1
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Kraus S, Fletcher ML, Łapińska U, Chawla K, Baker E, Attrill EL, O'Neill P, Farbos A, Jeffries A, Galyov EE, Korbsrisate S, Barnes KB, Harding SV, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Phage-induced efflux down-regulation boosts antibiotic efficacy. PLoS Pathog 2024; 20:e1012361. [PMID: 38941361 PMCID: PMC11239113 DOI: 10.1371/journal.ppat.1012361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/11/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms at the basis of these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage ΦBp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is facilitated by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations.
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Affiliation(s)
- Samuel Kraus
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Megan L Fletcher
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Krina Chawla
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Evan Baker
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Audrey Farbos
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Aaron Jeffries
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Thailand
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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2
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Attrill EL, Łapińska U, Westra ER, Harding SV, Pagliara S. Slow growing bacteria survive bacteriophage in isolation. ISME COMMUNICATIONS 2023; 3:95. [PMID: 37684358 PMCID: PMC10491631 DOI: 10.1038/s43705-023-00299-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The interactions between bacteria and bacteriophage have important roles in the global ecosystem; in turn changes in environmental parameters affect the interactions between bacteria and phage. However, there is a lack of knowledge on whether clonal bacterial populations harbour different phenotypes that respond to phage in distinct ways and whether the abundance of such phenotypes within bacterial populations is affected by variations in environmental parameters. Here we study the impact of variations in nutrient availability, bacterial growth rate and phage abundance on the interactions between the phage T4 and individual Escherichia coli cells confined in spatial refuges. Surprisingly, we found that fast growing bacteria survive together with all of their clonal kin cells, whereas slow growing bacteria survive in isolation. We also discovered that the number of bacteria that survive in isolation decreases at increasing phage doses possibly due to lysis inhibition in the presence of secondary adsorptions. We further show that these changes in the phenotypic composition of the E. coli population have important consequences on the bacterial and phage population dynamics and should therefore be considered when investigating bacteria-phage interactions in ecological, health or food production settings in structured environments.
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Affiliation(s)
- Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK.
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3
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Zhang Y, Kepiro I, Ryadnov MG, Pagliara S. Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes. Microbiol Spectr 2023; 11:e0366722. [PMID: 36651776 PMCID: PMC9927147 DOI: 10.1128/spectrum.03667-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
With the spread of multidrug-resistant bacteria, there has been an increasing focus on molecular classes that have not yet yielded an antibiotic. A key capability for assessing and prescribing new antibacterial treatments is to compare the effects antibacterial agents have on bacterial growth at a phenotypic, single-cell level. Here, we combined time-lapse microscopy with microfluidics to investigate the concentration-dependent killing kinetics of stationary-phase Escherichia coli cells. We used antibacterial agents from three different molecular classes, β-lactams and fluoroquinolones, with the known antibiotics ampicillin and ciprofloxacin, respectively, and a new experimental class, protein Ψ-capsids. We found that bacterial cells elongated when treated with ampicillin and ciprofloxacin used at their minimum inhibitory concentration (MIC). This was in contrast to Ψ-capsids, which arrested bacterial elongation within the first two hours of treatment. At concentrations exceeding the MIC, all the antibacterial agents tested arrested bacterial growth within the first 2 h of treatment. Further, our single-cell experiments revealed differences in the modes of action of three different agents. At the MIC, ampicillin and ciprofloxacin caused the lysis of bacterial cells, whereas at higher concentrations, the mode of action shifted toward membrane disruption. The Ψ-capsids killed cells by disrupting their membranes at all concentrations tested. Finally, at increasing concentrations, ampicillin and Ψ-capsids reduced the fraction of the population that survived treatment in a viable but nonculturable state, whereas ciprofloxacin increased this fraction. This study introduces an effective capability to differentiate the killing kinetics of antibacterial agents from different molecular classes and offers a high content analysis of antibacterial mechanisms at the single-cell level. IMPORTANCE Antibiotics act against bacterial pathogens by inhibiting their growth or killing them directly. Different modes of action determine different antibacterial responses, whereas phenotypic differences in bacteria can challenge the efficacy of antibiotics. Therefore, it is important to be able to differentiate the concentration-dependent killing kinetics of antibacterial agents at a single-cell level, in particular for molecular classes which have not yielded an antibiotic before. Here, we measured single-cell responses using microfluidics-enabled imaging, revealing that a novel class of antibacterial agents, protein Ψ-capsids, arrests bacterial elongation at the onset of treatment, whereas elongation continues for cells treated with β-lactam and fluoroquinolone antibiotics. The study advances our current understanding of antibacterial function and offers an effective strategy for the comparative design of new antibacterial therapies, as well as clinical antibiotic susceptibility testing.
