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Ding P, Wahn H, Chen FD, Li J, Mu X, Stalmashonak A, Luo X, Lo GQ, Poon JKS, Sacher WD. Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging. NEUROPHOTONICS 2024; 11:S11503. [PMID: 38322247 PMCID: PMC10846542 DOI: 10.1117/1.nph.11.s1.s11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
Significance Light-sheet fluorescence microscopy is widely used for high-speed, high-contrast, volumetric imaging. Application of this technique to in vivo brain imaging in non-transparent organisms has been limited by the geometric constraints of conventional light-sheet microscopes, which require orthogonal fluorescence excitation and collection objectives. We have recently demonstrated implantable photonic neural probes that emit addressable light sheets at depth in brain tissue, miniaturizing the excitation optics. Here, we propose a microendoscope consisting of a light-sheet neural probe packaged together with miniaturized fluorescence collection optics based on an image fiber bundle for lensless, light-field, computational fluorescence imaging. Aim Foundry-fabricated, silicon-based, light-sheet neural probes can be packaged together with commercially available image fiber bundles to form microendoscopes for light-sheet light-field fluorescence imaging at depth in brain tissue. Approach Prototype microendoscopes were developed using light-sheet neural probes with five addressable sheets and image fiber bundles. Fluorescence imaging with the microendoscopes was tested with fluorescent beads suspended in agarose and fixed mouse brain tissue. Results Volumetric light-sheet light-field fluorescence imaging was demonstrated using the microendoscopes. Increased imaging depth and enhanced reconstruction accuracy were observed relative to epi-illumination light-field imaging using only a fiber bundle. Conclusions Our work offers a solution toward volumetric fluorescence imaging of brain tissue with a compact size and high contrast. The proof-of-concept demonstrations herein illustrate the operating principles and methods of the imaging approach, providing a foundation for future investigations of photonic neural probe enabled microendoscopes for deep-brain fluorescence imaging in vivo.
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Affiliation(s)
- Peisheng Ding
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
| | - Hannes Wahn
- Max Planck Institute of Microstructure Physics, Halle, Germany
| | - Fu-Der Chen
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Jianfeng Li
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Xin Mu
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | | | | | | | - Joyce K. S. Poon
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Wesley D. Sacher
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
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2
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Hao S, Suebka S, Su J. Single 5-nm quantum dot detection via microtoroid optical resonator photothermal microscopy. LIGHT, SCIENCE & APPLICATIONS 2024; 13:195. [PMID: 39160151 PMCID: PMC11333578 DOI: 10.1038/s41377-024-01536-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024]
Abstract
Label-free detection techniques for single particles and molecules play an important role in basic science, disease diagnostics, and nanomaterial investigations. While fluorescence-based methods are tools for single molecule detection and imaging, they are limited by available molecular probes and photoblinking and photobleaching. Photothermal microscopy has emerged as a label-free imaging technique capable of detecting individual nanoabsorbers with high sensitivity. Whispering gallery mode (WGM) microresonators can confine light in a small volume for enhanced light-matter interaction and thus are a promising ultra-sensitive photothermal microscopy platform. Previously, microtoroid optical resonators were combined with photothermal microscopy to detect 250 nm long gold nanorods and 100 nm long polymers. Here, we combine microtoroids with photothermal microscopy to spatially detect single 5 nm diameter quantum dots (QDs) with a signal-to-noise ratio exceeding 104. Photothermal images were generated by point-by-point scanning of the pump laser. Single particle detection was confirmed for 18 nm QDs by high sensitivity fluorescence imaging and for 5 nm QDs via comparison with theory. Our system demonstrates the capability to detect a minimum heat dissipation of 0.75 pW. To achieve this, we integrated our microtoroid based photothermal microscopy setup with a low amplitude modulated pump laser and utilized the proportional-integral-derivative controller output as the photothermal signal source to reduce noise and enhance signal stability. The heat dissipation of these QDs is below that from single dye molecules. We anticipate that our work will have application in a wide variety of fields, including the biological sciences, nanotechnology, materials science, chemistry, and medicine.
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Affiliation(s)
- Shuang Hao
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Sartanee Suebka
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Judith Su
- Wyant College of Optical Sciences and Department of Biomedical Engineering, University of Arizona, Tucson, AZ, 85721, USA.
