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Johnson GE, Fei C, Wingreen NS, Bassler BL. Single-cell gene-expression measurements in Vibrio cholerae biofilms reveal spatiotemporal patterns underlying development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603784. [PMID: 39071398 PMCID: PMC11275835 DOI: 10.1101/2024.07.17.603784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bacteria commonly exist in multicellular, surface-attached communities called biofilms. Biofilms are central to ecology, medicine, and industry. The Vibrio cholerae pathogen forms biofilms from single founder cells that, via cell division, mature into three-dimensional structures with distinct, yet reproducible, regional architectures. To define mechanisms underlying biofilm developmental transitions, we establish a single-molecule fluorescence in situ hybridization (smFISH) approach that enables accurate quantitation of spatiotemporal gene-expression patterns in biofilms at individual-cell resolution. smFISH analyses of V. cholerae biofilm regulatory and structural genes demonstrate that, as biofilms mature, matrix gene expression decreases, and simultaneously, a pattern emerges in which matrix gene expression is largely confined to peripheral biofilm cells. Both quorum sensing and c-di-GMP-signaling are required to generate the proper temporal pattern of matrix gene expression, while c-di-GMP-signaling sets the regional expression pattern without input from quorum sensing. The smFISH strategy provides insight into mechanisms conferring particular fates to individual biofilm cells.
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Affiliation(s)
- Grace E. Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lead Contact
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2
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Prentice JA, Kasivisweswaran S, van de Weerd R, Bridges AA. Biofilm dispersal patterns revealed using far-red fluorogenic probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603607. [PMID: 39071379 PMCID: PMC11275749 DOI: 10.1101/2024.07.15.603607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious. Here, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae. To do so, we first developed a far-red cell-labeling strategy that overcomes pitfalls of fluorescent protein-based approaches. We reveal that dispersal initiates at the biofilm periphery and ~25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression and the formation of dynamic channels. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate.
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Affiliation(s)
- Jojo A. Prentice
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA, USA
| | | | - Robert van de Weerd
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA, USA
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh PA, USA
| | - Andrew A. Bridges
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA, USA
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3
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Black ME, Fei C, Alert R, Wingreen NS, Shaevitz JW. Capillary interactions drive the self-organization of bacterial colonies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596252. [PMID: 38853967 PMCID: PMC11160631 DOI: 10.1101/2024.05.28.596252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.
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4
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Li C, Nijjer J, Feng L, Zhang Q, Yan J, Zhang S. Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms. SOFT MATTER 2024; 20:3401-3410. [PMID: 38563244 DOI: 10.1039/d3sm01535a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Living active collectives have evolved with remarkable self-patterning capabilities to adapt to the physical and biological constraints crucial for their growth and survival. However, the intricate process by which complex multicellular patterns emerge from a single founder cell remains elusive. In this study, we utilize an agent-based model, validated through single-cell microscopy imaging, to track the three-dimensional (3D) morphodynamics of cells within growing bacterial biofilms encased by agarose gels. The confined growth conditions give rise to a spatiotemporally heterogeneous stress landscape within the biofilm. In the core of the biofilm, where high hydrostatic and low shear stresses prevail, cell packing appears disordered. In contrast, near the gel-cell interface, a state of high shear stress and low hydrostatic stress emerges, driving nematic ordering, albeit with a time delay inherent to shear stress relaxation. Strikingly, we observe a robust spatiotemporal correlation between stress anisotropy and nematic ordering within these confined biofilms. This correlation suggests a mechanism whereby stress anisotropy plays a pivotal role in governing the spatial organization of cells. The reciprocity between stress anisotropy and cell ordering in confined biofilms opens new avenues for innovative 3D mechanically guided patterning techniques for living active collectives, which hold significant promise for a wide array of environmental and biomedical applications.
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Affiliation(s)
- Changhao Li
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| | - Luyi Feng
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
| | - Qiuting Zhang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Material Science and Engineering, Pennsylvania State University, University Park, PA, USA
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5
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Prentice JA, van de Weerd R, Bridges AA. Cell-lysis sensing drives biofilm formation in Vibrio cholerae. Nat Commun 2024; 15:2018. [PMID: 38443393 PMCID: PMC10914755 DOI: 10.1038/s41467-024-46399-1] [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] [Received: 11/06/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Matrix-encapsulated communities of bacteria, called biofilms, are ubiquitous in the environment and are notoriously difficult to eliminate in clinical and industrial settings. Biofilm formation likely evolved as a mechanism to protect resident cells from environmental challenges, yet how bacteria undergo threat assessment to inform biofilm development remains unclear. Here we find that population-level cell lysis events induce the formation of biofilms by surviving Vibrio cholerae cells. Survivors detect threats by sensing a cellular component released through cell lysis, which we identify as norspermidine. Lysis sensing occurs via the MbaA receptor with genus-level specificity, and responsive biofilm cells are shielded from phage infection and attacks from other bacteria. Thus, our work uncovers a connection between bacterial lysis and biofilm formation that may be broadly conserved among microorganisms.
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Affiliation(s)
- Jojo A Prentice
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Robert van de Weerd
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andrew A Bridges
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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6
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Xu H, Wu Y. Self-enhanced mobility enables vortex pattern formation in living matter. Nature 2024; 627:553-558. [PMID: 38480895 DOI: 10.1038/s41586-024-07114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/24/2024] [Indexed: 03/22/2024]
Abstract
Ranging from subcellular organelle biogenesis to embryo development, the formation of self-organized structures is a hallmark of living systems. Whereas the emergence of ordered spatial patterns in biology is often driven by intricate chemical signalling that coordinates cellular behaviour and differentiation1-4, purely physical interactions can drive the formation of regular biological patterns such as crystalline vortex arrays in suspensions of spermatozoa5 and bacteria6. Here we discovered a new route to self-organized pattern formation driven by physical interactions, which creates large-scale regular spatial structures with multiscale ordering. Specifically we found that dense bacterial living matter spontaneously developed a lattice of mesoscale, fast-spinning vortices; these vortices each consisted of around 104-105 motile bacterial cells and were arranged in space at greater than centimetre scale and with apparent hexagonal order, whereas individual cells in the vortices moved in coordinated directions with strong polar and vortical order. Single-cell tracking and numerical simulations suggest that the phenomenon is enabled by self-enhanced mobility in the system-that is, the speed of individual cells increasing with cell-generated collective stresses at a given cell density. Stress-induced mobility enhancement and fluidization is prevalent in dense living matter at various scales of length7-9. Our findings demonstrate that self-enhanced mobility offers a simple physical mechanism for pattern formation in living systems and, more generally, in other active matter systems10 near the boundary of fluid- and solid-like behaviours11-17.
