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Zakharov A, Awan M, Cheng T, Gopinath A, Lee SJJ, Ramasubramanian AK, Dasbiswas K. Clots reveal anomalous elastic behavior of fiber networks. SCIENCE ADVANCES 2024; 10:eadh1265. [PMID: 38198546 PMCID: PMC10780871 DOI: 10.1126/sciadv.adh1265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024]
Abstract
The adaptive mechanical properties of soft and fibrous biological materials are relevant to their functionality. The emergence of the macroscopic response of these materials to external stress and intrinsic cell traction from local deformations of their structural components is not well understood. Here, we investigate the nonlinear elastic behavior of blood clots by combining microscopy, rheology, and an elastic network model that incorporates the stretching, bending, and buckling of constituent fibrin fibers. By inhibiting fibrin cross-linking in blood clots, we observe an anomalous softening regime in the macroscopic shear response as well as a reduction in platelet-induced clot contractility. Our model explains these observations from two independent macroscopic measurements in a unified manner, through a single mechanical parameter, the bending stiffness of individual fibers. Supported by experimental evidence, our mechanics-based model provides a framework for predicting and comprehending the nonlinear elastic behavior of blood clots and other active biopolymer networks in general.
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Affiliation(s)
- Andrei Zakharov
- Department of Physics, University of California, Merced, Merced, CA 95343, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Myra Awan
- Department of Chemical and Materials Engineering, San José State University, San José, CA 95192, USA
| | - Terrence Cheng
- Department of Chemical and Materials Engineering, San José State University, San José, CA 95192, USA
| | - Arvind Gopinath
- Department of Bioengineering, University of California, Merced, Merced, CA 95343, USA
| | - Sang-Joon John Lee
- Department of Mechanical Engineering, San José State University, San José, CA 95192, USA
| | - Anand K. Ramasubramanian
- Department of Chemical and Materials Engineering, San José State University, San José, CA 95192, USA
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, Merced, CA 95343, USA
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Lin WH, Zhu Z, Ravikumar V, Sharma V, Tolkacheva EG, McAlpine MC, Ogle BM. A Bionic Testbed for Cardiac Ablation Tools. Int J Mol Sci 2022; 23:ijms232214444. [PMID: 36430922 PMCID: PMC9692733 DOI: 10.3390/ijms232214444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/22/2022] Open
Abstract
Bionic-engineered tissues have been proposed for testing the performance of cardiovascular medical devices and predicting clinical outcomes ex vivo. Progress has been made in the development of compliant electronics that are capable of monitoring treatment parameters and being coupled to engineered tissues; however, the scale of most engineered tissues is too small to accommodate the size of clinical-grade medical devices. Here, we show substantial progress toward bionic tissues for evaluating cardiac ablation tools by generating a centimeter-scale human cardiac disk and coupling it to a hydrogel-based soft-pressure sensor. The cardiac tissue with contiguous electromechanical function was made possible by our recently established method to 3D bioprint human pluripotent stem cells in an extracellular matrix-based bioink that allows for in situ cell expansion prior to cardiac differentiation. The pressure sensor described here utilized electrical impedance tomography to enable the real-time spatiotemporal mapping of pressure distribution. A cryoablation tip catheter was applied to the composite bionic tissues with varied pressure. We found a close correlation between the cell response to ablation and the applied pressure. Under some conditions, cardiomyocytes could survive in the ablated region with more rounded morphology compared to the unablated controls, and connectivity was disrupted. This is the first known functional characterization of living human cardiomyocytes following an ablation procedure that suggests several mechanisms by which arrhythmia might redevelop following an ablation. Thus, bionic-engineered testbeds of this type can be indicators of tissue health and function and provide unique insight into human cell responses to ablative interventions.
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Affiliation(s)
- Wei-Han Lin
- Department of Biomedical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Zhijie Zhu
- Department of Mechanical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Vasanth Ravikumar
- Department of Electrical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Vinod Sharma
- Cardiac Rhythm and Heart Failure Division, Medtronic Inc., Minneapolis, MN 55432, USA
| | - Elena G. Tolkacheva
- Department of Biomedical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Lillehei Heart Institute, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Institute for Engineering in Medicine, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Michael C. McAlpine
- Department of Mechanical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Institute for Engineering in Medicine, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Correspondence: (M.C.M.); (B.M.O.)
| | - Brenda M. Ogle
- Department of Biomedical Engineering, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Lillehei Heart Institute, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Institute for Engineering in Medicine, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Correspondence: (M.C.M.); (B.M.O.)