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Affiliation(s)
- Yuewen Zhang
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- National Physical Laboratory, Teddington, United Kingdom
| | - Ibolya Kepiro
- National Physical Laboratory, Teddington, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Teddington, United Kingdom
- Department of Physics, King’s College London, London, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
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4
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Attrill EL, Claydon R, Łapińska U, Recker M, Meaden S, Brown AT, Westra ER, Harding SV, Pagliara S. Individual bacteria in structured environments rely on phenotypic resistance to phage. PLoS Biol 2021; 19:e3001406. [PMID: 34637438 PMCID: PMC8509860 DOI: 10.1371/journal.pbio.3001406] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria–phage interactions in naturally structured environments. Bacteriophages represent a promising avenue to overcome the current antibiotic resistance crisis, but evolution of phage resistance remains a concern. This study shows that in the presence of spatial refuges, genetic resistance to phage is less of a problem than commonly assumed, but the persistence of genetically susceptible bacteria suggests that eradicating bacterial pathogens from structured environments may require combined phage-antibiotic therapies.
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Affiliation(s)
- Erin L. Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rory Claydon
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Sean Meaden
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Aidan T. Brown
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Edze R. Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
| | - Sarah V. Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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5
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Goode O, Smith A, Łapińska U, Bamford R, Kahveci Z, Glover G, Attrill E, Carr A, Metz J, Pagliara S. Heterologous Protein Expression Favors the Formation of Protein Aggregates in Persister and Viable but Nonculturable Bacteria. ACS Infect Dis 2021; 7:1848-1858. [PMID: 34000805 DOI: 10.1021/acsinfecdis.1c00154] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Environmental and intracellular stresses can perturb protein homeostasis and trigger the formation and accumulation of protein aggregates. It has been recently suggested that the level of protein aggregates accumulated in bacteria correlates with the frequency of persister and viable but nonculturable cells that transiently survive treatment with multiple antibiotics. However, these findings have often been obtained employing fluorescent reporter strains. This enforced heterologous protein expression facilitates the visualization of protein aggregates but could also trigger the formation and accumulation of protein aggregates. Using microfluidics-based single-cell microscopy and a library of green fluorescent protein reporter strains, we show that heterologous protein expression favors the formation of protein aggregates. We found that persister and viable but nonculturable bacteria surviving treatment with antibiotics are more likely to contain protein aggregates and downregulate the expression of heterologous proteins. Our data also suggest that such aggregates are more basic with respect to the rest of the cell. These findings provide evidence for a strong link between heterologous protein expression, protein aggregation, intracellular pH, and phenotypic survival to antibiotics, suggesting that antibiotic treatments against persister and viable but nonculturable cells could be developed by modulating protein aggregation and pH regulation.
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Affiliation(s)
- Olivia Goode
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Ashley Smith
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Rosemary Bamford
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Zehra Kahveci
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Georgina Glover
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Erin Attrill
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Alice Carr
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Jeremy Metz
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
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6
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Morrish R, Yim KHW, Pagliara S, Palombo F, Chahwan R, Stone N. Single Cell Label-Free Probing of Chromatin Dynamics During B Lymphocyte Maturation. Front Cell Dev Biol 2021; 9:646616. [PMID: 33842468 PMCID: PMC8033168 DOI: 10.3389/fcell.2021.646616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/08/2021] [Indexed: 01/11/2023] Open
Abstract
Large-scale intracellular signaling during developmental growth or in response to environmental alterations are largely orchestrated by chromatin within the cell nuclei. Chemical and conformational modifications of the chromatin architecture are critical steps in the regulation of differential gene expression and ultimately cell fate determination. Therefore, establishing chemical properties of the nucleus could provide key markers for phenotypic characterization of cellular processes on a scale of individual cells. Raman microscopy is a sensitive technique that is capable of probing single cell chemical composition—and sub-cellular regions—in a label-free optical manner. As such, it has great potential in both clinical and basic research. However, perceived limitations of Raman spectroscopy such as low signal intensity and the difficulty in linking alterations in vibrational signals directly with ensuing biological effects have hampered advances in the field. Here we use immune B lymphocyte development as a model to assess chromatin and transcriptional changes using confocal Raman microscopy in combination with microfluidic devices and correlative transcriptomics, thereby linking changes in chemical and structural properties to biological outcomes. Live B lymphocytes were assessed before and after maturation. Multivariate analysis was applied to distinguish cellular components within each cell. The spectral differences between non-activated and activated B lymphocytes were then identified, and their correlation with known intracellular biological changes were assessed in comparison to conventional RNA-seq analysis. Our data shows that spectral analysis provides a powerful tool to study gene activation that can complement conventional molecular biology techniques and opens the way for mapping the dynamics in the biochemical makeup of individual cells.
