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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. BIOPHYSICAL REPORTS 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] [Abstract] [MESH Headings] [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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Amini S, Zhu T, Biswas A, Charsooghi MA, Kim K, Reber S, Dauphin Y, Fratzl P. Calcitic Prisms of The Giant Seashell Pinna Nobilis Form Light Guide Arrays. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304166. [PMID: 37450944 DOI: 10.1002/adma.202304166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The shells of the Pinnidae family are based on a double layer of single-crystal-like calcitic prisms and inner aragonitic nacre, a structure known for its outstanding mechanical performance. However, on the posterior side, shells are missing the nacreous layer, which raises the question of whether there can be any functional role in giving up this mechanical performance. Here, it is demonstrated that the prismatic part of the Pinna nobilis shell exhibits unusual optical properties, whereby each prism acts as an individual optical fiber guiding the ambient light to the inner shell cavity by total internal reflection. This pixelated light channeling enhances both spatial resolution and contrast while reducing angular blurring, an apt combination for acute tracking of a moving object. These findings offer insights into the evolutionary aspects of light-sensing and imaging and demonstrate how an architectured optical system for efficient light-tracking can be based on birefringent ceramics.
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Affiliation(s)
- Shahrouz Amini
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Tingting Zhu
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Abin Biswas
- Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
| | | | - Kyoohyun Kim
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
| | - Simone Reber
- Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Yannicke Dauphin
- UMR 7205 ISYEB, Museum National d'histoire Naturelle, CNRS UPMC EPHE, 57 rue Cuvier, Paris, 75005, France
| | - Peter Fratzl
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
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Valdez VA, Neahring L, Petry S, Dumont S. Mechanisms underlying spindle assembly and robustness. Nat Rev Mol Cell Biol 2023; 24:523-542. [PMID: 36977834 PMCID: PMC10642710 DOI: 10.1038/s41580-023-00584-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 03/30/2023]
Abstract
The microtubule-based spindle orchestrates chromosome segregation during cell division. Following more than a century of study, many components and pathways contributing to spindle assembly have been described, but how the spindle robustly assembles remains incompletely understood. This process involves the self-organization of a large number of molecular parts - up to hundreds of thousands in vertebrate cells - whose local interactions give rise to a cellular-scale structure with emergent architecture, mechanics and function. In this Review, we discuss key concepts in our understanding of spindle assembly, focusing on recent advances and the new approaches that enabled them. We describe the pathways that generate the microtubule framework of the spindle by driving microtubule nucleation in a spatially controlled fashion and present recent insights regarding the organization of individual microtubules into structural modules. Finally, we discuss the emergent properties of the spindle that enable robust chromosome segregation.
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Affiliation(s)
| | - Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA
| | - Sabine Petry
- Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA.
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA.
- Department of Biochemistry & Biophysics, UCSF, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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4
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Ng SC, Biswas A, Huyton T, Schünemann J, Reber S, Görlich D. Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length. Nat Commun 2023; 14:747. [PMID: 36765044 PMCID: PMC9918544 DOI: 10.1038/s41467-023-36331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
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Affiliation(s)
- Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abin Biswas
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Biological Optomechanics, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Simone Reber
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Kletter T, Biswas A, Reber S. Engineering metaphase spindles: Construction site and building blocks. Curr Opin Cell Biol 2022; 79:102143. [PMID: 36436307 DOI: 10.1016/j.ceb.2022.102143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/08/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022]
Abstract
In an active, crowded cytoplasm, eukaryotic cells construct metaphase spindles from conserved building blocks to segregate chromosomes. Yet, spindles execute their function in a stunning variety of cell shapes and sizes across orders of magnitude. Thus, the current challenge is to understand how unique mesoscale spindle characteristics emerge from the interaction of molecular collectives. Key components of these collectives are tubulin dimers, which polymerise into microtubules. Despite all conservation, tubulin is a genetically and biochemically complex protein family, and we only begin to uncover how tubulin diversity affects microtubule dynamics and thus spindle assembly. Moreover, it is increasingly appreciated that spindles are dynamically intertwined with the cytoplasm that itself exhibits cell-type specific emergent properties with yet mostly unexplored consequences for spindle construction. Therefore, on our way toward a quantitative picture of spindle function, we need to understand molecular behaviour of the building blocks and connect it to the entire cellular context.
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Affiliation(s)
- Tobias Kletter
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Abin Biswas
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Max-Planck-Institute for the Science of Light, 91058 Erlangen, Germany
| | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; University of Applied Sciences Berlin, 13353 Berlin, Germany.