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Khalil H, Legin E, Kurek B, Perre P, Taidi B. Morphological growth pattern of Phanerochaete chrysosporium cultivated on different Miscanthus x giganteus biomass fractions. BMC Microbiol 2021; 21:318. [PMID: 34784888 PMCID: PMC8597199 DOI: 10.1186/s12866-021-02350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Solid-state fermentation is a fungal culture technique used to produce compounds and products of industrial interest. The growth behaviour of filamentous fungi on solid media is challenging to study due to the intermixity of the substrate and the growing organism. Several strategies are available to measure indirectly the fungal biomass during the fermentation such as following the biochemical production of mycelium-specific components or microscopic observation. The microscopic observation of the development of the mycelium, on lignocellulosic substrate, has not been reported. In this study, we set up an experimental protocol based on microscopy and image processing through which we investigated the growth pattern of Phanerochaete chrysosporium on different Miscanthus x giganteus biomass fractions. RESULTS Object coalescence, the occupied surface area, and radial expansion of the colony were measured in time. The substrate was sterilized by autoclaving, which could be considered a type of pre-treatment. The fastest growth rate was measured on the unfractionated biomass, followed by the soluble fraction of the biomass, then the residual solid fractions. The growth rate on the different fractions of the substrate was additive, suggesting that both the solid and soluble fractions were used by the fungus. Based on the FTIR analysis, there were differences in composition between the solid and soluble fractions of the substrate, but the main components for growth were always present. We propose using this novel method for measuring the very initial fungal growth by following the variation of the number of objects over time. Once growth is established, the growth can be followed by measurement of the occupied surface by the mycelium. CONCLUSION Our data showed that the growth was affected from the very beginning by the nature of the substrate. The most extensive colonization of the surface was observed with the unfractionated substrate containing both soluble and solid components. The methodology was practical and may be applied to investigate the growth of other fungi, including the influence of environmental parameters on the fungal growth.
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Affiliation(s)
- Hassan Khalil
- LGPM, CentraleSupélec, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), Université Paris-Saclay, 3 Rue des Rouges Terres, 51110, Pomacle, France
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Estelle Legin
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Bernard Kurek
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Patrick Perre
- LGPM, CentraleSupélec, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), Université Paris-Saclay, 3 Rue des Rouges Terres, 51110, Pomacle, France
- LGPM, CentraleSupélec, Université Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France
| | - Behnam Taidi
- LGPM, CentraleSupélec, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), Université Paris-Saclay, 3 Rue des Rouges Terres, 51110, Pomacle, France.
- LGPM, CentraleSupélec, Université Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France.
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Galloni C, Carra D, Abella JV, Kjær S, Singaravelu P, Barry DJ, Kogata N, Guérin C, Blanchoin L, Way M. MICAL2 enhances branched actin network disassembly by oxidizing Arp3B-containing Arp2/3 complexes. J Cell Biol 2021; 220:e202102043. [PMID: 34106209 PMCID: PMC8193582 DOI: 10.1083/jcb.202102043] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/27/2021] [Accepted: 05/20/2021] [Indexed: 01/24/2023] Open
Abstract
The mechanisms regulating the disassembly of branched actin networks formed by the Arp2/3 complex still remain to be fully elucidated. In addition, the impact of Arp3 isoforms on the properties of Arp2/3 are also unexplored. We now demonstrate that Arp3 and Arp3B isocomplexes promote actin assembly equally efficiently but generate branched actin networks with different disassembly rates. Arp3B dissociates significantly faster than Arp3 from the network, and its depletion increases actin stability. This difference is due to the oxidation of Arp3B, but not Arp3, by the methionine monooxygenase MICAL2, which is recruited to the actin network by coronin 1C. Substitution of Arp3B Met293 by threonine, the corresponding residue in Arp3, increases actin network stability. Conversely, replacing Arp3 Thr293 with glutamine to mimic Met oxidation promotes disassembly. The ability of MICAL2 to enhance network disassembly also depends on cortactin. Our observations demonstrate that coronin 1C, cortactin, and MICAL2 act together to promote disassembly of branched actin networks by oxidizing Arp3B-containing Arp2/3 complexes.