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Affiliation(s)
- Rikke Morrish
- School of Physics and Astronomy, University of Exeter, Exeter, United Kingdom.,Living Systems Institute and School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Kevin Ho Wai Yim
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Stefano Pagliara
- Living Systems Institute and School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Francesca Palombo
- School of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nicholas Stone
- School of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
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7
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The concept of protein folding/unfolding and its impacts on human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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8
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Cai SC, Shen YX, Io CW. The mesoscopic collective motion of self-propelling active particle suspension confined in two-dimensional micro-channel. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:095101. [PMID: 31722320 DOI: 10.1088/1361-648x/ab5772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mesoscopic collective motion of self-propelling active particle suspension confined in high aspect ratio two-dimensional micro-channel is numerically studied through coupled [Formula: see text] equation by considering background thermal fluctuation, inter-particle interaction, self-propulsion and micro-channel confinement. Both the self-propulsion and micro-channel confinement are the factors driving the system away from equilibrium and sustaining heterogeneous motion. In such system, the propulsion induced particle accumulation around the channel walls is a universal phenomenon with spatial heterogeneity, where large fraction of particles are caged inside the accumulated cluster with local oscillation coexisting with few fast propelling particles in the center region. Although the formation mechanism of the induced accumulation is well studied, post the cluster formation, how the cluster evolves and its dynamical properties is rarely discussed. Based on the merits of [Formula: see text] equation, the dynamical evolution of induced accumulation is revealed by particle trajectories. It is found that the induced accumulation can be dissociated through the slow re-orientation process of few jammed particles. By using the idea of force chain network, how the transverse confinement couples the transverse displacement with the longitudinal displacement is evidenced. It is further verified by the statistical measurement of correlation probability between transverse and longitudinal displacements. The suppressed displacements in both directions is the origin leading to the slow dynamics of cluster evolution. Temporally, within the orientational relaxation time, this system exhibits non-trivial anomalous diffusion under the competition between the counter effects of self-propulsion (enhanced diffusion) and micro-channel confinement (suppressed diffusion). Additionally, by considering the orientational coupling, the deep hysteresis of accumulation has been found even for very weak orientational coupling strength.
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Affiliation(s)
- Sin-Cen Cai
- Many-body System Laboratory, Department of Physics, National Chung-Cheng University, Chiayi 62102, Taiwan, Republic of China. Department of Physics, Republic of China Military Academy, Kaohsiung, 83059, Taiwan, Republic of China
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9
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Kepiro IE, Marzuoli I, Hammond K, Ba X, Lewis H, Shaw M, Gunnoo SB, De Santis E, Łapińska U, Pagliara S, Holmes MA, Lorenz CD, Hoogenboom BW, Fraternali F, Ryadnov MG. Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters. ACS NANO 2020; 14:1609-1622. [PMID: 31794180 DOI: 10.1021/acsnano.9b06814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.
