1
|
Cayrol B, Colella S, Uzest M. Coupling clearing and hybridization chain reaction approaches to investigate gene expression in organs inside intact insect heads. Microsc Res Tech 2024. [PMID: 38558482 DOI: 10.1002/jemt.24561] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Detecting RNA molecules within their natural environment inside intact arthropods has long been challenging, particularly in small organisms covered by a tanned and pigmented cuticle. Here, we have developed a methodology that enables high-resolution analysis of the spatial distribution of transcripts of interest without having to dissect tiny organs or tissues, thereby preserving their integrity. We have combined an in situ amplification approach based on hybridization chain reaction, which enhances the signal-to-noise ratio, and a clearing approach that allows the visualization of inner organs beneath the cuticle. We have implemented this methodology for the first time in Hemiptera, mapping two salivary aphid (Acyrthosiphon pisum) transcripts, the effector c002 and the salivary sheath protein SHP. With a multiplex approach, we could simultaneously detect different mRNAs in mounted pea aphid head-thorax samples and show that they were distributed in distinct secretory cells of salivary glands. RESEARCH HIGHLIGHTS: Combining hybridisation chain reaction and clearing allows the detection of transcripts in intact aphids heads. The transcripts of the two salivary proteins c002 and SHP are compartmentalized in distinct secretory cells of the principal glands.
Collapse
Affiliation(s)
- Bastien Cayrol
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stefano Colella
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marilyne Uzest
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
2
|
Ensikat HJ, Malekhosseini M, Rust J, Weigend M. Visualization of calcium oxalate crystal macropatterns in plant leaves using an improved fast preparation method. J Microsc 2023; 290:168-177. [PMID: 37060298 DOI: 10.1111/jmi.13187] [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: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
Leaves of the majority of plants contain calcium oxalate (CaOx) crystals or druses which often occur in spectacular distribution patterns. Numerous studies on CaOx in plant tissues across many different plant groups have been published, since it can be visualized readily under a light microscope (LM). However, there is surprisingly limited knowledge on the actual, precise distribution of CaOx in the leaves of quite ordinary plants such as common native and exotic trees. Traditional sample preparation for the documentation of the distribution of CaOx crystals in a given sample - including overall distribution - requires time-consuming clearing procedures. Here we present a refined fast preparation method to visualize the overall CaOx complement in a sample: The plant material is ashed and the ash viewed under the polarizing microscope. This is a rapid method which overcomes many shortcomings of other methods and permits the visualization of the entire CaOx content in most leaf samples. Pros and cons in comparison with the conventional clearing technique are discussed. Further aspects for CaOx investigations by micro-CT and scanning electron microscopy are discussed. This article is protected by copyright. All rights reserved Lay description: Striking patterns of calcium oxalate (CaOx) crystals and druses (crystal aggregates) can be found in leaves of higher plants such as common trees and shrubs. They are easily visible under a light microscope, but this requires a chemical clearing procedure to render the samples transparent for polarizing microscopy. Here we present a refined fast preparation method to visualize the overall CaOx complement in a sample: The plant material is incinerated and the ash viewed under the polarizing microscope after immersion in oil. This rapid method overcomes the shortcomings of other methods; burning eliminates all organic components such as cellulose which would cause a disturbing background signal, and oil immersion provides good transparency of the samples. Thus, the burnt CaOx crystals are clearly visible whereas other ash components appear invisible in the polarizing microscope. Pros and cons in comparison with the conventional clearing technique are discussed. With this simple preparation method, CaOx distribution patterns in leaves may not only become favourable motives for amateur microscopists; for botanists they are a key for the understanding of their functions which are still in parts enigmatic and a matter of speculations.
Collapse
Affiliation(s)
- Hans-Jürgen Ensikat
- Nees-Institut für Biodiversität der Pflanzen der Universität Bonn, Bonn, Germany
| | - Mahdieh Malekhosseini
- Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
| | - Jes Rust
- Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
| | - Maximilian Weigend
- Nees-Institut für Biodiversität der Pflanzen der Universität Bonn, Bonn, Germany
| |
Collapse
|
3
|
de Caro A, Bellard E, Kolosnjaj-Tabi J, Golzio M, Rols MP. Gene Electrotransfer Efficiency in 2D and 3D Cancer Cell Models Using Different Electroporation Protocols: A Comparative Study. Pharmaceutics 2023; 15:pharmaceutics15031004. [PMID: 36986866 PMCID: PMC10053976 DOI: 10.3390/pharmaceutics15031004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Electroporation, a method relying on a pulsed electric field to induce transient cell membrane permeabilization, can be used as a non-viral method to transfer genes in vitro and in vivo. Such transfer holds great promise for cancer treatment, as it can induce or replace missing or non-functioning genes. Yet, while efficient in vitro, gene-electrotherapy remains challenging in tumors. To assess the differences of gene electrotransfer in respect to applied pulses in multi-dimensional (2D, 3D) cellular organizations, we herein compared pulsed electric field protocols applicable to electrochemotherapy and gene electrotherapy and different "High Voltage-Low Voltage" pulses. Our results show that all protocols can result in efficient permeabilization of 2D- and 3D-grown cells. However, their efficiency for gene delivery varies. The gene-electrotherapy protocol is the most efficient in cell suspensions, with a transfection rate of about 50%. Conversely, despite homogenous permeabilization of the entire 3D structure, none of the tested protocols allowed gene delivery beyond the rims of multicellular spheroids. Taken together, our findings highlight the importance of electric field intensity and the occurrence of cell permeabilization, and underline the significance of pulses' duration, impacting plasmids' electrophoretic drag. The latter is sterically hindered in 3D structures and prevents the delivery of genes into spheroids' core.
Collapse
Affiliation(s)
- Alexia de Caro
- Institut de Pharmacologie et de Biologie Structurale du CNRS UMR 5089, 205, Route de Narbonne, 31077 Toulouse CEDEX, France
| | - Elisabeth Bellard
- Institut de Pharmacologie et de Biologie Structurale du CNRS UMR 5089, 205, Route de Narbonne, 31077 Toulouse CEDEX, France
| | - Jelena Kolosnjaj-Tabi
- Institut de Pharmacologie et de Biologie Structurale du CNRS UMR 5089, 205, Route de Narbonne, 31077 Toulouse CEDEX, France
| | - Muriel Golzio
- Institut de Pharmacologie et de Biologie Structurale du CNRS UMR 5089, 205, Route de Narbonne, 31077 Toulouse CEDEX, France
| | - Marie-Pierre Rols
- Institut de Pharmacologie et de Biologie Structurale du CNRS UMR 5089, 205, Route de Narbonne, 31077 Toulouse CEDEX, France
| |
Collapse
|
4
|
Kiemen AL, Damanakis AI, Braxton AM, He J, Laheru D, Fishman EK, Chames P, Pérez CA, Wu PH, Wirtz D, Wood LD, Hruban RH. Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer. Med 2023; 4:75-91. [PMID: 36773599 PMCID: PMC9922376 DOI: 10.1016/j.medj.2022.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/06/2022] [Accepted: 11/23/2022] [Indexed: 01/26/2023]
Abstract
Pancreatic cancer is currently the third leading cause of cancer death in the United States. The clinical hallmarks of this disease include abdominal pain that radiates to the back, the presence of a hypoenhancing intrapancreatic lesion on imaging, and widespread liver metastases. Technologies such as tissue clearing and three-dimensional (3D) reconstruction of digitized serially sectioned hematoxylin and eosin-stained slides can be used to visualize large (up to 2- to 3-centimeter cube) tissues at cellular resolution. When applied to human pancreatic cancers, these 3D visualization techniques have provided novel insights into the basis of a number of the clinical characteristics of this disease. Here, we describe the clinical features of pancreatic cancer, review techniques for clearing and the 3D reconstruction of digitized microscope slides, and provide examples that illustrate how 3D visualization of human pancreatic cancer at the microscopic level has revealed features not apparent in 2D microscopy and, in so doing, has closed the gap between bench and bedside. Compared with animal models and 2D microscopy, studies of human tissues in 3D can reveal the difference between what can happen and what does happen in human cancers.