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3
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Rauf SA, Ahmed R, Hussain T, Saad M, Shah HH, Jamalvi SA, Yogeeta F, Devi M, Subash A, Gul M, Ahmed S, Haque MA. Fluorescence in neurosurgery: its therapeutic and diagnostic significance - a comprehensive review. Ann Med Surg (Lond) 2024; 86:4255-4261. [PMID: 38989178 PMCID: PMC11230751 DOI: 10.1097/ms9.0000000000002218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/15/2024] [Indexed: 07/12/2024] Open
Abstract
This review provides a comprehensive overview of the therapeutic and diagnostic implications of fluorescence imaging in neurosurgery. Fluorescence imaging has become a valuable intraoperative visualization and guidance tool, facilitating precise surgical interventions. The therapeutic role of fluorescence is examined, including its application in photodynamic therapy and tumor-targeted therapy. It also explores its diagnostic capabilities in tumor detection, margin assessment, and blood-brain barrier evaluation. Drawing from clinical and preclinical studies, the review underscores the growing evidence supporting the efficacy of fluorescence imaging in neurosurgical practice. Furthermore, it discusses current limitations and future directions, emphasizing the potential for emerging technologies to enhance the utility and accessibility of fluorescence imaging, ultimately improving patient outcomes in neurosurgery.
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Affiliation(s)
| | | | - Tooba Hussain
- Dow University of Health Sciences, Karachi, Pakistan
| | | | | | | | | | | | - Arun Subash
- Dow University of Health Sciences, Karachi, Pakistan
| | - Maryam Gul
- Dow University of Health Sciences, Karachi, Pakistan
| | - Shaheer Ahmed
- Dow University of Health Sciences, Karachi, Pakistan
| | - Md Ariful Haque
- Department of Public Health, Atish Dipankar University of Science and Technology
- Voice of Doctors Research School, Dhaka, Bangladesh
- Department of Orthopaedic Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, People's Republic of China
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4
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Lucidi M, Capecchi G, Visaggio D, Gasperi T, Parisi M, Cincotti G, Rampioni G, Visca P, Kolmakov K. Expanding the microbiologist toolbox via new far-red-emitting dyes suitable for bacterial imaging. Microbiol Spectr 2024; 12:e0369023. [PMID: 38095476 PMCID: PMC10782969 DOI: 10.1128/spectrum.03690-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE By harnessing the versatility of fluorescence microscopy and super-resolution imaging, bacteriologists explore critical aspects of bacterial physiology and resolve bacterial structures sized beyond the light diffraction limit. These techniques are based on fluorophores with profitable photochemical and tagging properties. The paucity of available far-red (FR)-emitting dyes for bacterial imaging strongly limits the multicolor choice of bacteriologists, hindering the possibility of labeling multiple structures in a single experiment. The set of FR fluorophores characterized in this study expands the palette of dyes useful for microbiologists, as they can be used for bacterial LIVE/DEAD staining and for tagging the membranes of viable Escherichia coli and Bacillus subtilis cells. The absence of toxicity makes these dyes suitable for live-cell imaging and allows monitoring of bacterial membrane biogenesis. Moreover, a newly synthesized FR-fluorophore can be employed for imaging bacterial membranes with stimulated emission depletion microscopy, a super-resolution technique capable of increasing the resolving power of conventional microscopes.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Rome, Italy
| | - Miranda Parisi
- Department of Engineering, University Roma Tre, Rome, Italy
| | | | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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5
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Rahman Bhuiyan MZ, Solanki S, Del Rio Mendoza LE, Borowicz P, Lakshman DK, Qi A, Ameen G, Khan MFR. Histopathological Investigation of Varietal Responses to Cercospora beticola Infection Process on Sugar Beet Leaves. PLANT DISEASE 2023; 107:3906-3912. [PMID: 37330633 DOI: 10.1094/pdis-03-23-0562-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cercospora leaf spot (CLS) is the most destructive foliar disease in sugar beet (Beta vulgaris). It is caused by Cercospora beticola Sacc., a fungal pathogen that produces toxins and enzymes which affect membrane permeability and cause cell death during infection. In spite of its importance, little is known about the initial stages of leaf infection by C. beticola. Therefore, we investigated the progression of C. beticola on leaf tissues of susceptible and resistant sugar beet varieties at 12-h intervals during the first 5 days after inoculation using confocal microscopy. Inoculated leaf samples were collected and stored in DAB (3,3'-diaminobenzidine) solution until processed. Samples were stained with Alexa Fluor-488-WGA dye to visualize fungal structures. Fungal biomass accumulation, reactive oxygen species (ROS) production, and the area under the disease progress curve were evaluated and compared. ROS production was not detected on any variety before 36 h postinoculation (hpi). C. beticola biomass accumulation, percentage leaf cell death, and disease severity were all significantly greater in the susceptible variety compared with the resistant variety (P < 0.05). Conidia penetrated directly through stomata between 48 to 60 hpi and produced appressoria on stomatal guard cells at 60 to 72 hpi in susceptible and resistant varieties, respectively. Penetration of hyphae inside the parenchymatous tissues varied in accordance with time postinoculation and varietal genotypes. Overall, this study provides a detailed account to date of events leading to CLS disease development in two contrasting varieties.
