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Recouvreux P, Pai P, Dunsing V, Torro R, Ludanyi M, Mélénec P, Boughzala M, Bertrand V, Lenne PF. Transfer of polarity information via diffusion of Wnt ligands in C. elegans embryos. Curr Biol 2024:S0960-9822(24)00370-1. [PMID: 38604167 DOI: 10.1016/j.cub.2024.03.030] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 10/26/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Different signaling mechanisms concur to ensure robust tissue patterning and cell fate instruction during animal development. Most of these mechanisms rely on signaling proteins that are produced, transported, and detected. The spatiotemporal dynamics of signaling molecules are largely unknown, yet they determine signal activity's spatial range and time frame. Here, we use the Caenorhabditis elegans embryo to study how Wnt ligands, an evolutionarily conserved family of signaling proteins, dynamically organize to establish cell polarity in a developing tissue. We identify how Wnt ligands, produced in the posterior half of the embryos, spread extracellularly to transmit information to distant target cells in the anterior half. With quantitative live imaging and fluorescence correlation spectroscopy, we show that Wnt ligands diffuse through the embryo over a timescale shorter than the cell cycle, in the intercellular space, and outside the tissue below the eggshell. We extracted diffusion coefficients of Wnt ligands and their receptor Frizzled and characterized their co-localization. Integrating our different measurements and observations in a simple computational framework, we show how fast diffusion in the embryo can polarize individual cells through a time integration of the arrival of the ligands at the target cells. The polarity established at the tissue level by a posterior Wnt source can be transferred to the cellular level. Our results support a diffusion-based long-range Wnt signaling, which is consistent with the dynamics of developing processes.
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Affiliation(s)
- Pierre Recouvreux
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France.
| | - Pritha Pai
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Valentin Dunsing
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Rémy Torro
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Monika Ludanyi
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Pauline Mélénec
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Mariem Boughzala
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Pierre-François Lenne
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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Belhadj J, Surina S, Hengstschläger M, Lomakin AJ. Form follows function: Nuclear morphology as a quantifiable predictor of cellular senescence. Aging Cell 2023; 22:e14012. [PMID: 37845808 PMCID: PMC10726876 DOI: 10.1111/acel.14012] [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: 07/10/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Enlarged or irregularly shaped nuclei are frequently observed in tissue cells undergoing senescence. However, it remained unclear whether this peculiar morphology is a cause or a consequence of senescence and how informative it is in distinguishing between proliferative and senescent cells. Recent research reveals that nuclear morphology can act as a predictive biomarker of senescence, suggesting an active role for the nucleus in driving senescence phenotypes. By employing deep learning algorithms to analyze nuclear morphology, accurate classification of cells as proliferative or senescent is achievable across various cell types and species both in vitro and in vivo. This quantitative imaging-based approach can be employed to establish links between senescence burden and clinical data, aiding in the understanding of age-related diseases, as well as assisting in disease prognosis and treatment response.
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Affiliation(s)
- Jakub Belhadj
- Center for Pathobiochemistry & Genetics, Institute of Medical GeneticsMedical University of ViennaViennaAustria
- Center for Pathobiochemistry & Genetics, Institute of Medical Chemistry and PathobiochemistryMedical University of ViennaViennaAustria
| | - Surina Surina
- Center for Pathobiochemistry & Genetics, Institute of Medical GeneticsMedical University of ViennaViennaAustria
- Center for Pathobiochemistry & Genetics, Institute of Medical Chemistry and PathobiochemistryMedical University of ViennaViennaAustria
- School of Medical SciencesUniversity of Campania Luigi VanvitelliNapoliItaly
| | - Markus Hengstschläger
- Center for Pathobiochemistry & Genetics, Institute of Medical GeneticsMedical University of ViennaViennaAustria
| | - Alexis J. Lomakin
- Center for Pathobiochemistry & Genetics, Institute of Medical GeneticsMedical University of ViennaViennaAustria
- Center for Pathobiochemistry & Genetics, Institute of Medical Chemistry and PathobiochemistryMedical University of ViennaViennaAustria
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3
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Waters CS, Angenent SB, Altschuler SJ, Wu LF. A PINK1 input threshold arises from positive feedback in the PINK1/Parkin mitophagy decision circuit. Cell Rep 2023; 42:113260. [PMID: 37851575 PMCID: PMC10668033 DOI: 10.1016/j.celrep.2023.113260] [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: 11/11/2022] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Mechanisms that prevent accidental activation of the PINK1/Parkin mitophagy circuit on healthy mitochondria are poorly understood. On the surface of damaged mitochondria, PINK1 accumulates and acts as the input signal to a positive feedback loop of Parkin recruitment, which in turn promotes mitochondrial degradation via mitophagy. However, PINK1 is also present on healthy mitochondria, where it could errantly recruit Parkin and thereby activate this positive feedback loop. Here, we explore emergent properties of the PINK1/Parkin circuit by quantifying the relationship between mitochondrial PINK1 concentrations and Parkin recruitment dynamics. We find that Parkin is recruited to mitochondria only if PINK1 levels exceed a threshold and then only after a delay that is inversely proportional to PINK1 levels. Furthermore, these two regulatory properties arise from the input-coupled positive feedback topology of the PINK1/Parkin circuit. These results outline an intrinsic mechanism by which the PINK1/Parkin circuit can avoid errant activation on healthy mitochondria.
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Affiliation(s)
- Christopher S Waters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sigurd B Angenent
- Mathematics Department, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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Petrich A, Chiantia S. Influenza A Virus Infection Alters Lipid Packing and Surface Electrostatic Potential of the Host Plasma Membrane. Viruses 2023; 15:1830. [PMID: 37766238 PMCID: PMC10537794 DOI: 10.3390/v15091830] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The pathogenesis of influenza A viruses (IAVs) is influenced by several factors, including IAV strain origin and reassortment, tissue tropism and host type. While such factors were mostly investigated in the context of virus entry, fusion and replication, little is known about the viral-induced changes to the host lipid membranes which might be relevant in the context of virion assembly. In this work, we applied several biophysical fluorescence microscope techniques (i.e., Förster energy resonance transfer, generalized polarization imaging and scanning fluorescence correlation spectroscopy) to quantify the effect of infection by two IAV strains of different origin on the plasma membrane (PM) of avian and human cell lines. We found that IAV infection affects the membrane charge of the inner leaflet of the PM. Moreover, we showed that IAV infection impacts lipid-lipid interactions by decreasing membrane fluidity and increasing lipid packing. Because of such alterations, diffusive dynamics of membrane-associated proteins are hindered. Taken together, our results indicate that the infection of avian and human cell lines with IAV strains of different origins had similar effects on the biophysical properties of the PM.
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Affiliation(s)
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
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Balaghi N, Erdemci-Tandogan G, McFaul C, Fernandez-Gonzalez R. Myosin waves and a mechanical asymmetry guide the oscillatory migration of Drosophila cardiac progenitors. Dev Cell 2023:S1534-5807(23)00238-1. [PMID: 37295436 DOI: 10.1016/j.devcel.2023.05.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Heart development begins with the formation of a tube as cardiac progenitors migrate from opposite sides of the embryo. Abnormal cardiac progenitor movements cause congenital heart defects. However, the mechanisms of cell migration during early heart development remain poorly understood. Using quantitative microscopy, we found that in Drosophila embryos, cardiac progenitors (cardioblasts) migrated through a sequence of forward and backward steps. Cardioblast steps were associated with oscillatory non-muscle myosin II waves that induced periodic shape changes and were necessary for timely heart tube formation. Mathematical modeling predicted that forward cardioblast migration required a stiff boundary at the trailing edge. Consistent with this, we found a supracellular actin cable at the trailing edge of the cardioblasts that limited the amplitude of the backward steps, thus biasing the direction of cell movement. Our results indicate that periodic shape changes coupled with a polarized actin cable produce asymmetrical forces that promote cardioblast migration.
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Affiliation(s)
- Negar Balaghi
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Gonca Erdemci-Tandogan
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Christopher McFaul
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Rodrigo Fernandez-Gonzalez
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada; Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
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Bogomolovas J, Zhang Z, Wu T, Chen J. Automated quantification and statistical assessment of proliferating cardiomyocyte rates in embryonic hearts. Am J Physiol Heart Circ Physiol 2023; 324:H288-H292. [PMID: 36563012 PMCID: PMC9886340 DOI: 10.1152/ajpheart.00483.2022] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of digital image analysis and count regression models contributes to the reproducibility and rigor of histological studies in cardiovascular research. The use of formalized computer-based quantification strategies of histological images essentially removes potential researcher bias, allows for higher analysis throughput, and enables easy sharing of formalized quantification tools, contributing to research transparency, and data transferability. Moreover, the use of count regression models rather than ratios in statistical analysis of cell population data incorporates the extent of sampling into analysis and acknowledges the non-Gaussian nature of count distributions. Using quantification of proliferating cardiomyocytes in embryonic murine hearts as an example, we describe how these improvements can be implemented using open-source artificial intelligence-based image analysis tools and novel count regression models to efficiently analyze real-life data.
