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Canales-Huerta N, Cádiz M, Ulloa MT, Chilet LA, Palma K, Jara-Wilde J, Cuevas F, González MJ, Navarro N, Toledo J, Castañeda V, Scavone P, Härtel S. Delayed biofilm formation in non-motile uropathogenic Escherichia coli strain in static and dynamic growth conditions. Microb Pathog 2025; 206:107712. [PMID: 40412736 DOI: 10.1016/j.micpath.2025.107712] [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: 12/12/2024] [Revised: 05/04/2025] [Accepted: 05/15/2025] [Indexed: 05/27/2025]
Abstract
Urinary tract infections associated with the placement of indwelling urinary catheters are a significant concern in hospital settings, as they are linked to an increased risk of severe infections and complications due to biofilm formation. These infections are primarily caused by uropathogens such as Escherichia coli (UPEC). UPEC possesses peritrichous flagella, which facilitates its motility, adhesion to surfaces, and biofilm formation. Understanding the development of UPEC communities is essential for developing effective treatment and eradication strategies. In this study, we characterized the biofilm formation of a clinical non-motile UPEC strain under both static and dynamic culture conditions that simulate the urinary catheter environment. We developed a dynamic culture system coupled with light sheet fluorescence microscopy (LSFM) to quantify the stages of biofilm formation over time. Our results demonstrate that flagella play a crucial role in the initial phase of biofilm formation. The non-motile strain exhibited a delay in the adhesion phase compared to motile strains but ultimately formed biofilms of similar volume during subsequent stages. These findings highlight the significance of flagella in dynamic biofilm formation models and provide valuable insights for modeling the evolution of bacterial communities in nosocomial environments using LSFM.
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Affiliation(s)
- Nicole Canales-Huerta
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Martín Cádiz
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | - Lucas Alé Chilet
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Karina Palma
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jorge Jara-Wilde
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Fabrizio Cuevas
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - María José González
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Nicolás Navarro
- Advanced Center for Chronic Diseases ACCDiS, Santiago, Chile; Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jorge Toledo
- Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Victor Castañeda
- Departamento de Tecnología Médica, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Paola Scavone
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Steffen Härtel
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile; Centro Nacional en Sistemas de Información en Salud CENS, Santiago, Chile; Centro de Modelamiento Matemático CMM, Universidad de Chile, Santiago, Beauchef 851, Casilla 170-3, Santiago, Chile.
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2
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Espinoza Miranda SS, Abbaszade G, Hess WR, Drescher K, Saliba AE, Zaburdaev V, Chai L, Dreisewerd K, Grünberger A, Westendorf C, Müller S, Mascher T. Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges. Microbiol Mol Biol Rev 2025; 89:e0013824. [PMID: 39853129 PMCID: PMC11948493 DOI: 10.1128/mmbr.00138-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2025] Open
Abstract
SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.
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Affiliation(s)
| | | | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | | | - Antoine-Emmanuel Saliba
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Alexander Grünberger
- Microsystems in Bioprocess Engineering (μBVT), Institute of Process Engineering in Life Sciences (BLT), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Christian Westendorf
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Susann Müller
- Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Thorsten Mascher
- General Microbiology, Technische Universität Dresden, Dresden, Germany
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3
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Gao W, Bai Y, Yang Y, Jia L, Mi Y, Cui W, Liu D, Shakoor A, Zhao L, Li J, Luo T, Sun D, Jiang Z. Intelligent sensing for the autonomous manipulation of microrobots toward minimally invasive cell surgery. APPLIED PHYSICS REVIEWS 2024; 11. [DOI: 10.1063/5.0211141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
Abstract
The physiology and pathogenesis of biological cells have drawn enormous research interest. Benefiting from the rapid development of microfabrication and microelectronics, miniaturized robots with a tool size below micrometers have widely been studied for manipulating biological cells in vitro and in vivo. Traditionally, the complex physiological environment and biological fragility require human labor interference to fulfill these tasks, resulting in high risks of irreversible structural or functional damage and even clinical risk. Intelligent sensing devices and approaches have been recently integrated within robotic systems for environment visualization and interaction force control. As a consequence, microrobots can be autonomously manipulated with visual and interaction force feedback, greatly improving accuracy, efficiency, and damage regulation for minimally invasive cell surgery. This review first explores advanced tactile sensing in the aspects of sensing principles, design methodologies, and underlying physics. It also comprehensively discusses recent progress on visual sensing, where the imaging instruments and processing methods are summarized and analyzed. It then introduces autonomous micromanipulation practices utilizing visual and tactile sensing feedback and their corresponding applications in minimally invasive surgery. Finally, this work highlights and discusses the remaining challenges of current robotic micromanipulation and their future directions in clinical trials, providing valuable references about this field.