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Affiliation(s)
- Ibolya E Kepiro
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Irene Marzuoli
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Katharine Hammond
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Xiaoliang Ba
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Helen Lewis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Michael Shaw
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Computer Science , University College London , London , WC1 6BT , U.K
| | - Smita B Gunnoo
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Emiliana De Santis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Urszula Łapińska
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Stefano Pagliara
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Mark A Holmes
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Christian D Lorenz
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
| | - Bart W Hoogenboom
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
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10
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Łapińska U, Glover G, Capilla-Lasheras P, Young AJ, Pagliara S. Bacterial ageing in the absence of external stressors. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180442. [PMID: 31587633 PMCID: PMC6792439 DOI: 10.1098/rstb.2018.0442] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/03/2022] Open
Abstract
Evidence of ageing in the bacterium Escherichia coli was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in E. coli in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the 'maternal old pole' progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Urszula Łapińska
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Georgina Glover
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Pablo Capilla-Lasheras
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J. Young
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Stefano Pagliara
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
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11
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Tottori S, Misiunas K, Keyser UF, Bonthuis DJ. Nonlinear Electrophoresis of Highly Charged Nonpolarizable Particles. PHYSICAL REVIEW LETTERS 2019; 123:014502. [PMID: 31386414 DOI: 10.1103/physrevlett.123.014502] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 05/28/2023]
Abstract
Nonlinear field dependence of electrophoresis in high fields has been investigated theoretically, yet experimental studies have failed to reach consensus on the effect. In this Letter, we present a systematic study on the nonlinear electrophoresis of highly charged submicron particles in applied electric fields of up to several kV/cm. First, the particles are characterized in the low-field regime at different salt concentrations and the surface charge density is estimated. Subsequently, we use microfluidic channels and video tracking to systematically characterize the nonlinear response over a range of field strengths. Using velocity measurements on the single particle level, we prove that nonlinear effects are present at electric fields and surface charge densities that are accessible in practical conditions. Finally, we show that nonlinear behavior leads to unexpected particle trapping in channels.
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Affiliation(s)
- Soichiro Tottori
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Karolis Misiunas
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Douwe Jan Bonthuis
- Institute of Theoretical and Computational Physics, Graz University of Technology, 8010 Graz, Austria
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12
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Misiunas K, Keyser UF. Density-Dependent Speed-up of Particle Transport in Channels. PHYSICAL REVIEW LETTERS 2019; 122:214501. [PMID: 31283305 DOI: 10.1103/physrevlett.122.214501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 06/09/2023]
Abstract
Collective transport through channels shows surprising properties under one-dimensional confinement: particles in a single file exhibit subdiffusive behavior, while liquid confinement causes distance-independent correlations between the particles. Such interactions in channels are well studied for passive Brownian motion, but driven transport remains largely unexplored. Here, we demonstrate gating of transport due to a speed-up effect for actively driven particle transport through microfluidic channels. We prove that particle velocity increases with particle density in the channel due to hydrodynamic interactions under electrophoretic and gravitational forces. Numerical models demonstrate that the observed speed-up of transport originates from a hydrodynamic pistonlike effect. Our discovery is fundamentally important for understanding protein channels and transport through porous materials and for designing novel sensors and filters.
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Affiliation(s)
- Karolis Misiunas
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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13
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Bolze H, Erfle P, Riewe J, Bunjes H, Dietzel A, Burg TP. A Microfluidic Split-Flow Technology for Product Characterization in Continuous Low-Volume Nanoparticle Synthesis. MICROMACHINES 2019; 10:mi10030179. [PMID: 30857317 PMCID: PMC6470898 DOI: 10.3390/mi10030179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
A key aspect of microfluidic processes is their ability to perform chemical reactions in small volumes under continuous flow. However, a continuous process requires stable reagent flow over a prolonged period. This can be challenging in microfluidic systems, as bubbles or particles easily block or alter the flow. Online analysis of the product stream can alleviate this problem by providing a feedback signal. When this signal exceeds a pre-defined range, the process can be re-adjusted or interrupted to prevent contamination. Here we demonstrate the feasibility of this concept by implementing a microfluidic detector downstream of a segmented-flow system for the synthesis of lipid nanoparticles. To match the flow rate through the detector to the measurement bandwidth independent of the synthesis requirements, a small stream is sidelined from the original product stream and routed through a measuring channel with 2 × 2 µm cross-section. The small size of the measuring channel prevents the entry of air plugs, which are inherent to our segmented flow synthesis device. Nanoparticles passing through the small channel were detected and characterized by quantitative fluorescence measurements. With this setup, we were able to count single nanoparticles. This way, we were able to detect changes in the particle synthesis affecting the size, concentration, or velocity of the particles in suspension. We envision that the flow-splitting scheme demonstrated here can be transferred to detection methods other than fluorescence for continuous monitoring and feedback control of microfluidic nanoparticle synthesis.
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Affiliation(s)
- Holger Bolze
- Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany.
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig 38106, Germany.
| | - Peer Erfle
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig 38106, Germany.
- Institute of Microtechnology, Technische Universität Braunschweig, Braunschweig 38124, Germany.
| | - Juliane Riewe
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig 38106, Germany.
