1
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Möckel C, Beck T, Kaliman S, Abuhattum S, Kim K, Kolb J, Wehner D, Zaburdaev V, Guck J. Estimation of the mass density of biological matter from refractive index measurements. Biophys Rep (N Y) 2024; 4:100156. [PMID: 38718671 PMCID: PMC11090064 DOI: 10.1016/j.bpr.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/04/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
The quantification of physical properties of biological matter gives rise to novel ways of understanding functional mechanisms. One of the basic biophysical properties is the mass density (MD). It affects the dynamics in sub-cellular compartments and plays a major role in defining the opto-acoustical properties of cells and tissues. As such, the MD can be connected to the refractive index (RI) via the well known Lorentz-Lorenz relation, which takes into account the polarizability of matter. However, computing the MD based on RI measurements poses a challenge, as it requires detailed knowledge of the biochemical composition of the sample. Here we propose a methodology on how to account for assumptions about the biochemical composition of the sample and respective RI measurements. To this aim, we employ the Biot mixing rule of RIs alongside the assumption of volume additivity to find an approximate relation of MD and RI. We use Monte-Carlo simulations and Gaussian propagation of uncertainty to obtain approximate analytical solutions for the respective uncertainties of MD and RI. We validate this approach by applying it to a set of well-characterized complex mixtures given by bovine milk and intralipid emulsion and employ it to estimate the MD of living zebrafish (Danio rerio) larvae trunk tissue. Our results illustrate the importance of implementing this methodology not only for MD estimations but for many other related biophysical problems, such as mechanical measurements using Brillouin microscopy and transient optical coherence elastography.
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Affiliation(s)
- Conrad Möckel
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany; Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Timon Beck
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Sara Kaliman
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Shada Abuhattum
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Kyoohyun Kim
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Julia Kolb
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany; Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel Wehner
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany; Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany; Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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2
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Angeloni M, van Doeveren T, Lindner S, Volland P, Schmelmer J, Foersch S, Matek C, Stoehr R, Geppert CI, Heers H, Wach S, Taubert H, Sikic D, Wullich B, van Leenders GJLH, Zaburdaev V, Eckstein M, Hartmann A, Boormans JL, Ferrazzi F, Bahlinger V. A deep-learning workflow to predict upper tract urothelial carcinoma protein-based subtypes from H&E slides supporting the prioritization of patients for molecular testing. J Pathol Clin Res 2024; 10:e12369. [PMID: 38504364 PMCID: PMC10951050 DOI: 10.1002/2056-4538.12369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
Upper tract urothelial carcinoma (UTUC) is a rare and aggressive, yet understudied, urothelial carcinoma (UC). The more frequent UC of the bladder comprises several molecular subtypes, associated with different targeted therapies and overlapping with protein-based subtypes. However, if and how these findings extend to UTUC remains unclear. Artificial intelligence-based approaches could help elucidate UTUC's biology and extend access to targeted treatments to a wider patient audience. Here, UTUC protein-based subtypes were identified, and a deep-learning (DL) workflow was developed to predict them directly from routine histopathological H&E slides. Protein-based subtypes in a retrospective cohort of 163 invasive tumors were assigned by hierarchical clustering of the immunohistochemical expression of three luminal (FOXA1, GATA3, and CK20) and three basal (CD44, CK5, and CK14) markers. Cluster analysis identified distinctive luminal (N = 80) and basal (N = 42) subtypes. The luminal subtype mostly included pushing, papillary tumors, whereas the basal subtype diffusely infiltrating, non-papillary tumors. DL model building relied on a transfer-learning approach by fine-tuning a pre-trained ResNet50. Classification performance was measured via three-fold repeated cross-validation. A mean area under the receiver operating characteristic curve of 0.83 (95% CI: 0.67-0.99), 0.8 (95% CI: 0.62-0.99), and 0.81 (95% CI: 0.65-0.96) was reached in the three repetitions. High-confidence DL-based predicted subtypes showed significant associations (p < 0.001) with morphological features, i.e. tumor type, histological subtypes, and infiltration type. Furthermore, a significant association was found with programmed cell death ligand 1 (PD-L1) combined positive score (p < 0.001) and FGFR3 mutational status (p = 0.002), with high-confidence basal predictions containing a higher proportion of PD-L1 positive samples and high-confidence luminal predictions a higher proportion of FGFR3-mutated samples. Testing of the DL model on an independent cohort highlighted the importance to accommodate histological subtypes. Taken together, our DL workflow can predict protein-based UTUC subtypes, associated with the presence of targetable alterations, directly from H&E slides.
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Affiliation(s)
- Miriam Angeloni
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Thomas van Doeveren
- Department of UrologyErasmus MC Urothelial Cancer Research GroupRotterdamThe Netherlands
| | - Sebastian Lindner
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Patrick Volland
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Jorina Schmelmer
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | | | - Christian Matek
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Carol I Geppert
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Hendrik Heers
- Department of UrologyPhilipps‐Universität MarburgMarburgGermany
| | - Sven Wach
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of Urology and Pediatric UrologyUniversity Hospital Erlangen, Friedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Helge Taubert
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of Urology and Pediatric UrologyUniversity Hospital Erlangen, Friedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Danijel Sikic
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of Urology and Pediatric UrologyUniversity Hospital Erlangen, Friedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Bernd Wullich
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of Urology and Pediatric UrologyUniversity Hospital Erlangen, Friedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Geert JLH van Leenders
- Department of PathologyErasmus MC Cancer Institute, University Medical CentreRotterdamthe Netherlands
| | - Vasily Zaburdaev
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
| | - Joost L Boormans
- Department of UrologyErasmus MC Urothelial Cancer Research GroupRotterdamThe Netherlands
| | - Fulvia Ferrazzi
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of NephropathologyInstitute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Veronika Bahlinger
- Institute of Pathology, University Hospital Erlangen‐Nürnberg, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN)ErlangenGermany
- Bavarian Cancer Research Center (BZKF)ErlangenGermany
- Department of Pathology and NeuropathologyUniversity Hospital and Comprehensive Cancer Center TübingenTübingenGermany
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3
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Chai L, Shank EA, Zaburdaev V. Where bacteria and eukaryotes meet. J Bacteriol 2024; 206:e0004923. [PMID: 38289062 PMCID: PMC10882991 DOI: 10.1128/jb.00049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.
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Affiliation(s)
- Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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4
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Ye Y, Ghrayeb M, Miercke S, Arif S, Müller S, Mascher T, Chai L, Zaburdaev V. Residual cells and nutrient availability guide wound healing in bacterial biofilms. Soft Matter 2024; 20:1047-1060. [PMID: 38205608 DOI: 10.1039/d3sm01032e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex eukaryotic tissues is being drawn. One illustrative example of where this analogy can be practically useful is the process of wound healing. While it has been extensively studied in eukaryotic tissues, the mechanism of wound healing in biofilms is virtually unexplored. Combining experiments in Bacillus subtilis bacteria, a model organism for biofilm formation, and a lattice-based theoretical model of biofilm growth, we studied how biofilms recover after macroscopic damage. We suggest that nutrient gradients and the abundance of proliferating cells are key factors augmenting wound closure. Accordingly, in the model, cell quiescence, nutrient fluxes, and biomass represented by cells and self-secreted extracellular matrix are necessary to qualitatively recapitulate the experimental results for damage repair. One of the surprising experimental findings is that residual cells, persisting in a damaged area after removal of a part of the biofilm, prominently affect the healing process. Taken together, our results outline the important roles of nutrient gradients and residual cells on biomass regrowth on macroscopic scales of the whole biofilm. The proposed combined experiment-simulation framework opens the way to further investigate the possible relation between wound healing, cell signaling and cell phenotype alternation in the local microenvironment of the wound.
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Affiliation(s)
- Yusong Ye
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Mnar Ghrayeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Sania Arif
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | | | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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5
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Tschurikow X, Gadzekpo A, Tran MP, Chatterjee R, Sobucki M, Zaburdaev V, Göpfrich K, Hilbert L. Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus. Nano Lett 2023; 23:7815-7824. [PMID: 37586706 PMCID: PMC10510709 DOI: 10.1021/acs.nanolett.3c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and we achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Increasing amphiphile concentrations induce rounding of droplets, prevent droplet fusion, and, at high concentrations, cause full dispersal of droplets. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that the addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of transcriptional cluster formation in biological cells using relatively simple DNA sequence-programmable nanostructures, opening novel ways to control the mesoscopic organization of synthetic nanomaterials.