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Ti SC. Reconstituting Microtubules: A Decades-Long Effort From Building Block Identification to the Generation of Recombinant α/β-Tubulin. Front Cell Dev Biol 2022; 10:861648. [PMID: 35573669 PMCID: PMC9096264 DOI: 10.3389/fcell.2022.861648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubules are cytoskeletal filaments underlying the morphology and functions of all eukaryotic cells. In higher eukaryotes, the basic building blocks of these non-covalent polymers, ɑ- and β-tubulins, are encoded by expanded tubulin family genes (i.e., isotypes) at distinct loci in the genome. While ɑ/β-tubulin heterodimers have been isolated and examined for more than 50 years, how tubulin isotypes contribute to the microtubule organization and functions that support diverse cellular architectures remains a fundamental question. To address this knowledge gap, in vitro reconstitution of microtubules with purified ɑ/β-tubulin proteins has been employed for biochemical and biophysical characterization. These in vitro assays have provided mechanistic insights into the regulation of microtubule dynamics, stability, and interactions with other associated proteins. Here we survey the evolving strategies of generating purified ɑ/β-tubulin heterodimers and highlight the advances in tubulin protein biochemistry that shed light on the roles of tubulin isotypes in determining microtubule structures and properties.
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Schlüßler R, Kim K, Nötzel M, Taubenberger A, Abuhattum S, Beck T, Müller P, Maharana S, Cojoc G, Girardo S, Hermann A, Alberti S, Guck J. Correlative all-optical quantification of mass density and mechanics of subcellular compartments with fluorescence specificity. eLife 2022; 11:e68490. [PMID: 35001870 PMCID: PMC8816383 DOI: 10.7554/elife.68490] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 01/08/2022] [Indexed: 01/06/2023] Open
Abstract
Quantitative measurements of physical parameters become increasingly important for understanding biological processes. Brillouin microscopy (BM) has recently emerged as one technique providing the 3D distribution of viscoelastic properties inside biological samples - so far relying on the implicit assumption that refractive index (RI) and density can be neglected. Here, we present a novel method (FOB microscopy) combining BM with optical diffraction tomography and epifluorescence imaging for explicitly measuring the Brillouin shift, RI, and absolute density with specificity to fluorescently labeled structures. We show that neglecting the RI and density might lead to erroneous conclusions. Investigating the nucleoplasm of wild-type HeLa cells, we find that it has lower density but higher longitudinal modulus than the cytoplasm. Thus, the longitudinal modulus is not merely sensitive to the water content of the sample - a postulate vividly discussed in the field. We demonstrate the further utility of FOB on various biological systems including adipocytes and intracellular membraneless compartments. FOB microscopy can provide unexpected scientific discoveries and shed quantitative light on processes such as phase separation and transition inside living cells.
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Affiliation(s)
- Raimund Schlüßler
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Kyoohyun Kim
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Martin Nötzel
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Anna Taubenberger
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Shada Abuhattum
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Timon Beck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Paul Müller
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Shovamaye Maharana
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Department of Microbiology and Cell Biology, Indian Institute of ScienceBengaluruIndia
| | - Gheorghe Cojoc
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Salvatore Girardo
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht Kossel", University Rostock, and German Center for Neurodegenerative Diseases (DZNE)Rostock/GreifswaldGermany
| | - Simon Alberti
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Physics of Life, Technische Universität DresdenDresdenGermany
| | - Jochen Guck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
- Physics of Life, Technische Universität DresdenDresdenGermany
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8
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Lee AJ, Yoon D, Han S, Hugonnet H, Park W, Park JK, Nam Y, Park Y. Label-free monitoring of 3D cortical neuronal growth in vitro using optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:6928-6939. [PMID: 34858689 PMCID: PMC8606138 DOI: 10.1364/boe.439404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/10/2023]
Abstract
The highly complex central nervous systems of mammals are often studied using three-dimensional (3D) in vitro primary neuronal cultures. A coupled confocal microscopy and immunofluorescence labeling are widely utilized for visualizing the 3D structures of neurons. However, this requires fixation of the neurons and is not suitable for monitoring an identical sample at multiple time points. Thus, we propose a label-free monitoring method for 3D neuronal growth based on refractive index tomograms obtained by optical diffraction tomography. The 3D morphology of the neurons was clearly visualized, and the developmental processes of neurite outgrowth in 3D spaces were analyzed for individual neurons.
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Affiliation(s)
- Ariel J Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Contributed equally
| | - DongJo Yoon
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
- Contributed equally
| | - SeungYun Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Applied Physics, Yale University, New Haven, CT 06520, USA
- Contributed equally
| | - Herve Hugonnet
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - WeiSun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YoonKey Nam
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon, Republic of Korea
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9
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Tanaka M, Shimamoto Y. Local body weight measurement of the spindle. Dev Cell 2021; 56:871-872. [PMID: 33823131 DOI: 10.1016/j.devcel.2021.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The spindle is a micron-sized chromosome segregation machine built from microtubules and many other proteins. In this issue of Developmental Cell, Biswas et al. (2021) use sophisticated imaging and Xenopus egg extracts to show that the spindle's mass density is only as much as the surrounding cytoplasm, contrary to popular belief.
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Affiliation(s)
- Masahito Tanaka
- Physics and Cell Biology Laboratory, Department of Chromosome Science, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yuta Shimamoto
- Physics and Cell Biology Laboratory, Department of Chromosome Science, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI University, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
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