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Melian C, Ploper D, Chehín R, Vignolo G, Castellano P. Impairment of Listeria monocytogenes biofilm developed on industrial surfaces by Latilactobacillus curvatus CRL1579 bacteriocin. Food Microbiol 2024; 121:104491. [PMID: 38637093 DOI: 10.1016/j.fm.2024.104491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 04/20/2024]
Abstract
The effect of lactocin AL705, bacteriocin produced by Latilactobacillus (Lat.) curvatus CRL1579 against Listeria biofilms on stainless steel (SS) and polytetrafluoroethylene (PTFE) coupons at 10 °C was investigated. L. monocytogenes FBUNT showed the greatest adhesion on both surfaces associated to the hydrophobicity of cell surface. Partially purified bacteriocin (800 UA/mL) effectively inhibited L. monocytogenes preformed biofilm through displacement strategy, reducing the pathogen by 5.54 ± 0.26 and 4.74 ± 0.05 log cycles at 3 and 6 days, respectively. The bacteriocin-producer decreased the pathogen biofilm by ∼2.84 log cycles. Control and Bac- treated samples reached cell counts of 7.05 ± 0.18 and 6.79 ± 0.06 log CFU/cm2 after 6 days of incubation. Confocal scanning laser microscopy (CLSM) allowed visualizing the inhibitory effect of lactocin AL705 on L. monocytogenes preformed biofilms under static and hydrodynamic flow conditions. A greater effect of the bacteriocin was found at 3 days independently of the surface matrix and pathogen growth conditions at 10 °C. As a more realistic approach, biofilm displacement strategy under continuous flow conditions showed a significant loss of biomass, mean thickness and substratum coverage of pathogen biofilm. These findings highlight the anti-biofilm capacity of lactocin AL705 and their potential application in food industries.
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Affiliation(s)
- Constanza Melian
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000ILC, Tucumán, Argentina
| | - Diego Ploper
- IMMCA (Instituto de Investigación en Medicina Molecular y Celular Aplicada, CONICET-Universidad Nacional de Tucumán-Ministerio de Salud Pública, Gobierno de Tucumán, Pje. Dorrego 1080, San Miguel de Tucumán, 4000, Tucumán, Argentina
| | - Rosana Chehín
- IMMCA (Instituto de Investigación en Medicina Molecular y Celular Aplicada, CONICET-Universidad Nacional de Tucumán-Ministerio de Salud Pública, Gobierno de Tucumán, Pje. Dorrego 1080, San Miguel de Tucumán, 4000, Tucumán, Argentina
| | - Graciela Vignolo
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000ILC, Tucumán, Argentina
| | - Patricia Castellano
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000ILC, Tucumán, Argentina.
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Christiansen Reinold E, Cardoso Anastacio A, Gonçalves de Mendonça-Filho L, Luís Dos Santos Lima A, Nichele J. Characterization of industrial TNT in ammunition shells: An in-depth study of artificial aging effects using Fourier-Transform infrared spectroscopy and gas chromatography-mass spectrometry. Spectrochim Acta A Mol Biomol Spectrosc 2024; 314:124220. [PMID: 38560952 DOI: 10.1016/j.saa.2024.124220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/09/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
In this study, we comprehensively investigated the degradation of industrial trinitrotoluene (TNT), focusing on the effects of aging and direct contact with steel surfaces, mirroring real-world usage conditions. While practical knowledge exists regarding this degradation, the existing literature lacks in-depth insights into the underlying processes. To address this gap, we conducted experiments using small steel samples, representative of military ammunition casings, which were coated with TNT and subjected to 30 days of heating at 75 °C under vacuum conditions. A subset of these samples was coated with a protective red alkyd paint. After the aging process, the TNT was carefully removed from the metal surfaces and subjected to a comprehensive analysis encompassing scanning electron microscopy, Fourier-transform infrared spectroscopy, and gas chromatography-mass spectrometry. Our results reveal a remarkable preservation of the chemical integrity of industrial TNT, even in the presence of thermal stress and direct steel contact. Although superficial changes were observed in the TNT's appearance, all analytical data consistently demonstrated the maintenance of its chemical composition. Notably, the sole change in composition was attributed to the presence of degradation products associated with the alkyd paint coating, rather than intrinsic TNT degradation. These findings underscore the negligible impact of degradation processes on TNT in scenarios involving the solid-phase thermal stress of TNT in direct contact with metal, significantly enhancing our understanding of TNT safety when packaged within steel artifacts-a common context in military ammunition.
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Affiliation(s)
- Erich Christiansen Reinold
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil; Brazilian Navy Weapon System Directorate, Rio de Janeiro, RJ, Brazil
| | - Aline Cardoso Anastacio
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | | | | | - Jakler Nichele
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil; Defense Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.
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Teixeira P, Galland R, Chevrollier A. Super-resolution microscopies, technological breakthrough to decipher mitochondrial structure and dynamic. Semin Cell Dev Biol 2024; 159-160:38-51. [PMID: 38310707 DOI: 10.1016/j.semcdb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/06/2024]
Abstract
Mitochondria are complex organelles with an outer membrane enveloping a second inner membrane that creates a vast matrix space partitioned by pockets or cristae that join the peripheral inner membrane with several thin junctions. Several micrometres long, mitochondria are generally close to 300 nm in diameter, with membrane layers separated by a few tens of nanometres. Ultrastructural data from electron microscopy revealed the structure of these mitochondria, while conventional optical microscopy revealed their extraordinary dynamics through fusion, fission, and migration processes but its limited resolution power restricted the possibility to go further. By overcoming the limits of light diffraction, Super-Resolution Microscopy (SRM) now offers the potential to establish the links between the ultrastructure and remodelling of mitochondrial membranes, leading to major advances in our understanding of mitochondria's structure-function. Here we review the contributions of SRM imaging to our understanding of the relationship between mitochondrial structure and function. What are the hopes for these new imaging approaches which are particularly important for mitochondrial pathologies?
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Affiliation(s)
- Pauline Teixeira
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France
| | - Rémi Galland
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Arnaud Chevrollier
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France.
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Flores P, Luo J, Mueller DW, Muecklich F, Zea L. Space biofilms - An overview of the morphology of Pseudomonas aeruginosa biofilms grown on silicone and cellulose membranes on board the international space station. Biofilm 2024; 7:100182. [PMID: 38370151 PMCID: PMC10869243 DOI: 10.1016/j.bioflm.2024.100182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/22/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024] Open
Abstract
Microorganisms' natural ability to live as organized multicellular communities - also known as biofilms - provides them with unique survival advantages. For instance, bacterial biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment with antibiotics. Bacterial biofilms are also capable of strongly attaching to surfaces, where their metabolic by-products could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecraft surfaces, it is impossible to prevent human-associated bacteria from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that bacterial biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The bacterial component of Space Biofilms project, performed on the International Space Station in early 2020, contributes to such understanding by characterizing the morphology and gene expression of bacterial biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism due to its relevance in biofilm studies and its ability to cause urinary tract infections as an opportunistic pathogen. Biofilm formation was characterized at one, two, and three days of incubation (37 °C) over six different materials. Materials reported in this manuscript include catheter grade silicone, selected due to its medical relevance in hospital acquired infections, catheter grade silicone with ultrashort pulsed direct laser interference patterning, included to test microtopographies as a potential biofilm control strategy, and cellulose membrane to replicate the column and canopy structure previously reported from a microgravity study. We here present an overview of the biofilm morphology, including 3D images of the biofilms to represent the distinctive morphology observed in each material tested, and some of the key differences in biofilm thickness, mass, and surface area coverage. We also present the impact of the surface microtopography in biofilm formation across materials, incubation time, and gravitational conditions. The Space Biofilms project (bacterial side) is supported by the National Aeronautics and Space Administration under Grant No. 80NSSC17K0036 and 80NSSC21K1950.
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Affiliation(s)
- Pamela Flores
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado, 3775 Discovery Drive, Boulder, CO, USA, 80309
| | - Jiaqi Luo
- Saarland University, 66123, Saarbrücken, Saarland, Germany
| | | | | | - Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado, 3775 Discovery Drive, Boulder, CO, USA, 80309
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Helman E, Dellarupe A, Steffen KD, Bernstein M, Moré G. Morphological and molecular characterization of Sarcocystis spp. in pigs (Sus scrofa domestica) from Argentina. Parasitol Int 2024; 100:102859. [PMID: 38199523 DOI: 10.1016/j.parint.2024.102859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Sarcocystis spp. are intracellular protozoan parasites with an obligatory heteroxenous life cycle. The objective of this study was to identify Sarcocystis spp. in pig muscles from Argentina, by light and transmission electron microscopy (TEM), and molecular studies. Muscles samples from 561 pigs (Sus scrofa domestica) were classified according to the breeding system in: intensive farming (IF, n = 295; animals kept in confinement during most of their productive cycle), or semi-extensive farming (SEF, n = 266; animals bred outdoors, generally family or backyard production). Results showed that 24.8% (139/561) were positive by light microscopy, with a significantly higher prevalence in the SEF (34.6%; 92/266) than the IF pigs (15.9%; 47/295) (p < 0.05). Of the 202 samples analyzed by PCR, 96 were positive (47.5%) for the 18S rRNA (18S ribosomal RNA) fragment. All samples analyzed by the S. suihominis specific coxI (mitochondrial cytochrome c oxidase subunit I) PCR (n = 235; 96 positives by 18S rRNA PCR and 139 positives by light microscopy) were negative. Fourteen individual cysts were positive for the 18S rRNA PCR and sequenced. Consensus sequences obtained from the 18S rRNA fragment PCR ranged from 613 to 880 bp and showed 100% of identity between them and with previously reported S. miescheriana sequences. In all the pig samples analyzed by TEM, cyst wall ultrastructure was compatible with S. miescheriana. This is the first study that provides infection rates and describes and identifies morphological and molecular features of Sarcocystis spp. cysts in pigs from Argentina.
