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Datta SS, Battiato I, Fernø MA, Juanes R, Parsa S, Prigiobbe V, Santanach-Carreras E, Song W, Biswal SL, Sinton D. Lab on a chip for a low-carbon future. LAB ON A CHIP 2023; 23:1358-1375. [PMID: 36789954 DOI: 10.1039/d2lc00020b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transitioning our society to a sustainable future, with low or net-zero carbon emissions to the atmosphere, will require a wide-spread transformation of energy and environmental technologies. In this perspective article, we describe how lab-on-a-chip (LoC) systems can help address this challenge by providing insight into the fundamental physical and geochemical processes underlying new technologies critical to this transition, and developing the new processes and materials required. We focus on six areas: (I) subsurface carbon sequestration, (II) subsurface hydrogen storage, (III) geothermal energy extraction, (IV) bioenergy, (V) recovering critical materials, and (VI) water filtration and remediation. We hope to engage the LoC community in the many opportunities within the transition ahead, and highlight the potential of LoC approaches to the broader community of researchers, industry experts, and policy makers working toward a low-carbon future.
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Affiliation(s)
- Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton NJ, USA.
| | - Ilenia Battiato
- Department of Energy Science and Engineering, Stanford University, Palo Alto CA, USA
| | - Martin A Fernø
- Department of Physics and Technology, University of Bergen, 5020, Bergen, Norway
| | - Ruben Juanes
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Shima Parsa
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester NY, USA
| | - Valentina Prigiobbe
- Department of Civil, Environmental, and Ocean Engineering, Stevens Institute of Technology, Hoboken NJ, USA
- Department of Geosciences, University of Padova, Padova, Italy
| | | | - Wen Song
- Hildebrand Department of Petroleum and Geosystems Engineering, University of Texas at Austin, Austin TX, USA
| | - Sibani Lisa Biswal
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto ON, Canada.
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2
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Zhao X, Ford RM. Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient. Biotechnol Bioeng 2022; 119:2564-2573. [PMID: 35716141 DOI: 10.1002/bit.28161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/20/2022] [Accepted: 06/08/2022] [Indexed: 11/07/2022]
Abstract
In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, α-methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted bacteria response to chemoeffector mixtures. Migration of E. coli toward α-methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xueying Zhao
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - Roseanne M Ford
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
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3
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Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oil pollution in soil-groundwater systems is difficult to remove, and a large amount of residual oil is trapped in the low permeable layer of the heterogeneous aquifer. Aromatic hydrocarbons in oil have high toxicity and low solubility in water, which are harmful to the ecological environment. Chemotactic degrading bacteria can perceive the concentration gradient of non-aqueous phase liquid (NAPL) pollutants in the groundwater environment, and enrich and proliferate around the pollutants, thus achieving a more efficient and thorough remediation effect. However, the existing theoretical models are relatively simple. The physical fields of oil–water two-phase flow and oil-phase solute convection and diffusion in water are not coupled, which further restricts the accuracy of studies on bacterial chemotaxis to NAPL. In this study, geometric models based on the actual microfluidic experimental study were constructed. Based on the phase field model, diffusion convection equation and chemotaxis velocity equation, the effects of heterogeneity of porous media, wall wettability and groundwater flow rate on the residual oil and the concentration distribution of chemotaxis bacteria were studied. Under all of the simulation conditions, the residual oil in the high permeable area was significantly lower than that in the low permeable area, and the wall hydrophilicity enhanced the water flooding effect. Chemotactic bacteria could react to the concentration gradient of pollutants dissolved into water in the oil phase, and enrich near the oil–water interface with high concentration of NAPL, and the density of chemotactic bacteria at the oil–water interface can be up to 1.8–2 times higher than that in the water phase at flow rates from 1.13 to 6.78 m/d.