Collapse
Affiliation(s)
- Ashley L Kiemen
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Alexander Ioannis Damanakis
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of General, Visceral, Cancer and Transplant Surgery, University Hospital of Cologne, Cologne, Germany
| | - Alicia M Braxton
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel Laheru
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elliot K Fishman
- Department of Radiology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Patrick Chames
- Antibody Therapeutics and Immunotargeting Team, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Cristina Almagro Pérez
- Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Pei-Hsun Wu
- Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Denis Wirtz
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| |
Collapse
|
5
|
Bedenbaugh MN, Brener SC, Maldonado J, Lippert RN, Sweeney P, Cone RD, Simerly RB. Organization of neural systems expressing melanocortin-3 receptors in the mouse brain: Evidence for sexual dimorphism. J Comp Neurol 2022; 530:2835-2851. [PMID: 35770983 PMCID: PMC9724692 DOI: 10.1002/cne.25379] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/15/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 01/13/2023]
Abstract
The central melanocortin system is fundamentally important for controlling food intake and energy homeostasis. Melanocortin-3 receptor (MC3R) is one of two major receptors of the melanocortin system found in the brain. In contrast to the well-characterized melanocortin-4 receptor (MC4R), little is known regarding the organization of MC3R-expressing neural circuits. To increase our understanding of the intrinsic organization of MC3R neural circuits, identify specific differences between males and females, and gain a neural systems level perspective of this circuitry, we conducted a brain-wide mapping of neurons labeled for MC3R and characterized the distribution of their projections. Analysis revealed MC3R neuronal and terminal labeling in multiple brain regions that control a diverse range of physiological functions and behavioral processes. Notably, dense labeling was observed in the hypothalamus, as well as areas that share considerable connections with the hypothalamus, including the cortex, amygdala, thalamus, and brainstem. Additionally, MC3R neuronal labeling was sexually dimorphic in several areas, including the anteroventral periventricular area, arcuate nucleus, principal nucleus of the bed nucleus of the stria terminalis, and ventral premammillary region. Altogether, anatomical evidence reported here suggests that MC3R has the potential to influence several different classes of motivated behavior that are essential for survival, including ingestive, reproductive, defensive, and arousal behaviors, and is likely to modulate these behaviors differently in males and females.
Collapse
Affiliation(s)
- Michelle N. Bedenbaugh
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Samantha C. Brener
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Jose Maldonado
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Rachel N. Lippert
- Department of Neurocircuit Development and Function, German Institute of Human Nutrition Potsdam-Rehbruecke, Potsdam, Germany
| | - Patrick Sweeney
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Roger D. Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard B. Simerly
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
6
|
Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [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] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| |
Collapse
|
7
|
Munck S, Cawthorne C, Escamilla-Ayala A, Kerstens A, Gabarre S, Wesencraft K, Battistella E, Craig R, Reynaud EG, Swoger J, McConnell G. Challenges and advances in optical 3D mesoscale imaging. J Microsc 2022; 286:201-219. [PMID: 35460574 PMCID: PMC9325079 DOI: 10.1111/jmi.13109] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022]
Abstract
Optical mesoscale imaging is a rapidly developing field that allows the visualisation of larger samples than is possible with standard light microscopy, and fills a gap between cell and organism resolution. It spans from advanced fluorescence imaging of micrometric cell clusters to centimetre‐size complete organisms. However, with larger volume specimens, new problems arise. Imaging deeper into tissues at high resolution poses challenges ranging from optical distortions to shadowing from opaque structures. This manuscript discusses the latest developments in mesoscale imaging and highlights limitations, namely labelling, clearing, absorption, scattering, and also sample handling. We then focus on approaches that seek to turn mesoscale imaging into a more quantitative technique, analogous to quantitative tomography in medical imaging, highlighting a future role for digital and physical phantoms as well as artificial intelligence.
Collapse
Affiliation(s)
- Sebastian Munck
- VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | | | - Abril Escamilla-Ayala
- VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Axelle Kerstens
- VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Sergio Gabarre
- VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | | | | | - Rebecca Craig
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Emmanuel G Reynaud
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Belfield, Ireland
| | - Jim Swoger
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| |
Collapse
|
8
|
Kahan A, Greenbaum A, Jang MJ, Robinson JE, Cho JR, Chen X, Kassraian P, Wagenaar DA, Gradinaru V. Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses. Cell Rep 2021; 36:109744. [PMID: 34592157 PMCID: PMC8552649 DOI: 10.1016/j.celrep.2021.109744] [Citation(s) in RCA: 5] [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: 11/25/2020] [Revised: 06/22/2021] [Accepted: 08/31/2021] [Indexed: 01/30/2023] Open
Abstract
Optical implants to control and monitor neuronal activity in vivo have become foundational tools of neuroscience. Standard two-dimensional histology of the implant location, however, often suffers from distortion and loss during tissue processing. To address that, we developed a three-dimensional post hoc histology method called “light-guided sectioning” (LiGS), which preserves the tissue with its optical implant in place and allows staining and clearing of a volume up to 500 μm in depth. We demonstrate the use of LiGS to determine the precise location of an optical fiber relative to a deep brain target and to investigate the implant-tissue interface. We show accurate cell registration of ex vivo histology with single-cell, two-photon calcium imaging, obtained through gradient refractive index (GRIN) lenses, and identify subpopulations based on immunohistochemistry. LiGS provides spatial information in experimental paradigms that use optical fibers and GRIN lenses and could help increase reproducibility through identification of fiber-to-target localization and molecular profiling. Kahan et al. describe a 3D histology method (LiGS) to investigate with high fidelity the vicinity of an intact optical implant (e.g., GRIN lenses and optical fibers). LiGS is compatible with immunohistochemistry and single-molecule imaging. With the use of two-photon microscopy, LiGS can also link the functional properties of cells to their molecular identity.
Collapse
Affiliation(s)
- Anat Kahan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alon Greenbaum
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Min J Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - J Elliott Robinson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jounhong Ryan Cho
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pegah Kassraian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daniel A Wagenaar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
9
|
Toulemonde P, Risoud M, Lemesre PE, Beck C, Wattelet J, Tardivel M, Siepmann J, Vincent C. Evaluation of the Efficacy of Dexamethasone-Eluting Electrode Array on the Post-Implant Cochlear Fibrotic Reaction by Three-Dimensional Immunofluorescence Analysis in Mongolian Gerbil Cochlea. J Clin Med 2021; 10:jcm10153315. [PMID: 34362099 PMCID: PMC8347204 DOI: 10.3390/jcm10153315] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Cochlear implant is the method of choice for the rehabilitation of severe to profound sensorineural hearing loss. The study of the tissue response to cochlear implantation and the prevention of post-cochlear-implant damages are areas of interest in hearing protection research. The objective was to assess the efficacy of dexamethasone-eluting electrode array on endo canal fibrosis formation by three-dimensional immunofluorescence analysis in implanted Mongolian gerbil cochlea. Two trials were conducted after surgery using Mongolian gerbil implanted with dexamethasone-eluting or non-eluting intracochlear electrode arrays. The animals were then euthanised 10 weeks after implantation. The cochleae were prepared (electrode array in place) according to a 29-day protocol with immunofluorescent labelling and tissue clearing. The acquisition was carried out using light-sheet microscopy. Imaris software was then used for three-dimensional analysis of the cochleae and quantification of the fibrotic volume. The analysis of 12 cochleae showed a significantly different mean volume of fibrosis (2.16 × 108 μm3 ± 0.15 in the dexamethasone eluting group versus 3.17 × 108 μm3 ± 0.54 in the non-eluting group) (p = 0.004). The cochlear implant used as a corticosteroid delivery system appears to be an encouraging device for the protection of the inner ear against fibrosis induced by implantation. Three-dimensional analysis of the cochlea by light-sheet microscopy was suitable for studying post-implantation tissue damage.
