201
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Wang Z, Natekar P, Tea C, Tamir S, Hakozaki H, Schöneberg J. MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data. PLoS Comput Biol 2023; 19:e1011060. [PMID: 37083820 PMCID: PMC10184899 DOI: 10.1371/journal.pcbi.1011060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 05/15/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Mitochondria form a network in the cell that rapidly changes through fission, fusion, and motility. Dysregulation of this four-dimensional (4D: x,y,z,time) network is implicated in numerous diseases ranging from cancer to neurodegeneration. While lattice light-sheet microscopy has recently made it possible to image mitochondria in 4D, quantitative analysis methods for the resulting datasets have been lacking. Here we present MitoTNT, the first-in-class software for Mitochondrial Temporal Network Tracking in 4D live-cell fluorescence microscopy data. MitoTNT uses spatial proximity and network topology to compute an optimal tracking assignment. To validate the accuracy of tracking, we created a reaction-diffusion simulation to model mitochondrial network motion and remodeling events. We found that our tracking is >90% accurate for ground-truth simulations and agrees well with published motility results for experimental data. We used MitoTNT to quantify 4D mitochondrial networks from human induced pluripotent stem cells. First, we characterized sub-fragment motility and analyzed network branch motion patterns. We revealed that the skeleton node motion is correlated along branch nodes and is uncorrelated in time. Second, we identified fission and fusion events with high spatiotemporal resolution. We found that mitochondrial skeleton nodes near the fission/fusion sites move nearly twice as fast as random skeleton nodes and that microtubules play a role in mediating selective fission/fusion. Finally, we developed graph-based transport simulations that model how material would distribute on experimentally measured mitochondrial temporal networks. We showed that pharmacological perturbations increase network reachability but decrease network resilience through a combination of altered mitochondrial fission/fusion dynamics and motility. MitoTNT's easy-to-use tracking module, interactive 4D visualization capability, and powerful post-tracking analyses aim at making temporal network tracking accessible to the wider mitochondria research community.
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Affiliation(s)
- Zichen Wang
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Parth Natekar
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Challana Tea
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Sharon Tamir
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
| | - Johannes Schöneberg
- Department of Pharmacology, University of California, San Diego, San Diego, California, United States of America
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California, United States of America
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202
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van der Beek J, Veenendaal T, de Heus C, van Dijk S, Ten Brink C, Liv N, Klumperman J. Ultrastructural Localization of Endogenous LC3 by On-Section Correlative Light-Electron Microscopy. J Vis Exp 2023. [PMID: 37067272 DOI: 10.3791/65067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The visualization of autophagic organelles at the ultrastructural level by electron microscopy (EM) is essential to establish their identity and reveal details that are important for understanding the autophagic process. However, EM methods often lack molecular information, obstructing the correlation of ultrastructural information obtained by EM to fluorescence microscopy-based localization of specific autophagy proteins. Furthermore, the rarity of autophagosomes in unaltered cellular conditions hampers investigation by EM, which requires high magnification, and hence provides a limited field of view. In answer to both challenges, an on-section correlative light-electron microscopy (CLEM) method based on fluorescent labeling was applied to correlate a common autophagosomal marker, LC3, to EM ultrastructure. The method was used to rapidly screen cells in fluorescence microscopy for LC3 labeling in combination with other relevant markers. Subsequently, the underlying ultrastructural features of selected LC3-labeled spots were identified by CLEM. The method was applied to starved cells without adding inhibitors of lysosomal acidification. In these conditions, LC3 was found predominantly on autophagosomes and rarely in autolysosomes, in which LC3 is rapidly degraded. These data show both the feasibility and sensitivity of this approach, demonstrating that CLEM can be used to provide ultrastructural insights on LC3-mediated autophagy in native conditions-without drug treatments or genetic alterations. Overall, this method presents a valuable tool for ultrastructural localization studies of autophagy proteins and other scarce antigens by bridging light microscopy to EM data.
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Affiliation(s)
- Jan van der Beek
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Tineke Veenendaal
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Cecilia de Heus
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Suzanne van Dijk
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Corlinda Ten Brink
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Nalan Liv
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Judith Klumperman
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University;
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203
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Lindqvist A, Hao Z, Akopyan K. Using an ImageJ-based script to detect replication stress and associated cell cycle exit from G2 phase by fluorescence microscopy. Methods Cell Biol 2023; 182:187-197. [PMID: 38359976 DOI: 10.1016/bs.mcb.2023.02.003] [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] [Indexed: 03/29/2023]
Abstract
Replication stress risks genomic integrity. Depending on the level, replication stress can lead to slower progression through S phase and entry into G2 phase with DNA damage. In G2 phase, cells either recover and eventually enter mitosis or permanently withdraw from the cell cycle. Here we describe a method to detect cell cycle distribution, replication stress and cell cycle exit from G2 phase using fluorescence microscopy. We provide a script to automate the analysis using ImageJ. The focus has been to make a script and setup that is accessible to people without extensive computer knowledge.
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Affiliation(s)
- Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Zhiyu Hao
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Akopyan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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204
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Ren ZW, Yang M, McKenna BA, Lian XM, Zhao FJ, Kopittke PM, Lombi E, Wang P. Fast X-ray fluorescence microscopy provides high-throughput phenotyping of element distribution in seeds. Plant Physiol 2023; 191:1520-1534. [PMID: 36423229 PMCID: PMC10022620 DOI: 10.1093/plphys/kiac534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
The concentration, chemical speciation, and spatial distribution of essential and toxic mineral elements in cereal seeds have important implications for human health. To identify genes responsible for element uptake, translocation, and storage, high-throughput phenotyping methods are needed to visualize element distribution and concentration in seeds. Here, we used X-ray fluorescence microscopy (μ-XRF) as a method for rapid and high-throughput phenotyping of seed libraries and developed an ImageJ-based pipeline to analyze the spatial distribution of elements. Using this method, we nondestructively scanned 4,190 ethyl methanesulfonate (EMS)-mutagenized M1 rice (Oryza sativa) seeds and 533 diverse rice accessions in a genome-wide association study (GWAS) panel to simultaneously measure concentrations and spatial distribution of elements in the embryo, endosperm, and aleurone layer. A total of 692 putative mutants and 65 loci associated with the spatial distribution of elements in rice seed were identified. This powerful method provides a basis for investigating the genetics and molecular mechanisms controlling the accumulation and spatial variations of mineral elements in plant seeds.
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Affiliation(s)
- Zi-Wen Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Meng Yang
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Brigid A McKenna
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Xing-Ming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Center for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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205
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Ramakrishna P. Grain scans: fast X-ray fluorescence microscopy for high-throughput elemental mapping of rice seeds. Plant Physiol 2023; 191:1465-1467. [PMID: 36548955 PMCID: PMC10022604 DOI: 10.1093/plphys/kiac598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Priya Ramakrishna
- Laboratory for Biological Geochemistry, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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206
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Bruggeman CW, Haasnoot GH, Peterman EJG. Microfluidics and fluorescence microscopy protocol to study the response of C. elegans to chemosensory stimuli. STAR Protoc 2023; 4:102121. [PMID: 36853676 PMCID: PMC9958070 DOI: 10.1016/j.xpro.2023.102121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Here, we present a protocol to use microfluidics in combination with fluorescence microscopy to expose the C. elegans tail to chemosensory stimuli. We describe steps for the preparation of microfluidic chips and sample preparation through the sedation of C. elegans. We detail flow calibration and imaging of C. elegans through fluorescence microscopy to determine their molecular and/or cellular response to chemosensory stimuli. This protocol can also be applied to amphid neurons by inserting the worm in the chip head-first. For complete details on the use and execution of this protocol, please refer to Bruggeman et al. (2022).1.
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Affiliation(s)
- Christine W Bruggeman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Guus H Haasnoot
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
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207
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Lan T, Ji N, Tian QQ, Zhan Y, He W. An edoplasmic reticulum-targeted NIR fluorescent probe with a large Stokes shift for hypoxia imaging. Spectrochim Acta A Mol Biomol Spectrosc 2023; 288:122201. [PMID: 36463622 DOI: 10.1016/j.saa.2022.122201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Hypoxia is closely linked to various diseases, including solid tumors. The level of nitroreductase (NTR) is usually abnormally upregulated in hypoxic conditions, which can be a biomarker of hypoxia. Herein, the first endoplasmic reticulum-targeting NIR fluorescent probe, ISO-NTR, was developed for highly selective and sensitive detection of NTR. It shows a large Stokes shift (185 nm) and a 5-fold increases in fluorescence intensity. Meanwhile, the ISO-NTR probe with a dicyanoisophorone derivative has excellent endoplasmic reticulum targeting in living systems with high Pearson's correlation coefficients (Rr = 0.9489). Molecular docking calculations and high binding energy between the probe and NTR (-10.78 kcal·mol-1) may explain the high selectivity of ISO-NTR. Additionally, it has been successfully applied to NTR imaging in vitro and vivo due to its good sensitivity, high selectivity and large Stokes shift, which may provide an effective method for studying the physiological and pathological functions of NTR in living systems. This probe could be developed as a potential imaging tool to further explore the pathogenesis of hypoxia-related diseases in endoplasmic reticulum stress.
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Affiliation(s)
- Ting Lan
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, PR China
| | - Nan Ji
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, PR China
| | - Qin-Qin Tian
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, PR China
| | - Yu Zhan
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, PR China
| | - Wei He
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, PR China.