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4
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Tahir U, Aslam F, Nawaz S, Khan UH, Yasmin A. Annotation of chemotaxis gene clusters and proteins involved in chemotaxis of Bacillus subtilis strain MB378 capable of biodecolorizing different dyes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3510-3520. [PMID: 34389949 DOI: 10.1007/s11356-021-15634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
This study explores the chemotactic potential of Bacillus subtilis MB378 against industrial dyes. Initial screening with swim plate assay showed significant movement of Bacillus subtilis MB378 towards test compounds. According to quantitative capillary assay, B. subtilis MB378 exhibited high chemotaxis potential towards Acid Orange 52 (CI: 9.52), followed by Direct Red 28 (CI: 8.39) and Basic Green 4 (CI: 5.21) in glucose-supplemented medium. Sequencing and gene annotation results evidently showed presence of chemotaxis genes and flagellar motor proteins in Bacillus subtilis draft genome. Methyl-accepting proteins (involved in chemotaxis regulation) belonged to pfam00672, pfam00072, and pfam00015 protein families. Annotated chemotaxis machinery of MB378 comprised 8 Che genes, 5 chemoreceptor genes, associated flagellar proteins, and rotary motors. Chemotaxis genes of B. subtilis MB378 were compared with genes of closely related Bacillus strains (168, WK1, and HTA426), depicting highly conserved regions showing evolutionary relation between them. Considering results of present study, it can be speculated that test compounds triggered chemotactic genes, which made these compounds bioavailable to the bacterium. Hence, the bacterium recognized and approached these compounds and facilitated biodegradation and detoxification of these compounds.
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Affiliation(s)
- Uruj Tahir
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
- Department of Environmental Sciences, Faculty of Natural Sciences, University of Okara, Okara, 56130, Pakistan.
| | - Fozia Aslam
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
| | - Shiza Nawaz
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Umair Hassan Khan
- School of Agriculture and Environment, The University of Western Australia, Crawley, Perth, Australia
| | - Azra Yasmin
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
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5
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Kerk YJ, Jameel A, Xing X, Zhang C. Recent advances of integrated microfluidic suspension cell culture system. ENGINEERING BIOLOGY 2021; 5:103-119. [PMID: 36970555 PMCID: PMC9996741 DOI: 10.1049/enb2.12015] [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: 07/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.
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Affiliation(s)
- Yi Jing Kerk
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Aysha Jameel
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Xin‐Hui Xing
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| | - Chong Zhang
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
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Middlebrooks SA, Zhao X, Ford RM, Cummings PT. A mathematical model for Escherichia coli chemotaxis to competing stimuli. Biotechnol Bioeng 2021; 118:4678-4686. [PMID: 34463958 DOI: 10.1002/bit.27930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 11/12/2022]
Abstract
Chemotactic bacteria sense and respond to temporal and spatial gradients of chemical cues in their surroundings. This phenomenon plays a critical role in many microbial processes such as groundwater bioremediation, microbially enhanced oil recovery, nitrogen fixation in legumes, and pathogenesis of the disease. Chemical heterogeneity in these natural systems may produce numerous competing signals from various directions. Predicting the migration behavior of bacterial populations under such conditions is necessary for designing effective treatment schemes. In this study, experimental studies and mathematical models are reported for the chemotactic response of Escherichia coli to a combination of attractant (α-methylaspartate) and repellent (NiCl2 ), which bind to the same transmembrane receptor complex. The model describes the binding of chemoeffectors and phosphorylation of the kinase in the signal transduction mechanism. Chemotactic parameters of E. coli (signaling efficiency σ , stimuli sensitivity coefficient γ , and repellent sensitivity coefficient κ ) were determined by fitting the model with experimental results for individual stimuli. Interestingly, our model naturally identifies NiCl2 as a repellent for κ > 1 . The model is capable of describing quantitatively the response to the individual attractant and repellent, and correctly predicts the change in direction of bacterial population migration for competing stimuli with a twofold increase in repellent concentration.
