1
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Living material assembly of bacteriogenic protocells. Nature 2022; 609:1029-1037. [DOI: 10.1038/s41586-022-05223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/10/2022] [Indexed: 11/08/2022]
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2
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Morsby JJ, Dharmarwardana M, McGarraugh H, Smith BD. Supramolecular optimization of the visual contrast for colorimetric indicator assays that release resorufin dye. Chem Commun (Camb) 2020; 56:9296-9299. [PMID: 32666982 PMCID: PMC7429340 DOI: 10.1039/d0cc03551c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A tetralactam macrocycle acts as a novel supramolecular adjuvant to capture a released resorufin dye and create a higher contrasting yellow/blue color change for enhanced naked eye interpretation of a colorimetric indicator assay.
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Affiliation(s)
- Janeala J Morsby
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
| | - Madushani Dharmarwardana
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
| | - Hannah McGarraugh
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
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3
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Hakala T, Bialas F, Toprakcioglu Z, Bräuer B, Baumann KN, Levin A, Bernardes GJL, Becker CFW, Knowles TPJ. Continuous Flow Reactors from Microfluidic Compartmentalization of Enzymes within Inorganic Microparticles. ACS APPLIED MATERIALS & INTERFACES 2020; 12:32951-32960. [PMID: 32589387 PMCID: PMC7383928 DOI: 10.1021/acsami.0c09226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Compartmentalization and selective transport of molecular species are key aspects of chemical transformations inside the cell. In an artificial setting, the immobilization of a wide range of enzymes onto surfaces is commonly used for controlling their functionality but such approaches can restrict their efficacy and expose them to degrading environmental conditions, thus reducing their activity. Here, we employ an approach based on droplet microfluidics to generate enzyme-containing microparticles that feature an inorganic silica shell that forms a semipermeable barrier. We show that this porous shell permits selective diffusion of the substrate and product while protecting the enzymes from degradation by proteinases and maintaining their functionality over multiple reaction cycles. We illustrate the power of this approach by synthesizing microparticles that can be employed to detect glucose levels through simultaneous encapsulation of two distinct enzymes that form a controlled reaction cascade. These results demonstrate a robust, accessible, and modular approach for the formation of microparticles containing active but protected enzymes for molecular sensing applications and potential novel diagnostic platforms.
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Affiliation(s)
- Tuuli
A. Hakala
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Friedrich Bialas
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Zenon Toprakcioglu
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Birgit Bräuer
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Kevin N. Baumann
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Aviad Levin
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Instituto
de Medicina Molecular, Faculdade de Medicina
de Universidad de Lisboa, 1649-028 Lisboa, Portugal
| | - Christian F. W. Becker
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Street 38, 1090 Vienna, Austria
| | - Tuomas P. J. Knowles
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cavendish
Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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4
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Singh H, Tiwari K, Tiwari R, Pramanik SK, Das A. Small Molecule as Fluorescent Probes for Monitoring Intracellular Enzymatic Transformations. Chem Rev 2019; 119:11718-11760. [DOI: 10.1021/acs.chemrev.9b00379] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Harwinder Singh
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India
| | - Karishma Tiwari
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India
| | - Rajeshwari Tiwari
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India
| | - Sumit Kumar Pramanik
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India
| | - Amitava Das
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India
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5
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Schick D, Schwack W. Planar yeast estrogen screen with resorufin-β-d-galactopyranoside as substrate. J Chromatogr A 2017; 1497:155-163. [PMID: 28359553 DOI: 10.1016/j.chroma.2017.03.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/24/2022]
Abstract
For the planar yeast estrogen screen (pYES), 4-methylumbelliferyl-β-d-galactopyranoside was generally employed as substrate, delivering blue fluorescing 4-methylumbelliferone after enzymatic cleavage by the YES reporter β-d-galactosidase as the positive signal for the presence of estrogen active compounds (EAC). As environmental samples like waste water also contain blue fluorescent components, it is difficult to differentiate them from pYES signals. Therefore, resorufin-β-d-galactopyranoside (RGP), providing the orange fluorescing resorufin after enzymatic cleavage, was introduced as pYES substrate to determine EAC. With 17β-estradiol (E2) and 17α-ethinylestradiol (EE2), mean limits of detection and quantitation of 3.5 and 6.5pg/zone, respectively, were determined. Obtained recoveries for both E2 and EE2 from spiked water samples in a concentration range of 2-20ng/L were close to 100%. The application of the RGP-pYES on waste water influent and effluent samples showed the clear detection of EAC without interferences. Estrone (E1), Estriol, E2, and an unknown EAC were found in the influent sample (E2 with a mean of 16.9 ng/L and a precision of 11% RSD; n=4), while another unknown EAC was observed in the effluent sample. In addition, the presence of conjugated EAC in the influent was demonstrated by hydrolysis with β-glucuronidase, when the signals of E1 and the unknown increased by about 25% and 100%, respectively.