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208
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Karrobi K, Tank A, Fuzail MA, Kalidoss M, Tilbury K, Zaman M, Ferruzzi J, Roblyer D. Fluorescence Lifetime Imaging Microscopy (FLIM) reveals spatial-metabolic changes in 3D breast cancer spheroids. Sci Rep 2023; 13:3624. [PMID: 36869092 PMCID: PMC9984376 DOI: 10.1038/s41598-023-30403-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Cancer cells are mechanically sensitive to physical properties of the microenvironment, which can affect downstream signaling to promote malignancy, in part through the modulation of metabolic pathways. Fluorescence Lifetime Imaging Microscopy (FLIM) can be used to measure the fluorescence lifetime of endogenous fluorophores, such as the metabolic co-factors NAD(P)H and FAD, in live samples. We used multiphoton FLIM to investigate the changes in cellular metabolism of 3D breast spheroids derived from MCF-10A and MD-MB-231 cell lines embedded in collagen with varying densities (1 vs. 4 mg/ml) over time (Day 0 vs. Day 3). MCF-10A spheroids demonstrated spatial gradients, with the cells closest to the spheroid edge exhibiting FLIM changes consistent with a shift towards oxidative phosphorylation (OXPHOS) while the spheroid core had changes consistent with a shift towards glycolysis. The MDA-MB-231 spheroids had a large shift consistent with increased OXPHOS with a more pronounced change at the higher collagen concentration. The MDA-MB-231 spheroids invaded into the collagen gel over time and cells that traveled the farthest had the largest changes consistent with a shift towards OXPHOS. Overall, these results suggest that the cells in contact with the extracellular matrix (ECM) and those that migrated the farthest had changes consistent with a metabolic shift towards OXPHOS. More generally, these results demonstrate the ability of multiphoton FLIM to characterize how spheroids metabolism and spatial metabolic gradients are modified by physical properties of the 3D ECM.
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Affiliation(s)
- Kavon Karrobi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Anup Tank
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | - Madhumathi Kalidoss
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Karissa Tilbury
- Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Muhammad Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Jacopo Ferruzzi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Darren Roblyer
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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209
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Cesaretti A, Calzoni E, Montegiove N, Bianconi T, Alebardi M, La Serra MA, Consiglio G, Fortuna CG, Elisei F, Spalletti A. Lighting-Up the Far-Red Fluorescence of RNA-Selective Dyes by Switching from Ortho to Para Position. Int J Mol Sci 2023; 24:ijms24054812. [PMID: 36902248 PMCID: PMC10003335 DOI: 10.3390/ijms24054812] [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: 12/24/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Fluorescence imaging is constantly searching for new far-red emitting probes whose turn-on response is selective upon the interaction with specific biological targets. Cationic push-pull dyes could indeed respond to these requirements due to their intramolecular charge transfer (ICT) character, by which their optical properties can be tuned, and their ability to interact strongly with nucleic acids. Starting from the intriguing results recently achieved with some push-pull dimethylamino-phenyl dyes, two isomers obtained by switching the cationic electron acceptor head (either a methylpyridinium or a methylquinolinium) from the ortho to the para position have been scrutinized for their ICT dynamics, their affinity towards DNA and RNA, and in vitro behavior. By exploiting the marked fluorescence enhancement observed upon complexation with polynucleotides, fluorimetric titrations were employed to evaluate the dyes' ability as efficient DNA/RNA binders. The studied compounds exhibited in vitro RNA-selectivity by localizing in the RNA-rich nucleoli and within the mitochondria, as demonstrated by fluorescence microscopy. The para-quinolinium derivative showed some modest antiproliferative effect on two tumor cell lines as well as improved properties as an RNA-selective far-red probe in terms of both turn-on response (100-fold fluorescence enhancement) and localized staining ability, attracting interest as a potential theranostic agent.
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Affiliation(s)
- Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Correspondence:
| | - Eleonora Calzoni
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Nicolò Montegiove
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Tommaso Bianconi
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Martina Alebardi
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Maria Antonietta La Serra
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Giuseppe Consiglio
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Cosimo Gianluca Fortuna
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
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210
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Tsuda N, Fukagawa R, Sueda S. Does the nuclear envelope retain its identity during mitosis? FEBS Lett 2023; 597:682-692. [PMID: 36528783 DOI: 10.1002/1873-3468.14568] [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: 09/28/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
During mitosis in metazoan species, the nuclear envelope (NE) undergoes breakdown, and its fragments are absorbed within the membranous network of the endoplasmic reticulum (ER). Past observations by fluorescence microscopy led researchers to think that the NE loses its identity when it is absorbed within the ER membrane. However, in our previous work, we developed a more specific labelling method and found evidence that the NE does not completely lose its identity during mitosis. In the present work, we conduct further experiments, the results of which support the idea that the NE partially retains its identity during mitosis.
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Affiliation(s)
- Natsumi Tsuda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
| | - Ryohei Fukagawa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
| | - Shinji Sueda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
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211
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Sarfraz N, Moscoso E, Oertel T, Lee HJ, Ranjit S, Braselmann E. Visualizing orthogonal RNAs simultaneously in live mammalian cells by fluorescence lifetime imaging microscopy (FLIM). Nat Commun 2023; 14:867. [PMID: 36797241 PMCID: PMC9935525 DOI: 10.1038/s41467-023-36531-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Visualization of RNAs in live cells is critical to understand biology of RNA dynamics and function in the complex cellular environment. Detection of RNAs with a fluorescent marker frequently involves genetically fusing an RNA aptamer tag to the RNA of interest, which binds to small molecules that are added to live cells and have fluorescent properties. Engineering efforts aim to improve performance and add versatile features. Current efforts focus on adding multiplexing capabilities to tag and visualize multiple RNAs simultaneously in the same cell. Here, we present the fluorescence lifetime-based platform Riboglow-FLIM. Our system requires a smaller tag and has superior cell contrast when compared with intensity-based detection. Because our RNA tags are derived from a large bacterial riboswitch sequence family, the riboswitch variants add versatility for using multiple tags simultaneously. Indeed, we demonstrate visualization of two RNAs simultaneously with orthogonal lifetime-based tags.
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Affiliation(s)
- Nadia Sarfraz
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Emilia Moscoso
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Therese Oertel
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Harrison J Lee
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
- Microscopy & Imaging Shared Resource, Georgetown University, Washington, DC, USA
| | - Esther Braselmann
- Department of Chemistry, Georgetown University, Washington, DC, USA.
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212
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Brogna C, Costanzo V, Brogna B, Bisaccia DR, Brogna G, Giuliano M, Montano L, Viduto V, Cristoni S, Fabrowski M, Piscopo M. Analysis of Bacteriophage Behavior of a Human RNA Virus, SARS-CoV-2, through the Integrated Approach of Immunofluorescence Microscopy, Proteomics and D-Amino Acid Quantification. Int J Mol Sci 2023; 24:3929. [PMID: 36835341 PMCID: PMC9965620 DOI: 10.3390/ijms24043929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
SARS-CoV-2, one of the human RNA viruses, is widely studied around the world. Significant efforts have been made to understand its molecular mechanisms of action and how it interacts with epithelial cells and the human microbiome since it has also been observed in gut microbiome bacteria. Many studies emphasize the importance of surface immunity and also that the mucosal system is critical in the interaction of the pathogen with the cells of the oral, nasal, pharyngeal, and intestinal epithelium. Recent studies have shown how bacteria in the human gut microbiome produce toxins capable of altering the classical mechanisms of interaction of viruses with surface cells. This paper presents a simple approach to highlight the initial behavior of a novel pathogen, SARS-CoV-2, on the human microbiome. The immunofluorescence microscopy technique can be combined with spectral counting performed at mass spectrometry of viral peptides in bacterial cultures, along with identification of the presence of D-amino acids within viral peptides in bacterial cultures and in patients' blood. This approach makes it possible to establish the possible expression or increase of viral RNA viruses in general and SARS-CoV-2, as discussed in this study, and to determine whether or not the microbiome is involved in the pathogenetic mechanisms of the viruses. This novel combined approach can provide information more rapidly, avoiding the biases of virological diagnosis and identifying whether a virus can interact with, bind to, and infect bacteria and epithelial cells. Understanding whether some viruses have bacteriophagic behavior allows vaccine therapies to be focused either toward certain toxins produced by bacteria in the microbiome or toward finding inert or symbiotic viral mutations with the human microbiome. This new knowledge opens a scenario on a possible future vaccine: the probiotics vaccine, engineered with the right resistance to viruses that attach to both the epithelium human surface and gut microbiome bacteria.
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Affiliation(s)
- Carlo Brogna
- Department of Research, Craniomed Group Facility Srl., 20091 Bresso, Italy
| | - Vincenzo Costanzo
- Biogem, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy
| | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy
| | | | - Giancarlo Brogna
- Department of Research, Craniomed Group Facility Srl., 20091 Bresso, Italy
| | - Marino Giuliano
- Marsanconsulting Srl. Public Health Company, Via dei Fiorentini, 80133 Napoli, Italy
| | - Luigi Montano
- Andrology Unit and Service of LifeStyle Medicine in Uro-Andrology, Local Health Authority (ASL), 84124 Salerno, Italy
| | - Valentina Viduto
- Long COVID-19 Foundation, Brookfield Court, Garforth, Leeds LS25 1NB, UK
| | | | - Mark Fabrowski
- Department of Emergency Medicine, Royal Sussex County Hospital, University Hospitals Sussex, Eastern Road, Brighton BN2 5BE, UK
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
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213
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Iida T, Ando J, Shinoda H, Makino A, Yoshimura M, Murai K, Mori M, Takeuchi H, Noda T, Nishimasu H, Watanabe R. Compact wide-field femtoliter-chamber imaging system for high-speed and accurate digital bioanalysis. Lab Chip 2023; 23:684-691. [PMID: 36255223 DOI: 10.1039/d2lc00741j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The femtoliter-chamber array is a bioanalytical platform that enables highly sensitive and quantitative analysis of biological reactions at the single-molecule level. This feature has been considered a key technology for "digital bioanalysis" in the biomedical field; however, its versatility is limited by the need for a large and expensive setup such as a fluorescence microscope, which requires a long time to acquire the entire image of a femtoliter-chamber array. To address these issues, we developed a compact and inexpensive wide-field imaging system (COWFISH) that can acquire fluorescence images with a large field of view (11.8 mm × 7.9 mm) and a high spatial resolution of ∼ 3 μm, enabling high-speed analysis of sub-million femtoliter chambers in 20 s. Using COWFISH, we demonstrated a CRISPR-Cas13a-based digital detection of viral RNA of SARS-CoV-2 with an equivalent detection sensitivity (limit of detection: 480 aM) and a 10-fold reduction in total imaging time, as compared to confocal fluorescence microscopy. In addition, we demonstrated the feasibility of COWFISH to discriminate between SARS-CoV-2-positive and -negative clinical specimens with 95% accuracy, showing its application in COVID-19 diagnosis. Therefore, COWFISH can serve as a compact and inexpensive imaging system for high-speed and accurate digital bioanalysis, paving a way for various biomedical applications, such as diagnosis of viral infections.
