1
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Pardeshi S, Shede P. A Novel Device and Method for Assay of Bacterial Chemotaxis Towards Chemoattractants. Indian J Microbiol 2024; 64:990-999. [PMID: 39282202 PMCID: PMC11399546 DOI: 10.1007/s12088-024-01194-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/01/2024] [Indexed: 09/18/2024] Open
Abstract
Capillary assemblies and microfluidic devices used for bacterial chemotaxis assays have certain inherent limitations. This opens opportunities for innovation in the area. The present study describes an innovative economical device called chemotaxis plate and also a method to use this device for chemotaxis assay. Two type cultures, Pseudomonas putida MCC 2989 and Bacillus subtilis MCC 2049, chemotactic to L-aspartate, were used to validate the new device and establish the protocol for assay. 100 to 1000 fold higher number of cells were recovered in presence of chemoattractant as compared to control (p < 0.05). This novel assay technique showed 100% sensitivity and 99.21% specificity for chemotaxis assay of Pseudomonas putida MCC 2989 towards 3 mM L-aspartate over 50 min assay time. The device was also used to isolate bacteria chemotactic to caffeine directly from environmental samples. Very high chemotaxis response indices were reported for the first-time using chemotaxis plate.
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Affiliation(s)
- Sheetal Pardeshi
- Department of Microbiology, PES Modern College of Arts, Science and Commerce (Autonomous), Shivajinagar, Pune, 411005 India
- Department of Microbiology, MES Abasaheb Garware College (Autonomous), Karve Road, Pune, 411004 India
| | - Prafulla Shede
- Department of Microbiology, MES Abasaheb Garware College (Autonomous), Karve Road, Pune, 411004 India
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2
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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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3
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Bondoc-Naumovitz KG, Laeverenz-Schlogelhofer H, Poon RN, Boggon AK, Bentley SA, Cortese D, Wan KY. Methods and Measures for Investigating Microscale Motility. Integr Comp Biol 2023; 63:1485-1508. [PMID: 37336589 PMCID: PMC10755196 DOI: 10.1093/icb/icad075] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023] Open
Abstract
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks, and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we summarize the main mechanisms of microscale motility and give an overview of different experimental, analytical, and mathematical methods used to study them across different scales encompassing the molecular-, individual-, to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.
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Affiliation(s)
| | | | - Rebecca N Poon
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
| | - Alexander K Boggon
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
| | - Samuel A Bentley
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
| | - Dario Cortese
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
| | - Kirsty Y Wan
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
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4
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Altenburger B, Andersson C, Levin S, Westerlund F, Fritzsche J, Langhammer C. Label-Free Imaging of Catalytic H 2O 2 Decomposition on Single Colloidal Pt Nanoparticles Using Nanofluidic Scattering Microscopy. ACS NANO 2023; 17:21030-21043. [PMID: 37847543 PMCID: PMC10655234 DOI: 10.1021/acsnano.3c03977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023]
Abstract
Single-particle catalysis aims at determining factors that dictate the nanoparticle activity and selectivity. Existing methods often use fluorescent model reactions at low reactant concentrations, operate at low pressures, or rely on plasmonic enhancement effects. Hence, methods to measure single-nanoparticle activity under technically relevant conditions and without fluorescence or other enhancement mechanisms are still lacking. Here, we introduce nanofluidic scattering microscopy of catalytic reactions on single colloidal nanoparticles trapped inside nanofluidic channels to fill this gap. By detecting minuscule refractive index changes in a liquid flushed trough a nanochannel, we demonstrate that local H2O2 concentration changes in water can be accurately measured. Applying this principle, we analyze the H2O2 concentration profiles adjacent to single colloidal Pt nanoparticles during catalytic H2O2 decomposition into O2 and H2O and derive the particles' individual turnover frequencies from the growth rate of the O2 gas bubbles formed in their respective nanochannel during reaction.
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Affiliation(s)
- Björn Altenburger
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Carl Andersson
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Sune Levin
- Department
of Life Sciences, Chalmers University of
Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Life Sciences, Chalmers University of
Technology, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Christoph Langhammer
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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5
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Stehnach MR, Henshaw RJ, Floge SA, Guasto JS. Multiplexed microfluidic screening of bacterial chemotaxis. eLife 2023; 12:e85348. [PMID: 37486823 PMCID: PMC10365836 DOI: 10.7554/elife.85348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Microorganism sensing of and responding to ambient chemical gradients regulates a myriad of microbial processes that are fundamental to ecosystem function and human health and disease. The development of efficient, high-throughput screening tools for microbial chemotaxis is essential to disentangling the roles of diverse chemical compounds and concentrations that control cell nutrient uptake, chemorepulsion from toxins, and microbial pathogenesis. Here, we present a novel microfluidic multiplexed chemotaxis device (MCD) which uses serial dilution to simultaneously perform six parallel bacterial chemotaxis assays that span five orders of magnitude in chemostimulant concentration on a single chip. We first validated the dilution and gradient generation performance of the MCD, and then compared the measured chemotactic response of an established bacterial chemotaxis system (Vibrio alginolyticus) to a standard microfluidic assay. Next, the MCD's versatility was assessed by quantifying the chemotactic responses of different bacteria (Psuedoalteromonas haloplanktis, Escherichia coli) to different chemoattractants and chemorepellents. The MCD vastly accelerates the chemotactic screening process, which is critical to deciphering the complex sea of chemical stimuli underlying microbial responses.
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Affiliation(s)
- Michael R Stehnach
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Richard J Henshaw
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston-Salem, United States
| | - Jeffrey S Guasto
- Department of Mechanical Engineering, Tufts University, Medford, United States
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6
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Abstract
Bacteria thrive in environments rich in fluid flow, such as the gastrointestinal tract, bloodstream, aquatic systems, and the urinary tract. Despite the importance of flow, how flow affects bacterial life is underappreciated. In recent years, the combination of approaches from biology, physics, and engineering has led to a deeper understanding of how bacteria interact with flow. Here, we highlight the wide range of bacterial responses to flow, including changes in surface adhesion, motility, surface colonization, quorum sensing, virulence factor production, and gene expression. To emphasize the diversity of flow responses, we focus our review on how flow affects four ecologically distinct bacterial species: Escherichia coli, Staphylococcus aureus, Caulobacter crescentus, and Pseudomonas aeruginosa. Additionally, we present experimental approaches to precisely study bacteria in flow, discuss how only some flow responses are triggered by shear force, and provide perspective on flow-sensitive bacterial signaling.
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Affiliation(s)
- Gilberto C. Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexander M. Shuppara
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica-Jae S. Palalay
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anuradha Sharma
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph E. Sanfilippo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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7
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Ramos G, Toulouze C, Rima M, Liot O, Duru P, Davit Y. Ultraviolet control of bacterial biofilms in microfluidic chips. BIOMICROFLUIDICS 2023; 17:024107. [PMID: 37124629 PMCID: PMC10132849 DOI: 10.1063/5.0135722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Polydimethylsiloxane (PDMS) microfluidic systems have been instrumental in better understanding couplings between physical mechanisms and bacterial biofilm processes, such as hydrodynamic effects. However, precise control of the growth conditions, for example, the initial distribution of cells on the substrate or the boundary conditions in a flow system, has remained challenging. Furthermore, undesired bacterial colonization in crucial parts of the systems, in particular, in mixing zones or tubing, is an important factor that strongly limits the duration of the experiments and, therefore, impedes our ability to study the biophysics of biofilm evolving over long periods of time, as found in the environment, in engineering, or in medicine. Here, we develop a new approach that uses ultraviolet-C (UV-C) light-emitting diodes (LEDs) to confine bacterial development to specific zones of interest in the flow channels. The LEDs are integrated into a 3D printed light guide that is positioned upon the chip and used to irradiate germicidal UV-C directly through the PDMS. We first demonstrate that this system is successful in controlling undesired growth of Pseudomonas aeruginosa biofilm in inlet and outlet mixing zones during 48 h. We further illustrate how this can be used to define the initial distribution of bacteria to perturb already formed biofilms during an experiment and to control colonization for seven days-and possibly longer periods of time-therefore opening the way toward long-term biofilm experiments in microfluidic devices. Our approach is easily generalizable to existing devices at low cost and may, thus, become a standard in biofilm experiments in PDMS microfluidics.