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Affiliation(s)
- Julius Bogomolovas
- Department of Medicine, University of California at San Diego, San Diego, California
| | - Zengming Zhang
- Department of Medicine, University of California at San Diego, San Diego, California
| | - Tongbin Wu
- Department of Medicine, University of California at San Diego, San Diego, California
| | - Ju Chen
- Department of Medicine, University of California at San Diego, San Diego, California
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Knapp TG, Duan S, Merchant JL, Sawyer TW. Quantitative characterization of duodenal gastrinoma autofluorescence using multiphoton microscopy. Lasers Surg Med 2023; 55:208-225. [PMID: 36515355 PMCID: PMC9957894 DOI: 10.1002/lsm.23619] [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: 06/17/2022] [Revised: 10/04/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Duodenal gastrinomas (DGASTs) are neuroendocrine tumors that develop in the submucosa of the duodenum and produce the hormone gastrin. Surgical resection of DGASTs is complicated by the small size of these tumors and the tendency for them to develop diffusely in the duodenum. Endoscopic mucosal resection of DGASTs is an increasingly popular method for treating this disease due to its low complication rate but suffers from poor rates of pathologically negative margins. Multiphoton microscopy can capture high-resolution images of biological tissue with contrast generated from endogenous fluorescence (autofluorescence [AF]) through two-photon excited fluorescence (2PEF). Second harmonic generation is another popular method of generating image contrast with multiphoton microscopy (MPM) and is a light-scattering phenomenon that occurs predominantly from structures such as collagen in biological samples. Some molecules that contribute to AF change in abundance from processes related to the cancer disease process (e.g., metabolic changes, oxidative stress, and angiogenesis). STUDY DESIGN/MATERIALS AND METHODS MPM was used to image 12 separate patient samples of formalin-fixed and paraffin-embedded duodenal gastrinoma slides with a second-harmonic generation (SHG) channel and four 2PEF channels. The excitation and emission profiles of each 2PEF channel were tuned to capture signal dominated by distinct fluorophores with well-characterized fluorescent spectra and known connections to the physiologic changes that arise in cancerous tissue. RESULTS We found that there was a significant difference in the relative abundance of signal generated in the 2PEF channels for regions of DGASTs in comparison to the neighboring tissues of the duodenum. Data generated from texture feature extraction of the MPM images were used in linear discriminant analysis models to create classifiers for tumor versus all other tissue types before and after principal component analysis (PCA). PCA improved the classifier accuracy and reduced the number of features required to achieve maximum accuracy. The linear discriminant classifier after PCA distinguished between tumor and other tissue types with an accuracy of 90.6%-93.8%. CONCLUSIONS These results suggest that multiphoton microscopy 2PEF and SHG imaging is a promising label-free method for discriminating between DGASTs and normal duodenal tissue which has implications for future applications of in vivo assessment of resection margins with endoscopic MPM.
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Affiliation(s)
- Thomas G. Knapp
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | - Suzann Duan
- College of Medicine, University of Arizona, Tucson, Arizona, USA
| | | | - Travis W. Sawyer
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
- College of Medicine, University of Arizona, Tucson, Arizona, USA
- Wyant College of Optical Sciences, University of Arizona, Tucson, Arizona, USA
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8
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Mazzarini M, Arciprete F, Picconi O, Valeri M, Verachi P, Martelli F, Migliaccio AR, Falchi M, Zingariello M. Single cell analysis of the localization of the hematopoietic stem cells within the bone marrow architecture identifies niche-specific proliferation dynamics. Front Med (Lausanne) 2023; 10:1166758. [PMID: 37188088 PMCID: PMC10175646 DOI: 10.3389/fmed.2023.1166758] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction Hematopoietic stem cells (HSC) reside in the bone marrow (BM) in specialized niches which provide support for their self-replication and differentiation into the blood cells. Recently, numerous studies using sophisticated molecular and microscopic technology have provided snap-shots information on the identity of the BM niches in mice. In adults, HSC are localized around arterioles and sinusoids/venules whereas in juvenile mice they are in close to the osteoblasts. However, although it is well recognized that in mice the nature of the hematopoietic niche change with age or after exposure to inflammatory insults, much work remains to be done to identify changes occurring under these conditions. The dynamic changes occurring in niche/HSC interactions as HSC enter into cycle are also poorly defined. Methods We exploit mice harboring the hCD34tTA/Tet-O-H2BGFP transgene to establish the feasibility to assess interactions of the HSC with their niche as they cycle. In this model, H2BGFP expression is driven by the TET trans-activator under the control of the human CD34 promoter which in mice is active only in the HSC. Since Doxycycline inhibits TET, HSC exposed to this drug no longer express H2BGFP and loose half of their label every division allowing establishing the dynamics of their first 1-3 divisions. To this aim, we first validated user-friendly confocal microscopy methods to determine HSC divisions by hemi-decrement changes in levels of GFP expression. We then tracked the interaction occurring in old mice between the HSC and their niche during the first HSC divisions. Results We determined that in old mice, most of the HSC are located around vessels, both arterioles which sustain quiescence and self-replication, and venules/sinusoids, which sustain differentiation. After just 1 week of exposure to Doxycycline, great numbers of the HSC around the venules lost most of their GFP label, indicating that they had cycled. By contrast, the few HSC surrounding the arterioles retained maximal levels of GFP expression, indicating that they are either dormant or cycle at very low rates. Conclusion These results reveal that in old mice, HSC cycle very dynamically and are biased toward interactions with the niche that instructs them to differentiate.
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Affiliation(s)
- Maria Mazzarini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
| | - Francesca Arciprete
- Unit of Microscopic and Ultrastructural Anatomy, University Campus Bio-Medico, Rome, Italy
| | - Orietta Picconi
- National Center for HIV/AIDS Research, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Valeri
- Center for Animal Experimentation and Well-Being, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Verachi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Martelli
- National Center for Preclinical and Clinical Research and Evaluation of Pharmaceutical Drugs, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Rita Migliaccio
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
- Unit of Microscopic and Ultrastructural Anatomy, University Campus Bio-Medico, Rome, Italy
- *Correspondence: Anna Rita Migliaccio ;
| | - Mario Falchi
- National Center for HIV/AIDS Research, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Zingariello
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
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Lauriola A, Davalli P, Marverti G, Caporali A, Mai S, D’Arca D. Telomere Dysfunction Is Associated with Altered DNA Organization in Trichoplein/Tchp/Mitostatin (TpMs) Depleted Cells. Biomedicines 2022; 10:biomedicines10071602. [PMID: 35884905 PMCID: PMC9312488 DOI: 10.3390/biomedicines10071602] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/02/2022] Open
Abstract
Recently, we highlighted a novel role for the protein Trichoplein/TCHP/Mitostatin (TpMs), both as mitotic checkpoint regulator and guardian of chromosomal stability. TpMs-depleted cells show numerical and structural chromosome alterations that lead to genomic instability. This condition is a major driving force in malignant transformation as it allows for the cells acquiring new functional capabilities to proliferate and disseminate. Here, the effect of TpMs depletion was investigated in different TpMs-depleted cell lines by means of 3D imaging and 3D Structured illumination Microscopy. We show that TpMs depletion causes alterations in the 3D architecture of telomeres in colon cancer HCT116 cells. These findings are consistent with chromosome alterations that lead to genomic instability. Furthermore, TpMs depletion changes the spatial arrangement of chromosomes and other nuclear components. Modified nuclear architecture and organization potentially induce variations that precede the onset of genomic instability and are considered as markers of malignant transformation. Our present observations connect the tumor suppression ability of TpMs with its novel functions in maintaining the proper chromosomal segregation as well as the proper telomere and nuclear architecture. Further investigations will investigate the connection between alterations in telomeres and nuclear architecture with the progression of human tumors with the aim of developing personalized therapeutic interventions.
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Affiliation(s)
- Angela Lauriola
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
| | - Pierpaola Davalli
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
| | - Gaetano Marverti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
| | - Andrea Caporali
- The Queen’s Medical Research Institute, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH10 4AH, UK;
| | - Sabine Mai
- CancerCare Manitoba Research Institute, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: (S.M.); (D.D.); Tel.: +1-204-272-3174 (S.M.); +39-059-205-5610 (D.D.)
| | - Domenico D’Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
- Correspondence: (S.M.); (D.D.); Tel.: +1-204-272-3174 (S.M.); +39-059-205-5610 (D.D.)
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10
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Kochová P, Malečková A, Pálek R, Liška V, Bońkowski T, Horák M, Grajciarová M, Tonar Z. Porcine spleen as a model organ for blunt injury impact tests: An experimental and histological study. Anat Histol Embryol 2022; 51:576-586. [PMID: 35751561 DOI: 10.1111/ahe.12831] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
The spleen is a large and highly vascularized secondary lymphatic organ. Spleen injuries are among the most frequent trauma-related injuries in the abdominal region. The aims of the study were to assess the volume fractions of the main splenic tissue components (red pulp, white pulp, trabeculae and reticular fibres) and to determine the severity of splenic injury due to the experimental impact test. Porcine spleens (n = 17) were compressed by 6.22 kg wooden plate using a drop tower technique from three impact heights (50, 100 and 150 mm corresponding to velocities 0.79, 1.24 and 1.58 m/s). The pressure was measured via catheters placed in the splenic vein. The impact velocity was measured using lasers. The severity of induced injuries was analysed on the macroscopic level. The volume fractions of splenic components were assessed microscopically using stereology. The volume fraction of the red pulp was 76.4%, white pulp 21.3% and trabeculae 2.7% respectively. All impact tests, even with the low impact velocities, led to injuries that occurred mostly in the dorsal extremity of the spleen, and were accompanied by bleeding, capsule rupture and parenchyma crushing. Higher impact height (impact velocity and impact energy) caused more severe injury. Porcine spleen had the same volume fraction of tissue components as human spleen, therefore we concluded that the porcine spleen was a suitable organ model for mechanical experiments. Based on our observations, regions around hilum and the diaphragmatic surface of the dorsal extremity, that contained fissures and notches, were the most prone to injury and required considerable attention during splenic examination after injury. The primary mechanical data are now available for the researchers focused on the splenic trauma modelling.
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Affiliation(s)
- Petra Kochová
- European Centre of Excellence NTIS, Faculty of Applied Sciences, University of West Bohemia, Pilsen, Czech Republic
| | - Anna Malečková
- Department of Histology and Embryology and Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Richard Pálek
- Department of Surgery and Biomedical Center, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Václav Liška
- Department of Surgery and Biomedical Center, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Tomasz Bońkowski
- New Technologies - Research Centre, University of West Bohemia, Pilsen, Czech Republic
| | - Miroslav Horák
- Department of Mechanics, Faculty of Applied Sciences, University of West Bohemia, Pilsen, Czech Republic
| | - Martina Grajciarová
- Department of Histology and Embryology and Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Zbyněk Tonar
- European Centre of Excellence NTIS, Faculty of Applied Sciences, University of West Bohemia, Pilsen, Czech Republic
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Abstract
Since its first demonstration, stimulated Raman scattering (SRS) microscopy has become a powerful chemical imaging tool that shows promise in numerous biological and biomedical applications. The spectroscopic capability of SRS enables identification and tracking of specific molecules or classes of molecules, often without labeling. SRS microscopy also has the hallmark advantage of signal strength that is directly proportional to molecular concentration, allowing for in situ quantitative analysis of chemical composition of heterogeneous samples with submicron spatial resolution and subminute temporal resolution. However, it is important to recognize that quantification through SRS microscopy requires assumptions regarding both system and sample. Such assumptions are often taken axiomatically, which may lead to erroneous conclusions without proper validation. In this review, we focus on the tacitly accepted, yet complex, quantitative aspect of SRS microscopy. We discuss the various approaches to quantitative analysis, examples of such approaches, challenges in different systems, and potential solutions. Through our examination of published literature, we conclude that a scrupulous approach to experimental design can further expand the powerful and incisive quantitative capabilities of SRS microscopy.