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Affiliation(s)
- Xenia Tschurikow
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Aaron Gadzekpo
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Mai P. Tran
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Rakesh Chatterjee
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Marcel Sobucki
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Vasily Zaburdaev
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Kerstin Göpfrich
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Lennart Hilbert
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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6
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Zhang X, Penkov S, Kurzchalia TV, Zaburdaev V. Periodic ethanol supply as a path toward unlimited lifespan of Caenorhabditis elegans dauer larvae. Front Aging 2023; 4:1031161. [PMID: 37731965 PMCID: PMC10507685 DOI: 10.3389/fragi.2023.1031161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
The dauer larva is a specialized stage of worm development optimized for survival under harsh conditions that have been used as a model for stress resistance, metabolic adaptations, and longevity. Recent findings suggest that the dauer larva of Caenorhabditis elegans may utilize external ethanol as an energy source to extend their lifespan. It was shown that while ethanol may serve as an effectively infinite source of energy, some toxic compounds accumulating as byproducts of its metabolism may lead to the damage of mitochondria and thus limit the lifespan of larvae. A minimal mathematical model was proposed to explain the connection between the lifespan of a dauer larva and its ethanol metabolism. To explore theoretically if it is possible to extend even further the lifespan of dauer larvae, we incorporated two natural mechanisms describing the recovery of damaged mitochondria and elimination of toxic compounds, which were previously omitted in the model. Numerical simulations of the revised model suggested that while the ethanol concentration is constant, the lifespan still stays limited. However, if ethanol is supplied periodically, with a suitable frequency and amplitude, the dauer could survive as long as we observe the system. Analytical methods further help to explain how feeding frequency and amplitude affect lifespan extension. Based on the comparison of the model with experimental data for fixed ethanol concentration, we proposed the range of feeding protocols that could lead to even longer dauer survival and it can be tested experimentally.
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Affiliation(s)
- Xingyu Zhang
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Sider Penkov
- Center of Membrane Biochemistry and Lipid Research, University Clinic and Faculty of Medicine, Dresden, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic and Faculty of Medicine, Dresden, Germany
| | | | - Vasily Zaburdaev
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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7
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Tran MP, Chatterjee R, Dreher Y, Fichtler J, Jahnke K, Hilbert L, Zaburdaev V, Göpfrich K. A DNA Segregation Module for Synthetic Cells. Small 2023; 19:e2202711. [PMID: 35971190 DOI: 10.1002/smll.202202711] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The bottom-up construction of an artificial cell requires the realization of synthetic cell division. Significant progress has been made toward reliable compartment division, yet mechanisms to segregate the DNA-encoded informational content are still in their infancy. Herein, droplets of DNA Y-motifs are formed by liquid-liquid phase separation. DNA droplet segregation is obtained by cleaving the linking component between two populations of DNA Y-motifs. In addition to enzymatic cleavage, photolabile sites are introduced for spatio-temporally controlled DNA segregation in bulk as well as in cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). Notably, the segregation process is slower in confinement than in bulk. The ionic strength of the solution and the nucleobase sequences are employed to regulate the segregation dynamics. The experimental results are corroborated in a lattice-based theoretical model which mimics the interactions between the DNA Y-motif populations. Altogether, engineered DNA droplets, reconstituted in GUVs, can represent a strategy toward a DNA segregation module within bottom-up assembled synthetic cells.
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Affiliation(s)
- Mai P Tran
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Rakesh Chatterjee
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 11, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Yannik Dreher
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Julius Fichtler
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Lennart Hilbert
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Zoological Institute, Department of Systems Biology / Bioinformatics, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 11, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
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8
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Abuhattum S, Kuan HS, Müller P, Guck J, Zaburdaev V. Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals. Biophys Rep (N Y) 2022; 2:100054. [PMID: 36425327 PMCID: PMC9680806 DOI: 10.1016/j.bpr.2022.100054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/24/2022] [Indexed: 06/16/2023]
Abstract
The mechanical response of materials to dynamic loading is often quantified by the frequency-dependent complex modulus. Probing materials directly in the frequency domain faces technical challenges such as a limited range of frequencies, long measurement times, or small sample sizes. Furthermore, many biological samples, such as cells or tissues, can change their properties upon repetitive probing at different frequencies. Therefore, it is common practice to extract the material properties by fitting predefined mechanical models to measurements performed in the time domain. This practice, however, precludes the probing of unique and yet unexplored material properties. In this report, we demonstrate that the frequency-dependent complex modulus can be robustly retrieved in a model-independent manner directly from time-dependent stress-strain measurements. While applying a rolling average eliminates random noise and leads to a reliable complex modulus in the lower frequency range, a Fourier transform with a complex frequency helps to recover the material properties at high frequencies. Finally, by properly designing the probing procedure, the recovery of reliable mechanical properties can be extended to an even wider frequency range. Our approach can be used with many state-of-the-art experimental methods to interrogate the mechanical properties of biological and other complex materials.
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Affiliation(s)
- Shada Abuhattum
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Hui-Shun Kuan
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Paul Müller
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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9
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Clopés J, Shin J, Jahnel M, Grill SW, Zaburdaev V. Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins. Phys Rev E 2021; 104:054403. [PMID: 34942783 DOI: 10.1103/physreve.104.054403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/18/2021] [Indexed: 11/07/2022]
Abstract
Recently, it has been shown that the long coiled-coil membrane tether protein early endosome antigen 1 (EEA1) switches from a rigid to a flexible conformation upon binding of a signaling protein to its free end. This flexibility switch represents a motorlike activity, allowing EEA1 to generate a force that moves vesicles closer to the membrane they will fuse with. It was hypothesized that the binding-induced signal could propagate along the coiled coil and lead to conformational changes through the localized domains of the protein chain that deviate from a perfect coiled-coil structure. To elucidate, if upon binding of a single protein the corresponding mechanical signal could propagate through the whole 200-nm-long chain, we propose a simplified description of the coiled coil as a one-dimensional Frenkel-Kontorova chain. Using numerical simulations, we find that an initial perturbation of the chain can propagate along its whole length in the presence of thermal fluctuations. This may enable the change of the configuration of the entire molecule and thereby affect its stiffness. Our work sheds light on intramolecular communication and force generation in long coiled-coil proteins.
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Affiliation(s)
- Judit Clopés
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Jaeoh Shin
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Biotechnology Center, Technical University Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Biotechnology Center, Technical University Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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10
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Pancholi A, Klingberg T, Zhang W, Prizak R, Mamontova I, Noa A, Sobucki M, Kobitski AY, Nienhaus GU, Zaburdaev V, Hilbert L. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin. Mol Syst Biol 2021; 17:e10272. [PMID: 34569155 PMCID: PMC8474054 DOI: 10.15252/msb.202110272] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid-liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super-resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid-phase condensation at concentrations that are too low for canonical liquid-liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface-associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.
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Affiliation(s)
- Agnieszka Pancholi
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Tim Klingberg
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Weichun Zhang
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Roshan Prizak
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Irina Mamontova
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Amra Noa
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Marcel Sobucki
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Andrei Yu Kobitski
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Gerd Ulrich Nienhaus
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Department of PhysicsUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Vasily Zaburdaev
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Lennart Hilbert
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
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11
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Anchang CG, Xu C, Raimondo MG, Atreya R, Maier A, Schett G, Zaburdaev V, Rauber S, Ramming A. The Potential of OMICs Technologies for the Treatment of Immune-Mediated Inflammatory Diseases. Int J Mol Sci 2021; 22:ijms22147506. [PMID: 34299122 PMCID: PMC8306614 DOI: 10.3390/ijms22147506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Immune-mediated inflammatory diseases (IMIDs), such as inflammatory bowel diseases and inflammatory arthritis (e.g., rheumatoid arthritis, psoriatic arthritis), are marked by increasing worldwide incidence rates. Apart from irreversible damage of the affected tissue, the systemic nature of these diseases heightens the incidence of cardiovascular insults and colitis-associated neoplasia. Only 40–60% of patients respond to currently used standard-of-care immunotherapies. In addition to this limited long-term effectiveness, all current therapies have to be given on a lifelong basis as they are unable to specifically reprogram the inflammatory process and thus achieve a true cure of the disease. On the other hand, the development of various OMICs technologies is considered as “the great hope” for improving the treatment of IMIDs. This review sheds light on the progressive development and the numerous approaches from basic science that gradually lead to the transfer from “bench to bedside” and the implementation into general patient care procedures.
