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Poteaux P, Ripoll C, Sarrazin A, Blanchard MP, Guillou-Duvoid A, Gourbal B, Hirbec H, Duval D. Breaking Biomphalaria black box by in situ revelation of fluorescent Schistosoma mansoni parasites. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109800. [PMID: 39096981 DOI: 10.1016/j.fsi.2024.109800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Tissue clearing is an old-fashioned method developed in the 1900's and used to turn an opaque biological object into a 3D visualizable transparent structure. Developed and diversified over the last decade, this method is most of the time applied to mammals' tissues, and especially mouse and human tissues for cytological, histological and pathophysiological studies. Through autofluorescence, immunofluorescence, in situ hybridization, intercalating agents, fluorescent transfection markers or fluorescent particle uptake, optically cleared samples can be monitored to discover new biological structures and cellular interactions through 3D-visualization, which can be more challenging in some extend through classical histological methods. Most of the tissue clearing procedures have been developed for specific applications like endogenous fluorescence visualization, immunolabeling or for revealing specific organs. Thus, choosing the adapted protocol may be empirical for non-model species, especially for mollusks for which very little related literature is available. Herein, we suggest an effective optical tissue clearing procedure for the freshwater snail Biomphalaria glabrata, known as the intermediate host of the human parasite Schistosoma mansoni. This clearing procedure involves solvents with a minimal toxicity, preserves the endogenous fluorescence of labeled parasites inside snail tissues and is compatible with an immunolabeling procedure.
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Affiliation(s)
- Pierre Poteaux
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, 58 avenue Paul Alduy, 66860, Perpignan, France.
| | - Chantal Ripoll
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Amélie Sarrazin
- MRI, BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Marie-Pierre Blanchard
- MRI, BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Anne Guillou-Duvoid
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Benjamin Gourbal
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, 58 avenue Paul Alduy, 66860, Perpignan, France
| | - Hélène Hirbec
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - David Duval
- IHPE, Université de Perpignan Via Domitia, CNRS, Ifremer, Université de Montpellier, 58 avenue Paul Alduy, 66860, Perpignan, France
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2
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Tait CC, Ramirez MD, Katz PS. Egg-laying hormone expression in identified neurons across developmental stages and reproductive states of the nudibranch Berghia stephanieae. Horm Behav 2024; 164:105578. [PMID: 38925074 PMCID: PMC11330727 DOI: 10.1016/j.yhbeh.2024.105578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Neuropeptides play essential roles in coordinating reproduction. Egg-laying hormone (ELH) is conserved in genetic sequence and behavioral function across molluscs, where neuronal clusters secrete ELH to modulate and induce egg-laying. Here we investigated ELH in the nudibranch mollusc, Berghia stephanieae. ELH preprohormone gene orthologs, which showed clade-specific differences at the C-terminus of the predicted bioactive peptide, were identified in brain transcriptomes across several nudipleuran species, including B. stephanieae. ELH shares deep homology with the corticotropin-releasing hormone gene family, which has roles broadly in stress response. Injection of synthesized B. stephanieae ELH peptide into mature individuals induced egg-laying. ELH gene expression in the brain and body was mapped using in-situ hybridization chain reaction. Across the adult brain, 300-400 neurons expressed ELH. Twenty-one different cell types were identified in adults, three of which were located unilaterally on the right side, which corresponds to the location of the reproductive organs. Ten cell types were present in pre-reproductive juvenile stages. An asymmetric cluster of approximately 100 small neurons appeared in the right pedal ganglion of late-stage juveniles. Additional neurons in the pleural and pedal ganglia expressed ELH only in adults that were actively laying eggs and sub-adults that were on the verge of doing so, implicating their direct role in reproduction. Outside the brain, ELH was expressed on sensory appendages, including in presumptive sensory neurons. Its widespread expression in the nudibranch B. stephanieae suggests that ELH plays a role beyond reproduction in gastropod molluscs.
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Affiliation(s)
- Cheyenne C Tait
- Department of Biology, University of Massachusetts Amherst, United States of America.
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, United States of America
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, United States of America; Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, United States of America
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3
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Kuo DH, Szczupak L, Weisblat DA, Portiansky EL, Winchell CJ, Lee JR, Tsai FY. Transgenesis enables mapping of segmental ganglia in the leech Helobdella austinensis. J Exp Biol 2024; 227:jeb247419. [PMID: 38940760 DOI: 10.1242/jeb.247419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
The analysis of how neural circuits function in individuals and change during evolution is simplified by the existence of neurons identified as homologous within and across species. Invertebrates, including leeches, have been used for these purposes in part because their nervous systems comprise a high proportion of identified neurons, but technical limitations make it challenging to assess the full extent to which assumptions of stereotypy hold true. Here, we introduce Minos plasmid-mediated transgenesis as a tool for introducing transgenes into the embryos of the leech Helobdella austinensis (Spiralia; Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae). We identified an enhancer driving pan-neuronal expression of markers, including histone2B:mCherry, which allowed us to enumerate neurons in segmental ganglia. Unexpectedly, we found that the segmental ganglia of adult transgenic H. austinensis contain fewer and more variable numbers of neurons than in previously examined leech species.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
- Museum of Zoology, National Taiwan University, Taipei, Taiwan106
| | - Lidia Szczupak
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBYNE UBA-CONICET, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - David A Weisblat
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Enrique L Portiansky
- Laboratory of Image Analysis, School of Veterinary Sciences, National University of La Plata, CONICET, B1900 La Plata, Argentina
| | - Christopher J Winchell
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jun-Ru Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
| | - Fu-Yu Tsai
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
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Clarke DN, Formery L, Lowe CJ. See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates. EvoDevo 2024; 15:8. [PMID: 38918798 PMCID: PMC11201320 DOI: 10.1186/s13227-024-00228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Studies of morphology and developmental patterning in adult stages of many invertebrates are hindered by opaque structures, such as shells, skeletal elements, and pigment granules that block or refract light and necessitate sectioning for observation of internal features. An inherent challenge in studies relying on surgical approaches is that cutting tissue is semi-destructive, and delicate structures, such as axonal processes within neural networks, are computationally challenging to reconstruct once disrupted. To address this problem, we developed See-Star, a hydrogel-based tissue clearing protocol to render the bodies of opaque and calcified invertebrates optically transparent while preserving their anatomy in an unperturbed state, facilitating molecular labeling and observation of intact organ systems. The resulting protocol can clear large (> 1 cm3) specimens to enable deep-tissue imaging, and is compatible with molecular techniques, such as immunohistochemistry and in situ hybridization to visualize protein and mRNA localization. To test the utility of this method, we performed a whole-mount imaging study of intact nervous systems in juvenile echinoderms and molluscs and demonstrate that See-Star allows for comparative studies to be extended far into development, facilitating insights into the anatomy of juveniles and adults that are usually not amenable to whole-mount imaging.