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Affiliation(s)
- Bryce Manifold
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
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12
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Oh S, Lee C, Yang W, Li A, Mukherjee A, Basan M, Ran C, Yin W, Tabin CJ, Fu D, Xie XS, Kirschner MW. Protein and lipid mass concentration measurement in tissues by stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A 2022; 119:e2117938119. [PMID: 35452314 PMCID: PMC9169924 DOI: 10.1073/pnas.2117938119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/06/2021] [Accepted: 02/21/2022] [Indexed: 01/10/2023] Open
Abstract
Cell mass and chemical composition are important aggregate cellular properties that are especially relevant to physiological processes, such as growth control and tissue homeostasis. Despite their importance, it has been difficult to measure these features quantitatively at the individual cell level in intact tissue. Here, we introduce normalized Raman imaging (NoRI), a stimulated Raman scattering (SRS) microscopy method that provides the local concentrations of protein, lipid, and water from live or fixed tissue samples with high spatial resolution. Using NoRI, we demonstrate that protein, lipid, and water concentrations at the single cell are maintained in a tight range in cells under the same physiological conditions and are altered in different physiological states, such as cell cycle stages, attachment to substrates of different stiffness, or by entering senescence. In animal tissues, protein and lipid concentration varies with cell types, yet an unexpected cell-to-cell heterogeneity was found in cerebellar Purkinje cells. The protein and lipid concentration profile provides means to quantitatively compare disease-related pathology, as demonstrated using models of Alzheimer’s disease. This demonstration shows that NoRI is a broadly applicable technique for probing the biological regulation of protein mass, lipid mass, and water mass for studies of cellular and tissue growth, homeostasis, and disease.
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Affiliation(s)
- Seungeun Oh
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Wenlong Yang
- Center for Advanced Imaging, Harvard University, Cambridge, MA 20138
| | - Ang Li
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Avik Mukherjee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Markus Basan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | - Wei Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | | | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - X. Sunney Xie
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871; China
| | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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13
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Iglesias I. Use of a Rotating Square Spatial-Frequency Filter to Map the Optical Path Length Variation in Microscopic Biological Samples. Sensors (Basel) 2022; 22:1842. [PMID: 35270988 PMCID: PMC8915107 DOI: 10.3390/s22051842] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Gradient images can be obtained using a rotating square mask to filter the angular spectra of the wavefront generated by a complex transmittance object. This method can be applied to measure the three-dimensional structure of microscopic biological samples through the relationship of the phase with the optical path length. This work describes the implementation of a system using an inverted optical microscope and shows the experimental results of phase maps generated by boar sperm cells.
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Affiliation(s)
- Ignacio Iglesias
- Departamento de Física, CEIR Campus Mare Nostrum (CMN), Universidad de Murcia, 30100 Murcia, Spain
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14
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Kolinko Y, Malečková A, Kochová P, Grajciarová M, Blassová T, Kural T, Trailin A, Červenková L, Havránková J, Vištejnová L, Tonarová P, Moulisová V, Jiřík M, Zavaďáková A, Tichánek F, Liška V, Králíčková M, Witter K, Tonar Z. Using virtual microscopy for the development of sampling strategies in quantitative histology and design-based stereology. Anat Histol Embryol 2021; 51:3-22. [PMID: 34806204 DOI: 10.1111/ahe.12765] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/31/2021] [Indexed: 02/03/2023]
Abstract
Only a fraction of specimens under study are usually selected for quantification in histology. Multilevel sampling or tissue probes, slides and fields of view (FOVs) in the regions of interest (ROIs) are required. In general, all parts of the organs under study should be given the same probability to be taken into account; that is, the sampling should be unbiased on all levels. The objective of our study was to provide an overview of the use of virtual microscopy in the context of developing sampling strategies of FOVs for stereological quantification. We elaborated this idea on 18 examples from multiple fields of histology, including quantification of extracellular matrix and muscle tissue, quantification of organ and tumour microvessels and tumour-infiltrating lymphocytes, assessing osseointegration of bone implants, healing of intestine anastomoses and osteochondral defects, counting brain neurons, counting nuclei in vitro cell cultures and others. We provided practical implications for the most common situations, such as exhaustive sampling of ROIs, sampling ROIs of different sizes, sampling the same ROIs for multiple histological methods, sampling more ROIs with variable intensities or using various objectives, multistage sampling and virtual sampling. Recommendations were provided for pilot studies on systematic uniform random sampling of FOVs as a part of optimizing the efficiency of histological quantification to prevent over- or undersampling. We critically discussed the pros and cons of using virtual sections for sampling FOVs from whole scanned sections. Our review demonstrated that whole slide scans of histological sections facilitate the design of sampling strategies for quantitative histology.
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Affiliation(s)
- Yaroslav Kolinko
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Anna Malečková
- Faculty of Applied Sciences, European Centre of Excellence NTIS, University of West Bohemia, Pilsen, Czech Republic
| | - Petra Kochová
- Faculty of Applied Sciences, European Centre of Excellence NTIS, University of West Bohemia, Pilsen, Czech Republic
| | - Martina Grajciarová
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Tereza Blassová
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Tomáš Kural
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Andriy Trailin
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Lenka Červenková
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jiřina Havránková
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Lucie Vištejnová
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Pavla Tonarová
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Vladimíra Moulisová
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Miroslav Jiřík
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic.,Faculty of Applied Sciences, European Centre of Excellence NTIS, University of West Bohemia, Pilsen, Czech Republic
| | - Anna Zavaďáková
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Filip Tichánek
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Václav Liška
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Surgery and Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milena Králíčková
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Kirsti Witter
- Institute of Morphology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Zbyněk Tonar
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czech Republic
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15
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Herdly L, Janin P, Bauer R, van de Linde S. Tunable Wide-Field Illumination and Single-Molecule Photoswitching with a Single MEMS Mirror. ACS Photonics 2021; 8:2728-2736. [PMID: 34553004 PMCID: PMC8447260 DOI: 10.1021/acsphotonics.1c00843] [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] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Homogeneous illumination in single-molecule localization microscopy (SMLM) is key for the quantitative analysis of super-resolution images. Therefore, different approaches for flat-field illumination have been introduced as alternative to the conventional Gaussian illumination. Here, we introduce a single microelectromechanical systems (MEMS) mirror as a tunable and cost-effective device for adapting wide-field illumination in SMLM. In flat-field mode the MEMS allowed for consistent SMLM metrics across the entire field of view. Employing single-molecule photoswitching, we developed a simple yet powerful routine to benchmark different illumination schemes on the basis of local emitter brightness and ON-state lifetime. Moreover, we propose that tuning the MEMS beyond optimal flat-field conditions enables to study the kinetics of photoswitchable fluorophores within a single acquisition.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Paul Janin
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Ralf Bauer
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
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16
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da Rocha-Azevedo B, Lee S, Dasgupta A, Vega AR, de Oliveira LR, Kim T, Kittisopikul M, Malik ZA, Jaqaman K. Heterogeneity in VEGF Receptor-2 Mobility and Organization on the Endothelial Cell Surface Leads to Diverse Models of Activation by VEGF. Cell Rep 2021; 32:108187. [PMID: 32997988 PMCID: PMC7541195 DOI: 10.1016/j.celrep.2020.108187] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 01/09/2020] [Revised: 07/17/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
The dynamic nanoscale organization of cell surface receptors plays an important role in signaling. We determine this organization and its relation to activation of VEGF receptor-2 (VEGFR-2), a critical receptor tyrosine kinase in endothelial cells (ECs), by combining single-molecule imaging of endogenous VEGFR-2 in live ECs with multiscale computational analysis. We find that surface VEGFR-2 can be mobile or exhibit restricted mobility and be monomeric or non-monomeric, with a complex interplay between the two. This basal heterogeneity results in heterogeneity in the sequence of steps leading to VEGFR-2 activation by VEGF. Specifically, we find that VEGF can bind to monomeric and non-monomeric VEGFR-2 and that, when binding to monomeric VEGFR-2, its effect on dimerization depends on the mobility of VEGFR-2. Our study highlights the dynamic and heterogeneous nature of cell surface receptor organization and the need for multiscale, single-molecule-based analysis to determine its relationship to receptor activation and signaling. da Rocha-Azevedo et al. show that VEGFR-2 exhibits mobility and interaction heterogeneity on the endothelial cell surface. The sequence of steps leading to VEGFR-2 activation by VEGF depends on the basal state of VEGFR-2. Thus, there is not one model but multiple co-existing models of VEGFR-2 activation by VEGF.
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Affiliation(s)
| | - Sungsoo Lee
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aparajita Dasgupta
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anthony R Vega
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Tae Kim
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachariah A Malik
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Khuloud Jaqaman
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Stoltzfus CR, Sivakumar R, Kunz L, Olin Pope BE, Menietti E, Speziale D, Adelfio R, Bacac M, Colombetti S, Perro M, Gerner MY. Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated With Anti-Tumor Immunity. Front Immunol 2021; 12:726492. [PMID: 34421928 PMCID: PMC8375665 DOI: 10.3389/fimmu.2021.726492] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Tumors are populated by a multitude of immune cell types with varied phenotypic and functional properties, which can either promote or inhibit anti-tumor responses. Appropriate localization and function of these cells within tumors is critical for protective immunity, with CD8 T cell infiltration being a biomarker of disease outcome and therapeutic efficacy. Recent multiplexed imaging approaches have revealed highly complex patterns of localization for these immune cell subsets and the generation of distinct tumor microenvironments (TMEs), which can vary among cancer types, individuals, and within individual tumors. While it is recognized that TMEs play a pivotal role in disease progression, a better understanding of their composition, organization, and heterogeneity, as well as how distinct TMEs are reshaped with immunotherapy, is necessary. Here, we performed spatial analysis using multi-parameter confocal imaging, histocytometry, and CytoMAP to study the microanatomical organization of immune cells in two widely used preclinical cancer models, the MC38 colorectal and KPC pancreatic murine tumors engineered to express human carcinoembryonic antigen (CEA). Immune responses were examined in either unperturbed tumors or after immunotherapy with a CEA T cell bispecific (CEA-TCB) surrogate antibody and anti-PD-L1 treatment. CEA-TCB mono and combination immunotherapy markedly enhanced intra-tumoral cellularity of CD8 T cells, dominantly driven by the expansion of TCF1-PD1+ effector T cells and with more minor increases in TCF1+PD1+ resource CD8 T cells. The majority of infiltrating T cells, particularly resource CD8 T cells, were colocalized with dendritic cells (DCs) or activated MHCII+ macrophages, but largely avoided the deeper tumor nest regions composed of cancer cells and non-activated macrophages. These myeloid cell - T cell aggregates were found in close proximity to tumor blood vessels, generating perivascular immune niches. This perivascular TME was present in untreated samples and markedly increased after CEA-TCB therapy, with its relative abundance positively associated with response to therapy. Together, these studies demonstrate the utility of advanced spatial analysis in cancer research by revealing that blood vessels are key organizational hubs of innate and adaptive immune cells within tumors, and suggesting the likely relevance of the perivascular immune TME in disease outcome.