- Institut für Pharmazeutische Technologie, Technische Universität Braunschweig, Braunschweig 38106, Germany.
| | - Heike Bunjes
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig 38106, Germany.
- Institut für Pharmazeutische Technologie, Technische Universität Braunschweig, Braunschweig 38106, Germany.
| | - Andreas Dietzel
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig 38106, Germany.
- Institute of Microtechnology, Technische Universität Braunschweig, Braunschweig 38124, Germany.
| | - Thomas P Burg
- Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany.
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, 64283 Darmstadt, Germany.
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14
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Zuo Y, Zhu X, Shi Y, Liang L, Yang Y. Light Manipulation in Inhomogeneous Liquid Flow and Its Application in Biochemical Sensing. MICROMACHINES 2018; 9:mi9040163. [PMID: 30424097 PMCID: PMC6187708 DOI: 10.3390/mi9040163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 02/06/2023]
Abstract
Light manipulation has always been the fundamental subject in the field of optics since centuries ago. Traditional optical devices are usually designed using glasses and other materials, such as semiconductors and metals. Optofluidics is the combination of microfluidics and optics, which brings a host of new advantages to conventional solid systems. The capabilities of light manipulation and biochemical sensing are inherent alongside the emergence of optofluidics. This new research area promotes advancements in optics, biology, and chemistry. The development of fast, accurate, low-cost, and small-sized biochemical micro-sensors is an urgent demand for real-time monitoring. However, the fluid flow in the on-chip sensor is usually non-uniformed, which is a new and emerging challenge for the accuracy of optical detection. It is significant to reveal the principle of light propagation in an inhomogeneous liquid flow and the interaction between biochemical samples and light in flowing liquids. In this review, we summarize the current state of optofluidic lab-on-a-chip techniques from the perspective of light modulation by the unique dynamic properties of fluid in heterogeneous media, such as diffusion, heat transfer, and centrifugation etc. Furthermore, this review introduces several novel photonic phenomena in an inhomogeneous liquid flow and demonstrates their application in biochemical sensing.
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Affiliation(s)
- Yunfeng Zuo
- School of Physics and Technology, Wuhan University, Wuhan 430070, China.
| | - Xiaoqiang Zhu
- School of Physics and Technology, Wuhan University, Wuhan 430070, China.
| | - Yang Shi
- School of Physics and Technology, Wuhan University, Wuhan 430070, China.
| | - Li Liang
- School of Physics and Technology, Wuhan University, Wuhan 430070, China.
| | - Yi Yang
- School of Physics and Technology, Wuhan University, Wuhan 430070, China.
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15
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Bamford RA, Smith A, Metz J, Glover G, Titball RW, Pagliara S. Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy. BMC Biol 2017; 15:121. [PMID: 29262826 PMCID: PMC5738893 DOI: 10.1186/s12915-017-0465-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/30/2017] [Indexed: 11/29/2022] Open
Abstract
Background Clonal microbial populations often harbor rare phenotypic variants that are typically hidden within the majority of the remaining cells, but are crucial for the population’s resilience to external perturbations. Persister and viable but non-culturable (VBNC) cells are two important clonal bacterial subpopulations that can survive antibiotic treatment. Both persister and VBNC cells pose a serious threat to human health. However, unlike persister cells, which quickly resume growth following drug removal, VBNC cells can remain non-growing for prolonged periods of time, thus eluding detection via traditional microbiological assays. Therefore, understanding the molecular mechanisms underlying the formation of VBNC cells requires the characterization of the clonal population with single-cell resolution. A combination of microfluidics, time-lapse microscopy, and fluorescent reporter strains offers the perfect platform for investigating individual cells while manipulating their environment. Methods Here, we report a novel single-cell approach to investigate VBNC cells. We perform drug treatment, bacterial culturing, and live/dead staining in series by using transcriptional reporter strains and novel adaptations to the mother machine technology. Since we track each cell throughout the experiment, we are able to quantify the size, morphology and fluorescence that each VBNC cell displayed before, during and after drug treatment. Results We show that VBNC cells are not dead or dying cells but share similar phenotypic features with persister cells, suggesting a link between these two subpopulations, at least in the Escherichia coli strain under investigation. We strengthen this link by demonstrating that, before drug treatment, both persister and VBNC cells can be distinguished from the remainder of the population by their lower fluorescence when using a reporter strain for tnaC, encoding the leader peptide of the tnaCAB operon responsible for tryptophan metabolism. Conclusion Our data demonstrates the suitability of our approach for studying the physiology of non-growing cells in response to external perturbations. Our approach will allow the identification of novel biomarkers for the isolation of VBNC and persister cells and will open new opportunities to map the detailed biochemical makeup of these clonal subpopulations. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0465-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosemary A Bamford
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, UK.,Living Systems Institute, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - Ashley Smith
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, UK.,Living Systems Institute, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - Jeremy Metz
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, UK.,Living Systems Institute, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - Georgina Glover
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, UK.,Living Systems Institute, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | | | - Stefano Pagliara
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, UK. .,Living Systems Institute, University of Exeter, Exeter, Devon, EX4 4QD, UK.
