1
|
Zhuang S, Semenec L, Nagy SS, Cain AK, Inglis DW. High-precision screening and sorting of double emulsion droplets. Cytometry A 2024. [PMID: 38634684 DOI: 10.1002/cyto.a.24842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Mounting evidence suggests that cell populations are extremely heterogeneous, with individual cells fulfilling different roles within the population. Flow cytometry (FC) is a high-throughput tool for single-cell analysis that works at high optical resolution. Sub-populations with unique properties can be screened, isolated and sorted through fluorescence-activated cell sorting (FACS), using intracellular fluorescent products or surface-tagged fluorescent products of interest. However, traditional FC and FACS methods cannot identify or isolate cells that secrete extracellular products of interest. Double emulsion (DE) droplets are an innovative approach to retaining these extracellular products so cells producing them can be identified and isolated with FC and FACS. The water-in-oil-in-water structure makes DE droplets compatible with the sheath flow of flow cytometry. Single cells can be encapsulated with other reagents into DEs, which act as pico-reactors. These droplets allow biological activities to take place while allowing for cell cultivation monitoring, rare mutant identification, and cellular events characterization. However, using DEs in FACS presents technical challenges, including rupture of DEs, poor accuracy and low sorting efficiency. This study presents high-performance sorting using fluorescent beads (as simulants for cells). This study aims to guide researchers in the use of DE-based flow cytometry, offering insights into how to resolve the technical difficulties associated with DE-based screening and sorting using FC.
Collapse
Affiliation(s)
- Siyuan Zhuang
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Lucie Semenec
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie S Nagy
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Amy K Cain
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
| |
Collapse
|
2
|
Chen H, Liu R, Cai S, Zhang Y, Zhu C, Yu H, Li S. Intermediate product control in cascade reaction for one-pot production of ε-caprolactone by Escherichia coli. Biotechnol J 2024; 19:e2300210. [PMID: 38403458 DOI: 10.1002/biot.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 02/27/2024]
Abstract
ε-Caprolactone is an important non-toxic compound for polymer synthesis like polycaprolactone which has been widely used in drug delivery and degradable plastics. To meet the demand for a green economy, a bi-enzymatic cascade, consisting of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO), was designed and introduced into Escherichia coli to synthesize ε-caprolactone from cyclohexanol with a self-sufficient NADPH-cofactor regeneration system. To further improve the catalytic efficiency, a carbonyl group-dependent colorimetric method using inexpensive 2,4-dinitrophenylhydrazine (DNPH) was developed for assay of cyclohexanone, an intermediate production of cascade reaction. It can be used to screen mutant strains with high catalytic efficiency from high-throughput library by detecting the absorbance value in microtiter plates (MTP) instead of gas chromatography (GC) analysis. Moreover, an RBS combinatorial library was constructed for balancing the expression of ADH and CHMO from two independent transcriptional units. After the high-throughput screening based on intermediate product control, an optimal variant with higher substrate tolerance and long-term stability was obtained from RBS combinatorial library. Through a fed-batch process, ε-caprolactone production reached 148.2 mM after 70 h of reaction under the optimized conditions, which was the highest yield achieved to date.
Collapse
Affiliation(s)
- Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ran Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shengliang Cai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingjiao Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
3
|
Zhao W, Shang X, Zhang B, Yuan D, Nguyen BTT, Wu W, Zhang JB, Peng N, Liu AQ, Duan F, Chin LK. Squeezed state in the hydrodynamic focusing regime for Escherichia coli bacteria detection. LAB ON A CHIP 2023; 23:5039-5046. [PMID: 37909299 DOI: 10.1039/d3lc00434a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Flow cytometry is an essential technique in single particle analysis and cell sorting for further downstream diagnosis, exhibiting high-throughput and multiplexing capabilities for many biological and biomedical applications. Although many hydrodynamic focusing-based microfluidic cytometers have been demonstrated with reduced size and cost to adapt to point-of-care settings, the operating conditions are not characterized systematically. This study presents the flow transition process in the hydrodynamic focusing mechanism when the flow rate or the Reynolds number increases. The characteristics of flow fields and mass transport were studied under various operating conditions, including flow rates and microchannel heights. A transition from the squeezed focusing state to the over-squeezed anti-focusing state in the hydrodynamic focusing regime was observed when the Reynolds number increased above 30. Parametric studies illustrated that the focusing width increased with the Reynolds number but decreased with the microchannel height in the over-squeezed state. The microfluidic cytometric analyses using microbeads and E. coli show that the recovery rate was maintained by limiting the Reynolds number to 30. The detailed analysis of the flow transition will provide new insight into microfluidic cytometric analyses with a broad range of applications in food safety, water monitoring and healthcare sectors.
Collapse
Affiliation(s)
- Wenhan Zhao
- Institute State Key Laboratory for Manufacturing Systems Engineering, School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710054, China
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Xiaopeng Shang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Boran Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane 4072, Australia
| | - Binh Thi Thanh Nguyen
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Wenshuai Wu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Jing Bo Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Niancai Peng
- Institute State Key Laboratory for Manufacturing Systems Engineering, School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710054, China
| | - Ai Qun Liu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore.