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Affiliation(s)
- Gabriel Ramos
- Institut de Mécanique des Fluides (IMFT), CNRS and Université de Toulouse, 31400 Toulouse, France
| | - Clara Toulouze
- Institut de Mécanique des Fluides (IMFT), CNRS and Université de Toulouse, 31400 Toulouse, France
| | - Maya Rima
- Laboratoire de Génie Chimique (LGC), Université de Toulouse, CNRS, INPT, UPS, 31062 Toulouse, France
| | - Olivier Liot
- Institut de Mécanique des Fluides (IMFT), CNRS and Université de Toulouse, 31400 Toulouse, France
| | - Paul Duru
- Institut de Mécanique des Fluides (IMFT), CNRS and Université de Toulouse, 31400 Toulouse, France
| | - Yohan Davit
- Institut de Mécanique des Fluides (IMFT), CNRS and Université de Toulouse, 31400 Toulouse, France
- Author to whom correspondence should be addressed:
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8
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Bouvard J, Douarche C, Mergaert P, Auradou H, Moisy F. Direct measurement of the aerotactic response in a bacterial suspension. Phys Rev E 2022; 106:034404. [PMID: 36266851 DOI: 10.1103/physreve.106.034404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ∝c^{-2}, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.
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Affiliation(s)
- J Bouvard
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - C Douarche
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - P Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - H Auradou
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - F Moisy
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
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9
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Shim S. Diffusiophoresis, Diffusioosmosis, and Microfluidics: Surface-Flow-Driven Phenomena in the Presence of Flow. Chem Rev 2022; 122:6986-7009. [PMID: 35285634 DOI: 10.1021/acs.chemrev.1c00571] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Diffusiophoresis is the spontaneous motion of particles under a concentration gradient of solutes. Since the first recognition by Derjaguin and colleagues in 1947 in the form of capillary osmosis, the phenomenon has been broadly investigated theoretically and experimentally. Early studies were mostly theoretical and were largely interested in surface coating applications, which considered the directional transport of coating particles. In the past decade, advances in microfluidics enabled controlled demonstrations of diffusiophoresis of micro- and nanoparticles. The electrokinetic nature and the typical scales of interest of the phenomenon motivated various experimental studies using simple microfluidic configurations. In this review, I will discuss studies that report diffusiophoresis in microfluidic systems, with the focus on the fundamental aspects of the reported results. In particular, parameters and influences of diffusiophoresis and diffusioosmosis in microfluidic systems and their combinations are highlighted.
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Affiliation(s)
- Suin Shim
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
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10
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Jimenez-Martinez J, Nguyen J, Or D. Controlling pore-scale processes to tame subsurface biomineralization. RE/VIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2022; 21:27-52. [PMID: 35221831 PMCID: PMC8831379 DOI: 10.1007/s11157-021-09603-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.
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Affiliation(s)
- Joaquin Jimenez-Martinez
- Department of Water Resources and Drinking Water, Eawag, Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Jen Nguyen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Dani Or
- Division of Hydrologic Sciences, Desert Research Institute, Reno, NV USA
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11
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Zhu X, Wang K, Yan H, Liu C, Zhu X, Chen B. Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:711-731. [PMID: 34985862 DOI: 10.1021/acs.est.1c03899] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.
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Affiliation(s)
- Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Xiaoying Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
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12
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Narla AV, Cremer J, Hwa T. A traveling-wave solution for bacterial chemotaxis with growth. Proc Natl Acad Sci U S A 2021; 118:e2105138118. [PMID: 34819366 PMCID: PMC8640786 DOI: 10.1073/pnas.2105138118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.
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Affiliation(s)
- Avaneesh V Narla
- Department of Physics, University of California San Diego, La Jolla, CA 92093
| | - Jonas Cremer
- Biology Department, Stanford University, Stanford, CA 94305
| | - Terence Hwa
- Department of Physics, University of California San Diego, La Jolla, CA 92093;
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13
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Yanagisawa N, Kozgunova E, Grossmann G, Geitmann A, Higashiyama T. Microfluidics-Based Bioassays and Imaging of Plant Cells. PLANT & CELL PHYSIOLOGY 2021; 62:1239-1250. [PMID: 34027549 PMCID: PMC8579190 DOI: 10.1093/pcp/pcab067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/13/2021] [Accepted: 05/23/2021] [Indexed: 05/03/2023]
Abstract
Many plant processes occur in the context of and in interaction with a surrounding matrix such as soil (e.g. root growth and root-microbe interactions) or surrounding tissues (e.g. pollen tube growth through the pistil), making it difficult to study them with high-resolution optical microscopy. Over the past decade, microfabrication techniques have been developed to produce experimental systems that allow researchers to examine cell behavior in microstructured environments that mimic geometrical, physical and/or chemical aspects of the natural growth matrices and that cannot be generated using traditional agar plate assays. These microfabricated environments offer considerable design flexibility as well as the transparency required for high-resolution, light-based microscopy. In addition, microfluidic platforms have been used for various types of bioassays, including cellular force assays, chemoattraction assays and electrotropism assays. Here, we review the recent use of microfluidic devices to study plant cells and organs, including plant roots, root hairs, moss protonemata and pollen tubes. The increasing adoption of microfabrication techniques by the plant science community may transform our approaches to investigating how individual plant cells sense and respond to changes in the physical and chemical environment.
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Affiliation(s)
- Naoki Yanagisawa
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Elena Kozgunova
- Department of Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestr. 1, Freiburg, Baden-Württemberg 79104, Germany
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Anja Geitmann
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Québec H9X 3V9, Canada
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-0033, Japan
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14
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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation. Commun Biol 2021; 4:1226. [PMID: 34702996 PMCID: PMC8548513 DOI: 10.1038/s42003-021-02736-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Lund, Sweden
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15
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Liu Y, Lehnert T, Gijs MAM. Effect of inoculum size and antibiotics on bacterial traveling bands in a thin microchannel defined by optical adhesive. MICROSYSTEMS & NANOENGINEERING 2021; 7:86. [PMID: 34745645 PMCID: PMC8536744 DOI: 10.1038/s41378-021-00309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Phenotypic diversity in bacterial flagella-induced motility leads to complex collective swimming patterns, appearing as traveling bands with transient locally enhanced cell densities. Traveling bands are known to be a bacterial chemotactic response to self-generated nutrient gradients during growth in resource-limited microenvironments. In this work, we studied different parameters of Escherichia coli (E. coli) collective migration, in particular the quantity of bacteria introduced initially in a microfluidic chip (inoculum size) and their exposure to antibiotics (ampicillin, ciprofloxacin, and gentamicin). We developed a hybrid polymer-glass chip with an intermediate optical adhesive layer featuring the microfluidic channel, enabling high-content imaging of the migration dynamics in a single bacterial layer, i.e., bacteria are confined in a quasi-2D space that is fully observable with a high-magnification microscope objective. On-chip bacterial motility and traveling band analysis was performed based on individual bacterial trajectories by means of custom-developed algorithms. Quantifications of swimming speed, tumble bias and effective diffusion properties allowed the assessment of phenotypic heterogeneity, resulting in variations in transient cell density distributions and swimming performance. We found that incubation of isogeneic E. coli with different inoculum sizes eventually generated different swimming phenotype distributions. Interestingly, incubation with antimicrobials promoted bacterial chemotaxis in specific cases, despite growth inhibition. Moreover, E. coli filamentation in the presence of antibiotics was assessed, and the impact on motility was evaluated. We propose that the observation of traveling bands can be explored as an alternative for fast antimicrobial susceptibility testing.