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Affiliation(s)
- Scott A Middlebrooks
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Xueying Zhao
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Roseanne M Ford
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Peter T Cummings
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
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7
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Xie Z, Pu H, Sun DW. Computer simulation of submicron fluid flows in microfluidic chips and their applications in food analysis. Compr Rev Food Sci Food Saf 2021; 20:3818-3837. [PMID: 34056852 DOI: 10.1111/1541-4337.12766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/24/2021] [Accepted: 04/15/2021] [Indexed: 01/01/2023]
Abstract
In recent years, countries around the world have maintained a zero-tolerance attitude toward safety problems in the food industry. In order to ensure human health, a fast, sensitive, and high-throughput analysis of food contaminants is necessary to ensure safe food products on the market. Microfluidics, as a high-efficiency and sensitive detection technology, has many advantages in the detection of food contaminants, including foodborne pathogens, pesticides, heavy metal ions, toxic substances, and so forth, especially in conjunction with a variety of submicron fluid driving methods, making food detection and analysis more efficient and accurate. This review introduces the principle of submicron fluid driving modes and discusses the driving simulation of submicron fluid in microfluidic chips. In addition, the latest developments in the application of simulation in food analysis from 2006 to 2020 are discussed, and the computer simulation of submicron fluid flow in microfluidic chips and its application and development trend in food analysis are also highlighted. The review indicates that microfluidic technology, using numerical simulation as an auxiliary tool, combined with traditional methods has greatly improved the detection and analysis of food products. In addition, microfluidics combined with a variety of control methods embodies the ability of specific, multifunctional, and sensitive detection and analysis of food products. The development of high-sensitivity, high-throughput, portable, integrated microfluidic chips will enable the technology to be applied in practice.
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Affiliation(s)
- Zhaoda Xie
- School of Mechanical and Electrical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology, School of Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Dublin, Ireland
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8
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Ly KL, Hu P, Pham LHP, Luo X. Flow-assembled chitosan membranes in microfluidics: recent advances and applications. J Mater Chem B 2021; 9:3258-3283. [PMID: 33725061 PMCID: PMC8369861 DOI: 10.1039/d1tb00045d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integration of membranes in microfluidic devices has been extensively exploited for various chemical engineering and bioengineering applications over the past few decades. To augment the applicability of membrane-integrated microfluidic platforms for biomedical and tissue engineering studies, a biologically friendly fabrication process with naturally occurring materials is highly desired. The in situ preparation of membranes involving interfacial reactions between parallel laminar flows in microfluidic networks, known as the flow-assembly technique, is one of the most biocompatible approaches. Membranes of many types with flexible geometries have been successfully assembled inside complex microchannels using this facile and versatile flow-assembly approach. Chitosan is a naturally abundant polysaccharide known for its pronounced biocompatibility, biodegradability, good mechanical stability, ease of modification and processing, and film-forming ability under near-physiological conditions. Chitosan membranes assembled by flows in microfluidics are freestanding, robust, semipermeable, and well-aligned in microstructure, and show high affinity to bioactive reagents and biological components (e.g. biomolecules, nanoparticles, or cells) that provide facile biological functionalization of microdevices. Here, we discuss the recent developments and optimizations in the flow-assembly of chitosan membranes and chitosan-based membranes in microfluidics. Furthermore, we recapitulate the applications of the chitosan membrane-integrated microfluidic platforms dedicated to biology, biochemistry, and drug release fields, and envision the future developments of this important platform with versatile functions.
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Affiliation(s)
- Khanh L Ly
- Department of Biomedical Engineering, The Catholic University of America, Washington, DC 20064, USA
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9
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Abstract
Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.
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10
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Ly KL, Raub CB, Luo X. Tuning the porosity of biofabricated chitosan membranes in microfluidics with co-assembled nanoparticles as templates. MATERIALS ADVANCES 2020; 1:34-44. [PMID: 33073238 PMCID: PMC7518516 DOI: 10.1039/d0ma00073f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 05/04/2023]
Abstract
Biopolymer membranes assembled in microfluidic devices offer many biological process- and analysis-related applications. One of the key characteristics of bio-fabricated membranes is their porosity, which regulates the transport of molecules, ions, or particles and contributes to their semi-permeability and selectivity. This study aims to tune the porosity of biofabricated chitosan membranes (CM) using incorporated nanoparticles as templates. CM with polystyrene nanoparticles (CM-np) were assembled by flow in microchannel networks. The membranes with incorporated nanoparticles were crosslinked with glutaraldehyde, and then the nanoparticles were dissolved with dimethyl sulfoxide. The in situ synthesized porous CM (pCM) were characterized with scanning electron microscopy and polarized light microscopy. Permeability tests confirmed the increased pore sizes of the pCM and enhanced permeability to macromolecules. Sharper static gradients in three-channel microfluidic devices were demonstrated with the pCM as compared to those with the original CM. The capability to customize the porosity of flow-assembled, freestanding and robust biopolymer membranes inside a microfluidic network is attractive and broadens the applications of these membranes in biomolecular and cellular studies.