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Affiliation(s)
- Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China.
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7
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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8
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Böhning J, Tarafder AK, Bharat TA. The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochem J 2024; 481:245-263. [PMID: 38358118 PMCID: PMC10903470 DOI: 10.1042/bcj20210301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.
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Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Abul K. Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
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9
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Krajnc M, Fei C, Košmrlj A, Kalin M, Stopar D. Mechanical constraints to unbound expansion of B. subtilis on semi-solid surfaces. Microbiol Spectr 2024; 12:e0274023. [PMID: 38047692 PMCID: PMC10783106 DOI: 10.1128/spectrum.02740-23] [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] [Received: 07/06/2023] [Accepted: 10/13/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE How bacterial cells colonize new territory is a problem of fundamental microbiological and biophysical interest and is key to the emergence of several phenomena of biological, ecological, and medical relevance. Here, we demonstrate how bacteria stuck in a colony of finite size can resume exploration of new territory by aquaplaning and how they fine tune biofilm viscoelasticity to surface material properties that allows them differential mobility. We show how changing local interfacial forces and colony viscosity results in a plethora of bacterial morphologies on surfaces with different physical and mechanical properties.
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Affiliation(s)
- Mojca Krajnc
- Biotechnical Faculty, Department of Microbiology, University of Ljubljana, Ljubljana, Slovenia
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Carl C. Icahn Laboratory, Princeton University, Princeton, New Jersey, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, USA
- Princeton Materials Institute, Princeton University, Princeton, New Jersey, USA
| | - Mitjan Kalin
- Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - David Stopar
- Biotechnical Faculty, Department of Microbiology, University of Ljubljana, Ljubljana, Slovenia
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10
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Nijjer J, Li C, Kothari M, Henzel T, Zhang Q, Tai JSB, Zhou S, Cohen T, Zhang S, Yan J. Biofilms as self-shaping growing nematics. NATURE PHYSICS 2023; 19:1936-1944. [PMID: 39055904 PMCID: PMC11271743 DOI: 10.1038/s41567-023-02221-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 08/23/2023] [Indexed: 07/28/2024]
Abstract
Active nematics are the nonequilibrium analogue of passive liquid crystals. They consist of anisotropic units that consume free energy to drive emergent behaviour. Like liquid crystal molecules in displays, ordering and dynamics in active nematics are sensitive to boundary conditions. However, unlike passive liquid crystals, active nematics have the potential to regulate their boundaries through self-generated stresses. Here, we show how a three-dimensional, living nematic can actively shape itself and its boundary to regulate its internal architecture through growth-induced stresses, using bacterial biofilms confined by a hydrogel as a model system. We show that biofilms exhibit a sharp transition in shape from domes to lenses upon changing environmental stiffness or cell-substrate friction, which is explained by a theoretical model that considers the competition between confinement and interfacial forces. The growth mode defines the progression of the boundary, which in turn determines the trajectories and spatial distribution of cell lineages. We further demonstrate that the evolving boundary and corresponding stress anisotropy define the orientational ordering of cells and the emergence of topological defects in the biofilm interior. Our findings may provide strategies for the development of programmed microbial consortia with emergent material properties.
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Affiliation(s)
- Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Changhao Li
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA
| | - Mrityunjay Kothari
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, University of New Hampshire, Durham, NH, USA
| | - Thomas Henzel
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qiuting Zhang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Jung-Shen B Tai
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Shuang Zhou
- Department of Physics, University of Massachusetts Amherst, Amherst, MA, USA
| | - Tal Cohen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
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11
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Pokhrel AR, Steinbach G, Krueger A, Day TC, Tijani J, Ng SL, Hammer BK, Yunker PJ. The biophysical basis of bacterial colony growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567592. [PMID: 38014274 PMCID: PMC10680802 DOI: 10.1101/2023.11.17.567592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth-the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is controlled by the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.
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12
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Skinner DJ, Jeckel H, Martin AC, Drescher K, Dunkel J. Topological packing statistics of living and nonliving matter. SCIENCE ADVANCES 2023; 9:eadg1261. [PMID: 37672580 PMCID: PMC10482333 DOI: 10.1126/sciadv.adg1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
Complex disordered matter is of central importance to a wide range of disciplines, from bacterial colonies and embryonic tissues in biology to foams and granular media in materials science to stellar configurations in astrophysics. Because of the vast differences in composition and scale, comparing structural features across such disparate systems remains challenging. Here, by using the statistical properties of Delaunay tessellations, we introduce a mathematical framework for measuring topological distances between general three-dimensional point clouds. The resulting system-agnostic metric reveals subtle structural differences between bacterial biofilms as well as between zebrafish brain regions, and it recovers temporal ordering of embryonic development. We apply the metric to construct a universal topological atlas encompassing bacterial biofilms, snowflake yeast, plant shoots, zebrafish brain matter, organoids, and embryonic tissues as well as foams, colloidal packings, glassy materials, and stellar configurations. Living systems localize within a bounded island-like region of the atlas, reflecting that biological growth mechanisms result in characteristic topological properties.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Hannah Jeckel
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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13
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McGenity TJ, Laissue PP. Bacteria stretch and bend oil to feed their appetite. Science 2023; 381:728-729. [PMID: 37590354 DOI: 10.1126/science.adj4430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Microbes reshape oil droplets to speed biodegradation.
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Affiliation(s)
- Terry J McGenity
- School of Life Sciences, University of Essex, Wivenhoe Park, CO4 3SQ, UK
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14
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Ma Y, Deng Y, Hua H, Khoo BL, Chua SL. Distinct bacterial population dynamics and disease dissemination after biofilm dispersal and disassembly. THE ISME JOURNAL 2023; 17:1290-1302. [PMID: 37270584 PMCID: PMC10356768 DOI: 10.1038/s41396-023-01446-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
Microbial communities that form surface-attached biofilms must release and disperse their constituent cells into the environment to colonize fresh sites for continued survival of their species. For pathogens, biofilm dispersal is crucial for microbial transmission from environmental reservoirs to hosts, cross-host transmission, and dissemination of infections across tissues within the host. However, research on biofilm dispersal and its consequences in colonization of fresh sites remain poorly understood. Bacterial cells can depart from biofilms via stimuli-induced dispersal or disassembly due to direct degradation of the biofilm matrix, but the complex heterogeneity of bacterial populations released from biofilms rendered their study difficult. Using a novel 3D-bacterial "biofilm-dispersal-then-recolonization" (BDR) microfluidic model, we demonstrated that Pseudomonas aeruginosa biofilms undergo distinct spatiotemporal dynamics during chemical-induced dispersal (CID) and enzymatic disassembly (EDA), with contrasting consequences in recolonization and disease dissemination. Active CID required bacteria to employ bdlA dispersal gene and flagella to depart from biofilms as single cells at consistent velocities but could not recolonize fresh surfaces. This prevented the disseminated bacteria cells from infecting lung spheroids and Caenorhabditis elegans in on-chip coculture experiments. In contrast, EDA by degradation of a major biofilm exopolysaccharide (Psl) released immotile aggregates at high initial velocities, enabling the bacteria to recolonize fresh surfaces and cause infections in the hosts efficiently. Hence, biofilm dispersal is more complex than previously thought, where bacterial populations adopting distinct behavior after biofilm departure may be the key to survival of bacterial species and dissemination of diseases.