- Institute of Quantum Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR
| | - Fei Duan
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Lip Ket Chin
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR.
| |
Collapse
|
4
|
McCully AL, Loop Yao M, Brower KK, Fordyce PM, Spormann AM. Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes. ISME COMMUNICATIONS 2023; 3:47. [PMID: 37160952 PMCID: PMC10169782 DOI: 10.1038/s43705-023-00241-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
Collapse
Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - McKenna Loop Yao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
| |
Collapse
|
5
|
Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
Collapse
Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| |
Collapse
|
6
|
Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
Collapse
Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
7
|
Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting. Nat Protoc 2023; 18:1090-1136. [PMID: 36707723 DOI: 10.1038/s41596-022-00796-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/09/2022] [Indexed: 01/28/2023]
Abstract
Droplet microfluidics has revolutionized quantitative high-throughput bioassays and screening, especially in the field of single-cell analysis where applications include cell characterization, antibody discovery and directed evolution. However, droplet microfluidic platforms capable of phenotypic, fluorescence-based readouts and sorting are still mostly found in specialized labs, because their setup is complex. Complementary to conventional FACS, microfluidic droplet sorters allow the screening of cell libraries for secreted factors, or even for the effects of secreted or surface-displayed factors on a second cell type. Furthermore, they also enable PCR-activated droplet sorting for the isolation of genetic material harboring specific markers. In this protocol, we provide a detailed step-by-step guide for the construction of a high-throughput droplet analyzer and sorter, which can be accomplished in ~45 working hours by nonspecialists. The resulting instrument is equipped with three lasers to excite the fluorophores in droplets and photosensors that acquire fluorescence signals in the blue (425-465 nm), green (505-545 nm) and red (580-630 nm) spectrum. This instrument also allows transmittance-activated droplet sorting by analyzing the brightfield light intensity transmitting through the droplets. The setup is validated by sorting droplets containing fluorescent beads at 200 Hz with 99.4% accuracy. We show results from an experiment where droplets hosting single cells were sorted on the basis of increased matrix metalloprotease activity as an application of our workstation in single-cell molecular biology, e.g., to analyze molecular determinants of cancer metastasis.
Collapse
|
8
|
Khariton M, McClune CJ, Brower KK, Klemm S, Sattely ES, Fordyce PM, Wang B. Alleviating Cell Lysate-Induced Inhibition to Enable RT-PCR from Single Cells in Picoliter-Volume Double Emulsion Droplets. Anal Chem 2023; 95:935-945. [PMID: 36598332 DOI: 10.1021/acs.analchem.2c03475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microfluidic droplet assays enable single-cell polymerase chain reaction (PCR) and sequencing analyses at unprecedented scales, with most methods encapsulating cells within nanoliter-sized single emulsion droplets (water-in-oil). Encapsulating cells within picoliter double emulsion (DE) (water-in-oil-in-water) allows sorting droplets with commercially available fluorescence-activated cell sorter (FACS) machines, making it possible to isolate single cells based on phenotypes of interest for downstream analyses. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. This poses challenges for molecular biology, as prior reports suggest that reverse transcription (RT) and PCR amplification cannot proceed efficiently at volumes below 1 nL due to cell lysate-induced inhibition. To overcome this limitation, we used a plate-based RT-PCR assay designed to mimic reactions in picoliter droplets to systematically quantify and ameliorate the inhibition. We find that RT-PCR is blocked by lysate-induced cleavage of nucleic acid probes and primers, which can be efficiently alleviated through heat lysis. We further show that the magnitude of inhibition depends on the cell type, but that RT-PCR can proceed in low-picoscale reaction volumes for most mouse and human cell lines tested. Finally, we demonstrate one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS. These results open up new avenues for improving picoscale droplet RT-PCR reactions and expanding microfluidic droplet-based single-cell analysis technologies.
Collapse
Affiliation(s)
- Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Conor J McClune
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, California94305, United States
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, California94305, United States.,Department of Genetics, Stanford University, Stanford, California94305, United States.,ChEM-H Institute, Stanford University, Stanford, California94305, United States.,Chan Zuckerberg Biohub, San Francisco, California94110, United States
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| |
Collapse
|
9
|
Cowell T, Han HS. Double Emulsion Flow Cytometry for Rapid Single Genome Detection. Methods Mol Biol 2023; 2689:155-167. [PMID: 37430053 DOI: 10.1007/978-1-0716-3323-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Established techniques in droplet microfluidics have utilized single emulsion (SE) drops to compartmentalize and analyze single cells achieving high-throughput, low input analysis. Building upon this foundation, double emulsion (DE) droplet microfluidics has emerged with distinct advantages in terms of stable compartmentalization, resistance to merging, and most importantly direct compatibility with flow cytometry. In this chapter, we describe a simple-to-fabricate, single-layer DE drop generation device that achieves spatial control over surface wetting with a plasma treatment step. This easy-to-operate device allows for the robust production of single-core DEs with excellent control over the monodispersity. We further explain the use of these DE drops for single-molecule and single-cell assays. Detailed protocols are described to perform single molecule detection using droplet digital PCR in DE drops and automated detection of DE drops on a fluorescence-activated cell sorter (FACS). Due to the wide availability of FACS instruments, DE methods can facilitate the broader adoption of drop-based screening. As the applications of FACS-compatible DE droplets are immensely varied and extend well beyond what can be explored here, this chapter should be seen as an introduction to DE microfluidics.
