170
|
Di Girolamo S, Puorger C, Lipps G. Stable and selective permeable hydrogel microcapsules for high-throughput cell cultivation and enzymatic analysis. Microb Cell Fact 2020; 19:170. [PMID: 32854709 PMCID: PMC7451113 DOI: 10.1186/s12934-020-01427-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Miniaturization of biochemical reaction volumes within artificial microcompartments has been the key driver for directed evolution of several catalysts in the past two decades. Typically, single cells are co-compartmentalized within water-in-oil emulsion droplets with a fluorogenic substrate whose conversion allows identification of catalysts with improved performance. However, emulsion droplet-based technologies prevent cell proliferation to high density and preclude the feasibility of biochemical reactions that require the exchange of small molecule substrates. Here, we report on the development of a high-throughput screening method that addresses these shortcomings and that relies on a novel selective permeable polymer hydrogel microcapsule. RESULTS Hollow-core polyelectrolyte-coated chitosan alginate microcapsules (HC-PCAMs) with selective permeability were successfully constructed by jet break-up and layer-by-layer (LBL) technology. We showed that HC-PCAMs serve as miniaturized vessels for single cell encapsulation, enabling cell growth to high density and cell lysis to generate monoclonal cell lysate compartments suitable for high-throughput analysis using a large particle sorter (COPAS). The feasibility of using HC-PCAMs as reaction compartments which exchange small molecule substrates was demonstrated using the transpeptidation reaction catalyzed by the bond-forming enzyme sortase F from P. acnes. The polyelectrolyte shell surrounding microcapsules allowed a fluorescently labelled peptide substrate to enter the microcapsule and take part in the transpeptidation reaction catalyzed by the intracellularly expressed sortase enzyme retained within the capsule upon cell lysis. The specific retention of fluorescent transpeptidation products inside microcapsules enabled the sortase activity to be linked with a fluorescent readout and allowed clear separation of microcapsules expressing the wild type SrtF from those expressing the inactive variant. CONCLUSION A novel polymer hydrogel microcapsule-based method, which allows for high-throughput analysis based on encapsulation of single cells has been developed. The method has been validated for the transpeptidation activity of sortase enzymes and represents a powerful tool for screening of libraries of sortases, other bond-forming enzymes, as well as of binding affinities in directed evolution experiments. Moreover, selective permeable microcapsules encapsulating microcolonies provide a new and efficient means for preparing novel caged biocatalyst and biosensor agents.
Collapse
Affiliation(s)
- Salvatore Di Girolamo
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Chasper Puorger
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland.
| |
Collapse
|
171
|
Zhang Y, Herling TW, Kreida S, Peter QAE, Kartanas T, Törnroth-Horsefield S, Linse S, Knowles TPJ. A microfluidic strategy for the detection of membrane protein interactions. LAB ON A CHIP 2020; 20:3230-3238. [PMID: 32744557 DOI: 10.1039/d0lc00205d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Membrane proteins perform a vast range of vital biological functions and are the gatekeepers for exchange of information and matter between the intracellular and extracellular environment. However, membrane protein interactions can be challenging to characterise in a quantitative manner due to the low solubility and large size of the membrane protein complex with associated lipid or detergent molecules. Here, we show that measurements of the changes in charge and diffusivity on the micron scale allow for non-disruptive studies of membrane protein interactions in solution. The approach presented here uses measurements of key physical properties of membrane proteins and their ligands to characterise the binding equilibrium parameters. We demonstrate this approach for human aquaporins (AQPs), key membrane proteins in the regulation of water homeostasis in cells. We perform quantitative measurements to characterise the interactions between two full-length AQP isoforms and the regulatory protein, calmodulin (CaM), and show that CaM selectively binds AQP0. Through direct measurements of the diffusivity and mobility in an external electric field, the diffusion coefficients and electrophoretic mobilities are determined for the individual components and the resulting AQP0-CaM complex. Furthermore, we obtain directly the binding equilibrium parameters and effective charge of each component. These results open up a route towards the use of microfluidics as a general platform in protein science and open up new possibilities for the characterisation of membrane protein interactions in solution.
Collapse
Affiliation(s)
- Yuewen Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Therese W Herling
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Stefan Kreida
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Quentin A E Peter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tadas Kartanas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| |
Collapse
|
172
|
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: 113] [Impact Index Per Article: 28.3] [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.