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Affiliation(s)
- D N Clarke
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - L Formery
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - C J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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5
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Hu Y, Hruscha A, Pan C, Schifferer M, Schmidt MK, Nuscher B, Giera M, Kostidis S, Burhan Ö, van Bebber F, Edbauer D, Arzberger T, Haass C, Schmid B. Mis-localization of endogenous TDP-43 leads to ALS-like early-stage metabolic dysfunction and progressive motor deficits. Mol Neurodegener 2024; 19:50. [PMID: 38902734 PMCID: PMC11188230 DOI: 10.1186/s13024-024-00735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The key pathological signature of ALS/ FTLD is the mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm. However, TDP-43 gain of function in the cytoplasm is still poorly understood since TDP-43 animal models recapitulating mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm are missing. METHODS CRISPR/Cas9 technology was used to generate a zebrafish line (called CytoTDP), that mis-locates endogenous TDP-43 from the nucleus to the cytoplasm. Phenotypic characterization of motor neurons and the neuromuscular junction was performed by immunostaining, microglia were immunohistochemically localized by whole-mount tissue clearing and muscle ultrastructure was analyzed by scanning electron microscopy. Behavior was investigated by video tracking and quantitative analysis of swimming parameters. RNA sequencing was used to identify mis-regulated pathways with validation by molecular analysis. RESULTS CytoTDP fish have early larval phenotypes resembling clinical features of ALS such as progressive motor defects, neurodegeneration and muscle atrophy. Taking advantage of zebrafish's embryonic development that solely relys on yolk usage until 5 days post fertilization, we demonstrated that microglia proliferation and activation in the hypothalamus is independent from food intake. By comparing CytoTDP to a previously generated TDP-43 knockout line, transcriptomic analyses revealed that mis-localization of endogenous TDP-43, rather than TDP-43 nuclear loss of function, leads to early onset metabolic dysfunction. CONCLUSIONS The new TDP-43 model mimics the ALS/FTLD hallmark of progressive motor dysfunction. Our results suggest that functional deficits of the hypothalamus, the metabolic regulatory center, might be the primary cause of weight loss in ALS patients. Cytoplasmic gain of function of endogenous TDP-43 leads to metabolic dysfunction in vivo that are reminiscent of early ALS clinical non-motor metabolic alterations. Thus, the CytoTDP zebrafish model offers a unique opportunity to identify mis-regulated targets for therapeutic intervention early in disease progression.
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Affiliation(s)
- Yiying Hu
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Metabolic Biochemistry, Biomedical Centre (BMC), Faculty of Medicine, Ludwig-Maximilian University, Munich, Germany
- Munich Medical Research School (MMRS), Munich, Germany
| | - Alexander Hruscha
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Chenchen Pan
- Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Michael K Schmidt
- Zentrum Für Neuropathologie, Ludwig-Maximilians University, Munich, Germany
| | - Brigitte Nuscher
- Metabolic Biochemistry, Biomedical Centre (BMC), Faculty of Medicine, Ludwig-Maximilian University, Munich, Germany
| | - Martin Giera
- Leiden University Medical Center, Leiden, Netherlands
| | | | - Özge Burhan
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Frauke van Bebber
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Metabolic Biochemistry, Biomedical Centre (BMC), Faculty of Medicine, Ludwig-Maximilian University, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Thomas Arzberger
- Zentrum Für Neuropathologie, Ludwig-Maximilians University, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Metabolic Biochemistry, Biomedical Centre (BMC), Faculty of Medicine, Ludwig-Maximilian University, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bettina Schmid
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.
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Ramirez MD, Bui TN, Katz PS. Cellular-resolution gene expression mapping reveals organization in the head ganglia of the gastropod, Berghia stephanieae. J Comp Neurol 2024; 532:e25628. [PMID: 38852042 PMCID: PMC11198006 DOI: 10.1002/cne.25628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 06/10/2024]
Abstract
Gastropod molluscs such as Aplysia, Lymnaea, and Tritonia have been important for determining fundamental rules of motor control, learning, and memory because of their large, individually identifiable neurons. Yet only a small number of gastropod neurons have known molecular markers, limiting the ability to establish brain-wide structure-function relations. Here we combine high-throughput, single-cell RNA sequencing with in situ hybridization chain reaction in the nudibranch Berghia stephanieae to identify and visualize the expression of markers for cell types. Broad neuronal classes were characterized by genes associated with neurotransmitters, like acetylcholine, glutamate, serotonin, and GABA, as well as neuropeptides. These classes were subdivided by other genes including transcriptional regulators and unannotated genes. Marker genes expressed by neurons and glia formed discrete, previously unrecognized regions within and between ganglia. This study provides the foundation for understanding the fundamental cellular organization of gastropod nervous systems.
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Affiliation(s)
| | - Thi N. Bui
- Department of Biology, University of Massachusetts Amherst
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst
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7
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Häfker NS, Holcik L, Mat AM, Ćorić A, Vadiwala K, Beets I, Stockinger AW, Atria CE, Hammer S, Revilla-i-Domingo R, Schoofs L, Raible F, Tessmar-Raible K. Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior. PLoS Biol 2024; 22:e3002572. [PMID: 38603542 PMCID: PMC11008795 DOI: 10.1371/journal.pbio.3002572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/29/2024] [Indexed: 04/13/2024] Open
Abstract
The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were maintained for several weeks. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wild-type worms showed that 24-h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. The prominent role of the neuropeptide pigment-dispersing factor (PDF) in Drosophila circadian behavior prompted us to test for a possible functional involvement of Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts overall activity levels but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, rhythmic phenotypes exist as a continuum, with no distinct "boundaries" between rhythmicity and arrhythmicity. We suggest that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous or changing marine environments. In times of massive sequencing, our work also emphasizes the importance of time series and functional tests.
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Affiliation(s)
- N. Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laurenz Holcik
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Audrey M. Mat
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Isabel Beets
- Division of animal Physiology and Neurobiology, KU Leuven, Leuven, Belgium
| | - Alexander W. Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Carolina E. Atria
- Department of Neuro- and Developmental Biology, University of Vienna, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells, University of Vienna, Vienna, Austria
| | - Stefan Hammer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Neuro- and Developmental Biology, University of Vienna, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells, University of Vienna, Vienna, Austria
| | - Liliane Schoofs
- Division of animal Physiology and Neurobiology, KU Leuven, Leuven, Belgium
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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8
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Krimpenfort LT, Garcia-Collado M, van Leeuwen T, Locri F, Luik AL, Queiro-Palou A, Kanatani S, André H, Uhlén P, Jakobsson L. Anatomy of the complete mouse eye vasculature explored by light-sheet fluorescence microscopy exposes subvascular-specific remodeling in development and pathology. Exp Eye Res 2023; 237:109674. [PMID: 37838300 DOI: 10.1016/j.exer.2023.109674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Eye development and function rely on precise establishment, regression and maintenance of its many sub-vasculatures. These crucial vascular properties have been extensively investigated in eye development and disease utilizing genetic and experimental mouse models. However, due to technical limitations, individual studies have often restricted their focus to one specific sub-vasculature. Here, we apply a workflow that allows for visualization of complete vasculatures of mouse eyes of various developmental stages. Through tissue depigmentation, immunostaining, clearing and light-sheet fluorescence microscopy (LSFM) entire vasculatures of the retina, vitreous (hyaloids) and uvea were simultaneously imaged at high resolution. In silico dissection provided detailed information on their 3D architecture and interconnections. By this method we describe successive remodeling of the postnatal iris vasculature, involving sprouting and pruning, following its disconnection from the embryonic feeding hyaloid vasculature. In addition, we demonstrate examples of conventional and LSFM-mediated analysis of choroidal neovascularization after laser-induced wounding, showing added value of the presented workflow in analysis of modelled eye disease. These advancements in visualization and analysis of the respective eye vasculatures in development and complex eye disease open for novel observations of their functional interplay at a whole-organ level.