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Affiliation(s)
- Yeping Ma
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Yanlin Deng
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Haojun Hua
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China.
- Hong Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Kowloon, Hong Kong SAR, 999077, China.
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen-Futian Research Institute, Shenzhen, 518057, China.
| | - Song Lin Chua
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.
- Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen, China.
- Research Centre for Deep Space Explorations (RCDSE), The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.
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15
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Han E, Fei C, Alert R, Copenhagen K, Koch MD, Wingreen NS, Shaevitz JW. Local polar order controls mechanical stress and triggers layer formation in developing Myxococcus xanthus colonies. ARXIV 2023:arXiv:2308.00368v1. [PMID: 37576128 PMCID: PMC10418523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Colonies of the social bacterium Myxococcus xanthus go through a morphological transition from a thin colony of cells to three-dimensional droplet-like fruiting bodies as a strategy to survive starvation. The biological pathways that control the decision to form a fruiting body have been studied extensively. However, the mechanical events that trigger the creation of multiple cell layers and give rise to droplet formation remain poorly understood. By measuring cell orientation, velocity, polarity, and force with cell-scale resolution, we reveal a stochastic local polar order in addition to the more obvious nematic order. Average cell velocity and active force at topological defects agree with predictions from active nematic theory, but their fluctuations are anomalously large due to polar active forces generated by the self-propelled rod-shaped cells. We find that M. xanthus cells adjust their reversal frequency to tune the magnitude of this local polar order, which in turn controls the mechanical stresses and triggers layer formation in the colonies.
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Affiliation(s)
- Endao Han
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ricard Alert
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstraße 108, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Katherine Copenhagen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Matthias D. Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Joshua W. Shaevitz
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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16
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Shi J, Wang Y, He W, Ye Z, Liu M, Zhao Z, Lam JWY, Zhang P, Kwok RTK, Tang BZ. Precise Molecular Engineering of Type I Photosensitizer with Aggregation-Induced Emission for Image-Guided Photodynamic Eradication of Biofilm. Molecules 2023; 28:5368. [PMID: 37513241 PMCID: PMC10385678 DOI: 10.3390/molecules28145368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Biofilm-associated infections exert more severe and harmful attacks on human health since they can accelerate the generation and development of the antibiotic resistance of the embedded bacteria. Anti-biofilm materials and techniques that can eliminate biofilms effectively are in urgent demand. Therefore, we designed a type I photosensitizer (TTTDM) with an aggregation-induced emission (AIE) property and used F-127 to encapsulate the TTTDM into nanoparticles (F-127 AIE NPs). The NPs exhibit highly efficient ROS generation by enhancing intramolecular D-A interaction and confining molecular non-radiative transitions. Furthermore, the NPs can sufficiently penetrate the biofilm matrix and then detect and eliminate mature bacterial biofilms upon white light irradiation. This strategy holds great promise for the rapid detection and eradication of bacterial biofilms.
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Affiliation(s)
- Jinghong Shi
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yucheng Wang
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wei He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen 518057, China
| | - Ziyue Ye
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Mengli Liu
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zheng Zhao
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen 518172, China
- HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen 518057, China
| | - Jacky Wing Yip Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Pengfei Zhang
- Shenzhen Key Laboratory for Molecular Imaging, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ryan Tsz Kin Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen 518057, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen 518172, China
- HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen 518057, China
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17
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Hallatschek O, Datta SS, Drescher K, Dunkel J, Elgeti J, Waclaw B, Wingreen NS. Proliferating active matter. NATURE REVIEWS. PHYSICS 2023; 5:1-13. [PMID: 37360681 PMCID: PMC10230499 DOI: 10.1038/s42254-023-00593-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.
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Affiliation(s)
- Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA US
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Sujit S. Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| | | | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Jens Elgeti
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Bartek Waclaw
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry PAN, Warsaw, Poland
- School of Physics and Astronomy, The University of Edinburgh, JCMB, Edinburgh, UK
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
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18
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Ricci-Tam C, Kuipa S, Kostman MP, Aronson MS, Sgro AE. Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity. Semin Cell Dev Biol 2023; 141:50-62. [PMID: 35537929 DOI: 10.1016/j.semcdb.2022.04.014] [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: 03/01/2022] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
Abstract
While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are coordinated naturally.
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Affiliation(s)
- Chiara Ricci-Tam
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sophia Kuipa
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Maya Peters Kostman
- Biological Design Center, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA
| | - Mark S Aronson
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Allyson E Sgro
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA.
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19
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Supekar R, Song B, Hastewell A, Choi GPT, Mietke A, Dunkel J. Learning hydrodynamic equations for active matter from particle simulations and experiments. Proc Natl Acad Sci U S A 2023; 120:e2206994120. [PMID: 36763535 PMCID: PMC9963139 DOI: 10.1073/pnas.2206994120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Recent advances in high-resolution imaging techniques and particle-based simulation methods have enabled the precise microscopic characterization of collective dynamics in various biological and engineered active matter systems. In parallel, data-driven algorithms for learning interpretable continuum models have shown promising potential for the recovery of underlying partial differential equations (PDEs) from continuum simulation data. By contrast, learning macroscopic hydrodynamic equations for active matter directly from experiments or particle simulations remains a major challenge, especially when continuum models are not known a priori or analytic coarse graining fails, as often is the case for nondilute and heterogeneous systems. Here, we present a framework that leverages spectral basis representations and sparse regression algorithms to discover PDE models from microscopic simulation and experimental data, while incorporating the relevant physical symmetries. We illustrate the practical potential through a range of applications, from a chiral active particle model mimicking nonidentical swimming cells to recent microroller experiments and schooling fish. In all these cases, our scheme learns hydrodynamic equations that reproduce the self-organized collective dynamics observed in the simulations and experiments. This inference framework makes it possible to measure a large number of hydrodynamic parameters in parallel and directly from video data.