Collapse
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
| |
Collapse
|
173
|
Radziwon K, Weeks AM. Protein engineering for selective proteomics. Curr Opin Chem Biol 2020; 60:10-19. [PMID: 32768891 DOI: 10.1016/j.cbpa.2020.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
Post-translational modifications, complex formation, subcellular localization, and cell-type-specific expression create functionally distinct protein subpopulations that enable living systems to execute rapid and precise responses to changing conditions. Systems-level analysis of these subproteomes remains challenging, requiring preservation of spatial information or enrichment of species that are transient and present at low abundance. Engineered proteins have emerged as important tools for selective proteomics based on their capacity for highly specific molecular recognition and their genetic targetability. Here, we focus on new developments in protein engineering for selective proteomics of post-translational modifications, protein complexes, subcellular compartments, and cell types. We also address remaining challenges and future opportunities to integrate engineered protein tools across different subproteome scales to map the proteome with unprecedented depth and detail.
Collapse
Affiliation(s)
- Katarzyna Radziwon
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Amy M Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
174
|
Wang X, Xin Y, Ren L, Sun Z, Zhu P, Ji Y, Li C, Xu J, Ma B. Positive dielectrophoresis-based Raman-activated droplet sorting for culture-free and label-free screening of enzyme function in vivo. SCIENCE ADVANCES 2020; 6:eabb3521. [PMID: 32821836 PMCID: PMC7413728 DOI: 10.1126/sciadv.abb3521] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/26/2020] [Indexed: 05/19/2023]
Abstract
The potential of Raman-activated cell sorting (RACS) is inherently limited by conflicting demands for signal quality and sorting throughput. Here, we present positive dielectrophoresis-based Raman-activated droplet sorting (pDEP-RADS), where a periodical pDEP force was exerted to trap fast-moving cells, followed by simultaneous microdroplet encapsulation and sorting. Screening of yeasts for triacylglycerol (TAG) content demonstrated near-theoretical-limit accuracy, ~120 cells min-1 throughput and full-vitality preservation, while sorting fatty acid degree of unsaturation (FA-DU) featured ~82% accuracy at ~40 cells min-1. From a yeast library expressing algal diacylglycerol acyltransferases (DGATs), a pDEP-RADS run revealed all reported TAG-synthetic variants and distinguished FA-DUs of enzyme products. Furthermore, two previously unknown DGATs producing low levels of monounsaturated fatty acid-rich TAG were discovered. This first demonstration of RACS for enzyme discovery represents hundred-fold saving in time consumables and labor versus culture-based approaches. The ability to automatically flow-sort resonance Raman-independent phenotypes greatly expands RACS' application.
Collapse
Affiliation(s)
- Xixian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lihui Ren
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zhu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Qingdao Single-cell Biotechnology Co., Ltd., Qingdao, Shandong, China
| | - Chunyu Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Corresponding author. (B.M.); (J.X.)
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Corresponding author. (B.M.); (J.X.)
| |
Collapse
|
175
|
Samlali K, Ahmadi F, Quach ABV, Soffer G, Shih SCC. One Cell, One Drop, One Click: Hybrid Microfluidics for Mammalian Single Cell Isolation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002400. [PMID: 32705796 DOI: 10.1002/smll.202002400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Generating a stable knockout cell line is a complex process that can take several months to complete. In this work, a microfluidic method that is capable of isolating single cells in droplets, selecting successful edited clones, and expansion of these isoclones is introduced. Using a hybrid microfluidics method, droplets in channels can be individually addressed using a co-planar electrode system. In the hybrid microfluidics device, it is shown that single cells can be trapped and subsequently encapsulate them on demand into pL-sized droplets. Furthermore, droplets containing single cells are either released, kept in the traps, or merged with other droplets by the application of an electric potential to the electrodes that is actuated through an in-house user interface. This high precision control is used to successfully sort and recover single isoclones to establish monoclonal cell lines, which is demonstrated with a heterozygous NCI-H1299 lung squamous cell population resulting from loss-of-function eGFP and RAF1 gene knockout transfections.