Collapse
Affiliation(s)
- Thomas Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
10
|
Sun G, Wu Y, Huang Z, Liu Y, Li J, Du G, Lv X, Liu L. Directed evolution of diacetylchitobiose deacetylase via high-throughput droplet sorting with a novel, bacteria-based biosensor. Biosens Bioelectron 2023; 219:114818. [PMID: 36327560 DOI: 10.1016/j.bios.2022.114818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Numerous biological disciplines rely on high-throughput cell sorting. Flow cytometry, the current gold standard, is capable of ultrahigh-throughput cell sorting, but measurements are primarily limited to cell size and surface marker. Droplet sorting technology is gaining increasing attention with the ability to provide an individual environment for the analysis of single-cell secretion. Although various droplet detecting methods, such as fluorescence, absorbance, mass spectrum, imaging analysis, have been developed for droplet sorting, it remains challenging to establish high-throughput sorting methods for numerous analytes. We aim to develop a high-throughput sorting system based on the glucosamine (GlcN) measurement for the directed evolution of diacetylchitobiose deacetylase (Dac), the key enzyme for GlcN production. To overcome the limitation that no high-throughput sorting system existed for GlcN, we designed a novel bacteria-based biosensor capable of converting GlcN to a positively correlated fluorescence signal. Through characterization and optimization, it was possible to detect GlcN in droplets for high-throughput droplet sorting. We recovered the best Dac mutant S60I/R157T/F168S after sorting ∼0.2 million Dac mutants; its activity was 48.6 ± 1.5 U/mL, which was 1.8-times that of our previously discovered Dac mutant R157T (27.2 ± 1.8 U/mL). This result successfully demonstrated the combination of high-throughput droplet sorting technology and a bacteria-based biosensor, which could facilitate the industrial production of GlcN and serve as a model for similar droplet sorting applications.
Collapse
Affiliation(s)
- Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Ziyang Huang
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
11
|
Cowell TW, Dobria A, Han HS. Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20528-20537. [PMID: 35502700 DOI: 10.1021/acsami.1c22692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.
Collapse
Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Andrew Dobria
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave., Urbana, Illinois 61801, United States
| |
Collapse
|
12
|
Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| |
Collapse
|
13
|
|
14
|
Hilton SH, White IM. Advances in the analysis of single extracellular vesicles: A critical review. SENSORS AND ACTUATORS REPORTS 2021; 3:100052. [PMID: 35098157 PMCID: PMC8792802 DOI: 10.1016/j.snr.2021.100052] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There is an ever-growing need for new cancer diagnostic approaches that provide earlier diagnosis as well as richer diagnostic, prognostic, and resistance information. Extracellular vesicles (EVs) recovered from a liquid biopsy have paradigm-shifting potential to offer earlier and more complete diagnostic information in the form of a minimally invasive liquid biopsy. However, much remains unknown about EVs, and current analytical approaches are unable to provide precise information about the contents and source of EVs. New approaches have emerged to analyze EVs at the single particle level, providing the opportunity to study biogenesis, correlate markers for higher specificity, and connect EV cargo with the source or destination. In this critical review we describe and analyze methods for single EV analysis that have emerged over the last five years. In addition, we note that current methods are limited in their adoption due to cost and complexity and we offer opportunities for the research community to address this challenge.
Collapse
|
15
|
Wu L, Xu S, Wang J, Paguirigan AL, Radich JP, Qin Y, Chiu DT. Capillary-Mediated Single-Cell Dispenser. Anal Chem 2021; 93:10750-10755. [PMID: 34319086 DOI: 10.1021/acs.analchem.1c01879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-cell manipulation, sorting, and dispensing into multiwell plates is useful for single-cell multiomics studies. Here, we develop a single-cell dispenser inspired by electrohydrodynamic jet printing that achieves accurate droplet generation and single-cell sorting and dispensing using fused silica capillary tubing as both the optical detection window and nozzle for droplet dispensing. Parameters that affect droplet dispensing performance-capillary inner and outer diameter, flow rate, applied voltage, and solution properties-were optimized systematically with COMSOL simulations and experimentation. Small (5-10 nL) droplets were obtained by using 100-μm inner diameter and 160-μm outer diameter capillary tubing and allowed efficient encapsulation and dispensing of single cells. We demonstrate an application of this easy-to-assemble single-cell dispenser by sorting and dispensing cells into multiwell plates for single-cell PCR analysis.