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Affiliation(s)
- Yang Liu
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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16
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Yang CY, Erickstad M, Tadrist L, Ronan E, Gutierrez E, Wong-Ng J, Groisman A. Aggregation Temperature of Escherichia coli Depends on Steepness of the Thermal Gradient. Biophys J 2020; 118:2816-2828. [PMID: 32348719 DOI: 10.1016/j.bpj.2020.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/14/2020] [Accepted: 02/03/2020] [Indexed: 11/30/2022] Open
Abstract
Bacterial chemotaxis, the directed migration of bacteria in a gradient of chemoattractant, is one of the most well-studied and well-understood processes in cell biology. On the other hand, bacterial thermotaxis, the directed migration of bacteria in a gradient of temperature, is understood relatively poorly, with somewhat conflicting reports by different groups. One of the reasons for that is the relative technical difficulty of the generation of well-defined gradients of temperature that are sufficiently steep to elicit readily detectable thermotaxis. Here, we used a specially designed microfluidic device to study thermotaxis of Escherichia coli in a broad range of thermal gradients with a high rate of data collection. We found that in shallow temperature gradients with narrow temperature ranges, E. coli tended to aggregate near a sidewall of the gradient channel at either the lowest or the highest temperature. On the other hand, in sufficiently steep gradients with wide temperature ranges, E. coli aggregated at intermediate temperatures, with maximal cell concentrations found away from the sidewalls. We observed this intermediate temperature aggregation in a motility buffer that did not contain any major chemoattractants of E. coli, in contradiction to some previous reports, which suggested that this type of aggregation required the presence of at least one major chemoattractant in the medium. Even more surprisingly, the aggregation temperature strongly depended on the gradient steepness, decreasing by ∼10° as the steepness was increased from 27 to 53°C/mm. Our experiments also highlight the fact that assessments of thermal gradients by changes in fluorescence of temperature-sensitive fluorescent dyes need to account for thermophoresis of the dyes.
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Affiliation(s)
- Chih-Yu Yang
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Michael Erickstad
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Loïc Tadrist
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Edward Ronan
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Edgar Gutierrez
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Jérôme Wong-Ng
- Department of Physics, University of California, San Diego, La Jolla, California.
| | - Alex Groisman
- Department of Physics, University of California, San Diego, La Jolla, California.
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Grigolato F, Egholm C, Impellizzieri D, Arosio P, Boyman O. Establishment of a scalable microfluidic assay for characterization of population-based neutrophil chemotaxis. Allergy 2020; 75:1382-1393. [PMID: 31971608 DOI: 10.1111/all.14195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Regulation of neutrophil chemotaxis and activation plays crucial roles in immunity, and dysregulated neutrophil responses can lead to pathology as seen in neutrophilic asthma. Neutrophil recruitment is key for initiating immune defense and inflammation, and its modulation is a promising therapeutic target. Microfluidic technology is an attractive tool for characterization of neutrophil migration. Compared to transwell assays, microfluidic approaches could offer several advantages, including precis e control of defined chemokine gradients in space and time, automated quantitative analysis of chemotaxis, and high throughput. METHODS We established a microfluidic device for fully automated, quantitative assessment of neutrophil chemotaxis. Freshly isolated mouse neutrophils from bone marrow or human neutrophils from peripheral blood were assessed in real time using an epifluorescence microscope for their migration toward the potent chemoattractants C-X-C-motif ligand 2 (CXCL2) and CXCL8, without or with interleukin-4 (IL-4) pre-incubation. RESULTS Our microfluidic device allowed the precise and reproducible determination of the optimal CXCL2 and CXCL8 concentrations for mouse and human neutrophil chemotaxis, respectively. Furthermore, our microfluidic assay was able to measure the equilibrium and real-time dynamic effects of specific modulators of neutrophil chemotaxis. We demonstrated this concept by showing that IL-4 receptor signaling in mouse and human neutrophils inhibited their migration toward CXCL2 and CXCL8, respectively, and this inhibition was time-dependent. CONCLUSION Collectively, our microfluidic device shows several advantages over traditional transwell migration assays and its design is amenable to future integration into multiplexed high-throughput platforms for screening of molecules that modulate the chemotaxis of different immune cells.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology, Zurich Zurich Switzerland
| | - Cecilie Egholm
- Department of Immunology University Hospital Zurich Zurich Switzerland
| | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology, Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
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18
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Chen X, Miller A, Cao S, Gan Y, Zhang J, He Q, Wang RQ, Yong X, Qin P, Lapizco-Encinas BH, Du K. Rapid Escherichia coli Trapping and Retrieval from Bodily Fluids via a Three-Dimensional Bead-Stacked Nanodevice. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7888-7896. [PMID: 31939648 DOI: 10.1021/acsami.9b19311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel micro- and nanofluidic device stacked with magnetic beads has been developed to efficiently trap, concentrate, and retrieve Escherichia coli (E. coli) from the bacterial suspension and pig plasma. The small voids between the magnetic beads are used to physically isolate the bacteria in the device. We used computational fluid dynamics, three-dimensional (3D) tomography technology, and machine learning to probe and explain the bead stacking in a small 3D space with various flow rates. A combination of beads with different sizes is utilized to achieve a high capture efficiency (∼86%) with a flow rate of 50 μL/min. Leveraging the high deformability of this device, an E. coli sample can be retrieved from the designated bacterial suspension by applying a higher flow rate followed by rapid magnetic separation. This unique function is also utilized to concentrate E. coli cells from the original bacterial suspension. An on-chip concentration factor of ∼11× is achieved by inputting 1300 μL of the E. coli sample and then concentrating it in 100 μL of buffer. Importantly, this multiplexed, miniaturized, inexpensive, and transparent device is easy to fabricate and operate, making it ideal for pathogen separation in both laboratory and point-of-care settings.