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Affiliation(s)
- Luc Thomas Krimpenfort
- Department of Medical Biochemistry and Biophysics, Div. of Vascular Biology, Karolinska Institutet, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Maria Garcia-Collado
- Department of Medical Biochemistry and Biophysics, Div. of Vascular Biology, Karolinska Institutet, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Tom van Leeuwen
- Department of Medical Biochemistry and Biophysics, Div. of Molecular Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Filippo Locri
- Department of Clinical Neuroscience, Division of Eye and Vision, St Erik Eye Hospital, Karolinska Institutet, Eugeniavägen 12, 171 77, Stockholm, Sweden
| | - Anna-Liisa Luik
- Department of Medical Biochemistry and Biophysics, Div. of Vascular Biology, Karolinska Institutet, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Antonio Queiro-Palou
- Department of Medical Biochemistry and Biophysics, Div. of Vascular Biology, Karolinska Institutet, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Shigeaki Kanatani
- Department of Medical Biochemistry and Biophysics, Div. of Molecular Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Helder André
- Department of Clinical Neuroscience, Division of Eye and Vision, St Erik Eye Hospital, Karolinska Institutet, Eugeniavägen 12, 171 77, Stockholm, Sweden
| | - Per Uhlén
- Department of Medical Biochemistry and Biophysics, Div. of Molecular Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Jakobsson
- Department of Medical Biochemistry and Biophysics, Div. of Vascular Biology, Karolinska Institutet, Solnavägen 9, 171 77, Stockholm, Sweden.
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9
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Ćorić A, Stockinger AW, Schaffer P, Rokvić D, Tessmar-Raible K, Raible F. A Fast And Versatile Method for Simultaneous HCR, Immunohistochemistry And Edu Labeling (SHInE). Integr Comp Biol 2023; 63:372-381. [PMID: 36866518 PMCID: PMC10445416 DOI: 10.1093/icb/icad007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Access to newer, fast, and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is an increased need for in situ visualization of gene expression or encoded proteins to validate, localize, or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here, we introduce a versatile protocol that combines in situ hybridization chain reaction, immunohistochemistry, and proliferative cell labeling using 5-ethynyl-2'-deoxyuridine, and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression, and protein localization in bristleworm heads and trunks.
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Affiliation(s)
- Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Alexander W Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Petra Schaffer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Dunja Rokvić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Carl-von-Ossietzky University, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
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10
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Altbürger C, Holzhauser J, Driever W. CRISPR/Cas9-based QF2 knock-in at the tyrosine hydroxylase ( th) locus reveals novel th-expressing neuron populations in the zebrafish mid- and hindbrain. Front Neuroanat 2023; 17:1196868. [PMID: 37603776 PMCID: PMC10433395 DOI: 10.3389/fnana.2023.1196868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
Catecholaminergic neuron clusters are among the most conserved neuromodulatory systems in vertebrates, yet some clusters show significant evolutionary dynamics. Because of their disease relevance, special attention has been paid to mammalian midbrain dopaminergic systems, which have important functions in motor control, reward, motivation, and cognitive function. In contrast, midbrain dopaminergic neurons in teleosts were thought to be lost secondarily. Here, we generated a CRISPR/Cas9-based knock-in transgene at the th locus, which allows the expression of the Q-system transcription factor QF2 linked to the Tyrosine hydroxylase open reading frame by an E2A peptide. The QF2 knock-in allele still expresses Tyrosine hydroxylase in catecholaminergic neurons. Coexpression analysis of QF2 driven expression of QUAS fluorescent reporter transgenes and of th mRNA and Th protein revealed that essentially all reporter expressing cells also express Th/th. We also observed a small group of previously unidentified cells expressing the reporter gene in the midbrain and a larger group close to the midbrain-hindbrain boundary. However, we detected no expression of the catecholaminergic markers ddc, slc6a3, or dbh in these neurons, suggesting that they are not actively transmitting catecholamines. The identified neurons in the midbrain are located in a GABAergic territory. A coexpression analysis with anatomical markers revealed that Th-expressing neurons in the midbrain are located in the tegmentum and those close to the midbrain-hindbrain boundary are located in the hindbrain. Our data suggest that zebrafish may still have some evolutionary remnants of midbrain dopaminergic neurons.
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Affiliation(s)
- Christian Altbürger
- Developmental Biology, Faculty of Biology, Institute of Biology I, Albert Ludwigs University Freiburg, Freiburg, Germany
- CIBSS and BIOSS - Centres for Biological Signalling Studies, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Jens Holzhauser
- Developmental Biology, Faculty of Biology, Institute of Biology I, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Wolfgang Driever
- Developmental Biology, Faculty of Biology, Institute of Biology I, Albert Ludwigs University Freiburg, Freiburg, Germany
- CIBSS and BIOSS - Centres for Biological Signalling Studies, Albert Ludwigs University Freiburg, Freiburg, Germany
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11
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Schubert R, Bae T, Simic B, Smith SN, Park SH, Nagy-Davidescu G, Gradinaru V, Plückthun A, Hur JK. CRISPR-clear imaging of melanin-rich B16-derived solid tumors. Commun Biol 2023; 6:370. [PMID: 37016073 PMCID: PMC10073193 DOI: 10.1038/s42003-023-04614-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/21/2023] [Indexed: 04/06/2023] Open
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful technology to expand classical histological techniques. Current techniques have been optimized for imaging sparsely pigmented organs such as the mammalian brain. In contrast, melanin-rich pigmented tissue, of great interest in the investigation of melanomas, remains challenging. To address this challenge, we have developed a CRISPR-based gene editing approach that is easily incorporated into existing tissue-clearing workflows such the PACT clearing method. We term this method CRISPR-Clear. We demonstrate its applicability to highly melanin-rich B16-derived solid tumors, including one made transgenic for HER2, constituting one of very few syngeneic mouse tumors that can be used in immunocompetent models. We demonstrate the utility in detailed tumor characterization by staining for targeting antibodies and nanoparticles, as well as expressed fluorescent proteins. With CRISPR-Clear we have unprecedented access to optical interrogation in considerable portions of intact melanoma tissue for stained surface markers, expressed fluorescent proteins, of subcellular compartments, and of the vasculature.