Collapse
Affiliation(s)
- Li Wu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, Washington 98195, United States.,School of Public Health, Nantong University, Nantong, Jiangsu 226019, P. R. China
| | - Shihan Xu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Jingang Wang
- Department of Chemistry and Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Amy L Paguirigan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Yuling Qin
- Department of Chemistry and Bioengineering, University of Washington, Seattle, Washington 98195, United States.,School of Public Health, Nantong University, Nantong, Jiangsu 226019, P. R. China
| | - Daniel T Chiu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
16
|
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
|
17
|
Brower KK, Khariton M, Suzuki PH, Still C, Kim G, Calhoun SGK, Qi LS, Wang B, Fordyce PM. Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS. Anal Chem 2020; 92:13262-13270. [PMID: 32900183 DOI: 10.1021/acs.analchem.0c02499] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput screening via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying sizes and morphologies as well as a heterogeneous cell mixture of a whole dissociated flatworm (5-25 μm in diameter) within highly monodisperse double emulsions (35 μm in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS screening of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional phenotyping.
Collapse
Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States.,Chem-H Institute, Stanford University, Stanford, California 94305, United States
| | - Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Chris Still
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, United States
| | - Gaeun Kim
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Suzanne G K Calhoun
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States.,Chem-H Institute, Stanford University, Stanford, California 94305, United States.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States.,Department of Developmental Biology, Stanford University, Stanford, California 94305, United States
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States.,Chem-H Institute, Stanford University, Stanford, California 94305, United States.,Department of Genetics, Stanford University, Stanford, California 94305, United States.,Chan Zuckerburg BioHub, San Francisco, California 94158, United States
| |
Collapse
|
18
|
Hedde PN, Bouzin M, Abram TJ, Chen X, Toosky MN, Vu T, Li Y, Zhao W, Gratton E. Rapid isolation of rare targets from large fluid volumes. Sci Rep 2020; 10:12458. [PMID: 32719382 PMCID: PMC7385493 DOI: 10.1038/s41598-020-69315-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/26/2020] [Indexed: 11/24/2022] Open
Abstract
Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.
Collapse
Affiliation(s)
- Per Niklas Hedde
- Department of Biomedical Engineering, University of California, Irvine, CA, USA. .,Department of Biochemistry, University of Hawaii at Manoa, Manoa, HI, USA.
| | - Margaux Bouzin
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | | | - Xiaoming Chen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | | | - Tam Vu
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Yiyan Li
- Department of Physics and Engineering, Fort Lewis College, Durango, CO, USA
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
| |
Collapse
|
19
|
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
|
20
|
Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
Collapse
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
| | | | | | | | | | | |
Collapse
|
21
|
Ma C, Tan ZL, Lin Y, Han S, Xing X, Zhang C. Gel microdroplet–based high-throughput screening for directed evolution of xylanase-producing Pichia pastoris. J Biosci Bioeng 2019; 128:662-668. [DOI: 10.1016/j.jbiosc.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
|
22
|
Qin Y, Wu L, Wang J, Han R, Shen J, Wang J, Xu S, Paguirigan AL, Smith JL, Radich JP, Chiu DT. A Fluorescence-Activated Single-Droplet Dispenser for High Accuracy Single-Droplet and Single-Cell Sorting and Dispensing. Anal Chem 2019; 91:6815-6819. [PMID: 31050286 DOI: 10.1021/acs.analchem.9b01017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ability to sort and dispense droplets accurately is essential to droplet-based single-cell analysis. Here, we describe a fluorescence-activated single-droplet dispenser (FASD) that is analogous to a conventional fluorescence-activated cell sorter, but sorts droplets containing single cells within an oil emulsion. The FASD system uses cytometric detection and electrohydrodynamic actuation-based single-droplet manipulation, allowing droplet isolation and dispensing with high efficiency and accuracy. The system is compatible with multiwell plates and can be integrated with existing microfluidic devices and large-scale screening systems. By enabling sorting based on single-cell reactions such as PCR, this platform will help expand the basis of cell sorting from mainly protein biomarkers to nucleic acid sequences and secreted biomolecules.
Collapse
Affiliation(s)
- Yuling Qin
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jingang Wang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Rui Han
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jingyu Shen
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jiasi Wang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Shihan Xu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Amy L Paguirigan
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Jordan L Smith
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Jerald P Radich
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| |
Collapse
|
23
|
Segaliny AI, Li G, Kong L, Ren C, Chen X, Wang JK, Baltimore D, Wu G, Zhao W. Functional TCR T cell screening using single-cell droplet microfluidics. LAB ON A CHIP 2018; 18:3733-3749. [PMID: 30397689 PMCID: PMC6279597 DOI: 10.1039/c8lc00818c] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Adoptive T cell transfer, in particular TCR T cell therapy, holds great promise for cancer immunotherapy with encouraging clinical results. However, finding the right TCR T cell clone is a tedious, time-consuming, and costly process. Thus, there is a critical need for single cell technologies to conduct fast and multiplexed functional analyses followed by recovery of the clone of interest. Here, we use droplet microfluidics for functional screening and real-time monitoring of single TCR T cell activation upon recognition of target tumor cells. Notably, our platform includes a tracking system for each clone as well as a sorting procedure with 100% specificity validated by downstream single cell reverse-transcription PCR and sequencing of TCR chains. Our TCR screening prototype will facilitate immunotherapeutic screening and development of T cell therapies.