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Affiliation(s)
| | - Shyam Solanki
- South Dakota State University, Brookings, SD 57007, U.S.A
| | | | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Aiming Qi
- Centre for Agriculture, Food, and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, U.K
| | - Gazala Ameen
- South Dakota State University, Brookings, SD 57007, U.S.A
| | - Mohamed F R Khan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
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Yoon J, Moon JH, Chung J, Kim YJ, Kim K, Kang HS, Jeon YS, Oh E, Lee SH, Han K, Lee D, Lee CH, Kim YK, Lee D. Exploring the Magnetic Properties of Individual Barcode Nanowires using Wide-Field Diamond Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304129. [PMID: 37264689 DOI: 10.1002/smll.202304129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/22/2023] [Indexed: 06/03/2023]
Abstract
A barcode magnetic nanowire typically comprises a multilayer magnetic structure in a single body with more than one segment type. Interestingly, due to selective functionalization and novel interactions between the layers, it has attracted significant attention, particularly in bioengineering. However, analyzing the magnetic properties at the individual nanowire level remains challenging. Herein, the characterization of a single magnetic nanowire is investigated at room temperature under ambient conditions based on magnetic images obtained via wide-field quantum microscopy with nitrogen-vacancy centers in diamond. Consequently, critical magnetic properties of a single nanowire can be extracted, such as saturation magnetization and coercivity, by comparing the experimental result with that of micromagnetic simulation. This study opens up the possibility for a versatile in situ characterization method suited to individual magnetic nanowires.
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Affiliation(s)
- Jungbae Yoon
- Department of Physics, Korea University, Seoul, 02841, Republic of Korea
| | - Jun Hwan Moon
- Department of Materials Science and Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jugyeong Chung
- Department of Physics, Korea University, Seoul, 02841, Republic of Korea
| | - Yu Jin Kim
- Institute for High Technology Materials and Devices, Korea University, Seoul, 02841, Republic of Korea
| | - Kihwan Kim
- Department of Physics, Korea University, Seoul, 02841, Republic of Korea
| | - Hee Seong Kang
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Yoo Sang Jeon
- Center for Hydrogen∙Fuel Cell Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Eunsoo Oh
- Department of Materials Science and Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sun Hwa Lee
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Dongmin Lee
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Anatomy, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Chul-Ho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Keun Kim
- Department of Materials Science and Engineering, Korea University, Seoul, 02841, Republic of Korea
- Institute for High Technology Materials and Devices, Korea University, Seoul, 02841, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, 02841, Republic of Korea
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7
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Thakkar RN, Kioutchoukova IP, Griffin I, Foster DT, Sharma P, Valero EM, Lucke-Wold B. Mapping the Glymphatic Pathway Using Imaging Advances. J 2023; 6:477-491. [PMID: 37601813 PMCID: PMC10439810 DOI: 10.3390/j6030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023] Open
Abstract
The glymphatic system is a newly discovered waste-clearing system that is analogous to the lymphatic system in our central nervous system. Furthermore, disruption in the glymphatic system has also been associated with many neurodegenerative disorders (e.g., Alzheimer's disease), traumatic brain injury, and subarachnoid hemorrhage. Thus, understanding the function and structure of this system can play a key role in researching the progression and prognoses of these diseases. In this review article, we discuss the current ways to map the glymphatic system and address the advances being made in preclinical mapping. As mentioned, the concept of the glymphatic system is relatively new, and thus, more research needs to be conducted in order to therapeutically intervene via this system.