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Affiliation(s)
- Caleb R. Stoltzfus
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States
| | - Ramya Sivakumar
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States
| | - Leo Kunz
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Brandy E. Olin Pope
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States
| | - Elena Menietti
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Dario Speziale
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Roberto Adelfio
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Marina Bacac
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Sara Colombetti
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Mario Perro
- Pharmaceutical Research & Early Development (pRED), Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Michael Y. Gerner
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States
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18
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de Man SMA, Zwanenburg G, van der Wal T, Hink MA, van Amerongen R. Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics. eLife 2021; 10:e66440. [PMID: 34190040 PMCID: PMC8341982 DOI: 10.7554/elife.66440] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/11/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
WNT/CTNNB1 signaling regulates tissue development and homeostasis in all multicellular animals, but the underlying molecular mechanism remains incompletely understood. Specifically, quantitative insight into endogenous protein behavior is missing. Here, we combine CRISPR/Cas9-mediated genome editing and quantitative live-cell microscopy to measure the dynamics, diffusion characteristics and absolute concentrations of fluorescently tagged, endogenous CTNNB1 in human cells under both physiological and oncogenic conditions. State-of-the-art imaging reveals that a substantial fraction of CTNNB1 resides in slow-diffusing cytoplasmic complexes, irrespective of the activation status of the pathway. This cytoplasmic CTNNB1 complex undergoes a major reduction in size when WNT/CTNNB1 is (hyper)activated. Based on our biophysical measurements, we build a computational model of WNT/CTNNB1 signaling. Our integrated experimental and computational approach reveals that WNT pathway activation regulates the dynamic distribution of free and complexed CTNNB1 across different subcellular compartments through three regulatory nodes: the destruction complex, nucleocytoplasmic shuttling, and nuclear retention.
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Affiliation(s)
- Saskia MA de Man
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Gooitzen Zwanenburg
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Tanne van der Wal
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Mark A Hink
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
- van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
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19
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Willy NM, Colombo F, Huber S, Smith AC, Norton EG, Kural C, Cocucci E. CALM supports clathrin-coated vesicle completion upon membrane tension increase. Proc Natl Acad Sci U S A 2021; 118:e2010438118. [PMID: 34155137 DOI: 10.1073/pnas.2010438118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The most represented components of clathrin-coated vesicles (CCVs) are clathrin triskelia and the adaptors clathrin assembly lymphoid myeloid leukemia protein (CALM) and the heterotetrameric complex AP2. Investigation of the dynamics of AP180-amino-terminal-homology (ANTH) recruitment during CCV formation has been hampered by CALM toxicity upon overexpression. We used knock-in gene editing to express a C-terminal-attached fluorescent version of CALM, while preserving its endogenous expression levels, and cutting-edge live-cell microscopy approaches to study CALM recruitment at forming CCVs. Our results demonstrate that CALM promotes vesicle completion upon membrane tension increase as a function of the amount of this adaptor present. Since the expression of adaptors, including CALM, differs among cells, our data support a model in which the efficiency of clathrin-mediated endocytosis is tissue specific and explain why CALM is essential during embryogenesis and red blood cell development.
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20
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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21
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Pape C, Remme R, Wolny A, Olberg S, Wolf S, Cerrone L, Cortese M, Klaus S, Lucic B, Ullrich S, Anders-Össwein M, Wolf S, Cerikan B, Neufeldt CJ, Ganter M, Schnitzler P, Merle U, Lusic M, Boulant S, Stanifer M, Bartenschlager R, Hamprecht FA, Kreshuk A, Tischer C, Kräusslich HG, Müller B, Laketa V. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera: A semi-quantitative, high throughput, microscopy-based assay expands existing approaches to measure SARS-CoV-2 specific antibody levels in human sera. Bioessays 2020; 43:e2000257. [PMID: 33377226 PMCID: PMC7883048 DOI: 10.1002/bies.202000257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/28/2022]
Abstract
Emergence of the novel pathogenic coronavirus SARS-CoV-2 and its rapid pandemic spread presents challenges that demand immediate attention. Here, we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA, and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay that complements the portfolio of SARS-CoV-2 serological assays. Sensitive, specific and quantitative serological assays are urgently needed for a better understanding of humoral immune response against the virus as a basis for developing public health strategies to control viral spread. The procedure described here has been used for clinical studies and provides a general framework for the application of quantitative high-throughput microscopy to rapidly develop serological assays for emerging virus infections.
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Affiliation(s)
- Constantin Pape
- HCI/IWR, Heidelberg University, Heidelberg, Germany.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Roman Remme
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | - Adrian Wolny
- HCI/IWR, Heidelberg University, Heidelberg, Germany.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sylvia Olberg
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Steffen Wolf
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | | | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Severina Klaus
- Department of Infectious Diseases, Parasitology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephanie Ullrich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Maria Anders-Össwein
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefanie Wolf
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Ganter
- Department of Infectious Diseases, Parasitology, University Hospital Heidelberg, Heidelberg, Germany
| | - Paul Schnitzler
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Uta Merle
- Department of Gastroenterology and Hepatology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.,Research Group "Cellular polarity and viral infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Megan Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany.,Research Group "Cellular polarity and viral infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | | | - Anna Kreshuk
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
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22
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Radtke AJ, Kandov E, Lowekamp B, Speranza E, Chu CJ, Gola A, Thakur N, Shih R, Yao L, Yaniv ZR, Beuschel RT, Kabat J, Croteau J, Davis J, Hernandez JM, Germain RN. IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. Proc Natl Acad Sci U S A 2020; 117:33455-65. [PMID: 33376221 DOI: 10.1073/pnas.2018488117] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The diverse composition of mammalian tissues poses challenges for understanding the cell-cell interactions required for organ homeostasis and how spatial relationships are perturbed during disease. Existing methods such as single-cell genomics, lacking a spatial context, and traditional immunofluorescence, capturing only two to six molecular features, cannot resolve these issues. Imaging technologies have been developed to address these problems, but each possesses limitations that constrain widespread use. Here we report a method that overcomes major impediments to highly multiplex tissue imaging. "Iterative bleaching extends multiplexity" (IBEX) uses an iterative staining and chemical bleaching method to enable high-resolution imaging of >65 parameters in the same tissue section without physical degradation. IBEX can be employed with various types of conventional microscopes and permits use of both commercially available and user-generated antibodies in an "open" system to allow easy adjustment of staining panels based on ongoing marker discovery efforts. We show how IBEX can also be used with amplified staining methods for imaging strongly fixed tissues with limited epitope retention and with oligonucleotide-based staining, allowing potential cross-referencing between flow cytometry, cellular indexing of transcriptomes and epitopes by sequencing, and IBEX analysis of the same tissue. To facilitate data processing, we provide an open-source platform for automated registration of iterative images. IBEX thus represents a technology that can be rapidly integrated into most current laboratory workflows to achieve high-content imaging to reveal the complex cellular landscape of diverse organs and tissues.
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23
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Mazzarini M, Falchi M, Bani D, Migliaccio AR. Evolution and new frontiers of histology in bio-medical research. Microsc Res Tech 2020; 84:217-237. [PMID: 32915487 DOI: 10.1002/jemt.23579] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
Histology refers to the study of the morphology of cells within their natural tissue environment. As a bio-medical discipline, it dates back to the development of first microscopes which allowed to override the physical visual limitation of the human eye. Since the first observations, it was understood that cell shape predicts function and, therefore, shape alterations can identify and explain dysfunction and diseases. The advancements in morphological investigation techniques have allowed to extend our understanding of the shape-function relationships close to the molecular level of organization of tissues, as well as to derive reliable data not only from fixed, and hence static, biological samples but also living cells and tissues and even for extended time periods. These modern approaches, which encompass quantitative microscopy, precision microscopy, and dynamic microscopy, represent the new frontier of morphology. This article summarizes how the microscopy techniques have evolved to properly face the challenges of biomedical sciences, thus transforming histology from a merely qualitative discipline, which played an ancillary role to traditional "major" sciences such as anatomy, to a modern experimental science capable of driving knowledge progress in biology and medicine.
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Affiliation(s)
- Maria Mazzarini
- Biomedical and Neuromotor Sciences, Alma Mater University Bologna, Bologna, Italy
| | - Mario Falchi
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Daniele Bani
- Research Unit of Histology & Embryology, Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
| | - Anna Rita Migliaccio
- Biomedical and Neuromotor Sciences, Alma Mater University Bologna, Bologna, Italy.,Myeloproliferative Neoplasm-Research Consortium, New York City, New York, USA
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24
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Xing W, Muhlrad D, Parker R, Rosen MK. A quantitative inventory of yeast P body proteins reveals principles of composition and specificity. eLife 2020; 9:56525. [PMID: 32553117 PMCID: PMC7373430 DOI: 10.7554/elife.56525] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 03/31/2020] [Accepted: 06/18/2020] [Indexed: 01/01/2023] Open
Abstract
P bodies are archetypal biomolecular condensates that concentrate proteins and RNA without a surrounding membrane. While dozens of P body proteins are known, the concentrations of components in the compartment have not been measured. We used live cell imaging to generate a quantitative inventory of the major proteins in yeast P bodies. Only seven proteins are highly concentrated in P bodies (5.1–15µM); the 24 others examined are appreciably lower (most ≤ 2.6µM). P body concentration correlates inversely with cytoplasmic exchange rate. Sequence elements driving Dcp2 concentration into P bodies are distributed across the protein and act synergistically. Our data indicate that P bodies, and probably other condensates, are compositionally simpler than suggested by proteomic analyses, with implications for specificity, reconstitution and evolution.