Collapse
MESH Headings
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Cell Line, Tumor
- Equipment Design
- Humans
- Immunotherapy, Adoptive
- Microfluidic Analytical Techniques/instrumentation
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/analysis
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
- T-Lymphocytes/chemistry
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
Collapse
Affiliation(s)
- Aude I. Segaliny
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Ci Ren
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Xiaoming Chen
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Jessica K. Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - Guikai Wu
- Amberstone Biosciences LLC, Irvine, CA 92617, U.S.A
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| |
Collapse
|
24
|
Zhu X, Shi X, Chu J, Ye B, Zuo P, Wang Y. Quantitative analysis of the growth of individual Bacillus coagulans cells by microdroplet technology. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0229-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
25
|
Tan Z, Heemstra JM. High-Throughput Measurement of Small-Molecule Enantiopurity by Using Flow Cytometry. Chembiochem 2018; 19:1853-1857. [PMID: 30126025 DOI: 10.1002/cbic.201800341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Fluorescence-activated cell sorting (FACS) offers a powerful approach to high-throughput library screening in directed evolution experiments. However, FACS is rarely used in the evolution of stereoselective enzymes, due to the difficulty of designing fluorescence-based assays for measuring enantiopurity. Here, we describe a new FACS-based enantiopurity analysis approach that overcomes these limitations by using enantiomeric DNA biosensors labeled with orthogonal fluorophores. By co-encapsulating the biosensors with a mixture of target enantiomers in microfluidic droplets, we could demonstrate the use of FACS to differentiate between droplets having various levels of target enantiopurity. We envision the utility of this method for high-throughput screening of enantiopurity in the directed evolution of stereoselective enzymes, thereby facilitating the discovery of new asymmetric biocatalysts for the synthesis of pharmaceuticals and other high-value chemicals.
Collapse
Affiliation(s)
- Zhesen Tan
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.,Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| |
Collapse
|
26
|
Abstract
![]()
The compartmentalization of reactions
in monodispersed droplets
is valuable for applications across biology. However, the requirement
of microfluidics to partition the sample into monodispersed droplets
is a significant barrier that impedes implementation. Here, we introduce
particle-templated emulsification, a method to encapsulate samples
in monodispersed emulsions without microfluidics. By vortexing a mixture
of hydrogel particles and sample solution, we encapsulate the sample
in monodispersed emulsions that are useful for most droplet applications.
We illustrate the method with ddPCR and single cell culture. The ability
to encapsulate samples in monodispersed droplets without microfluidics
should facilitate the implementation of compartmentalized reactions
in biology.
Collapse
Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Samuel C Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
| |
Collapse
|
27
|
Vian A, Reuse B, Amstad E. Scalable production of double emulsion drops with thin shells. LAB ON A CHIP 2018; 18:1936-1942. [PMID: 29881836 DOI: 10.1039/c8lc00282g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Double emulsions are often used as containers to perform high throughput screening assays and as templates for capsules. These applications require double emulsions to be mechanically stable such that they do not coalesce during processing and storage. A possibility to increase their stability is to reduce the thickness of their shells to sufficiently low values that lubrication effects hinder coalescence. However, the controlled fabrication of double emulsions with such thin shells is difficult. Here, we introduce a new microfluidic device, the aspiration device, that reduces the shell thickness of double emulsions down to 240 nm at a high throughput; thereby, the shell volume is reduced by up to 95%. The shell thickness of the resulting double emulsions depends on the pressure profile in the device and hence on the fluid flow rates in the channels and is independent of the shell thickness of the injected double emulsions. Therefore, this device enables converting double emulsions with polydisperse shell thicknesses into double emulsions with well-defined, uniform thin shells.
Collapse
Affiliation(s)
- A Vian
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | | | | |
Collapse
|
28
|
Gamboa-Melendez H, Larroude M, Park YK, Trebul P, Nicaud JM, Ledesma-Amaro R. Synthetic Biology to Improve the Production of Lipases and Esterases (Review). Methods Mol Biol 2018; 1835:229-242. [PMID: 30109656 DOI: 10.1007/978-1-4939-8672-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology is an emergent field of research whose aim is to make biology an engineering discipline, thus permitting to design, control, and standardize biological processes. Synthetic biology is therefore expected to boost the development of biotechnological processes such as protein production and enzyme engineering, which can be significantly relevant for lipases and esterases.
Collapse
Affiliation(s)
- Heber Gamboa-Melendez
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Macarena Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Young Kyoung Park
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pauline Trebul
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Sythetic Biology, Imperial College London, London, UK.
| |
Collapse
|
29
|
Sukovich DJ, Kim SC, Ahmed N, Abate AR. Bulk double emulsification for flow cytometric analysis of microfluidic droplets. Analyst 2017; 142:4618-4622. [PMID: 29131209 PMCID: PMC5997486 DOI: 10.1039/c7an01695f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Droplet microfluidics is valuable for applications in chemistry and biology, but generates massive numbers of droplets that must be analyzed and sorted. Here, we describe a simple approach to bulk double emulsify microfluidic emulsions for analysis and sorting with commercial flow cytometers. We illustrate the method by using it to identify droplets based on nucleic acid content. Though simple, our method provides a general approach for analyzing and sorting microfluidic droplets without custom microfluidic double emulsifiers or sorters.