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Affiliation(s)
- Rajvi N. Thakkar
- College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Ian Griffin
- College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Devon T. Foster
- College of Medicine, Florida International University, Miami, FL 33199, USA
| | | | | | - Brandon Lucke-Wold
- Department of Neurosurgery, University of Florida, 1600 SW Archer Rd., Gainesville, FL 32610, USA
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8
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Venken KJ, Matinyan N, Gonzalez Y, Dierick HA. Serial Recombineering Cloning to Build Selectable and Tagged Genomic P[acman] BAC Clones for Selection Transgenesis and Functional Gene Analysis using Drosophila melanogaster. Curr Protoc 2023; 3:e675. [PMID: 36757632 PMCID: PMC9923880 DOI: 10.1002/cpz1.675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Transgenes with genomic DNA fragments that encompass genes of interest are the gold standard for complementing null alleles in rescue experiments in the fruit fly Drosophila melanogaster. Of particular interest are genomic DNA clones available as bacterial artificial chromosomes (BACs) or fosmids from publicly available genomic DNA libraries. Genes contained within BAC and fosmid clones can be easily modified by recombineering cloning to insert peptide or protein tags to localize, visualize, or manipulate gene products, and to create point mutations or deletions for structure-function analysis of the inserted genes. However, since transgenesis efficiency is inversely correlated with transgene size, obtaining transgenic animals for increasingly larger BAC and fosmid clones requires increasingly laborious screening efforts using the transgenesis marker commonly used for these transgenes, the dominant eye color marker white+ . We recently described a drug-based selectable genetic platform for Drosophila melanogaster, which included four resistance markers that allow direct selection of transgenic animals, eliminating the need to identify transgenic progeny by laborious phenotypic screening. By integrating these resistance markers into BAC transgenes, we were able to isolate animals containing large transgenes by direct selection, avoiding laborious screening. Here we present procedures on how to upgrade BAC clones by serial recombineering cloning to build both selectable and tagged BAC transgenes, for selection transgenesis and functional gene analysis, respectively. We illustrate these procedures using a BAC clone encompassing the gene encoding the synaptic vesicle protein, cysteine string protein. We demonstrate that the modified BAC clone, serially recombineered with a selectable marker for selection transgenesis and an N-terminal green fluorescent protein tag for gene expression analysis, is functional by showing the expression pattern obtained after successful selection transgenesis. The protocols cover: (1) cloning and preparation of the recombineering templates needed for serial recombineering cloning to incorporate selectable markers and protein tags; (2) preparing electrocompetent cells needed to perform serial recombineering cloning; and (3) the serial recombineering workflow to generate both selectable and tagged genomic BAC reporter transgenes for selection transgenesis and functional gene analysis in Drosophila melanogaster. The protocols we describe can be easily adapted to incorporate any of four selectable markers, protein tags, or any other modification for structure-function analysis of the genes present within any of the BAC or fosmid clones. A protocol for generating transgenic animals using serially recombineered BAC clones is presented in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023a). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cloning and preparation of recombineering templates used for serial recombineering cloning. Basic Protocol 2: Making electrocompetent cells of the bacterial strains used to perform serial recombineering cloning or induction of plasmid copy number. Basic Protocol 3: Serial recombineering cloning to generate both selectable and tagged genomic P[acman] BAC reporter transgenes for selection transgenesis and gene expression analysis in Drosophila melanogaster.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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de Jong H, van de Belt J, Fransz P. Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations. Methods Mol Biol 2023; 2672:247-256. [PMID: 37335481 DOI: 10.1007/978-1-0716-3226-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The final step in a long period of chromosome slide experiments is the publication of DAPI and multicolor fluorescence images. Quite often the result of published artwork is disappointing due to insufficient knowledge of image processing and presentation. In this chapter we describe some errors of fluorescence photomicrographs and how to avoid them. We include suggestions of processing chromosome images with simple examples of image processing in Photoshop® or the like, without the need of complex knowledge of the software programs.
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Affiliation(s)
- Hans de Jong
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands.