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Affiliation(s)
- Chiara Galloni
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Davide Carra
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Jasmine V.G. Abella
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Pavithra Singaravelu
- CytoMorpho Lab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble-Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Grenoble, France
- CytoMorpho Lab, Institut de Recherche Saint Louis, University of Paris, Institut National de la Santé et de la Recherche Médicale, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Paris, France
| | - David J. Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Naoko Kogata
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Christophe Guérin
- CytoMorpho Lab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble-Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Grenoble, France
- CytoMorpho Lab, Institut de Recherche Saint Louis, University of Paris, Institut National de la Santé et de la Recherche Médicale, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Paris, France
| | - Laurent Blanchoin
- CytoMorpho Lab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble-Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Grenoble, France
- CytoMorpho Lab, Institut de Recherche Saint Louis, University of Paris, Institut National de la Santé et de la Recherche Médicale, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Paris, France
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College, London, UK
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Wershof E, Park D, Barry DJ, Jenkins RP, Rullan A, Wilkins A, Schlegelmilch K, Roxanis I, Anderson KI, Bates PA, Sahai E. A FIJI macro for quantifying pattern in extracellular matrix. Life Sci Alliance 2021; 4:e202000880. [PMID: 33504622 PMCID: PMC7898596 DOI: 10.26508/lsa.202000880] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/24/2022] Open
Abstract
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.
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Affiliation(s)
- Esther Wershof
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Danielle Park
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - David J Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Robert P Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Antonio Rullan
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Anna Wilkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Ioannis Roxanis
- Breast Cancer Research Division, Toby Robins Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Kurt I Anderson
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
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Tesche S, Krull R. An image analysis method to quantify heterogeneous filamentous biomass based on pixel intensity values – Interrelation of macro- and micro-morphology in Actinomadura namibiensis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cardini A, Pellegrino E, Del Dottore E, Gamper HA, Mazzolai B, Ercoli L. HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia. MYCORRHIZA 2020; 30:229-242. [PMID: 32300867 DOI: 10.1007/s00572-020-00956-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.
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Affiliation(s)
- Alessio Cardini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Elisa Pellegrino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Emanuela Del Dottore
- Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy
| | - Hannes A Gamper
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- Free University of Bozen-Bolzano, Faculty of Science and Technology, Universitätsplatz 5 - piazza Università 5, 39100, Bozen-Bolzano, Italy
| | - Barbara Mazzolai
- Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy
| | - Laura Ercoli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
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Wershof E, Park D, Jenkins RP, Barry DJ, Sahai E, Bates PA. Matrix feedback enables diverse higher-order patterning of the extracellular matrix. PLoS Comput Biol 2019; 15:e1007251. [PMID: 31658254 PMCID: PMC6816557 DOI: 10.1371/journal.pcbi.1007251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
The higher-order patterning of extra-cellular matrix in normal and pathological tissues has profound consequences on tissue function. Whilst studies have documented both how fibroblasts create and maintain individual matrix fibers and how cell migration is altered by the fibers they interact with, a model unifying these two aspects of tissue organization is lacking. Here we use computational modelling to understand the effect of this interconnectivity between fibroblasts and matrix at the mesoscale level. We created a unique adaptation to the Vicsek flocking model to include feedback from a second layer representing the matrix, and use experimentation to parameterize our model and validate model-driven hypotheses. Our two-layer model demonstrates that feedback between fibroblasts and matrix increases matrix diversity creating higher-order patterns. The model can quantitatively recapitulate matrix patterns of tissues in vivo. Cells follow matrix fibers irrespective of when the matrix fibers were deposited, resulting in feedback with the matrix acting as temporal 'memory' to collective behaviour, which creates diversity in topology. We also establish conditions under which matrix can be remodelled from one pattern to another. Our model elucidates how simple rules defining fibroblast-matrix interactions are sufficient to generate complex tissue patterns.