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Affiliation(s)
- Xinye Chen
- Department of Microsystems Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
- Department of Mechanical Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
| | - Abbi Miller
- Department of Biomedical Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
| | - Shengting Cao
- Department of Electrical and Computer Engineering , University of Alabama , Tuscaloosa , Alabama 35401 , United States
| | - Yu Gan
- Department of Electrical and Computer Engineering , University of Alabama , Tuscaloosa , Alabama 35401 , United States
| | - Jie Zhang
- Carollo Engineers, Inc. , Seattle , Washington 98101 , United States
| | - Qian He
- Department of Mechanical Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
- Center of Precision Medicine and Healthcare , Tsinghua-Berkeley Shenzhen Institute , Shenzhen , Guangdong Province 518055 , China
| | - Ruo-Qian Wang
- Department of Civil and Environmental Engineering , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08854 , United States
| | - Xin Yong
- Department of Mechanical Engineering , The State University of New York , Binghamton , New York 13902 , United States
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare , Tsinghua-Berkeley Shenzhen Institute , Shenzhen , Guangdong Province 518055 , China
| | - Blanca H Lapizco-Encinas
- Department of Biomedical Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
| | - Ke Du
- Department of Microsystems Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
- Department of Mechanical Engineering , Rochester Institute of Technology , Rochester , New York 14623 , United States
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Gaines A, Ludovice M, Xu J, Zanghi M, Meinersmann RJ, Berrang M, Daley W, Britton D. The dialogue between protozoa and bacteria in a microfluidic device. PLoS One 2019; 14:e0222484. [PMID: 31596855 PMCID: PMC6784911 DOI: 10.1371/journal.pone.0222484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/30/2019] [Indexed: 01/28/2023] Open
Abstract
In nature, protozoa play a major role in controlling bacterial populations. This paper proposes a microfluidic device for the study of protozoa behaviors change due to their chemotactic response in the presence of bacterial cells. A three-channel microfluidic device was designed using a nitrocellulose membrane into which channels were cut using a laser cutter. The membrane was sandwiched between two glass slides; a Euglena suspension was then allowed to flow through the central channel. The two side channels were filled with either, 0.1% peptone as a negative control, or a Listeria suspension respectively. The membrane design prevented direct interaction but allowed Euglena cells to detect Listeria cells as secretions diffused through the nitrocellulose membrane. A significant number of Euglena cells migrated toward the chambers near the bacterial cells, indicating a positive chemotactic response of Euglena toward chemical cues released from Listeria cells. Filtrates collected from Listeria suspension with a series of molecular weight cutoffs (3k, 10k and 100k) were examined in Euglena chemotaxis tests. Euglena cells were attracted to all filtrates collected from the membrane filtration with different molecular weight cutoffs, suggesting small molecules from Listeria might be the chemical cues to attract protozoa. Headspace volatile organic compounds (VOC) released from Listeria were collected, spiked to 0.1% peptone and tested as the chemotactic effectors. It was discovered that the Euglena cells responded quickly to Listeria VOCs including decanal, 3,5- dimethylbenzaldehyde, ethyl acetate, indicating bacterial VOCs were used by Euglena to track the location of bacteria.
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Affiliation(s)
- Anna Gaines
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Miranda Ludovice
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jie Xu
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Marc Zanghi
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Richard J. Meinersmann
- Richard B. Russell Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Mark Berrang
- Richard B. Russell Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Wayne Daley
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Doug Britton
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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20
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Shim S, Stone HA, Ford RM. Chemotaxis in shear flow: Similarity solutions of the steady‐state chemoattractant and bacterial distributions. AIChE J 2019. [DOI: 10.1002/aic.16713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Suin Shim
- Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey
| | - Howard A. Stone
- Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey
| | - Roseanne M. Ford
- Department of Chemical Engineering School of Engineering and Applied Science, University of Virginia Charlottesville Virginia
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21
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Improvement of a diffusion-based microfluidic chemotaxis assay through stable formation of a chemical gradient. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Study on the Attachment of Escherichia coli to Sediment Particles at a Single-Cell Level: The Effect of Particle Size. WATER 2019. [DOI: 10.3390/w11040819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The attachment of bacteria to sediment particles has a significant impact on the level of bacterial contamination in water. In this work, the attachment of Escherichia coli to particles was investigated with emphasis on the effect of particle size. To exclude the impact of other facts, e.g., the irregularity of particles, we used regular spherical glass particles in addition to natural sediment particles. Both types of particles are mainly composed of SiO2 and are similar in density. Through a bacterial tracking method together with microfluidic techniques, the attachment of single Escherichia coli cells on the particles was observed. The results showed that only a small portion of the cells that approach the particles remain attached and that the attachment probability per approach increases with surface area for both sediment and glass particles within the size range (8–62 μm) examined in this study. Therefore, finer sediments with more surface area have a higher E. coli attachment capacity. The attachment probability is higher on sediment particles than on glass microspheres of equivalent size, indicating preferential attachment of E. coli to sediment particles. The partition coefficient of the commonly used linear partition model was calculated based on microscopic measurements and the obtained relation of the partition coefficient with attachment probability and particle size was validated with data from the published literature.
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23
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Walker M, Humphries S. 3D Printing: Applications in evolution and ecology. Ecol Evol 2019; 9:4289-4301. [PMID: 31016005 PMCID: PMC6468079 DOI: 10.1002/ece3.5050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/17/2019] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
In the commercial and medical sectors, 3D printing is delivering on its promise to enable a revolution. However, in the fields of Ecology and Evolution we are only on the brink of embracing the advantages that 3D printing can offer. Here we discuss examples where the process has enabled researchers to develop new techniques, work with novel species, and to enhance the impact of outreach activities. Our aim is to showcase the potential that 3D printing offers in terms of improved experimental techniques, greater flexibility, reduced costs and promoting open science, while also discussing its limitations. By taking a general overview of studies using the technique from fields across the broad range of Ecology and Evolution, we show the flexibility of 3D printing technology and aim to inspire the next generation of discoveries.
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Futai N, Tamura M, Ogawa T, Tanaka M. Microfluidic Long-Term Gradient Generator with Axon Separation Prototyped by 185 nm Diffused Light Photolithography of SU-8 Photoresist. MICROMACHINES 2018; 10:mi10010009. [PMID: 30586941 PMCID: PMC6356992 DOI: 10.3390/mi10010009] [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: 11/15/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023]
Abstract
We have developed a cast microfluidic chip for concentration gradient generation that contains a thin (~5 µm2 cross-sectional area) microchannel. The diffusion of diffused 185 nm ultraviolet (UV) light from an inexpensive low-pressure mercury lamp exposed a layer of the SU-8 photoresist from the backside and successfully patterned durable 2 µm-high microchannel mold features with smooth bell-shaped sidewalls. The thin channel had appropriate flow resistance and simultaneously satisfied both the rapid introduction of test substance and long-term maintenance of gradients. The average height and width at the half height of the channel, defined by a 2 µm-wide line mask pattern, were 2.00 ± 0.19 µm, and 2.14 ± 0.89 µm, respectively. We were able to maintain the concentration gradient of Alexa Fluor 488 fluorescent dye inside or at the exit of the thin microchannel in an H-shaped microfluidic configuration for at least 48 h. We also demonstrated the cultivation of chick embryo dorsal root ganglion neuronal cells for 96 h, and the directional elongation of axons under a nerve growth factor concentration gradient.
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Affiliation(s)
- Nobuyuki Futai
- Department of Mechanical Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan.
| | - Makoto Tamura
- Department of Mechanical Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan.
| | - Tomohisa Ogawa
- Department of Human Pathology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
| | - Masato Tanaka
- Division of Life Science, Tokyo Denki University, Hiki-gun, Saitama 350-0394, Japan.