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Affiliation(s)
- Khanh L Ly
- Department of Biomedical Engineering , Catholic University of America , Washington , DC 20064 , USA
| | - Christopher B Raub
- Department of Biomedical Engineering , Catholic University of America , Washington , DC 20064 , USA
| | - Xiaolong Luo
- Department of Mechanical Engineering , Catholic University of America , Washington , DC 20064 , USA .
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11
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Yang L, Chen X, Zeng X, Radosevich M, Ripp S, Zhuang J, Sayler GS. Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through Soils. Front Microbiol 2019; 10:2691. [PMID: 32038503 PMCID: PMC6988784 DOI: 10.3389/fmicb.2019.02691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/06/2019] [Indexed: 12/25/2022] Open
Abstract
Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L−1), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).
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Affiliation(s)
- Liqiong Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xijuan Chen
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Steven Ripp
- Department of Microbiology, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Jie Zhuang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Gary S Sayler
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
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12
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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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13
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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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14
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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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15
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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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Pham P, Vo T, Luo X. Steering air bubbles with an add-on vacuum layer for biopolymer membrane biofabrication in PDMS microfluidics. LAB ON A CHIP 2017; 17:248-255. [PMID: 27942655 DOI: 10.1039/c6lc01362g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Membrane functionality is crucial in microfluidics for realizing operations such as filtration, separation, concentration, signaling among cells and gradient generation. Currently, common methods often sandwich commercially available membranes in multi-layer devices, or use photopolymerization or temperature-induced gelation to fabricate membrane structures in one-layer devices. Biofabrication offers an alternative to forming membrane structures with biomimetic materials and mechanisms in mild conditions. We have recently developed a biofabrication strategy to form parallel biopolymer membranes in gas-permeable polydimethylsiloxane (PDMS) microfluidic devices, which used positive pressure to dissipate air bubbles through PDMS to initiate membrane formation but required careful pressure balancing between two flows. Here, we report a technical innovation by simply placing as needed an add-on PDMS vacuum layer on PDMS microfluidic devices to dissipate air bubbles and guide the biofabrication of biopolymer membranes. Vacuuming through PDMS was simply achieved by either withdrawing a syringe or releasing a squeezed nasal aspirator. Upon vacuuming, air bubbles dissipated within minutes, membranes were effortlessly formed, and the add-on vacuum layer can be removed. Subsequent membrane growth could be robustly controlled with the flows and pH of solutions. This new process is user-friendly and has achieved a 100% success rate in more than 200 trials in membrane biofabrication.
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Affiliation(s)
- Phu Pham
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Thanh Vo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
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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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Luo X, Vo T, Jambi F, Pham P, Choy JS. Microfluidic partition with in situ biofabricated semipermeable biopolymer membranes for static gradient generation. LAB ON A CHIP 2016; 16:3815-3823. [PMID: 27713976 DOI: 10.1039/c6lc00742b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We report an in situ biofabrication strategy that conveniently partitions microfluidic networks into physically separated while chemically communicating microchannels with semipermeable biopolymer membranes, which enable the facile generation of static gradients for biomedical applications. The biofabrication of parallel biopolymer membranes was initiated with the dissipation of trapped air bubbles in parallel apertures in polydimethylsiloxane (PDMS) microfluidic devices, followed by tunable membrane growth with precise temporal and spatial control to the desired thickness. Static gradients were generated within minutes and well maintained over time by pure diffusion of molecules through the biofabricated semipermeable membranes. As an example application, the static gradient of alpha factor was generated to study the development of the "shmoo" morphology of yeast over time. The in situ biofabrication provides a simple approach to generate static gradients and an ideal platform for biological applications where flow-free static gradients are indispensable.