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Affiliation(s)
- Dinah Schick
- Institute of Food Chemistry, University of Hohenheim, Garbenstraße 28, D-70599 Stuttgart, Germany
| | - Wolfgang Schwack
- Institute of Food Chemistry, University of Hohenheim, Garbenstraße 28, D-70599 Stuttgart, Germany.
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6
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Magro G, Bain RES, Woodall CA, Matthews RL, Gundry SW, Davis AP. Synthesis and application of resorufin β-D-glucuronide, a low-cost chromogenic substrate for detecting Escherichia coli in drinking water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9624-9631. [PMID: 25035967 DOI: 10.1021/es502319n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The development of low-cost tests for Escherichia coli is hampered by the expense and limited choice of enzyme substrates. Most chromogenic substrates are required in costly amounts, while fluorogenic substrates require an additional apparatus (e.g., an ultraviolet lamp) to be detected. Herein, we propose an alternative chromogenic substrate, resorufin β-d-glucuronide (REG), which is exceptionally sensitive and may be employed in very small amounts. We show that REG can be produced similarly to other simple glucuronides and should therefore be no more expensive. The compound is used by both healthy and injured E. coli, resulting in a pronounced color change from orange to a bright pink. Because the released dye (resorufin) has a high extinction coefficient, substantially lower amounts are needed than for commercially available substrates. The potential of this substrate is demonstrated by a presence/absence test requiring just 0.1 mg of REG/100 mL of water sample, one hundredth of the quantity needed for common chromogenic substrates, with an estimated bulk cost of ≤0.1 U.S. cents/test. REG shows promise as a chromogenic substrate for E. coli detection and should be considered in the development of new water tests, especially for low-income settings.
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Affiliation(s)
- Germinal Magro
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
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7
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Goodacre R, Trew S, Wrigley-Jones C, Neal MJ, Maddock J, Ottley TW, Porter N, Kell DB. Rapid screening for metabolite overproduction in fermentor broths, using pyrolysis mass spectrometry with multivariate calibration and artificial neural networks. Biotechnol Bioeng 2012; 44:1205-16. [PMID: 18618547 DOI: 10.1002/bit.260441008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Binary mixtures of model systems consisting of the antibiotic ampicillin with either Escherichia coli or Staphylococcus auresu were subjected to pyrolysis mass spectrometry (PyMS). To deconvolute the pyrolysis mass spectra, so as to obtain quantitative information on the concentration of ampicilin in the mixtures, partial least squares regression (PLS), principal components regression (PCR), and fully interconnected feedforward artificial neural networks (ANNs) were studied. In the latter case, the weights were modified using the standard backpropagation algorithm, and the nodes used a sigmoidal squsahing funciton. It was found that each of the methods could be used to provide calibration models which gave excellent predictions for the concentrations of ampicillin in samples on which they had not been trained. Furthermore, ANNs trained to predict the amount of ampicilin in E. coli were able to generalise so as to predict the concentration of ampicillin in a S. aureus background, illustrating the robustness of ANNs to rather substantial variations in the biological background. The PyMS of the complex mixture of ampicilin in bacteria could not be expressed simply in terms of additive combinations of the spectra describing the pure components of the mixtures and their relative concentrations. Intermolecular reactions took place in the pyrolysate, leading to a lack of superposition of the spectral components and to a dependence of the normalized mass spectrum on sample size. Samples from fermentations of a single organism in a complex production medium were also analyzed quantitatively for a drug of commercial interest. The drug could also be quantified in a variety of mutant-producing strains cultivated in the same medium. The combination of PyMS and ANNs constitutes a novel, rapid, and convenient method for exploitation in strain improvement screening programs. (c) 1994 John Wiley & Sons, Inc.