Collapse
Affiliation(s)
- Kenza Samlali
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Angela B V Quach
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| |
Collapse
|
176
|
Neun S, Zurek PJ, Kaminski TS, Hollfelder F. Ultrahigh throughput screening for enzyme function in droplets. Methods Enzymol 2020; 643:317-343. [PMID: 32896286 DOI: 10.1016/bs.mie.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Water-in-oil droplets, made and handled in microfluidic devices, provide a new experimental format, in which ultrahigh throughput experiments can be conducted faster and with minimal reagent consumption. An increasing number of studies have emerged that applied this approach to directed evolution and metagenomic screening of enzyme catalysts. Here, we review the considerations necessary to implement robust workflows, based on choices of device design, detection modes, emulsion formulations and substrates, and scope out which enzyme classes have become amenable to droplet screening.
Collapse
Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Zurek
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
177
|
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: 83] [Impact Index Per Article: 20.8] [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.
Collapse
Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | | | | | | |
Collapse
|
178
|
Frazier CL, Weeks AM. Engineered peptide ligases for cell signaling and bioconjugation. Biochem Soc Trans 2020; 48:1153-1165. [PMID: 32539119 PMCID: PMC8350744 DOI: 10.1042/bst20200001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Enzymes that catalyze peptide ligation are powerful tools for site-specific protein bioconjugation and the study of cellular signaling. Peptide ligases can be divided into two classes: proteases that have been engineered to favor peptide ligation, and protease-related enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications, advantages, and limitations associated with each enzyme. Finally, we address future challenges and opportunities for further development of peptide ligases as tools for biological research.
Collapse
Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
179
|
Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins. Curr Opin Struct Biol 2020; 63:123-133. [PMID: 32615371 DOI: 10.1016/j.sbi.2020.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.
Collapse
|
180
|
Farka Z, Mickert MJ, Pastucha M, Mikušová Z, Skládal P, Gorris HH. Fortschritte in der optischen Einzelmoleküldetektion: Auf dem Weg zu höchstempfindlichen Bioaffinitätsassays. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zdeněk Farka
- CEITEC – Central European Institute of TechnologyMasaryk University 625 00 Brno Czech Republic
| | - Matthias J. Mickert
- Institut für Analytische Chemie, Chemo- und BiosensorikUniversität Regensburg Universitätsstraße 31 93040 Regensburg Deutschland
| | - Matěj Pastucha
- CEITEC – Central European Institute of TechnologyMasaryk University 625 00 Brno Czech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University 625 00 Brno Czech Republic
| | - Zuzana Mikušová
- CEITEC – Central European Institute of TechnologyMasaryk University 625 00 Brno Czech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University 625 00 Brno Czech Republic
| | - Petr Skládal
- CEITEC – Central European Institute of TechnologyMasaryk University 625 00 Brno Czech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University 625 00 Brno Czech Republic
| | - Hans H. Gorris
- Institut für Analytische Chemie, Chemo- und BiosensorikUniversität Regensburg Universitätsstraße 31 93040 Regensburg Deutschland
| |
Collapse
|
181
|
Farka Z, Mickert MJ, Pastucha M, Mikušová Z, Skládal P, Gorris HH. Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays. Angew Chem Int Ed Engl 2020; 59:10746-10773. [PMID: 31869502 PMCID: PMC7318240 DOI: 10.1002/anie.201913924] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/20/2019] [Indexed: 12/11/2022]
Abstract
The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.