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Affiliation(s)
- Wenmin Xing
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
| | - Denise Muhlrad
- Department of Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, United States
| | - Roy Parker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, United States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
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25
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Konstandinou C, Kostopoulos S, Glotsos D, Pappa D, Ravazoula P, Michail G, Kalatzis I, Asvestas P, Lavdas E, Cavouras D, Sakellaropoulos G. GPU-enabled design of an adaptable pattern recognition system for discriminating squamous intraepithelial lesions of the cervix. ACTA ACUST UNITED AC 2020; 65:315-325. [PMID: 31747374 DOI: 10.1515/bmt-2019-0040] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/30/2019] [Indexed: 11/15/2022]
Abstract
The aim of the present study was to design an adaptable pattern recognition (PR) system to discriminate low- from high-grade squamous intraepithelial lesions (LSIL and HSIL, respectively) of the cervix using microscopy images of hematoxylin and eosin (H&E)-stained biopsy material from two different medical centers. Clinical material comprised H&E-stained biopsies of 66 patients diagnosed with LSIL (34 cases) or HSIL (32 cases). Regions of interest were selected from each patient's digitized microscopy images. Seventy-seven features were generated, regarding the texture, morphology and spatial distribution of nuclei. The probabilistic neural network (PNN) classifier, the exhaustive search feature selection method, the leave-one-out (LOO) and the bootstrap validation methods were used to design the PR system and to assess its precision. Optimal PR system design and evaluation were made feasible by the employment of graphics processing unit (GPU) and Compute Unified Device Architecture (CUDA) technologies. The accuracy of the PR-system was 93% and 88.6% when using the LOO and bootstrap validation methods, respectively. The proposed PR system for discriminating LSIL from HSIL of the cervix was designed to operate in a clinical environment, having the capability of being redesigned when new verified cases are added to its repository and when data from other medical centers are included, following similar biopsy material preparation procedures.
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Affiliation(s)
- Christos Konstandinou
- Department of Medical Physics, School of Health Sciences, Faculty of Medicine, University of Patras, Rio, Patras, Greece
| | - Spiros Kostopoulos
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Ag. Spyridonos Street, Egaleo, 122 43 Athens, Greece
| | - Dimitris Glotsos
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Dimitra Pappa
- Department of Pathology, IASO Thessalias, Larissa, Greece
| | | | - George Michail
- Department of Obstetrics and Gynecology, University Hospital of Patras, Rio, Greece
| | - Ioannis Kalatzis
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Pantelis Asvestas
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Eleftherios Lavdas
- Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Dionisis Cavouras
- Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - George Sakellaropoulos
- Department of Medical Physics, School of Health Sciences, Faculty of Medicine, University of Patras, Rio, Patras, Greece
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26
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Stoltzfus CR, Filipek J, Gern BH, Olin BE, Leal JM, Wu Y, Lyons-Cohen MR, Huang JY, Paz-Stoltzfus CL, Plumlee CR, Pöschinger T, Urdahl KB, Perro M, Gerner MY. CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues. Cell Rep 2020; 31:107523. [PMID: 32320656 PMCID: PMC7233132 DOI: 10.1016/j.celrep.2020.107523] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [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: 11/07/2019] [Revised: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 12/21/2022] Open
Abstract
Recently developed approaches for highly multiplexed imaging have revealed complex patterns of cellular positioning and cell-cell interactions with important roles in both cellular- and tissue-level physiology. However, tools to quantitatively study cellular patterning and tissue architecture are currently lacking. Here, we develop a spatial analysis toolbox, the histo-cytometric multidimensional analysis pipeline (CytoMAP), which incorporates data clustering, positional correlation, dimensionality reduction, and 2D/3D region reconstruction to identify localized cellular networks and reveal features of tissue organization. We apply CytoMAP to study the microanatomy of innate immune subsets in murine lymph nodes (LNs) and reveal mutually exclusive segregation of migratory dendritic cells (DCs), regionalized compartmentalization of SIRPα- dermal DCs, and preferential association of resident DCs with select LN vasculature. The findings provide insights into the organization of myeloid cells in LNs and demonstrate that CytoMAP is a comprehensive analytics toolbox for revealing features of tissue organization in imaging datasets.
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Affiliation(s)
- Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jakub Filipek
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Benjamin H Gern
- Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Brandy E Olin
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Joseph M Leal
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Yajun Wu
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | | | - Jessica Y Huang
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | | | | | - Thomas Pöschinger
- Roche Innovation Center Munich, Pharmaceutical Research & Early Development (pRED), Discovery Pharmacology, Nonnenwald 2, 82377 Penzberg, Germany
| | - Kevin B Urdahl
- Department of Immunology, University of Washington, Seattle, WA 98109, USA; Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Mario Perro
- Roche Innovation Center Zurich, Pharmaceutical Research & Early Development (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA 98109, USA.
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27
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Bracaglia LG, Piotrowski-Daspit AS, Lin CY, Moscato ZM, Wang Y, Tietjen GT, Saltzman WM. High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents. Proc Natl Acad Sci U S A 2020; 117:3502-8. [PMID: 32015123 DOI: 10.1073/pnas.1915450117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accurate analysis of blood concentration and circulation half-life is an important consideration for any intravenously administered agent in preclinical development or for therapeutic application. However, the currently available tools to measure these parameters are laborious, expensive, and inefficient for handling multiple samples from complex multivariable experiments. Here we describe a robust high-throughput quantitative microscopy-based method to measure the blood concentration and circulation half-life of any fluorescently labeled agent using only a small (2 µL) amount of blood volume, enabling additional end-point measurements to be assessed in the same subject. To validate this method, we demonstrate its use to measure the circulation half-life in mice of two types of fluorescently labeled polymeric nanoparticles of different sizes and surface chemistries and of a much smaller fluorescently labeled monoclonal antibody. Furthermore, we demonstrate the improved accuracy of this method compared to previously described methods.
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28
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Akamatsu M, Vasan R, Serwas D, Ferrin MA, Rangamani P, Drubin DG. Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis. eLife 2020; 9:49840. [PMID: 31951196 PMCID: PMC7041948 DOI: 10.7554/elife.49840] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [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: 07/02/2019] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Force generation by actin assembly shapes cellular membranes. An experimentally constrained multiscale model shows that a minimal branched actin network is sufficient to internalize endocytic pits against membrane tension. Around 200 activated Arp2/3 complexes are required for robust internalization. A newly developed molecule-counting method determined that ~200 Arp2/3 complexes assemble at sites of clathrin-mediated endocytosis in human cells. Simulations predict that actin self-organizes into a radial branched array with growing ends oriented toward the base of the pit. Long actin filaments bend between attachment sites in the coat and the base of the pit. Elastic energy stored in bent filaments, whose presence was confirmed by cryo-electron tomography, contributes to endocytic internalization. Elevated membrane tension directs more growing filaments toward the base of the pit, increasing actin nucleation and bending for increased force production. Thus, spatially constrained actin filament assembly utilizes an adaptive mechanism enabling endocytosis under varying physical constraints. The outer membrane of a cell is a tight but elastic barrier that controls what enters or leaves the cell. Large molecules typically cannot cross this membrane unaided. Instead, to enter the cell, they must be packaged into a pocket of the membrane that is then pulled inside. This process, called endocytosis, shuttles material into a cell hundreds of times a minute. Endocytosis relies on molecular machines that assemble and disassemble at the membrane as required. One component, a protein called actin, self-assembles near the membrane into long filaments with many repeated subunits. These filaments grow against the membrane, pulling it inwards. But it was not clear how actin filaments organize in such a way that allows them to pull on the membrane with enough force – and without a template to follow. Akamatsu et al. set about identifying how actin operates during endocytosis by using computer simulations that were informed by measurements made in living cells. The simulations included information about the location of actin and other essential molecules, along with the details of how these molecules work individually and together. Akamatsu et al. also developed a method to count the numbers of molecules of a key protein at individual sites of endocytosis. High-resolution imaging was then used to create 3D pictures of actin and endocytosis in action in human cells grown in the laboratory. The analysis showed the way actin filaments arrange themselves depends on the starting positions of a few key molecules that connect to actin. Imaging confirmed that, like a pole-vaulting pole, the flexible actin filaments bend to store energy and then release it to pull the membrane inwards during endocytosis. Finally, the simulations predicted that the collection of filaments adapts its shape and size in response to the resistance of the elastic membrane. This makes the system opportunistic and adaptable to the unpredictable environment within cells.
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Affiliation(s)
- Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, United States
| | - Daniel Serwas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Michael A Ferrin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, United States
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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29
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Abstract
The endoplasmic reticulum (ER) is the site for folding and maturation of secreted and membrane proteins. When the ER protein-folding machinery is overwhelmed, misfolded proteins trigger ER stress, which is frequently linked to human diseases, including cancer and neurodegeneration. Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident sensor that assembles into large clusters of previously unknown organization upon its activation by unfolded peptides. We demonstrate that IRE1 clusters are topologically complex dynamic structures that remain contiguous with the ER membrane throughout their lifetime. The majority of clustered IRE1 molecules are diffusionally trapped inside the clusters until IRE1 signaling attenuates, at which point they are released back into the ER through a pathway that is functionally distinct from cluster assembly. The endoplasmic reticulum (ER) membrane-resident stress sensor inositol-requiring enzyme 1 (IRE1) governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined superresolution microscopy, single-particle tracking, fluorescence recovery, and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that: 1) In contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (∼5%) of the total IRE1 in the cell; 2) IRE1 clusters have complex topologies that display features of higher-order organization; 3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates; 4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network; 5) when IRE1 clusters disappear at later time points of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded; 6) IRE1 cluster assembly and disassembly are mechanistically distinct; and 7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins.