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Affiliation(s)
- Elisa Helman
- Argentinean National Council of Scientific and Technological Research (CONICET), Godoy Cruz 2290 (C1425FQB) CABA, Buenos Aires, Argentina; Laboratory of Immunoparasitology (LAINPA), Faculty of Veterinary Sciences, National University of La Plata (FCV-UNLP), La Plata 1900, Argentina
| | - Andrea Dellarupe
- Argentinean National Council of Scientific and Technological Research (CONICET), Godoy Cruz 2290 (C1425FQB) CABA, Buenos Aires, Argentina; Laboratory of Immunoparasitology (LAINPA), Faculty of Veterinary Sciences, National University of La Plata (FCV-UNLP), La Plata 1900, Argentina.
| | - Kevin Denis Steffen
- Argentinean National Council of Scientific and Technological Research (CONICET), Godoy Cruz 2290 (C1425FQB) CABA, Buenos Aires, Argentina; Laboratory of Immunoparasitology (LAINPA), Faculty of Veterinary Sciences, National University of La Plata (FCV-UNLP), La Plata 1900, Argentina
| | - Mariana Bernstein
- Argentinean National Council of Scientific and Technological Research (CONICET), Godoy Cruz 2290 (C1425FQB) CABA, Buenos Aires, Argentina; Laboratory of Immunoparasitology (LAINPA), Faculty of Veterinary Sciences, National University of La Plata (FCV-UNLP), La Plata 1900, Argentina
| | - Gastón Moré
- Argentinean National Council of Scientific and Technological Research (CONICET), Godoy Cruz 2290 (C1425FQB) CABA, Buenos Aires, Argentina; Laboratory of Immunoparasitology (LAINPA), Faculty of Veterinary Sciences, National University of La Plata (FCV-UNLP), La Plata 1900, Argentina; Institute of Parasitology, Vetsuisse Faculty, University of Berne, Langgasssstrasse 122, Bern 3012, Switzerland
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Amambo GN, Fombad FF, Chounna Ndongmo PW, Abong RA, Njouendou AJ, Beng AA, Nji TM, Esum ME, Fru-Cho J, Manuel R, Kebede D, Enyong PI, Hoerauf A, Koudou B, Bockarie M, Wanji S. Impact of repeated mass ivermectin administration using a community directed approach on L. loa infection in Chrysops silacea of the rain forest and forest savanna of Cameroon. Parasite Epidemiol Control 2024; 25:e00343. [PMID: 38405181 PMCID: PMC10884510 DOI: 10.1016/j.parepi.2024.e00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 09/22/2023] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Background Loiasis is an endemic filarial infection in the rainforest zone of West and Central Africa. Repeated annual community-directed treatment with ivermectin (CDTI) delivered for several years to control onchocerciasis has been shown to reduce the prevalence and intensity of Loiasis in some Loa loa-Onchocerca volvulus co-endemic areas. However, the impact of these multiple rounds of CDTI on entomological indicators of loiasis transmission is not known, and was therefore assessed in this study in areas with contrasting histories of CDTI. Methods The study was conducted in the East, North-west and South-west 1 CDTI project sites of Cameroon. Two communities per CDTI project were selected for fly collection and dissection. Ivermectin treatment coverage was documented in these areas, and this was correlated to Chrysops infection and infective rates. A total of 7029 female Chrysops were collected from 6 communities of the 3 CDTI projects (East, North-west, and South-west 1) and from 2 communities in a non-CDTI district (East). Results Chrysops biting densities and parous rates were significantly reduced in the North-west and South-west sites post-CDTI, while in the East, biting densities were similar in non-CDTI and CDTI sites, with higher parous rates observed in the non-CDTI site. Infection and infective rates in the East non-CDTI site were 4.4% and 1.8% respectively, as compared to 3.3% and 1.3% in the CDTI site after 10 ivermectin rounds (there were no baseline data for the latter). In the North-west site, significant reductions in Chrysops infection and infective rates from 10.2% and 4.2% respectively, to 3.5% and 1.2 (after 9 rounds of ivermectin treatment), were recorded following CDTI. In the South-west, infection rate significantly increased from 1.74% to 2.8% and infective rate remained statistically unchanged after 14 rounds of CDTI (0.45% - 0.40%). Similar trends in Mean Head L3 were observed except in the East site where this indicator was similar in both CDTI and control sites. Only in the North-west site did monthly transmission potentials decrease significantly. Conclusion This study demonstrated that the impact of repeated annual treatment with ivermectin for the control of onchocerciasis using community directed delivery approach on the entomological indicators of loiasis varies with bioecological zones. Community directed treatment with ivermectin induced a significant reduction in the entomological indicators of loiasis in the North-West project site which lies in forest savanna area. A non-significant decrease was observed in the East project site and in contrast, a significant increase was observed in the South-West 1 project site which both lies in the rainforest zones.
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Affiliation(s)
- Glory N. Amambo
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
- Centre for Neglected Tropical Diseases (Incorporating the Lymphatic Filariasis Support Centre), Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Bonn, Germany
| | - Fanny F. Fombad
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Patrick W. Chounna Ndongmo
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Raphael Awah Abong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Abdel Jelil Njouendou
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Department of Biomedical Science, Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Amuam Andrew Beng
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Theobald Mue Nji
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
- Department of Sociology and Anthropology, Faculty of Social and Management Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Mathias Eyong Esum
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Jerome Fru-Cho
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Ritter Manuel
- Institute of Medical Microbiology, Immunology, and Parasitology, University Hospital Bonn, Germany
| | - Deribe Kebede
- Global Health and Infection Department, Brighton and Sussex Medical School, Brighton BN1 9PX, United Kingdom
- School of Public Health, College of Health Sciences, Addis Ababa University, Ethiopia
| | - Peter Ivo Enyong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology, and Parasitology, University Hospital Bonn, Germany
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Bonn, Germany
| | - Benjamin Koudou
- Unité de Formation et de Recherche Sciences de la Nature, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Moses Bockarie
- Centre for Neglected Tropical Diseases (Incorporating the Lymphatic Filariasis Support Centre), Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- European & Developing Countries Clinical Trials Partnership, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Samuel Wanji
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Res1earch Foundation for Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
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Ornowska S, Wudarski M, Dziewięcka E, Olesińska M. Naifold capillaroscopy in mixed connective tissue disease patients. Clin Rheumatol 2024; 43:1703-1709. [PMID: 38509242 DOI: 10.1007/s10067-024-06879-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Mixed connective tissue disease (MCTD) is a rare systemic disease characterized by overlapping features of systemic lupus erythematosus (SLE), systemic sclerosis (SSc), dermato-/polymyositis (DM/PM), and rheumatoid arthritis (RA). Naifold capillaroscopy (NFC) is a non-invasive test for evaluating the capillaries of the nail shaft used in the diagnosis of rheumatic diseases. OBJECTIVES To determine whether there are characteristic abnormalities in NFC in MCTD patients, and whether the type of NFC lesions correlates with organ involvement in these patients. METHODS Clinical picture and NFC patterns were analyzed in 43 patients with MCTD. Capillaroscopic images were divided into scleroderma-like pattern (SD-like pattern) according to the Cutolo classification, non-specific lesions, and normal images. Relationships between the clinical aspects considered in the MCTD classification criteria and the changes in the capillaroscopic images were evaluated. RESULTS SD-like pattern was present in 20 MCTD patients (46.51%) with a predominance of the "early" pattern. Giant, branched, dilated capillaries and reduced capillary density were found more frequently in MCTD patients compared to the control group (p-values 0.0005, 0.005, 0.02, < 0.0001 respectively). There were associations found between the presence of a reduced number of vessels, avascular areas, and SD-like pattern with the presence of sclerodactyly in MCTD patients (p = 0.002, p = 0.006, p = 0.02, respectively), alongside an association between the presence of branched vessels and the subpapillary plexus with pulmonary arterial hypertension (PAH) (p = 0.04 and p = 0.005, respectively). CONCLUSIONS MCTD patients are significantly more likely to have abnormalities upon NFC. It is worthwhile to perform capillaroscopic examination in MCTD patients. Key Points • Scleroderma-like pattern was found in more than half of the MCTD patients. • Reduced capillary density was found to be a significant predictor of the diagnosis of MCTD. • There were relationships between the presence of reduced capillary density, avascular areas, and SD-like with the presence of sclerodactyly in the MCTD patients. • There was an association between the presence of branched vessels and the visibility of the subpapillary plexus and pulmonary arterial hypertension (PAH).
