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Xia W, Lin H, Zhou X, Wang Y, Cao S, Liu J, Xu A, Dong W, Jiang M. Screening of polyurethane-degrading microbes using a quenching fluorescence probe by microfluidic droplet sorting. CHEMOSPHERE 2024; 364:143060. [PMID: 39121966 DOI: 10.1016/j.chemosphere.2024.143060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/28/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Excessive use of polyurethane (PU) polymers has led contributed to serious environmental pollution. The plastic recycling technology using microorganisms and enzymes as catalysts offers a promising green and low-carbon approach for managing plastic waste. However, current methods for screening PU-degrading strains suffer from drawbacks such as being time-consuming and inefficient. Herein, we present a novel approach for screening PU-degrading microorganisms using a quenching fluorescent probe along with the fluorescence-activated droplet sorting (FADS). The FPAP could specifically recognize the 4,4'-methylenedianiline (MDA) derivates released from PU degradation, with fluorescence quenching as a response. Based on the approach, we successfully screen two PU-degrading strains (Burkholderia sp. W38 and Bacillus sp. C1). After 20 d of cultivation, strain W38 and C1 could degrade 41.58% and 31.45% of polyester-PU film, respectively. Additionally, three metabolites were identified during the degradation of PU monomer (2,4-toluene diamine, 2,4-TDA) and a proposed degradation pathway was established. Consequently, the fluorescence probe integrated with microfluidic droplet systems, demonstrates potential for the development of innovative PU-biocatalysts. Furthermore, the identification of the 2,4-TDA degradation pathway provides valuable insights that can propel advancements in the field of PU biodegradation.
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Affiliation(s)
- Wei Xia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Haohong Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xinyu Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yihu Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Shixiang Cao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jiawei Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Anming Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
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2
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Pourmasoumi F, Hengoju S, Beck K, Stephan P, Klopfleisch L, Hoernke M, Rosenbaum MA, Kries H. Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics. Chembiochem 2023; 24:e202300680. [PMID: 37804133 DOI: 10.1002/cbic.202300680] [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: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Katharina Beck
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lukas Klopfleisch
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Hoernke
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
- Faculty of Chemistry, Martin-Luther-Universität, Von-Danckelmann-Platz 4, 06108, Halle (S.), Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstrasse 30, 95440, Bayreuth, Germany
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3
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:1073. [PMID: 37240718 PMCID: PMC10221674 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
| | - Anton P. Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
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4
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Xu A, Liu J, Cao S, Xu B, Guo C, Yu Z, Chen X, Zhou J, Dong W, Jiang M. Application of a novel fluorogenic polyurethane analogue probe in polyester-degrading microorganisms screening by microfluidic droplet. Microb Biotechnol 2022; 16:474-480. [PMID: 35881631 PMCID: PMC9871523 DOI: 10.1111/1751-7915.14121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 01/27/2023] Open
Abstract
Application of polyester-degrading microorganisms or enzymes should be considered as an eco-friendly alternative to chemical recycling due to the huge plastic waste disposal nowadays. However, current impranil DLN-based screening of polyester-degrading microorganisms is time-consuming, labour-intensive and unable to distinguish polyesterases from other protease- or amidase-like enzymes. Herein, we present an approach that combined a novel synthetic fluorescent polyurethane analogue probe (FPAP), along with the droplet-based microfluidics to screen polyurethane-degrading microorganisms through fluorescence-activated droplet sorting (FADS) pipeline. The fluorescent probe FPAP exhibited a fluorescence enhancement effect once hydrolysed by polyesterases, along with a strong specificity in discriminating polyesterases from other non-active enzymes. Application of FPAP in a microfluidic droplet system demonstrated that this probe exhibited high sensitivity and efficiency in selecting positive droplets containing leaf-branch compost cutinase (LCC) enzymes. This novel fluorogenic probe, FPAP, combined with the droplet microfluidic system has the potential to be used in the exploitation of novel PUR-biocatalysts for biotechnological and environmental applications.