Collapse
Affiliation(s)
- David J Sukovich
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA.
| | | | | | | |
Collapse
|
30
|
Scheler O, Pacocha N, Debski PR, Ruszczak A, Kaminski TS, Garstecki P. Optimized droplet digital CFU assay (ddCFU) provides precise quantification of bacteria over a dynamic range of 6 logs and beyond. LAB ON A CHIP 2017; 17:1980-1987. [PMID: 28480460 DOI: 10.1039/c7lc00206h] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Standard digital assays need a large number of compartments for precise quantification of a sample over a broad dynamic range. We address this issue with an optimized droplet digital approach that uses a drastically reduced number of compartments for quantification. We generate serial logarithmic dilutions of an initial bacterial sample as an array of microliter-sized droplet plugs. In a subsequent step, these droplets are split into libraries of nanoliter droplets and pooled together for incubation and analysis. We show that our technology is at par with traditional dilution plate count for quantification of bacteria, but has the advantage of simplifying the experimental setup and reducing the manual workload. The method also has the potential to reduce the assay time significantly.
Collapse
Affiliation(s)
- O Scheler
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - N Pacocha
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - P R Debski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - A Ruszczak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - T S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - P Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| |
Collapse
|
31
|
Sequence specific sorting of DNA molecules with FACS using 3dPCR. Sci Rep 2017; 7:39385. [PMID: 28051104 PMCID: PMC5209659 DOI: 10.1038/srep39385] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 12/04/2022] Open
Abstract
Genetic heterogeneity is an important feature of many biological systems, but introduces technical challenges to their characterization. Even with the best modern instruments, only a small fraction of DNA molecules present in a sample can be read, and they are recovered in the form of short, hundred-base reads. In this paper, we introduce 3dPCR, a method to sort DNA molecules with sequence specificity. 3dPCR allows heterogeneous populations of DNA to be sorted to recover long targets for deep sequencing. It is valuable whenever a target sequence is rare in a mixed population, such as for characterizing mutations in heterogeneous cancer cell populations or identifying cells containing a specific genetic sequence or infected with a target virus.
Collapse
|
32
|
Lim SW, Lance ST, Stedman KM, Abate AR. PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts. J Virol Methods 2016; 242:14-21. [PMID: 28042018 DOI: 10.1016/j.jviromet.2016.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 01/27/2023]
Abstract
Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the "gold standard" of virus enumeration, the plaque assay.
Collapse
Affiliation(s)
- Shaun W Lim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Shea T Lance
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Kenneth M Stedman
- Biology Department and Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.
| |
Collapse
|
33
|
Lance ST, Sukovich DJ, Stedman KM, Abate AR. Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry. Virol J 2016; 13:201. [PMID: 27906039 PMCID: PMC5131442 DOI: 10.1186/s12985-016-0655-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 11/21/2022] Open
Abstract
Background Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts of viruses. Methods PAVS enables specific sorting of viruses with flow cytometry. A sample containing a virus population is processed through a microfluidic device to encapsulate it into droplets, such that the droplets contain different viruses from the sample. TaqMan PCR reagents are also included targeting specific virus species such that, upon thermal cycling, droplets containing the species become fluorescent. The target viruses are then recovered via droplet sorting. The recovered virus genomes can then be analyzed with qPCR and next generation sequencing. Results and Conclusions We describe the PAVS workflow and demonstrate its specificity for identifying target viruses in a heterogeneous population. In addition, we demonstrate recovery of the target viruses via droplet sorting and analysis of their nucleic acids with qPCR. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0655-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shea T Lance
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - David J Sukovich
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - Kenneth M Stedman
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, Oregon, USA
| | - Adam R Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA. .,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
34
|
Bawazer LA, McNally CS, Empson CJ, Marchant WJ, Comyn TP, Niu X, Cho S, McPherson MJ, Binks BP, deMello A, Meldrum FC. Combinatorial microfluidic droplet engineering for biomimetic material synthesis. SCIENCE ADVANCES 2016; 2:e1600567. [PMID: 27730209 PMCID: PMC5055387 DOI: 10.1126/sciadv.1600567] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/31/2016] [Indexed: 05/19/2023]
Abstract
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine.
Collapse
Affiliation(s)
- Lukmaan A. Bawazer
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
- Corresponding author. (F.C.M.); (L.A.B.)
| | | | | | | | - Tim P. Comyn
- Institute for Materials Research, School of Process, Environmental and Materials Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Xize Niu
- Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, U.K
| | - Soongwon Cho
- Samsung Display, 465, Beonyeong-ro, Seobuk-gu, Cheonan-si, Chungcheongnam-do, Republic of Korea
| | - Michael J. McPherson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Bernard P. Binks
- Surfactant & Colloid Group, Department of Chemistry, University of Hull, Hull HU6 7RX, U.K
| | - Andrew deMello
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Fiona C. Meldrum
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
- Corresponding author. (F.C.M.); (L.A.B.)