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Affiliation(s)
- Esther Wershof
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Danielle Park
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Robert P. Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David J. Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, United Kingdom
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, United Kingdom
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Sachs CC, Koepff J, Wiechert W, Grünberger A, Nöh K. mycelyso - high-throughput analysis of Streptomyces mycelium live cell imaging data. BMC Bioinformatics 2019; 20:452. [PMID: 31484491 PMCID: PMC6727546 DOI: 10.1186/s12859-019-3004-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/13/2019] [Indexed: 11/19/2022] Open
Abstract
Background Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked to their growth morphology. Microfluidic lab-on-a-chip cultivation systems, coupled with automated time-lapse imaging, generate spatio-temporal insights into the mycelium development of streptomycetes, therewith extending the biotechnological toolset by spatio-temporal screening under well-controlled and reproducible conditions. However, the analysis of the complex mycelial structure formation is limited by the extent of manual interventions required during processing of the acquired high-volume image data. These interventions typically lead to high evaluation times and, therewith, limit the analytic throughput and exploitation of microfluidic-based screenings. Results We present the tool mycelyso (MYCElium anaLYsis SOftware), an image analysis system tailored to fully automated hyphae-level processing of image stacks generated by time-lapse microscopy. With mycelyso, the developing hyphal streptomycete network is automatically segmented and tracked over the cultivation period. Versatile key growth parameters such as mycelium network structure, its development over time, and tip growth rates are extracted. Results are presented in the web-based exploration tool mycelyso Inspector, allowing for user friendly quality control and downstream evaluation of the extracted information. In addition, 2D and 3D visualizations show temporal tracking for detailed inspection of morphological growth behaviors. For ease of getting started with mycelyso, bundled Windows packages as well as Docker images along with tutorial videos are available. Conclusion mycelyso is a well-documented, platform-independent open source toolkit for the automated end-to-end analysis of Streptomyces image stacks. The batch-analysis mode facilitates the rapid and reproducible processing of large microfluidic screenings, and easy extraction of morphological parameters. The objective evaluation of image stacks is possible by reproducible evaluation workflows, useful to unravel correlations between morphological, molecular and process parameters at the hyphae- and mycelium-levels with statistical power. Electronic supplementary material The online version of this article (10.1186/s12859-019-3004-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian Carsten Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Joachim Koepff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, 52074, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.,Multiscale Bioengineering, Bielefeld University, Universitätsstr. 25, Bielefeld, 33615, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.
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11
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Schmideder S, Barthel L, Friedrich T, Thalhammer M, Kovačević T, Niessen L, Meyer V, Briesen H. An X‐ray microtomography‐based method for detailed analysis of the three‐dimensional morphology of fungal pellets. Biotechnol Bioeng 2019; 116:1355-1365. [DOI: 10.1002/bit.26956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Stefan Schmideder
- Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Process Systems EngineeringFreising Germany
| | - Lars Barthel
- Department of Applied and Molecular MicrobiologyInstitute of Biotechnology, Technische Universität BerlinBerlin Germany
| | - Tiaan Friedrich
- Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Process Systems EngineeringFreising Germany
| | - Michaela Thalhammer
- Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Process Systems EngineeringFreising Germany
| | - Tijana Kovačević
- Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Process Systems EngineeringFreising Germany
| | - Ludwig Niessen
- Lehrstuhl für Technische MikrobiologieTechnical University of MunichFreising Germany
| | - Vera Meyer
- Department of Applied and Molecular MicrobiologyInstitute of Biotechnology, Technische Universität BerlinBerlin Germany
| | - Heiko Briesen
- Technical University of Munich, School of Life Sciences Weihenstephan, Chair of Process Systems EngineeringFreising Germany
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HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi. Sci Rep 2018; 8:605. [PMID: 29330515 PMCID: PMC5766585 DOI: 10.1038/s41598-017-19103-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/22/2017] [Indexed: 11/22/2022] Open
Abstract
The dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains.
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Abstract
ABSTRACT
The characteristic growth pattern of fungal mycelia as an interconnected network has a major impact on how cellular events operating on a micron scale affect colony behavior at an ecological scale. Network structure is intimately linked to flows of resources across the network that in turn modify the network architecture itself. This complex interplay shapes the incredibly plastic behavior of fungi and allows them to cope with patchy, ephemeral resources, competition, damage, and predation in a manner completely different from multicellular plants or animals. Here, we try to link network structure with impact on resource movement at different scales of organization to understand the benefits and challenges of organisms that grow as connected networks. This inevitably involves an interdisciplinary approach whereby mathematical modeling helps to provide a bridge between information gleaned by traditional cell and molecular techniques or biophysical approaches at a hyphal level, with observations of colony dynamics and behavior at an ecological level.
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