Collapse
Affiliation(s)
- Philippine Toulemonde
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
- Correspondence: ; Tel.: +33-6851-91052
| | - Michaël Risoud
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| | - Pierre Emmanuel Lemesre
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| | - Cyril Beck
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| | - Jean Wattelet
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| | - Meryem Tardivel
- BioImaging Center Lille-Nord de France (BICeL), University of Lille 2 Henri Warembourg, F-59000 Lille, France;
| | - Juergen Siepmann
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| | - Christophe Vincent
- Department of Otology and Neurotology, CHU Lille, University of Lille 2 Henri Warembourg, F-59000 Lille, France; (M.R.); (P.E.L.); (C.B.); (J.W.); (J.S.); (C.V.)
- INSERM U1008—Controlled Drug Delivery Systems and Biomaterials, F-59000 Lille, France
| |
Collapse
|
10
|
Hahn A, Bode J, Alexander A, Karimian-Jazi K, Schregel K, Schwarz D, Sommerkamp AC, Krüwel T, Abdollahi A, Wick W, Platten M, Bendszus M, Tews B, Kurz FT, Breckwoldt MO. Large-scale characterization of the microvascular geometry in development and disease by tissue clearing and quantitative ultramicroscopy. J Cereb Blood Flow Metab 2021; 41:1536-1546. [PMID: 33043767 PMCID: PMC8217891 DOI: 10.1177/0271678x20961854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Three-dimensional assessment of optically cleared, entire organs and organisms has recently become possible by tissue clearing and selective plane illumination microscopy ("ultramicroscopy"). Resulting datasets can be highly complex, encompass over a thousand images with millions of objects and data of several gigabytes per acquisition. This constitutes a major challenge for quantitative analysis. We have developed post-processing tools to quantify millions of microvessels and their distribution in three-dimensional datasets from ultramicroscopy and demonstrate the capabilities of our pipeline within entire mouse brains and embryos. Using our developed acquisition, segmentation, and analysis platform, we quantify physiological vascular networks in development and the healthy brain. We compare various geometric vessel parameters (e.g. vessel density, radius, tortuosity) in the embryonic spinal cord and brain as well as in different brain regions (basal ganglia, corpus callosum, cortex). White matter tract structures (corpus callosum, spinal cord) showed lower microvascular branch densities and longer vessel branch length compared to grey matter (cortex, basal ganglia). Furthermore, we assess tumor neoangiogenesis in a mouse glioma model to compare tumor core and tumor border. The developed methodology allows rapid quantification of three-dimensional datasets by semi-automated segmentation of fluorescently labeled objects with conventional computer hardware. Our approach can aid preclinical investigations and paves the way towards "quantitative ultramicroscopy".
Collapse
Affiliation(s)
- Artur Hahn
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany.,Department of Physics and Astronomy, University of Heidelberg, Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Allen Alexander
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Katharina Schregel
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Schwarz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexander C Sommerkamp
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Krüwel
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium and Heidelberg Institute of Radiation Oncology, National Center for Radiation Research in Oncology, Heidelberg, Germany.,Heidelberg University School of Medicine, Heidelberg University, Heidelberg, Germany.,Translational Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany
| | - Martin Bendszus
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Felix T Kurz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael O Breckwoldt
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
11
|
Abstract
Expansion microscopy (ExM) is a technique that physically expands preserved cells and tissues before microscope imaging, so that conventional diffraction-limited microscopes can perform nanoscale-resolution imaging. In ExM, biomolecules or their markers are linked to a dense, swellable gel network synthesized throughout a specimen. Mechanical homogenization of the sample (e.g., by protease digestion) and the addition of water enable isotropic swelling of the gel, so that the relative positions of biomolecules are preserved. We previously presented ExM protocols for analyzing proteins and RNAs in cells and tissues. Here we describe a cookbook-style ExM protocol for expanding cultured HeLa cells with immunostained microtubules, aimed to help newcomers familiarize themselves with the experimental setups and skills required to successfully perform ExM. Our aim is to help beginners, or students in a wet-lab classroom setting, learn all the key steps of ExM. © 2020 The Authors.
Collapse
Affiliation(s)
- Chi Zhang
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Current address, Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts
| |
Collapse
|
12
|
Colombini M, Pasierbek P, Masselink W. A safe and reusable imaging chamber compatible with organic solvents. ACTA ACUST UNITED AC 2021; 69:321-323. [PMID: 32332999 DOI: 10.1093/jmicro/dfaa020] [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: 03/05/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/12/2022]
Abstract
High refractive index organic solvents are commonly used as an imaging medium in tissue clearing approaches. While effective, such solvents provide serious concerns for the safety of users and the equipment, especially in a central microscopy unit. To overcome these concerns, we have developed a large and reusable imaging chamber compatible with the universal mounting frame AK (PeCon GmbH). This chamber is easy to assemble and significantly improves the working environment in a central microscopy unit, where hazardous chemicals could negatively affect equipment and people. To encourage the uptake of these chambers, the design is made publicly available for download.
Collapse
Affiliation(s)
- Martin Colombini
- Research Institute of Molecular Pathology, Vienna BioCenter, Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wouter Masselink
- Research Institute of Molecular Pathology, Vienna BioCenter, Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| |
Collapse
|
13
|
Imoto A, Yamada M, Sakamoto T, Okuyama A, Ishida T, Sawa S, Aida M. A ClearSee-Based Clearing Protocol for 3D Visualization of Arabidopsis thaliana Embryos. Plants (Basel) 2021; 10:190. [PMID: 33498275 DOI: 10.3390/plants10020190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 11/17/2022]
Abstract
Tissue clearing methods combined with confocal microscopy have been widely used for studying developmental biology. In plants, ClearSee is a reliable clearing method that is applicable to a wide range of tissues and is suitable for gene expression analysis using fluorescent reporters, but its application to the Arabidopsis thaliana embryo, a model system to study morphogenesis and pattern formation, has not been described in the original literature. Here, we describe a ClearSee-based clearing protocol which is suitable for obtaining 3D images of Arabidopsis thaliana embryos. The method consists of embryo dissection, fixation, washing, clearing, and cell wall staining and enables high-quality 3D imaging of embryo morphology and expression of fluorescent reporters with the cellular resolution. Our protocol provides a reliable method that is applicable to the analysis of morphogenesis and gene expression patterns in Arabidopsis thaliana embryos.