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Affiliation(s)
- Sylwia Ornowska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, ul. Spartańska 1, 02-637, Warsaw, Poland.
| | - Mariusz Wudarski
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, ul. Spartańska 1, 02-637, Warsaw, Poland
| | - Ewa Dziewięcka
- Department of Cardiac and Vascular Diseases, Jagiellonian University Collegium Medicum, Cardiac Institute, John Paul II Hospital, Kraków, Poland
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, ul. Spartańska 1, 02-637, Warsaw, Poland
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Shin M, Seo M, Lee K, Yoon K. Super-resolution techniques for biomedical applications and challenges. Biomed Eng Lett 2024; 14:465-496. [PMID: 38645589 PMCID: PMC11026337 DOI: 10.1007/s13534-024-00365-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 04/23/2024] Open
Abstract
Super-resolution (SR) techniques have revolutionized the field of biomedical applications by detailing the structures at resolutions beyond the limits of imaging or measuring tools. These techniques have been applied in various biomedical applications, including microscopy, magnetic resonance imaging (MRI), computed tomography (CT), X-ray, electroencephalogram (EEG), ultrasound, etc. SR methods are categorized into two main types: traditional non-learning-based methods and modern learning-based approaches. In both applications, SR methodologies have been effectively utilized on biomedical images, enhancing the visualization of complex biological structures. Additionally, these methods have been employed on biomedical data, leading to improvements in computational precision and efficiency for biomedical simulations. The use of SR techniques has resulted in more detailed and accurate analyses in diagnostics and research, essential for early disease detection and treatment planning. However, challenges such as computational demands, data interpretation complexities, and the lack of unified high-quality data persist. The article emphasizes these issues, underscoring the need for ongoing development in SR technologies to further improve biomedical research and patient care outcomes.
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Affiliation(s)
- Minwoo Shin
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Minjee Seo
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyunghyun Lee
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyungho Yoon
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS Nano 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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Rodríguez CL, Strub C, Fontana A, Verheecke-Vaessen C, Durand N, Beugré C, Guehi T, Medina A, Schorr-Galindo S. Biocontrol activities of yeasts or lactic acid bacteria isolated from Robusta coffee against Aspergillus carbonarius growth and ochratoxin A production in vitro. Int J Food Microbiol 2024; 415:110638. [PMID: 38430685 DOI: 10.1016/j.ijfoodmicro.2024.110638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Biocontrol Agents (BCAs) can be an eco-friendly alternative to fungicides to reduce the contamination with mycotoxigenic fungi on coffee. In the present study, different strains of bacteria and yeasts were isolated from Ivorian Robusta coffee. Their ability to reduce fungal growth and Ochratoxin A (OTA) production during their confrontation against Aspergillus carbonarius was screened on solid media. Some strains were able to reduce growth and OTA production by 85 % and 90 % and were molecularly identified as two yeasts, Rhodosporidiobolus ruineniae and Meyerozyma caribbica. Subsequent tests on liquid media with A. carbonarius or solely with OTA revealed adhesion of R. ruineniae to the mycelium of A. carbonarius through Scanning Electron Microscopy, and an OTA adsorption efficiency of 50 %. For M. caribbica potential degradation of OTA after 24 h incubation was observed. Both yeasts could be potential BCAs good candidates for Ivorian Robusta coffee protection against A. carbonarius and OTA contamination.
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Affiliation(s)
- Claudia López Rodríguez
- Qualisud, Univ Montpellier, CIRAD, Institut Agro, IRD, Avignon Univ, Univ de La Réunion, Montpellier, France; Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, UK
| | - Caroline Strub
- Qualisud, Univ Montpellier, CIRAD, Institut Agro, IRD, Avignon Univ, Univ de La Réunion, Montpellier, France.
| | - Angélique Fontana
- Qualisud, Univ Montpellier, CIRAD, Institut Agro, IRD, Avignon Univ, Univ de La Réunion, Montpellier, France
| | | | - Noël Durand
- Qualisud, Univ Montpellier, CIRAD, Institut Agro, IRD, Avignon Univ, Univ de La Réunion, Montpellier, France; CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Corinne Beugré
- Laboratory of Microbiology and Molecular Biology, Department of Food Science and Technology, University of Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Tagro Guehi
- Laboratory of Microbiology and Molecular Biology, Department of Food Science and Technology, University of Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Angel Medina
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, UK
| | - Sabine Schorr-Galindo
- Qualisud, Univ Montpellier, CIRAD, Institut Agro, IRD, Avignon Univ, Univ de La Réunion, Montpellier, France
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Idelfonso-García OG, Pacheco-Rivera R, Alarcón-Sánchez BR, Serrano-Luna J, Baltiérrez-Hoyos R, Vásquez-Garzón VR, Muriel P, Villa-Treviño S, Pérez-Carreón JI, Arellanes-Robledo J. Protocol to detect senescence-associated β-galactosidase and immunoperoxidase activity in fresh-frozen murine tissues. STAR Protoc 2024; 5:103009. [PMID: 38602869 PMCID: PMC11017356 DOI: 10.1016/j.xpro.2024.103009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Double labeling to identify different markers in the same tissue section represents a useful tool either for in situ diagnosis or characterization of molecular associations. Here, we present a protocol to detect senescence-associated β-galactosidase (SA-βGal) and immunoperoxidase (IPO) activity in fresh-frozen murine tissues. We describe steps for tissue collection, solution preparation, SA-βGal staining, IPO staining, hematoxylin counterstaining, microscopic observation, and signal quantification. This protocol can be used to detect in situ proteins alongside SA-βGal activity. For complete details on the use and execution of this protocol, please refer to Pacheco-Rivera et al.1.
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Affiliation(s)
- Osiris Germán Idelfonso-García
- Laboratory of Liver Diseases, National Institute of Genomic Medicine - INMEGEN, Mexico City 14610, Mexico; Department of Health Sciences, Metropolitan Autonomous University - Iztapalapa Campus - UAM-I, Mexico City 09340, Mexico.
| | - Ruth Pacheco-Rivera
- Laboratory of Molecular Diagnostics, Department of Biochemistry, National School of Biological Sciences of the National Polytechnic Institute, Mexico City 07738, Mexico
| | - Brisa Rodope Alarcón-Sánchez
- Laboratory of Liver Diseases, National Institute of Genomic Medicine - INMEGEN, Mexico City 14610, Mexico; Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute - CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Jesús Serrano-Luna
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute - CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Rafael Baltiérrez-Hoyos
- Laboratory of Fibrosis and Cancer, Faculty of Medicine and Surgery, "Benito Juárez" Autonomous University of Oaxaca - UABJO, Mexico City 68120, Mexico; Deputy Directorate of Humanistic and Scientific Research, National Council of Humanities, Sciences and Technologies - CONAHCYT, Mexico City 03940, Mexico
| | - Verónica Rocío Vásquez-Garzón
- Laboratory of Fibrosis and Cancer, Faculty of Medicine and Surgery, "Benito Juárez" Autonomous University of Oaxaca - UABJO, Mexico City 68120, Mexico; Deputy Directorate of Humanistic and Scientific Research, National Council of Humanities, Sciences and Technologies - CONAHCYT, Mexico City 03940, Mexico
| | - Pablo Muriel
- Laboratory of Experimental Hepatology, Department of Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute - CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Saúl Villa-Treviño
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute - CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Julio Isael Pérez-Carreón
- Laboratory of Liver Diseases, National Institute of Genomic Medicine - INMEGEN, Mexico City 14610, Mexico
| | - Jaime Arellanes-Robledo
- Laboratory of Liver Diseases, National Institute of Genomic Medicine - INMEGEN, Mexico City 14610, Mexico; Deputy Directorate of Humanistic and Scientific Research, National Council of Humanities, Sciences and Technologies - CONAHCYT, Mexico City 03940, Mexico.
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12
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F Shida J, Ma K, Toll HW, Salinas O, Ma X, Peng CS. Multicolor Long-Term Single-Particle Tracking Using 10 nm Upconverting Nanoparticles. Nano Lett 2024; 24:4194-4201. [PMID: 38497588 DOI: 10.1021/acs.nanolett.4c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Single-particle tracking (SPT) is a powerful technique to unveil molecular behaviors crucial to the understanding of many biological processes, but it is limited by factors such as probe photostability and spectral orthogonality. To overcome these limitations, we develop upconverting nanoparticles (UCNPs), which are photostable over several hours at the single-particle level, enabling long-term multicolor SPT. We investigate the brightness of core-shell UCNPs as a function of inert shell thickness to minimize particle size while maintaining sufficient signal for SPT. We explore different rare-earth dopants to optimize for the brightest probes and find that UCNPs doped with 2% Tm3+/30% Yb3+, 10% Er3+/90% Yb3+, and 15% Tm3+/85% Yb3+ represent the optimal probes for blue, green, and near-infrared emission, respectively. The multiplexed 10 nm probes enable three-color single-particle tracking on live HeLa cells for tens of minutes using a single, near-infrared excitation source. These photostable and multiplexed probes open new avenues for numerous biological applications.