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Affiliation(s)
- R Goodacre
- Institute of Biological Sciences, University of Wales, Aberystwyth, Dyfed SY23 3DA, United Kingdom
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8
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Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles. Proc Natl Acad Sci U S A 2012; 109:E1437-43. [PMID: 22562794 DOI: 10.1073/pnas.1116670109] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule level. Individual HRP molecules are trapped within surface-tethered lipid vesicles, and their reaction with a fluorogenic substrate is probed. While the substrate readily penetrates into the vesicles, the charged product (resorufin) gets trapped and accumulates inside the vesicles. Surprisingly, individual enzyme molecules are found to stall when a few tens of product molecules accumulate. Bulk enzymology experiments verify that the enzyme is noncompetitively inhibited by resorufin. The initial reaction velocity of individual enzyme molecules and the number of product molecules required for their complete inhibition are broadly distributed and dynamically disordered. The two seemingly unrelated parameters, however, are found to be substantially correlated with each other in each enzyme molecule and over long times. These results suggest that, as a way to counter disorder, enzymes have evolved the means to correlate fluctuations at structurally distinct functional sites.
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9
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Abstract
A quantitative assay of beta-galactosidase activity in single cells of Saccharomyces cerevisiae has been developed using a fluorogenic substrate and flow cytometry [reported in Wittrup & Bailey, Cytometry, 9,394 (1988)]. The beta-galactosidase activity is expressed in yeast from the Escherichia coli lacZ gene under the control of the yeast GAL10 promoter, and is used as a marker for multicopy plasmid content. A nonfluorescent fluorogenic substrate is enzymatically cleaved by intracellular beta-galactosidase to form a fluorescent product. The accumulation of fluorescent product in single cells was found to depend on bulk substrate concentration and single-cell enzyme activity in a fashion that could not be described by a Michaelis-Menten kinetic rate form. It has been demonstrated that diffusion limitation rather than enzyme activity can determine the level of single-cell fluorescence under certain assay conditions, and a mathematical model has; been formulated which accounts for substrate and product diffusion. Guided by the mathematical model, the assay conditions were modified to allow measurement of single-cell enzyme activity rather than diffusion rates.
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Affiliation(s)
- K D Wittrup
- Department of Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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10
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Wittrup KD, Bailey JE, Ratzkin B, Patel A. Propagation of an amplifiable recombinant plasmid in Saccharomyces cerevisiae: flow cytometry studies and segregated modeling. Biotechnol Bioeng 2009; 35:565-77. [PMID: 18592552 DOI: 10.1002/bit.260350604] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Efficient expression of a foreign protein product by the yeast Saccharomyces cerevisiae requires a stable recombinant vector present at a high number of copies per cell. A conditional centromere yeast plasmid was constructed which can be amplified to high copy number by a process of unequal partitioning at cell division, followed by selection for increased copy number. However, in the absence of selection pressure for plasmid amplification, copy number rapidly drops from 25 plasmids/cell to 6 plasmids/cell in less than 10 generations of growth. Copy number subsequently decreases from 6 plasmids/cell to 2 plasmids/cell over a span of 50 generations. A combination of flow cytometric measurement of copy number distributions and segregated mathematical modeling were applied to test the predictions of a conceptual model of conditional centromere plasmid propagation. Measured distributions of plasmid content displayed a significant subpopulation of cells with a copy number of 4-6, even in a population whose mean copy number was 13.5. This type of copy number distribution was reproduced by a mathematical model which assumes that a maximum of 4-6 centromere plasmids per cell can be stably partitioned at cell division. The model also reproduces the observed biphasic kinetics of plasmid number instability. The agreement between simulation and experimental results provides support for the proposed model and demonstrates the utility of the flow cytometry/segregated modeling approach for the study of multicopy recombinant vector propagation.