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25
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Alam MK, Koomson E, Zou H, Yi C, Li CW, Xu T, Yang M. Recent advances in microfluidic technology for manipulation and analysis of biological cells (2007–2017). Anal Chim Acta 2018; 1044:29-65. [DOI: 10.1016/j.aca.2018.06.054] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
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26
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Zhang Y, Li C, Wu Y, Zhang Y, Zhou Z, Cao B. A microfluidic gradient mixer-flow chamber as a new tool to study biofilm development under defined solute gradients. Biotechnol Bioeng 2018; 116:54-64. [DOI: 10.1002/bit.26852] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/17/2018] [Accepted: 10/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yingdan Zhang
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Cheng Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yichao Wu
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yilei Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
| | - Zhi Zhou
- Division of Environmental and Ecological Engineering and School of Civil Engineering, Purdue University; Indiana USA
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
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27
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Abstract
A micro-level technique so-called “microfluidic technology or simply microfluidic” has gained a special place as a powerful tool in bioengineering and biomedical engineering research due to its core advantages in modern science and engineering. Microfluidic technology has played a substantial role in numerous applications with special reference to bioscience, biomedical and biotechnological research. It has facilitated noteworthy development in various sectors of bio-research and upsurges the efficacy of research at the molecular level, in recent years. Microfluidic technology can manipulate sample volumes with precise control outside cellular microenvironment, at micro-level. Thus, enable the reduction of discrepancies between in vivo and in vitro environments and reduce the overall reaction time and cost. In this review, we discuss various integrations of microfluidic technologies into biotechnology and its paradigmatic significance in bio-research, supporting mechanical and chemical in vitro cellular microenvironment. Furthermore, specific innovations related to the application of microfluidics to advance microbial life, solitary and co-cultures along with a multiple-type cell culturing, cellular communications, cellular interactions, and population dynamics are also discussed.
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28
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Seo Y, Hwang J, Lee E, Kim YJ, Lee K, Park C, Choi Y, Jeon H, Choi J. Engineering copper nanoparticles synthesized on the surface of carbon nanotubes for anti-microbial and anti-biofilm applications. NANOSCALE 2018; 10:15529-15544. [PMID: 29985503 DOI: 10.1039/c8nr02768d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biofilms adhere to surfaces to produce extracellular polymeric substances (EPSs). EPSs grow and protect themselves from external stresses. Their formation causes a foul odor and may lead to chronic infectious diseases in animals and people. Biofilms also inhibit the contact between bacteria and antibiotics, thereby reducing their antibacterial activity. Thus, we describe novel nanostructures, a fusion of copper and multi-walled carbon nanotubes (MWCNTs), which increase antimicrobial activity against biofilms without being toxic to human cells. Simulations based on the stochastic response were performed to predict the efficiency of synthesizing nanostructures. The synthesized Cu/MWCNTs inhibit the growth of Methylobacterium spp., which forms biofilms; antimicrobial testing and cytotoxicity assessments showed that the Cu/MWCNTs were not cytotoxic to human cells. The Cu/MWCNTs come in direct contact with the bacterial cell surface, damage the cell wall, and cause secondary oxidation of reactive oxygen species. Furthermore, the Cu/MWCNTs release copper ions, which inhibit the quorum sensing in Methylobacterium spp., thereby inhibiting the expression of the genes that form biofilms. Additionally, we confirmed excellent electrical and thermal conductivity of Cu/MWCNTs as well as biofilm removal efficiency in the microfluidic channel.
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Affiliation(s)
- Youngmin Seo
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
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29
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Parthasarathy R. Monitoring microbial communities using light sheet fluorescence microscopy. Curr Opin Microbiol 2018; 43:31-37. [PMID: 29175679 PMCID: PMC5963963 DOI: 10.1016/j.mib.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 01/20/2023]
Abstract
Microbes often live in dense, dynamic, multi-species communities whose architecture and function are intimately intertwined. Imaging these complex, three-dimensional ensembles presents considerable technical challenges, however. In this review, I describe light sheet fluorescence microscopy, a technique that enables rapid acquisition of three-dimensional images over large fields of view and over long durations, and I highlight recent applications of this method to microbial systems that include artificial closed ecosystems, bacterial biofilms, and gut microbiota. I comment also on the history of light sheet imaging and the many variants of the method. Light sheet techniques have tremendous potential for illuminating the workings of microbial communities, a potential that is just beginning to be realized.
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30
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Nikoleli GP, Nikolelis DP, Siontorou CG, Karapetis S, Varzakas T. Novel Biosensors for the Rapid Detection of Toxicants in Foods. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 84:57-102. [PMID: 29555073 DOI: 10.1016/bs.afnr.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The modern environmental and food analysis requires sensitive, accurate, and rapid methods. The growing field of biosensors represents an answer to this demand. Unfortunately, most biosensor systems have been tested only on distilled water or buffered solutions, although applications to real samples are increasingly appearing in recent years. In this context, biosensors for potential food applications continue to show advances in areas such as genetic modification of enzymes and microorganisms, improvement of recognition element immobilization, and sensor interfaces. This chapter investigates the progress in the development of biosensors for the rapid detection of food toxicants for online applications. Recent progress in nanotechnology has produced affordable, mass-produced devices, and to integrate these into components and systems (including portable ones) for mass market applications for food toxicants monitoring. Sensing includes chemical and microbiological food toxicants, such as toxins, insecticides, pesticides, herbicides, microorganisms, bacteria, viruses and other microorganisms, phenolic compounds, allergens, genetically modified foods, hormones, dioxins, etc. Therefore, the state of the art of recent advances and future targets in the development of biosensors for food monitoring is summarized as follows: biosensors for food analysis will be highly sensitive, selective, rapidly responding, real time, massively parallel, with no or minimum sample preparation, and platform suited to portable and handheld nanosensors for the rapid detection of food toxicants for online uses even by nonskilled personnel.
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Affiliation(s)
- Georgia-Paraskevi Nikoleli
- Laboratory of Inorganic & Analytical Chemistry, School of Chemical Engineering, Chemical Sciences, National Technical University of Athens, Athens, Greece
| | | | - Christina G Siontorou
- Laboratory of Simulation of Industrial Processes, School of Maritime and Industry, University of Piraeus, Piraeus, Greece
| | - Stephanos Karapetis
- Laboratory of Inorganic & Analytical Chemistry, School of Chemical Engineering, Chemical Sciences, National Technical University of Athens, Athens, Greece
| | - Theo Varzakas
- Laboratory of Inorganic Chemistry, University of Athens, Athens, Greece; Technological Educational Institute of Peloponnese, Kalamata, Greece
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A Static Microfluidic Device for Investigating the Chemotaxis Response to Stable, Non-linear Gradients. Methods Mol Biol 2018. [PMID: 29429081 DOI: 10.1007/978-1-4939-7577-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Microfluidic technology allows fast and precise measurement of chemotaxis responses to both attractant and repellent signals. One of the major drawbacks of current microfluidic chemotaxis assays is the presence of bacterial cells within the concentration gradient flow field, which has the potential for flow effects masking the chemotaxis response. This chapter describes a new microfluidic device for producing stable concentration gradients and measuring the response of cells to the gradient without exposing them to any flow. Unlike other methods described in the literature, this method is capable of producing gradients of any shape, almost instantaneously, allowing the measurement of time-dependent response of cells to a variety of signals.
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Showalter GM, Deming JW. Low-temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:92-101. [PMID: 29235725 DOI: 10.1111/1758-2229.12610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviours remain understudied in cold habitats. Here, we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8°C to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8°C and -1°C). Results indicate that C. psychrerythraea 34H is capable of chemotaxis at all temperatures tested, with strongest chemotaxis at the temperature at which it was first grown, whether 8°C or -1°C. This model marine psychrophile also showed significant halotaxis towards 15 and 55 ppt solutions, as well as strong substrate-specific chemohalotaxis. We suggest that such patterns of taxis may enable bacteria to colonize sea ice, position themselves optimally within its extremely cold, hypersaline and temporally fluctuating microenvironments, and respond to various chemical signals therein.