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Affiliation(s)
- Rohit Supekar
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alasdair Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Gary P. T. Choi
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alexander Mietke
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
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20
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Breakdown of clonal cooperative architecture in multispecies biofilms and the spatial ecology of predation. Proc Natl Acad Sci U S A 2023; 120:e2212650120. [PMID: 36730197 PMCID: PMC9963355 DOI: 10.1073/pnas.2212650120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biofilm formation, including adherence to surfaces and secretion of extracellular matrix, is common in the microbial world, but we often do not know how interaction at the cellular spatial scale translates to higher-order biofilm community ecology. Here we explore an especially understudied element of biofilm ecology, namely predation by the bacterium Bdellovibrio bacteriovorus. This predator can kill and consume many different Gram-negative bacteria, including Vibrio cholerae and Escherichia coli. V. cholerae can protect itself from predation within densely packed biofilm structures that it creates, whereas E. coli biofilms are highly susceptible to B. bacteriovorus. We explore how predator-prey dynamics change when V. cholerae and E. coli are growing in biofilms together. We find that in dual-species prey biofilms, E. coli survival under B. bacteriovorus predation increases, whereas V. cholerae survival decreases. E. coli benefits from predator protection when it becomes embedded within expanding groups of highly packed V. cholerae. But we also find that the ordered, highly packed, and clonal biofilm structure of V. cholerae can be disrupted if V. cholerae cells are directly adjacent to E. coli cells at the start of biofilm growth. When this occurs, the two species become intermixed, and the resulting disordered cell groups do not block predator entry. Because biofilm cell group structure depends on initial cell distributions at the start of prey biofilm growth, the surface colonization dynamics have a dramatic impact on the eventual multispecies biofilm architecture, which in turn determines to what extent both species survive exposure to B. bacteriovorus.
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21
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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: 0] [Impact Index Per Article: 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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22
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Moreau A, Mukherjee S, Yan J. Mechanical Characterization and Single‐Cell Imaging of Bacterial Biofilms. Isr J Chem 2023. [DOI: 10.1002/ijch.202200075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Alexis Moreau
- Department of Molecular, Cellular and Developmental Biology, Quantitative Biology Institute Yale University 260 Whitney Ave. New Haven CT 06511 USA
| | - Sampriti Mukherjee
- Department of Molecular Genetics & Cell Biology University of Chicago 920 E. 58th Street, Suite 1106 Chicago IL 60637
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Quantitative Biology Institute Yale University 260 Whitney Ave. New Haven CT 06511 USA
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23
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Sugimoto S, Kinjo Y. Instantaneous Clearing of Biofilm (iCBiofilm): an optical approach to revisit bacterial and fungal biofilm imaging. Commun Biol 2023; 6:38. [PMID: 36690667 PMCID: PMC9870912 DOI: 10.1038/s42003-022-04396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Whole-biofilm imaging at single-cell resolution is necessary for system-level analysis of cellular heterogeneity, identification of key matrix component functions and response to immune cells and antimicrobials. To this end, we developed a whole-biofilm clearing and imaging method, termed instantaneous clearing of biofilm (iCBiofilm). iCBiofilm is a simple, rapid, and efficient method involving the immersion of biofilm samples in a refractive index-matching medium, enabling instant whole-biofilm imaging with confocal laser scanning microscopy. We also developed non-fixing iCBiofilm, enabling live and dynamic imaging of biofilm development and actions of antimicrobials. iCBiofilm is applicable for multicolor imaging of fluorescent proteins, immunostained matrix components, and fluorescence labeled cells in biofilms with a thickness of several hundred micrometers. iCBiofilm is scalable from bacterial to fungal biofilms and can be used to observe biofilm-neutrophil interactions. iCBiofilm therefore represents an important advance for examining the dynamics and functions of biofilms and revisiting bacterial and fungal biofilm formation.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
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24
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Tai JSB, Ferrell MJ, Yan J, Waters CM. New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:17-39. [PMID: 36792869 PMCID: PMC10726288 DOI: 10.1007/978-3-031-22997-8_2] [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] [Indexed: 02/17/2023]
Abstract
With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.
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Affiliation(s)
- Jung-Shen B Tai
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Micah J Ferrell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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25
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Cao Y, Lee S, Kim K, Kang SH. Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging. Anal Chem 2022; 94:17877-17884. [PMID: 36509731 DOI: 10.1021/acs.analchem.2c03729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.
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Affiliation(s)
- Yingying Cao
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
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26
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Winans JB, Wucher BR, Nadell CD. Multispecies biofilm architecture determines bacterial exposure to phages. PLoS Biol 2022; 20:e3001913. [PMID: 36548227 PMCID: PMC9778933 DOI: 10.1371/journal.pbio.3001913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Numerous ecological interactions among microbes-for example, competition for space and resources, or interaction among phages and their bacterial hosts-are likely to occur simultaneously in multispecies biofilm communities. While biofilms formed by just a single species occur, multispecies biofilms are thought to be more typical of microbial communities in the natural environment. Previous work has shown that multispecies biofilms can increase, decrease, or have no measurable impact on phage exposure of a host bacterium living alongside another species that the phages cannot target. The reasons underlying this variability are not well understood, and how phage-host encounters change within multispecies biofilms remains mostly unexplored at the cellular spatial scale. Here, we study how the cellular scale architecture of model 2-species biofilms impacts cell-cell and cell-phage interactions controlling larger scale population and community dynamics. Our system consists of dual culture biofilms of Escherichia coli and Vibrio cholerae under exposure to T7 phages, which we study using microfluidic culture, high-resolution confocal microscopy imaging, and detailed image analysis. As shown previously, sufficiently mature biofilms of E. coli can protect themselves from phage exposure via their curli matrix. Before this stage of biofilm structural maturity, E. coli is highly susceptible to phages; however, we show that these bacteria can gain lasting protection against phage exposure if they have become embedded in the bottom layers of highly packed groups of V. cholerae in co-culture. This protection, in turn, is dependent on the cell packing architecture controlled by V. cholerae biofilm matrix secretion. In this manner, E. coli cells that are otherwise susceptible to phage-mediated killing can survive phage exposure in the absence of de novo resistance evolution. While co-culture biofilm formation with V. cholerae can confer phage protection to E. coli, it comes at the cost of competing with V. cholerae and a disruption of normal curli-mediated protection for E. coli even in dual species biofilms grown over long time scales. This work highlights the critical importance of studying multispecies biofilm architecture and its influence on the community dynamics of bacteria and phages.