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Affiliation(s)
| | - Jun Ando
- Cluster for Pioneering Research, RIKEN, Japan.
| | | | | | | | - Kazue Murai
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Makiko Mori
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University, Japan
| | - Takeshi Noda
- Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Japan
- RCAST, The University of Tokyo, Japan
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214
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Bao L, Running MP. 3-D Time-Lapse Imaging of Cell Wall Dynamics Using Calcofluor in the Moss Physcomitrium patens. J Vis Exp 2023. [PMID: 36847393 DOI: 10.3791/64651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Time-lapse imaging with fluorescence microscopy allows observation of the dynamic changes of growth and development at cellular and subcellular levels. In general, for observations over a long period, the technique requires transformation of a fluorescent protein; however, for most systems, genetic transformation is either time-consuming or technically unavailable. This manuscript presents a protocol for 3-D time-lapse imaging of cell wall dynamics over a 3 day period using calcofluor dye (which stains cellulose in the plant cell wall), developed in the moss Physcomitrium patens. The calcofluor dye signal from the cell wall is stable and can last for 1 week without obvious decay. Using this method, it has been shown that the detachment of cells in ggb mutants (in which the protein geranylgeranyltransferase-I beta subunit is knocked out) is caused by unregulated cell expansion and cell wall integrity defects. Moreover, the patterns of calcofluor staining change over time; less intensely stained regions correlate with the future cell expansion/branching sites in the wild type. This method can be applied to many other systems that contain cell walls and that can be stained by calcofluor.
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Affiliation(s)
- Liang Bao
- Department of Biology, University of Louisville;
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215
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Sakr N, Glazova O, Shevkova L, Onyanov N, Kaziakhmedova S, Shilova A, Vorontsova MV, Volchkov P. Characterizing and Quenching Autofluorescence in Fixed Mouse Adrenal Cortex Tissue. Int J Mol Sci 2023; 24:ijms24043432. [PMID: 36834842 PMCID: PMC9968082 DOI: 10.3390/ijms24043432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Tissue autofluorescence of fixed tissue sections is a major concern of fluorescence microscopy. The adrenal cortex emits intense intrinsic fluorescence that interferes with signals from fluorescent labels, resulting in poor-quality images and complicating data analysis. We used confocal scanning laser microscopy imaging and lambda scanning to characterize the mouse adrenal cortex autofluorescence. We evaluated the efficacy of tissue treatment methods in reducing the intensity of the observed autofluorescence, such as trypan blue, copper sulfate, ammonia/ethanol, Sudan Black B, TrueVIEWTM Autofluorescence Quenching Kit, MaxBlockTM Autofluorescence Reducing Reagent Kit, and TrueBlackTM Lipofuscin Autofluorescence Quencher. Quantitative analysis demonstrated autofluorescence reduction by 12-95%, depending on the tissue treatment method and excitation wavelength. TrueBlackTM Lipofuscin Autofluorescence Quencher and MaxBlockTM Autofluorescence Reducing Reagent Kit were the most effective treatments, reducing the autofluorescence intensity by 89-93% and 90-95%, respectively. The treatment with TrueBlackTM Lipofuscin Autofluorescence Quencher preserved the specific fluorescence signals and tissue integrity, allowing reliable detection of fluorescent labels in the adrenal cortex tissue. This study demonstrates a feasible, easy-to-perform, and cost-effective method to quench tissue autofluorescence and improve the signal-to-noise ratio in adrenal tissue sections for fluorescence microscopy.
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Affiliation(s)
- Nawar Sakr
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Olga Glazova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Liudmila Shevkova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Nikita Onyanov
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Samira Kaziakhmedova
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Alena Shilova
- Faculty of Medicine, M.V. Lomonosov Moscow State University, 27-1, Lomonosovsky Prospect, Moscow 117192, Russia
| | - Maria V. Vorontsova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Pavel Volchkov
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
- Correspondence:
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216
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Sellam AZ, Benlamoudi A, Cid CA, Dobelle L, Slama A, El Hillali Y, Taleb-Ahmed A. Deep Learning Solution for Quantification of Fluorescence Particles on a Membrane. Sensors (Basel) 2023; 23:1794. [PMID: 36850392 PMCID: PMC9967937 DOI: 10.3390/s23041794] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The detection and quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus particles in ambient waters using a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) method can play an important role in large-scale environmental surveillance for early warning of potential outbreaks. However, counting particles or cells in fluorescence microscopy is an expensive, time-consuming, and tedious task that only highly trained technicians and researchers can perform. Although such objects are generally easy to identify, manually annotating cells is occasionally prone to fatigue errors and arbitrariness due to the operator's interpretation of borderline cases. In this research, we proposed a method to detect and quantify multiscale and shape variant SARS-CoV-2 fluorescent cells generated using a portable (mgLAMP) system and captured using a smartphone camera. The proposed method is based on the YOLOv5 algorithm, which uses CSPnet as its backbone. CSPnet is a recently proposed convolutional neural network (CNN) that duplicates gradient information within the network using a combination of Dense nets and ResNet blocks, and bottleneck convolution layers to reduce computation while at the same time maintaining high accuracy. In addition, we apply the test time augmentation (TTA) algorithm in conjunction with YOLO's one-stage multihead detection heads to detect all cells of varying sizes and shapes. We evaluated the model using a private dataset provided by the Linde + Robinson Laboratory, California Institute of Technology, United States. The model achieved a mAP@0.5 score of 90.3 in the YOLOv5-s6.
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Affiliation(s)
- Abdellah Zakaria Sellam
- Institute of Applied Sciences and Intelligent Systems, National Research Council of Italy, 73100 Lecce, Italy
| | - Azeddine Benlamoudi
- Laboratoire de Génie Électrique, Faculté des Nouvelles Technologies de l’Information et de la Communication, Université Ouargla, Ouargla 30000, Algeria
| | - Clément Antoine Cid
- Linde Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leopold Dobelle
- Linde Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amina Slama
- Faculty of Humanities and Social Sciences, Mohamed Khider University of Biskra, Biskra 07000, Algeria
| | - Yassin El Hillali
- Institut d’Electronique de Microélectronique et de Nanotechnologie (IEMN), UMR 8520, Université Polytechnique Hauts de France, Université de Lille, CNRS, 59313 Valenciennes, France
| | - Abdelmalik Taleb-Ahmed
- Institut d’Electronique de Microélectronique et de Nanotechnologie (IEMN), UMR 8520, Université Polytechnique Hauts de France, Université de Lille, CNRS, 59313 Valenciennes, France
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217
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Xiong Q, Zhao K, Cheng Y, He C, Lai Y, Shi M, Ming X, Jin F, Tao D, Liao R, Liu Y. Optical properties, bioimaging and theoretical calculation of a Zn(II) complex based on triphenylamine derivative. Spectrochim Acta A Mol Biomol Spectrosc 2023; 286:122012. [PMID: 36308823 DOI: 10.1016/j.saa.2022.122012] [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] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
A luminescent material with various optical properties based on a triphenylamine Zn(II) complex is described. The ultraviolet-visible absorption, one-photon excited fluorescence (OPEF) and two-photon excited fluorescence (TPEF) of the complex indicate that the material has good OPEF and TPEF properties. And the results of one- and two-photon HepG2 cells imaging experiments show the potential of the complex in fluorescence microscopy bioimaging. The experimental Stokes shift and the FWHM (full-width at half-maximum) in different solvents were correlated with the rMPI polarity of the solvent, and the perfect Boltzmann curves were obtained, where the Boltzmann correlation between Stokes shift and solvent polarity is reported for the second time. But the Boltzmann correlation between FWHM and solvent polarity is reported for the first time. In addition, the computational results indicate that, the covalent bond within the salt ZnBr2 is strengthened by the coordination, and the newly formed coordination bond Zn-N is stronger than the original covalent bond Zn-Br.