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Affiliation(s)
- João F Shida
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Kaibo Ma
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Harrison W Toll
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Omar Salinas
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Xiaojie Ma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
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13
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Coker ZN, Troyanova-Wood M, Steelman ZA, Ibey BL, Bixler JN, Scully MO, Yakovlev VV. Brillouin microscopy monitors rapid responses in subcellular compartments. Photonix 2024; 5:9. [PMID: 38618142 PMCID: PMC11006764 DOI: 10.1186/s43074-024-00123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/12/2024] [Accepted: 03/11/2024] [Indexed: 04/16/2024]
Abstract
Measurements and imaging of the mechanical response of biological cells are critical for understanding the mechanisms of many diseases, and for fundamental studies of energy, signal and force transduction. The recent emergence of Brillouin microscopy as a powerful non-contact, label-free way to non-invasively and non-destructively assess local viscoelastic properties provides an opportunity to expand the scope of biomechanical research to the sub-cellular level. Brillouin spectroscopy has recently been validated through static measurements of cell viscoelastic properties, however, fast (sub-second) measurements of sub-cellular cytomechanical changes have yet to be reported. In this report, we utilize a custom multimodal spectroscopy system to monitor for the very first time the rapid viscoelastic response of cells and subcellular structures to a short-duration electrical impulse. The cytomechanical response of three subcellular structures - cytoplasm, nucleoplasm, and nucleoli - were monitored, showing distinct mechanical changes despite an identical stimulus. Through this pioneering transformative study, we demonstrate the capability of Brillouin spectroscopy to measure rapid, real-time biomechanical changes within distinct subcellular compartments. Our results support the promising future of Brillouin spectroscopy within the broad scope of cellular biomechanics.
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Affiliation(s)
- Zachary N. Coker
- Department of Physics & Astronomy, Texas A&M University, 4242 TAMU, College Station, TX 77843 USA
- SAIC, Fort Sam Houston, TX 78234 USA
| | | | - Zachary A. Steelman
- Air Force Research Laboratory, JBSA Fort Sam Houston, Fort Sam Houston, TX 78234 USA
| | - Bennett L. Ibey
- Air Force Research Laboratory, JBSA Fort Sam Houston, Fort Sam Houston, TX 78234 USA
| | - Joel N. Bixler
- Air Force Research Laboratory, JBSA Fort Sam Houston, Fort Sam Houston, TX 78234 USA
| | - Marlan O. Scully
- Department of Physics & Astronomy, Texas A&M University, 4242 TAMU, College Station, TX 77843 USA
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, TX 77843 USA
| | - Vladislav V. Yakovlev
- Department of Physics & Astronomy, Texas A&M University, 4242 TAMU, College Station, TX 77843 USA
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, TX 77843 USA
- Department of Biomedical Engineering, Texas A&M University, 3120 TAMU, 101 Bizzell Street, College Station, TX 77843 USA
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14
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Delgadillo-Guevara M, Halte M, Erhardt M, Popp PF. Fluorescent tools for the standardized work in Gram-negative bacteria. J Biol Eng 2024; 18:25. [PMID: 38589953 PMCID: PMC11003136 DOI: 10.1186/s13036-024-00420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.
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Affiliation(s)
- Mario Delgadillo-Guevara
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Halte
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Marc Erhardt
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, 10117, Germany
| | - Philipp F Popp
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany.
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15
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Manrique-Castano D, ElAli A. Unbiased quantification of the spatial distribution of murine cells using point pattern analysis. STAR Protoc 2024; 5:102989. [PMID: 38568817 PMCID: PMC10999708 DOI: 10.1016/j.xpro.2024.102989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/09/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
CNS injuries are associated with profound changes in cell organization. This protocol presents a stepwise approach to quantitatively describe the spatiotemporal changes in glial cell rearrangement in the injured murine brain, which is applicable to other biological contexts. Herein, we apply common immunolabeling of neurons and glial cells and wide-field microscopy imaging. Then, we employ computational tools for alignment to the Allen Brain Atlas, unbiased/automatic detection of cells, generation of point patterns, and data analysis. For complete details on the use and execution of this protocol, please refer to Manrique-Castano et al.1.
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Affiliation(s)
- Daniel Manrique-Castano
- Neuroscience Axis, Research Center of CHU de Québec - Université Laval, Quebec City, QC G1V 0A6, Canada; Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada.
| | - Ayman ElAli
- Neuroscience Axis, Research Center of CHU de Québec - Université Laval, Quebec City, QC G1V 0A6, Canada; Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada.
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16
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Bolz S, Kaempf N, Muehlbauer M, Löwe D, Haucke V. Phosphoinositide detection at synapses of fixed murine hippocampal neurons. STAR Protoc 2024; 5:102945. [PMID: 38573863 PMCID: PMC10999879 DOI: 10.1016/j.xpro.2024.102945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
The minor phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is crucial for neurotransmission and has been implicated in Parkinson's disease. Here, we present a staining protocol for the analysis of activity-dependent changes of PI(4,5)P2 at synapses. We describe steps for stimulating and fixing murine hippocampal neurons, staining with probes for PI(4,5)P2 and a synaptic marker, and analysis by high-resolution microscopy. Our approach gives insights into local PI(4,5)P2 synthesis and turnover at synapses and can be extended to phosphoinositide lipids other than PI(4,5)P2. For complete details on the use and execution of this protocol, please refer to Bolz et al.1.
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Affiliation(s)
- Svenja Bolz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Natalie Kaempf
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Maria Muehlbauer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Delia Löwe
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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Palacios-Rápalo SN, Hernández-Castillo J, Cordero-Rivera CD, Benítez-Vega ML, De Jesús-González LA, Reyes-Ruiz JM, Farfan-Morales CN, Osuna-Ramos JF, Gonzalez-Gonzalez AM, Cruz R, Del Ángel RM. Protocol to evaluate the antiviral effect of FDA-approved drugs against dengue virus in Huh7 cells and AG129 mice. STAR Protoc 2024; 5:102992. [PMID: 38568816 PMCID: PMC10999876 DOI: 10.1016/j.xpro.2024.102992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Finding an effective therapy against diseases caused by flaviviruses remains a challenge. Here, we present a protocol to test Food and Drug Administration-approved drugs that inhibit host nuclear protein import, promoting a reduction of dengue infection. We describe steps for analyzing the drug effect on nuclear import inhibition of cellular and viral proteins by confocal microscopy or western blotting. We then describe procedures for measuring the antiviral drug effects on virus-infected cells by flow cytometry and testing drug efficacy in dengue-infected AG129 mice by survival assays. For complete details on the use and execution of this protocol, please refer to Palacios-Rápalo et al.1.
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Affiliation(s)
- Selvin Noé Palacios-Rápalo
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico
| | - Jonathan Hernández-Castillo
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico
| | - Carlos Daniel Cordero-Rivera
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico
| | - Magda Lizbeth Benítez-Vega
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico
| | | | - José Manuel Reyes-Ruiz
- Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 14, Centro Médico Nacional "Adolfo Ruiz Cortines", Instituto Mexicano del Seguro Social (IMSS), Veracruz 91897, México; Facultad de Medicina, Región Veracruz, Universidad Veracruzana (UV), Veracruz 91700, México
| | - Carlos Noe Farfan-Morales
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico; Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana (UAM), Unidad Cuajimalpa, Ciudad de México 05348, México
| | | | - Arely M Gonzalez-Gonzalez
- Laboratorio de Ingeniería Tisular y Medicina Traslacional, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de Mexico (UNAM), Mexico City 54090, Mexico
| | - Raymundo Cruz
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico
| | - Rosa María Del Ángel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico.