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Affiliation(s)
- James B. Winans
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
| | - Benjamin R. Wucher
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
| | - Carey D. Nadell
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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27
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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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [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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Puri D, Fang X, Allison KR. Evidence of a possible multicellular life cycle in Escherichia coli. iScience 2022; 26:105795. [PMID: 36594031 PMCID: PMC9804144 DOI: 10.1016/j.isci.2022.105795] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biofilms are surface-attached multicellular microbial communities. Their genetics have been extensively studied, but the cell-scale morphogenetic events of their formation are largely unknown. Here, we recorded the entirety of morphogenesis in Escherichia coli, and discovered a previously unknown multicellular self-assembly process. Unattached, single-cells formed 4-cell rosettes which grew into constant-width chains. After ∼10 cell generations, these multicellular chains attached to surfaces and stopped growing. Chains remained clonal throughout morphogenesis. We showed that this process generates biofilms, which we found are composed of attached clonal chains, aligned in parallel. We investigated genetics of chain morphogenesis: Ag43 facilitates rosette formation and clonality; type-1 fimbriae and curli promote stability and configuration; and extracellular polysaccharide production facilitates attachment. Our study establishes that E. coli, a unicellular organism, can follow a multistage, clonal, genetically-regulated, rosette-initiated multicellular life cycle. These findings have implications for synthetic biology, multicellular development, and the treatment and prevention of bacterial diseases.
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Affiliation(s)
- Devina Puri
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Xin Fang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Kyle R. Allison
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA,Corresponding author
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A novel time-lapse imaging method for studying developing bacterial biofilms. Sci Rep 2022; 12:21120. [PMID: 36476631 PMCID: PMC9729682 DOI: 10.1038/s41598-022-24431-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
In nature, bacteria prevailingly reside in the form of biofilms. These elaborately organized surface-bound assemblages of bacterial cells show numerous features of multicellular organization. We recently showed that biofilm growth is a true developmental process, which resembles developmental processes in multicellular eukaryotes. To study the biofilm growth in a fashion of eukaryotic ontogeny, it is essential to define dynamics and critical transitional phases of this process. The first step in this endeavor is to record the gross morphological changes of biofilm ontogeny under standardized conditions. This visual information is instrumental in guiding the sampling strategy for the later omics analyses of biofilm ontogeny. However, none of the currently available visualizations methods is specifically tailored for recording gross morphology across the whole biofilm development. To address this void, here we present an affordable Arduino-based approach for time-lapse visualization of complete biofilm ontogeny using bright field stereomicroscopy with episcopic illumination. The major challenge in recording biofilm development on the air-solid interphase is water condensation, which compromises filming directly through the lid of a Petri dish. To overcome these trade-offs, we developed an Arduino microcontroller setup which synchronizes a robotic arm, responsible for opening and closing the Petri dish lid, with the activity of a stereomicroscope-mounted camera and lighting conditions. We placed this setup into a microbiological incubator that maintains temperature and humidity during the biofilm growth. As a proof-of-principle, we recorded biofilm development of five Bacillus subtilis strains that show different morphological and developmental dynamics.
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Chen YG, Li CX, Zhang Y, Qi YD, Liu XH, Feng J, Zhang XZ. Hybrid suture coating for dual-staged control over antibacterial actions to match well wound healing progression. MATERIALS HORIZONS 2022; 9:2824-2834. [PMID: 36039967 DOI: 10.1039/d2mh00591c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Absorbable sutures have moved to the forefront in surgical fields with a huge market. Antibacterial activity is one indispensable feature for the next generation of absorbable sutures. This study develops a simple and cost-effective coating method to endow sutures with staged control over antibacterial actions to achieve enhanced dual stages of the wound healing process. This method is achieved in aqueous solution under mild conditions without the usage of any organic solvent and reserves the fundamental properties of suture materials, based on the pH-dependent reversible self-polymerization of tannic acid (TA) together with the strong adhesion of poly (tannic acid) (PTA) not only toward the suture surface but also with TA. Just by changing pH of TA solution, a hybrid coating (MPTA) composed of PTA and TA could be readily formed on the commercialized sutures originating from synthetic and natural materials. In the initial post-surgery stage, wound sites are susceptible to aseptic and/or bacterial inflammation. The resulting acid conditions induce burst release of antibacterial TA mostly coming from the adsorbed TA monomer. In the later stage, TA release is tailored totally depending on the pH conditions determined by the healing degree of wounds, allowing the sustained antibacterial prevention in a biologically adjustable manner. Thus, antibacterial MPTA coating meets the rigid requirements that differ distinctly during two major wound healing stages. Nontoxic MPTA coating on sutures leads to excellent post-implantation outcomes regarding bacterial prevention/elimination, anti-inflammation, tissue repair and wound healing. Moreover, MPTA coating provides sutures with a robust platform for functional expansion due to the matrix-independent adhesive ability of PTA.
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Affiliation(s)
- Ying-Ge Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Chu-Xin Li
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Yu Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Yong-Dan Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Jun Feng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
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Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species. PLoS Biol 2022; 20:e3001846. [PMID: 36288405 PMCID: PMC9605341 DOI: 10.1371/journal.pbio.3001846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Bacterial biofilms are among the most abundant multicellular structures on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. However, general principles that govern the emergence of biofilm architecture across different species remain unknown. Here, we combine experiments, simulations, and statistical analysis to identify shared biophysical mechanisms that determine early biofilm architecture development at the single-cell level, for the species Vibrio cholerae, Escherichia coli, Salmonella enterica, and Pseudomonas aeruginosa grown as microcolonies in flow chambers. Our data-driven analysis reveals that despite the many molecular differences between these species, the biofilm architecture differences can be described by only 2 control parameters: cellular aspect ratio and cell density. Further experiments using single-species mutants for which the cell aspect ratio and the cell density are systematically varied, and mechanistic simulations show that tuning these 2 control parameters reproduces biofilm architectures of different species. Altogether, our results show that biofilm microcolony architecture is determined by mechanical cell-cell interactions, which are conserved across different species.
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Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles. Nat Commun 2022; 13:6063. [PMID: 36229546 PMCID: PMC9561665 DOI: 10.1038/s41467-022-33816-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a ΔrbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.