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Affiliation(s)
- Anming Xu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Jiawei Liu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Shixiang Cao
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Bin Xu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Chengzhi Guo
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Ziyi Yu
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Xiaoqiang Chen
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Jie Zhou
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Min Jiang
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
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5
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Viebrock K, Rabl D, Meinen S, Wunder P, Meyer JA, Frey LJ, Rasch D, Dietzel A, Mayr T, Krull R. Microsensor in Microbioreactors: Full Bioprocess Characterization in a Novel Capillary-Wave Microbioreactor. BIOSENSORS 2022; 12:bios12070512. [PMID: 35884315 PMCID: PMC9312480 DOI: 10.3390/bios12070512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Microbioreactors (MBRs) with a volume below 1 mL are promising alternatives to established cultivation platforms such as shake flasks, lab-scale bioreactors and microtiter plates. Their main advantages are simple automatization and parallelization and the saving of expensive media components and test substances. These advantages are particularly pronounced in small-scale MBRs with a volume below 10 µL. However, most described small-scale MBRs are lacking in process information from integrated sensors due to limited space and sensor technology. Therefore, a novel capillary-wave microbioreactor (cwMBR) with a volume of only 7 µL has the potential to close this gap, as it combines a small volume with integrated sensors for biomass, pH, dissolved oxygen (DO) and glucose concentration. In the cwMBR, pH and DO are measured by established luminescent optical sensors on the bottom of the cwMBR. The novel glucose sensor is based on a modified oxygen sensor, which measures the oxygen uptake of glucose oxidase (GOx) in the presence of glucose up to a concentration of 15 mM. Furthermore, absorbance measurement allows biomass determination. The optical sensors enabled the characterization of an Escherichia coli batch cultivation over 8 h in the cwMBR as proof of concept for further bioprocesses. Hence, the cwMBR with integrated optical sensors has the potential for a wide range of microscale bioprocesses, including cell-based assays, screening applications and process development.
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Affiliation(s)
- Kevin Viebrock
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
| | - Dominik Rabl
- Institute of Analytical Chemistry and Food Chemistry, Technische Universität Graz, 8010 Graz, Austria; (D.R.); (T.M.)
| | - Sven Meinen
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
- Institute of Microtechnology, Technische Universität Braunschweig, 38124 Braunschweig, Germany
| | - Paul Wunder
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
| | - Jan-Angelus Meyer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
| | - Lasse Jannis Frey
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
| | - Detlev Rasch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
| | - Andreas Dietzel
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
- Institute of Microtechnology, Technische Universität Braunschweig, 38124 Braunschweig, Germany
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry, Technische Universität Graz, 8010 Graz, Austria; (D.R.); (T.M.)
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (K.V.); (P.W.); (J.-A.M.); (L.J.F.); (D.R.)
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (S.M.); (A.D.)
- Correspondence:
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6
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Oberpaul M, Spohn MS, Brinkmann S, Mihajlovic S, Marner M, Patras MA, Toti L, Kurz M, Hammann PE, Vilcinskas A, Glaeser J, Schäberle TF. Trichoderma-derived pentapeptides from the infected nest mycobiome of the subterranean termite Coptotermes testaceus. Chembiochem 2022; 23:e202100698. [PMID: 35298064 PMCID: PMC9321192 DOI: 10.1002/cbic.202100698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Indexed: 11/07/2022]
Abstract
Termites live in a dynamic environment where colony health is strongly influenced by surrounding microbes. However, little is known about the mycobiomes of lower termites and their nests, and how these change in response to disease. Here we compared the individual and nest mycobiomes of a healthy subterranean termite colony (Coptotermes testaceus) to one infected and ultimately eradicated by a fungal pathogen. We identified Trichoderma species in the materials of both nests, but they were also abundant in the infected termites. Methanolic extracts of Trichoderma sp. FHG000531, isolated from the infected nest, were screened for secondary metabolites by UHPLC‐HR MS/MS‐guided molecular networking. We identified many bioactive compounds with potential roles in the eradication of the infected colony, as well as a cluster of six unknown peptides. The novel peptide FE011 was isolated and characterized by NMR spectroscopy. The function of this novel peptide family as well as the role of Trichoderma species in dying termite colonies therefore requires further investigation.