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Di Pizio A. A bitter taste receptor activated in a surprising way. Nature 2024; 628:506-507. [PMID: 38600187 DOI: 10.1038/d41586-024-00712-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
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19
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Lindstrom AP, Conny JM, Ortiz-Montalvo DL. Sampling of microplastics at a materials recovery facility. Anal Bioanal Chem 2024:10.1007/s00216-024-05231-x. [PMID: 38558307 DOI: 10.1007/s00216-024-05231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Detecting, separating, and characterizing airborne microplastics from other airborne particulates is currently challenging due to the various instrumental constraints and related sample preparation hurdles that must be overcome. The ability to measure these real-world environments is needed to better assess the risks associated with microplastics. To that end, the current study focused on developing a methodology for sampling and characterizing airborne microplastics. Particulate sampling was carried out at a municipal materials recovery facility near a conveyer belt containing sorted plastic materials to collect airborne environmental particles on filters. Nucleopore filters were mounted on Teflon support rings, coated with 100 nm aluminum to reduce the background signal for micro-Raman spectroscopy, and marked with a fiducial pattern using a laser engraver. The fiducial pattern was crucial in identifying samples, relocating particles, and efficiently enabling orthogonal measurements on the same samples. Optimum sampling conditions of 2 h at 25 L/min were determined using light microscopy to evaluate the particle loadings. The filters were then cut into slices which were attached to sections of thin beryllium-copper sheeting for easy transfer of the filter between microscopy platforms. Scanning electron microscopy was used to identify carbon-rich particles. Light microscopy was used to identify colored particles which were also carbon-rich which were then analyzed using micro-Raman spectroscopy to identify specific polymers.
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Affiliation(s)
- Abigail P Lindstrom
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | - Joseph M Conny
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Diana L Ortiz-Montalvo
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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20
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da Rocha RFP, da Costa MPM, da Costa ACA, de Mello Ferreira IL. Study of the degradation in an ultisol of alginate-chitosan complex and its stability and applicability as a soil conditioner. Int J Biol Macromol 2024; 264:130384. [PMID: 38395282 DOI: 10.1016/j.ijbiomac.2024.130384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The present work describes the process of degradation of a polyelectrolytic complex (PEC) based on sodium alginate (ALG) and chitosan (CHI), buried for different time intervals, in a clayey soil (ultisol) collected from the municipality of Campos dos Goytacazes, in the northern region of the state of Rio de Janeiro, Brazil. The influence of PEC on soil moisture was also investigated. The results showed that soil moisture increased with the presence of PEC after 7 days of testing, and remained high until the end of the study. FTIR and Raman spectra showed that the breaking of the glycosidic bond (C-O-C) was responsible for the PEC degradation. Thermogravimetry results revealed that alginate was possibly degraded faster than chitosan. Microscopic analysis of the PEC revealed a fragile and fragmented surface of the samples that were buried, in comparison with those not buried. The microbiological assays of the soil confirmed the biodegradation of the polysaccharides. Chemical analysis of soil indicated that PEC did not significantly influence soil fertility. Therefore, we conclude that the PEC (ALG: CHI), formed only by electrostatic interaction, buried in clayey soil, even being biodegraded, can be a promising soil conditioner for agricultural applications.
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21
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Welter EM, Benavides S, Archer TK, Kosyk O, Zannas AS. Machine learning-based morphological quantification of replicative senescence in human fibroblasts. GeroScience 2024; 46:2425-2439. [PMID: 37985642 PMCID: PMC10828145 DOI: 10.1007/s11357-023-01007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/28/2023] [Indexed: 11/22/2023] Open
Abstract
Although aging has been investigated extensively at the organismal and cellular level, the morphological changes that individual cells undergo along their replicative lifespan have not been precisely quantified. Here, we present the results of a readily accessible machine learning-based pipeline that uses standard fluorescence microscope and open access software to quantify the minute morphological changes that human fibroblasts undergo during their replicative lifespan in culture. Applying this pipeline in a widely used fibroblast cell line (IMR-90), we find that advanced replicative age robustly increases (+28-79%) cell surface area, perimeter, number and total length of pseudopodia, and nuclear surface area, while decreasing cell circularity, with phenotypic changes largely occurring as replicative senescence is reached. These senescence-related morphological changes are recapitulated, albeit to a variable extent, in primary dermal fibroblasts derived from human donors of different ancestry, age, and sex groups. By performing integrative analysis of single-cell morphology, our pipeline further classifies senescent-like cells and quantifies how their numbers increase with replicative senescence in IMR-90 cells and in dermal fibroblasts across all tested donors. These findings provide quantitative insights into replicative senescence, while demonstrating applicability of a readily accessible computational pipeline for high-throughput cell phenotyping in aging research.
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Affiliation(s)
- Emma M Welter
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Sofia Benavides
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Oksana Kosyk
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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22
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Wehrle E, Günther D, Mathavan N, Singh A, Müller R. Protocol for preparing formalin-fixed paraffin-embedded musculoskeletal tissue samples from mice for spatial transcriptomics. STAR Protoc 2024; 5:102986. [PMID: 38555590 PMCID: PMC10998190 DOI: 10.1016/j.xpro.2024.102986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/29/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Here, we present a protocol for using spatial transcriptomics in bone and multi-tissue musculoskeletal formalin-fixed paraffin-embedded (FFPE) samples from mice. We describe steps for tissue harvesting, sample preparation, paraffin embedding, and FFPE sample selection. We detail procedures for sectioning and placement on spatial slides prior to imaging, decrosslinking, library preparation, and final analyses of the sequencing data. The complete protocol takes ca. 18 days for mouse femora with adjacent muscle; of this time, >50% is required for mineralized tissue decalcification. For complete details on the use and execution of this protocol, please refer to Wehrle et al.1 and Mathavan et al.2.
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Affiliation(s)
- Esther Wehrle
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland; AO Research Institute Davos, Davos Platz, Switzerland.
| | - Denise Günther
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | | | - Amit Singh
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Ralph Müller
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
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23
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Ma C, Zhu Y, Zhang Z, Chen X, Ji Z, Zhang LN, Xu Q. Ratiometric electrochemiluminescence sensing and intracellular imaging of ClO - via resonance energy transfer. Anal Bioanal Chem 2024:10.1007/s00216-024-05236-6. [PMID: 38512384 DOI: 10.1007/s00216-024-05236-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Electrochemiluminescence resonance energy transfer (ECL-RET) is a versatile signal transduction strategy widely used in the fabrication of chem/biosensors. However, this technique has not yet been applied in visualized imaging analysis of intracellular species due to the insulating nature of the cell membrane. Here, we construct a ratiometric ECL-RET analytical method for hypochlorite ions (ClO-) by ECL luminophore, with a luminol derivative (L-012) as the donor and a fluorescence probe (fluorescein hydrazide) as the acceptor. L-012 can emit a strong blue ECL signal and fluorescein hydrazide has negligible absorbance and fluorescence signal in the absence of ClO-. Thus, the ECL-RET process is turned off at this time. In the presence of ClO-, however, the closed-loop hydrazide structure in fluorescein hydrazide is opened via specific recognition with ClO-, accompanied with intensified absorbance and fluorescence signal. Thanks to the spectral overlap between the ECL spectrum of L-012 and the absorption spectrum of fluorescein, the ECL-RET effect is gradually recovered with the addition of ClO-. Furthermore, the ECL-RET system has been successfully applied to image intracellular ClO-. Although the insulating nature of the cell itself can generate a shadow ECL pattern in the cellular region, extracellular ECL emission penetrates the cell membrane and excites intracellular fluorescein generated by the reactions between fluorescein hydrazide and ClO-. The cell imaging strategy via ECL-RET circumvents the blocking of the cell membrane and enables assays of intracellular species. The importance of the ECL-RET platform lies in calibrating the fluctuation from the external environment and improving the selectivity by using fluorescent probes. Therefore, this ratiometric ECL sensor has shown broad application prospects in the identification of targets in clinical diagnosis and environmental monitoring.
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Affiliation(s)
- Cheng Ma
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China.
| | - Yujing Zhu
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China
| | - Zhichen Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China
| | - Xuan Chen
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China
| | - Zhengping Ji
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China
| | - Lu-Nan Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China
| | - Qin Xu
- School of Chemistry and Chemical Engineering, Yangzhou University, YangzhouJiangsu, 225002, China.
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24
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Travisano SI, Lien CL. Protocol for the isolation and single-nuclei multiomic analyses of the human fetal epicardium. STAR Protoc 2024; 5:102973. [PMID: 38517898 PMCID: PMC10978535 DOI: 10.1016/j.xpro.2024.102973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
The characterization of cell populations that reside in the outer layer of the heart has been hindered by difficulties in their isolation. Here, we present a protocol for isolation and single-nuclei multiomic analyses of the human fetal epicardium. We describe steps for microdissection, isolation, and enrichment of epicardial cells by mechanical dissociations and direct lysis. We then detail procedures for integrating transcriptome and chromatin accessibility datasets. This approach allows the analysis of diverse cell populations, marked by unique cis-regulatory elements. For complete details on the use and execution of this protocol, please refer to Travisano et al.1.
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Affiliation(s)
| | - Ching-Ling Lien
- The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Surgery, Biochemistry, and Molecular Medicine, Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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25
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Landajuela A, Braun M, Rodrigues CDA, Karatekin E. Detection of membrane fission in single Bacillus subtilis cells during endospore formation with high temporal resolution. STAR Protoc 2024; 5:102965. [PMID: 38502684 DOI: 10.1016/j.xpro.2024.102965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/17/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Membrane fission is an essential process in all domains of life. The underlying mechanisms remain poorly understood in bacteria, partly because suitable assays are lacking. Here, we describe an assay to detect membrane fission during endospore formation in single Bacillus subtilis cells with a temporal resolution of ∼1 min. Other cellular processes can be quantified and temporally aligned to the membrane fission event in individual cells, revealing correlations and causal relationships. For complete details on the use and execution of this protocol, please refer to Landajuela et al.1.