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Affiliation(s)
- K D Wittrup
- Department of Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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11
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Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci 2009; 5:500-16. [PMID: 19680472 PMCID: PMC2726447 DOI: 10.7150/ijbs.5.500] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/21/2009] [Indexed: 11/05/2022] Open
Abstract
Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.
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Affiliation(s)
- Miranda Maki
- Biorefining Research Initiative, Lakehead University, Thunder Bay, Ontario, Canada
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12
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Ivanen DR, Rongjina NL, Shishlyannikov SM, Litviakova GI, Isaeva-Ivanova LS, Shabalin KA, Kulminskaya AA. Novel precipitated fluorescent substrates for the screening of cellulolytic microorganisms. J Microbiol Methods 2008; 76:295-300. [PMID: 19150471 DOI: 10.1016/j.mimet.2008.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Revised: 12/11/2008] [Accepted: 12/15/2008] [Indexed: 12/01/2022]
Abstract
New substrates, 2-(2'-benzothiazolyl)-phenyl (BTP) cellooligosaccharides with degree of polymerization (d.p.) 2-4 (BTPG(2-4)) were synthesized for the screening of microbial cellulolytic activity in plate assays. The substrates were very efficient that was shown for several cellulolytic bacteria, including yeast-like isolates from Kamchatka hot springs. Three tested bacterial strains and eighteen of 30 of the yeast isolates showed ability to degrade cellulose with cellobiohydrolase, beta-glucosidase and endo-cellulase activities measured with standard substrates. The structures of 2-(2'-benzothiazolyl)-phenyl oligosaccharides were solved by NMR- and mass-spectrometry. The usefulness of the 2-(2'-benzothiazolyl)-phenyl substrates were also shown during purification of the B. polymyxa cellulolytic complex, which consists of at least three types of the enzymes: cellobiohydrolase, endo-beta-d-glucanase and beta-glucosidase.
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Affiliation(s)
- Dina R Ivanen
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biophysics Division, 188300, Orlova roscha 1, Gatchina, Leningrad District, Russia
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13
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Mastrobattista E, Taly V, Chanudet E, Treacy P, Kelly BT, Griffiths AD. High-Throughput Screening of Enzyme Libraries: In Vitro Evolution of a β-Galactosidase by Fluorescence-Activated Sorting of Double Emulsions. ACTA ACUST UNITED AC 2005; 12:1291-300. [PMID: 16356846 DOI: 10.1016/j.chembiol.2005.09.016] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 09/22/2005] [Accepted: 09/22/2005] [Indexed: 11/29/2022]
Abstract
We describe a completely in vitro high-throughput screening system for directed evolution of enzymes based on in vitro compartmentalization (IVC). Single genes are transcribed and translated inside the aqueous droplets of a water-in-oil emulsion. Enzyme activity generates a fluorescent product and, after conversion into a water-in-oil-in-water double emulsion, fluorescent droplets are sorted using a fluorescence-activated cell sorter (FACS). Earlier in vivo studies have demonstrated that Ebg, a protein of unknown function, can evolve to allow Escherichia coli lacking the lacZ beta-galactosidase gene to grow on lactose. Here we demonstrate that we can evolve Ebg into an enzyme with significant beta-galactosidase activity in vitro. Only two specific mutations were ever seen to provide this improvement in Ebg beta-galactosidase activity in vivo. In contrast, nearly all the improved beta-galactosidases selected in vitro resulted from different mutations.