Collapse
Affiliation(s)
- Zdeněk Farka
- CEITEC – Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
| | - Matthias J. Mickert
- Institute of Analytical Chemistry, Chemo- and BiosensorsUniversity of RegensburgUniversitätsstraße 3193040RegensburgGermany
| | - Matěj Pastucha
- CEITEC – Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University625 00BrnoCzech Republic
| | - Zuzana Mikušová
- CEITEC – Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University625 00BrnoCzech Republic
| | - Petr Skládal
- CEITEC – Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
- Department of BiochemistryFaculty of ScienceMasaryk University625 00BrnoCzech Republic
| | - Hans H. Gorris
- Institute of Analytical Chemistry, Chemo- and BiosensorsUniversity of RegensburgUniversitätsstraße 3193040RegensburgGermany
| |
Collapse
|
182
|
FACS-Based Functional Protein Screening via Microfluidic Co-encapsulation of Yeast Secretor and Mammalian Reporter Cells. Sci Rep 2020; 10:10182. [PMID: 32576855 PMCID: PMC7311539 DOI: 10.1038/s41598-020-66927-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
In this study, we present a straightforward approach for functional cell-based screening by co-encapsulation of secretor yeast cells and reporter mammalian cells in millions of individual agarose-containing microdroplets. Our system is compatible with ultra-high-throughput selection utilizing standard fluorescence-activated cell sorters (FACS) without need of extensive adaptation and optimization. In a model study we co-encapsulated murine interleukin 3 (mIL-3)-secreting S. cerevisiae cells with murine Ba/F3 reporter cells, which express green fluorescent protein (GFP) upon stimulation with mIL-3, and could observe specific and robust induction of fluorescence signal compared to a control with yeast cells secreting a non-functional mIL-3 mutant. We demonstrate the successful enrichment of activating mIL-3 wt-secreting yeast cells from a 1:10,000 dilution in cells expressing the inactive cytokine variant by two consecutive cycles of co-encapsulation and FACS. This indicates the suitability of the presented strategy for functional screening of high-diversity yeast-based libraries and demonstrates its potential for the efficient isolation of clones secreting bioactive recombinant proteins.
Collapse
|
183
|
Rho HS, Gardeniers H. Microfluidic Droplet-Storage Array. MICROMACHINES 2020; 11:mi11060608. [PMID: 32585943 PMCID: PMC7344826 DOI: 10.3390/mi11060608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023]
Abstract
A microfluidic droplet-storage array that is capable of the continuous operation of droplet formation, storing, repositioning, retrieving, injecting and restoring is demonstrated. The microfluidic chip comprised four valve-assisted droplet generators and a 3 × 16 droplet-storage array. The integrated pneumatically actuated microvalves enable the precise control of aqueous phase dispensing, as well as carrier fluid flow path and direction for flexible manipulating water-in-oil droplets in the chip. The size of droplets formed by the valve-assisted droplet generators was validated under various operating conditions such as pressures for introducing solutions and dispensing time. In addition, flexible droplet addressing in the storage array was demonstrated by storing droplets with various numbers and compositions in different storage units as well as rearranging their stored positions. Moreover, serial injections of new droplets into a retrieved droplet from a storage unit was performed to show the potential of the platform in sequential dosing on incubated droplet-based reactors at the desired timeline. The droplet-storage array with great freedom and flexibility in droplet handling could be applied for performing complex chemical and biologic reactions, especially in which incubation and dosing steps are necessary.
Collapse
Affiliation(s)
- Hoon Suk Rho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands;
- Mesoscale Chemical Systems Group, MESA+ Institute, University of Twente, 7522 NB Enschede, The Netherlands
| | - Han Gardeniers
- Mesoscale Chemical Systems Group, MESA+ Institute, University of Twente, 7522 NB Enschede, The Netherlands
- Correspondence: ; Tel.: +31-(0)53-489-4356
| |
Collapse
|
184
|
Azimi-Boulali J, Madadelahi M, Madou MJ, Martinez-Chapa SO. Droplet and Particle Generation on Centrifugal Microfluidic Platforms: A Review. MICROMACHINES 2020; 11:mi11060603. [PMID: 32580516 PMCID: PMC7344714 DOI: 10.3390/mi11060603] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 01/09/2023]
Abstract
The use of multiphase flows in microfluidics to carry dispersed phase material (droplets, particles, bubbles, or fibers) has many applications. In this review paper, we focus on such flows on centrifugal microfluidic platforms and present different methods of dispersed phase material generation. These methods are classified into three specific categories, i.e., step emulsification, crossflow, and dispenser nozzle. Previous works on these topics are discussed and related parameters and specifications, including the size, material, production rate, and rotational speed are explicitly mentioned. In addition, the associated theories and important dimensionless numbers are presented. Finally, we discuss the commercialization of these devices and show a comparison to unveil the pros and cons of the different methods so that researchers can select the centrifugal droplet/particle generation method which better suits their needs.