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The long and the short of Periscope Proteins. Biochem Soc Trans 2022; 50:1293-1302. [PMID: 36196877 DOI: 10.1042/bst20220194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Bacteria sense, interact with, and modify their environmental niche by deploying a molecular ensemble at the cell surface. The changeability of this exposed interface, combined with extreme changes in the functional repertoire associated with lifestyle switches from planktonic to adherent and biofilm states necessitate dynamic variability. Dynamic surface changes include chemical modifications to the cell wall; export of diverse extracellular biofilm components; and modulation of expression of cell surface proteins for adhesion, co-aggregation and virulence. Local enrichment for highly repetitive proteins with high tandem repeat identity has been an enigmatic phenomenon observed in diverse bacterial species. Preliminary observations over decades of research suggested these repeat regions were hypervariable, as highly related strains appeared to express homologues with diverse molecular mass. Long-read sequencing data have been interrogated to reveal variation in repeat number; in combination with structural, biophysical and molecular dynamics approaches, the Periscope Protein class has been defined for cell surface attached proteins that dynamically expand and contract tandem repeat tracts at the population level. Here, I review the diverse high-stability protein folds and coherent interdomain linkages culminating in the formation of highly anisotropic linear repeat arrays, so-called rod-like protein 'stalks', supporting roles in bacterial adhesion, biofilm formation, cell surface spatial competition, and immune system modulation. An understanding of the functional impacts of dynamic changes in repeat arrays and broader characterisation of the unusual protein folds underpinning this variability will help with the design of immunisation strategies, and contribute to synthetic biology approaches including protein engineering and microbial consortia construction.
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Bottura B, Rooney LM, Hoskisson PA, McConnell G. Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness. Biofilm 2022; 4:100084. [PMID: 36254115 PMCID: PMC9568850 DOI: 10.1016/j.bioflm.2022.100084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 02/02/2023] Open
Abstract
Nutrient-transporting channels have been recently discovered in mature Escherichia coli biofilms, however the relationship between intra-colony channel structure and the surrounding environmental conditions is poorly understood. Using a combination of fluorescence mesoscopy and a purpose-designed open-source quantitative image analysis pipeline, we show that growth substrate composition and nutrient availability have a profound effect on the morphology of intra-colony channels in mature E. coli biofilms. Under all nutrient conditions, intra-colony channel width was observed to increase non-linearly with radial distance from the centre of the biofilm. Notably, the channels were around 25% wider at the centre of carbon-limited biofilms compared to nitrogen-limited biofilms. Channel density also differed in colonies grown on rich and minimal media, with the former creating a network of tightly packed channels and the latter leading to well-separated, wider channels with defined edges. Our approach paves the way for measurement of internal patterns in a wide range of biofilms, offering the potential for new insights into infection and pathogenicity.
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Affiliation(s)
- Beatrice Bottura
- Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, UK,Corresponding author.
| | - Liam M. Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, UK
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Zhang Y, Cai Y, Zeng L, Liu P, Ma LZ, Liu J. A Microfluidic Approach for Quantitative Study of Spatial Heterogeneity in Bacterial Biofilms. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yuzhen Zhang
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
| | - Yumin Cai
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Lingbin Zeng
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Peng Liu
- Department of Biomedical Engineering School of Medicine Tsinghua University Beijing 100084 China
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Jintao Liu
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
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36
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Microbial silver resistance mechanisms: recent developments. World J Microbiol Biotechnol 2022; 38:158. [PMID: 35821348 DOI: 10.1007/s11274-022-03341-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/19/2022] [Indexed: 01/12/2023]
Abstract
In this mini-review, after a brief introduction into the widespread antimicrobial use of silver ions and nanoparticles against bacteria, fungi and viruses, the toxicity of silver compounds and the molecular mechanisms of microbial silver resistance are discussed, including recent studies on bacteria and fungi. The similarities and differences between silver ions and silver nanoparticles as antimicrobial agents are also mentioned. Regarding bacterial ionic silver resistance, the roles of the sil operon, silver cation efflux proteins, and copper-silver efflux systems are explained. The importance of bacterially produced exopolysaccharides as a physiological (biofilm) defense mechanism against silver nanoparticles is also emphasized. Regarding fungal silver resistance, the roles of metallothioneins, copper-transporting P-type ATPases and cell wall are discussed. Recent evolutionary engineering (adaptive laboratory evolution) studies are also discussed which revealed that silver resistance can evolve rapidly in bacteria and fungi. The cross-resistance observed between silver resistance and resistance to other heavy metals and antibiotics in bacteria and fungi is also explained as a clinically and environmentally important issue. The use of silver against bacterial and fungal biofilm formation is also discussed. Finally, the antiviral effects of silver and the use of silver nanoparticles against SARS-CoV-2 and other viruses are mentioned. To conclude, silver compounds are becoming increasingly important as antimicrobial agents, and their widespread use necessitates detailed understanding of microbial silver response and resistance mechanisms, as well as the ecological effects of silver compounds. Figure created with BioRender.com.
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37
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Chen YG, Li CX, Zhang Y, Qi YD, Feng J, Zhang XZ. Antibacterial Sutures Coated with Smooth Chitosan Layer by Gradient Deposition. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2770-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Dawan J, Ahn J. Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10071385. [PMID: 35889104 PMCID: PMC9322497 DOI: 10.3390/microorganisms10071385] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Korea
- Correspondence: ; Tel.: +82-33-250-6564
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Abstract
Active crystals are highly ordered structures that emerge from the self-organization of motile objects, and have been widely studied in synthetic1,2 and bacterial3,4 active matter. Whether persistent crystalline order can emerge in groups of autonomously developing multicellular organisms is currently unknown. Here we show that swimming starfish embryos spontaneously assemble into chiral crystals that span thousands of spinning organisms and persist for tens of hours. Combining experiments, theory and simulations, we demonstrate that the formation, dynamics and dissolution of these living crystals are controlled by the hydrodynamic properties and the natural development of embryos. Remarkably, living chiral crystals exhibit self-sustained chiral oscillations as well as various unconventional deformation response behaviours recently predicted for odd elastic materials5,6. Our results provide direct experimental evidence for how non-reciprocal interactions between autonomous multicellular components may facilitate non-equilibrium phases of chiral active matter.
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40
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Liu X, Inda ME, Lai Y, Lu TK, Zhao X. Engineered Living Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201326. [PMID: 35243704 PMCID: PMC9250645 DOI: 10.1002/adma.202201326] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Indexed: 05/31/2023]
Abstract
Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.