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Affiliation(s)
- Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Thanh Vo
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Fahad Jambi
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - Phu Pham
- Department of Mechanical Engineering, The Catholic University of America, Washington, D.C. 20064, USA.
| | - John S Choy
- Department of Biology, The Catholic University of America, Washington, D.C. 20064, USA
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Oliveira AF, Pessoa ACSN, Bastos RG, de la Torre LG. Microfluidic tools toward industrial biotechnology. Biotechnol Prog 2016; 32:1372-1389. [DOI: 10.1002/btpr.2350] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/15/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Aline F. Oliveira
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
| | - Amanda C. S. N. Pessoa
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
| | - Reinaldo G. Bastos
- Department of Agroindustrial Technology and Rural Socioeconomy, Center of Agricultural Sciences, Federal University of São Carlos; Km 174 Anhanguera Highway Araras P.O. Box 153
| | - Lucimara G. de la Torre
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
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Wang X, Lanning LM, Ford RM. Enhanced Retention of Chemotactic Bacteria in a Pore Network with Residual NAPL Contamination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:165-172. [PMID: 26633578 DOI: 10.1021/acs.est.5b03872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nonaqueous-phase liquid (NAPL) contaminants are difficult to eliminate from natural aquifers due, in part, to the heterogeneous structure of the soil. Chemotaxis enhances the mixing of bacteria with contaminant sources in low-permeability regions, which may not be readily accessible by advection and dispersion alone. A microfluidic device was designed to mimic heterogeneous features of a contaminated groundwater aquifer. NAPL droplets (toluene) were trapped within a fine pore network, and bacteria were injected through a highly conductive adjacent macrochannel. Chemotactic bacteria (Pseudomonas putida F1) exhibited greater accumulation near the pore network at 0.5 m/day than both the nonchemotactic control and the chemotactic bacteria at a higher groundwater velocity of 5 m/day. Chemotactic bacteria accumulated in the vicinity of NAPL droplets, and the accumulation was 15% greater than a nonchemotactic mutant. Indirect evidence showed that chemotactic bacteria were retained within the contaminated low-permeability region longer than nonchemotactic bacteria at 0.25 m/day. This retention was diminished at 5 m/day. Numerical solutions of the bacterial-transport equations were consistent with the experimental results. Because toluene is degraded by P. putida F1, the accumulation of chemotactic bacteria around NAPL sources is expected to increase contaminant consumption and improve the efficiency of bioremediation.
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Affiliation(s)
- Xiaopu Wang
- School of Petroleum Engineering, China University of Petroleum , Qingdao, Shandong, China 266580
- Department of Chemical Engineering, School of Engineering and Applied Science, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Larry M Lanning
- Department of Chemical Engineering, School of Engineering and Applied Science, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Roseanne M Ford
- Department of Chemical Engineering, School of Engineering and Applied Science, University of Virginia , Charlottesville, Virginia 22904, United States
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Liu C, Yamaguchi Y, Sekine S, Ni Y, Li Z, Zhu X, Dou X. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis. J Sep Sci 2015; 39:986-92. [PMID: 26648455 DOI: 10.1002/jssc.201501087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/09/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment.
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Affiliation(s)
- Chenchen Liu
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, China.,Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China
| | - Yoshinori Yamaguchi
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Shinichi Sekine
- Division of Special Care Dentistry, Osaka University Dental Hospital, Osaka University, Osaka, Japan.,Department of Preventive Dentistry, Osaka University Graduate School of Dentistry Osaka University, Osaka, Japan
| | - Yi Ni
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China
| | - Zhenqing Li
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, China
| | - Xifang Zhu
- School of Optoelectronic Engineering, ChangZhou Institute of Technology, Changzhou, Jiangsu, China
| | - Xiaoming Dou
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China.,School of Optoelectronic Engineering, ChangZhou Institute of Technology, Changzhou, Jiangsu, China
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