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Affiliation(s)
- Charles Gwellem Anchang
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Cong Xu
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Maria Gabriella Raimondo
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Raja Atreya
- Department of Internal Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany;
| | - Andreas Maier
- Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Georg Schett
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, 91054 Erlangen, Germany;
- Department of Biology, Mathematics in Life Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Simon Rauber
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Andreas Ramming
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
- Correspondence: ; Tel.: +49-9131-8543048; Fax: +49-9131-8536448
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12
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Noa A, Kuan HS, Aschmann V, Zaburdaev V, Hilbert L. The hierarchical packing of euchromatin domains can be described as multiplicative cascades. PLoS Comput Biol 2021; 17:e1008974. [PMID: 33951053 PMCID: PMC8128263 DOI: 10.1371/journal.pcbi.1008974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 05/17/2021] [Accepted: 04/16/2021] [Indexed: 01/24/2023] Open
Abstract
The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such hierarchical packing is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into this hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. Specifically, we can pinpoint the values required to mimic a microphase-separated state of euchromatin. We suggest that the concept of multiplicative cascades can also be applied to images of other types of chromatin. Here, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin.
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Affiliation(s)
- Amra Noa
- Institute of Biological and Chemical Systems, Dept. Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Hui-Shun Kuan
- Chair of Mathematics in Life Sciences, Dept. Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Vera Aschmann
- Master’s Program Biology, Faculty for Chemistry and Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Vasily Zaburdaev
- Chair of Mathematics in Life Sciences, Dept. Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Lennart Hilbert
- Institute of Biological and Chemical Systems, Dept. Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Zoological Institute, Dept. Systems Biology and Bioinformatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
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13
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Kuan HS, Pönisch W, Jülicher F, Zaburdaev V. Continuum Theory of Active Phase Separation in Cellular Aggregates. Phys Rev Lett 2021; 126:018102. [PMID: 33480767 DOI: 10.1103/physrevlett.126.018102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Dense cellular aggregates are common in biology, ranging from bacterial biofilms to organoids, cell spheroids, and tumors. Their dynamics, driven by intercellular forces, is intrinsically out of equilibrium. Motivated by bacterial colonies as a model system, we present a continuum theory to study dense, active, cellular aggregates. We describe the process of aggregate formation as an active phase separation phenomenon, while the merging of aggregates is rationalized as a coalescence of viscoelastic droplets where the key timescales are linked to the turnover of the active force. Our theory provides a general framework for studying the rheology and nonequilibrium dynamics of dense cellular aggregates.
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Affiliation(s)
- Hui-Shun Kuan
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Max Planck Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Wolfram Pönisch
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3DY Cambridge, United Kingdom
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Max Planck Zentrum für Physik und Medizin, 91058 Erlangen, Germany
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14
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Lühr JJ, Alex N, Amon L, Kräter M, Kubánková M, Sezgin E, Lehmann CHK, Heger L, Heidkamp GF, Smith AS, Zaburdaev V, Böckmann RA, Levental I, Dustin ML, Eggeling C, Guck J, Dudziak D. Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition. Front Immunol 2020; 11:590121. [PMID: 33329576 PMCID: PMC7728921 DOI: 10.3389/fimmu.2020.590121] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/15/2020] [Indexed: 01/02/2023] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells of the immune system. Upon sensing pathogenic material in their environment, DCs start to mature, which includes cellular processes, such as antigen uptake, processing and presentation, as well as upregulation of costimulatory molecules and cytokine secretion. During maturation, DCs detach from peripheral tissues, migrate to the nearest lymph node, and find their way into the correct position in the net of the lymph node microenvironment to meet and interact with the respective T cells. We hypothesize that the maturation of DCs is well prepared and optimized leading to processes that alter various cellular characteristics from mechanics and metabolism to membrane properties. Here, we investigated the mechanical properties of monocyte-derived dendritic cells (moDCs) using real-time deformability cytometry to measure cytoskeletal changes and found that mature moDCs were stiffer compared to immature moDCs. These cellular changes likely play an important role in the processes of cell migration and T cell activation. As lipids constitute the building blocks of the plasma membrane, which, during maturation, need to adapt to the environment for migration and DC-T cell interaction, we performed an unbiased high-throughput lipidomics screening to identify the lipidome of moDCs. These analyses revealed that the overall lipid composition was significantly changed during moDC maturation, even implying an increase of storage lipids and differences of the relative abundance of membrane lipids upon maturation. Further, metadata analyses demonstrated that lipid changes were associated with the serum low-density lipoprotein (LDL) and cholesterol levels in the blood of the donors. Finally, using lipid packing imaging we found that the membrane of mature moDCs revealed a higher fluidity compared to immature moDCs. This comprehensive and quantitative characterization of maturation associated changes in moDCs sets the stage for improving their use in clinical application.
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Affiliation(s)
- Jennifer J. Lühr
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
- Nano-Optics, Max-Planck Institute for the Science of Light, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Nils Alex
- Department of Physics, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Martin Kräter
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biological Optomechanics, Max-Planck Institute for the Science of Light, Erlangen, Germany
| | - Markéta Kubánková
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biological Optomechanics, Max-Planck Institute for the Science of Light, Erlangen, Germany
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Raddcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Christian H. K. Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Gordon F. Heidkamp
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
- Roche Innovation Center Munich, Roche Pharmaceutical Research and Early Development, pRED, Munich, Germany
| | - Ana-Sunčana Smith
- PULS Group, Department of Physics, IZNF, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Mathematics in Life Sciences, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Medical Immunology Campus Erlangen, Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ilya Levental
- McGovern Medical School, The University of Texas Health Science Center, Houston, TX, United States
| | - Michael L. Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Raddcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Institute for Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Leibniz Institute of Photonic Technologies e.V., Jena, Germany
| | - Jochen Guck
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Biological Optomechanics, Max-Planck Institute for the Science of Light, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
- Medical Immunology Campus Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Erlangen, Germany
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15
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Taylor RW, Holler C, Mahmoodabadi RG, Küppers M, Dastjerdi HM, Zaburdaev V, Schambony A, Sandoghdar V. High-Precision Protein-Tracking With Interferometric Scattering Microscopy. Front Cell Dev Biol 2020; 8:590158. [PMID: 33224953 PMCID: PMC7669747 DOI: 10.3389/fcell.2020.590158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023] Open
Abstract
The mobility of proteins and lipids within the cell, sculpted oftentimes by the organization of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behavior. Interferometric scattering (iSCAT) microscopy is an emerging technique well-suited for visualizing the diffusion of gold nanoparticle-labeled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualizing the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.
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Affiliation(s)
- Richard W Taylor
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Cornelia Holler
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Reza Gholami Mahmoodabadi
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Michelle Küppers
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Physics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Houman Mirzaalian Dastjerdi
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Computer Science, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexandra Schambony
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Physics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
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16
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Abstract
We studied the rotational and translational diffusion of a single gold nanorod linked to a supported lipid bilayer with ultrahigh temporal resolution of two microseconds. By using a home-built polarization-sensitive dark-field microscope, we recorded particle trajectories with lateral precision of 3 nm and rotational precision of 4°. The large number of trajectory points in our measurements allows us to characterize the statistics of rotational diffusion with unprecedented detail. Our data show apparent signatures of anomalous diffusion such as sublinear scaling of the mean-squared angular displacement and negative values of angular correlation function at small lag times. However, a careful analysis reveals that these effects stem from the residual noise contributions and confirms normal diffusion. Our experimental approach and observations can be extended to investigate diffusive processes of anisotropic nanoparticles in other fundamental systems such as cellular membranes or other two-dimensional fluids.