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Affiliation(s)
- Qijuan Xiong
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Kaipeng Zhao
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Yuling Cheng
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Changjun He
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Yuting Lai
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Mengyun Shi
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Xin Ming
- College of Biology and Food Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Feng Jin
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China.
| | - Dongliang Tao
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Rongbao Liao
- College of Chemistry and Material Engineering, Fuyang Normal University, Fuyang 236037, China
| | - Yong Liu
- College of Biology and Food Engineering, Fuyang Normal University, Fuyang 236037, China
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218
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Place BC, Troublefield CA, Murphy RD, Sinai AP, Patwardhan AR. Machine learning based classification of mitochondrial morphologies from fluorescence microscopy images of Toxoplasma gondii cysts. PLoS One 2023; 18:e0280746. [PMID: 36730225 PMCID: PMC9894464 DOI: 10.1371/journal.pone.0280746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/07/2023] [Indexed: 02/03/2023] Open
Abstract
The mitochondrion is intimately linked to energy and overall metabolism and therefore the morphology of mitochondrion can be very informative for inferring the metabolic state of cells. In this study we report an approach for automatic classification of mitochondrial morphologies using supervised machine learning to efficiently classify them from a large number of cells at a time. Fluorescence microscopy images of the chronic encysted form of parasite Toxoplasma gondii were used for this development. Manually classifying these morphologies from the hundreds of parasites within typical tissue cysts is tedious and error prone. In addition, because of inherent biological heterogeneity in morphologies, there can be variability and lack of reproducibility in manual classification. We used image segmentation to detect mitochondrial shapes and used features extracted from them in a multivariate logistic regression model to classify the detected shapes into five morphological classes: Blobs, Tadpoles, Lasso/Donuts, Arcs, and Other. The detected shapes from a subset of images were first used to obtain consensus classification among expert users to obtain a labeled set. The model was trained using the labeled set from five cysts and its performance was tested on the mitochondrial morphologies from ten other cysts that were not used in training. Results showed that the model had an average overall accuracy of 87%. There was high degree of confidence in the classification of Blobs and Arcs (average F scores 0.91 and 0.73) which constituted the majority of morphologies (85%). Although the current development used microscopy images from tissue cysts of Toxoplasma gondii, the approach is adaptable with minor adjustments and can be used to automatically classify morphologies of organelles from a variety of cells.
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Affiliation(s)
- Brooke C. Place
- F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, United States of America
| | - Cortni A. Troublefield
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Robert D. Murphy
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Anthony P. Sinai
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Abhijit R. Patwardhan
- F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, United States of America
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219
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Smith HA, Taylor CW. Dissociation of inositol 1,4,5-trisphosphate from IP 3 receptors contributes to termination of Ca 2+ puffs. J Biol Chem 2023; 299:102871. [PMID: 36621623 PMCID: PMC9971896 DOI: 10.1016/j.jbc.2023.102871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023] Open
Abstract
Ca2+ puffs are brief, localized Ca2+ signals evoked by physiological stimuli that arise from the coordinated opening of a few clustered inositol 1,4,5-trisphosphate receptors (IP3Rs). However, the mechanisms that control the amplitude and termination of Ca2+ puffs are unresolved. To address these issues, we expressed SNAP-tagged IP3R3 in HEK cells without endogenous IP3Rs and used total internal reflection fluorescence microscopy to visualize the subcellular distribution of IP3Rs and the Ca2+ puffs that they evoke. We first confirmed that SNAP-IP3R3 were reliably identified and that they evoked normal Ca2+ puffs after photolysis of a caged analog of IP3. We show that increased IP3R expression caused cells to assemble more IP3R clusters, each of which contained more IP3Rs, but the mean amplitude of Ca2+ puffs (indicative of the number of open IP3Rs) was unaltered. We thus suggest that functional interactions between IP3Rs constrain the number of active IP3Rs within a cluster. Furthermore, Ca2+ puffs evoked by IP3R with reduced affinity for IP3 had undiminished amplitude, but the puffs decayed more quickly. The selective effect of reducing IP3 affinity on the decay times of Ca2+ puffs was not mimicked by exposing normal IP3R to a lower concentration of IP3. We conclude that distinct mechanisms constrain recruitment of IP3Rs during the rising phase of a Ca2+ puff and closure of IP3Rs during the falling phase, and that only the latter is affected by the rate of IP3 dissociation.
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Affiliation(s)
- Holly A Smith
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
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220
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Haffer H, Chiapparelli E, Moser M, Muellner M, Dodo Y, Adl Amini D, Zhu J, Miller TT, Han YX, Donnelly E, Shue J, Sama AA, Cammisa FP, Girardi FP, Hughes AP. Dermal ultrasound measurements for bone quality assessment : An investigation of advanced glycation endproducts derived from confocal fluorescence microscopy. J Orthop Res 2023; 41:345-354. [PMID: 35470915 PMCID: PMC9596615 DOI: 10.1002/jor.25350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023]
Abstract
Bone quality is increasingly being recognized in the assessment of fracture risk. Nonenzymatic collagen cross-linking with the accumulation of advanced glycation end products stiffens and embrittles collagen fibers thus increasing bone fragility. Echogenicity is an ultrasound (US) parameter that provides information regarding the skin collagen structure. We hypothesized that both skin and bone collagen degrade in parallel fashion. Prospectively collected data of 110 patients undergoing posterior lumbar fusion was analyzed. Preoperative skin US measurements were performed in the lumbar region to assess dermal thickness and echogenicity. Intraoperative bone biopsies from the posterior superior iliac spine were obtained and analyzed with confocal fluorescence microscopy for fluorescent advanced glycation endproducts (fAGEs). Pearson's correlation was calculated to examine relationships between (1) US and fAGEs, and (2) age and fAGEs stratified by sex. Multivariable linear regression analysis with adjustments for age, sex, body mass index (BMI), diabetes mellitus, and hemoglobin A1c (HbA1c) was used to investigate associations between US and fAGEs. One hundred and ten patients (51.9% female, 61.6 years, BMI 29.8 kg/m2 ) were included in the analysis. In the univariate analysis cortical and trabecular fAGEs decreased with age, but only in women (cortical: r = -0.32, p = 0.031; trabecular: r = -0.32; p = 0.031). After adjusting for age, sex, BMI, diabetes mellitus, and HbA1c, lower dermal (β = 1.01; p = 0.012) and subcutaneous (β = 1.01; p = 0.021) echogenicity increased with increasing cortical fAGEs and lower dermal echogenicity increased with increasing trabecular fAGEs (β = 1.01; p = 0.021). This is the first study demonstrating significant associations between skin US measurements and in vivo bone quality parameters in lumbar fusion patients. As a noninvasive assessment tool, skin US measurements might be incorporated into future practice to investigate bone quality in spine surgery patients.
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Affiliation(s)
- Henryk Haffer
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Erika Chiapparelli
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Manuel Moser
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
- Department of Spine Surgery, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | - Maximilian Muellner
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yusuke Dodo
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Dominik Adl Amini
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiaqi Zhu
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Theodore T. Miller
- Department of Radiology and Imaging, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Yi Xin Han
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Donnelly
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
- Musculoskeletal Integrity Program, Research Institute, Hospital for Special Surgery, New York City, NY, USA
| | - Jennifer Shue
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Andrew A. Sama
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Frank P. Cammisa
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Federico P. Girardi
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Alexander P. Hughes
- Department of Orthopaedic Surgery, Hospital for Special Surgery, Weill Cornell Medicine, New York City, NY, USA
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221
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Hartl I, Brumovska V, Striedner Y, Yasari A, Schütz GJ, Sevcsik E, Tiemann-Boege I. Measurement of FGFR3 signaling at the cell membrane via total internal reflection fluorescence microscopy to compare the activation of FGFR3 mutants. J Biol Chem 2023; 299:102832. [PMID: 36581204 PMCID: PMC9900515 DOI: 10.1016/j.jbc.2022.102832] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) initiate signal transduction via the RAS/mitogen-activated protein kinase pathway by their tyrosine kinase activation known to determine cell growth, tissue differentiation, and apoptosis. Recently, many missense mutations have been reported for FGFR3, but we only know the functional effect for a handful of them. Some mutations result in aberrant FGFR3 signaling and are associated with various genetic disorders and oncogenic conditions. Here, we employed micropatterned surfaces to specifically enrich fluorophore-tagged FGFR3 (monomeric GFP [mGFP]-FGFR3) in certain areas of the plasma membrane of living cells. We quantified receptor activation via total internal reflection fluorescence microscopy of FGFR3 signaling at the cell membrane that captured the recruitment of the downstream signal transducer growth factor receptor-bound 2 (GRB2) tagged with mScarlet (GRB2-mScarlet) to FGFR3 micropatterns. With this system, we tested the activation of FGFR3 upon ligand addition (fgf1 and fgf2) for WT and four FGFR3 mutants associated with congenital disorders (G380R, Y373C, K650Q, and K650E). Our data showed that ligand addition increased GRB2 recruitment to WT FGFR3, with fgf1 having a stronger effect than fgf2. For all mutants, we found an increased basal receptor activity, and only for two of the four mutants (G380R and K650Q), activity was further increased upon ligand addition. Compared with previous reports, two mutant receptors (K650Q and K650E) had either an unexpectedly high or low activation state, respectively. This can be attributed to the different methodology, since micropatterning specifically captures signaling events at the plasma membrane. Collectively, our results provide further insight into the functional effects of mutations to FGFR3.
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Affiliation(s)
- Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Atena Yasari
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Eva Sevcsik
- Insitute of Applied Physics, TU Wien, Vienna, Austria.