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Affiliation(s)
- Xinyue Liu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Maria Eugenia Inda
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yong Lai
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xuanhe Zhao
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Babayekhorasani F, Hosseini M, Spicer PT. Molecular and Colloidal Transport in Bacterial Cellulose Hydrogels. Biomacromolecules 2022; 23:2404-2414. [PMID: 35544686 DOI: 10.1021/acs.biomac.2c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. The design of diverse applications of these bacterial cellulose films also relies on understanding and controlling transport through the fiber mesh, and transport simulations of the films are most accurate when guided by experimental characterization of the structures and the resultant diffusion inside. Diffusion through such films is a function of their key microstructural length scales, determining how molecules, as well as particles and microorganisms, permeate them. We use microscopy to study the unique bacterial cellulose film via its pore structure and quantify the mobility dynamics of various sizes of tracer particles and macromolecules. Mobility is hindered within the films, as confinement and local movement strongly depend on the void size relative to diffusing tracers. The biofilms have a naturally periodic structure of alternating dense and porous layers of nanofiber mesh, and we tune the magnitude of the spacing via fermentation conditions. Micron-sized particles can diffuse through the porous layers but cannot penetrate the dense layers. Tracer mobility in the porous layers is isotropic, indicating a largely random pore structure there. Molecular diffusion through the whole film is only slightly reduced by the structural tortuosity. Knowledge of transport variations within bacterial cellulose networks can be used to guide the design of symbiotic cultures in these structures and enhance their use in applications like biomedical implants, wound dressings, lab-grown meat, clothing textiles, and sensors.
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Affiliation(s)
| | - Maryam Hosseini
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Patrick T Spicer
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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Hu J, Chen S, Yang Y, Li L, Cheng X, Cheng Y, Huang Q. A Smart Hydrogel with Anti-Biofilm and Anti-Virulence Activities to Treat Pseudomonas aeruginosa Infections. Adv Healthc Mater 2022; 11:e2200299. [PMID: 35306745 DOI: 10.1002/adhm.202200299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/26/2022] [Indexed: 01/04/2023]
Abstract
Biofilm is the main culprit of refractory infections and seriously threaten to the human health. Here, a smart hydrogel consisted of norspermidine, aminoglycosides, and oxidized polysaccharide is prepared via the formation of acid-labile imine linkage to treat Pseudomonas aeruginosa biofilm infections in several animal models. The increased acidity caused by bacterial infection triggers the release of norspermidine and aminoglycosides covalently bound with the polymer scaffold. The released norspermidine inhibits biofilm formation and virulence production by regulating the quorum sensing of P. aeruginosa, while the aminoglycoside antibiotics effectively kill the released bacteria. The gel thoroughly inhibits biofilm formation on various medical devices and decreases bacteria pathogenicity. It efficiently inhibits implantation-associated biofilm infections and chronic wound infections, and shows great promise to prevent and treat biofilm-induced refractory infection in clinics.
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Affiliation(s)
- Jingjing Hu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Sijia Chen
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yongxin Yang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lin Li
- Department of Orthopedics Oncology, Changzheng Hospital, Navy Medical University, Shanghai, 200003, China
| | - Xuejing Cheng
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Quan Huang
- Department of Orthopedics Oncology, Changzheng Hospital, Navy Medical University, Shanghai, 200003, China
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43
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Choi H, Zaki FR, Monroy GL, Won J, Boppart SA. Imaging and characterization of transitions in biofilm morphology via anomalous diffusion following environmental perturbation. BIOMEDICAL OPTICS EXPRESS 2022; 13:1654-1670. [PMID: 35414993 PMCID: PMC8973182 DOI: 10.1364/boe.449131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Microorganisms form macroscopic structures for the purpose of environmental adaptation. Sudden environmental perturbations induce dynamics that cause bacterial biofilm morphology to transit to another equilibrium state, thought to be related to anomalous diffusion processes. Here, detecting the super-diffusion characteristics would offer a long-sought goal for a rapid detection method of biofilm phenotypes based on their dynamics, such as growth or dispersal. In this paper, phase-sensitive Doppler optical coherence tomography (OCT) and dynamic light scattering (DLS) are combined to demonstrate wide field-of-view and label-free internal dynamic imaging of biofilms. The probability density functions (PDFs) of phase displacement of the backscattered light and the dynamic characteristics of the PDFs are estimated by a simplified mixed Cauchy and Gaussian model. This model can quantify the super-diffusion state and estimate the dynamic characteristics and macroscopic responses in biofilms that may further describe dispersion and growth in biofilm models.
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Affiliation(s)
- Honggu Choi
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Farzana R. Zaki
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Guillermo L. Monroy
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Jungeun Won
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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44
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Pettygrove BA, Smith HJ, Pallister KB, Voyich JM, Stewart PS, Parker AE. Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidence. Front Microbiol 2022; 12:785182. [PMID: 35095798 PMCID: PMC8793059 DOI: 10.3389/fmicb.2021.785182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a large imaging dataset consisting of 16 independent CLSM microscopy experiments was leveraged. These experiments were designed to study interactions between human neutrophils and single cells or aggregates of Staphylococcus aureus (S. aureus) during the initial stages of biofilm formation. Results suggest that in untreated control experiments, variability differed substantially between growth phases (i.e., lag or exponential). When studying the effect of an antimicrobial treatment (in this case, neutrophil challenge), regardless of the inoculation level or of growth phase, variability changed as a frown-shaped function of treatment efficacy (i.e., the reduction in biofilm surface coverage). These findings were used to predict the best experimental designs for future imaging studies of early biofilms by considering differing (i) numbers of independent experiments; (ii) numbers of fields of view (FOV) per experiment; and (iii) frame capture rates per hour. A spreadsheet capable of assessing any user-specified design is included that requires the expected mean log reduction and variance components from user-generated experimental results. The methodology outlined in this study can assist researchers in designing their CLSM studies of antimicrobial treatments with a high level of statistical confidence.
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Affiliation(s)
- Brian A. Pettygrove
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Kyler B. Pallister
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Jovanka M. Voyich
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Philip S. Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, United States
| | - Albert E. Parker
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, United States
- *Correspondence: Albert E. Parker
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45
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Bridier A, Briandet R. Microbial Biofilms: Structural Plasticity and Emerging Properties. Microorganisms 2022; 10:138. [PMID: 35056587 PMCID: PMC8778831 DOI: 10.3390/microorganisms10010138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation- from a single-cell to a multicellular scale- to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.