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Affiliation(s)
- Mahdi Mazaheri
- Max
Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany
| | - Jens Ehrig
- Max
Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany
| | - Alexey Shkarin
- Max
Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany
| | - Vasily Zaburdaev
- Department
of Biology, Friedrich Alexander University
Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany
- Max-Planck-Zentrum
für Physik und Medizin, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max
Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany
- Max-Planck-Zentrum
für Physik und Medizin, 91058 Erlangen, Germany
- Department
of Physics, Friedrich Alexander University
Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany
- E-mail:
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17
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Kaptan D, Penkov S, Zhang X, Gade VR, Raghuraman BK, Galli R, Sampaio JL, Haase R, Koch E, Shevchenko A, Zaburdaev V, Kurzchalia TV. Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation. Aging Cell 2020; 19:e13214. [PMID: 32898317 PMCID: PMC7576309 DOI: 10.1111/acel.13214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/01/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
The dauer larva of Caenorhabditis elegans, destined to survive long periods of food scarcity and harsh environment, does not feed and has a very limited exchange of matter with the exterior. It was assumed that the survival time is determined by internal energy stores. Here, we show that ethanol can provide a potentially unlimited energy source for dauers by inducing a controlled metabolic shift that allows it to be metabolized into carbohydrates, amino acids, and lipids. Dauer larvae provided with ethanol survive much longer and have greater desiccation tolerance. On the cellular level, ethanol prevents the deterioration of mitochondria caused by energy depletion. By modeling the metabolism of dauers of wild‐type and mutant strains with and without ethanol, we suggest that the mitochondrial health and survival of an organism provided with an unlimited source of carbon depends on the balance between energy production and toxic product(s) of lipid metabolism.
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Affiliation(s)
- Damla Kaptan
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Sider Penkov
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden Dresden Germany
- Institute for Clinical Chemistry and Laboratory Medicine University Clinic and Medical FacultyTU Dresden Dresden Germany
| | - Xingyu Zhang
- Max Planck Institute for the Physics of Complex Systems Dresden Germany
- Friedrich‐Alexander‐University Erlangen‐Nuremberg Erlangen Germany
- Max‐Planck‐Zentrum für Physik und Medizin Erlangen Germany
| | - Vamshidhar R. Gade
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | | | - Roberta Galli
- Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring Faculty of Medicine Carl Gustav Carus TU Dresden Dresden Germany
| | - Júlio L. Sampaio
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Robert Haase
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Edmund Koch
- Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring Faculty of Medicine Carl Gustav Carus TU Dresden Dresden Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems Dresden Germany
- Friedrich‐Alexander‐University Erlangen‐Nuremberg Erlangen Germany
- Max‐Planck‐Zentrum für Physik und Medizin Erlangen Germany
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18
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Adame-Arana O, Weber CA, Zaburdaev V, Prost J, Jülicher F. Liquid Phase Separation Controlled by pH. Biophys J 2020; 119:1590-1605. [PMID: 33010236 DOI: 10.1016/j.bpj.2020.07.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 12/31/2022] Open
Abstract
We present a minimal model to study the effects of pH on liquid phase separation of macromolecules. Our model describes a mixture composed of water and macromolecules that exist in three different charge states and have a tendency to phase separate. This phase separation is affected by pH via a set of chemical reactions describing protonation and deprotonation of macromolecules, as well as self-ionization of water. We consider the simple case in which interactions are captured by Flory-Huggins interaction parameters corresponding to Debye screening lengths shorter than a nanometer, which is relevant to proteins inside biological cells under physiological conditions. We identify the conjugate thermodynamic variables at chemical equilibrium and discuss the effective free energy at fixed pH. First, we study phase diagrams as a function of macromolecule concentration and temperature at the isoelectric point of the macromolecules. We find a rich variety of phase diagram topologies, including multiple critical points, triple points, and first-order transition points. Second, we change the pH relative to the isoelectric point of the macromolecules and study how phase diagrams depend on pH. We find that these phase diagrams as a function of pH strongly depend on whether oppositely charged macromolecules or neutral macromolecules have a stronger tendency to phase separate. One key finding is that we predict the existence of a reentrant behavior as a function of pH. In addition, our model predicts that the region of phase separation is typically broader at the isoelectric point. This model could account for both in vitro phase separation of proteins as a function of pH and protein phase separation in yeast cells for pH values close to the isoelectric point of many cytosolic proteins.
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Affiliation(s)
- Omar Adame-Arana
- Max-Planck-Institut für Physik komplexer Systeme, Dresden, Germany
| | - Christoph A Weber
- Max-Planck-Institut für Physik komplexer Systeme, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Jacques Prost
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Frank Jülicher
- Max-Planck-Institut für Physik komplexer Systeme, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany.
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19
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Sato Y, Hilbert L, Oda H, Wan Y, Heddleston JM, Chew TL, Zaburdaev V, Keller P, Lionnet T, Vastenhouw N, Kimura H. Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis. Development 2019; 146:146/19/dev179127. [PMID: 31570370 PMCID: PMC6803375 DOI: 10.1242/dev.179127] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022]
Abstract
Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique to monitor the changes in histone modification levels during zygotic genome activation (ZGA) in living zebrafish embryos. Among various histone modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating in two nuclear foci in the 64- to 1k-cell-stage embryos. The elongating form of RNA polymerase II, which is phosphorylated at Ser2 in heptad repeats within the C-terminal domain (RNAP2 Ser2ph), and miR-430 transcripts were also concentrated in foci closely associated with H3K27ac. When treated with α-amanitin to inhibit transcription or JQ-1 to inhibit binding of acetyl-reader proteins, H3K27ac foci still appeared but RNAP2 Ser2ph and miR-430 morpholino were not concentrated in foci, suggesting that H3K27ac precedes active transcription during ZGA. We anticipate that the method presented here could be applied to a variety of developmental processes in any model and non-model organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Lennart Hilbert
- Center for Systems Biology Dresden, Dresden 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yinan Wan
- Howard Hughes Medical Institute, Janelia Research Campus, VA 20147, USA
| | - John M Heddleston
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, VA 20147, USA
| | - Vasily Zaburdaev
- Center for Systems Biology Dresden, Dresden 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
| | - Philipp Keller
- Howard Hughes Medical Institute, Janelia Research Campus, VA 20147, USA
| | - Timothee Lionnet
- Institute for Systems Genetics and Department of Cell Biology, New York University Langone Health, NY 10016, USA
| | - Nadine Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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20
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Abstract
Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple pili. It was shown experimentally that the substrate motility of Neisseria gonorrhoeae cells can be described as a persistent random walk with a persistence length that exceeds the mean pili length. Moreover, the persistence length increases for a higher number of pili per cell. With the help of a simple, tractable stochastic model, we test whether a tug of war without directional memory can explain the persistent motion of single Neisseria gonorrhoeae cells. While persistent motion of single cells indeed emerges naturally in the model, a tug of war alone is not capable of explaining the motility of microcolonies, which becomes weaker with increasing colony size. We suggest sliding friction between the microcolonies and the substrate as the missing ingredient. While such friction almost does not affect the general mechanism of single cell motility, it has a strong effect on colony motility. We validate the theoretical predictions by using a three-dimensional computational model that includes explicit details of the pili dynamics, force generation, and geometry of cells.
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Affiliation(s)
- Wolfram Pönisch
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Institute of Supercomputing Technologies, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603140, Russia.,Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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21
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Abstract
Loop geometry is a frequent encounter in synthetic and biological polymers. Here we provide an analytical theory to characterize the shapes of polymer loops subjected to an external force field. We show how to calculate the polymer density, gyration radius and its distribution. Interestingly, the distribution of the gyration radius shows a non-monotonic behavior as a function of the external force. Furthermore, we analyzed the gyration tensor of the polymer loop characterizing its overall shape. Two parameters called asphericity and the nature of asphericity derived from the gyration tensor, along with the gyration radius, can be used to quantify the shape of polymer loops in theory and experiments.
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Affiliation(s)
- Wenwen Huang
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, D-01187 Dresden, Germany.
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22
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Passucci G, Brasch ME, Henderson JH, Zaburdaev V, Manning ML. Identifying the mechanism for superdiffusivity in mouse fibroblast motility. PLoS Comput Biol 2019; 15:e1006732. [PMID: 30763309 PMCID: PMC6392322 DOI: 10.1371/journal.pcbi.1006732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/27/2019] [Accepted: 12/20/2018] [Indexed: 12/02/2022] Open
Abstract
We seek to characterize the motility of mouse fibroblasts on 2D substrates. Utilizing automated tracking techniques, we find that cell trajectories are super-diffusive, where displacements scale faster than t1/2 in all directions. Two mechanisms have been proposed to explain such statistics in other cell types: run and tumble behavior with Lévy-distributed run times, and ensembles of cells with heterogeneous speed and rotational noise. We develop an automated toolkit that directly compares cell trajectories to the predictions of each model and demonstrate that ensemble-averaged quantities such as the mean-squared displacements and velocity autocorrelation functions are equally well-fit by either model. However, neither model correctly captures the short-timescale behavior quantified by the displacement probability distribution or the turning angle distribution. We develop a hybrid model that includes both run and tumble behavior and heterogeneous noise during the runs, which correctly matches the short-timescale behaviors and indicates that the run times are not Lévy distributed. The analysis tools developed here should be broadly useful for distinguishing between mechanisms for superdiffusivity in other cells types and environments.