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222
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Kodama Y, Fujishima M. Role of host ciliate Paramecium bursaria mitochondria and trichocysts for symbiotic Chlorella variabilis attachment beneath the host cell cortex. FEMS Microbiol Lett 2023; 370:fnad088. [PMID: 37660246 DOI: 10.1093/femsle/fnad088] [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: 03/02/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023] Open
Abstract
Symbiotic Chlorella variabilis is encased in the perialgal vacuole (PV) membrane of ciliate Paramecium bursaria. The PV membrane is stably anchored below the host cell cortex by adhesion to host mitochondria. Host trichocysts, which are defensive organelles against predators, are present in the mitochondria and PV membrane vicinity. The mechanism by which PV attaches beneath the host cell cortex remains unknown. When P. bursaria is centrifuged at high speed, the symbiotic algae are displaced from the host cell cortex and concentrate at the posterior end. When centrifugation is stopped, the dislocated algae reattach beneath the host cell cortex with fast cytoplasmic streaming. The densities of mitochondria and trichocysts before and after centrifugation were compared using indirect immunofluorescence microscopy with monoclonal antibodies. Almost all trichocysts were shed by high-speed centrifugation, but dislocated algae could reattach even in the absence of trichocysts. In contrast, host mitochondria were unaffected in localization and number, and the dislocated algae also reattached. These findings suggest trichocysts are unnecessary for algal relocalization and that mitochondria are colocalized with the algae. However, many mitochondria were also present in the cell's anterior region without symbiotic algae. Therefore, not all areas with mitochondria contained algae, but there was an algal localization bias within the host cell.
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Affiliation(s)
- Yuuki Kodama
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu-cho, Matsue-shi, Shimane 690-8504, Japan
| | - Masahiro Fujishima
- Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, Yoshida 1677-1, Yamaguchi 753-8512, Japan
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223
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Prigent S, Dutertre S, Bidaud-Meynard A, Bertolin G, Michaux G, Kervrann C. Sparse denoising and adaptive estimation enhances the resolution and contrast of fluorescence emission difference microscopy based on an array detector. Opt Lett 2023; 48:498-501. [PMID: 36638494 DOI: 10.1364/ol.474883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
An array detector allows a resolution gain for confocal microscopy by combining images sensed by a set of photomultipliers tubes (or sub-detectors). Several methods have been proposed to reconstruct a high-resolution image by linearly combining sub-detector images, especially the fluorescence emission difference (FED) technique. To improve the resolution and contrast of FED microscopy based on an array detector, we propose to associate sparse denoising with spatial adaptive estimation. We show on both calibration slides and real data that our approach applied to the full stack of spatially reassigned detector signals, enables us to achieve a higher reconstruction performance in terms of resolution, image contrast, and noise reduction.
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224
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Gahan CG, Van Lehn RC, Blackwell HE, Lynn DM. Interactions of Bacterial Quorum Sensing Signals with Model Lipid Membranes: Influence of Membrane Composition on Membrane Remodeling. Langmuir 2023; 39:295-307. [PMID: 36534123 PMCID: PMC10038191 DOI: 10.1021/acs.langmuir.2c02506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report the influence of membrane composition on the multiscale remodeling of multicomponent lipid bilayers initiated by contact with the amphiphilic bacterial quorum sensing signal N-(3-oxo)-dodecanoyl-l-homoserine lactone (3-oxo-C12-AHL) and its anionic headgroup hydrolysis product, 3-oxo-C12-HS. We used fluorescence microscopy and quartz crystal microbalance with dissipation (QCM-D) to characterize membrane reformation that occurs when these amphiphiles are placed in contact with supported lipid bilayers (SLBs) composed of (i) 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) containing varying amounts of cholesterol or (ii) mixtures of DOPC and either 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE, a conical zwitterionic lipid) or 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS, a model anionic lipid). In general, we observe these mixed-lipid membranes to undergo remodeling events, including the formation and subsequent collapse of long tubules and the formation of hemispherical caps, upon introduction to biologically relevant concentrations of 3-oxo-C12-AHL and 3-oxo-C12-HS in ways that differ substantially from those observed in single-component DOPC membranes. These differences in bilayer reformation and their associated dynamics can be understood in terms of the influence of membrane composition on the time scales of molecular flip-flop, lipid packing defects, and lipid phase segregation in these materials. The lipid components investigated here are representative of classes of lipids that comprise both naturally occurring cell membranes and many useful synthetic soft materials. These studies thus represent a first step toward understanding the ways in which membrane composition can impact interactions with this important class of bacterial signaling molecules.
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Affiliation(s)
- Curran G. Gahan
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - David M. Lynn
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
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225
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Pu Y, Bassham DC. Detection of Autophagy in Plants by Fluorescence Microscopy. Methods Mol Biol 2023; 2581:135-147. [PMID: 36413316 DOI: 10.1007/978-1-0716-2784-6_11] [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] [Indexed: 06/16/2023]
Abstract
Autophagy is a key process for degradation and recycling of proteins or organelles in eukaryotes. Autophagy in plants has been shown to function in stress responses, pathogen immunity, and senescence, while a basal level of autophagy plays a housekeeping role in cells. Upon activation of autophagy, vesicles termed autophagosomes are formed to deliver proteins or organelles to the vacuole for degradation. The number of autophagosomes can thus be used to indicate the level of autophagy. Here we describe two common methods used for detection of autophagosomes, staining of autophagosomes with the fluorescent dye monodansylcadaverine and expression of a fusion between GFP and the autophagosomal membrane protein ATG8.
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Affiliation(s)
- Yunting Pu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
- Plant Sciences Institute, Iowa State University, Ames, IA, USA.
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226
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Abstract
Biomolecular condensates of ribonucleoproteins (RNPs) such as the transactivation response element (TAR) DNA-binding protein 43 (TDP-43) arise from liquid-liquid phase separation (LLPS) and play vital roles in various biological processes including the formation-dissolution of stress granules (SGs). These condensates are thought to be directly linked to neurodegenerative diseases, providing a depot of aggregation-prone proteins and serving as a cauldron of protein aggregation and fibrillation. Despite recent research efforts, biochemical processes and rearrangements within biomolecular condensates that trigger subsequent protein misfolding and aggregation remain to be elucidated. Fluorescence lifetime imaging microscopy (FLIM) provides a minimally intrusive high-sensitivity and high-resolution imaging method to monitor in-droplet spatiotemporal changes that initiate and lead to protein aggregation. In this chapter, we describe a FLIM application for characterizing chemical chaperone-assisted decoupling of TDP-43 liquid-liquid phase separation and aggregation/fibrillation, highlighting potential therapeutic strategies to combat pathological RNP-associated aggregates without compromising cellular stress responses.
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Affiliation(s)
- My Diem Quan
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
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227
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Jiao Y, Gu L, Jiang Y, Weng M, Yang M. Digitally predicting protein localization and manipulating protein activity in fluorescence images using 4D reslicing GAN. Bioinformatics 2023; 39:6827288. [PMID: 36373962 PMCID: PMC9805574 DOI: 10.1093/bioinformatics/btac719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/28/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
MOTIVATION While multi-channel fluorescence microscopy is a vital imaging method in biological studies, the number of channels that can be imaged simultaneously is limited by technical and hardware limitations such as emission spectra cross-talk. One solution is using deep neural networks to model the localization relationship between two proteins so that the localization of one protein can be digitally predicted. Furthermore, the input and predicted localization implicitly reflect the modeled relationship. Accordingly, observing the response of the prediction via manipulating input localization could provide an informative way to analyze the modeled relationships between the input and the predicted proteins. RESULTS We propose a protein localization prediction (PLP) method using a cGAN named 4D Reslicing Generative Adversarial Network (4DR-GAN) to digitally generate additional channels. 4DR-GAN models the joint probability distribution of input and output proteins by simultaneously incorporating the protein localization signals in four dimensions including space and time. Because protein localization often correlates with protein activation state, based on accurate PLP, we further propose two novel tools: digital activation (DA) and digital inactivation (DI) to digitally activate and inactivate a protein, in order to observing the response of the predicted protein localization. Compared with genetic approaches, these tools allow precise spatial and temporal control. A comprehensive experiment on six pairs of proteins shows that 4DR-GAN achieves higher-quality PLP than Pix2Pix, and the DA and DI responses are consistent with the known protein functions. The proposed PLP method helps simultaneously visualize additional proteins, and the developed DA and DI tools provide guidance to study localization-based protein functions. AVAILABILITY AND IMPLEMENTATION The open-source code is available at https://github.com/YangJiaoUSA/4DR-GAN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Jiao
- Department of Electrical and Computer Engineering, University of Nevada, Las Vegas, NV 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Yingtao Jiang
- Department of Electrical and Computer Engineering, University of Nevada, Las Vegas, NV 89154, USA
| | - Mo Weng
- To whom correspondence should be addressed. or
| | - Mei Yang
- To whom correspondence should be addressed. or
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228
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Abstract
Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a key biochemical method for the comparative analysis of complex protein mixtures. The technique focuses on the identification and characterization of individual protein species following gel electrophoretic separation making it an important analytical tool of top-down proteomics. In order to verify changes in the expression levels of a particular protein, as determined by 2D-DIGE analysis, and evaluate the subcellular localization of the proteoform of interest, immunofluorescence microscopy is very well suited. This chapter describes in detail the preparation of tissue specimens and the process of cryo-sectioning, as well as incubation with primary antibodies and fluorescently labeled secondary antibodies, followed by image analysis. As illustrative examples, the co-detection of immuno-labeled dystrophin and the Y-chromosome in skeletal muscle are shown, and the localization of calbindin in the cerebellum is presented.