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Affiliation(s)
- Wendi Gao
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Yunfei Bai
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Yujie Yang
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Lanlan Jia
- Department of Electronic Engineering, Ocean University of China 2 , Qingdao 266400,
| | - Yingbiao Mi
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Wenji Cui
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Dehua Liu
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Adnan Shakoor
- Department of Control and Instrumentation Engineering, King Fahd University of Petroleum and Minerals 3 , Dhahran 31261,
| | - Libo Zhao
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
| | - Junyang Li
- Department of Electronic Engineering, Ocean University of China 2 , Qingdao 266400,
| | - Tao Luo
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University 4 , Xiamen 361102,
| | - Dong Sun
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
- Department of Biomedical Engineering, City University of Hong Kong 5 , Hong Kong 999099,
| | - Zhuangde Jiang
- State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Overseas Expertise Introduction Center for Micro/Nano Manufacturing and Nano Measurement Technologies Discipline Innovation, Xi'an Jiaotong University (Yantai) Research Institute for Intelligent Sensing Technology and System, School of Instrument Science and Technology, Xi'an Jiaotong University 1 , Xi'an 710049,
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4
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Chow DJX, Schartner EP, Corsetti S, Upadhya A, Morizet J, Gunn-Moore FJ, Dunning KR, Dholakia K. Quantifying DNA damage following light sheet and confocal imaging of the mammalian embryo. Sci Rep 2024; 14:20760. [PMID: 39237572 PMCID: PMC11377761 DOI: 10.1038/s41598-024-71443-x] [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: 12/22/2023] [Accepted: 08/28/2024] [Indexed: 09/07/2024] Open
Abstract
Embryo quality assessment by optical imaging is increasing in popularity. Among available optical techniques, light sheet microscopy has emerged as a superior alternative to confocal microscopy due to its geometry, enabling faster image acquisition with reduced photodamage to the sample. However, previous assessments of photodamage induced by imaging may have failed to measure more subtle impacts. In this study, we employed DNA damage as a sensitive indicator of photodamage. We use light sheet microscopy with excitation at a wavelength of 405 nm for imaging embryo autofluorescence and compare its performance to laser scanning confocal microscopy. At an equivalent signal-to-noise ratio for images acquired with both modalities, light sheet microscopy reduced image acquisition time by ten-fold, and did not induce DNA damage when compared to non-imaged embryos. In contrast, imaging with confocal microscopy led to significantly higher levels of DNA damage within embryos and had a higher photobleaching rate. Light sheet imaging is also capable of inducing DNA damage within the embryo but requires multiple cycles of volumetric imaging. Collectively, this study confirms that light sheet microscopy is faster and safer than confocal microscopy for imaging live embryos, indicating its potential as a label-free diagnostic for embryo quality.
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Affiliation(s)
- Darren J X Chow
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
| | - Erik P Schartner
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
| | - Stella Corsetti
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK.
| | - Avinash Upadhya
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
| | - Josephine Morizet
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Frank J Gunn-Moore
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Kylie R Dunning
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia
| | - Kishan Dholakia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia.
- Centre of Light for Life, The University of Adelaide, Adelaide, Australia.
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, UK.