Collapse
|
14
|
Masselink W, Tanaka EM. Toward whole tissue imaging of axolotl regeneration. Dev Dyn 2020; 250:800-806. [PMID: 33336514 PMCID: PMC8247021 DOI: 10.1002/dvdy.282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
The axolotl is a highly regenerative organism and has been studied in laboratories for over 150 years. Despite a long‐standing fascination with regeneration in general and axolotl specifically, we are still scratching the surface trying to visualize and understand the complex cellular behavior that underlies axolotl regeneration. In this review, we will discuss the progress that has been made in visualizing these processes focusing on four major aspects: cell labeling approaches, the removal of pigmentation, reductionist approaches to perform live cell imaging, and finally recent developments applying tissue clearing strategies to visualize the processes that underly regeneration. We also provide several suggestions that the community could consider exploring, notably the generation of novel alleles that further reduce pigmentation as well as improvements in tissue clearing strategies. Historical perspective on axolotl imaging and lineage tracing Description of tissue clearing approaches Refractive index matching strategies Strategies to further reduce pigmentation in axolotl
Collapse
Affiliation(s)
- Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BiocCenter (VBC), Vienna, Austria
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BiocCenter (VBC), Vienna, Austria
| |
Collapse
|
15
|
Lallemant L, Lebreton C, Garfa-Traoré M. Comparison of different clearing and acquisition methods for 3D imaging of murine intestinal organoids. J Biol Methods 2020; 7:e141. [PMID: 33564693 PMCID: PMC7865078 DOI: 10.14440/jbm.2020.334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 01/17/2023] Open
Abstract
An organoid is a three-dimensional multicellular structure that shows realistic micro-anatomy of an organ. This in vitro model mimics the in vivo environment, architecture and multi-lineage differentiation of the original organs and allows to answer many interesting biological questions. For these reasons, they are widely used in stem cell, regenerative medicine, toxicology, pharmacology, and host-microbe interactions research. In order to study organoids, microscopy is very useful: It is possible to make three-dimensional reconstruction of serial sections but it is time consuming and error-prone. Here we propose an alternative solution: Tissue clearing reduces the dispersion of light because it homogenizes the refractive index of the tissue, allowing sample observation throughout its thickness. We have compared different clearing techniques on mouse intestinal organoids using different acquisition methods.
Collapse
Affiliation(s)
- Louison Lallemant
- Cell Imaging Platform, INSERM-US24-CNRS UMS 3633 Structure Fédérative de Recherche Necker, Paris University, Paris 75015, France
| | - Corinne Lebreton
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR1163, Paris 75015, France
| | - Meriem Garfa-Traoré
- Cell Imaging Platform, INSERM-US24-CNRS UMS 3633 Structure Fédérative de Recherche Necker, Paris University, Paris 75015, France
| |
Collapse
|
16
|
Steinberg E, Orehov N, Tischenko K, Schwob O, Zamir G, Hubert A, Manevitch Z, Benny O. Rapid Clearing for High Resolution 3D Imaging of Ex Vivo Pancreatic Cancer Spheroids. Int J Mol Sci 2020; 21:E7703. [PMID: 33081011 PMCID: PMC7589457 DOI: 10.3390/ijms21207703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/25/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
The currently accepted imaging methods have been a central hurdle to imaging the finer details of tumor behavior in three-dimensional (3D) ex vivo multicellular culture models. In our search for an improved way of imaging tumor behavior in its physiological-like niche, we developed a simple, efficient, and straightforward procedure using standard reagents and imaging equipment that significantly enhanced 3D imaging up to a ~200-micron depth. We tested its efficacy on pancreatic spheroids, prototypes of high-density tissues that are difficult to image. We found we could both save time with this method and extract information about pancreatic tumor spheroids that previously was difficult to obtain. We were able to discern clear differences in the organization of pancreatic tumor spheroids generated from different origins, suggesting cell-specific, inherent, bottom-up organization with a correlation to the level of malignancy. We also examined the dynamic changes in the spheroids at predetermined time points, providing important information related to tissue morphogenesis and its metabolic state. Lastly, this process enabled us to assess a drug vehicle's potential to penetrate dense tumor tissue by improving our view of the inert particles' diffusion in the 3D spheroid. This clearing method, a simple procedure, can open the door to more accurate imaging and reveal more about cancer behavior.
Collapse
Affiliation(s)
- Eliana Steinberg
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.S.); (N.O.); (K.T.); (O.S.)
| | - Natalie Orehov
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.S.); (N.O.); (K.T.); (O.S.)
| | - Katerina Tischenko
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.S.); (N.O.); (K.T.); (O.S.)
| | - Ouri Schwob
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.S.); (N.O.); (K.T.); (O.S.)
| | - Gideon Zamir
- Department of Surgery and Transplantation Unit, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 91120, Israel;
| | - Ayala Hubert
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 91120, Israel;
| | - Zakhariya Manevitch
- The Core Research Facility, The Hebrew University of Jerusalem, Jerusalem 91120, Israel;
| | - Ofra Benny
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.S.); (N.O.); (K.T.); (O.S.)
| |
Collapse
|
17
|
Gauch HL, Bisio V, Rossin S, Montomoli F, Tagarielli VL. Predictions of the transient loading on box-like objects by arbitrary pressure waves in air. Proc Math Phys Eng Sci 2019; 475:20190360. [PMID: 31611730 PMCID: PMC6784400 DOI: 10.1098/rspa.2019.0360] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/14/2019] [Indexed: 11/12/2022] Open
Abstract
This study investigates the transient loading on rigid, isolated, box-like objects by impinging pressure waves of variable intensity and time duration. A numerical solver is used to predict the transient flow around the object and the consequent pressure on the object's surface. An analytical model is developed which is capable of predicting the transient loading history on the faces of a box-like object; it was found in good agreement with the numerical predictions. The numerical and analytical models are then used to construct non-dimensional design maps. Different regimes of loading are identified and explored.
Collapse
Affiliation(s)
- H. L. Gauch
- Department of Aeronautics, Imperial College London, London SW7 2AZ, UK
| | - V. Bisio
- Baker Hughes, a GE company, Via Felice Matteucci 2, 50127 Firenze FI, Italy
| | - S. Rossin
- Baker Hughes, a GE company, Via Felice Matteucci 2, 50127 Firenze FI, Italy
| | - F. Montomoli
- Department of Aeronautics, Imperial College London, London SW7 2AZ, UK
| | - V. L. Tagarielli
- Department of Aeronautics, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
18
|
Lerch ML, Bauer DR, Theiss A, Chafin D, Otter M, Baird GS. Monitoring Dehydration and Clearing in Tissue Processing for High-Quality Clinical Pathology. Biopreserv Biobank 2019; 17:303-311. [PMID: 31107113 PMCID: PMC6703239 DOI: 10.1089/bio.2018.0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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] [Indexed: 01/20/2023] Open
Abstract
The development of precision testing for disease diagnosis has advanced medicine by specifically matching patients with drugs to treat specific diseases. High-quality diagnostics start with high-quality tissue specimens. The development and optimization of tissue handling and processing have lagged behind bioassay development. Ultrasound time-of-flight (TOF) technology has been successfully used to monitor the critical processing step of tissue fixation with formalin. In this study, we expand the use of this technology to monitor tissue dehydration and clearing by analyzing TOF signals from 270 different specimens, representing 13 different tissue types obtained through surgical resections. We determined the time constant τ90 for each tissue type for the following tissue processing solvents: 70% ethanol, 90% ethanol, 100% ethanol, and xylene. The TOF signals were correlated with tissue morphology to ensure that high-quality tissue was produced. Tissues can be grouped into those exhibiting fast and slow reagent diffusion. We monitored incomplete dehydration of tissue by skipping a key processing step, dehydration in absolute ethanol, and then correlated the τ90 with poor histomorphology, demonstrating that the technique can detect significant processing errors. Ultrasound TOF technology can therefore be used to monitor all phases of tissue processing cycle and yields an important preanalytical quality metric.