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30
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Min J, Yao B, Trendafilova V, Ketelhut S, Kastl L, Greve B, Kemper B. Quantitative phase imaging of cells in a flow cytometry arrangement utilizing Michelson interferometer-based off-axis digital holographic microscopy. J Biophotonics 2019; 12:e201900085. [PMID: 31169960 DOI: 10.1002/jbio.201900085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 03/06/2019] [Revised: 05/13/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
We combined Michelson-interferometer-based off-axis digital holographic microscopy (DHM) with a common flow cytometry (FCM) arrangement. Utilizing object recognition procedures and holographic autofocusing during the numerical reconstruction of the acquired off-axis holograms, sharply focused quantitative phase images of suspended cells in flow were retrieved without labeling, from which biophysical cellular features of distinct cells, such as cell radius, refractive index and dry mass, can be subsequently retrieved in an automated manner. The performance of the proposed concept was first characterized by investigations on microspheres that were utilized as test standards. Then, we analyzed two types of pancreatic tumor cells with different morphology to further verify the applicability of the proposed method for quantitative live cell imaging. The retrieved biophysical datasets from cells in flow are found in good agreement with results from comparative investigations with previously developed DHM methods under static conditions, which demonstrates the effectiveness and reliability of our approach. Our results contribute to the establishment of DHM in imaging FCM and prospect to broaden the application spectrum of FCM by providing complementary quantitative imaging as well as additional biophysical cell parameters which are not accessible in current high-throughput FCM measurements.
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Affiliation(s)
- Junwei Min
- Biomedical Technology Center, University of Muenster, Muenster, Germany
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, China
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, China
| | | | - Steffi Ketelhut
- Biomedical Technology Center, University of Muenster, Muenster, Germany
| | - Lena Kastl
- Biomedical Technology Center, University of Muenster, Muenster, Germany
| | - Burkhard Greve
- Department of Radiotherapy-Radiooncology-, University Hospital Muenster, Muenster, Germany
| | - Björn Kemper
- Biomedical Technology Center, University of Muenster, Muenster, Germany
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31
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Narayana SKK, Gopi DK, Rubeena M, Parameswaran SR. Macro‑micro‑morphological diagnosis of leaves of two species of Cinnamomum ( C. sulphuratum and C. verum) used as resource of bay leaf. Ayu 2019; 40:196-203. [PMID: 33281398 PMCID: PMC7685258 DOI: 10.4103/ayu.ayu_194_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 09/14/2017] [Revised: 10/18/2017] [Accepted: 06/13/2020] [Indexed: 11/21/2022] Open
Abstract
Background: Cinnamomumverum (true cinnamon or Tejpatra) is a well‑known spice with immense medicinal properties. Its adulteration with leaf and bark of other species belonging to genus Cinnamomum is found to be a common practice in India. Aims: Cinnamomumsulphuratum is used as a substitute of C. verum owing to its apparent macroscopic similarities. Materials and Methods: Fresh leaves of C. verum and C. sulphuratum growing in South India were collected and studied to establish their macro–microscopic identity with pharmacognostical perspective. Results: Detailed microscopic evaluation by transverse section, maceration, and powder microscopy was conducted to delineate the two species. Detailed macroscopic identification served the purpose of identification of the entire drug on the spot, and microscopy has helped in the identification of fragmented and powdered form of the drugs. Conclusion: Further chemical and biological studies may be necessary to confirm whether these leaves can be used as a substitute or adulterant for other species Cinnamon.
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Affiliation(s)
- Sunil Kumar Koppala Narayana
- Department of Pharmacognosy and , (Central Council for Research in Siddha, Ministry of AYUSH, Government of India), Chennai, Tamil Nadu, India
| | - Divya Kallingilkalathil Gopi
- Department of Pharmacognosy and , (Central Council for Research in Siddha, Ministry of AYUSH, Government of India), Chennai, Tamil Nadu, India
| | - Mattummal Rubeena
- Department of Pharmacognosy and , (Central Council for Research in Siddha, Ministry of AYUSH, Government of India), Chennai, Tamil Nadu, India
| | - Sathiya Rajeswaran Parameswaran
- Department of Director Incharge, Siddha Central Research Institute, (Central Council for Research in Siddha, Ministry of AYUSH, Government of India), Chennai, Tamil Nadu, India
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32
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Royer CA. Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy. Protein Sci 2019; 28:1210-1221. [PMID: 31012169 DOI: 10.1002/pro.3630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 11/12/2022]
Abstract
Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super-resolution.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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33
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Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM. Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma. SLAS Discov 2018; 23:1030-1039. [PMID: 30074852 DOI: 10.1177/2472555218791414] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Image-based analysis is an increasingly important tool to characterize the effect of drugs in large-scale chemical screens. Herein, we present image and data analysis methods to investigate population cell-cycle dynamics in patient-derived brain tumor cells. Images of glioblastoma cells grown in multiwell plates were used to extract per-cell descriptors, including nuclear DNA content. We reduced the DNA content data from per-cell descriptors to per-well frequency distributions, which were used to identify compounds affecting cell-cycle phase distribution. We analyzed cells from 15 patient cases representing multiple subtypes of glioblastoma and searched for clusters of cell-cycle phase distributions characterizing similarities in response to 249 compounds at 11 doses. We show that this approach applied in a blind analysis with unlabeled substances identified drugs that are commonly used for treating solid tumors as well as other compounds that are well known for inducing cell-cycle arrest. Redistribution of nuclear DNA content signals is thus a robust metric of cell-cycle arrest in patient-derived glioblastoma cells.
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Affiliation(s)
- Damian J Matuszewski
- 1 Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,2 Centre for Image Analysis, Uppsala University, Uppsala, Sweden
| | - Carolina Wählby
- 1 Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,2 Centre for Image Analysis, Uppsala University, Uppsala, Sweden
| | - Cecilia Krona
- 3 Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Sven Nelander
- 1 Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,3 Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
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34
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Kiss A, Fischer I, Kleele T, Misgeld T, Propst F. Neuronal Growth Cone Size-Dependent and -Independent Parameters of Microtubule Polymerization. Front Cell Neurosci 2018; 12:195. [PMID: 30065631 PMCID: PMC6056669 DOI: 10.3389/fncel.2018.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/25/2018] [Accepted: 06/17/2018] [Indexed: 01/16/2023] Open
Abstract
Migration and pathfinding of neuronal growth cones during neurite extension is critically dependent on dynamic microtubules. In this study we sought to determine, which aspects of microtubule polymerization relate to growth cone morphology and migratory characteristics. We conducted a multiscale quantitative microscopy analysis using automated tracking of microtubule plus ends in migrating growth cones of cultured murine dorsal root ganglion (DRG) neurons. Notably, this comprehensive analysis failed to identify any changes in microtubule polymerization parameters that were specifically associated with spontaneous extension vs. retraction of growth cones. This suggests that microtubule dynamicity is a basic mechanism that does not determine the polarity of growth cone response but can be exploited to accommodate diverse growth cone behaviors. At the same time, we found a correlation between growth cone size and basic parameters of microtubule polymerization including the density of growing microtubule plus ends and rate and duration of microtubule growth. A similar correlation was observed in growth cones of neurons lacking the microtubule-associated protein MAP1B. However, MAP1B-null growth cones, which are deficient in growth cone migration and steering, displayed an overall reduction in microtubule dynamicity. Our results highlight the importance of taking growth cone size into account when evaluating the influence on growth cone microtubule dynamics of different substrata, guidance factors or genetic manipulations which all can change growth cone morphology and size. The type of large scale multiparametric analysis performed here can help to separate direct effects that these perturbations might have on microtubule dynamics from indirect effects resulting from perturbation-induced changes in growth cone size.
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Affiliation(s)
- Alexa Kiss
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Irmgard Fischer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Tatjana Kleele
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich Cluster for Systems Neurology (SyNergy) and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich Cluster for Systems Neurology (SyNergy) and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Friedrich Propst
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
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35
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Schlichthaerle T, Eklund AS, Schueder F, Strauss MT, Tiede C, Curd A, Ries J, Peckham M, Tomlinson DC, Jungmann R. Site-Specific Labeling of Affimers for DNA-PAINT Microscopy. Angew Chem Int Ed Engl 2018; 57:11060-11063. [PMID: 29873161 DOI: 10.1002/anie.201804020] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/11/2018] [Indexed: 12/17/2022]
Abstract
Optical super-resolution techniques allow fluorescence imaging below the classical diffraction limit of light. From a technology standpoint, recent methods are approaching molecular-scale spatial resolution. However, this remarkable achievement is not easily translated to imaging of cellular components, since current labeling approaches are limited by either large label sizes (antibodies) or the sparse availability of small and efficient binders (nanobodies, aptamers, genetically-encoded tags). In this work, we combined recently developed Affimer reagents with site-specific DNA modification for high-efficiency labeling and imaging using DNA-PAINT. We assayed our approach using an actin Affimer. The small DNA-conjugated affinity binders could provide a solution for efficient multitarget super-resolution imaging in the future.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Tiede
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Alistair Curd
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Michelle Peckham
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
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36
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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37
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Wang IH, Burckhardt CJ, Yakimovich A, Greber UF. Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton. Viruses. 2018;10. [PMID: 29614729 PMCID: PMC5923460 DOI: 10.3390/v10040166] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/27/2022] Open
Abstract
Viruses have a dual nature: particles are “passive substances” lacking chemical energy transformation, whereas infected cells are “active substances” turning-over energy. How passive viral substances convert to active substances, comprising viral replication and assembly compartments has been of intense interest to virologists, cell and molecular biologists and immunologists. Infection starts with virus entry into a susceptible cell and delivers the viral genome to the replication site. This is a multi-step process, and involves the cytoskeleton and associated motor proteins. Likewise, the egress of progeny virus particles from the replication site to the extracellular space is enhanced by the cytoskeleton and associated motor proteins. This overcomes the limitation of thermal diffusion, and transports virions and virion components, often in association with cellular organelles. This review explores how the analysis of viral trajectories informs about mechanisms of infection. We discuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking. Virus visualization and tracking are increasingly enhanced by computational analyses of virus trajectories as well as in silico modeling. Combined approaches reveal previously unrecognized features of virus-infected cells. Using select examples of complementary methodology, we highlight the role of actin filaments and microtubules, and their associated motors in virus infections. In-depth studies of single virion dynamics at high temporal and spatial resolutions thereby provide deep insight into virus infection processes, and are a basis for uncovering underlying mechanisms of how cells function.