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Affiliation(s)
- Rajib Schubert
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Research and early development, Roche Sequencing Solutions, Pleasanton, CA, USA.
| | - Taegeun Bae
- Department of Medicine, Graduate School, Kyung Hee University, Seoul, South Korea
- College of Pharmacy, The Catholic University of Korea, Gyeonggi-do, South Korea
| | - Branko Simic
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
- Vector BioPharma AG, Basel, Switzerland
| | - Sheena N Smith
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
- Vector BioPharma AG, Basel, Switzerland
| | - Seong-Ho Park
- Department of Medicine, Major in Medical Genetics, Graduate School, Hanyang University, Seoul, South Korea
| | | | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, South Korea.
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul, South Korea.
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12
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Masselink W, Tanaka EM. Ethyl Cinnamate-Based Tissue Clearing Strategies. Methods Mol Biol 2023; 2562:123-133. [PMID: 36272071 DOI: 10.1007/978-1-0716-2659-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tissue clearing turns otherwise turbid and opaque tissue transparent, enabling imaging deep within tissues. The nontransparent nature of most tissues is due to the refractive index mismatch between its three major constituent components (lipids, proteins, and water). All tissue clearing methods rectify this mismatch by homogenizing the refractive index within the tissue and carefully matching it to the surrounding media. Here we describe a detailed protocol to clear a wide range of salamander tissues. We also include several optional steps such as depigmentation, antibody staining, and tissue mounting. These steps are optional, and do not change anything in the steps needed for tissue clearing. Depending on the fluorescent signal and optics employed, images up to several millimeters inside of the tissue can be acquired.
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Affiliation(s)
- Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Wien, Austria.
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Wien, Austria
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13
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Murawala P, Oliveira CR, Okulski H, Yun MH, Tanaka EM. Baculovirus Production and Infection in Axolotls. Methods Mol Biol 2023; 2562:369-387. [PMID: 36272088 PMCID: PMC9665047 DOI: 10.1007/978-1-0716-2659-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Salamanders have served as an excellent model for developmental and tissue regeneration studies. While transgenic approaches are available for various salamander species, their long generation time and expensive maintenance have driven the development of alternative gene delivery methods for functional studies. We have previously developed pseudotyped baculovirus (BV) as a tool for gene delivery in the axolotl (Oliveira et al. Dev Biol 433(2):262-275, 2018). Since its initial conception, we have refined our protocol of BV production and usage in salamander models. In this chapter, we describe a detailed and versatile protocol for BV-mediated transduction in urodeles.
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Affiliation(s)
- Prayag Murawala
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, ME, USA.
- Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany.
| | - Catarina R Oliveira
- Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Dresden, Germany
- Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, Portugal
| | - Helena Okulski
- Research - Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Maximina H Yun
- Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Elly M Tanaka
- Research - Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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14
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Dunlap GS, Leigh ND. Best Practices to Promote Data Utility and Reuse by the Non-Traditional Model Organism Community. Methods Mol Biol 2023; 2562:461-469. [PMID: 36272094 DOI: 10.1007/978-1-0716-2659-7_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The dramatic increase in accessibility to sequencing technologies has opened new avenues into studying different processes, cells, and animal models. In the amphibian models used for regeneration research, these new datasets have uncovered a variety of information about what genes define the regenerating limb as well as how genes and cells change over the course of regeneration. The accumulation of data from these studies undoubtedly increases our understanding of regeneration. Throughout these studies, it is important to consider how data can be made most useful not only for the primary study but also for reuse within the scientific community. This chapter will focus on best practices for data collection and handling as well as principles to promote access and reuse of big datasets. However, the deposition and thorough description of data of all sizes generated for a publication (e.g., images, fcs files, etc.) can also be done following this generic workflow. The aim is to lower hurdles for reuse, access, and re-evaluation of data which will in turn increase the utility of these datasets and accelerate scientific progress.
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Affiliation(s)
- Garrett S Dunlap
- Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Nicholas D Leigh
- Molecular Medicine and Gene Therapy, Wallenberg Centre for Molecular Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden.
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15
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MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens. Sci Rep 2022; 12:19508. [PMID: 36376344 PMCID: PMC9663452 DOI: 10.1038/s41598-022-23376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
Transparency of biological specimens is crucial to obtaining detailed 3-dimensional images and understanding the structure and function of biological specimens. This transparency or tissue clearing can be achieved by adjusting the refractive index (RI) with embedding media and removing light barriers such as lipids, inorganic deposits, and pigments. Many currently available protocols consist of multiple steps to achieve sufficient transparency, making the process complex and time-consuming. Thus, in this study, we tailored the recipe for RI adjustment media named MAX based on the recently reported MACS protocol to achieve a single-step procedure, especially for ECM-rich tissues. This was achieved by the improvement of the tissue penetrability of the RI-matching reagent by combining MXDA with sucrose or iodixanol. While this was sufficient for the 3D imaging in many applications, MAX can also be combined with modular processes for de-lipidation, de-coloration, and de-calcification to further maximize the transparency depending on the special features of the tissues. Our approach provides an easy alternative for tissue clearing and 3D imaging.
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16
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A hypothalamic dopamine locus for psychostimulant-induced hyperlocomotion in mice. Nat Commun 2022; 13:5944. [PMID: 36209152 PMCID: PMC9547883 DOI: 10.1038/s41467-022-33584-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
The lateral septum (LS) has been implicated in the regulation of locomotion. Nevertheless, the neurons synchronizing LS activity with the brain’s clock in the suprachiasmatic nucleus (SCN) remain unknown. By interrogating the molecular, anatomical and physiological heterogeneity of dopamine neurons of the periventricular nucleus (PeVN; A14 catecholaminergic group), we find that Th+/Dat1+ cells from its anterior subdivision innervate the LS in mice. These dopamine neurons receive dense neuropeptidergic innervation from the SCN. Reciprocal viral tracing in combination with optogenetic stimulation ex vivo identified somatostatin-containing neurons in the LS as preferred synaptic targets of extrahypothalamic A14 efferents. In vivo chemogenetic manipulation of anterior A14 neurons impacted locomotion. Moreover, chemogenetic inhibition of dopamine output from the anterior PeVN normalized amphetamine-induced hyperlocomotion, particularly during sedentary periods. Cumulatively, our findings identify a hypothalamic locus for the diurnal control of locomotion and pinpoint a midbrain-independent cellular target of psychostimulants. The psychostimulant-sensitive neural mechanism linking the circadian clock to locomotion is unknown. Here, hypothalamic A14 neurons are shown to time diurnal activity by entraining the lateral septum, and their activity is shown to be sensitive to amphetamine.