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Affiliation(s)
- Enrico Mastrobattista
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
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14
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Shim H, Karlström A, Touami SM, Fuller RP, Barbas CF. Flow cytometric screening of aldolase catalytic antibodies. Bioorg Med Chem Lett 2004; 14:4065-8. [PMID: 15225727 DOI: 10.1016/j.bmcl.2004.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 05/14/2004] [Accepted: 05/14/2004] [Indexed: 10/26/2022]
Abstract
High-throughput screening of cells expressing active catalytic antibody clones by flow cytometry is described. A fluorogenic retro-aldol retro-Michael substrate was designed and synthesized with incorporation of a chloromethyl moiety for intracellular retention. Hybridoma or transfected mammalian cells expressing catalytic antibody molecules could be rapidly isolated.
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Affiliation(s)
- Hyunbo Shim
- The Skaggs Institute for Chemical Biology and Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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15
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Schilling EA, Kamholz AE, Yager P. Cell lysis and protein extraction in a microfluidic device with detection by a fluorogenic enzyme assay. Anal Chem 2002; 74:1798-804. [PMID: 11985310 DOI: 10.1021/ac015640e] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A critical requirement for achieving a micro total analytical system for the analysis of cells and their constituent proteins is to integrate the lysis and fractionation steps on-chip. Here, an experimental microfluidic system integrating the lysis of bacterial cells and the extraction of a large intracellular enzyme, beta-galactosidase, is demonstrated. The beta-galactosidase is detected and quantified using a fluorogenic enzyme assay and a numerical model. While the focus is on the lysis of typical gram-negative bacterial cells (E. coli), the techniques described here could, in principle, be applied to a variety of different cell types.
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Affiliation(s)
- Eric A Schilling
- Department of Bioengineering, University of Washington, Seattle 98195, USA
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16
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Abstract
This unit promotes increased interest in the use of flow cytometry in several new environments. The author provides protocols and descriptive detail on measurements of cell cycle, viability, respiratory activity, and beta-galactosidase activity. Many of these assays are described for other biological systems in CPC, but are now provided in detail for yeasts. Despite the increasing usefulness of digital imaging techniques, flow cytometry remains the method of choice for the resolution of population heterogeneities.
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Affiliation(s)
- D Lloyd
- University of Wales, Cardiff, United Kingdom
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17
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Abstract
Classical microbiology techniques are relatively slow in comparison to other analytical techniques, in many cases due to the need to culture the microorganisms. Furthermore, classical approaches are difficult with unculturable microorganisms. More recently, the emergence of molecular biology techniques, particularly those on antibodies and nucleic acid probes combined with amplification techniques, has provided speediness and specificity to microbiological diagnosis. Flow cytometry (FCM) allows single- or multiple-microbe detection in clinical samples in an easy, reliable, and fast way. Microbes can be identified on the basis of their peculiar cytometric parameters or by means of certain fluorochromes that can be used either independently or bound to specific antibodies or oligonucleotides. FCM has permitted the development of quantitative procedures to assess antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly reproducible way. Furthermore, this technique allows the monitoring of in vitro antimicrobial activity and of antimicrobial treatments ex vivo. The most outstanding contribution of FCM is the possibility of detecting the presence of heterogeneous populations with different responses to antimicrobial treatments. Despite these advantages, the application of FCM in clinical microbiology is not yet widespread, probably due to the lack of access to flow cytometers or the lack of knowledge about the potential of this technique. One of the goals of this review is to attempt to mitigate this latter circumstance. We are convinced that in the near future, the availability of commercial kits should increase the use of this technique in the clinical microbiology laboratory.