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Affiliation(s)
- Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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229
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Rademacher A, Erdel F, Weinmann R, Rippe K. Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation. Methods Mol Biol 2023; 2563:395-411. [PMID: 36227485 DOI: 10.1007/978-1-0716-2663-4_20] [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] [Indexed: 06/16/2023]
Abstract
Phase separation is emerging as a key mechanism to describe the formation of membraneless organelles in the cell. It depends on the multivalent (self-) interaction properties of the macromolecules involved and can be observed in aqueous solutions under controlled conditions in vitro with purified components. However, to experimentally demonstrate that this process indeed occurs in the complex environment of living cells remains difficult. Here, we describe an assay based on light-induced association of proteins into complexes termed optodroplets that are in the hundred nm to μm size range. The formation and dissociation of these optodroplets can be followed over time in living cells by fluorescence microscopy to evaluate the propensity of proteins to demix and to form phase-separated subcompartments. The optodroplet assay is based on the fusion of a protein of interest with the photolyase homology region (PHR) protein domain from Arabidopsis thaliana, which can undergo reversible homo-oligomerization upon illumination with blue light. Using this approach, candidate proteins and their interaction-deficient or interaction-enhanced variants can be compared to each other or to reference proteins with known phase separation features. By quantifying the resulting microscopy images, the propensity of a given protein construct to assemble into a phase-separated subcompartment can be assessed.
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Affiliation(s)
- Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Robin Weinmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
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230
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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. Biochemistry Moscow 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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231
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Zupančič D, Kreft ME, Romih R. Combined Lectin- and Immuno-histochemistry (CLIH) for Fluorescence Microscopy. Methods Mol Biol 2023; 2566:99-110. [PMID: 36152245 DOI: 10.1007/978-1-0716-2675-7_8] [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] [Indexed: 06/16/2023]
Abstract
The function of glycoproteins depends both on their polypeptide chain and sugar residues. For detection and localization of glycoproteins in tissue sections, methods of immunohistochemistry (IHC) and lectin histochemistry (LHC) are usually used separately. For a better understanding of the expression and distribution of variants of glycoproteins, tissue sections can be analyzed by combined lectin- and immuno-histochemistry (CLIH). CLIH exploits the advantages of both IHC and LHC and can therefore contribute to research in glycobiology and other fields of cell biology. Since cancer transformation is accompanied by alterations in the glycosylation of some glycoproteins, CLIH could also be exploited for improved classification of cancers. The chapter considers how CLIH could be employed on paraffin sections and semithin cryosections for fluorescence microscopy. Five different protocols of CLIH are described in detail as well as appropriate negative controls.
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Affiliation(s)
- Daša Zupančič
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Mateja Erdani Kreft
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Romih
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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232
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Tanno Y. Preparation of Mitotic Cells for Fluorescence Microscopy. Methods Mol Biol 2023; 2519:27-40. [PMID: 36066707 DOI: 10.1007/978-1-0716-2433-3_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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cell cycle-dependent regulation of chromosome is a dynamic event. After replication in S phase, sister chromatids show dynamic behavior including condensation, alignment, and segregation in M phase. These beautiful behaviors of chromosomes observed through the microscope have fascinated people since more than 100 years ago, and now we can sketch the dynamics of regulatory proteins and their posttranscriptional modifications through the fluorescent microscope. The purpose of this chapter is describing the basic methods of immunofluorescence analysis of mitotic cells and chromosomes. Besides, the key ideas for improving the preparation of the specimen are also described. Because the characteristic of the proteins of your interest differs one by one, modifying the method might cause the crucial improvement in the observation.
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Affiliation(s)
- Yuji Tanno
- Bioscience Department, Veritas Corporation, Minato-ku, Tokyo, Japan.
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233
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Mahato J, Ray S, Maji SK, Chowdhury A. Spectrally Resolved FRET Microscopy of α-Synuclein Phase-Separated Liquid Droplets. Methods Mol Biol 2023; 2551:425-447. [PMID: 36310218 DOI: 10.1007/978-1-0716-2597-2_27] [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] [Indexed: 06/16/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged as an important phenomenon associated with formation of membraneless organelles. Recently, LLPS has been shown to act as nucleation centers for disease-associated protein aggregation and amyloid fibril formation. Phase-separated α-synuclein droplets gradually rigidify during the course of protein aggregation, and it is very challenging to understand the biomolecular interactions that lead to liquid-like to solid-like transition using conventional ensemble measurements. Here, we describe a spectrally-resolved fluorescence microscopy based Förster resonance energy transfer (FRET) imaging to probe interactions of α-synuclein in individual droplets during LLPS-mediated aggregation. By acquiring entire emission spectral profiles of individual droplets upon sequential excitation of acceptors and donors therein, this technique allows for the quantification of sensitized emission proportional to the extent of FRET, which enables interrogation of the evolution of local interactions of donor-/acceptor-labeled α-synuclein molecules within each droplet. The present study on single droplets is not only an important development for studying LLPS but can also be used to investigate self-assembly or aggregation in biomolecular systems and soft materials.
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Affiliation(s)
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India.
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234
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Middelhauve V, Siebrasse JP, Kubitscheck U. Expansion Microscopy of Bacillus subtilis. Methods Mol Biol 2023; 2601:191-202. [PMID: 36445585 DOI: 10.1007/978-1-0716-2855-3_10] [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] [Indexed: 06/16/2023]
Abstract
Expansion microscopy enables super-resolved visualization of specimen without the need of highly sophisticated and expensive optical instruments. Instead, the method is executed with conventional chemicals and lab equipment. Imaging of bacteria is performed using standard fluorescence microscopy. This chapter describes a protocol for the expansion microscopy of Bacillus subtilis expressing DivIVA-GFP. In addition, the cell wall was labeled by wheat germ agglutinin. Here, we place emphasis on the challenges of selecting the protein and organism of interest.
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Affiliation(s)
- Viola Middelhauve
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Jan Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.
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235
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Ishida CT, Shao W, Espenshade PJ. Assaying Sterol-Regulated ER-to-Golgi Transport of SREBP Cleavage-Activating Protein Using Immunofluorescence Microscopy. Methods Mol Biol 2023; 2557:755-764. [PMID: 36512249 PMCID: PMC10494790 DOI: 10.1007/978-1-0716-2639-9_45] [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] [Indexed: 12/15/2022]
Abstract
Sterol regulatory element-binding proteins (SREBPs) are a family of membrane-bound transcription factors that regulate the uptake and synthesis of cholesterol and fatty acids in mammalian cells. SREBP cleavage-activating protein (SCAP) is an endoplasmic reticulum (ER) protein that binds newly synthesized SREBP, retaining it in the ER where SREBP is inactive. SCAP binds cholesterol and functions as the cholesterol sensor in this regulatory system. Under low cholesterol conditions, SCAP escorts SREBP from the ER to the Golgi apparatus where two proteases sequentially cleave and activate SREBP. Given their central importance in maintaining cellular lipid homeostasis, other mechanisms exist to regulate SREBP activity, such as control of protein synthesis and degradation. Here, we describe methods to assay ER-to-Golgi transport of SCAP in vitro using immunofluorescence microscopy and two different cell systems, Chinese hamster ovary (CHO) cells stably expressing hamster GFP-SCAP and human HeLa cells transiently expressing human GFP-SCAP. These methods will permit investigators to determine if cellular perturbations act by affecting the ER-to-Golgi transport of SCAP.
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Affiliation(s)
- Chiaki T Ishida
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Shao
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter J Espenshade
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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236
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Abstract
Fluorescence microscopy assays enable the investigation of endogenous biomolecular condensates directly in their cellular context. With appropriate experimental designs, these assays yield quantitative information on condensate material properties and inform on biophysical mechanisms of condensate formation. Single-molecule super-resolution and tracking experiments grant access to the smallest condensates and early condensation stages not resolved by conventional imaging approaches. Here, we discuss considerations for using single-molecule assays to extract quantitative information about biomolecular condensates directly in their cellular context.
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Affiliation(s)
- Ganesh Pandey
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA
| | - Alisha Budhathoki
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
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237
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Cheli F, Falsini S, Salvatici MC, Ristori S, Schiff S, Corti E, Costantini I, Gonnelli C, Pavone FS, Papini A. Fluorescent Labeling of Lignin Nanocapsules with Fluorol Yellow 088. Methods Mol Biol 2023; 2566:345-353. [PMID: 36152265 DOI: 10.1007/978-1-0716-2675-7_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 06/16/2023]
Abstract
The microscopic visualization of nanoparticles in plants is crucial to elucidate the mechanisms of their uptake through the cell wall and plasma membrane and to localize the possible sites of their extracellular or intracellular accumulation. Lignin nanocarriers are polymeric hollow nanocapsules able to contain and transport several bioactive substances inside plant tissues. We describe here a method for the preparation of Fluorol Yellow 088-labeled lignin nanocapsules that allow their localization in plant organs and tissues by fluorescence microscopy.
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Affiliation(s)
- Franco Cheli
- LENS - European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | - Sara Falsini
- Department of Biology, University of Florence, Florence, Italy.
| | - Maria Cristina Salvatici
- Institute of Chemistry of Organometallic Compounds (ICCOM)-Electron Microscopy Centre (Ce.M. E.), National Research Council (CNR), Florence, Italy
| | - Sandra Ristori
- Department of Chemistry, University of Florence, Florence, Italy
| | - Silvia Schiff
- Department of Biology, University of Florence, Florence, Italy
| | - Emilio Corti
- Department of Biology, University of Florence, Florence, Italy
| | - Irene Costantini
- LENS - European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | | | | | - Alessio Papini
- Department of Biology, University of Florence, Florence, Italy
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238
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Oddi S, Ciaramellano F, Scipioni L, Dainese E, Maccarrone M. Visualization of Endocannabinoids in the Cell. Methods Mol Biol 2023; 2576:453-459. [PMID: 36152209 DOI: 10.1007/978-1-0716-2728-0_37] [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] [Indexed: 06/16/2023]
Abstract
A still unsolved, although critical, issue in endocannabinoid research is the mechanism by which the lipophilic anandamide (AEA) moves from its site of synthesis, crosses the aqueous milieu, and reaches the different intracellular membrane compartments, where its metabolic and signaling pathways take place. The difficulty of studying intracellular AEA transport and distribution results from the lack of specific probes and techniques to track and visualize this bioactive lipid within the cells. Herein, we describe the use of a biotinylated, non-hydrolyzable derivative of AEA (biotin-AEA, b-AEA) for visualizing the subcellular distribution of this endocannabinoid by means of confocal fluorescence microscopy.