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38
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Vanhecke D, Kuhn DA, Jimenez de Aberasturi D, Balog S, Milosevic A, Urban D, Peckys D, de Jonge N, Parak WJ, Petri-Fink A, Rothen-Rutishauser B. Involvement of two uptake mechanisms of gold and iron oxide nanoparticles in a co-exposure scenario using mouse macrophages. Beilstein J Nanotechnol 2017; 8:2396-2409. [PMID: 29234575 PMCID: PMC5704759 DOI: 10.3762/bjnano.8.239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 10/11/2017] [Indexed: 05/26/2023]
Abstract
Little is known about the simultaneous uptake of different engineered nanoparticle types, as it can be expected in our daily life. In order to test such co-exposure effects, murine macrophages (J774A.1 cell line) were incubated with gold (AuNPs) and iron oxide nanoparticles (FeO x NPs) either alone or combined. Environmental scanning electron microscopy revealed that single NPs of both types bound within minutes on the cell surface but with a distinctive difference between FeO x NPs and AuNPs. Uptake analysis studies based on laser scanning microscopy, transmission electron microscopy, and inductively coupled plasma optical emission spectrometry revealed intracellular appearance of both NP types in all exposure scenarios and a time-dependent increase. This increase was higher for both AuNPs and FeO x NPs during co-exposure. Cells treated with endocytotic inhibitors recovered after co-exposure, which additionally hinted that two uptake mechanisms are involved. Cross-talk between uptake pathways is relevant for toxicological studies: Co-exposure acts as an uptake accelerant. If the goal is to maximize the cellular uptake, e.g., for the delivery of pharmaceutical agents, this can be beneficial. However, co-exposure should also be taken into account in the case of risk assessment of occupational settings. The demonstration of co-exposure-invoked pathway interactions reveals that synergetic nanoparticle effects, either positive or negative, must be considered for nanotechnology and nanomedicine in particular to develop to its full potential.
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Affiliation(s)
- Dimitri Vanhecke
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Dagmar A Kuhn
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | | | - Sandor Balog
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Ana Milosevic
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Dominic Urban
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Diana Peckys
- Department of Biophysics, CIPMM Geb. 48, Saarland University, 66421 Homburg/Saar, Germany
| | - Niels de Jonge
- Department of Biophysics, CIPMM Geb. 48, Saarland University, 66421 Homburg/Saar, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Wolfgang J Parak
- CIC Biomagune, Miramon Ibilbidea 182, 20014 Donostia, Gipuzkoa, San Sebastian, Spain
- Fachbereich Physik, Philipps Universität Marburg, Renthof 7, 35037 Marburg, Germany
| | - Alke Petri-Fink
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
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Abstract
Coxiella burnetii is the causative agent of human Q fever, a zoonotic disease that can cause a debilitating, flu-like illness in acute cases, or a life-threatening endocarditis in chronic patients. An obligate intracellular bacterial pathogen, Coxiella survives and multiplies in a large lysosome-like vacuole known as the Coxiella parasitophorous vacuole (CPV). A unique characteristic of the CPV is the acidic environment (pH ∼5.0), which is required to activate Coxiella metabolism and the Coxiella type 4 secretion system (T4SS), a major virulence factor required for intracellular survival. Further, inhibiting or depleting vacuolar ATPase, a host cell protein that regulates lysosomal pH, inhibits intracellular Coxiella growth. Together, these data suggest that CPV pH is an important limiting factor for Coxiella growth and virulence. This unit describes a method to determine CPV pH using live cell microscopy of a pH-sensitive fluorophore conjugated to dextran. This technique is useful to measure changes in CPV pH during infection or in response to drug treatment. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Dhritiman Samanta
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stacey D. Gilk
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana
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40
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Li W, Germain RN, Gerner MY. Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C e3D). Proc Natl Acad Sci U S A 2017; 114:E7321-30. [PMID: 28808033 DOI: 10.1073/pnas.1708981114] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques.
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41
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Abstract
The gram-negative bacterium Coxiella burnetii causes human Q fever, a disease characterized by a debilitating flu-like illness in acute cases and endocarditis in chronic patients. An obligate intracellular pathogen, Coxiella burnetii survives within a large, lysosome-like vacuole inside the host cell. A unique feature of the Coxiella parasitophorous vacuole (PV) is high levels of fusion with the host endocytic pathway, with PV-endosome fusion critical for Coxiella survival within the host cell. This unit describes quantitating PV-endosome fusion by measuring delivery of the fluid phase endosome marker dextran to the PV using live cell imaging. To study the effect of host cell proteins involved in PV-endosome fusion, details are provided for using siRNA knockdown host cells. This method is a powerful tool for understanding mechanisms underlying Coxiella's ability to manipulate host cell trafficking pathways. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth Winfree
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stacey D Gilk
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana
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42
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AkhavanAghdam Z, Sinha J, Tabbaa OP, Hao N. Dynamic control of gene regulatory logic by seemingly redundant transcription factors. eLife 2016; 5. [PMID: 27690227 PMCID: PMC5047750 DOI: 10.7554/elife.18458] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 06/03/2016] [Accepted: 09/12/2016] [Indexed: 12/24/2022] Open
Abstract
Many transcription factors co-express with their homologs to regulate identical target genes, however the advantages of such redundancies remain elusive. Using single-cell imaging and microfluidics, we study the yeast general stress response transcription factor Msn2 and its seemingly redundant homolog Msn4. We find that gene regulation by these two factors is analogous to logic gate systems. Target genes with fast activation kinetics can be fully induced by either factor, behaving as an 'OR' gate. In contrast, target genes with slow activation kinetics behave as an 'AND' gate, requiring distinct contributions from both factors, upon transient stimulation. Furthermore, such genes become an 'OR' gate when the input duration is prolonged, suggesting that the logic gate scheme is not static but rather dependent on the input dynamics. Therefore, Msn2 and Msn4 enable a time-based mode of combinatorial gene regulation that might be applicable to homologous transcription factors in other organisms. DOI:http://dx.doi.org/10.7554/eLife.18458.001 Cells respond to environmental signals by activating proteins called transcription factors. These bind to the DNA that is stored in the cell nucleus and turn on specific genes to make gene products. Many of these transcription factors move in and out of the nucleus once activated. Different environmental signals affect the amount of transcription factor that appears in the nucleus in different ways, and this is important in determining which genes should be turned on and how many copies of gene products should be made. Many transcription factors co-exist with a similar version of themselves in the same cell. These closely related proteins, called homologous transcription factors, respond to the same signals and bind to the same place on the DNA to turn on the same genes. It was not clear what advantages the cells gain from having two molecules that perform the same roles. Two homologous transcription factors called Msn2 and Msn4 are found in baker's yeast. These transcription factors respond to a wide variety of environmental stresses by moving rapidly into the nucleus, where they remain for a short time to turn on hundreds of target genes that are needed for the cell to survive. AkhavanAghdam, Sinha, Tabbaa et al. investigated the roles of Msn2 and Msn4 by tracking where the proteins localized to and which genes they switched on inside the same single cell. Genes that can be turned on quickly could be activated by either Msn2 or Msn4, and both factors activated the genes to a similar extent. By contrast, both Msn2 and Msn4 were required to activate those genes that take a long time to be turned on. In these cases, Msn2 served as a 'switch' that governed the 'on' and 'off' state of the genes, while Msn4 behaved as a 'rheostat' to tune how much gene product was made. This cooperation between the two transcription factors is equivalent to a design commonly found in electrical circuits and may help the cell to survive in rapidly changing environments. Further studies are now needed to investigate the mechanisms that provide Msn2 and Msn4 with distinct roles in gene regulation. Technological advances that allow the full genetic material of a single cell to be analyzed could also determine whether other homologous transcription factors regulate their target genes in similar ways. DOI:http://dx.doi.org/10.7554/eLife.18458.002
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Affiliation(s)
- Zohreh AkhavanAghdam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Joydeb Sinha
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Omar P Tabbaa
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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43
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Abstract
Zebrafish ( Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.
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Affiliation(s)
- Omer Ishaq
- 1 Centre for Image Analysis/SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Carolina Wählby
- 1 Centre for Image Analysis/SciLifeLab, Uppsala University, Uppsala, Sweden
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44
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Kroll T, Schmidt D, Schwanitz G, Ahmad M, Hamann J, Schlosser C, Lin YC, Böhm KJ, Tuckermann J, Ploubidou A. High-Content Microscopy Analysis of Subcellular Structures: Assay Development and Application to Focal Adhesion Quantification. ACTA ACUST UNITED AC 2016; 77:12.43.1-12.43.44. [PMID: 27367288 DOI: 10.1002/cpcy.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-content analysis (HCA) converts raw light microscopy images to quantitative data through the automated extraction, multiparametric analysis, and classification of the relevant information content. Combined with automated high-throughput image acquisition, HCA applied to the screening of chemicals or RNAi-reagents is termed high-content screening (HCS). Its power in quantifying cell phenotypes makes HCA applicable also to routine microscopy. However, developing effective HCA and bioinformatic analysis pipelines for acquisition of biologically meaningful data in HCS is challenging. Here, the step-by-step development of an HCA assay protocol and an HCS bioinformatics analysis pipeline are described. The protocol's power is demonstrated by application to focal adhesion (FA) detection, quantitative analysis of multiple FA features, and functional annotation of signaling pathways regulating FA size, using primary data of a published RNAi screen. The assay and the underlying strategy are aimed at researchers performing microscopy-based quantitative analysis of subcellular features, on a small scale or in large HCS experiments. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Torsten Kroll
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.,These authors contributed equally to this work
| | - David Schmidt
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.,Current address: Max Planck Institute for Molecular Biomedicine, Münster, Germany.,These authors contributed equally to this work
| | - Georg Schwanitz
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Mubashir Ahmad
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.,Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Jana Hamann
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | | | - Yu-Chieh Lin
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Konrad J Böhm
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Jan Tuckermann
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
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45
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Zacharias AL, Murray JI. Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time. Genesis 2016; 54:182-97. [PMID: 26915329 DOI: 10.1002/dvg.22928] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/19/2022]
Abstract
Understanding how a single cell, the zygote, can divide and differentiate to produce the diverse animal cell types is a central goal of developmental biology research. The model organism Caenorhabditis elegans provides a system that enables a truly comprehensive understanding of this process across all cells. Its invariant cell lineage makes it possible to identify all of the cells in each individual and compare them across organisms. Recently developed methods automate the process of cell identification, allowing high-throughput gene expression characterization and phenotyping at single cell resolution. In this Review, we summarize the sequences of events that pattern the lineage including establishment of founder cell identity, the signaling pathways that diversify embryonic fate, and the regulators involved in patterning within these founder lineages before cells adopt their terminal fates. We focus on insights that have emerged from automated approaches to lineage tracking, including insights into mechanisms of robustness, context-specific regulation of gene expression, and temporal coordination of differentiation. We suggest a model by which lineage history produces a combinatorial code of transcription factors that act, often redundantly, to ensure terminal fate.