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5
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Chen Y, Chauhan S, Gong C, Dayton H, Xu C, De La Cruz ED, Tsai YYW, Datta MS, Rosoklija GB, Dwork AJ, Mann JJ, Boldrini M, Leong KW, Dietrich LEP, Tomer R. Low-cost and scalable projected light-sheet microscopy for the high-resolution imaging of cleared tissue and living samples. Nat Biomed Eng 2024; 8:1109-1123. [PMID: 39209948 DOI: 10.1038/s41551-024-01249-9] [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: 08/06/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Light-sheet fluorescence microscopy (LSFM) is a widely used technique for imaging cleared tissue and living samples. However, high-performance LSFM systems are typically expensive and not easily scalable. Here we introduce a low-cost, scalable and versatile LSFM framework, which we named 'projected light-sheet microscopy' (pLSM), with high imaging performance and small device and computational footprints. We characterized the capabilities of pLSM, which repurposes readily available consumer-grade components, optimized optics, over-network control architecture and software-driven light-sheet modulation, by performing high-resolution mapping of cleared mouse brains and of post-mortem pathological human brain samples, and via the molecular phenotyping of brain and blood-vessel organoids derived from human induced pluripotent stem cells. We also report a method that leverages pLSM for the live imaging of the dynamics of sparsely labelled multi-layered bacterial pellicle biofilms at an air-liquid interface. pLSM can make high-resolution LSFM for biomedical applications more accessible, affordable and scalable.
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Affiliation(s)
- Yannan Chen
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Cheng Gong
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Yu-Young Wesley Tsai
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Malika S Datta
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
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Ohmura T, Skinner DJ, Neuhaus K, Choi GPT, Dunkel J, Drescher K. In Vivo Microrheology Reveals Local Elastic and Plastic Responses Inside 3D Bacterial Biofilms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314059. [PMID: 38511867 DOI: 10.1002/adma.202314059] [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] [Revised: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Bacterial biofilms are highly abundant 3D living materials capable of performing complex biomechanical and biochemical functions, including programmable growth, self-repair, filtration, and bioproduction. Methods to measure internal mechanical properties of biofilms in vivo with spatial resolution on the cellular scale have been lacking. Here, thousands of cells are tracked inside living 3D biofilms of the bacterium Vibrio cholerae during and after the application of shear stress, for a wide range of stress amplitudes, periods, and biofilm sizes, which revealed anisotropic elastic and plastic responses of both cell displacements and cell reorientations. Using cellular tracking to infer parameters of a general mechanical model, spatially-resolved measurements of the elastic modulus inside the biofilm are obtained, which correlate with the spatial distribution of the polysaccharides within the biofilm matrix. The noninvasive microrheology and force-inference approach introduced here provides a general framework for studying mechanical properties with high spatial resolution in living materials.
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Affiliation(s)
- Takuya Ohmura
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| | - Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60201, USA
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Gary P T Choi
- Department of Mathematics, The Chinese University of Hong Kong, N.T., Hong Kong
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
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7
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Kume D, Kozawa Y, Kawakami R, Ishii H, Watakabe Y, Uesugi Y, Imamura T, Nemoto T, Sato S. Graded arc beam in light needle microscopy for axially resolved, rapid volumetric imaging without nonlinear processes. OPTICS EXPRESS 2024; 32:7289-7306. [PMID: 38439413 DOI: 10.1364/oe.516437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
High-speed three-dimensional (3D) imaging is essential for revealing the structure and functions of biological specimens. Confocal laser scanning microscopy has been widely employed for this purpose. However, it requires a time-consuming image-stacking procedure. As a solution, we previously developed light needle microscopy using a Bessel beam with a wavefront-engineered approach [Biomed. Opt. Express13, 1702 (2022)10.1364/BOE.449329]. However, this method applies only to multiphoton excitation microscopy because of the requirement to reduce the sidelobes of the Bessel beam. Here, we introduce a beam that produces a needle spot while eluding the intractable artifacts due to the sidelobes. This beam can be adopted even in one-photon excitation fluorescence 3D imaging. The proposed method can achieve real-time, rapid 3D observation of 200-nm particles in water at a rate of over 50 volumes per second. In addition, fine structures, such as the spines of neurons in fixed mouse brain tissue, can be visualized in 3D from a single raster scan of the needle spot. The proposed method can be applied to various modalities in biological imaging, enabling rapid 3D image acquisition.