| |
Collapse
|
35
|
Ma F, Fischer M, Han Y, Withers SG, Feng Y, Yang GY. Substrate Engineering Enabling Fluorescence Droplet Entrapment for IVC-FACS-Based Ultrahigh-Throughput Screening. Anal Chem 2016; 88:8587-95. [DOI: 10.1021/acs.analchem.6b01712] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Fuqiang Ma
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Michael Fischer
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yunbin Han
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Stephen G. Withers
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yan Feng
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guang-Yu Yang
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Shanghai
Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
36
|
Kaminski TS, Scheler O, Garstecki P. Droplet microfluidics for microbiology: techniques, applications and challenges. LAB ON A CHIP 2016; 16:2168-87. [PMID: 27212581 DOI: 10.1039/c6lc00367b] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
Collapse
Affiliation(s)
- Tomasz S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | | | | |
Collapse
|
37
|
Affiliation(s)
- Alexander K. Price
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| |
Collapse
|
38
|
Li S, Gong X, Mc Nally CS, Zeng M, Gaule T, Anduix-Canto C, Kulak AN, Bawazer LA, McPherson MJ, Meldrum FC. Rapid preparation of highly reliable PDMS double emulsion microfluidic devices. RSC Adv 2016. [DOI: 10.1039/c6ra03225g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article presents a simple and highly reliable method for preparing PDMS microfluidic double emulsion devices that employs a single-step oxidative plasma treatment to both pattern the wettability of the microchannels and to bond the chips.
Collapse
Affiliation(s)
- Shunbo Li
- School of Chemistry
- University of Leeds
- Leeds
- UK
| | | | | | - Muling Zeng
- School of Chemistry
- University of Leeds
- Leeds
- UK
| | - Thembaninkosi Gaule
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | | | | | | | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | | |
Collapse
|
39
|
Cole RH, Tran TM, Abate AR. Double Emulsion Generation Using a Polydimethylsiloxane (PDMS) Co-axial Flow Focus Device. J Vis Exp 2015:e53516. [PMID: 26780079 DOI: 10.3791/53516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Double emulsions are useful in a number of biological and industrial applications in which it is important to have an aqueous carrier fluid. This paper presents a polydimethylsiloxane (PDMS) microfluidic device capable of generating water/oil/water double emulsions using a coaxial flow focusing geometry that can be fabricated entirely using soft lithography. Similar to emulsion devices using glass capillaries, double emulsions can be formed in channels with uniform wettability and with dimensions much smaller than the channel sizes. Three dimensional flow focusing geometry is achieved by casting a pair of PDMS slabs using two layer soft lithography, then mating the slabs together in a clamshell configuration. Complementary locking features molded into the PDMS slabs enable the accurate registration of features on each of the slab surfaces. Device testing demonstrates formation of double emulsions from 14 µm to 50 µm in diameter while using large channels that are robust against fouling and clogging.
Collapse
Affiliation(s)
- Russell H Cole
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Tuan M Tran
- Joint UCSF/UCB Bioengineering Graduate Group, University of California, San Francisco
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; California Institute for Quantitative Biosciences, University of California, San Francisco;
| |
Collapse
|
40
|
Labanieh L, Nguyen TN, Zhao W, Kang DK. Floating Droplet Array: An Ultrahigh-Throughput Device for Droplet Trapping, Real-time Analysis and Recovery. MICROMACHINES 2015; 6:1469-1482. [PMID: 27134760 PMCID: PMC4849166 DOI: 10.3390/mi6101431] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We describe the design, fabrication and use of a dual-layered microfluidic device for ultrahigh-throughput droplet trapping, analysis, and recovery using droplet buoyancy. To demonstrate the utility of this device for digital quantification of analytes, we quantify the number of droplets, which contain a β-galactosidase-conjugated bead among more than 100,000 immobilized droplets. In addition, we demonstrate that this device can be used for droplet clustering and real-time analysis by clustering several droplets together into microwells and monitoring diffusion of fluorescein, a product of the enzymatic reaction of β-galactosidase and its fluorogenic substrate FDG, between droplets.
Collapse
Affiliation(s)
| | | | - Weian Zhao
- Correspondence: (W.Z.); (D.-K.K.); Tel.: +1-949-824-8035- (D.-K.K.)
| | - Dong-Ku Kang
- Correspondence: (W.Z.); (D.-K.K.); Tel.: +1-949-824-8035- (D.-K.K.)
| |
Collapse
|
41
|
Petzold CJ, Chan LJG, Nhan M, Adams PD. Analytics for Metabolic Engineering. Front Bioeng Biotechnol 2015; 3:135. [PMID: 26442249 PMCID: PMC4561385 DOI: 10.3389/fbioe.2015.00135] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/20/2022] Open
Abstract
Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.
Collapse
Affiliation(s)
- Christopher J Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Melissa Nhan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Paul D Adams
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| |
Collapse
|
42
|
Colin PY, Zinchenko A, Hollfelder F. Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 2015; 33:42-51. [PMID: 26311177 DOI: 10.1016/j.sbi.2015.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/12/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Abstract
The success of a directed evolution approach to creating custom-made enzymes relies in no small part on screening as many clones as possible. The miniaturisation of assays into pico to femtoliter compartments (emulsion droplets, vesicles or gel-shell beads) makes directed evolution campaigns practically more straightforward than current large scale industrial screening that requires liquid handling equipment and much manpower. Several recent experimental formats have established protocols to screen more than 10 million compartments per day, representing unprecedented throughput at low cost. This review introduces the emerging approaches towards making biomimetic man-made compartments that are poised to be adapted by a wider circle of researchers. In addition to cost and time saving, control of selection pressures and conditions, the quantitative readout that reports on every library members and the ability to develop strategies based on these data will increase the degrees of freedom in designing and testing strategies for directed evolution experiments.