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17
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Genina EA. Tissue Optical Clearing: State of the Art and Prospects. Diagnostics (Basel) 2022; 12:diagnostics12071534. [PMID: 35885440 PMCID: PMC9324581 DOI: 10.3390/diagnostics12071534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Elina A. Genina
- Optics and Biophotonics Department, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia;
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, 36 Lenin’s Av., 634050 Tomsk, Russia
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18
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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: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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Affiliation(s)
- Sebastian Munck
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | | | - Abril Escamilla‐Ayala
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | - Axelle Kerstens
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | - Sergio Gabarre
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | | | | | - Rebecca Craig
- Department of Physics, SUPAUniversity of StrathclydeGlasgowUK
| | - Emmanuel G. Reynaud
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinBelfieldIreland
| | - Jim Swoger
- European Molecular Biology Laboratory (EMBL) BarcelonaBarcelonaSpain
| | - Gail McConnell
- Department of Physics, SUPAUniversity of StrathclydeGlasgowUK
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19
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Elagoz AM, Styfhals R, Maccuro S, Masin L, Moons L, Seuntjens E. Optimization of Whole Mount RNA Multiplexed in situ Hybridization Chain Reaction With Immunohistochemistry, Clearing and Imaging to Visualize Octopus Embryonic Neurogenesis. Front Physiol 2022; 13:882413. [PMID: 35711315 PMCID: PMC9196907 DOI: 10.3389/fphys.2022.882413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression analysis has been instrumental to understand the function of key factors during embryonic development of many species. Marker analysis is also used as a tool to investigate organ functioning and disease progression. As these processes happen in three dimensions, the development of technologies that enable detection of gene expression in the whole organ or embryo is essential. Here, we describe an optimized protocol of whole mount multiplexed RNA in situ hybridization chain reaction version 3.0 (HCR v3.0) in combination with immunohistochemistry (IHC), followed by fructose-glycerol clearing and light sheet fluorescence microscopy (LSFM) imaging on Octopus vulgaris embryos. We developed a code to automate probe design which can be applied for designing HCR v3.0 type probe pairs for fluorescent in situ mRNA visualization. As proof of concept, neuronal (Ov-elav) and glial (Ov-apolpp) markers were used for multiplexed HCR v3.0. Neural progenitor (Ov-ascl1) and precursor (Ov-neuroD) markers were combined with immunostaining for phosphorylated-histone H3, a marker for mitosis. After comparing several tissue clearing methods, fructose-glycerol clearing was found optimal in preserving the fluorescent signal of HCR v3.0. The expression that was observed in whole mount octopus embryos matched with the previous expression data gathered from paraffin-embedded transverse sections. Three-dimensional reconstruction revealed additional spatial organization that had not been discovered using two-dimensional methods.
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Affiliation(s)
- Ali M. Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Sofia Maccuro
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Luca Masin
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Laboratory of Neural Circuit Development and Regeneration, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lieve Moons
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Laboratory of Neural Circuit Development and Regeneration, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
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20
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Pesce L, Scardigli M, Gavryusev V, Laurino A, Mazzamuto G, Brady N, Sancataldo G, Silvestri L, Destrieux C, Hof PR, Costantini I, Pavone FS. 3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy. Commun Biol 2022; 5:447. [PMID: 35551498 PMCID: PMC9098858 DOI: 10.1038/s42003-022-03390-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/21/2022] [Indexed: 12/17/2022] Open
Abstract
The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H2O2-antigen Retrieval-TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.
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Affiliation(s)
- Luca Pesce
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Marina Scardigli
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Annunziatina Laurino
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy.
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy.
- Department of Biology, University of Florence, Florence, Italy.
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
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21
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Masselink W, Sandoval-Guzmán T, Yun MH. Meeting report: Salamander Models in Cross-disciplinary Biological Research Meeting. Dev Dyn 2022; 251:906-910. [PMID: 35451159 DOI: 10.1002/dvdy.481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
The 3rd annual meeting on 'Salamander Models in Cross-disciplinary Biological Research' took place online on August 2021, bringing together over 200 international researchers using salamanders as research models and encompassing diverse fields, ranging from Development and Regeneration through to Immunology, Pathogenesis and Evolution. The event was organized by Maximina H. Yun (Center for Regenerative Therapies Dresden, Germany) and Tatiana Sandoval-Guzmán (TU Dresden, Germany) with the generous support of the Deutsche Forschungsgemeinschaft, the Center for Regenerative Therapies Dresden, Technische Universität Dresden, and the Company of Biologists. Showcasing a number of emerging salamander models, innovative techniques and resources, and providing a platform for sharing both published and ongoing research, this meeting proved to be an excellent forum for exchanging ideas and moving research forwards. Here, we discuss the highlights stemming from this exciting scientific event. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-BioCenter 1, 1030, Vienna, Austria
| | - Tatiana Sandoval-Guzmán
- Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden of Helmholtz Centre Munich at University Clinic Carl Gustav Carus of TU Dresden Faculty of Medicine, Dresden, Germany
| | - Maximina H Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Germany.,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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22
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Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. NATURE REVIEWS. METHODS PRIMERS 2021; 1:84. [PMID: 35128463 PMCID: PMC8815095 DOI: 10.1038/s43586-021-00080-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 12/16/2022]
Abstract
Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.
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Affiliation(s)
- Douglas S. Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Katsuhiko Matsumoto
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Chenchen Pan
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Nano Biomedical Engineering (Nano BME) Graduate Program, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Jeff W. Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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23
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Bauer B, Mally A, Liedtke D. Zebrafish Embryos and Larvae as Alternative Animal Models for Toxicity Testing. Int J Mol Sci 2021; 22:13417. [PMID: 34948215 PMCID: PMC8707050 DOI: 10.3390/ijms222413417] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Prerequisite to any biological laboratory assay employing living animals is consideration about its necessity, feasibility, ethics and the potential harm caused during an experiment. The imperative of these thoughts has led to the formulation of the 3R-principle, which today is a pivotal scientific standard of animal experimentation worldwide. The rising amount of laboratory investigations utilizing living animals throughout the last decades, either for regulatory concerns or for basic science, demands the development of alternative methods in accordance with 3R to help reduce experiments in mammals. This demand has resulted in investigation of additional vertebrate species displaying favourable biological properties. One prominent species among these is the zebrafish (Danio rerio), as these small laboratory ray-finned fish are well established in science today and feature outstanding biological characteristics. In this review, we highlight the advantages and general prerequisites of zebrafish embryos and larvae before free-feeding stages for toxicological testing, with a particular focus on cardio-, neuro, hepato- and nephrotoxicity. Furthermore, we discuss toxicokinetics, current advances in utilizing zebrafish for organ toxicity testing and highlight how advanced laboratory methods (such as automation, advanced imaging and genetic techniques) can refine future toxicological studies in this species.