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Affiliation(s)
- G M Showalter
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - J W Deming
- School of Oceanography, University of Washington, Seattle, WA, USA
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Roggo C, Picioreanu C, Richard X, Mazza C, van Lintel H, van der Meer JR. Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips. Environ Microbiol 2017; 20:241-258. [DOI: 10.1111/1462-2920.13982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Clémence Roggo
- Department of Fundamental Microbiology; University of Lausanne; Lausanne Switzerland 1015
| | - Cristian Picioreanu
- Department of Biotechnology Faculty of Applied Sciences; Delft University of Technology; Delft 2629 HZ The Netherlands
| | - Xavier Richard
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Christian Mazza
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Harald van Lintel
- Microsystems Laboratory LMIS4; École Polytechnique Fédérale de Lausanne (EPFL), Station 17; Lausanne Switzerland CH-1015
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34
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ZANG XQ, LI ZY, ZHANG XY, JIANG L, REN NQ, SUN K. Advance in Bacteria Chemotaxis on Microfluidic Devices. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61050-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Cell-cell communication enhances bacterial chemotaxis toward external attractants. Sci Rep 2017; 7:12855. [PMID: 28993669 PMCID: PMC5634484 DOI: 10.1038/s41598-017-13183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022] Open
Abstract
Bacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using numerical simulations. Using a microfluidic approach, we find that E. coli cells respond to the gradient of chemoattractant not only by biasing their own random-walk swimming pattern through the well-understood intracellular chemotaxis signaling, but also by actively secreting a chemical signal into the extracellular medium, possibly through a hitherto unknown communication signal transduction pathway. This extracellular signaling molecule is a strong chemoattractant that attracts distant cells to the food source. The observed behavior may represent a common evolved solution to accelerate the function of biochemical networks of interacting cells.
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36
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Lambert BS, Raina JB, Fernandez VI, Rinke C, Siboni N, Rubino F, Hugenholtz P, Tyson GW, Seymour JR, Stocker R. A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nat Microbiol 2017; 2:1344-1349. [DOI: 10.1038/s41564-017-0010-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 07/19/2017] [Indexed: 11/09/2022]
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Murugesan N, Panda T, Das SK. Effect of gold nanoparticles on thermal gradient generation and thermotaxis of E. coli cells in microfluidic device. Biomed Microdevices 2017; 18:53. [PMID: 27246690 DOI: 10.1007/s10544-016-0077-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bacteria responds to changing chemical and thermal environment by moving towards or away from a particular location. In this report, we looked into thermal gradient generation and response of E. coli DH5α cells to thermal gradient in the presence and in the absence of spherical gold nanoparticles (size: 15 to 22 nm) in a static microfluidic environment using a polydimethylsiloxane (PDMS) made microfluidic device. A PDMS-agarose based microfluidic device for generating thermal gradient has been developed and the thermal gradient generation in the device has been validated with the numerical simulation. Our studies revealed that the presence of gold nanoparticles, AuNPs (0.649 μg/mL) has no effect on the thermal gradient generation. The E. coli DH5α cells have been treated with AuNPs of two different concentrations (0.649 μg/mL and 0.008 μg/mL). The thermotaxis behavior of cells in the presence of AuNPs has been studied and compared to the thermotaxis of E.coli DH5α cells in the absence of AuNPs. In case of thermotaxis, in the absence of the AuNPs, the E. coli DH5α cells showed better thermotaxis towards lower temperature range, whereas in the presence of AuNPs (0.649 μg/mL and 0.008 μg/mL) thermotaxis of the E. coli DH5α cells has been inhibited. The results show that the spherical AuNPs intervenes in the themotaxis of E. coli DH5α cells and inhibits the cell migration. The reason for the failure in thermotaxis response mechanism may be due to decreased F-type ATP synthase activity and collapse of membrane potential by AuNPs, which, in turn, leads to decreased ATP levels. This has been hypothesized since both thermotaxis and chemotaxis follows the same response mechanism for migration in which ATP plays critical role.
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Affiliation(s)
- Nithya Murugesan
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Tapobrata Panda
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sarit K Das
- Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India.
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Shang W, Tsao CY, Luo X, Teodoro M, McKay R, Quan DN, Wu HC, Payne GF, Bentley WE. A simple and reusable bilayer membrane-based microfluidic device for the study of gradient-mediated bacterial behaviors. BIOMICROFLUIDICS 2017; 11:044114. [PMID: 28868107 PMCID: PMC5566557 DOI: 10.1063/1.4993438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/10/2017] [Indexed: 05/11/2023]
Abstract
We have developed a user-friendly microfluidic device for the study of gradient-mediated bacterial behaviors, including chemotaxis. This device rapidly establishes linear concentration gradients by exploiting solute diffusion through porous membranes in the absence of convective flows. As such, the gradients are created rapidly and can be sustained for long time periods (e.g., hours), sufficient to evaluate cell phenotype. The device exploits a unique simple bilayer configuration that enables rapid setup and quick reproducible introduction of cells. Its reusability represents an additional advantage in that it need not be limited to settings with microfluidics expertise. We have successfully demonstrated the applicability of this tool in studying the chemotactic response of Escherichia coli to glucose. When coupled with our recent Python program, quantified metrics such as speed, ratio of tumble to run, and effective diffusivity can be obtained from slow frame rate videos. Moreover, we introduce a chemotaxis partition coefficient that conveniently scores swimming behavior on the single-cell level.
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Affiliation(s)
| | | | - Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, 20064, USA
| | | | | | | | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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39
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Abstract
Although the “adaptive” strategy used by Escherichia coli has dominated our understanding of bacterial chemotaxis, the environmental conditions under which this strategy emerged is still poorly understood. In this work, we study the performance of various chemotactic strategies under a range of stochastic time- and space-varying attractant distributions in silico. We describe a novel “speculator” response in which the bacterium compare the current attractant concentration to the long-term average; if it is higher then they tumble persistently, while if it is lower than the average, bacteria swim away in search of more favorable conditions. We demonstrate how this response explains the experimental behavior of aerobically-grown Rhodobacter sphaeroides and that under spatially complex but slowly-changing nutrient conditions the speculator response is as effective as the adaptive strategy of E. coli.
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Affiliation(s)
- Martin Godány
- Division of Infection & Immunity, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Bhavin S. Khatri
- Division of Infection & Immunity, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
- * E-mail:
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40
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The Aerotactic Response of Caulobacter crescentus. Biophys J 2017; 110:2076-84. [PMID: 27166815 DOI: 10.1016/j.bpj.2016.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 11/24/2022] Open
Abstract
Many motile microorganisms are able to detect chemical gradients in their surroundings to bias their motion toward more favorable conditions. In this study, we observe the swimming patterns of Caulobacter crescentus, a uniflagellated bacterium, in a linear oxygen gradient produced by a three-channel microfluidic device. Using low-magnification dark-field microscopy, individual cells are tracked over a large field of view and their positions within the oxygen gradient are recorded over time. Motor switching events are identified so that swimming trajectories are deconstructed into a series of forward and backward swimming runs. Using these data, we show that C. crescentus displays aerotactic behavior by extending the average duration of forward swimming runs while moving up an oxygen gradient, resulting in directed motility toward oxygen sources. Additionally, the motor switching response is sensitive both to the steepness of the gradient experienced and to background oxygen levels, exhibiting a logarithmic response.
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41
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Fernandez RE, Rohani A, Farmehini V, Swami NS. Review: Microbial analysis in dielectrophoretic microfluidic systems. Anal Chim Acta 2017; 966:11-33. [PMID: 28372723 PMCID: PMC5424535 DOI: 10.1016/j.aca.2017.02.024] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 12/13/2022]
Abstract
Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques.
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Affiliation(s)
- Renny E Fernandez
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Ali Rohani
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Vahid Farmehini
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Nathan S Swami
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA.