Collapse
Affiliation(s)
- Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| |
Collapse
|
43
|
Novak R, Hart K, Mathies RA. Single cell measurement of telomerase expression and splicing using microfluidic emulsion cultures. Nucleic Acids Res 2015. [PMID: 26202962 PMCID: PMC4652743 DOI: 10.1093/nar/gkv477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Telomerase is a reverse transcriptase that maintains telomeres on the ends of chromosomes, allowing rapidly dividing cells to proliferate while avoiding senescence and apoptosis. Understanding telomerase gene expression and splicing at the single cell level could yield insights into the roles of telomerase during normal cell growth as well as cancer development. Here we use droplet-based single cell culture followed by single cell or colony transcript abundance analysis to investigate the relationship between cell growth and transcript abundance of the telomerase genes encoding the RNA component (hTR) and protein component (hTERT) as well as hTERT splicing. Jurkat and K562 cells were examined under normal cell culture conditions and during exposure to curcumin, a natural compound with anti-carcinogenic and telomerase activity-reducing properties. Individual cells predominantly express single hTERT splice variants, with the α+/β− variant exhibiting significant transcript abundance bimodality that is sustained through cell division. Sub-lethal curcumin exposure results in reduced bimodality of all hTERT splice variants and significant upregulation of alpha splicing, suggesting a possible role in cellular stress response. The single cell culture and transcript abundance analysis method presented here provides the tools necessary for multiparameter single cell analysis which will be critical for understanding phenotypes of heterogeneous cell populations, disease cell populations and their drug response.
Collapse
Affiliation(s)
- Richard Novak
- UCSF/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Kristina Hart
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Richard A Mathies
- UCSF/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA Department of Chemistry, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
44
|
Uyeda A, Watanabe T, Kato Y, Watanabe H, Yomo T, Hohsaka T, Matsuura T. Liposome-Based in Vitro Evolution of Aminoacyl-tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation. Chembiochem 2015; 16:1797-802. [DOI: 10.1002/cbic.201500174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/09/2022]
|
45
|
Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci U S A 2015; 112:7159-64. [PMID: 26040002 DOI: 10.1073/pnas.1422285112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural enzymes are incredibly proficient catalysts, but engineering them to have new or improved functions is challenging due to the complexity of how an enzyme's sequence relates to its biochemical properties. Here, we present an ultrahigh-throughput method for mapping enzyme sequence-function relationships that combines droplet microfluidic screening with next-generation DNA sequencing. We apply our method to map the activity of millions of glycosidase sequence variants. Microfluidic-based deep mutational scanning provides a comprehensive and unbiased view of the enzyme function landscape. The mapping displays expected patterns of mutational tolerance and a strong correspondence to sequence variation within the enzyme family, but also reveals previously unreported sites that are crucial for glycosidase function. We modified the screening protocol to include a high-temperature incubation step, and the resulting thermotolerance landscape allowed the discovery of mutations that enhance enzyme thermostability. Droplet microfluidics provides a general platform for enzyme screening that, when combined with DNA-sequencing technologies, enables high-throughput mapping of enzyme sequence space.
Collapse
|
46
|
Eastburn DJ, Huang Y, Pellegrino M, Sciambi A, Ptáček LJ, Abate AR. Microfluidic droplet enrichment for targeted sequencing. Nucleic Acids Res 2015; 43:e86. [PMID: 25873629 PMCID: PMC4513844 DOI: 10.1093/nar/gkv297] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/26/2015] [Indexed: 02/07/2023] Open
Abstract
Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications.
Collapse
Affiliation(s)
- Dennis J Eastburn
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA Mission Bio, Inc., San Francisco, CA 94107, USA
| | - Yong Huang
- Department of Neurology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | | | - Adam Sciambi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA Mission Bio, Inc., San Francisco, CA 94107, USA
| | - Louis J Ptáček
- Department of Neurology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| |
Collapse
|
47
|
Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
Collapse
Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| |
Collapse
|
48
|
|
49
|
Lim SW, Tran TM, Abate AR. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes. PLoS One 2015; 10:e0113549. [PMID: 25629401 PMCID: PMC4309575 DOI: 10.1371/journal.pone.0113549] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS) can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS). This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.
Collapse
Affiliation(s)
- Shaun W. Lim
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, United States of America
| | - Tuan M. Tran
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, United States of America
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
50
|
Abstract
Fluorescence-activated droplet sorting is an important tool for droplet microfluidic workflows, but published approaches are unable to surpass throughputs of a few kilohertz. We present a new geometry that replaces the hard divider separating the outlets with a gapped divider, allowing sorting over ten times faster.
Collapse
Affiliation(s)
- Adam Sciambi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158 USA.
| | | |
Collapse
|