Collapse
Affiliation(s)
- Melissa L Lerch
- 1Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington
| | | | | | | | | | - Geoffrey S Baird
- 1Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington
| |
Collapse
|
19
|
Abstract
Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
Collapse
Affiliation(s)
- Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jennifer Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Kristin Overton
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA; .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.,H oward Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
20
|
Abstract
Multi-user core microscopy facilities are often faced with the challenge to adapt or modify existing instruments. This is essential in order to fulfill the requirements of the user community, who wants to image a wide range of model organisms with varying stains and sample thicknesses. In recent years, lightsheet microscopy has turned into an invaluable tool for both live and cleared sample imaging of many different specimens. This brought up new challenges in terms of sample mounting as the classical approach of attachment onto a coverslip cannot be universally applied. Here we describe the development of a diversified holder which extends the range of samples which can be imaged on a Zeiss Lightsheet microscope Z1. We focus on mounting strategies of cleared specimens; however, the holder and mounting strategy can be applied to live specimens too. The proposed methodology provides very high flexibility along with numerous possibilities for adaptation based on imaging specimen size, condition and available clearing reagents. Moreover, the described mounting strategies can be applied to other light sheet microscopes that can mount 1 mL syringes.
Collapse
Affiliation(s)
- Thierry Laroche
- Bioimaging and Optics Platform, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Olivier Burri
- Bioimaging and Optics Platform, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lalit Kumar Dubey
- Faculty of Biology and Medicine, Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Arne Seitz
- Bioimaging and Optics Platform, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
21
|
Dobkowski KA, Flanagan KD, Nordstrom JR. Factors influencing recruitment and appearance of bull kelp, Nereocystis luetkeana (phylum Ochrophyta). J Phycol 2019; 55:236-244. [PMID: 30565227 DOI: 10.1111/jpy.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/03/2017] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The dynamics of annual species are strongly tied to their capacity for recruitment each year. We examined how competition and propagule availability influence recruitment and appearance and tracked survivorship of an annual species of marine macroalgae, the bull kelp (Nereocystis luetkeana), which serves as major biogenic habitat in the Salish Sea of Washington State. We hypothesized that (i) juvenile N. luetkeana would exhibit a seasonal appearance as a cohort in the spring and (ii) competition for space would be more limiting than propagules (spores) to recruitment at sites adjacent to established N. luetkeana beds. We tagged N. luetkeana recruits in the field to track appearance and survivorship across seasons (spring, summer, fall, and winter), using a two-factor crossed design to assess effects of competition and propagule availability on appearance of new N. luetkeana sporophytes. Survivorship of N. luetkeana recruits was low and, whereas most new individuals arose in the spring, some appeared in every season. New N. luetkeana recruits also appeared the earliest (median 8 weeks vs. >20 weeks) after experimental "seeding" in the spring as compared to other seasons. Eliminating macroalgal competitors ("clearing") influenced the appearance of recruits more than enhancement of propagules in the spring. An improved understanding of factors regulating the seasonal appearance of new N. luetkeana sporophytes furthers our understanding of this crucial foundation species' appearance and persistence across seasons, which is increasingly important as global ocean conditions change, and highlights the importance of studying organisms with complex life histories across multiple stages and geographical regions.
Collapse
Affiliation(s)
- Katie A Dobkowski
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA
- Friday Harbor Laboratories, 620 University Rd, Friday Harbor, Washington, 98250, USA
| | - K Darby Flanagan
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA
- Friday Harbor Laboratories, 620 University Rd, Friday Harbor, Washington, 98250, USA
| | - Jessica R Nordstrom
- Friday Harbor Laboratories, 620 University Rd, Friday Harbor, Washington, 98250, USA
- Point Defiance Zoo and Aquarium, 5400 N Pearl St, Tacoma, Washington, 98407, USA
| |
Collapse
|
22
|
Cabrera J, Olmo R, Ruiz-Ferrer V, Abreu I, Hermans C, Martinez-Argudo I, Fenoll C, Escobar C. A Phenotyping Method of Giant Cells from Root-Knot Nematode Feeding Sites by Confocal Microscopy Highlights a Role for CHITINASE-LIKE 1 in Arabidopsis. Int J Mol Sci 2018; 19:E429. [PMID: 29389847 DOI: 10.3390/ijms19020429] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 12/21/2017] [Revised: 01/19/2018] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
Most effective nematicides for the control of root-knot nematodes are banned, which demands a better understanding of the plant-nematode interaction. Understanding how gene expression in the nematode-feeding sites relates to morphological features may assist a better characterization of the interaction. However, nematode-induced galls resulting from cell-proliferation and hypertrophy hinders such observation, which would require tissue sectioning or clearing. We demonstrate that a method based on the green auto-fluorescence produced by glutaraldehyde and the tissue-clearing properties of benzyl-alcohol/benzyl-benzoate preserves the structure of the nematode-feeding sites and the plant-nematode interface with unprecedented resolution quality. This allowed us to obtain detailed measurements of the giant cells’ area in an Arabidopsis line overexpressing CHITINASE-LIKE-1 (CTL1) from optical sections by confocal microscopy, assigning a role for CTL1 and adding essential data to the scarce information of the role of gene repression in giant cells. Furthermore, subcellular structures and features of the nematodes body and tissues from thick organs formed after different biotic interactions, i.e., galls, syncytia, and nodules, were clearly distinguished without embedding or sectioning in different plant species (Arabidopsis, cucumber or Medicago). The combination of this method with molecular studies will be valuable for a better understanding of the plant-biotic interactions.
Collapse
|
23
|
Bray ER, Noga M, Thakor K, Wang Y, Lemmon VP, Park KK, Tsoulfas P. 3D Visualization of Individual Regenerating Retinal Ganglion Cell Axons Reveals Surprisingly Complex Growth Paths. eNeuro 2017; 4:ENEURO. [PMID: 28856242 DOI: 10.1523/ENEURO.0093-17.2017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 03/20/2017] [Revised: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 01/28/2023] Open
Abstract
Retinal ganglion cells (RGCs), the sole output cells of the retina, are a heterogeneous population of neurons that project axons to visual targets in the brain. Like most CNS neurons, RGCs are considered incapable of mounting long distance axon regeneration. Using immunolabeling-enabled 3D imaging of solvent-cleared organs (iDISCO) in transgenic mice, we tracked the entire paths of individual RGC axons and show that adult RGCs are highly capable of spontaneous long-distance regeneration, even without any treatment. Our results show that the Thy1-H-YFP mouse sparsely labels RGCs, consisting predominantly of regeneration-competent α-type RGCs (αRGCs). Following optic nerve crush, many of the YFP-labeled RGC axons extend considerable distances proximal to the injury site with only a few penetrating through the lesion. This tortuous axon growth proximal to the lesion site is even more striking with intravitreal ciliary neurotrophic factor (CNTF) treatment. We further demonstrate that despite traveling more than 5 mm (i.e., a distance equal to the length of mouse optic nerve), many of these circuitous axons are confined to the injury area and fail to reach the brain. Our results re-evaluate the view that RGCs are naturally incapable of re-extending long axons, and shift the focus from promoting axon elongation, to understanding factors that prevent direct growth of axons through the lesion and the injured nerve.