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Affiliation(s)
- Giuseppe Passucci
- Physics Department, Syracuse University, Syracuse, New York, United States of America
| | - Megan E. Brasch
- Biomedical and Chemical Engineering Department, Syracuse University, Syracuse, New York, United States of America
| | - James H. Henderson
- Biomedical and Chemical Engineering Department, Syracuse University, Syracuse, New York, United States of America
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York, United States of America
| | - Vasily Zaburdaev
- Institute of Supercomputing Technologies, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - M. Lisa Manning
- Physics Department, Syracuse University, Syracuse, New York, United States of America
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York, United States of America
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23
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Pönisch W, Eckenrode KB, Alzurqa K, Nasrollahi H, Weber C, Zaburdaev V, Biais N. Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation. Sci Rep 2018; 8:16567. [PMID: 30410109 PMCID: PMC6224386 DOI: 10.1038/s41598-018-34754-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
Microcolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a significant change in bacterial physiology. Within a microcolony, bacteria forgo a single cell lifestyle for a communal lifestyle hallmarked by high cell density and physical interactions between cells potentially altering their behaviour. It is thus crucial to understand how initially identical single cells start to behave differently while assembling in these tight communities. Here we show that cells in the microcolonies formed by the human pathogen Neisseria gonorrhoeae (Ng) present differential motility behaviors within an hour upon colony formation. Observation of merging microcolonies and tracking of single cells within microcolonies reveal a heterogeneous motility behavior: cells close to the surface of the microcolony exhibit a much higher motility compared to cells towards the center. Numerical simulations of a biophysical model for the microcolonies at the single cell level suggest that the emergence of differential behavior within a multicellular microcolony of otherwise identical cells is of mechanical origin. It could suggest a route toward further bacterial differentiation and ultimately mature biofilms.
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Affiliation(s)
- Wolfram Pönisch
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany
- MRC Laboratory for Molecular Cell Biology, University City London, London, UK
| | - Kelly B Eckenrode
- Brooklyn College of CUNY, Department of Biology, Brooklyn, USA
- Graduate Center of CUNY, New York, USA
| | - Khaled Alzurqa
- Brooklyn College of CUNY, Department of Biology, Brooklyn, USA
| | - Hadi Nasrollahi
- Brooklyn College of CUNY, Department of Biology, Brooklyn, USA
| | - Christoph Weber
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany
| | - Vasily Zaburdaev
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Nicolas Biais
- Brooklyn College of CUNY, Department of Biology, Brooklyn, USA.
- Graduate Center of CUNY, New York, USA.
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24
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Schlüssler R, Abuhattum S, Cojoc G, Beck T, Reichel F, Kim K, Schürmann M, Müller P, Czarske J, Zaburdaev V, Franzmann T, Alberti S, Guck J. Biophysical Techniques for the Study of Phase Transitions in Protein Droplets and Cells. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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25
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Strelnikova N, Sauter N, Guizar-Sicairos M, Göllner M, Diaz A, Delivani P, Chacón M, Tolić IM, Zaburdaev V, Pfohl T. Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast. Sci Rep 2017; 7:13775. [PMID: 29061993 PMCID: PMC5653777 DOI: 10.1038/s41598-017-13175-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/21/2017] [Indexed: 01/04/2023] Open
Abstract
Seeing physiological processes at the nanoscale in living organisms without labeling is an ultimate goal in life sciences. Using X-ray ptychography, we explored in situ the dynamics of unstained, living fission yeast Schizosaccharomyces pombe cells in natural, aqueous environment at the nanoscale. In contrast to previous X-ray imaging studies on biological matter, in this work the eukaryotic cells were alive even after several ptychographic X-ray scans, which allowed us to visualize the chromatin motion as well as the autophagic cell death induced by the ionizing radiation. The accumulated radiation of the sequential scans allowed for the determination of a characteristic dose of autophagic vacuole formation and the lethal dose for fission yeast. The presented results demonstrate a practical method that opens another way of looking at living biological specimens and processes in a time-resolved label-free setting.
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Affiliation(s)
| | - Nora Sauter
- Department of Chemistry, University of Basel, Basel, Switzerland
| | | | - Michael Göllner
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Ana Diaz
- Paul Scherrer Institut, Villigen, Switzerland
| | - Petrina Delivani
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mariola Chacón
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Thomas Pfohl
- Department of Chemistry, University of Basel, Basel, Switzerland. .,Biomaterials Science Center, University of Basel, Basel, Switzerland. .,Institute of Physics, University of Freiburg, Freiburg, Germany.
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26
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Boothe T, Hilbert L, Heide M, Berninger L, Huttner WB, Zaburdaev V, Vastenhouw NL, Myers EW, Drechsel DN, Rink JC. A tunable refractive index matching medium for live imaging cells, tissues and model organisms. eLife 2017; 6. [PMID: 28708059 PMCID: PMC5582871 DOI: 10.7554/elife.27240] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/13/2017] [Indexed: 11/17/2022] Open
Abstract
In light microscopy, refractive index mismatches between media and sample cause spherical aberrations that often limit penetration depth and resolution. Optical clearing techniques can alleviate these mismatches, but they are so far limited to fixed samples. We present Iodixanol as a non-toxic medium supplement that allows refractive index matching in live specimens and thus substantially improves image quality in live-imaged primary cell cultures, planarians, zebrafish and human cerebral organoids. DOI:http://dx.doi.org/10.7554/eLife.27240.001 Light microscopy is a key tool in biomedical research. For perfect images, light needs to be able to pass through the sample, the material (or “mounting medium”) that holds the sample in place, and finally the image-detecting equipment in a straight line. However, in practice, light rays often deviate away from this line because they move at different speeds in different materials; how much the speed of light changes is related to a property called the refractive index of the material. This is exactly the effect that causes a stick stuck into water to look bent at the water’s surface. In light microscopy, mismatches in refractive index significantly reduce quality of the images that can be obtained. Live specimens are particularly challenging to image because different specimens have very different refractive indices compared to the mounting medium, which holds specimens in place but must also keep them alive. Although the addition of chemical compounds can theoretically match the refractive index of the mounting medium to that of the specimen, this approach has so far not been practical because such manipulations tend to kill the specimen. An important challenge has therefore been to identify a compound that can adjust, or “tune”, the refractive index of mounting media over a wide range, yet without harming the specimens. Now, Boothe et al. have identified a chemical called Iodixanol as an ideal and easy to use supplement for tuning the refractive index of water-based live imaging media. Adding Iodixanol to the mounting media did not appear to have any toxic effects on cell cultures, developing zebrafish embryos or regenerating planarian flatworms. Importantly, Boothe et al. found that Iodixanol significantly improved the quality of the images collected from all of these different specimens. It is important to stress that Iodixanol does not change the refractive index of the sample or cancel out refractive index differences within the sample – so it cannot render opaque specimens transparent. Nevertheless, Iodixanol supplementation is a simple and affordable technique to improve image quality in any live imaging application without having to resort to more expensive and highly specialized microscopes. DOI:http://dx.doi.org/10.7554/eLife.27240.002
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Affiliation(s)
- Tobias Boothe
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Lennart Hilbert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lea Berninger
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - David N Drechsel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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27
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Joseph SR, Pálfy M, Hilbert L, Kumar M, Karschau J, Zaburdaev V, Shevchenko A, Vastenhouw NL. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. eLife 2017; 6. [PMID: 28425915 PMCID: PMC5451213 DOI: 10.7554/elife.23326] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo. DOI:http://dx.doi.org/10.7554/eLife.23326.001 The DNA in a fertilized egg contains all the information required to form an animal’s body. In order for the animal to develop properly, particular genes encoded in the DNA are only active at specific times. The DNA is wrapped around proteins called histones, which allows the DNA to be tightly packed inside the cell. However, histones can block other proteins called transcription factors from binding to the DNA to activate the genes. Young embryos initially develop with all of their genes switched off, relying on the nutrients and other molecules provided by their mother. After some time, the embryo starts to switch on its own genes to take control of its own development, but it was not clear how this happens. Joseph et al. investigated how genes are activated in zebrafish embryos, which are often used as models to study how animals develop. The experiments show that competition between histones and transcription factors for binding to DNA controls when genes are switched on. In young fish embryos, there are so many histones present that transcription factors have no opportunity to bind to DNA. Over time, however, the numbers of histones decrease, allowing transcription factors to bind to DNA and switch on genes. Histones and transcription factors regulate the activity of genes throughout the life of the animal. Therefore, competition between these two types of protein may also control gene activity in other situations. A better understanding of how gene activity is controlled could allow researchers to more easily grow different types of cell in the laboratory or to reprogram specific cells in the body. As such, these new findings may aid the development of therapies to regenerate organs or tissues that have been damaged by injury or disease. DOI:http://dx.doi.org/10.7554/eLife.23326.002
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Affiliation(s)
- Shai R Joseph
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lennart Hilbert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jens Karschau
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Vasily Zaburdaev
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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28
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Shin J, Cherstvy AG, Kim WK, Zaburdaev V. Elasticity-based polymer sorting in active fluids: a Brownian dynamics study. Phys Chem Chem Phys 2017; 19:18338-18347. [DOI: 10.1039/c7cp02947k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different.