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Affiliation(s)
- Markus Oberpaul
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioresources, Ohlebergsweg 12, 35392, Gießen, GERMANY
| | - Marius S Spohn
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioressources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Stephan Brinkmann
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioresources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Sanja Mihajlovic
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioresources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Michael Marner
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioresources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Maria Alexandra Patras
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Bioresources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Luigi Toti
- Sanofi-Aventis Deutschland GmbH, Natural Product Research - Infectious Diseases, Industriepark Höchst, 65926, Frankfurt am Main, GERMANY
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, Industriepark Höchst, 65926, Frankfurt am Main, GERMANY
| | - Peter Eugen Hammann
- Evotec International GmbH, Evotec, Marie-Curie-Straße 7, 37079, Göttingen, GERMANY
| | - Andreas Vilcinskas
- Fraunhofer IME: Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Branch for Bioresources, Ohlebergsweg 12, 35392, Giessen, GERMANY
| | - Jens Glaeser
- Evotec International GmbH, Antiinfectives Lead Discovery from Natural Products, Marie-Curie-Straße 7, 37079, Göttingen, GERMANY
| | - Till Friedrich Schäberle
- University of Giessen, Institute for Insect Biotechnology, Heinrich-Buff-Ring 26-32, 35392, Giessen, GERMANY
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Matilla MA. Facing crises in the 21st century: microfluidics approaches for antibiotic discovery. Microb Biotechnol 2022; 15:392-394. [PMID: 34333833 PMCID: PMC8867967 DOI: 10.1111/1751-7915.13908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022] Open
Abstract
We urgently need new antibiotics to counteract the rising in the emergence of multidrug-resistant microorganisms. To improve the identification of antimicrobial compounds of microbial origin, numerous multidisciplinary approaches are being implemented. However, the development of innovative microbial cultivation strategies is necessary to exploit the full biosynthetic potential of non-culturable microorganisms. Here, I highlight various articles that employ high-throughput microfluidic-based strategies to identify novel antimicrobial metabolites based on bacterial activities. The rapid development of this technology will likely advance the field of antibiotic discovery.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biotechnology and Environmental ProtectionEstación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
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8
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Two-step generation of monodisperse agarose-solidified double emulsions (w/w/o) excluding an inner oil barrier. MethodsX 2021; 8:101565. [PMID: 35004199 PMCID: PMC8720838 DOI: 10.1016/j.mex.2021.101565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Miniaturization of biomedical and chemical research areas is performed using microfluidic techniques. Droplet-based microfluidic applications are of high interest for various applications, e.g., high-throughput screening assays. Many of them are based on simple water-in-oil (w/o) or oil-in-water (o/w) emulsions that are easily to produce. More complex assays based on separate compartments require the use of multiple emulsions, such as water-in-oil-in-water (w/o/w) or oil-in-water-in-oil (o/w/o) emulsions. In this study an easy, fast to establish method to generate agarose-solidified (w/w/o) double emulsions with ∼55 µm in diameter, in which both agarose-phases are not separated by a surfactant stabilized oil is described. An off-chip emulsion-breaking and washing step of the inner agarose droplets based on density gradient centrifugation was designed, offering new possibilities for high-throughput assays on picoliter scale. In brief, this paper reports:the protocol to generate agarose-solidified (w/w/o) double emulsions non-seperated by surfactant stabilized oil; an off-chip washing protocol of agarose-solidified emulsions based on density gradient centrifugation.
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