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8
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Wang N, Zhang C, Wei X, Yan T, Zhou W, Zhang J, Kang H, Yuan Z, Chen X. Harnessing the power of optical microscopy for visualization and analysis of histopathological images. BIOMEDICAL OPTICS EXPRESS 2023; 14:5451-5465. [PMID: 37854561 PMCID: PMC10581782 DOI: 10.1364/boe.501893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 10/20/2023]
Abstract
Histopathology is the foundation and gold standard for identifying diseases, and precise quantification of histopathological images can provide the pathologist with objective clues to make a more convincing diagnosis. Optical microscopy (OM), an important branch of optical imaging technology that provides high-resolution images of tissue cytology and structural morphology, has been used in the diagnosis of histopathology and evolved into a new disciplinary direction of optical microscopic histopathology (OMH). There are a number of ex-vivo studies providing applicability of different OMH approaches, and a transfer of these techniques toward in vivo diagnosis is currently in progress. Furthermore, combined with advanced artificial intelligence algorithms, OMH allows for improved diagnostic reliability and convenience due to the complementarity of retrieval information. In this review, we cover recent advances in OMH, including the exploration of new techniques in OMH as well as their applications, and look ahead to new challenges in OMH. These typical application examples well demonstrate the application potential and clinical value of OMH techniques in histopathological diagnosis.
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Affiliation(s)
- Nan Wang
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Chang Zhang
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
| | - Xinyu Wei
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
| | - Tianyu Yan
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Wangting Zhou
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Jiaojiao Zhang
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Huan Kang
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Zhen Yuan
- Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Xueli Chen
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
- Inovation Center for Advanced Medical Imaging and Intelligent Medicine, Guangzhou Institute of Technology, Xidian University, Guangzhou, Guangdong 510555, China
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9
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Kim J. Recent advances in oblique plane microscopy. NANOPHOTONICS (BERLIN, GERMANY) 2023; 12:2317-2334. [PMID: 39633752 PMCID: PMC11501266 DOI: 10.1515/nanoph-2023-0002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/10/2023] [Indexed: 12/07/2024]
Abstract
Oblique plane microscopy (OPM) directly captures object information in a plane tilted from the focal plane of the objective lens without the need for slow z-stack acquisition. This unconventional widefield imaging approach is made possible by using a remote focusing principle that eliminates optical aberrations for object points beyond the focal plane. Together with oblique lightsheet illumination, OPM can make conventional lightsheet imaging fully compatible with standard biological specimens prepared on microscope slides. OPM is not only an excellent high-speed volumetric imaging platform by sweeping oblique lightsheet illumination without mechanically moving either the sample or objective lens in sample space, but also provides a solution for direct oblique plane imaging along any orientation of interest on the sample in a single shot. Since its first demonstration in 2008, OPM has continued to evolve into an advanced microscope platform for biological, medical, and materials science applications. In recent years, many technological advances have been made in OPM with the goal of super-resolution, fast volumetric imaging, and a large imaging field of view, etc. This review gives an overview of OPM's working principle and imaging performance and introduces recent technical developments in OPM methods and applications. OPM has strong potential in a variety of research fields, including cellular and developmental biology, clinical diagnostics in histology and ophthalmology, flow cytometry, microfluidic devices, and soft materials.
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Affiliation(s)
- Jeongmin Kim
- Department of Applied Bioengineering, Graduate School of Convergence Science and Technology, Seoul National University, Seoul08826, Republic of Korea
- Research Institute for Convergence Science, Seoul National University, Seoul08826, Republic of Korea
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10
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Alnahhas RN, Dunlop MJ. Advances in linking single-cell bacterial stress response to population-level survival. Curr Opin Biotechnol 2023; 79:102885. [PMID: 36641904 PMCID: PMC9899315 DOI: 10.1016/j.copbio.2022.102885] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.
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Affiliation(s)
- Razan N Alnahhas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States.