Collapse
|
24
|
Lindsey BW, Kaslin J. Optical Projection Tomography as a Novel Method to Visualize and Quantitate Whole-Brain Patterns of Cell Proliferation in the Adult Zebrafish Brain. Zebrafish 2017; 14:574-577. [PMID: 28296621 DOI: 10.1089/zeb.2017.1418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 12/11/2022] Open
Abstract
How distinct cell populations are distributed in three-dimensional space under homeostasis or following injury, neurodegeneration, or with senescence can teach us much about brain-wide patterns and signaling along the neuroaxis. Visualizing individual cell populations in the mature vertebrate central nervous system (CNS) has remained a challenge as a result of difficulty clearing adult brain tissue or limitations in imaging depth or resolution. We have developed a simple clearing and imaging pipeline optimally suited for the adult zebrafish brain to investigate changes in patterns of cell proliferation in wild-type and transgenic backgrounds that can easily be quantified and represented using FIJI and IMARIS software.
Collapse
Affiliation(s)
- Benjamin W Lindsey
- Australian Regenerative Medicine Institute, Monash University , Clayton, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University , Clayton, Australia
| |
Collapse
|
25
|
Chovsepian A, Empl L, Correa D, Bareyre FM. Heterotopic Transcallosal Projections Are Present throughout the Mouse Cortex. Front Cell Neurosci 2017; 11:36. [PMID: 28270750 PMCID: PMC5318386 DOI: 10.3389/fncel.2017.00036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 12/11/2016] [Accepted: 02/06/2017] [Indexed: 11/13/2022] Open
Abstract
Transcallosal projection neurons are a population of pyramidal excitatory neurons located in layers II/III and to a lesser extent layer V of the cortex. Their axons form the corpus callosum thereby providing an inter-hemispheric connection in the brain. While transcallosal projection neurons have been described in some detail before, it is so far unclear whether they are uniformly organized throughout the cortex or whether different functional regions of the cortex contain distinct adaptations of their transcallosal connectivity. To address this question, we have therefore conducted a systematic analysis of transcallosal projection neurons and their axons across six distinct stereotactic coordinates in the mouse cortex that cover different areas of the motor and somatosensory cortices. Using anterograde and retrograde tracing techniques, we found that in agreement with previous studies, most of the transcallosal projections show a precise homotopic organization. The somata of these neurons are predominantly located in layer II/III and layer V but notably smaller numbers of these cells are also found in layer IV and layer VI. In addition, regional differences in the distribution of their somata and the precision of their projections exist indicating that while transcallosal neurons show a uniform organization throughout the mouse cortex, there is a sizeable fraction of these connections that are heterotopic. Our study thus provides a comprehensive characterization of transcallosal connectivity in different cortical areas that can serve as the basis for further investigations of the establishment of inter-hemispheric projections in development and their alterations in disease.
Collapse
Affiliation(s)
- Alexandra Chovsepian
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians Universität München Munich, Germany
| | - Laura Empl
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians Universität München Munich, Germany
| | - Daphne Correa
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians Universität München Munich, Germany
| | - Florence M Bareyre
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians Universität MünchenMunich, Germany; Munich Cluster of System Neurology (SyNergy), Ludwig-Maximilians Universität MünchenMunich, Germany
| |
Collapse
|
26
|
Koay JB, Natasya NN, Nashithatul M, Ihsanuddin R, Salleh FM, Azil AH. Using wintergreen oil for mounting mosquito larvae: a safer alternative to xylene. Biotech Histochem 2015; 91:63-70. [PMID: 26528914 DOI: 10.3109/10520295.2015.1074286] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Permanent mounting of fourth instar mosquito larvae is essential for identifying Aedes spp. This procedure requires extensive exposure to xylene, a clearing agent in the mounting process. We investigated wintergreen oil as a substitute for xylene. Five hundred larvae were mounted on slides to evaluate shrinkage or expansion of specimens after clearing using xylene or wintergreen oil. We examined the ventral brush and siphonal hair tufts for species identification and for preservation of morphological characteristics after clearing specimens in xylene or wintergreen oil. Shrinkage of the length of whole larvae and width of the head, thorax and abdomen after mounting was significantly greater after clearing with xylene than with wintergreen oil. The length of the comb scale nearest the ventral brush was similar for both clearing agents. The clarity of the specimens after mounting was improved by clearing with wintergreen oil, but the integrity of the ventral brush and siphonal hair tufts were similar for both clearing agents.
Collapse
Affiliation(s)
- J B Koay
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| | - N N Natasya
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| | - Mag Nashithatul
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| | - R Ihsanuddin
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| | - F M Salleh
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| | - A H Azil
- a Department of Parasitology and Medical Entomology , Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center , Kuala Lumpur , Malaysia
| |
Collapse
|
27
|
Kabadi PK, Vantangoli MM, Rodd AL, Leary E, Madnick SJ, Morgan JR, Kane A, Boekelheide K. Into the depths: Techniques for in vitro three-dimensional microtissue visualization. Biotechniques 2015; 59:279-86. [PMID: 26554505 DOI: 10.2144/000114353] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/31/2015] [Indexed: 01/28/2023] Open
Abstract
Three-dimensional (3-D) in vitro platforms have been shown to closely recapitulate human physiology when compared with conventional two-dimensional (2-D) in vitro or in vivo animal model systems. This confers a substantial advantage in evaluating disease mechanisms, pharmaceutical drug discovery, and toxicity testing. Despite the benefits of 3-D cell culture, limitations in visualization and imaging of 3-D microtissues present significant challenges. Here we optimized histology and microscopy techniques to overcome the constraints of 3-D imaging. For morphological assessment of 3-D microtissues of several cell types, different time points, and different sizes, a two-step glycol methacrylate embedding protocol for evaluating 3-D microtissues produced using agarose hydrogels improved resolution of nuclear and cellular histopathology characteristic of cell death and proliferation. Additional immunohistochemistry, immunofluorescence, and in situ immunostaining techniques were successfully adapted to these microtissues and enhanced by optical clearing. Utilizing the Clear(T2) protocol greatly increased fluorescence signal intensity, imaging depth, and clarity, allowing for more complete confocal fluorescence microscopy imaging of these 3-D microtissues compared with uncleared samples. The refined techniques presented here address the key challenges associated with 3-D imaging, providing new and alternative methods in evaluating disease pathogenesis, delineating toxicity pathways, and enhancing the versatility of 3-D in vitro testing systems in pharmacological and toxicological applications.
Collapse
|
28
|
Liu CY, Dubé PE, Girish N, Reddy AT, Polk DB. Optical reconstruction of murine colorectal mucosa at cellular resolution. Am J Physiol Gastrointest Liver Physiol 2015; 308:G721-35. [PMID: 25721303 PMCID: PMC4421015 DOI: 10.1152/ajpgi.00310.2014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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] [Received: 08/15/2014] [Accepted: 02/18/2015] [Indexed: 02/07/2023]
Abstract
The mucosal layer of the colon is a unique and dynamic site where host cells interface with one another and the microbiome, with major implications for physiology and disease. However, the cellular mechanisms mediating colonic regeneration, inflammation, dysplasia, and dysbiosis remain undercharacterized, partly because the use of thin tissue sections in many studies removes important volumetric context. To address these challenges in visualization, we have developed the deep mucosal imaging (DMI) method to reconstruct continuous extended volumes of mouse colorectal mucosa at cellular resolution. Use of ScaleA2 and SeeDB clearing agents enabled full visualization of the colonic crypt, the fundamental unit of adult colon. Confocal imaging of large colorectal expanses revealed epithelial structures involved in repair, inflammation, tumorigenesis, and stem cell function, in fluorescent protein-labeled, immunostained, paraffin-embedded, or human biopsy samples. We provide freely available software to reconstruct and explore on computers with standard memory allocations the large DMI datasets containing in toto representations of distal colonic mucosal volume. Extended-volume imaging of colonic mucosa through the novel, extensible, and readily adopted DMI approach will expedite mechanistic investigations of intestinal physiology and pathophysiology at intracrypt to multicrypt length scales.