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Affiliation(s)
- Jaeoh Shin
- Max Planck Institute for the Physics of Complex Systems
- 01187 Dresden
- Germany
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Won Kyu Kim
- Institut für Weiche Materie and Funktionale Materialen
- Helmholtz-Zentrum Berlin
- 14109 Berlin
- Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems
- 01187 Dresden
- Germany
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29
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Pönisch W, Weber CA, Juckeland G, Biais N, Zaburdaev V. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates. New J Phys 2017; 19:015003. [PMID: 34017216 PMCID: PMC8132470 DOI: 10.1088/1367-2630/aa5483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.
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Affiliation(s)
- Wolfram Pönisch
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Guido Juckeland
- Department of Information Services and Computing (FWC), Helmholtz-Zentrum Dresden-Rossendorf e.V, D-01314 Dresden, Germany
| | - Nicolas Biais
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA
- Graduate Center of CUNY, NY 10016, USA
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
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30
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Zaburdaev V, Fouxon I, Denisov S, Barkai E. Superdiffusive Dispersals Impart the Geometry of Underlying Random Walks. Phys Rev Lett 2016; 117:270601. [PMID: 28084765 DOI: 10.1103/physrevlett.117.270601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Indexed: 06/06/2023]
Abstract
It is recognized now that a variety of real-life phenomena ranging from diffusion of cold atoms to the motion of humans exhibit dispersal faster than normal diffusion. Lévy walks is a model that excelled in describing such superdiffusive behaviors albeit in one dimension. Here we show that, in contrast to standard random walks, the microscopic geometry of planar superdiffusive Lévy walks is imprinted in the asymptotic distribution of the walkers. The geometry of the underlying walk can be inferred from trajectories of the walkers by calculating the analogue of the Pearson coefficient.
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Affiliation(s)
- V Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
- Institute of Supercomputing Technologies, Lobachevsky State University of Nizhny Novgorod, 603140 Nizhny Novgorod, Russia
| | - I Fouxon
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - S Denisov
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, 603140 Nizhny Novgorod, Russia
- Sumy State University, Rimsky-Korsakov Street 2, 40007 Sumy, Ukraine
- Institute of Physics, University of Augsburg, Universitätsstrasse 1, D-86135 Augsburg, Germany
| | - E Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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31
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Munder MC, Midtvedt D, Franzmann T, Nüske E, Otto O, Herbig M, Ulbricht E, Müller P, Taubenberger A, Maharana S, Malinovska L, Richter D, Guck J, Zaburdaev V, Alberti S. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy. eLife 2016; 5. [PMID: 27003292 PMCID: PMC4850707 DOI: 10.7554/elife.09347] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 02/13/2016] [Indexed: 01/19/2023] Open
Abstract
Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state.
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Affiliation(s)
| | - Daniel Midtvedt
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oliver Otto
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maik Herbig
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Elke Ulbricht
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Paul Müller
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anna Taubenberger
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen Guck
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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32
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Hilbert L, Zaburdaev V, Vastenhouw N. Subnuclear Spatial Structuring of Chromatin and Polymerase II during Transcription Activation of the Zebrafish Zygotic Genome. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Lin YT, Frömberg D, Huang W, Delivani P, Chacón M, Tolić IM, Jülicher F, Zaburdaev V. Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes. Phys Rev Lett 2015; 115:208102. [PMID: 26613475 DOI: 10.1103/physrevlett.115.208102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 06/05/2023]
Abstract
During recombination, the DNA of parents exchange their genetic information to give rise to a genetically unique offspring. For recombination to occur, homologous chromosomes need to find each other and align with high precision. Fission yeast solves this problem by folding chromosomes in loops and pulling them through the viscous nucleoplasm. We propose a theory of pulled polymer loops to quantify the effect of drag forces on the alignment of chromosomes. We introduce an external force field to the concept of a Brownian bridge and thus solve for the statistics of loop configurations in space.
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Affiliation(s)
- Yen Ting Lin
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
| | - Daniela Frömberg
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
| | - Wenwen Huang
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
| | - Petrina Delivani
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
| | - Mariola Chacón
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
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34
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Abstract
Type IV pili (Tfp) are prokaryotic retractable appendages known to mediate surface attachment, motility, and subsequent clustering of cells. Tfp are the main means of motility for Neisseria gonorrhoeae, the causative agent of gonorrhea. Tfp are also involved in formation of the microcolonies, which play a crucial role in the progression of the disease. While motility of individual cells is relatively well understood, little is known about the dynamics of N. gonorrhoeae aggregation. We investigate how individual N. gonorrhoeae cells, initially uniformly dispersed on flat plastic or glass surfaces, agglomerate into spherical microcolonies within hours. We quantify the clustering process by measuring the area fraction covered by the cells, number of cell aggregates, and their average size as a function of time. We observe that the microcolonies are also able to move but their mobility rapidly vanishes as the size of the colony increases. After a certain critical size they become immobile. We propose a simple theoretical model which assumes a pili-pili interaction of cells as the main clustering mechanism. Numerical simulations of the model quantitatively reproduce the experimental data on clustering and thus suggest that the agglomeration process can be entirely explained by the Tfp-mediated interactions. In agreement with this hypothesis mutants lacking pili are not able to form colonies. Moreover, cells with deficient quorum sensing mechanism show similar aggregation as the wild-type bacteria. Therefore, our results demonstrate that pili provide an essential mechanism for colony formation, while additional chemical cues, for example quorum sensing, might be of secondary importance.
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Affiliation(s)
- Johannes Taktikos
- Harvard University, School of Engineering and Applied Sciences, Cambridge, MA, United States of America
- Technische Universität Berlin, Institut für Theoretische Physik, Berlin, Germany
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany
| | - Yen Ting Lin
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany
| | - Holger Stark
- Technische Universität Berlin, Institut für Theoretische Physik, Berlin, Germany
| | - Nicolas Biais
- Brooklyn College of City University of New York, Department of Biology, Brooklyn, NY, United States of America
- * E-mail: (NB); (VZ)
| | - Vasily Zaburdaev
- Harvard University, School of Engineering and Applied Sciences, Cambridge, MA, United States of America
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany
- * E-mail: (NB); (VZ)
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35
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Weber CA, Lin YT, Biais N, Zaburdaev V. Formation and dissolution of bacterial colonies. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:032704. [PMID: 26465495 DOI: 10.1103/physreve.92.032704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 06/05/2023]
Abstract
Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing the formation and dissolution of bacterial colonies are still poorly understood. Starting from a kinetic description of motile and interacting cells we derive a hydrodynamic equation for their density on a surface, where most of the kinetic coefficients are estimated from experimental data for N. gonorrhoeae bacteria. We use it to describe the formation of multiple colonies with sizes consistent with experimental observations. Finally, we show how the changes in the cell-to-cell interactions lead to the dissolution of the bacterial colonies. The successful application of kinetic theory to a complex far from equilibrium system such as formation and dissolution of living bacterial colonies potentially paves the way for the physical quantification of the initial stages of biofilm formation.