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Affiliation(s)
- Sergio Oddi
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy.
| | - Francesca Ciaramellano
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
| | - Lucia Scipioni
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Enrico Dainese
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Mauro Maccarrone
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
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239
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Digrazia JR, Engevik MA, Engevik AC. Identification of Differentiated Intestinal Epithelial Cells Using Immunostaining and Fluorescence Microscopy. Methods Mol Biol 2023; 2650:17-34. [PMID: 37310620 DOI: 10.1007/978-1-0716-3076-1_2] [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] [Indexed: 06/14/2023]
Abstract
Immunofluorescence imaging enables visualization of a wide range of molecules in diverse cells and tissues. Determining the localization and endogenous protein levels in cells using immunostaining can be highly informative for researchers studying cell structure and function. The small intestinal epithelium is composed of numerous cell types including absorptive enterocytes, mucus-producing goblet cells, lysozyme positive Paneth cells, proliferative stem cells, chemosensing tuft cells, and hormone-producing enteroendocrine cells. Each cell type in the small intestine has unique functions and structures that are critical for maintaining intestinal homeostasis and identifiable by immunofluorescence labeling. In this chapter we provide a detailed protocol and representative images of immunostaining of paraffin-embedded mouse small intestinal tissue. The method highlights antibodies and micrographs that identify differentiated cell types. These details are important because quality immunofluorescence imaging can provide novel insights and a greater understanding of healthy and disease states.
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Affiliation(s)
- Jessica R Digrazia
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Melinda A Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Amy C Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
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240
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Holub M, Birnie A, Japaridze A, van der Torre J, Ridder MD, de Ram C, Pabst M, Dekker C. Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments. Cell Rep Methods 2022; 2:100366. [PMID: 36590691 PMCID: PMC9795359 DOI: 10.1016/j.crmeth.2022.100366] [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] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/29/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%-100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a "genome-in-a-box" approach to study chromosome organization from the bottom up.
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Affiliation(s)
- Martin Holub
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Anthony Birnie
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Aleksandre Japaridze
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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241
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Tikhonova TN, Kolmogorov VS, Timoshenko RV, Vaneev AN, Cohen-Gerassi D, Osminkina LA, Gorelkin PV, Erofeev AS, Sysoev NN, Adler-Abramovich L, Shirshin EA. Sensing Cells-Peptide Hydrogel Interaction In Situ via Scanning Ion Conductance Microscopy. Cells 2022; 11:cells11244137. [PMID: 36552900 PMCID: PMC9776472 DOI: 10.3390/cells11244137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Peptide-based hydrogels were shown to serve as good matrices for 3D cell culture and to be applied in the field of regenerative medicine. The study of the cell-matrix interaction is important for the understanding of cell attachment, proliferation, and migration, as well as for the improvement of the matrix. Here, we used scanning ion conductance microscopy (SICM) to study the growth of cells on self-assembled peptide-based hydrogels. The hydrogel surface topography, which changes during its formation in an aqueous solution, were studied at nanoscale resolution and compared with fluorescence lifetime imaging microscopy (FLIM). Moreover, SICM demonstrated the ability to map living cells inside the hydrogel. A zwitterionic label-free pH nanoprobe with a sensitivity > 0.01 units was applied for the investigation of pH mapping in the hydrogel to estimate the hydrogel applicability for cell growth. The SICM technique that was applied here to evaluate the cell growth on the peptide-based hydrogel can be used as a tool to study functional living cells.
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Affiliation(s)
- Tatiana N. Tikhonova
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Vasilii S. Kolmogorov
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Roman V. Timoshenko
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Alexander N. Vaneev
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Dana Cohen-Gerassi
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Nanoscience and Nanotechnology, The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liubov A. Osminkina
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Petr V. Gorelkin
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Alexander S. Erofeev
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Nikolay N. Sysoev
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Nanoscience and Nanotechnology, The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evgeny A. Shirshin
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 8-2 Trubetskaya St., 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-4959391104
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Baccile N, Lorthioir C, Ba AA, Le Griel P, Pérez J, Hermida-Merino D, Soetaert W, Roelants SLKW. Topological Connection between Vesicles and Nanotubes in Single-Molecule Lipid Membranes Driven by Head-Tail Interactions. Langmuir 2022; 38:14574-14587. [PMID: 36410028 DOI: 10.1021/acs.langmuir.2c01824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Lipid nanotube-vesicle networks are important channels for intercellular communication and transport of matter. Experimentally observed in neighboring mammalian cells but also reproduced in model membrane systems, a broad consensus exists on their formation and stability. Lipid membranes must be composed of at least two molecular components, each stabilizing low (generally a phospholipid) and high curvatures. Strong anisotropy or enhanced conical shape of the second amphiphile is crucial for the formation of nanotunnels. Anisotropic driving forces generally favor nanotube protrusions from vesicles. In this work, we report the unique case of topologically connected nanotubes-vesicles obtained in the absence of directional forces, in single-molecule membranes, composed of an anisotropic bolaform glucolipid, above its melting temperature, Tm. Cryo-TEM and fluorescence confocal microscopy show the interconnection between vesicles and nanotubes in a single-phase region, between 60 and 90 °C under diluted conditions. Solid-state NMR demonstrates that the glucolipid can assume two distinct configurations, head-head and head-tail. These arrangements, seemingly of comparable energy above the Tm, could explain the existence and stability of the topologically connected vesicles and nanotubes, which are generally not observed for classical single-molecule phospholipid-based membranes above their Tm.
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Affiliation(s)
- Niki Baccile
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, Sorbonne Université, Paris75005, France
| | - Cédric Lorthioir
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, Sorbonne Université, Paris75005, France
| | - Abdoul Aziz Ba
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, Sorbonne Université, Paris75005, France
| | - Patrick Le Griel
- Centre National de la Recherche Scientifique, Laboratoire de Chimie de la Matière Condensée de Paris, LCMCP, Sorbonne Université, Paris75005, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, BP48, Gif-sur-Yvette Cedex91192, France
| | - Daniel Hermida-Merino
- Netherlands Organisation for Scientific Research (NWO), DUBBLE@ESRF BP CS40220, Grenoble38043, France
- Departamento de Física Aplicada, CINBIO, Universidade de Vigo, Campus Lagoas-Marcosende, Vigo36310, Spain
| | - Wim Soetaert
- InBio, Department of Biotechnology, Ghent University, Ghent9000, Belgium
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Rana DK, Bhattacharya SC. Implication toward a simple strategy to generate pH tunable FRET-based biosensing. Spectrochim Acta A Mol Biomol Spectrosc 2022; 282:121687. [PMID: 35940066 DOI: 10.1016/j.saa.2022.121687] [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] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The present contribution depicts a unique approach to generate tunable Förster resonance energy transfer (FRET) emission with variation of pH of the medium. The pH sensitive absorption of Doxorubicin leads to modification of spectral overlap between emission spectra of donor (Pyrazoline) and absorption spectra of acceptor (Doxorubicin) thereby sensing maximum FRET efficiency in an optimum pH (near pKa of Doxorubicin). This drug molecule exhibits an instantaneous conformation change at a particular pH, which consequences on abrupt ON-and-OFF FRET efficiency. At elevated pH, both the drug molecules exhibit conformational change and form stable fluorescent exciplex, switching off the FRET emission. Confocal fluorescence images of live HepG2 cells imply that the sensor can proficiently go through the cell membrane and can be applied in the controlled delivery of drug to the tumor cell lines.
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Affiliation(s)
- Dipak Kumar Rana
- Department of Chemistry, Saldiha College, Bankura - 722173, West Bengal, India.
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244
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Kahle ER, Patel N, Sreenivasappa HB, Marcolongo MS, Han L. Targeting cell-matrix interface mechanobiology by integrating AFM with fluorescence microscopy. Prog Biophys Mol Biol 2022; 176:67-81. [PMID: 36055517 PMCID: PMC9691605 DOI: 10.1016/j.pbiomolbio.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Mechanosensing at the interface of a cell and its surrounding microenvironment is an essential driving force of physiological processes. Understanding molecular activities at the cell-matrix interface has the potential to provide novel targets for improving tissue regeneration and early disease intervention. In the past few decades, the advancement of atomic force microscopy (AFM) has offered a unique platform for probing mechanobiology at this crucial microdomain. In this review, we describe key advances under this topic through the use of an integrated system of AFM (as a biomechanical testing tool) with complementary immunofluorescence (IF) imaging (as an in situ navigation system). We first describe the body of work investigating the micromechanics of the pericellular matrix (PCM), the immediate cell micro-niche, in healthy, diseased, and genetically modified tissues, with a focus on articular cartilage. We then summarize the key findings in understanding cellular biomechanics and mechanotransduction, in which, molecular mechanisms governing transmembrane ion channel-mediated mechanosensing, cytoskeleton remodeling, and nucleus remodeling have been studied in various cell and tissue types. Lastly, we provide an overview of major technical advances that have enabled more in-depth studies of mechanobiology, including the integration of AFM with a side-view microscope, multiple optomicroscopy, a fluorescence recovery after photobleaching (FRAP) module, and a tensile stretching device. The innovations described here have contributed greatly to advancing the fundamental knowledge of extracellular matrix biomechanics and cell mechanobiology for improved understanding, detection, and intervention of various diseases.