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16
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Tan Y, Gladrow J, Keyser UF, Dagdug L, Pagliara S. Particle transport across a channel via an oscillating potential. Phys Rev E 2017; 96:052401. [PMID: 29347788 DOI: 10.1103/physreve.96.052401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 06/07/2023]
Abstract
Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we study particle transport through a channel coupled with an energy well that oscillates its position between the two entrances of the channel. We optimize particle transport across the channel by adjusting the oscillation frequency. At the optimal oscillation frequency, the translocation rate through the channel is a hundred times higher with respect to free diffusion across the channel. Our findings reveal the effect of time-dependent potentials on particle transport across a channel and will be relevant for membrane transport and microfluidics application.
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Affiliation(s)
- Yizhou Tan
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jannes Gladrow
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Leonardo Dagdug
- Departamento de Fisica, Universidad Autonoma Metropolitana-Iztapalapa, 09340 Mexico City, Mexico
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom and Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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17
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Locatelli E, Pierno M, Baldovin F, Orlandini E, Tan Y, Pagliara S. Single-File Escape of Colloidal Particles from Microfluidic Channels. PHYSICAL REVIEW LETTERS 2016; 117:038001. [PMID: 27472142 DOI: 10.1103/physrevlett.117.038001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 06/06/2023]
Abstract
Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount to quantify the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy, and theoretical analysis we uncover the self-similar character of the escape process and provide closed-formula evaluations of the escape time. We find that the escape time scales inversely with the diffusion coefficient of the last particle to leave the channel. Importantly, we find that at the investigated microscale, bias forces as tiny as 10^{-15} N determine the magnitude of the escape time by drastically reducing interparticle collisions. Our findings provide crucial guidelines to optimize the design of micro- and nanodevices for a variety of applications including drug delivery, particle filtering, and transport in geometrical constrictions.
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Affiliation(s)
- Emanuele Locatelli
- Dipartimento di Fisica e Astronomia "G. Galilei" (DFA) and Sezione CNISM, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Matteo Pierno
- Dipartimento di Fisica e Astronomia "G. Galilei" (DFA) and Sezione CNISM, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Fulvio Baldovin
- Dipartimento di Fisica e Astronomia "G. Galilei" (DFA), Sezione INFN and Sezione CNISM, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia "G. Galilei" (DFA), Sezione INFN and Sezione CNISM, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Yizhou Tan
- Cavendish Laboratory, Cambridge CB30HE, United Kingdom
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18
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Misiunas K, Pagliara S, Lauga E, Lister JR, Keyser UF. Nondecaying Hydrodynamic Interactions along Narrow Channels. PHYSICAL REVIEW LETTERS 2015; 115:038301. [PMID: 26230830 DOI: 10.1103/physrevlett.115.038301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 06/04/2023]
Abstract
Particle-particle interactions are of paramount importance in every multibody system as they determine the collective behavior and coupling strength. Many well-known interactions such as electrostatic, van der Waals, or screened Coulomb interactions, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here we confine two particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance independent in these channels. This finding is of fundamental importance for the interpretation of experiments where dense mixtures of particles or molecules diffuse through finite length, water-filled channels or pore networks.