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Affiliation(s)
- Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden 01187, Germany
| | - Yen Ting Lin
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden 01187, Germany
| | - Nicolas Biais
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York 11210, USA
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden 01187, Germany
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36
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Froemberg D, Schmiedeberg M, Barkai E, Zaburdaev V. Asymptotic densities of ballistic Lévy walks. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:022131. [PMID: 25768482 DOI: 10.1103/physreve.91.022131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 06/04/2023]
Abstract
We propose an analytical method to determine the shape of density profiles in the asymptotic long-time limit for a broad class of coupled continuous-time random walks which operate in the ballistic regime. In particular, we show that different scenarios of performing a random-walk step, via making an instantaneous jump penalized by a proper waiting time or via moving with a constant speed, dramatically effect the corresponding propagators, despite the fact that the end points of the steps are identical. Furthermore, if the speed during each step of the random walk is itself a random variable, its distribution gets clearly reflected in the asymptotic density of random walkers. These features are in contrast with more standard nonballistic random walks.
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Affiliation(s)
- D Froemberg
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, D-01187 Dresden, Germany
| | - M Schmiedeberg
- Insitut für Theoretische Physik 2: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - E Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - V Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, D-01187 Dresden, Germany
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37
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Zaburdaev V, Biais N, Schmiedeberg M, Eriksson J, Jonsson AB, Sheetz MP, Weitz DA. Uncovering the mechanism of trapping and cell orientation during Neisseria gonorrhoeae twitching motility. Biophys J 2014; 107:1523-31. [PMID: 25296304 PMCID: PMC4190650 DOI: 10.1016/j.bpj.2014.07.061] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/16/2014] [Accepted: 07/22/2014] [Indexed: 11/22/2022] Open
Abstract
Neisseria gonorrheae bacteria are the causative agent of the second most common sexually transmitted infection in the world. The bacteria move on a surface by means of twitching motility. Their movement is mediated by multiple long and flexible filaments, called type IV pili, that extend from the cell body, attach to the surface, and retract, thus generating a pulling force. Moving cells also use pili to aggregate and form microcolonies. However, the mechanism by which the pili surrounding the cell body work together to propel bacteria remains unclear. Understanding this process will help describe the motility of N. gonorrheae bacteria, and thus the dissemination of the disease which they cause. In this article we track individual twitching cells and observe that their trajectories consist of alternating moving and pausing intervals, while the cell body is preferably oriented with its wide side toward the direction of motion. Based on these data, we propose a model for the collective pili operation of N. gonorrheae bacteria that explains the experimentally observed behavior. Individual pili function independently but can lead to coordinated motion or pausing via the force balance. The geometry of the cell defines its orientation during motion. We show that by changing pili substrate interactions, the motility pattern can be altered in a predictable way. Although the model proposed is tangibly simple, it still has sufficient robustness to incorporate further advanced pili features and various cell geometries to describe other bacteria that employ pili to move on surfaces.
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Affiliation(s)
- Vasily Zaburdaev
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Nicolas Biais
- Department of Biological Sciences, Columbia University, New York, New York; Department of Biology, Brooklyn College, New York, New York
| | - Michael Schmiedeberg
- Insitut für Theoretische Physik: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jens Eriksson
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ann-Beth Jonsson
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Michael P Sheetz
- Department of Biological Sciences, Columbia University, New York, New York
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts.
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38
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Theves M, Taktikos J, Zaburdaev V, Stark H, Beta C. A bacterial swimmer with two alternating speeds of propagation. Biophys J 2014; 105:1915-24. [PMID: 24138867 DOI: 10.1016/j.bpj.2013.08.047] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 08/18/2013] [Accepted: 08/22/2013] [Indexed: 11/29/2022] Open
Abstract
We recorded large data sets of swimming trajectories of the soil bacterium Pseudomonas putida. Like other prokaryotic swimmers, P. putida exhibits a motion pattern dominated by persistent runs that are interrupted by turning events. An in-depth analysis of their swimming trajectories revealed that the majority of the turning events is characterized by an angle of ϕ1 = 180° (reversals). To a lesser extent, turning angles of ϕ2 = 0° are also found. Remarkably, we observed that, upon a reversal, the swimming speed changes by a factor of two on average-a prominent feature of the motion pattern that, to our knowledge, has not been reported before. A theoretical model, based on the experimental values for the average run time and the rotational diffusion, recovers the mean-square displacement of P. putida if the two distinct swimming speeds are taken into account. Compared to a swimmer that moves with a constant intermediate speed, the mean-square displacement is strongly enhanced. We furthermore observed a negative dip in the directional autocorrelation at intermediate times, a feature that is only recovered in an extended model, where the nonexponential shape of the run-time distribution is taken into account.
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Affiliation(s)
- Matthias Theves
- Institut für Physik und Astronomie, Universität Potsdam, Potsdam, Germany
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39
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Abstract
Most bacteria at certain stages of their life cycle are able to move actively; they can swim in a liquid or crawl on various surfaces. A typical path of the moving cell often resembles the trajectory of a random walk. However, bacteria are capable of modifying their apparently random motion in response to changing environmental conditions. As a result, bacteria can migrate towards the source of nutrients or away from harmful chemicals. Surprisingly, many bacterial species that were studied have several distinct motility patterns, which can be theoretically modeled by a unifying random walk approach. We use this approach to quantify the process of cell dispersal in a homogeneous environment and show how the bacterial drift velocity towards the source of attracting chemicals is affected by the motility pattern of the bacteria. Our results open up the possibility of accessing additional information about the intrinsic response of the cells using macroscopic observations of bacteria moving in inhomogeneous environments.
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Affiliation(s)
- Johannes Taktikos
- Max-Planck-Institut für Physik komplexer Systeme, Dresden, Germany
- Technische Universität Berlin, Institut für Theoretische Physik, Berlin, Germany
- Harvard University, School of Engineering and Applied Sciences, Cambridge, Massachusetts, United States
- * E-mail:
| | - Holger Stark
- Technische Universität Berlin, Institut für Theoretische Physik, Berlin, Germany
| | - Vasily Zaburdaev
- Max-Planck-Institut für Physik komplexer Systeme, Dresden, Germany
- Harvard University, School of Engineering and Applied Sciences, Cambridge, Massachusetts, United States
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40
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Zaburdaev V, Denisov S, Hänggi P. Space-time velocity correlation function for random walks. Phys Rev Lett 2013; 110:170604. [PMID: 23679699 DOI: 10.1103/physrevlett.110.170604] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/11/2013] [Indexed: 06/02/2023]
Abstract
Space-time correlation functions constitute a useful instrument from the research toolkit of continuous-media and many-body physics. Here we adopt this concept for single-particle random walks and demonstrate that the corresponding space-time velocity autocorrelation functions reveal correlations which extend in time much longer than estimated with the commonly employed temporal correlation functions. A generic feature of considered random-walk processes is an effect of velocity echo identified by the existence of time-dependent regions where most of the walkers are moving in the direction opposite to their initial motion. We discuss the relevance of the space-time velocity correlation functions for the experimental studies of cold atom dynamics in an optical potential and charge transport on micro- and nanoscales.
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Affiliation(s)
- V Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
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41
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Abstract
Many bacteria on earth exist in surface-attached communities known as biofilms. These films are responsible for manifold problems, including hospital-acquired infections and biofouling, but they can also be beneficial. Biofilm growth depends on the transport of nutrients and waste, for which diffusion is thought to be the main source of transport. However, diffusion is ineffective for transport over large distances and thus should limit growth. Nevertheless, biofilms can grow to be very large. Here we report the presence of a remarkable network of well-defined channels that form in wild-type Bacillus subtilis biofilms and provide a system for enhanced transport. We observe that these channels have high permeability to liquid flow and facilitate the transport of liquid through the biofilm. In addition, we find that spatial variations in evaporative flux from the surface of these biofilms provide a driving force for the flow of liquid in the channels. These channels offer a remarkably simple system for liquid transport, and their discovery provides insight into the physiology and growth of biofilms.