Collapse
Affiliation(s)
- Javid Azimi-Boulali
- School of Engineering and Sciences, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico;
| | - Masoud Madadelahi
- School of Engineering and Sciences, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico;
- Correspondence: (M.M.); (S.O.M.-C.)
| | - Marc J. Madou
- Department of Mechanical and Aerospace Engineering, University of California Irvine, Irvine, CA 92697, USA;
| | - Sergio O. Martinez-Chapa
- School of Engineering and Sciences, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico;
- Correspondence: (M.M.); (S.O.M.-C.)
| |
Collapse
|
185
|
Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM. Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. LAB ON A CHIP 2020; 20:2062-2074. [PMID: 32417874 PMCID: PMC7670282 DOI: 10.1039/d0lc00261e] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics has made large impacts in diverse areas such as enzyme evolution, chemical product screening, polymer engineering, and single-cell analysis. However, while droplet reactions have become increasingly sophisticated, phenotyping droplets by a fluorescent signal and sorting them to isolate individual variants-of-interest at high-throughput remains challenging. Here, we present sdDE-FACS (s[combining low line]ingle d[combining low line]roplet D[combining low line]ouble E[combining low line]mulsion-FACS), a new method that uses a standard flow cytometer to phenotype, select, and isolate individual double emulsion droplets of interest. Using a 130 μm nozzle at high sort frequency (12-14 kHz), we demonstrate detection of droplet fluorescence signals with a dynamic range spanning 5 orders of magnitude and robust post-sort recovery of intact double emulsion (DE) droplets using 2 commercially-available FACS instruments. We report the first demonstration of single double emulsion droplet isolation with post-sort recovery efficiencies >70%, equivalent to the capabilities of single-cell FACS. Finally, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets via qPCR with little to no cross-contamination. sdDE-FACS marries the full power of droplet microfluidics with flow cytometry to enable a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis.
Collapse
Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California, USA.
| | | | | | | | | | | | | | | |
Collapse
|
186
|
Harmon JB, Gray HK, Young CC, Schwab KJ. Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters. PLoS One 2020; 15:e0233239. [PMID: 32516315 PMCID: PMC7282644 DOI: 10.1371/journal.pone.0233239] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/30/2020] [Indexed: 01/22/2023] Open
Abstract
Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and evaluates the utility of microfluidic droplets, also termed ultra-miniaturized bioreactors, for rapid detection of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash water acquired from a major Mid-Atlantic produce processing facility (denoted as Producer) in the U.S. Using a fluorescently-labeled anti-S. Typhimurium antibody and relative fluorescence intensities, paired with in-droplet incubation, S. Typhimurium was detected and identified with 100% specificity in less than 5 h. In initial optimization experiments using S. Typhimurium-spiked sterile water, the relative fluorescence intensity of S. Typhimurium was approximately two times that of the observed relative intensities of five non-S. Typhimurium negative controls at 4-h incubation in droplets containing Rappaport-Vasiliadis (RV) broth at 37°C: relative fluorescence intensity for S. Typhimurium = 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16), Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium- and E. aerogens-spiked shredded lettuce wash waters acquired from the Producer were then incubated 4 h in-droplet at 37°C with RV broth. The observed relative fluorescence of S. Typhimurium was significantly higher than that of E. aerogens, 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12), respectively. While further optimization focusing on compatible concentration methodologies for highly-dilute produce water samples is needed, this application of droplet microfluidics shows great promise in dramatically shortening the time necessary-from days to hours-to confirm viable bacterial contamination in ready-to-eat produce wash waters used throughout the domestic and international food industry.