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Affiliation(s)
- Karolis Misiunas
- Cavendish Laboratory, University of Cambridge, United Kingdom and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Stefano Pagliara
- Cavendish Laboratory, University of Cambridge, United Kingdom and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Eric Lauga
- Cavendish Laboratory, University of Cambridge, United Kingdom and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - John R Lister
- Cavendish Laboratory, University of Cambridge, United Kingdom and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, United Kingdom and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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19
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Pagliara S, Dettmer SL, Keyser UF. Channel-facilitated diffusion boosted by particle binding at the channel entrance. PHYSICAL REVIEW LETTERS 2014; 113:048102. [PMID: 25105657 DOI: 10.1103/physrevlett.113.048102] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Indexed: 06/03/2023]
Abstract
We investigate single-file diffusion of Brownian particles in arrays of closely confining microchannels permeated by a variety of attractive optical potentials and connecting two baths with equal particle concentration. We simultaneously test free diffusion in the channel, diffusion in optical traps coupled in the center of the channel, and diffusion in traps extending into the baths. We found that both classes of attractive optical potentials enhance the translocation rate through the channel with respect to free diffusion. Surprisingly, for the latter class of potentials we measure a 40-fold enhancement in the translocation rate with respect to free diffusion and find a sublinear power law dependence of the translocation rate on the average number of particles in the channel. Our results reveal the function of particle binding at the channel entrances for diffusive transport and open the way to a better understanding of membrane transport and design of synthetic membranes with enhanced diffusion rate.
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20
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Dettmer SL, Pagliara S, Misiunas K, Keyser UF. Anisotropic diffusion of spherical particles in closely confining microchannels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:062305. [PMID: 25019774 DOI: 10.1103/physreve.89.062305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 06/03/2023]
Abstract
We present here the measurement of the diffusivity of spherical particles closely confined by narrow microchannels. Our experiments yield a two-dimensional map of the position-dependent diffusion coefficients parallel and perpendicular to the channel axis with a resolution down to 129 nm. The diffusivity was measured simultaneously in the channel interior, the bulk reservoirs, as well as the channel entrance region. In the channel interior we found strongly anisotropic diffusion. While the perpendicular diffusion coefficient close to the confining walls decreased down to approximately 25% of the value on the channel axis, the parallel diffusion coefficient remained constant throughout the entire channel width. In addition to the experiment, we performed finite element simulations for the diffusivity in the channel interior and found good agreement with the measurements. Our results reveal the distinctive influence of strong confinement on Brownian motion, which is of significance to microfluidics as well as quantitative models of facilitated membrane transport.
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Affiliation(s)
- Simon L Dettmer
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Stefano Pagliara
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Karolis Misiunas
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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21
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Dettmer SL, Keyser UF, Pagliara S. Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:023708. [PMID: 24593372 DOI: 10.1063/1.4865552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces.
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Affiliation(s)
- Simon L Dettmer
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Stefano Pagliara
- Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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22
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Pagliara S, Schwall C, Keyser UF. Optimizing diffusive transport through a synthetic membrane channel. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:844-9. [PMID: 23161732 PMCID: PMC3594580 DOI: 10.1002/adma.201203500] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/11/2012] [Indexed: 05/02/2023]
Affiliation(s)
- Stefano Pagliara
- Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK.
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23
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Viscoelastic properties of differentiating blood cells are fate- and function-dependent. PLoS One 2012; 7:e45237. [PMID: 23028868 PMCID: PMC3459925 DOI: 10.1371/journal.pone.0045237] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/20/2012] [Indexed: 11/19/2022] Open
Abstract
Although cellular mechanical properties are known to alter during stem cell differentiation, understanding of the functional relevance of such alterations is incomplete. Here, we show that during the course of differentiation of human myeloid precursor cells into three different lineages, the cells alter their viscoelastic properties, measured using an optical stretcher, to suit their ultimate fate and function. Myeloid cells circulating in blood have to be advected through constrictions in blood vessels, engendering the need for compliance at short time-scales (<seconds). Intriguingly, only the two circulating myeloid cell types have increased short time scale compliance and flow better through microfluidic constrictions. Moreover, all three differentiated cell types reduce their steady-state viscosity by more than 50% and show over 140% relative increase in their ability to migrate through tissue-like pores at long time-scales (>minutes), compared to undifferentiated cells. These findings suggest that reduction in steady-state viscosity is a physiological adaptation for enhanced migration through tissues. Our results indicate that the material properties of cells define their function, can be used as a cell differentiation marker and could serve as target for novel therapies.
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Halpern AR, Donavan KC, Penner RM, Corn RM. Wafer-Scale Fabrication of Nanofluidic Arrays and Networks Using Nanoimprint Lithography and Lithographically Patterned Nanowire Electrodeposition Gold Nanowire Masters. Anal Chem 2012; 84:5053-8. [DOI: 10.1021/ac3007285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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