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42
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Roh C, Lee J, Kinger M, Kang C. In Vitro Studies on a Microfluidic Sensor with Embedded Obstacles Using New Antibacterial Synthetic Compounds (1-TDPPO) Mixed Prop-2-en-1-one with Difluoro Phenyl. SENSORS 2017; 17:s17040803. [PMID: 28397751 PMCID: PMC5422164 DOI: 10.3390/s17040803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/20/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022]
Abstract
This paper describes the use of an analytical microfluidic sensor for accelerating chemo-repellent response and strong anti-bacterial 1-(Thien-2-yl)-3-(2, 6-difluoro phenyl) prop-2-en-1-one (1-TDPPO). The chemically-synthesized antimicrobial agent, which included prop-2-en-1-one and difluoro phenyl groups, was moving through an optically transparent polydimethylsiloxane (PDMS) microfluidic sensor with circular obstacles arranged evenly. The response, growth and distribution of fluorescent labeling Pseudomonas aeruginosa PAO1 against the antimicrobial agent were monitored by confocal laser scanning microscope (CLSM). The microfluidic sensor along with 1-TDPPOin this study exhibits the following advantages: (i) Real-time chemo-repellent responses of cell dynamics; (ii) Rapid eradication of biofilm by embedded obstacles and powerful antibacterial agents, which significantly reduce the response time compared to classical methods; (iii) Minimal consumption of cells and antimicrobial agents; and (iv) Simplifying the process of the normalization of the fluorescence intensity and monitoring of biofilm by captured images and datasets.
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Affiliation(s)
- Changhyun Roh
- Biotechnology Research Division, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 1266, Sinjeong-Dong, Jeongeup, Jeonbuk 580-185, Korea.
| | - Jaewoong Lee
- Department of Textile Engineering and Technology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Mayank Kinger
- Department of Chemistry, Maharishi Markandeshwar University, Mullana, (Ambala) Haryana 133207, India.
| | - Chankyu Kang
- Ministry of Employment and Labor, Major Industrial Accident Prevention Center, 34 Yeosusandallo, Yeosu-Si, Jeonnam 59631, Korea.
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43
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Anielski A, Pfannes EKB, Beta C. Adaptive microfluidic gradient generator for quantitative chemotaxis experiments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:034301. [PMID: 28372375 DOI: 10.1063/1.4978535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chemotactic motion in a chemical gradient is an essential cellular function that controls many processes in the living world. For a better understanding and more detailed modelling of the underlying mechanisms of chemotaxis, quantitative investigations in controlled environments are needed. We developed a setup that allows us to separately address the dependencies of the chemotactic motion on the average background concentration and on the gradient steepness of the chemoattractant. In particular, both the background concentration and the gradient steepness can be kept constant at the position of the cell while it moves along in the gradient direction. This is achieved by generating a well-defined chemoattractant gradient using flow photolysis. In this approach, the chemoattractant is released by a light-induced reaction from a caged precursor in a microfluidic flow chamber upstream of the cell. The flow photolysis approach is combined with an automated real-time cell tracker that determines changes in the cell position and triggers movement of the microscope stage such that the cell motion is compensated and the cell remains at the same position in the gradient profile. The gradient profile can be either determined experimentally using a caged fluorescent dye or may be alternatively determined by numerical solutions of the corresponding physical model. To demonstrate the function of this adaptive microfluidic gradient generator, we compare the chemotactic motion of Dictyostelium discoideum cells in a static gradient and in a gradient that adapts to the position of the moving cell.
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Affiliation(s)
- Alexander Anielski
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Eva K B Pfannes
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
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44
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Murugesan N, Dhar P, Panda T, Das SK. Interplay of chemical and thermal gradient on bacterial migration in a diffusive microfluidic device. BIOMICROFLUIDICS 2017; 11:024108. [PMID: 28396712 PMCID: PMC5367144 DOI: 10.1063/1.4979103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/13/2017] [Indexed: 05/09/2023]
Abstract
Living systems are constantly under different combinations of competing gradients of chemical, thermal, pH, and mechanical stresses allied. The present work is about competing chemical and thermal gradients imposed on E. coli in a diffusive stagnant microfluidic environment. The bacterial cells were exposed to opposing and aligned gradients of an attractant (1 mM sorbitol) or a repellant (1 mM NiSO4) and temperature. The effects of the repellant/attractant and temperature on migration behavior, migration rate, and initiation time for migration have been reported. It has been observed that under competing gradients of an attractant and temperature, the nutrient gradient (gradient generated by cells itself) initiates directed migration, which, in turn, is influenced by temperature through the metabolic rate. Exposure to competing gradients of an inhibitor and temperature leads to the imposed chemical gradient governing the directed cell migration. The cells under opposing gradients of the repellant and temperature have experienced the longest decision time (∼60 min). The conclusion is that in a competing chemical and thermal gradient environment in the range of experimental conditions used in the present work, the migration of E. coli is always initiated and governed by chemical gradients (either generated by the cells in situ or imposed upon externally), but the migration rate and percentage of migration of cells are influenced by temperature, shedding insights into the importance of such gradients in deciding collective dynamics of such cells in physiological conditions.
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Affiliation(s)
- Nithya Murugesan
- Department of Chemical Engineering, Indian Institute of Technology Madras , Chennai 600 036, India
| | - Purbarun Dhar
- Department of Mechanical Engineering, Indian Institute of Technology Ropar , Rupnagar 140001, India
| | - Tapobrata Panda
- Department of Chemical Engineering, Indian Institute of Technology Madras , Chennai 600 036, India
| | - Sarit K Das
- Department of Mechanical Engineering, Indian Institute of Technology Madras , Chennai 600 036, India
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45
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Menolascina F, Rusconi R, Fernandez VI, Smriga S, Aminzare Z, Sontag ED, Stocker R. Logarithmic sensing in Bacillus subtilis aerotaxis. NPJ Syst Biol Appl 2017; 3:16036. [PMID: 28725484 PMCID: PMC5516866 DOI: 10.1038/npjsba.2016.36] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/13/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022] Open
Abstract
Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate favorable oxygen concentrations. Despite oxygen's fundamental role for life, even key aspects of aerotaxis remain poorly understood. In Bacillus subtilis, for example, there is conflicting evidence of whether migration occurs to the maximal oxygen concentration available or to an optimal intermediate one, and how aerotaxis can be maintained over a broad range of conditions. Using precisely controlled oxygen gradients in a microfluidic device, spanning the full spectrum of conditions from quasi-anoxic to oxic (60 n mol/l-1 m mol/l), we resolved B. subtilis' 'oxygen preference conundrum' by demonstrating consistent migration towards maximum oxygen concentrations ('monotonic aerotaxis'). Surprisingly, the strength of aerotaxis was largely unchanged over three decades in oxygen concentration (131 n mol/l-196 μ mol/l). We discovered that in this range B. subtilis responds to the logarithm of the oxygen concentration gradient, a rescaling strategy called 'log-sensing' that affords organisms high sensitivity over a wide range of conditions. In these experiments, high-throughput single-cell imaging yielded the best signal-to-noise ratio of any microbial taxis study to date, enabling the robust identification of the first mathematical model for aerotaxis among a broad class of alternative models. The model passed the stringent test of predicting the transient aerotactic response despite being developed on steady-state data, and quantitatively captures both monotonic aerotaxis and log-sensing. Taken together, these results shed new light on the oxygen-seeking capabilities of B. subtilis and provide a blueprint for the quantitative investigation of the many other forms of microbial taxis.