Collapse
Affiliation(s)
- J. Brian Harmon
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Asymmetric Operations Sector, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - Hannah K. Gray
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Charles C. Young
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Asymmetric Operations Sector, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - Kellogg J. Schwab
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| |
Collapse
|
187
|
|
188
|
Prodanović R, Ung WL, Ilić Đurđić K, Fischer R, Weitz DA, Ostafe R. A High-Throughput Screening System Based on Droplet Microfluidics for Glucose Oxidase Gene Libraries. Molecules 2020; 25:E2418. [PMID: 32455903 PMCID: PMC7287683 DOI: 10.3390/molecules25102418] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Glucose oxidase (GOx) is an important industrial enzyme that can be optimized for specific applications by mutagenesis and activity-based screening. To increase the efficiency of this approach, we have developed a new ultrahigh-throughput screening platform based on a microfluidic lab-on-chip device that allows the sorting of GOx mutants from a saturation mutagenesis library expressed on the surface of yeast cells. GOx activity was measured by monitoring the fluorescence of water microdroplets dispersed in perfluorinated oil. The signal was generated via a series of coupled enzyme reactions leading to the formation of fluorescein. Using this new method, we were able to enrich the yeast cell population by more than 35-fold for GOx mutants with higher than wild-type activity after two rounds of sorting, almost double the efficiency of our previously described flow cytometry platform. We identified and characterized novel GOx mutants, the most promising of which (M6) contained a combination of six point mutations that increased the catalytic constant kcat by 2.1-fold compared to wild-type GOx and by 1.4-fold compared to a parental GOx variant. The new microfluidic platform for GOx was therefore more sensitive than flow cytometry and supports comprehensive screens of gene libraries containing multiple mutations per gene.
Collapse
Affiliation(s)
- Radivoje Prodanović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12, 11000 Belgrade, Serbia;
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; (W.L.U.); (D.A.W.)
| | - W. Lloyd Ung
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; (W.L.U.); (D.A.W.)
| | - Karla Ilić Đurđić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12, 11000 Belgrade, Serbia;
| | - Rainer Fischer
- Departments of Biological Sciences and Chemistry, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA;
| | - David A. Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; (W.L.U.); (D.A.W.)
| | - Raluca Ostafe
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Molecular Evolution, Protein Engineering and Production, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA;
| |
Collapse
|
189
|
Liu L, Chen D, Wang J, Chen J. Advances of Single-Cell Protein Analysis. Cells 2020; 9:E1271. [PMID: 32443882 PMCID: PMC7290353 DOI: 10.3390/cells9051271] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.
Collapse
Affiliation(s)
- Lixing Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
190
|
Vallejo D, Nikoomanzar A, Chaput JC. Directed evolution of custom polymerases using droplet microfluidics. Methods Enzymol 2020; 644:227-253. [PMID: 32943147 DOI: 10.1016/bs.mie.2020.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA polymerases are critical tools for a large number of emerging applications in biotechnology, but oftentimes polymerases with desired functions are not readily available. Directed evolution provides a possible solution to this problem by enabling the creation of engineered polymerases that are better equipped to recognize a given unnatural substrate. Here we report a microfluidic-based method for evolving new polymerase functions that involves ultrahigh throughput sorting of fluorescent water-in-oil (w/o) microdroplets. The workflow entails the expression of a diverse population of polymerase variants in E. coli, production of microfluidic droplets containing one or less E. coli, bacteria lysis to release the polymerase and encoding plasmid into the surrounding droplet, a fluorescence-based activity assay to identify variants with a desired activity, isolation of fluorescent droplets using a fluorescence activated droplet sorting (FADS) device, and plasmid recovery with DNA sequencing to determine the identity of the functional variants. This technique is amenable to any type of unnatural nucleic acid and/or polymerase function, including DNA-templated synthesis, reverse transcription, and replication.
Collapse
Affiliation(s)
- Derek Vallejo
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology, and Biochemistry, University of California, Irvine, CA, United States
| | - Ali Nikoomanzar
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology, and Biochemistry, University of California, Irvine, CA, United States
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology, and Biochemistry, University of California, Irvine, CA, United States.
| |
Collapse
|
191
|
Xu P, Modavi C, Demaree B, Twigg F, Liang B, Sun C, Zhang W, Abate AR. Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery. Nucleic Acids Res 2020; 48:e48. [PMID: 32095820 PMCID: PMC7192590 DOI: 10.1093/nar/gkaa131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways.