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11
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BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations. NPJ Biofilms Microbiomes 2022; 8:99. [PMID: 36529755 PMCID: PMC9760640 DOI: 10.1038/s41522-022-00362-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Accurate detection and segmentation of single cells in three-dimensional (3D) fluorescence time-lapse images is essential for observing individual cell behaviors in large bacterial communities called biofilms. Recent progress in machine-learning-based image analysis is providing this capability with ever-increasing accuracy. Leveraging the capabilities of deep convolutional neural networks (CNNs), we recently developed bacterial cell morphometry in 3D (BCM3D), an integrated image analysis pipeline that combines deep learning with conventional image analysis to detect and segment single biofilm-dwelling cells in 3D fluorescence images. While the first release of BCM3D (BCM3D 1.0) achieved state-of-the-art 3D bacterial cell segmentation accuracies, low signal-to-background ratios (SBRs) and images of very dense biofilms remained challenging. Here, we present BCM3D 2.0 to address this challenge. BCM3D 2.0 is entirely complementary to the approach utilized in BCM3D 1.0. Instead of training CNNs to perform voxel classification, we trained CNNs to translate 3D fluorescence images into intermediate 3D image representations that are, when combined appropriately, more amenable to conventional mathematical image processing than a single experimental image. Using this approach, improved segmentation results are obtained even for very low SBRs and/or high cell density biofilm images. The improved cell segmentation accuracies in turn enable improved accuracies of tracking individual cells through 3D space and time. This capability opens the door to investigating time-dependent phenomena in bacterial biofilms at the cellular level.
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12
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Yin Y, Shen H. Common methods in mitochondrial research (Review). Int J Mol Med 2022; 50:126. [PMID: 36004457 PMCID: PMC9448300 DOI: 10.3892/ijmm.2022.5182] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yiyuan Yin
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Haitao Shen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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13
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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14
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Kozawa Y, Nakamura T, Uesugi Y, Sato S. Wavefront engineered light needle microscopy for axially resolved rapid volumetric imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:1702-1717. [PMID: 35415006 PMCID: PMC8973193 DOI: 10.1364/boe.449329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Increasing the acquisition speed of three-dimensional volumetric images is important-particularly in biological imaging-to unveil the structural dynamics and functionalities of specimens in detail. In conventional laser scanning fluorescence microscopy, volumetric images are constructed from optical sectioning images sequentially acquired by changing the observation plane, limiting the acquisition speed. Here, we present a novel method to realize volumetric imaging from two-dimensional raster scanning of a light needle spot without sectioning, even in the traditional framework of laser scanning microscopy. Information from multiple axial planes is simultaneously captured using wavefront engineering for fluorescence signals, allowing us to readily survey the entire depth range while maintaining spatial resolution. This technique is applied to real-time and video-rate three-dimensional tracking of micrometer-sized particles, as well as the prompt visualization of thick fixed biological specimens, offering substantially faster volumetric imaging.
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Affiliation(s)
- Yuichi Kozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoya Nakamura
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuuki Uesugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shunichi Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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15
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Zhang J, Zhang M, Wang Y, Donarski E, Gahlmann A. Optically Accessible Microfluidic Flow Channels for Noninvasive High-Resolution Biofilm Imaging Using Lattice Light Sheet Microscopy. J Phys Chem B 2021; 125:12187-12196. [PMID: 34714647 DOI: 10.1021/acs.jpcb.1c07759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Imaging platforms that enable long-term, high-resolution imaging of biofilms are required to study cellular level dynamics within bacterial biofilms. By combining high spatial and temporal resolution and low phototoxicity, lattice light sheet microscopy (LLSM) has made critical contributions to the study of cellular dynamics. However, the power of LLSM has not yet been leveraged for biofilm research because the open-on-top imaging geometry using water-immersion objective lenses is not compatible with living bacterial specimens; bacterial growth on the microscope's objective lenses makes long-term time-lapse imaging impossible and raises considerable safety concerns for microscope users. To make LLSM compatible with pathogenic bacterial specimens, we developed hermetically sealed, but optically accessible, microfluidic flow channels that can sustain bacterial biofilm growth for multiple days under precisely controllable physical and chemical conditions. To generate a liquid- and gas-tight seal, we glued a thin polymer film across a 3D-printed channel, where the top wall had been omitted. We achieved negligible optical aberrations by using polymer films that precisely match the refractive index of water. Bacteria do not adhere to the polymer film itself, so that the polymer window provides unobstructed optical access to the channel interior. Inside the flow channels, biofilms can be grown on arbitrary, even nontransparent, surfaces. By integrating this flow channel with LLSM, we were able to record the growth of S. oneidensis MR-1 biofilms over several days at cellular resolution without any observable phototoxicity or photodamage.
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Affiliation(s)
- Ji Zhang
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mingxing Zhang
- School of Materials Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yibo Wang
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Eric Donarski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Andreas Gahlmann
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
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