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Affiliation(s)
- Benedikt Bauer
- Institute of Pharmacology and Toxicology, Julius-Maximilians-University, 97078 Würzburg, Germany; (B.B.); (A.M.)
| | - Angela Mally
- Institute of Pharmacology and Toxicology, Julius-Maximilians-University, 97078 Würzburg, Germany; (B.B.); (A.M.)
| | - Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-University, 97074 Würzburg, Germany
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24
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Abstract
Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
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Affiliation(s)
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute – ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
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25
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Revilla-i-Domingo R, Rajan VBV, Waldherr M, Prohaczka G, Musset H, Orel L, Gerrard E, Smolka M, Stockinger A, Farlik M, Lucas RJ, Raible F, Tessmar-Raible K. Characterization of cephalic and non-cephalic sensory cell types provides insight into joint photo- and mechanoreceptor evolution. eLife 2021; 10:e66144. [PMID: 34350831 PMCID: PMC8367381 DOI: 10.7554/elife.66144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/04/2021] [Indexed: 12/11/2022] Open
Abstract
Rhabdomeric opsins (r-opsins) are light sensors in cephalic eye photoreceptors, but also function in additional sensory organs. This has prompted questions on the evolutionary relationship of these cell types, and if ancient r-opsins were non-photosensory. A molecular profiling approach in the marine bristleworm Platynereis dumerilii revealed shared and distinct features of cephalic and non-cephalic r-opsin1-expressing cells. Non-cephalic cells possess a full set of phototransduction components, but also a mechanosensory signature. Prompted by the latter, we investigated Platynereis putative mechanotransducer and found that nompc and pkd2.1 co-expressed with r-opsin1 in TRE cells by HCR RNA-FISH. To further assess the role of r-Opsin1 in these cells, we studied its signaling properties and unraveled that r-Opsin1 is a Gαq-coupled blue light receptor. Profiling of cells from r-opsin1 mutants versus wild-types, and a comparison under different light conditions reveals that in the non-cephalic cells light - mediated by r-Opsin1 - adjusts the expression level of a calcium transporter relevant for auditory mechanosensation in vertebrates. We establish a deep-learning-based quantitative behavioral analysis for animal trunk movements and identify a light- and r-Opsin-1-dependent fine-tuning of the worm's undulatory movements in headless trunks, which are known to require mechanosensory feedback. Our results provide new data on peripheral cell types of likely light sensory/mechanosensory nature. These results point towards a concept in which such a multisensory cell type evolved to allow for fine-tuning of mechanosensation by light. This implies that light-independent mechanosensory roles of r-opsins may have evolved secondarily.
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Affiliation(s)
- Roger Revilla-i-Domingo
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Vinoth Babu Veedin Rajan
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Monika Waldherr
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Günther Prohaczka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Hugo Musset
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Lukas Orel
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Elliot Gerrard
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Moritz Smolka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of ViennaViennaAustria
| | - Alexander Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Dermatology, Medical University of ViennaViennaAustria
| | - Robert J Lucas
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
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26
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Hofmann J, Keppler SJ. Tissue clearing and 3D imaging - putting immune cells into context. J Cell Sci 2021; 134:271108. [PMID: 34342351 DOI: 10.1242/jcs.258494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A better understanding of cell-cell and cell-niche interactions is crucial to comprehend the complexity of inflammatory or pathophysiological scenarios such as tissue damage during viral infections, the tumour microenvironment and neuroinflammation. Optical clearing and 3D volumetric imaging of large tissue pieces or whole organs is a rapidly developing methodology that holds great promise for the in-depth study of cells in their natural surroundings. These methods have mostly been applied to image structural components such as endothelial cells and neuronal architecture. Recent work now highlights the possibility of studying immune cells in detail within their respective immune niches. This Review summarizes recent developments in tissue clearing methods and 3D imaging, with a focus on the localization and quantification of immune cells. We first provide background to the optical challenges involved and their solutions before discussing published protocols for tissue clearing, the limitations of 3D imaging of immune cells and image analysis. Furthermore, we highlight possible applications for tissue clearing and propose future developments for the analysis of immune cells within homeostatic or inflammatory immune niches.
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Affiliation(s)
- Julian Hofmann
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
| | - Selina J Keppler
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
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27
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Takashima S, Takemoto S, Toyoshi K, Ohba A, Shimozawa N. Zebrafish model of human Zellweger syndrome reveals organ-specific accumulation of distinct fatty acid species and widespread gene expression changes. Mol Genet Metab 2021; 133:307-323. [PMID: 34016526 DOI: 10.1016/j.ymgme.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 11/24/2022]
Abstract
In Zellweger syndrome (ZS), lack of peroxisome function causes physiological and developmental abnormalities in many organs such as the brain, liver, muscles, and kidneys, but little is known about the exact pathogenic mechanism. By disrupting the zebrafish pex2 gene, we established a disease model for ZS and found that it exhibits pathological features and metabolic changes similar to those observed in human patients. By comprehensive analysis of the fatty acid profile, we found organ-specific accumulation and reduction of distinct fatty acid species, such as an accumulation of ultra-very-long-chain polyunsaturated fatty acids (ultra-VLC-PUFAs) in the brains of pex2 mutant fish. Transcriptome analysis using microarray also revealed mutant-specific gene expression changes that might lead to the symptoms, including reduction of crystallin, troponin, parvalbumin, and fatty acid metabolic genes. Our data indicated that the loss of peroxisomes results in widespread metabolic and gene expression changes beyond the causative peroxisomal function. These results suggest the genetic and metabolic basis of the pathology of this devastating human disease.
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Affiliation(s)
- Shigeo Takashima
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.
| | - Shoko Takemoto
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Kayoko Toyoshi
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Akiko Ohba
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Nobuyuki Shimozawa
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
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28
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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29
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Ishii N, Tajika Y, Murakami T, Galipon J, Shirahata H, Mukai R, Uehara D, Kaneko R, Yamazaki Y, Yoshimoto Y, Iwasaki H. Correlative microscopy and block-face imaging (CoMBI) method for both paraffin-embedded and frozen specimens. Sci Rep 2021; 11:13108. [PMID: 34162961 PMCID: PMC8222340 DOI: 10.1038/s41598-021-92485-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Correlative microscopy and block-face imaging (CoMBI), a method that we previously developed, is characterized by the ability to correlate between serial block-face images as 3-dimensional (3D) datasets and sections as 2-dimensional (2D) microscopic images. CoMBI has been performed for the morphological analyses of various biological specimens, and its use is expanding. However, the conventional CoMBI system utilizes a cryostat, which limits its compatibility to only frozen blocks and the resolution of the block-face image. We developed a new CoMBI system that can be applied to not only frozen blocks but also paraffin blocks, and it has an improved magnification for block-face imaging. The new system, called CoMBI-S, comprises sliding-type sectioning devices and imaging devices, and it conducts block slicing and block-face imaging automatically. Sections can also be collected and processed for microscopy as required. We also developed sample preparation methods for improving the qualities of the block-face images and 3D rendered volumes. We successfully obtained correlative 3D datasets and 2D microscopic images of zebrafish, mice, and fruit flies, which were paraffin-embedded or frozen. In addition, the 3D datasets at the highest magnification could depict a single neuron and bile canaliculus.