Collapse
Affiliation(s)
- Peng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA
| | - Frederick Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Benjamin Liang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
192
|
Panhwar MH, Czerwinski F, Dabbiru VAS, Komaragiri Y, Fregin B, Biedenweg D, Nestler P, Pires RH, Otto O. High-throughput cell and spheroid mechanics in virtual fluidic channels. Nat Commun 2020; 11:2190. [PMID: 32366850 PMCID: PMC7198589 DOI: 10.1038/s41467-020-15813-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 03/25/2020] [Indexed: 12/14/2022] Open
Abstract
Microfluidics by soft lithography has proven to be of key importance for biophysics and life science research. While being based on replicating structures of a master mold using benchtop devices, design modifications are time consuming and require sophisticated cleanroom equipment. Here, we introduce virtual fluidic channels as a flexible and robust alternative to microfluidic devices made by soft lithography. Virtual channels are liquid-bound fluidic systems that can be created in glass cuvettes and tailored in three dimensions within seconds for rheological studies on a wide size range of biological samples. We demonstrate that the liquid-liquid interface imposes a hydrodynamic stress on confined samples, and the resulting strain can be used to calculate rheological parameters from simple linear models. In proof-of-principle experiments, we perform high-throughput rheology inside a flow cytometer cuvette and show the Young's modulus of isolated cells exceeds the one of the corresponding tissue by one order of magnitude.
Collapse
Affiliation(s)
- Muzaffar H Panhwar
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Fabian Czerwinski
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Venkata A S Dabbiru
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Yesaswini Komaragiri
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Bob Fregin
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Doreen Biedenweg
- Klinik für Innere Medizin B, Universitätsmedizin Greifswald, Fleischmannstr. 8, 17475, Greifswald, Germany
| | - Peter Nestler
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Ricardo H Pires
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany
| | - Oliver Otto
- Zentrum für Innovationskompetenz: Humorale Immunreaktionen bei kardiovaskulären Erkrankungen, Universität Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany.
- Deutsches Zentrum für Herz-Kreislauf-Forschung e.V., Standort Greifswald, Universitätsmedizin Greifswald, Fleischmannstr. 42, 17489, Greifswald, Germany.
| |
Collapse
|
193
|
Femmer C, Bechtold M, Held M, Panke S. In vivo directed enzyme evolution in nanoliter reactors with antimetabolite selection. Metab Eng 2020; 59:15-23. [DOI: 10.1016/j.ymben.2020.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022]
|
194
|
Zielke C, Pan CW, Gutierrez Ramirez AJ, Feit C, Dobson C, Davidson C, Sandel B, Abbyad P. Microfluidic Platform for the Isolation of Cancer-Cell Subpopulations Based on Single-Cell Glycolysis. Anal Chem 2020; 92:6949-6957. [PMID: 32297730 DOI: 10.1021/acs.analchem.9b05738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
High rates of glycolysis in tumors have been associated with cancer metastasis, tumor recurrence, and poor outcomes. In this light, single cells that exhibit high glycolysis are specific targets for therapy. However, the study of these cells requires efficient tools for their isolation. We use a droplet microfluidic technique developed in our lab, Sorting by Interfacial Tension (SIFT), to isolate cancer cell subpopulations based on glycolysis without the use of labels or active sorting components. By controlling the flow conditions on chip, the threshold of selection can be modified, enabling the isolation of cells with different levels of glycolysis. Hypoxia in tumors, that can be simulated with treatment with CoCl2, leads to an increase in glycolysis, and more dangerous tumors. The device was used to enrich CoCl2 treated MDA-MB 231 breast cancer cells from an untreated population. It is also used to sort K562 human chronic myelogenous leukemia cells that have either been treated or untreated with 2-deoxy-d-glucose (2DG), a pharmaceutical that targets cell metabolism. The technique provides a facile and robust way of separating cells based on elevated glycolytic activity; a biomarker associated with cancer cell malignancy.