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Affiliation(s)
- Amanda L Zacharias
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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46
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Abstract
Genetically identical organisms in homogeneous environments have different lifespans and healthspans. These differences are often attributed to stochastic events, such as mutations and 'epimutations', changes in DNA methylation and chromatin that change gene function and expression. But work in the last 10 years has revealed differences in lifespan- and health-related phenotypes that are not caused by lasting changes in DNA or identified by modifications to DNA or chromatin. This work has demonstrated persistent differences in single-cell and whole-organism physiological states operationally defined by values of reporter gene signals in living cells. While some single-cell states, for example, responses to oxygen deprivation, were defined previously, others, such as a generally heightened ability to make proteins, were, revealed by direct experiment only recently, and are not well understood. Here, we review technical progress that promises to greatly increase the number of these measurable single-cell physiological variables and measureable states. We discuss concepts that facilitate use of single-cell measurements to provide insight into physiological states and state transitions. We assert that researchers will use this information to relate cell level physiological readouts to whole-organism outcomes, to stratify aging populations into groups based on different physiologies, to define biomarkers predictive of outcomes, and to shed light on the molecular processes that bring about different individual physiologies. For these reasons, quantitative study of single-cell physiological variables and state transitions should provide a valuable complement to genetic and molecular explanations of how organisms age.
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Affiliation(s)
| | - Monica Driscoll
- Department of Molecular Biology and BiochemistryRutgersThe State University of New JerseyPiscatawayNJUSA
| | - Roger Brent
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleWAUSA
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47
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Kwei J, Halstead FD, Dretzke J, Oppenheim BA, Moiemen NS. Protocol for a systematic review of quantitative burn wound microbiology in the management of burns patients. Syst Rev 2015; 4:150. [PMID: 26542240 PMCID: PMC4635620 DOI: 10.1186/s13643-015-0137-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/16/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Sepsis from burn injuries can result from colonisation of burn wounds, especially in large surface area burns. Reducing bacterial infection will reduce morbidity and mortality, and mortality for severe burns can be as high as 15 %. There are various quantitative and semi-quantitative techniques to monitor bacterial load on wounds. In the UK, burn wounds are typically monitored for the presence or absence of bacteria through the collection and culture of swabs, but no absolute count is obtained. Quantitative burn wound culture provides a measure of bacterial count and is gaining increased popularity in some countries. It is however more resource intensive, and evidence for its utility appears to be inconsistent. This systematic review therefore aims to assess the evidence on the utility and reliability of different quantitative microbiology techniques in terms of diagnosing or predicting clinical outcomes. METHODS/DESIGN Standard systematic review methods aimed at minimising bias will be employed for study identification, selection and data extraction. Bibliographic databases and ongoing trial registers will be searched and conference abstracts screened. Studies will be eligible if they are prospective studies or systematic reviews of burn patients (any age) for whom quantitative microbiology has been performed, whether it is compared to another method. Quality assessment will be based on quality assessment tools for diagnostic and prognostic studies and tailored to the review as necessary. Synthesis is likely to be primarily narrative, but meta-analysis may be considered where clinical and methodological homogeneity exists. DISCUSSION Given the increasing use of quantitative methods, this is a timely systematic review, which will attempt to clarify the evidence base. As far as the authors are aware, it will be the first to address this topic. TRIAL REGISTRATION PROSPERO, CRD42015023903.
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Affiliation(s)
- Johnny Kwei
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, England. .,Royal North Shore Hospital and Manly District Hospital, Northern Sydney Area Network, Sydney, NSW, Australia. .,The Healing Foundation Burns Research Centre, Birmingham, England.
| | - Fenella D Halstead
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, England. .,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, England.
| | - Janine Dretzke
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, England. .,Public Health, Epidemiology and Biostatistics, School of Health and Population Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, England.
| | - Beryl A Oppenheim
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, England. .,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, England.
| | - Naiem S Moiemen
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, England. .,The Healing Foundation Burns Research Centre, Birmingham, England. .,Birmingham Children's Hospital, Birmingham, England.
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Puigdellívol-Sánchez A, Giralt A, Casanovas A, Alberch J, Prats-Galino A. Cryostat Slice Irregularities May Introduce Bias in Tissue Thickness Estimation: Relevance for Cell Counting Methods. Microsc Microanal 2015; 21:893-901. [PMID: 26173483 DOI: 10.1017/s143192761501380x] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Stereological techniques using the optical disectors require estimation of final section thickness, but frozen tissue irregularities may interfere with this estimation. Cryostat slices from rodent nerve tissues (dorsal root ganglia, spinal cord, and brain), cut at 16, 40, and 50 μm, were digitized with a confocal microscope and visualized through 3D software. Geometric section thickness of tissue (T geom) was defined as tissue volume/area. Maximal section thicknesses (T max), from the top to the bottom of the section, were measured in a random sample of vertical ZX planes. Irregularities were mostly related to blood vessels traversing the tissue and neuronal somas protruding over the cut surfaces, with other neuron profiles showing a fragmented appearance. Irregularities contributed to increasing the distance between the tops and bottoms of slices sectioned in different laboratories. Significant differences were found between T max and T geom for all thickness studies and counting frames (p<0.01). The T geom/T max average rate was 68.4-85.7% in volumes around cell profiles (∼600-1,200 μm2) and 83.3-91.8% in subcellular samples (∼25-160 μm2). Confocal microscopy may help to assess tissue irregularities, which might lead to an overestimation of tissue volume if section thickness is estimated by focusing on the top and bottom of the sections.
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Affiliation(s)
- Anna Puigdellívol-Sánchez
- 1Human Anatomy and Embryology Unit,Facultat de Medicina,Universitat de Barcelona,c/Casanova 143,08036 Barcelona,Spain
| | - Albert Giralt
- 3Departament de Biologia Cellular,Immunologia i Neurociències,Facultat de Medicina,Universitat de Barcelona,c/Casanova 143,08036 Barcelona,Spain.Barcelona,Spain
| | - Anna Casanovas
- 6Unit of Cellular Neurobioloy,Departament de Medicina Experimental,Facultat de Medicina,Universitat de Lleida,c/Montserrat Roig 2,25008 Lleida,Spain
| | - Jordi Alberch
- 3Departament de Biologia Cellular,Immunologia i Neurociències,Facultat de Medicina,Universitat de Barcelona,c/Casanova 143,08036 Barcelona,Spain.Barcelona,Spain
| | - Alberto Prats-Galino
- 1Human Anatomy and Embryology Unit,Facultat de Medicina,Universitat de Barcelona,c/Casanova 143,08036 Barcelona,Spain
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49
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Righolt CH, Schmälter AK, Kuzyk A, Young IT, van Vliet LJ, Mai S. Measuring murine chromosome orientation in interphase nuclei. Cytometry A 2015; 87:733-40. [PMID: 25891972 DOI: 10.1002/cyto.a.22674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/25/2015] [Accepted: 03/31/2015] [Indexed: 11/08/2022]
Abstract
The nuclear architecture of a cell may change as a result of various diseases, including cancer. A variety of nuclear features are, therefore, of interest to cell biologists. Recently, several studies have investigated the orientation of chromosomes in the interphase nucleus either visually or semi-automatically. In this article an automated method to measure this orientation is presented. The theoretical difference between performing these measurements in two and three dimensions is discussed and experimentally verified. The results computed from measurements of murine nuclei correspond with results from visual inspection. We found significant differences in the orientation of chromosome 11 between nuclei from a PreB cell line of BALB/c origin and primary B nuclei from congenic [T38HxBALB/c]N wild-type mice. Since our new automatic method concurs with both the visual and semi-automatic methods, we conclude that the automatic method can replace these methods in assessing chromosome orientation.
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Affiliation(s)
- Christiaan H Righolt
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Ann-Kristin Schmälter
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Institute for Human Genetics, Ludwig Maximilian University, Munich, Germany
| | - Alexandra Kuzyk
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ian T Young
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Lucas J van Vliet
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Sabine Mai
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
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50
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Ulferts S, Delventhal R, Splivallo R, Karlovsky P, Schaffrath U. Abscisic acid negatively interferes with basal defence of barley against Magnaporthe oryzae. BMC Plant Biol 2015; 15:7. [PMID: 25604965 PMCID: PMC4307682 DOI: 10.1186/s12870-014-0409-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 10/16/2014] [Accepted: 12/29/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant hormones are well known regulators which balance plant responses to abiotic and biotic stresses. We investigated the role of abscisic acid (ABA) in resistance of barley (Hordeum vulgare L.) against the plant pathogenic fungus Magnaporthe oryzae. RESULTS Exogenous application of ABA prior to inoculation with M. oryzae led to more disease symptoms on barley leaves. This result contrasted the finding that ABA application enhances resistance of barley against the powdery mildew fungus. Microscopic analysis identified diminished penetration resistance as cause for enhanced susceptibility. Consistently, the barley mutant Az34, impaired in ABA biosynthesis, was less susceptible to infection by M. oryzae and displayed elevated penetration resistance as compared to the isogenic wild type cultivar Steptoe. Chemical complementation of Az34 mutant plants by exogenous application of ABA re-established disease severity to the wild type level. The role of ABA in susceptibility of barley against M. oryzae was corroborated by showing that ABA application led to increased disease severity in all barley cultivars under investigation except for the most susceptible cultivar Pallas. Interestingly, endogenous ABA concentrations did not significantly change after infection of barley with M. oryzae. CONCLUSION Our results revealed that elevated ABA levels led to a higher disease severity on barley leaves to M. oryzae. This supports earlier reports on the role of ABA in enhancing susceptibility of rice to the same pathogen and thereby demonstrates a host plant-independent function of this phytohormone in pathogenicity of monocotyledonous plants against M. oryzae.
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Affiliation(s)
- Sylvia Ulferts
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany.
| | - Rhoda Delventhal
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany.
| | - Richard Splivallo
- Institute for Molecular Biosciences, Goethe University of Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37077, Goettingen, Germany.
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany.
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