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18
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Alvarez-Barrientos A, Arroyo J, Cantón R, Nombela C, Sánchez-Pérez M. Applications of flow cytometry to clinical microbiology. Clin Microbiol Rev 2000; 13:167-95. [PMID: 10755996 PMCID: PMC100149 DOI: 10.1128/cmr.13.2.167] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Classical microbiology techniques are relatively slow in comparison to other analytical techniques, in many cases due to the need to culture the microorganisms. Furthermore, classical approaches are difficult with unculturable microorganisms. More recently, the emergence of molecular biology techniques, particularly those on antibodies and nucleic acid probes combined with amplification techniques, has provided speediness and specificity to microbiological diagnosis. Flow cytometry (FCM) allows single- or multiple-microbe detection in clinical samples in an easy, reliable, and fast way. Microbes can be identified on the basis of their peculiar cytometric parameters or by means of certain fluorochromes that can be used either independently or bound to specific antibodies or oligonucleotides. FCM has permitted the development of quantitative procedures to assess antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly reproducible way. Furthermore, this technique allows the monitoring of in vitro antimicrobial activity and of antimicrobial treatments ex vivo. The most outstanding contribution of FCM is the possibility of detecting the presence of heterogeneous populations with different responses to antimicrobial treatments. Despite these advantages, the application of FCM in clinical microbiology is not yet widespread, probably due to the lack of access to flow cytometers or the lack of knowledge about the potential of this technique. One of the goals of this review is to attempt to mitigate this latter circumstance. We are convinced that in the near future, the availability of commercial kits should increase the use of this technique in the clinical microbiology laboratory.
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Affiliation(s)
- A Alvarez-Barrientos
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
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19
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Rapid and quantitative analysis of metabolites in fermentor broths using pyrolysis mass spectrometry with supervised learning: application to the screening of Penicillium chrysogenum fermentations for the overproduction of penicillins. Anal Chim Acta 1995. [DOI: 10.1016/0003-2670(95)00170-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Chung JD, Conner S, Stephanopoulos G. Flow cytometric study of differentiating cultures of Bacillus subtilis. CYTOMETRY 1995; 20:324-33. [PMID: 7587720 DOI: 10.1002/cyto.990200408] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report on 1) the development of a flow cytometry-based technique for detecting beta-galactosidase in differentiating cultures of Bacillus subtilis and 2) the application of this technique in the study of early developmental gene expression. The problems associated with generating detectable signals (despite the small size of B. subtilis cells) have been overcome using the fluorogenic substrate 5-octanolyaminofluorescein di-beta-D-galactopyranoside (C8-FDG). Additionally, to control for background fluorescence during the staining process, we included a control population in the C8-FDG staining mixture that consists of cells devoid of the lacZ gene prestained with another dye, PKH26. The distinct emission spectra of C8-fluorescein and PKH26 allow nonspecific C8-FDG staining in this control population to be monitored using two-color analysis. This technique has been applied in the study of developmental gene expression in sporulating cultures of B. subtilis, and it has been found that such cultures are heterogeneous, comprising two cell populations. One population is induced for expression of early sporulation genes, which is determined using lacZ fusions, whereas the other remains uninduced. These results have allowed us to understand better the patterns of gene expression exhibited by wild-type and mutant cultures early during the development process of spore formation.
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Affiliation(s)
- J D Chung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, USA
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21
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Plovins A, Alvarez AM, Ibañez M, Molina M, Nombela C. Use of fluorescein-di-beta-D-galactopyranoside (FDG) and C12-FDG as substrates for beta-galactosidase detection by flow cytometry in animal, bacterial, and yeast cells. Appl Environ Microbiol 1994; 60:4638-41. [PMID: 7811104 PMCID: PMC202038 DOI: 10.1128/aem.60.12.4638-4641.1994] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Fluorescein-di-beta-D-galactopyranoside (FDG) was found to be a useful substrate for beta-galactosidase detection by flow cytometry in gram-negative bacteria, since it entered viable cells and gave a fluorescence emission proportional to the enzymatic activity. C12-FDG, a more lipophilic derivative, gave a very poor signal because of the lack of penetration. On the contrary, C12-FDG was more sensitive than FDG for beta-galactosidase activity determinations in animal cells. In contrast to previous reports, C12-FDG did not enter viable yeast cells, so that the use of the substrate required cell permeabilization. Without this treatment, C12-FDG penetrates only nonviable yeast cells that may occur in populations expressing beta-galactosidase.