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Affiliation(s)
- Elizabeth R Kahle
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Neil Patel
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Harini B Sreenivasappa
- Cell Imaging Center, Office of Research and Innovation, Drexel University, PA 19104, United States
| | - Michele S Marcolongo
- Department of Mechanical Engineering, Villanova University, Villanova, PA 19085, United States
| | - Lin Han
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States.
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245
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Gomez-Cruz C, Laguna S, Bachiller-Pulido A, Quilez C, Cañadas-Ortega M, Albert-Smet I, Ripoll J, Muñoz-Barrutia A. Single Plane Illumination Microscopy for Microfluidic Device Imaging. Biosensors (Basel) 2022; 12:1110. [PMID: 36551076 PMCID: PMC9775991 DOI: 10.3390/bios12121110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Three-dimensional imaging of live processes at a cellular level is a challenging task. It requires high-speed acquisition capabilities, low phototoxicity, and low mechanical disturbances. Three-dimensional imaging in microfluidic devices poses additional challenges as a deep penetration of the light source is required, along with a stationary setting, so the flows are not perturbed. Different types of fluorescence microscopy techniques have been used to address these limitations; particularly, confocal microscopy and light sheet fluorescence microscopy (LSFM). This manuscript proposes a novel architecture of a type of LSFM, single-plane illumination microscopy (SPIM). This custom-made microscope includes two mirror galvanometers to scan the sample vertically and reduce shadowing artifacts while avoiding unnecessary movement. In addition, two electro-tunable lenses fine-tune the focus position and reduce the scattering caused by the microfluidic devices. The microscope has been fully set up and characterized, achieving a resolution of 1.50 μm in the x-y plane and 7.93 μm in the z-direction. The proposed architecture has risen to the challenges posed when imaging microfluidic devices and live processes, as it can successfully acquire 3D volumetric images together with time-lapse recordings, and it is thus a suitable microscopic technique for live tracking miniaturized tissue and disease models.
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Affiliation(s)
- Clara Gomez-Cruz
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Sonia Laguna
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Ariadna Bachiller-Pulido
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Cristina Quilez
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Marina Cañadas-Ortega
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Ignacio Albert-Smet
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Jorge Ripoll
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28009 Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28009 Madrid, Spain
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246
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Berker Y, ElHarouni D, Peterziel H, Fiesel P, Witt O, Oehme I, Schlesner M, Oppermann S. Patient-by-Patient Deep Transfer Learning for Drug-Response Profiling Using Confocal Fluorescence Microscopy of Pediatric Patient-Derived Tumor-Cell Spheroids. IEEE Trans Med Imaging 2022; 41:3981-3999. [PMID: 36099221 DOI: 10.1109/tmi.2022.3205554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Image-based phenotypic drug profiling is receiving increasing attention in drug discovery and precision medicine. Compared to classical end-point measurements quantifying drug response, image-based profiling enables both the quantification of drug response and characterization of disease entities and drug-induced cell-death phenotypes. Here, we aim to quantify image-based drug responses in patient-derived 3D spheroid tumor cell cultures, tackling the challenges of a lack of single-cell-segmentation methods and limited patient-derived material. Therefore, we investigate deep transfer learning with patient-by-patient fine-tuning for cell-viability quantification. We fine-tune a convolutional neural network (pre-trained on ImageNet) with 210 control images specific to a single training cell line and 54 additional screen -specific assay control images. This method of image-based drug profiling is validated on 6 cell lines with known drug sensitivities, and further tested with primary patient-derived samples in a medium-throughput setting. Network outputs at different drug concentrations are used for drug-sensitivity scoring, and dense-layer activations are used in t-distributed stochastic neighbor embeddings of drugs to visualize groups of drugs with similar cell-death phenotypes. Image-based cell-line experiments show strong correlation to metabolic results ( R ≈ 0.7 ) and confirm expected hits, indicating the predictive power of deep learning to identify drug-hit candidates for individual patients. In patient-derived samples, combining drug sensitivity scoring with phenotypic analysis may provide opportunities for complementary combination treatments. Deep transfer learning with patient-by-patient fine-tuning is a promising, segmentation-free image-analysis approach for precision medicine and drug discovery.
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247
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Fu X, Kaur H, Rodgers ML, Montemayor EJ, Butcher SE, Hoskins AA. Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy. Proc Natl Acad Sci U S A 2022; 119:e2206815119. [PMID: 36417433 PMCID: PMC9860250 DOI: 10.1073/pnas.2206815119] [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: 04/23/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA 3'-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release. We have used colocalization single molecule spectroscopy (CoSMoS) to visualize Lsm2-8 dynamics during activation of Saccharomyces cerevisiae spliceosomes in vitro. Lsm2-8 is recruited as a component of the tri-snRNP and is released after integration of the Prp19-containing complex (NTC). Despite Lsm2-8 and the NTC being mutually exclusive in existing cryo-EM structures of yeast B complex spliceosomes, we identify a transient intermediate containing both ([Formula: see text]) and provide a kinetic framework for its formation and transformation during activation. Prior to [Formula: see text] assembly, the NTC rapidly and reversibly samples the spliceosome suggesting a mechanism for preventing NTC sequestration by defective spliceosomes that fail to properly activate. In complementary ensemble assays, we show that a base-pairing-dependent ternary complex can form between Lsm2-8 and U2 and U6 helix II RNAs. We propose that this interaction may play a role in formation of transient spliceosome intermediates formed during activation.
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Affiliation(s)
- Xingyang Fu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Margaret L. Rodgers
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Aaron A. Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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248
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Saha A, Mandal S, Arafiles JVV, Gómez‐González J, Hackenberger CPR, Brik A. Structure-Uptake Relationship Study of DABCYL Derivatives Linked to Cyclic Cell-Penetrating Peptides for Live-Cell Delivery of Synthetic Proteins. Angew Chem Int Ed Engl 2022; 61:e202207551. [PMID: 36004945 PMCID: PMC9828537 DOI: 10.1002/anie.202207551] [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: 05/23/2022] [Indexed: 01/12/2023]
Abstract
Modifying cyclic cell-penetrating deca-arginine (cR10) peptides with 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL) improves the uptake efficiency of synthetic ubiquitin (Ub) cargoes into living cells. To probe the role of the DABCYL moiety, we performed time-lapse microscopy and fluorescence lifetime imaging microscopy (FLIM) of fluorescent DABCYL-R10 to evaluate the impact on cell entry by the formation of nucleation zones. Furthermore, we performed a structure-uptake relationship study with 13 DABCYL derivatives coupled to CPP to examine their effect on the cell-uptake efficiency when conjugated to mono-Ub through disulfide linkages. Our results show that through structure variations of the DABCYL moiety alone we could reach, at nanomolar concentration, an additional threefold increase in the cytosolic delivery of Ub, which will enable studies on various intracellular processes related to Ub signaling.
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Affiliation(s)
- Abhishek Saha
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Shaswati Mandal
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Jan Vincent V. Arafiles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
| | - Jacobo Gómez‐González
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Str.2Berlin12489Germany
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
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249
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Abstract
Despite the enormous progress in genomics and proteomics, it is still challenging to assess the states of organelles in living cells with high spatiotemporal resolution. Based on our recent finding of enzyme-instructed self-assembly of a thiophosphopeptide that targets the Golgi Apparatus (GA) instantly, we use the thiophosphopeptide, which is enzymatically responsive and redox active, as an integrative probe for revealing the state of the GA of live cells at the single cell level. By imaging the probe in the GA of live cells over time, our results show that the accumulation of the probe at the GA depends on cell types. By comparison to a conventional Golgi probe, this self-assembling probe accumulates at the GA much faster and are sensitive to the expression of alkaline phosphatases. In addition, subtle changes of the fluorophore results in slightly different GA responses. This work illustrates a novel class of active molecular probes that combine enzyme-instructed self-assembly and redox reaction for high-resolution imaging of the states of subcellular organelles over a large area and extended times.
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Affiliation(s)
- Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, 415 South St., Waltham, MA 02453, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
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250
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Shen Z, Gao Y, Li M, Zhang Y, Xu K, Gong S, Wang Z, Wang S. Development and application of a novel β-diketone difluoroboron-derivatized fluorescent probe for sensitively detecting H 2S. Spectrochim Acta A Mol Biomol Spectrosc 2022; 281:121609. [PMID: 35839692 DOI: 10.1016/j.saa.2022.121609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Hydrogen sulfide{Wang, 2018 #4}{Wang, 2018 #4}{Zhong, 2020 #9} (H2S) is a poisonous and harmful gas molecule. Certain concentrations of H2S{Liu, 2021 #8} can irritate the eyes, respiratory system, and central nervous system of human beings. Therefore, it was an urgent need for highly selective, anti-interference, and sensitive detection technology for hydrogen sulfide. Herein, a novel "turn-on" fluorescent probe 1-(2-(6,6-dimethylbicyclo[3.1.1]heptyl-2-ene-2-yl))-9-(4-(dimethylaminophenyl))non-1,6,8-triene-3,5-dione boron difluoride complex (MCBF) was designed and synthesized for detecting H2S sensitively. MCBF displayed a remarkable fluorescence enhancement response to H2S with a large Stokes shift of 220 nm. The sensitive detection of MCBF towards H2S owned good selectivity, fast response time (6 min), excellent photostability, and low detection limit (0.44 μM). The sensing mechanism of MCBF towards H2S was well confirmed by HRMS analysis, 1H NMR titration, and density functional theory (DFT) calculations. What's more, probe MCBF was successfully applied to detect the contained H2S in red wine, which showed the potential practicability of MCBF in real samples analysis.
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Affiliation(s)
- Zheyu Shen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Gao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Mingxin Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yan Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Kai Xu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Shuai Gong
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhonglong Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Shifa Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
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