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Affiliation(s)
- Ane Landajuela
- Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA.
| | - Martha Braun
- Nanobiology Institute, Yale University, West Haven, CT, USA; Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Erdem Karatekin
- Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA; Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Université de Paris, Saints-Pères Paris Institute for the Neurosciences (SPPIN), Centre National de la Recherche Scientifique (CNRS), 75006 Paris, France.
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26
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Liang W, Najor RH, Gustafsson ÅB. Protocol to separate small and large extracellular vesicles from mouse and human cardiac tissues. STAR Protoc 2024; 5:102914. [PMID: 38386549 PMCID: PMC10897917 DOI: 10.1016/j.xpro.2024.102914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
Extracellular vesicles (EVs) are secreted by cells under various conditions and can contribute to the disease progression in tissues. Here, we present a protocol to separate small and large EVs from mouse hearts and cardiac tissues collected from patients. We describe steps for utilizing enzymatic digestion for release of EVs from interstitial space followed by differential centrifugation and immunoaffinity purification. The isolated EVs can be used for various experiments to gain insight into their in vivo functions. For complete details on the use and execution of this protocol, please refer to Liang et al. (2023).1.
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Affiliation(s)
- Wenjing Liang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Rita H Najor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Åsa B Gustafsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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27
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Ilamathi HS, Benhammouda S, Chatel-Chaix L, Germain M. Protocol for measuring interorganelle contact sites in primary cells using a modified proximity ligation assay. STAR Protoc 2024; 5:102915. [PMID: 38393951 PMCID: PMC10901140 DOI: 10.1016/j.xpro.2024.102915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Interorganelle contact sites regulate lipid metabolism, organelle dynamics and positioning, as well as apoptosis and autophagy. Here, we present a proximity ligation assay (PLA) protocol for measuring the association of two organelles in fixed cells. We describe steps for primary cell culture, primary cell transfection, and the assay itself. We then detail procedures for manual and image J-based analysis of PLA foci. This protocol optimizes the use of assay products and improves the identification of PLA foci labeling actual contact sites. For complete details on the use and execution of this protocol, please refer to Ilamathi et al. (2023).1.
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Affiliation(s)
- Hema Saranya Ilamathi
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3, Canada; Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Montréal, QC H3C 3P8, Canada; Réseau Intersectoriel de Recherche en Santé de l'Université du Québec (RISUQ), Québec, QC G1K 9H7, Canada
| | - Sara Benhammouda
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3, Canada; Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Montréal, QC H3C 3P8, Canada; Réseau Intersectoriel de Recherche en Santé de l'Université du Québec (RISUQ), Québec, QC G1K 9H7, Canada
| | - Laurent Chatel-Chaix
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Montréal, QC H3C 3P8, Canada; Réseau Intersectoriel de Recherche en Santé de l'Université du Québec (RISUQ), Québec, QC G1K 9H7, Canada; Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3, Canada; Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Montréal, QC H3C 3P8, Canada; Réseau Intersectoriel de Recherche en Santé de l'Université du Québec (RISUQ), Québec, QC G1K 9H7, Canada.
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28
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Desai JV, Lionakis MS. Evaluation of murine renal phagocyte-fungal interactions using intravital confocal microscopy and flow cytometry. STAR Protoc 2024; 5:102781. [PMID: 38113143 PMCID: PMC10770751 DOI: 10.1016/j.xpro.2023.102781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Myeloid phagocytes are essential for antifungal host defense during systemic candidiasis. Here, we present a protocol for assessing phagocyte-fungal interactions in vivo in the kidney, the primary target organ of the murine systemic candidiasis model. We describe steps for intravital confocal microscopy and flow cytometry. We also detail a kidney tissue dissociation procedure to obtain highly pure functional phagocytes for utilization in downstream ex vivo fungal uptake and killing assays.
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Affiliation(s)
- Jigar V Desai
- Fungal Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Michail S Lionakis
- Fungal Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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Kim M, Fèvre C, Lavina M, Disson O, Lecuit M. Protocol for live imaging of bacteria-cell interactions in genetically modified mouse small intestinal organoids. STAR Protoc 2024; 5:102773. [PMID: 38103194 PMCID: PMC10764352 DOI: 10.1016/j.xpro.2023.102773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Here, we present a protocol for microinjection of bacteria into mouse small intestinal organoids that recapitulates the natural route of infection of intestinal epithelial cells from the intestinal lumen. We describe steps for visualizing bacteria-cell interactions by live imaging of infected organoids using light sheet microscopy. We then detail procedures for generating doxycycline-inducible expression of mutant proteins in organoids to study essential gene functions. The different techniques described in this protocol can be used independently as required. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).1.
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Affiliation(s)
- Minhee Kim
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015 Paris, France.
| | - Cindy Fèvre
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Morgane Lavina
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Olivier Disson
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, 75015 Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France; Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75006 Paris, France.
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30
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Wijerathne T, Lacroix J. Voltage-clamp fluorometry to record flow-activated PIEZO1 currents and fluorometric signals. STAR Protoc 2024; 5:102789. [PMID: 38103195 PMCID: PMC10770629 DOI: 10.1016/j.xpro.2023.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/13/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
PIEZO channels sense mechanical forces through conformational rearrangements of a mechanosensory domain called blade. To probe these rearrangements in real time, we have inserted conformational-sensitive cyclic-permuted GFP into several positions of PIEZO1's blade. Here, we describe the step-by-step experimental procedure we developed to simultaneously measure flow-activated ionic currents and fluorometric signals in cells expressing these engineered constructs. We describe steps for performing transfection, seeding cells on coverslips, setting up a perfusion-based fluid shear application system, and performing voltage-clamp fluorometry. For complete details on the use and execution of this protocol, please refer to Ozkan et al. (2023).1.
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Affiliation(s)
- Tharaka Wijerathne
- Department of Basic Medical Sciences, Western University of Health Sciences, 309 East Second St., Pomona, CA 91766, USA
| | - Jerome Lacroix
- Department of Basic Medical Sciences, Western University of Health Sciences, 309 East Second St., Pomona, CA 91766, USA.
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31
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Popgeorgiev N, Gil C, Berthenet K, Bertolin G, Ichim G. Shedding light on mitochondrial outer-membrane permeabilization and membrane potential: State of the art methods and biosensors. Semin Cell Dev Biol 2024; 156:58-65. [PMID: 37438211 DOI: 10.1016/j.semcdb.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Membrane structural integrity is essential for optimal mitochondrial function. These organelles produce the energy needed for all vital processes, provided their outer and inner membranes are intact. This prevents the release of mitochondrial apoptogenic factors into the cytosol and ensures intact mitochondrial membrane potential (ΔΨm) to sustain ATP production. Cell death by apoptosis is generally triggered by outer mitochondrial membrane permeabilization (MOMP), tightly coupled with loss of ΔΨ m. As these two processes are essential for both mitochondrial function and cell death, researchers have devised various techniques to assess them. Here, we discuss current methods and biosensors available for detecting MOMP and measuring ΔΨ m, focusing on their advantages and limitations and discuss what new imaging tools are needed to improve our knowledge of mitochondrial function.
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Affiliation(s)
- Nikolay Popgeorgiev
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France; Institut Universitaire de France (IUF), Paris, France
| | - Clara Gil
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France
| | - Kevin Berthenet
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Institute of Genetics and Development of Rennes), Rennes, France.
| | - Gabriel Ichim
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France.
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32
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Hooshmandi M, Wong C, Lister KC, Brown N, Cai W, Ho-Tieng D, Stecum P, Backman T, Kostantin E, Khoutorsky A. Protocol for measuring protein synthesis in specific cell types in the mouse brain using in vivo non-canonical amino acid tagging. STAR Protoc 2024; 5:102775. [PMID: 38085640 PMCID: PMC10783633 DOI: 10.1016/j.xpro.2023.102775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/09/2023] [Accepted: 11/29/2023] [Indexed: 01/14/2024] Open
Abstract
The fluorescent non-canonical amino acid tagging (FUNCAT) technique has been used to visualize newly synthesized proteins in cell lines and tissues. Here, we present a protocol for measuring protein synthesis in specific cell types in the mouse brain using in vivo FUNCAT. We describe steps for metabolically labeling newly synthesized proteins with azidohomoalanine, which introduces an azide group into the polypeptide. We then detail procedures for binding a fluorophore-conjugated alkyne to the azide group to allow its visualization. For complete details on the use and execution of this protocol, please refer to tom Dieck et al. (2012)1 and Hooshmandi et al. (2023).2.