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Affiliation(s)
- Nobukazu Ishii
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.,Department of Neurosurgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yuki Tajika
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.
| | - Tohru Murakami
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Josephine Galipon
- Keio University Institute for Advanced Biosciences, Tsuruoka, Yamagata, Japan.,Nagoya University Neuroscience Institute of the Graduate School of Science, Nagoya, Japan
| | - Hiroyoshi Shirahata
- Keio University Institute for Advanced Biosciences, Tsuruoka, Yamagata, Japan.,Tsuruoka Chuo High School, Tsuruoka, Yamagata, Japan
| | - Ryo Mukai
- Department of Ophthalmology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Daisuke Uehara
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Ryosuke Kaneko
- Bioresource Center, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yuichi Yamazaki
- Department of Gastroenterology and Hepatology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yuhei Yoshimoto
- Department of Neurosurgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Hirohide Iwasaki
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.
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30
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Mano T, Murata K, Kon K, Shimizu C, Ono H, Shi S, Yamada RG, Miyamichi K, Susaki EA, Touhara K, Ueda HR. CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping. CELL REPORTS METHODS 2021; 1:100038. [PMID: 35475238 PMCID: PMC9017177 DOI: 10.1016/j.crmeth.2021.100038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 01/18/2023]
Abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
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Affiliation(s)
- Tomoyuki Mano
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Ken Murata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Hiroaki Ono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Kazunari Miyamichi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Etsuo A. Susaki
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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31
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Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc 2021; 16:2732-2748. [PMID: 34021294 PMCID: PMC10542857 DOI: 10.1038/s41596-021-00502-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).
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Affiliation(s)
- Kurt R Weiss
- Morgridge Institute for Research, Madison, WI, USA
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Douglas P Shepherd
- Department of Physics, Arizona State University, Tempe, AZ, USA
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA.
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32
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Cura Costa E, Otsuki L, Rodrigo Albors A, Tanaka EM, Chara O. Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration. eLife 2021; 10:e55665. [PMID: 33988504 PMCID: PMC8205487 DOI: 10.7554/elife.55665] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/13/2021] [Indexed: 01/05/2023] Open
Abstract
Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Albors et al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rost et al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modeling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during ~85 hours after amputation within ~830 μm of the injury. We adapted Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding bona fide spinal cord regeneration.
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Affiliation(s)
- Emanuel Cura Costa
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata (UNLP)La PlataArgentina
| | - Leo Otsuki
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Aida Rodrigo Albors
- Division of Cell and Developmental Biology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Osvaldo Chara
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata (UNLP)La PlataArgentina
- Center for Information Services and High Performance Computing, Technische Universität DresdenDresdenGermany
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33
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Nowoshilow S, Fei JF, Voss SR, Tanaka EM, Murawala P. Gene and transgenics nomenclature for the laboratory axolotl-Ambystoma mexicanum. Dev Dyn 2021; 251:913-921. [PMID: 33896069 DOI: 10.1002/dvdy.351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 01/10/2023] Open
Abstract
The laboratory axolotl (Ambystoma mexicanum) is widely used in biological research. Recent advancements in genetic and molecular toolkits are greatly accelerating the work using axolotl, especially in the area of tissue regeneration. At this juncture, there is a critical need to establish gene and transgenic nomenclature to ensure uniformity in axolotl research. Here, we propose guidelines for genetic nomenclature when working with the axolotl.
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Affiliation(s)
- Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Ji-Feng Fei
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - S Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA.,Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky, USA.,Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Prayag Murawala
- Mount Desert Island Biological laboratory (MDIBL), Salisbury Cove, USA.,Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
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Abstract
Advanced optical methods combined with various probes pave the way toward molecular imaging within living cells. However, major challenges are associated with the need to enhance the imaging resolution even further to the subcellular level for the imaging of larger tissues, as well as for in vivo studies. High scattering and absorption of opaque tissues limit the penetration of light into deep tissues and thus the optical imaging depth. Tissue optical clearing technique provides an innovative way to perform deep-tissue imaging. Recently, various optical clearing methods have been developed, which provide tissue clearing based on similar physical principles via different chemical approaches. Here, we introduce the mechanisms of the current clearing methods from fundamental physical and chemical perspectives, including the main physical principle, refractive index matching via various chemical approaches, such as dissociation of collagen, delipidation, decalcification, dehydration, and hyperhydration, to reduce scattering, as well as decolorization to reduce absorption.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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35
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Avilov SV. Navigating across multi-dimensional space of tissue clearing parameters. Methods Appl Fluoresc 2021; 9:022001. [PMID: 33592593 DOI: 10.1088/2050-6120/abe6fb] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.
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Affiliation(s)
- Sergiy V Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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36
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Expanding evolutionary neuroscience: insights from comparing variation in behavior. Neuron 2021; 109:1084-1099. [PMID: 33609484 DOI: 10.1016/j.neuron.2021.02.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 01/01/2023]
Abstract
Neuroscientists have long studied species with convenient biological features to discover how behavior emerges from conserved molecular, neural, and circuit level processes. With the advent of new tools, from viral vectors and gene editing to automated behavioral analyses, there has been a recent wave of interest in developing new, "nontraditional" model species. Here, we advocate for a complementary approach to model species development, that is, model clade development, as a way to integrate an evolutionary comparative approach with neurobiological and behavioral experiments. Capitalizing on natural behavioral variation in and investing in experimental tools for model clades will be a valuable strategy for the next generation of neuroscience discovery.
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37
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Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
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Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
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38
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Fontinha BM, Zekoll T, Al-Rawi M, Gallach M, Reithofer F, Barker AJ, Hofbauer M, Fischer RM, von Haeseler A, Baier H, Tessmar-Raible K. TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. PLoS Biol 2021; 19:e3001012. [PMID: 33411725 PMCID: PMC7837489 DOI: 10.1371/journal.pbio.3001012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/26/2021] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
Vertebrate behavior is strongly influenced by light. Light receptors, encoded by functional opsin proteins, are present inside the vertebrate brain and peripheral tissues. This expression feature is present from fishes to human and appears to be particularly prominent in diurnal vertebrates. Despite their conserved widespread occurrence, the nonvisual functions of opsins are still largely enigmatic. This is even more apparent when considering the high number of opsins. Teleosts possess around 40 opsin genes, present from young developmental stages to adulthood. Many of these opsins have been shown to function as light receptors. This raises the question of whether this large number might mainly reflect functional redundancy or rather maximally enables teleosts to optimally use the complex light information present under water. We focus on tmt-opsin1b and tmt-opsin2, c-opsins with ancestral-type sequence features, conserved across several vertebrate phyla, expressed with partly similar expression in non-rod, non-cone, non-retinal-ganglion-cell brain tissues and with a similar spectral sensitivity. The characterization of the single mutants revealed age- and light-dependent behavioral changes, as well as an impact on the levels of the preprohormone sst1b and the voltage-gated sodium channel subunit scn12aa. The amount of daytime rest is affected independently of the eyes, pineal organ, and circadian clock in tmt-opsin1b mutants. We further focused on daytime behavior and the molecular changes in tmt-opsin1b/2 double mutants, and found that-despite their similar expression and spectral features-these opsins interact in part nonadditively. Specifically, double mutants complement molecular and behavioral phenotypes observed in single mutants in a partly age-dependent fashion. Our work provides a starting point to disentangle the highly complex interactions of vertebrate nonvisual opsins, suggesting that tmt-opsin-expressing cells together with other visual and nonvisual opsins provide detailed light information to the organism for behavioral fine-tuning. This work also provides a stepping stone to unravel how vertebrate species with conserved opsins, but living in different ecological niches, respond to similar light cues and how human-generated artificial light might impact on behavioral processes in natural environments.