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Affiliation(s)
- Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35300 Fougères, France
| | - Romain Briandet
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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46
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Nercessian D, Busalmen JP. Cell Adhesion and Biofilm Formation Analysis. Methods Mol Biol 2022; 2522:407-417. [PMID: 36125767 DOI: 10.1007/978-1-0716-2445-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cell adhesion to surfaces and ulterior biofilm formation are critical processes in microbial development since living in biofilms is the preferred way of life within microorganisms. These processes are known to influence not only microorganisms development in the environment, but also their participation in biotechnological processes and have been the focus of intense research that as a matter of fact, was mainly directed to the bacterial domain. Archaea also adhere to surfaces and have been shown forming biofilms, but studies performed until present did not exploit the diversity of methods probed to be useful along bacterial biofilm research.An experimental setup is described here with the aim of stimulating archaeal biofilm research. It can be used for studying cell adhesion and biofilm formation under controlled flow conditions and allows performing in situ optical microscopy (phase contrast, fluorescence, or confocal) and/or spectroscopic techniques (UV-Vis, IR, or Raman) to determine structural and functional biofilm features and their evolution in time. Variants are described with specific aims as working in anaerobiosis and allow sampling of biological material along time.
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Affiliation(s)
- Débora Nercessian
- Instituto de Investigaciones Biológicas (CONICET-UNMdP), Mar del Plata, Argentina.
| | - Juan Pablo Busalmen
- Ingeniería de Interfases y Bioprocesos, INTEMA (CONICET-UNMdP), Mar del Plata, Argentina.
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47
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Moore RP, O'Shaughnessy EC, Shi Y, Nogueira AT, Heath KM, Hahn KM, Legant WR. A multi-functional microfluidic device compatible with widefield and light sheet microscopy. LAB ON A CHIP 2021; 22:136-147. [PMID: 34859808 PMCID: PMC9022779 DOI: 10.1039/d1lc00600b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present a microfluidic device compatible with high resolution light sheet and super-resolution microscopy. The device is a 150 μm thick chamber with a transparent fluorinated ethylene propylene (FEP) cover that has a similar refractive index (1.34) to water (1.33), making it compatible with top-down imaging used in light sheet microscopy. We provide a detailed fabrication protocol and characterize the optical performance of the device. We demonstrate that the device supports long-term imaging of cell growth and differentiation as well as the rapid addition and removal of reagents while simultaneously maintaining sterile culture conditions by physically isolating the sample from the dipping lenses used for imaging. Finally, we demonstrate that the device can be used for super-resolution imaging using lattice light sheet structured illumination microscopy (LLS-SIM) and DNA PAINT. We anticipate that FEP-based microfluidics, as shown here, will be broadly useful to researchers using light sheet microscopy due to the ability to switch reagents, image weakly adherent cells, maintain sterility, and physically isolate the specimen from the optics of the instruments.
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Affiliation(s)
- Regan P Moore
- Joint Biomedical Engineering Department, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, 27599, USA.
| | - Ellen C O'Shaughnessy
- Pharmacology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yu Shi
- Joint Biomedical Engineering Department, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, 27599, USA.
| | - Ana T Nogueira
- Pharmacology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katelyn M Heath
- Joint Biomedical Engineering Department, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, 27599, USA.
| | - Klaus M Hahn
- Pharmacology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wesley R Legant
- Joint Biomedical Engineering Department, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, 27599, USA.
- Pharmacology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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48
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Liu Y, Patko D, Engelhardt I, George TS, Stanley-Wall NR, Ladmiral V, Ameduri B, Daniell TJ, Holden N, MacDonald MP, Dupuy LX. Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proc Natl Acad Sci U S A 2021; 118:e2109176118. [PMID: 34819371 PMCID: PMC8640753 DOI: 10.1073/pnas.2109176118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm3 in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favored small pore spaces over the surface of soil particles, colonizing the root in a pulsatile manner. Migrations appeared to be directed toward the root cap, the point of "first contact," before the subsequent colonization of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
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Affiliation(s)
- Yangminghao Liu
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Daniel Patko
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Ilonka Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Timothy S George
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Vincent Ladmiral
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Bruno Ameduri
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola Holden
- Northern Faculty, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Michael P MacDonald
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom;
| | - Lionel X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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49
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Mondal D, Prabhune AG, Ramaswamy S, Sharma P. Strong confinement of active microalgae leads to inversion of vortex flow and enhanced mixing. eLife 2021; 10:e67663. [PMID: 34806977 PMCID: PMC8758135 DOI: 10.7554/elife.67663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms swimming through viscous fluids imprint their propulsion mechanisms in the flow fields they generate. Extreme confinement of these swimmers between rigid boundaries often arises in natural and technological contexts, yet measurements of their mechanics in this regime are absent. Here, we show that strongly confining the microalga Chlamydomonas between two parallel plates not only inhibits its motility through contact friction with the walls but also leads, for purely mechanical reasons, to inversion of the surrounding vortex flows. Insights from the experiment lead to a simplified theoretical description of flow fields based on a quasi-2D Brinkman approximation to the Stokes equation rather than the usual method of images. We argue that this vortex flow inversion provides the advantage of enhanced fluid mixing despite higher friction. Overall, our results offer a comprehensive framework for analyzing the collective flows of strongly confined swimmers.
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Affiliation(s)
- Debasmita Mondal
- Department of Physics, Indian Institute of ScienceBangaloreIndia
| | - Ameya G Prabhune
- Department of Physics, Indian Institute of ScienceBangaloreIndia
| | - Sriram Ramaswamy
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of ScienceBangaloreIndia
| | - Prerna Sharma
- Department of Physics, Indian Institute of ScienceBangaloreIndia
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50
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Nijjer J, Li C, Zhang Q, Lu H, Zhang S, Yan J. Mechanical forces drive a reorientation cascade leading to biofilm self-patterning. Nat Commun 2021; 12:6632. [PMID: 34789754 PMCID: PMC8599862 DOI: 10.1038/s41467-021-26869-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, surface-attached aggregates of bacterial cells embedded in an extracellular matrix that can exhibit community-scale orientational order. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order during biofilm development remains elusive. Here we report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core leads to a pattern of differential growth that drives radial alignment of the cells in the rim, while the growing rim generates compressive stresses that expand the verticalized core. Such self-patterning disappears in nonadherent mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling jointly reveal the strong interdependence of the driving forces underlying the differential ordering. Our findings offer insight into the developmental processes that shape bacterial communities and provide ways to engineer phenotypes and functions in living active matter.
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Affiliation(s)
- Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Changhao Li
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA
| | - Qiuting Zhang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Haoran Lu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA.
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