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Affiliation(s)
- Mehdi Hooshmandi
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada.
| | - Calvin Wong
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Kevin C Lister
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Nicole Brown
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Weihua Cai
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - David Ho-Tieng
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Patricia Stecum
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Thomas Backman
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Elie Kostantin
- Clinical Department of Laboratory Medicine, Cite-de-la-Sante Hospital, Optilab LLL and University of Montreal, Montreal, QC, Canada
| | - Arkady Khoutorsky
- Department of Anesthesia and Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada.
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33
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Mulder EJ, Moser B, Delgado J, Steinhardt R, Esser-Kahn AP. Protocol for localized macrophage stimulation with small-molecule TLR agonist via fluidic force microscopy. STAR Protoc 2024; 5:102873. [PMID: 38427566 PMCID: PMC10918328 DOI: 10.1016/j.xpro.2024.102873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 03/03/2024] Open
Abstract
Here, we present a protocol to deliver nanoliter volumes of Toll-like receptor (TLR) agonist onto a culture of nuclear factor κB (NF-κB) reporter macrophages using fluidic force microscopy and a micron-scale probe. We describe steps for quantifying the dose of agonist by modeling their diffusion with experimental inputs. We then detail procedures for quantifying and categorizing macrophage responses to individual and varied doses and combining agonist concentration and macrophage response to analyze the NF-κB response to localized TLR stimulation. For complete details on the use and execution of this protocol, please refer to Mulder et al. (2024).1.
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Affiliation(s)
| | - Brittany Moser
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer Delgado
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Rachel Steinhardt
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Aaron P Esser-Kahn
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.
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34
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Petratou D, Fragkiadaki P, Lionaki E, Tavernarakis N. Assessing locomotory rate in response to food for the identification of neuronal and muscular defects in C. elegans. STAR Protoc 2024; 5:102801. [PMID: 38159271 PMCID: PMC10805661 DOI: 10.1016/j.xpro.2023.102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
C. elegans is a bacteria-eating soil-dwelling nematode. Typical cultivation of laboratory-reared populations occurs on bacteria-covered solid media, where they move along with sinusoidal undulations. Nematodes decelerate when they encounter food. Dopaminergic and serotonergic neurotransmission regulate this behavior. Here, we describe the procedure for determining food-dependent locomotion rate of fed and fasting nematodes. We detail steps for assay plate preparation, C. elegans synchronization, and assessment of locomotion. The behaviors we describe provide information regarding the animal's physiological neuronal and muscular function. For complete details on the use and execution of this protocol, please refer to Petratou et al. (2023)1 and Sawin et al. (2000).2.
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Affiliation(s)
- Dionysia Petratou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013 Crete, Greece; Department of Basic Sciences, Medical School, University of Crete, Heraklion, 71003 Crete, Greece
| | - Persefoni Fragkiadaki
- Department of Toxicology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece
| | - Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013 Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, 70013 Crete, Greece; Department of Basic Sciences, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
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35
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Leites EP, Morais VA. Protocol for the isolation and culture of microglia, astrocytes, and neurons from the same mouse brain. STAR Protoc 2024; 5:102804. [PMID: 38206816 PMCID: PMC10825338 DOI: 10.1016/j.xpro.2023.102804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/08/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
Studying the intrinsic properties of microglia, astrocytes, and neurons is essential to our understanding of brain function. Here, we present a protocol to isolate and culture these neural cells from the same mouse brain. Using immunocapture magnetic beads, we describe steps for dissociating, cleaning, and sequentially separating brains from 9-day-old mice into microglia, astrocytes, and neurons. Following these detailed procedures for seeding and culturing of isolated cells, we can address critical questions related to brain function.
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Affiliation(s)
- Elvira P Leites
- iMM Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Vanessa A Morais
- iMM Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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36
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Li JSF, Tang PCT, Choi CKK, Chan ASW, Ng CSH, To KF, Tang PMK. Protocol to study immunodynamics in the tumor microenvironment using a tyramide signal amplification-based immunofluorescent multiplex panel. STAR Protoc 2024; 5:102823. [PMID: 38194342 PMCID: PMC10820311 DOI: 10.1016/j.xpro.2023.102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Immunodynamics in the tumor microenvironment can be precisely examined by using multiple antigen identification approaches. Here, we present a protocol for capturing expression levels of multiple target proteins in the same specimen at single-cell resolution using a tyramide signal amplification-based immunofluorescent multiplexing system. We describe steps for tumor tissue microarray preparation, multiplex immunohistochemistry staining, image acquisition, and quantification. This protocol can quantify immune cells in tissues from patients or experimental disease models at a protein level. For complete details on the use and execution of this protocol, please refer to Chung et al. (2023),1 Tang et al. (2022),2 and Tang et al. (2022).3.
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Affiliation(s)
- Jane Siu-Fan Li
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Philip Chiu-Tsun Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Kit K Choi
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alex Siu-Wing Chan
- Department of Applied Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Calvin Sze-Hang Ng
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Patrick Ming-Kuen Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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37
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Bjornson KJ, Cahill ME. Assessing protein distribution and dendritic spine morphology relationships using structured illumination microscopy in cultured neurons. STAR Protoc 2024; 5:102829. [PMID: 38236769 PMCID: PMC10827590 DOI: 10.1016/j.xpro.2023.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 02/03/2024] Open
Abstract
Dendritic spines are protrusions on dendrites forming the postsynaptic aspect of excitatory connections within the brain. Spine morphology is associated with synaptic functional strength and the spatial regulation of protein nanodomains within dendritic spines is an important determinant of spine structure and function. Here, we present a protocol to resolve the nanoscale localization of proteins within dendritic spines using structured illumination microscopy. We describe steps for the structural analysis of dendritic spine parameters, protein localization analysis, and data processing. For complete details on the use and execution of this protocol, please refer to Bjornson et al.1.
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Affiliation(s)
- Kathryn J Bjornson
- Department of Comparative Biosciences, University of Wisconsin, Madison, WI 53706, USA.
| | - Michael E Cahill
- Department of Comparative Biosciences, University of Wisconsin, Madison, WI 53706, USA.
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38
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Arellano-Caicedo C, Beech JP, Bengtsson M, Ohlsson P, Hammer EC. Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models. STAR Protoc 2024; 5:102784. [PMID: 38103191 PMCID: PMC10783617 DOI: 10.1016/j.xpro.2023.102784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/07/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1.
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Affiliation(s)
- Carlos Arellano-Caicedo
- Center of Microbiology and Environmental System Sciences, University of Vienna, 1030 Vienna, Austria; Department of Biology, Lund University, 22362 Lund, Sweden.
| | - Jason P Beech
- Division of Solid-State Physics, Lund University, 22363 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, 22363 Lund, Sweden
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, 22363 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, 22362 Lund, Sweden.
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39
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Sun N, Shao H, Zhang Y, Ci B, Yao H, Bai B, Tan T. Establishing a 3D culture system for early organogenesis of monkey embryos ex vivo and single-cell transcriptome analysis of cultured embryos. STAR Protoc 2024; 5:102835. [PMID: 38224493 PMCID: PMC10826423 DOI: 10.1016/j.xpro.2023.102835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
Creating in vitro culture platforms for monkey embryos is crucial for understanding the initial 4 weeks of early primate embryogenesis. Here, we present a protocol to culture cynomolgus monkey embryos in vitro for 25 days post-fertilization and to delineate the key developmental events of gastrulation and early organogenesis. We describe steps for culturing with a 3D system, immunofluorescence analysis, single-cell RNA sequencing, and bioinformatic analysis. For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1.
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Affiliation(s)
- Nianqin Sun
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Honglian Shao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Youyue Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Baiquan Ci
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Hui Yao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Bing Bai
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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40
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Tingey M, Junod SL, Rush C, Yang W. Protocol for live-cell super-resolution imaging of transport of pre-ribosomal subunits through the nuclear pore complex. STAR Protoc 2024; 5:102790. [PMID: 38113144 PMCID: PMC10770744 DOI: 10.1016/j.xpro.2023.102790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Here, we present a protocol for single-molecule super-resolution imaging of the nuclear export of pre-ribosomal subunits pre-40S and pre-60S through nuclear pore complexes. We describe steps for plating cells and co-transfecting cells. We then detail steps for using single-point edge-excitation sub-diffraction microscopy, allowing visualization of real-time dynamics of the pre-ribosomal subunits. For complete details on the use and execution of this protocol, please refer to Junod et al. (2023).1.
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Affiliation(s)
- Mark Tingey
- Temple University Department of Biology, Philadelphia, PA 19122, USA.
| | - Samuel L Junod
- Temple University Department of Biology, Philadelphia, PA 19122, USA
| | - Coby Rush
- Temple University Department of Biology, Philadelphia, PA 19122, USA
| | - Weidong Yang
- Temple University Department of Biology, Philadelphia, PA 19122, USA.