Collapse
Affiliation(s)
- Cambrian Y. Liu
- 1The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; ,2Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Philip E. Dubé
- 1The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; ,2Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Nandini Girish
- 1The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; ,2Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Ajay T. Reddy
- 1The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; ,2Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - D. Brent Polk
- 1The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; ,2Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California; and ,3Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California
| |
Collapse
|
29
|
Decroix L, Van Muylder V, Desender L, Sampaolesi M, Thorrez L. Tissue clearing for confocal imaging of native and bio-artificial skeletal muscle. Biotech Histochem 2015; 90:424-31. [PMID: 25893542 DOI: 10.3109/10520295.2015.1019564] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 11/13/2022] Open
Abstract
Novel clearing techniques have revolutionized three-dimensional confocal imaging of the brain without the need for physical tissue sectioning. We evaluated three clearing methods, ScaleA2, Clear(T2), and 3DISCO for visualizing native and tissue engineered muscle by confocal microscopy. We found that Clear(T2) treatment improved the depth of visualization of immunohistochemical staining slightly, but did not improve depth of visualization of endogenous green fluorescent protein (GFP). ScaleA2 preserved endogenous GFP signal better and permitted significantly deeper GFP imaging, but it was incompatible with tropomyosin immunohistochemical staining. 3DISCO treatment preserved both endogenous GFP and immunohistochemical staining, and permitted significantly deeper imaging. Clearing time for the 3DISCO procedure is short compared to ScaleA2 and Clear(T2). We suggest that 3DISCO is the preferable clearing method for native and tissue engineered skeletal muscle tissue.
Collapse
Affiliation(s)
- L Decroix
- Tissue Engineering Lab, Department of Development and Regeneration , KU Leuven campus Kulak, Kortrijk
| | | | | | | | | |
Collapse
|
30
|
Scott GD, Blum ED, Fryer AD, Jacoby DB. Tissue optical clearing, three-dimensional imaging, and computer morphometry in whole mouse lungs and human airways. Am J Respir Cell Mol Biol 2014; 51:43-55. [PMID: 24471696 DOI: 10.1165/rcmb.2013-0284oc] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In whole adult mouse lung, full identification of airway nerves (or other cellular/subcellular objects) has not been possible due to patchy distribution and micron-scale size. Here we describe a method using tissue clearing to acquire the first complete image of three-dimensional (3D) innervation in the lung. We then created a method to pair analysis of nerve (or any other colabeled epitope) images with identification of 3D tissue compartments and airway morphometry by using fluorescent casting and morphometry software (which we designed and are making available as open-source). We then tested our method to quantify a sparse heterogeneous nerve population by examining visceral pleural nerves. Finally, we demonstrate the utility of our method in human tissue to image full thickness innervation in irregular 3D tissue compartments and to quantify sparse objects (intrinsic airway ganglia). Overall, this method can uniquely pair the advantages of whole tissue imaging and cellular/subcellular fluorescence microscopy.
Collapse
Affiliation(s)
- Gregory D Scott
- Division of Pulmonary and Critical Care, Oregon Health and Sciences University, Portland, Oregon
| | | | | | | |
Collapse
|
31
|
Indu S, Ramesh V, Indu PC, Prashad KV, Premalatha B, Ramadoss K. Comparative efficacy of cedarwood oil and xylene in hematoxylin and eosin staining procedures: An experimental study. J Nat Sci Biol Med 2014; 5:284-7. [PMID: 25097399 PMCID: PMC4121899 DOI: 10.4103/0976-9668.136167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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] [Indexed: 11/09/2022] Open
Abstract
Background: Xylene is used as a clearing agent in hematoxylin and eosin (H and E) staining of tissue sections in routine histopathology based diagnosis. However, the hazards associated with exposure to xylene are of concern. Numerous solutions mainly essential oils have been evaluated in the past as clearing agents, which can possibly be substituted for xylene during the routine tissue processing. Aim: The aim of this study is to compare the efficacy of essential oil (cedarwood oil), as a possible replacement for xylene in H and E staining procedures. Materials and Methods: The study was carried out in the Department of Oral Pathology and Microbiology. Thirty paraffin blocks of the routine biopsy specimen were retrieved from the department archives. The cedarwood oil was procured from organic and essential oil dealer in the local market. Two to three paraffin sections of four micron thickness were cut from each of the 30 paraffin blocks of processed tissue specimens, were subjected to different clearing agents: Essential oil (8% cedarwood oil) or xylene and stained with H and E stain. The stained sections were scored based on nuclear and cytoplasmic details, clarity and uniformity of staining. Results: Significant correlation was observed between cedarwood oil and xylene in terms of the three staining quality parameters assessed. Conclusions: We conclude that cedarwood oil can be an effective, eco-friendly and safe alternative to xylene as a clearing agent in the histopathological laboratory.
Collapse
Affiliation(s)
- Sudip Indu
- Department of Oral Pathology and Microbiology, Mahatma Gandhi Post Graduate Institute of Dental Sciences, Puducherry, India
| | - V Ramesh
- Department of Oral Pathology and Microbiology, Mahatma Gandhi Post Graduate Institute of Dental Sciences, Puducherry, India
| | | | - Karthikshree V Prashad
- Department of Oral Pathology and Microbiology, Mahatma Gandhi Post Graduate Institute of Dental Sciences, Puducherry, India
| | - B Premalatha
- Department of Oral Pathology and Microbiology, Mahatma Gandhi Post Graduate Institute of Dental Sciences, Puducherry, India
| | - K Ramadoss
- Department of Oral Pathology and Microbiology, Mahatma Gandhi Post Graduate Institute of Dental Sciences, Puducherry, India
| |
Collapse
|
32
|
Villani TS, Koroch AR, Simon JE. An improved clearing and mounting solution to replace chloral hydrate in microscopic applications. Appl Plant Sci 2013; 1:apps1300016. [PMID: 25202549 PMCID: PMC4105042 DOI: 10.3732/apps.1300016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/22/2013] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY This study presents Visikol™, a new proprietary formulation that can be used as an efficient replacement for chloral hydrate as a clearing agent for microscopic examination. In the United States, chloral hydrate is regulated and therefore difficult to acquire. • METHODS AND RESULTS Fresh and dry samples of the following plants: ginger (Zingiber officinale), maté (Ilex paraguariensis), lime basil (Ocimum americanum), oregano (Origanum vulgare), and mouse-ear cress (Arabidopsis thaliana), were cleared using Visikol or chloral hydrate solution and compared using a light microscope. • CONCLUSIONS This new method can be used successfully to clear specimens, allowing identification of diagnostic characteristics for the identification of plant materials. Visikol is as effective as chloral hydrate in providing clarity and resolution of all tissues examined. Tissues become transparent, allowing observation of deeper layers of cells and making it effective in research, botanical and quality control, and for educational applications.