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Affiliation(s)
- A Plovins
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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22
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Hydrolysis of a novel lysosomotropic enzyme substrate for beta-galactosidase within intact cells. J Lipid Res 1994. [DOI: 10.1016/s0022-2275(20)40085-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Bylund JE, Zhang L, Haines MA, Higgins ML, Piggot PJ. Analysis by fluorescence microscopy of the development of compartment-specific gene expression during sporulation of Bacillus subtilis. J Bacteriol 1994; 176:2898-905. [PMID: 8188591 PMCID: PMC205445 DOI: 10.1128/jb.176.10.2898-2905.1994] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The use of a fluorogenic substrate, 5-octanoylaminofluorescein-di-beta-D-galactopyranoside, for beta-galactosidase has made it possible to visualize enzyme activity in individual cells of sporulating populations of Bacillus subtilis by fluorescence microscopy. lacZ fusions to different sporulation-associated genes have been used to investigate the cell compartmentalization of gene expression during sporulation. A strain with a lacZ fusion to sspA, a gene which is transcribed by E-sigma G at a late stage of sporulation, displayed predominantly compartment-specific fluorescence. Expression of the early-expressed spoIIA locus, which includes the structural gene for sigma F, was seen not to be compartmentalized. Populations of strains with lacZ fusions to gpr and dacF, genes which are transcribed by E-sigma F at intermediate stages of sporulation, included some organisms showing uncompartmentalized fluorescence and others showing compartment-specific fluorescence; the proportion showing compartment-specific fluorescence increased in samples taken later in sporulation. Several possible explanations of the results obtained with gpr and dacF are considered. A plausible interpretation is that sigma F activity is initially not compartmentalized and becomes compartmentalized as sporulation progresses. The progression to compartmentalization does not require the activities of the sporulation-specific factor sigma E or sigma G but may require some product of sigma F activity.
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Affiliation(s)
- J E Bylund
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
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24
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Miao F, Todd P, Kompala DS. A single-cell assay of ?-galactosidase in recombinantEscherichia coli using flow cytometry. Biotechnol Bioeng 1993; 42:708-15. [DOI: 10.1002/bit.260420605] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Degelau A, Freitag R, Linz F, Middendorf C, Scheper T, Bley T, Müller S, Stoll P, Reardon KF. Immuno- and flow cytometric analytical methods for biotechnological research and process monitoring. J Biotechnol 1992; 25:115-44. [PMID: 1368458 DOI: 10.1016/0168-1656(92)90112-m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this article, the applications of immunoanalysis and flow cytometry for research and process monitoring in biotechnology are discussed. Brief reviews of the two analytical methods are followed by descriptions of actual applications in various areas of biotechnology. In the case of immunoanalysis, emphasis is placed on systems for on-line bioprocess monitoring, and examples are given for a thermostable pullulanase, a mouse IgG, and antithrombin III. Although flow cytometry is not currently an on-line analytical technique, its value as an off-line method is illustrated by examples of the measurement of shear stress effects, lipid content, and sterol content.
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Affiliation(s)
- A Degelau
- Institut für Technische Chemie, Universität Hannover, Germany
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26
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Eitzman PD, Srienc F. Dynamics of activation of a galactose-inducible promoter in Saccharomyces cerevisiae. J Biotechnol 1991; 21:63-81. [PMID: 1367691 DOI: 10.1016/0168-1656(91)90261-s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have investigated the dynamics of accumulation of the Escherichia coli beta-galactosidase (beta-gal) under the control of a promoter containing the galactose-inducible upstream activating sequence (UASG) in single Saccharomyces cerevisiae cells. The accumulation of beta-gal in single cells following the addition of the inducer, galactose, was determined using an in situ combined DNA and immunofluorescent stain in conjunction with flow cytometry. Two strains were studied, D603/2i, which has two copies of the galactose-inducible fusion gene integrated into its genome, and D603/pLGSD5, which carries a 2 microns-based plasmid containing the fusion gene. Flow cytometry results indicate that accumulation of beta-gal within the first three hours following the addition of galactose is dependent on cell cycle position. Two proposed mechanisms explaining this observed behavior are (1) the cell-cycle-dependent synthesis of the fusion protein or (2) the unequal partitioning of the protein at cell division between mother and daughter cells.