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Affiliation(s)
- Bruno M. Fontinha
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Theresa Zekoll
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Mariam Al-Rawi
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Miguel Gallach
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Florian Reithofer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
| | | | - Maximilian Hofbauer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- loopbio, Vienna, Austria
| | - Ruth M. Fischer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform ‘‘Rhythms of Life,” University of Vienna, Vienna, Austria
- FENS-Kavli Network of Excellence, Brussels, Belgium
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39
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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] [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
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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
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40
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The cytokine MIF controls daily rhythms of symbiont nutrition in an animal-bacterial association. Proc Natl Acad Sci U S A 2020; 117:27578-27586. [PMID: 33067391 DOI: 10.1073/pnas.2016864117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The recent recognition that many symbioses exhibit daily rhythms has encouraged research into the partner dialogue that drives these biological oscillations. Here we characterized the pivotal role of the versatile cytokine macrophage migration inhibitory factor (MIF) in regulating a metabolic rhythm in the model light-organ symbiosis between Euprymna scolopes and Vibrio fischeri As the juvenile host matures, it develops complex daily rhythms characterized by profound changes in the association, from gene expression to behavior. One such rhythm is a diurnal shift in symbiont metabolism triggered by the periodic provision of a specific nutrient by the mature host: each night the symbionts catabolize chitin released from hemocytes (phagocytic immune cells) that traffic into the light-organ crypts, where the population of V. fischeri cells resides. Nocturnal migration of these macrophage-like cells, together with identification of an E. scolopes MIF (EsMIF) in the light-organ transcriptome, led us to ask whether EsMIF might be the gatekeeper controlling the periodic movement of the hemocytes. Western blots, ELISAs, and confocal immunocytochemistry showed EsMIF was at highest abundance in the light organ. Its concentration there was lowest at night, when hemocytes entered the crypts. EsMIF inhibited migration of isolated hemocytes, whereas exported bacterial products, including peptidoglycan derivatives and secreted chitin catabolites, induced migration. These results provide evidence that the nocturnal decrease in EsMIF concentration permits the hemocytes to be drawn into the crypts, delivering chitin. This nutritional function for a cytokine offers the basis for the diurnal rhythms underlying a dynamic symbiotic conversation.
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41
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Subiran Adrados C, Yu Q, Bolaños Castro LA, Rodriguez Cabrera LA, Yun MH. Salamander-Eci: An optical clearing protocol for the three-dimensional exploration of regeneration. Dev Dyn 2020; 250:902-915. [PMID: 33084146 DOI: 10.1002/dvdy.264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/07/2020] [Accepted: 10/11/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Salamander limb regeneration is a complex biological process that entails the orchestration of multiple cellular and molecular mechanisms in a three-dimensional space. Hence, a comprehensive understanding of this process requires whole-structure level explorations. Recent advances in imaging and optical clearing methods have transformed the study of regenerative phenomena, allowing the three-dimensional visualization of structures and entire organisms. RESULTS Here we introduce Salamander-Eci, a rapid and robust optical clearing protocol optimized for the widely used axolotl model, which allows simultaneous immunohistochemistry and Click-chemistry detection with minimal volume disruption. We provide examples of its application, from whole larva to adult limbs and organs, and complement it with an image analysis pipeline for volumetric cell quantification. Further, we offer a detailed 3D quantitation of cell proliferation throughout axolotl limb regeneration. CONCLUSIONS Salamander-Eci enables the comprehensive volumetric analysis of regenerative phenomena at both local and systemic levels.
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Affiliation(s)
| | - Qinghao Yu
- CRTD/Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | | | - Luis Alberto Rodriguez Cabrera
- CRTD/Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.,Department of Pediatrics, Neonatology and Pediatric Critical Care Medicine, Technische Universität Dresden, University Hospital and Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Maximina Hee Yun
- CRTD/Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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42
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Eme-Scolan E, Dando SJ. Tools and Approaches for Studying Microglia In vivo. Front Immunol 2020; 11:583647. [PMID: 33117395 PMCID: PMC7576994 DOI: 10.3389/fimmu.2020.583647] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Microglia are specialized resident macrophages of the central nervous system (CNS) that have important functions during neurodevelopment, homeostasis and disease. This mini-review provides an overview of the current tools and approaches for studying microglia in vivo. We focus on tools for labeling microglia, highlighting the advantages and limitations of microglia markers/antibodies and reporter mice. We also discuss techniques for imaging microglia in situ, including in vivo live imaging of brain and retinal microglia. Finally, we review microglia depletion approaches and their use to investigate microglial function in CNS homeostasis and disease.
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Affiliation(s)
- Elisa Eme-Scolan
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France.,Faculty of Health, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Samantha J Dando
- Faculty of Health, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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43
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Gómez-Gaviro MV, Sanderson D, Ripoll J, Desco M. Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease. iScience 2020; 23:101432. [PMID: 32805648 PMCID: PMC7452225 DOI: 10.1016/j.isci.2020.101432] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Three-dimensional (3D) optical imaging techniques can expand our knowledge about physiological and pathological processes that cannot be fully understood with 2D approaches. Standard diagnostic tests frequently are not sufficient to unequivocally determine the presence of a pathological condition. Whole-organ optical imaging requires tissue transparency, which can be achieved by using tissue clearing procedures enabling deeper image acquisition and therefore making possible the analysis of large-scale biological tissue samples. Here, we review currently available clearing agents, methods, and their application in imaging of physiological or pathological conditions in different animal and human organs. We also compare different optical tissue clearing methods discussing their advantages and disadvantages and review the use of different 3D imaging techniques for the visualization and image acquisition of cleared tissues. The use of optical tissue clearing resources for large-scale biological tissues 3D imaging paves the way for future applications in translational and clinical research.
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Affiliation(s)
- Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Daniel Sanderson
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Jorge Ripoll
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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