Collapse
Affiliation(s)
- Thomas S. Villani
- New Use Agriculture and Natural Plant Products Program, School of Environmental and Biological Sciences, and the New Jersey Agricultural Experiment Station (NJAES), Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901 USA
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, New Jersey 08854 USA
| | - Adolfina R. Koroch
- Science Department, City University of New York, Borough of Manhattan Community College, 199 Chambers Street, New York, New York 10007 USA
| | - James E. Simon
- New Use Agriculture and Natural Plant Products Program, School of Environmental and Biological Sciences, and the New Jersey Agricultural Experiment Station (NJAES), Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901 USA
- Author for correspondence:
| |
Collapse
|
33
|
Morawetz JJ. A clearing protocol for whole tissues: An example using haustoria of Orobanchaceae. Appl Plant Sci 2013; 1:apps1200361. [PMID: 25202483 PMCID: PMC4105356 DOI: 10.3732/apps.1200361] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/17/2012] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Due to lack of success in clearing whole tissues using only classical clearing techniques (e.g., Herr's 4½ solution, KOH, NaOH, lactic acid saturated with chloral hydrate), and because tissue degradation is often a result of harsh clearing agents (e.g., KOH, NaOH), a novel combined treatment was sought to improve the removal of obscuring tannins from intact haustoria. • METHODS AND RESULTS Stockwell's bleach proved to be useful in removing tannins from haustoria, usually within 3 d (up to 10 d), rendering them opaque to (rarely) translucent. After bleaching, haustoria were successfully cleared in 1-3 d in a solution of lactic acid saturated with chloral hydrate at 42°C. • CONCLUSIONS The two-step clearing protocol reported here will now facilitate structural studies on haustoria, such as those examining the presence and distribution of callose, and three-dimensional reconstruction using confocal microscopy. Tissues in this study did not suffer from the degradation in quality observed using harsher treatments. This protocol should be useful for other difficult-to-clear tissues that are unable to be cleared using classical protocols alone.
Collapse
Affiliation(s)
- Jeffery J. Morawetz
- Rancho Santa Ana Botanic Garden, 1500 N. College Avenue, Claremont, California 91711 USA
| |
Collapse
|
34
|
Clendenon SG, Young PA, Ferkowicz M, Phillips C, Dunn KW. Deep tissue fluorescent imaging in scattering specimens using confocal microscopy. Microsc Microanal 2011; 17:614-617. [PMID: 21729357 PMCID: PMC4428593 DOI: 10.1017/s1431927611000535] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [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] [Indexed: 05/31/2023]
Abstract
In scattering specimens, multiphoton excitation and nondescanned detection improve imaging depth by a factor of 2 or more over confocal microscopy; however, imaging depth is still limited by scattering. We applied the concept of clearing to deep tissue imaging of highly scattering specimens. Clearing is a remarkably effective approach to improving image quality at depth using either confocal or multiphoton microscopy. Tissue clearing appears to eliminate the need for multiphoton excitation for deep tissue imaging.
Collapse
Affiliation(s)
- Sherry G Clendenon
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, IN 46202, USA.
| | | | | | | | | |
Collapse
|
35
|
Oldham M, Sakhalkar H, Oliver T, Allan Johnson G, Dewhirst M. Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography. J Biomed Opt 2008; 13:021113. [PMID: 18465962 PMCID: PMC2746042 DOI: 10.1117/1.2907968] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [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] [Indexed: 05/18/2023]
Abstract
Optical computed tomography (optical-CT) and optical emission computed tomography (optical-ECT) are new techniques that enable unprecedented high-resolution 3-D multimodal imaging of tissue structure and function. Applications include imaging macroscopic gene expression and microvasculature structure in unsectioned biological specimens up to 8 cm(3). A key requisite for these imaging techniques is effective sample preparation including optical clearing, which enables light transport through the sample while preserving the signal (either light absorbing stain or fluorescent proteins) in representative form. We review recent developments in optical-CT and optical-ECT, and compatible "fluorescence-friendly" optical clearing protocols.
Collapse
Affiliation(s)
- Mark Oldham
- Duke University Medical Center, Department of Radiation Oncology, Durham, North Carolina 27710, USA.
| | | | | | | | | |
Collapse
|
36
|
Rahimi S, Shahi S, Yavari HR, Manafi H, Eskandarzadeh N. Root canal configuration of mandibular first and second premolars in an Iranian population. J Dent Res Dent Clin Dent Prospects 2007; 1:59-64. [PMID: 23277835 PMCID: PMC3525926 DOI: 10.5681/joddd.2007.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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: 06/19/2007] [Accepted: 09/01/2007] [Indexed: 11/17/2022] Open
Abstract
Background and aims
It is critical to have a proper knowledge of the normal anatomy of the pulp and its variations for the success of endodontic treatment. The aim of this study was to determine the canal configuration and the prevalence of C-shaped canals in mandibular first and second premolars in a North-Western Iranian population.
Materials and methods
A total of 163 extracted mandibular first and 103 mandibular second premolars were injected with India ink and demineralized . They were made clear and transparent with methyl salicylate and the anatomy of their canal(s) was studied.
Results
The results showed that 98% of mandibular first premolars had one root, 2% had two roots, 70.6% had one canal, 27.8% had two canals, 1.2% had three canals and the prevalence of C-shaped canals was 2.4%. All mandibular second premolars had one root, 80.5% had one canal, 17.5% had two canals and the prevalence of C-shaped canals was 2%.
Conclusion It is important that clinicians, before treatment of mandibular first and second premolars, pay complete attention to radiographs, have a true concept of the number of root(s) and canal(s), and prepare a correct access cavitiy.
Collapse
Affiliation(s)
- Saeed Rahimi
- Associate Professor, Department of Endodontics, Faculty of Dentistry, Tabriz University of Medical Sciences, Iran
| | | | | | | | | |
Collapse
|
37
|
LUX ALEXANDER, MORITA SHIGENORI, ABE JUN, ITO KAORI. An improved method for clearing and staining free-hand sections and whole-mount samples. Ann Bot 2005; 96:989-96. [PMID: 16192293 PMCID: PMC4247103 DOI: 10.1093/aob/mci266] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [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: 03/17/2005] [Revised: 05/25/2005] [Accepted: 08/10/2005] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Free-hand sectioning of living plant tissues allows fast microscopic observation of internal structures. The aim of this study was to improve the quality of preparations from roots with suberized cell walls. A whole-mount procedure that enables visualization of exo- and endodermal cells along the root axis was also established. METHODS Free-hand sections were cleared with lactic acid saturated with chloral hydrate, and observed with or without post-staining in toluidine blue O or aniline blue. Both white light and UV light were used for observation. Lactic acid was also used as a solvent for berberine, and fluorol yellow for clearing and staining the samples used for suberin observation. This procedure was also applied to whole-mount roots with suberized celllayers. KEY RESULTS Clearing of sections results in good image quality to observe the tissue structure and cell walls compared with non-cleared sections. The use of lactic acid as a solvent for fluorol yellow proved superior to previously used solvents such as polyethylene glycol-glycerol. Clearing and fluorescence staining of thin roots such as those of Arabidopsis thaliana were successful for suberin visualization in endodermal cells within whole-mount roots. For thicker roots, such as those of maize, sorghum or tea, this procedure could be used for visualizing the exodermis in a longitudinal view. Clearing and staining of peeled maize root segments enabled observation of endodermal cell walls. CONCLUSIONS The clearing procedure using lactic acid improves the quality of images from free-hand sections and clearings. This method enhances the study of plant root anatomy, in particular the histological development and changes of cell walls, when used in combination with fluorescence microscopy.
Collapse
Affiliation(s)
- ALEXANDER LUX
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina B-2,SK—842 15 Bratislava, Slovak Republic
| | - SHIGENORI MORITA
- Field Production Science Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - JUN ABE
- AE-Bio, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - KAORI ITO
- Field Production Science Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| |
Collapse
|