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Affiliation(s)
- Filippo Menolascina
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Scotland, UK.,SynthSys-Centre for Synthetic and Systems Biology, The University of Edinburgh, Scotland, UK
| | - Roberto Rusconi
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Vicente I Fernandez
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Steven Smriga
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Zahra Aminzare
- The Program in Applied and Computational Mathematics, Princeton, NJ, USA
| | - Eduardo D Sontag
- Department of Mathematics, Hill Center Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Roman Stocker
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
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46
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Hussain YH, Sadilek M, Salad S, Zimmer RK, Riffell JA. Individual female differences in chemoattractant production change the scale of sea urchin gamete interactions. Dev Biol 2017; 422:186-197. [PMID: 28088316 DOI: 10.1016/j.ydbio.2017.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/02/2017] [Accepted: 01/10/2017] [Indexed: 01/13/2023]
Abstract
Sperm selection by females is an important process influencing fertilization and, particularly in broadcast-spawning organisms, often occurs before sperm reach the egg. Waterborne sperm chemoattractants are one mechanism by which eggs selectively influence conspecific sperm behavior, but it remains an open question whether the eggs from different females produce different amounts of sperm chemoattractant, and how that might influence sperm behavior. Here, we quantify the differences in attractant production between females of the sea urchin species Lytechinus pictus and use computational models and microfluidic sperm chemotaxis assays to determine how differences in chemoattractant production between females affects their ability to attract sperm. Our study demonstrates that there is significant individual female variation in egg chemoattractant production, and that this variation changes the scope and strength of sperm attraction. These results provide evidence for the importance of individual female variability in differential sperm attraction and fertilization success.
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Affiliation(s)
- Yasmeen H Hussain
- University of Washington, Department of Biology, Seattle, WA 98195, USA
| | - Martin Sadilek
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Shukri Salad
- University of Washington, Department of Biology, Seattle, WA 98195, USA
| | - Richard K Zimmer
- University of California Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, CA 90095, USA
| | - Jeffrey A Riffell
- University of Washington, Department of Biology, Seattle, WA 98195, USA
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47
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Bhattacharjee N, Folch A. Large-scale microfluidic gradient arrays reveal axon guidance behaviors in hippocampal neurons. MICROSYSTEMS & NANOENGINEERING 2017; 3:17003. [PMID: 31057858 PMCID: PMC6445017 DOI: 10.1038/micronano.2017.3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/30/2016] [Accepted: 12/10/2016] [Indexed: 05/05/2023]
Abstract
High-throughput quantitative approaches to study axon growth behaviors have remained a challenge. We have developed a 1024-chamber microfluidic gradient generator array that enables large-scale investigations of axon guidance and growth dynamics from individual primary mammalian neurons, which are exposed to gradients of diffusible molecules. Our microfluidic method (a) generates statistically rich data sets, (b) produces a stable, reproducible gradient with negligible shear stresses on the culture surface, (c) is amenable to the long-term culture of primary neurons without any unconventional protocol, and (d) eliminates the confounding influence of cell-secreted factors. Using this platform, we demonstrate that hippocampal axon guidance in response to a netrin-1 gradient is concentration-dependent-attractive at higher concentrations and repulsive at lower concentrations. We also show that the turning of the growth cone depends on the angle of incidence of the gradient. Our study highlights the potential of microfluidic devices in producing large amounts of data from morphogen and chemokine gradients that play essential roles not only in axonal navigation but also in stem cell differentiation, cell migration, and immune response.
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Affiliation(s)
- Nirveek Bhattacharjee
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Foege N423-A, Seattle, WA 98195, USA
- ()
| | - Albert Folch
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Foege N423-A, Seattle, WA 98195, USA
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48
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Menachery A, Kumawat N, Qasaimeh MA. Merging orthogonal microfluidic flows to generate multi-profile concentration gradients. RSC Adv 2017. [DOI: 10.1039/c7ra09692e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This work describes a novel microfluidic device capable of generating multi-profile gradients that include sigmoidal, parabolic, and exponential concentration variations across its main channel.
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Affiliation(s)
- A. Menachery
- Division of Engineering
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - N. Kumawat
- Division of Engineering
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - M. A. Qasaimeh
- Division of Engineering
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
- Department of Mechanical and Aerospace Engineering
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49
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Wolfram CJ, Rubloff GW, Luo X. Perspectives in flow-based microfluidic gradient generators for characterizing bacterial chemotaxis. BIOMICROFLUIDICS 2016; 10:061301. [PMID: 27917249 PMCID: PMC5106431 DOI: 10.1063/1.4967777] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/31/2016] [Indexed: 05/08/2023]
Abstract
Chemotaxis is a phenomenon which enables cells to sense concentrations of certain chemical species in their microenvironment and move towards chemically favorable regions. Recent advances in microbiology have engineered the chemotactic properties of bacteria to perform novel functions, but traditional methods of characterizing chemotaxis do not fully capture the associated cell motion, making it difficult to infer mechanisms that link the motion to the microbiology which induces it. Microfluidics offers a potential solution in the form of gradient generators. Many of the gradient generators studied to date for this application are flow-based, where a chemical species diffuses across the laminar flow interface between two solutions moving through a microchannel. Despite significant research efforts, flow-based gradient generators have achieved mixed success at accurately capturing the highly subtle chemotactic responses exhibited by bacteria. Here we present an analysis encompassing previously published versions of flow-based gradient generators, the theories that govern their gradient-generating properties, and new, more practical considerations that result from experimental factors. We conclude that flow-based gradient generators present a challenge inherent to their design in that the residence time and gradient decay must be finely balanced, and that this significantly narrows the window for reliable observation and quantification of chemotactic motion. This challenge is compounded by the effects of shear on an ellipsoidal bacterium that causes it to preferentially align with the direction of flow and subsequently suppresses the cross-flow chemotactic response. These problems suggest that a static, non-flowing gradient generator may be a more suitable platform for chemotaxis studies in the long run, despite posing greater difficulties in design and fabrication.
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Affiliation(s)
- Christopher J Wolfram
- Department of Materials Science and Engineering, University of Maryland , College Park, Maryland 20742, USA
| | - Gary W Rubloff
- Department of Materials Science and Engineering, University of Maryland , College Park, Maryland 20742, USA
| | - Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America , Washington, DC 20064, USA
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Shin S, Ahmed I, Hwang J, Seo Y, Lee E, Choi J, Moon S, Hong JW. A Microfluidic Approach to Investigating a Synergistic Effect of Tobramycin and Sodium Dodecyl Sulfate on Pseudomonas aeruginosa Biofilms. ANAL SCI 2016; 32:67-73. [PMID: 26753708 DOI: 10.2116/analsci.32.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent years, a microfluidic technology has contributed a significant role in biological research, specifically for the study of biofilms. Bacterial biofilms are a source of infections and contamination in the environment due to an extra polymeric matrix. Inadequate uses of antibiotics make the bacterial biofilms antibiotic resistant. Therefore, it is important to determine the effective concentration of antibiotics in order to eliminate bacterial biofilms. The present microfluidic study was carried out to analyze the activities of tobramycin and sodium dodecyl sulfate (SDS) against Pseudomonas aeruginosa biofilms with a continuous flow in order to achieve a greater delivery of the agents. The results show that a co-treatment of tobramycin and SDS significantly reduced the biomass of biofilms (by more than 99%) after 24 h. Tobramycin and SDS killed and detached bacteria in the cores of biofilms. Evidently, our data suggest that a microchannel would be effective for both quantitative and qualitative evaluations in order to test combinatorial effect of drugs and chemicals on a complexed biological system including biofilm.
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Affiliation(s)
- Soojeong Shin
- Department of Bionano Engineering, Hanyang University
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