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Affiliation(s)
| | | | | | | | | | - David A. Weitz
- School of Engineering and Applied Sciences
- Department of Physics, Harvard University, Cambridge, MA 02138
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42
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Eule S, Zaburdaev V, Friedrich R, Geisel T. Langevin description of superdiffusive Lévy processes. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 86:041134. [PMID: 23214556 DOI: 10.1103/physreve.86.041134] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 04/25/2012] [Indexed: 06/01/2023]
Abstract
The description of diffusion processes is possible in different frameworks such as random walks or Fokker-Planck or Langevin equations. Whereas for classical diffusion the equivalence of these methods is well established, in the case of anomalous diffusion it often remains an open problem. In this paper we aim to bring three approaches describing anomalous superdiffusive behavior to a common footing. While each method clearly has its advantages it is crucial to understand how those methods relate and complement each other. In particular, by using the method of subordination, we show how the Langevin equation can describe anomalous diffusion exhibited by Lévy-walk-type models and further show the equivalence of the random walk models and the generalized Kramers-Fokker-Planck equation. As a result a synergetic and complementary description of anomalous diffusion is obtained which provides a much more flexible tool for applications in real-world systems.
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Affiliation(s)
- S Eule
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
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43
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Taktikos J, Zaburdaev V, Stark H. Collective dynamics of model microorganisms with chemotactic signaling. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 85:051901. [PMID: 23004782 DOI: 10.1103/physreve.85.051901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Indexed: 06/01/2023]
Abstract
Various microorganisms use chemotaxis for signaling among individuals-a common strategy for communication that is responsible for the formation of microcolonies. We model the microorganisms as autochemotactic active random walkers and describe them by an appropriate Langevin dynamics. It consists of rotational diffusion of the walker's velocity direction and a deterministic torque that aligns the velocity direction along the gradient of a self-generated chemical field. To account for finite size, each microorganism is treated as a soft disk. Its velocity is modified when it overlaps with other walkers according to a linear force-velocity relation and a harmonic repulsion force. We analyze two-walker collisions by presenting typical trajectories and by determining a state diagram that distinguishes between free walker, metastable, and bounded cluster states. We mention an analogy to Kramer's escape problem. Finally, we investigate relevant properties of many-walker systems and describe characteristics of cluster formation in unbounded geometry and in confinement.
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Affiliation(s)
- Johannes Taktikos
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
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44
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Abstract
The standard Lévy walk is performed by a particle that moves ballistically between randomly occurring collisions when the intercollision time is a random variable governed by a power-law distribution. During instantaneous collision events, the particle randomly changes the direction of motion but maintains the same constant speed. We generalize the standard model to incorporate velocity fluctuations into the process. Two types of models are considered, namely (i) with a walker changing the direction and absolute value of its velocity during collisions only, and (ii) with a walker whose velocity continuously fluctuates. We present a full analytic evaluation of both models and emphasize the importance of initial conditions. We show that, in the limit of weak velocity fluctuations, the integral diffusion characteristics and the bulk of diffusion profiles are identical to those for the standard Lévy walk. However, the type of underlying velocity fluctuations can be identified by looking at the ballistic regions of the diffusion profiles. Our analytical results are corroborated by numerical simulations.
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Affiliation(s)
- S Denisov
- Institute of Physics, University of Augsburg, Augsburg, Germany
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45
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Abstract
We develop a minimal model for the stochastic dynamics of microorganisms where individuals communicate via autochemotaxis. This means that microorganisms, such as bacteria, amoebae, or cells, follow the gradient of a chemical that they produce themselves to attract or repel each other. A microorganism is represented as a self-propelled particle or walker with constant speed while its velocity direction diffuses on the unit circle. We study the autochemotactic response of a single self-propelled walker whose dynamics is non-Markovian. We show that its long-time dynamics is always diffusive by deriving analytic expressions for its diffusion coefficient in the weak- and strong-coupling case. We confirm our findings by numerical simulations.
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Affiliation(s)
- Johannes Taktikos
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, D-10623 Berlin, Germany
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46
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Zaburdaev V, Uppaluri S, Pfohl T, Engstler M, Friedrich R, Stark H. Langevin dynamics deciphers the motility pattern of swimming parasites. Phys Rev Lett 2011; 106:208103. [PMID: 21668266 DOI: 10.1103/physrevlett.106.208103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 05/30/2023]
Abstract
The parasite African trypanosome swims in the bloodstream of mammals and causes the highly dangerous human sleeping sickness. Cell motility is essential for the parasite's survival within the mammalian host. We present an analysis of the random-walk pattern of a swimming trypanosome. From experimental time-autocorrelation functions for the direction of motion we identify two relaxation times that differ by an order of magnitude. They originate from the rapid deformations of the cell body and a slower rotational diffusion of the average swimming direction. Velocity fluctuations are athermal and increase for faster cells whose trajectories are also straighter. We demonstrate that such a complex dynamics is captured by two decoupled Langevin equations that decipher the complex trajectory pattern by referring it to the microscopic details of cell behavior.
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Affiliation(s)
- Vasily Zaburdaev
- School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
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47
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Zaburdaev V, Denisov S, Hänggi P. Perturbation spreading in many-particle systems: a random walk approach. Phys Rev Lett 2011; 106:180601. [PMID: 21635077 DOI: 10.1103/physrevlett.106.180601] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Indexed: 05/30/2023]
Abstract
The propagation of an initially localized perturbation via an interacting many-particle Hamiltonian dynamics is investigated. We argue that the propagation of the perturbation can be captured by the use of a continuous-time random walk where a single particle is traveling through an active, fluctuating medium. Employing two archetype ergodic many-particle systems, namely, (i) a hard-point gas composed of two unequal masses and (ii) a Fermi-Pasta-Ulam chain, we demonstrate that the corresponding perturbation profiles coincide with the diffusion profiles of the single-particle Lévy walk approach. The parameters of the random walk can be related through elementary algebraic expressions to the physical parameters of the corresponding test many-body systems.
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Affiliation(s)
- V Zaburdaev
- School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
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48
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Zaburdaev V, Schmiedeberg M, Stark H. Random walks with random velocities. Phys Rev E Stat Nonlin Soft Matter Phys 2008; 78:011119. [PMID: 18763931 DOI: 10.1103/physreve.78.011119] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 06/20/2008] [Indexed: 05/26/2023]
Abstract
We consider a random walk model that takes into account the velocity distribution of random walkers. Random motion with alternating velocities is inherent to various physical and biological systems. Moreover, the velocity distribution is often the first characteristic that is experimentally accessible. Here, we derive transport equations describing the dispersal process in the model and solve them analytically. The asymptotic properties of solutions are presented in the form of a phase diagram that shows all possible scaling regimes, including superdiffusive, ballistic, and superballistic motion. The theoretical results of this work are in excellent agreement with accompanying numerical simulations.
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Affiliation(s)
- Vasily Zaburdaev
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, Berlin, Germany.
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49
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Fingerle A, Herminghaus S, Zaburdaev V. Kolmogorov-Sinai entropy of the dilute wet granular gas. Phys Rev Lett 2005; 95:198001. [PMID: 16384026 DOI: 10.1103/physrevlett.95.198001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Indexed: 05/05/2023]
Abstract
We present an analytical expression for the Kolmogorov-Sinai entropy of a wet granular gas. The influence of the liquid is modeled by a hysteretic interaction force. For the dilute limit (two-particle collisions only), we find a simple expression accounting for the contribution of both the scattering states and the bound states in arbitrary dimensions. It is shown that the system is significantly more chaotic than a gas of (dry) hard spheres, as reflected by a pronounced increase of the Kolmogorov-Sinai entropy.
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Affiliation(s)
- Axel Fingerle
- Max-Planck-Institute for Dynamics and Self-Organization, Bunsenstrasse 10, 37073 Goettingen, Germany.
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50
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Chukbar K, Zaburdaev V. Subdiffusion in random compressible flows. Phys Rev E Stat Nonlin Soft Matter Phys 2005; 71:061105. [PMID: 16089720 DOI: 10.1103/physreve.71.061105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Revised: 03/28/2005] [Indexed: 05/03/2023]
Abstract
In this work, we study the diffusion of admixture particles in a one-dimensional velocity field given by a gradient of a random potential. This refers us to the case of random compressible flows, where previously only scaling estimates were available. We develop a general approach which allows to solve this problem analytically. With its help we derive the macroscopic transport equation and rigorously show in which cases transport can be subdiffusive. We find the Fourier-Laplace transform of the Green's function of this equation and prove that for some potential distributions it satisfies the subdiffusive equation with fractional derivative with respect to time.
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