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41
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Peko L, Katz S, Gattegno R, Ilovitsh T. Protocol to assess extravasation of fluorescent molecules in mice after ultrasound-mediated blood-brain barrier opening. STAR Protoc 2024; 5:102770. [PMID: 38160392 PMCID: PMC10805705 DOI: 10.1016/j.xpro.2023.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Blood-brain barrier disruption (BBBD) using focused ultrasound (FUS) and microbubbles (MBs) is an effective tool for therapeutic delivery to the brain. Here, we present an optimized protocol for quantifying fluorescent molecules extravasation in mice. We describe steps for ultrasound treatment, injection of MBs and fluorescent dyes, brain harvesting, microscopy imaging, and image postprocessing algorithm. Our protocol has proven to successfully conduct a diameter-dependent analysis that measures vascular leakage following FUS-mediated BBBD at a single blood vessel resolution. For complete details on the use and execution of this protocol, please refer to Katz et al.1.
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Affiliation(s)
- Lea Peko
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Katz
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roni Gattegno
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tali Ilovitsh
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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42
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Sell LB, Shi Q, Bhat MA. Protocol for isolating and processing mouse sciatic nerve fibers for confocal immunohistochemistry. STAR Protoc 2024; 5:102852. [PMID: 38277269 PMCID: PMC10840394 DOI: 10.1016/j.xpro.2024.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Many motor and neurodegenerative diseases affect the peripheral nervous system (PNS). The myelinated axons in the sciatic nerves offer valuable insights into the pathology of these diseases. Here, we present a protocol for isolating and processing mouse sciatic nerves for confocal immunohistochemistry. We describe steps for mouse perfusion, removing and fixing the sciatic nerve, transferring nerves onto slides, staining, and imaging. This protocol can assist in characterizing pathologies of myelinated fibers resulting from diseases affecting the PNS. For complete details on the use and execution of this protocol, please refer to Chang et al. (2023).1.
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Affiliation(s)
- Lacey B Sell
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; IBMS Neuroscience Graduate Program, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Qian Shi
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; IBMS Neuroscience Graduate Program, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Manzoor A Bhat
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; IBMS Neuroscience Graduate Program, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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43
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Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protoc 2024; 5:102795. [PMID: 38165800 PMCID: PMC10797208 DOI: 10.1016/j.xpro.2023.102795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/09/2023] [Accepted: 12/07/2023] [Indexed: 01/04/2024] Open
Abstract
Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects. For complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3.
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Affiliation(s)
- Andi H Hansen
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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44
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Yan D, Xue J, Xiao J, Lyu Z, Yang X. Protocol for single-molecule labeling and tracking of bacterial cell division proteins. STAR Protoc 2024; 5:102766. [PMID: 38085639 PMCID: PMC10733747 DOI: 10.1016/j.xpro.2023.102766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/11/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Here, we present a protocol for labeling and tracking individual molecules, particularly cell division proteins in live bacterial cells. The protocol encompasses strain construction, single-molecule imaging, trajectory segmentation, and motion property analysis. The protocol enables the identification of distinctive motion states associated with different cell division proteins. Subsequent assessments of the dynamic behaviors of these proteins provide insights into their activities and interactions at the septum during cell division. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021),1 Lyu et al. (2022),2 and Mahone et al. (2024).3.
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Affiliation(s)
- Di Yan
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Jinchan Xue
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Zhixin Lyu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Xinxing Yang
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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45
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Schroder AL, Fairbanks-Santana M, Rakotomamonjy J, Guemez-Gamboa A. Quantifying differentiation of progenitor populations using cerebral organoid models for neurodevelopmental disorders. STAR Protoc 2024; 5:102904. [PMID: 38427568 PMCID: PMC10918321 DOI: 10.1016/j.xpro.2024.102904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
Neurodevelopmental disorders are characterized by complex phenotypes that often result from concomitant dysregulation of cell proliferation, differentiation, or other crucial developmental processes. Here, we present a protocol to quantify differentiation of progenitor populations during early stages of neurogenesis in induced pluripotent stem cell (iPSC)-derived cerebral organoids. We describe steps for organoid differentiation and maturation, sample preparation, immunofluorescence, and imaging and analysis using epifluorescence microscopy. This protocol can be used to compare cerebral organoids from control and patient-derived iPSCs. For complete details on the use and execution of this protocol, please refer to Rakotomamonjy et al. (2023).1.
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Affiliation(s)
- Annika L Schroder
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Martin Fairbanks-Santana
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jennifer Rakotomamonjy
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alicia Guemez-Gamboa
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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46
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de Leeuw SM, Nuriel T. Intracellular cholesterol visualization in brain tissue using D4H ∗. STAR Protoc 2024; 5:102779. [PMID: 38100357 PMCID: PMC10762518 DOI: 10.1016/j.xpro.2023.102779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/31/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Studying cholesterol biology in the brain has been greatly hindered by the lack of adequate cholesterol visualization techniques. Here, we present a protocol for using a high-affinity cholesterol probe D4H∗-mCherry as a histology reagent in mouse or human brain tissue. We describe steps for D4H∗ tissue treatment and crosslinking leading to stable labeling of intracellular membrane cholesterol. Furthermore, co-labeling with Rab5 endosomal marker and optimized buffers to reduce background enable punctate cholesterol visualization within the organelle membranes.
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Affiliation(s)
- Sherida M de Leeuw
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, 630 West 168th Street, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
| | - Tal Nuriel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, 630 West 168th Street, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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47
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Blanco-Touriñán N. Quantification of xylem connection defects during lateral root development in Arabidopsis. STAR Protoc 2024; 5:102786. [PMID: 38113142 PMCID: PMC10767186 DOI: 10.1016/j.xpro.2023.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
The cellular and molecular mechanisms underlying the establishment of vascular connections between primary and lateral roots have recently gained significant attention. Here, I present a protocol to visualize and quantify xylem connection defects during lateral root development. I describe steps for employing stains to infer whether the defects observed in xylem bridges are associated with alterations in the xylem differentiation program, including programmed cell death and secondary cell wall deposition. For complete details on the use and execution of this protocol, please refer to Blanco-Touriñán et al. (2023) and Ursache et al. (2018).1,2.
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Affiliation(s)
- Noel Blanco-Touriñán
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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48
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Verstraelen P, Verschuuren M, De Vos WH. Integrated staging of morphofunctional connectivity in neuronal cultures. STAR Protoc 2024; 5:102957. [PMID: 38492228 PMCID: PMC10959717 DOI: 10.1016/j.xpro.2024.102957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/29/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Neurological disorders are defined by synaptic dysfunction. We present a workflow to quantify morphological and functional aspects of synaptic connectivity in neuronal cultures and obtain an integrated readout. We describe steps for measuring synchronous calcium bursting in GCaMP6f-transduced neurons and labeling mature synapses using a proximity ligation assay. The integration of functional and morphological information from the same cultures provides a rich fingerprint of synaptic connectivity, deployable in different experimental conditions. For complete details on the use and execution of this protocol, please refer to Verstraelen et al. and Verschuuren et al.1,2.
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Affiliation(s)
- Peter Verstraelen
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610 Wilrijk, Belgium; Antwerp Centre for Advanced Microscopy, University of Antwerp, Antwerp, Belgium; μNeuro Research Centre of Excellence, University of Antwerp, Antwerp, Belgium.
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Chen J, He K, Han Y, Dickman D. Ca 2+ imaging of synaptic compartments using subcellularly targeted GCaMP8f in Drosophila. STAR Protoc 2024; 5:102832. [PMID: 38198278 PMCID: PMC10820801 DOI: 10.1016/j.xpro.2023.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
GCaMP8f is a sensitive genetically encoded Ca2+ indicator that enables imaging of neuronal activity. Here, we present a protocol to perform Ca2+ imaging of the Drosophila neuromuscular junction using GCaMP8f targeted to pre- or postsynaptic compartments. We describe ratiometric Ca2+ imaging using GCaMP8f fused to mScarlet and synaptotagmin that reveals Ca2+ dynamics at presynaptic terminals. We then detail "quantal" imaging of miniature transmission events using GCaMP8f targeted to postsynaptic compartments by fusion to a PDZ-binding motif. For complete details on the use and execution of this protocol, please refer to Li et al.,1 Han et al.,2 Perry et al.,3 and Han et al.4.
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Affiliation(s)
- Jiawen Chen
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Kaikai He
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yifu Han
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA 90089, USA.
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Durrieu L, Bush A, Colman-Lerner A. Protocol for FRAP-based estimation of nuclear import and export rates in single yeast cells. STAR Protoc 2024; 5:102876. [PMID: 38349788 PMCID: PMC10876970 DOI: 10.1016/j.xpro.2024.102876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Here, we present a protocol for estimating nuclear transport parameters in single cells. We describe steps for performing four consecutive fluorescence recovery after photobleaching experiments, fitting the obtained data to an ordinary differential equations model, and statistical analysis of the fittings using a specialized R package. This protocol permits the estimation of import and export rates, nuclear or cytosolic fixed fractions, and total number of molecules. For complete details on the use and execution of this protocol, please refer to Durrieu et al.1.
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Affiliation(s)
- Lucía Durrieu
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
| | - Alan Bush
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Alejandro Colman-Lerner
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
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