Collapse
Affiliation(s)
- Claudia Zielke
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Ching W Pan
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Adriana J Gutierrez Ramirez
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Cameron Feit
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Chandler Dobson
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Catherine Davidson
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| | - Brody Sandel
- Department of Biology, Santa Clara University, Santa Clara, California 95053, United States
| | - Paul Abbyad
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, California 95053, United States
| |
Collapse
|
195
|
Lee H, Baek JI, Kim SJ, Kwon KK, Rha E, Yeom SJ, Kim H, Lee DH, Kim DM, Lee SG. Sensitive and Rapid Phenotyping of Microbes With Soluble Methane Monooxygenase Using a Droplet-Based Assay. Front Bioeng Biotechnol 2020; 8:358. [PMID: 32391352 PMCID: PMC7193049 DOI: 10.3389/fbioe.2020.00358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022] Open
Abstract
Methanotrophs with soluble methane monooxygenase (sMMO) show high potential for various ecological and biotechnological applications. Here, we developed a high throughput method to identify sMMO-producing microbes by integrating droplet microfluidics and a genetic circuit-based biosensor system. sMMO-producers and sensor cells were encapsulated in monodispersed droplets with benzene as the substrate and incubated for 5 h. The sensor cells were analyzed as the reporter for phenol-sensitive transcription activation of fluorescence. Various combinations of methanotrophs and biosensor cells were investigated to optimize the performance of our droplet-integrated transcriptional factor biosensor system. As a result, the conditions to ensure sMMO activity to convert the starting material, benzene, into phenol, were determined. The biosensor signals were sensitive and quantitative under optimal conditions, showing that phenol is metabolically stable within both cell species and accumulates in picoliter-sized droplets, and the biosensor cells are healthy enough to respond quantitatively to the phenol produced. These results show that our system would be useful for rapid evaluation of phenotypes of methanotrophs showing sMMO activity, while minimizing the necessity of time-consuming cultivation and enzyme preparation, which are required for conventional analysis of sMMO activity.
Collapse
Affiliation(s)
- Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ji In Baek
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Su Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Kil Koang Kwon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Dong-Myung Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
196
|
Synthesizing Chiral Drug Intermediates by Biocatalysis. Appl Biochem Biotechnol 2020; 192:146-179. [DOI: 10.1007/s12010-020-03272-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/13/2020] [Indexed: 01/16/2023]
|
197
|
Totlani K, Hurkmans JW, van Gulik WM, Kreutzer MT, van Steijn V. Scalable microfluidic droplet on-demand generator for non-steady operation of droplet-based assays. LAB ON A CHIP 2020; 20:1398-1409. [PMID: 32255441 DOI: 10.1039/c9lc01103j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We developed a microfluidic droplet on-demand (DoD) generator that enables the production of droplets with a volume solely governed by the geometry of the generator for a range of operating conditions. The prime reason to develop this novel type of DoD generator is that its robustness in operation enables scale out and operation under non-steady conditions, which are both essential features for the further advancement of droplet-based assays. We first detail the working principle of the DoD generator and study the sensitivity of the volume of the generated droplets with respect to the used fluids and control parameters. We next compare the performance of our DoD generator when scaled out to 8 parallel generators to the performance of a conventional DoD generator in which the droplet volume is not geometry-controlled, showing its superior performance. Further scale out to 64 parallel DoD generators shows that all generators produce droplets with a volume between 91% and 105% of the predesigned volume. We conclude the paper by presenting a simple droplet-based assay in which the DoD generator enables sequential supply of reagent droplets to a droplet stored in the device, illustrating its potential to be used in droplet-based assays for biochemical studies under non-steady operation conditions.
Collapse
Affiliation(s)
- Kartik Totlani
- Delft University of Technology, Faculty of Applied Sciences, Department of Chemical Engineering, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | | | | | | | | |
Collapse
|
198
|
Jian X, Guo X, Wang J, Tan ZL, Xing X, Wang L, Zhang C. Microbial microdroplet culture system (MMC): An integrated platform for automated, high‐throughput microbial cultivation and adaptive evolution. Biotechnol Bioeng 2020; 117:1724-1737. [DOI: 10.1002/bit.27327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/14/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
| | - Xiaojie Guo
- Luoyang TMAXTREE Biotechnology Co., Ltd. Luoyang China
| | - Jia Wang
- Biochemical Engineering Research Group, School of Chemical Engineering and TechnologyXi'an Jiaotong University Xi'an China
| | - Zheng Lin Tan
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- School of Life Science and TechnologyTokyo Institute of Technology, Midori‐ku Yokohama Kanagawa Prefecture Japan
| | - Xin‐hui Xing
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- Center for Synthetic & Systems BiologyTsinghua University Beijing China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd. Luoyang China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- Center for Synthetic & Systems BiologyTsinghua University Beijing China
| |
Collapse
|
199
|
Leavell MD, Singh AH, Kaufmann-Malaga BB. High-throughput screening for improved microbial cell factories, perspective and promise. Curr Opin Biotechnol 2020; 62:22-28. [DOI: 10.1016/j.copbio.2019.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/11/2023]
|
200
|
Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
Collapse
Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|