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Affiliation(s)
- P D Eitzman
- Institute of Advanced Studies in Biological Process Technology and Materials Science, University of Minnesota, St. Paul 55108
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27
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Kell DB, Ryder HM, Kaprelyants AS, Westerhoff HV. Quantifying heterogeneity: flow cytometry of bacterial cultures. Antonie Van Leeuwenhoek 1991; 60:145-58. [PMID: 1725477 DOI: 10.1007/bf00430362] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Flow cytometry is a technique which permits the characterisation of individual cells in populations, in terms of distributions in their properties such as DNA content, protein content, viability, enzyme activities and so on. We review the technique, and some of its recent applications to microbiological problems. It is concluded that cellular heterogeneity, in both batch and continuous axenic cultures, is far greater than is normally assumed. This has important implications for the quantitative analysis of microbial processes.
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Affiliation(s)
- D B Kell
- Department of Biological Sciences, University College of Wales, Aberystwyth, UK
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28
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Nir R, Yisraeli Y, Lamed R, Sahar E. Flow cytometry sorting of viable bacteria and yeasts according to beta-galactosidase activity. Appl Environ Microbiol 1990; 56:3861-6. [PMID: 2128011 PMCID: PMC185080 DOI: 10.1128/aem.56.12.3861-3866.1990] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We describe a novel method for quantitative measurement of beta-galactosidase (beta-gal) levels in bacteria and yeasts by using flow cytometry, a method which allows viable microbial cells to be sorted on the basis of the expressed activity and to be recultivated. The method is based on encapsulating single cells in agarose microbeads 20 to 30 microns in diameter and analyzing the beta-gal activity of the colonies that develop (containing several hundred cells) by using the fluorogenic substrate fluorescein-di-beta-D-galactopyranoside (FDG). Three strains of Escherichia coli, containing different levels of beta-gal, served as a model system. A high degree of correlation was found between the average fluorescence measured per bead and the level of the enzyme in extracts of the respective strain. Although the use of FDG necessitates cell permeabilization, conditions were found under which a small part of each colony remained viable, yet most of the enzyme was exposed to the substrate. This allowed sorting of microcolonies and plating with close to 100% efficiency. The potential of the technique was demonstrated by selecting beta-gal-positive cells from an artificial mixture of beta-gal-positive and beta-gal-negative E. coli strains.
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Affiliation(s)
- R Nir
- Department of Biotechnology, Tel-Aviv University, Israel
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29
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Eitzman PD, Hendrick JL, Srienc F. Quantitative immunofluorescence in single Saccharomyces cerevisiae cells. CYTOMETRY 1989; 10:475-83. [PMID: 2504565 DOI: 10.1002/cyto.990100417] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have developed a staining procedure that allows the simultaneous determination of intracellular amounts of DNA and an antigen in Saccharomyces cerevisiae with a single laser flow cytometer. The antigen, beta-galactosidase from a cloned lacZ gene, is inducible and is detected with an indirect immunofluorescent stain. Cell preparation procedures, specifically cell fixation and cell wall removal, have significant effects on measured levels of immunofluorescence and have been optimized to prevent cell loss and maximize immunofluorescence. Average immunofluorescent levels of cell populations expressing different levels of beta-galactosidase show excellent correlation with measurements of average beta-galactosidase activity per cell based on cleavage of o-nitrophenyl-beta-D-galactopyranoside. Experiments with yeast populations containing various numbers of copies of the cloned gene indicate that the relationship between immunofluorescence and antigen content also holds at the single-cell level. Correlated measurements of DNA and beta-galactosidase content on a single-cell level permit the investigation of cellular enzyme content as a function of cell cycle position under various conditions. The procedure can be easily modified to detect other antigens by changing the primary antibody used.
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Affiliation(s)
- P D Eitzman
- Institute for Advanced Studies in Biological Process Technology, University of Minnesota, St. Paul 55108
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