| | - José van de Belt
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Paul Fransz
- Wageningen University & Research, Laboratory of Genetics, Wageningen, The Netherlands
- Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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10
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Xie H, Liu Y, An H, Yi J, Li C, Wang X, Chai W. Recent advances in prevention, detection and treatment in prosthetic joint infections of bioactive materials. Front Bioeng Biotechnol 2022; 10:1053399. [PMID: 36440438 PMCID: PMC9685530 DOI: 10.3389/fbioe.2022.1053399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/31/2022] [Indexed: 11/07/2023] Open
Abstract
Prosthetic joint infection (PJI) is often considered as one of the most common but catastrophic complications after artificial joint replacement, which can lead to surgical failure, revision, amputation and even death. It has become a worldwide problem and brings great challenges to public health systems. A small amount of microbe attaches to the graft and forms a biofilm on its surface, which lead to the PJI. The current standard methods of treating PJI have limitations, but according to recent reports, bioactive materials have potential research value as a bioactive substance that can have a wide range of applications in the field of PJI. These include the addition of bioactive materials to bone cement, the use of antibacterial and anti-fouling materials for prosthetic coatings, the use of active materials such as bioactive glasses, protamine, hydrogels for prophylaxis and detection with PH sensors and fluorescent-labelled nanoparticles, and the use of antibiotic hydrogels and targeting delivery vehicles for therapeutic purposes. This review focus on prevention, detection and treatment in joint infections with bioactive materials and provide thoughts and ideas for their future applications.
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Affiliation(s)
- Hongbin Xie
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Yubo Liu
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Haoming An
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Jiafeng Yi
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Chao Li
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Xing Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Chai
- Senior Department of Orthopedics, Fourth Medical Center of People’s Liberation Army General Hospital, Beijing, China
- National Clinical Research Center for Orthopaedics, Sports Medicine & Rehabilitation, Beijing, China
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11
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Hussen BM, Faraj GSH, Rasul MF, Hidayat HJ, Salihi A, Baniahmad A, Taheri M, Ghafouri-Frad S. Strategies to overcome the main challenges of the use of exosomes as drug carrier for cancer therapy. Cancer Cell Int 2022; 22:323. [PMID: 36258195 PMCID: PMC9580186 DOI: 10.1186/s12935-022-02743-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Exosomes are naturally occurring nanosized particles that aid intercellular communication by transmitting biological information between cells. Exosomes have therapeutic efficacy that can transfer their contents between cells as natural carriers. In addition, the exosomal contents delivered to the recipient pathological cells significantly inhibit cancer progression. However, exosome-based tumor treatments are inadequately precise or successful, and various challenges should be adequately overcome. Here, we discuss the significant challenges that exosomes face as drug carriers used for therapeutic targets and strategies for overcoming these challenges in order to promote this new incoming drug carrier further and improve future clinical outcomes. We also present techniques for overcoming these challenges.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Goran Sedeeq Hama Faraj
- College of Medicine, Department of Medical Laboratory Sciences, Komar University of Science and Technology, Sulaymaniyah, Iraq
| | - Mohammad Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Erbil, Kurdistan Region, Iraq
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University, Erbil, Kurdistan Region, Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany. .,Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Frad
- Department of Medical Genetics,, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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12
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Refaat A, Yap ML, Pietersz G, Walsh APG, Zeller J, Del Rosal B, Wang X, Peter K. In vivo fluorescence imaging: success in preclinical imaging paves the way for clinical applications. J Nanobiotechnology 2022; 20:450. [PMID: 36243718 PMCID: PMC9571426 DOI: 10.1186/s12951-022-01648-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
Advances in diagnostic imaging have provided unprecedented opportunities to detect diseases at early stages and with high reliability. Diagnostic imaging is also crucial to monitoring the progress or remission of disease and thus is often the central basis of therapeutic decision-making. Currently, several diagnostic imaging modalities (computed tomography, magnetic resonance imaging, and positron emission tomography, among others) are routinely used in clinics and present their own advantages and limitations. In vivo near-infrared (NIR) fluorescence imaging has recently emerged as an attractive imaging modality combining low cost, high sensitivity, and relative safety. As a preclinical tool, it can be used to investigate disease mechanisms and for testing novel diagnostics and therapeutics prior to their clinical use. However, the limited depth of tissue penetration is a major challenge to efficient clinical use. Therefore, the current clinical use of fluorescence imaging is limited to a few applications such as image-guided surgery on tumors and retinal angiography, using FDA-approved dyes. Progress in fluorophore development and NIR imaging technologies holds promise to extend their clinical application to oncology, cardiovascular diseases, plastic surgery, and brain imaging, among others. Nanotechnology is expected to revolutionize diagnostic in vivo fluorescence imaging through targeted delivery of NIR fluorescent probes using antibody conjugation. In this review, we discuss the latest advances in in vivo fluorescence imaging technologies, NIR fluorescent probes, and current and future clinical applications.
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Affiliation(s)
- Ahmed Refaat
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Engineering Technologies, Swinburne University of Technology, Melbourne, VIC, Australia.,Pharmaceutics Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - May Lin Yap
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Geoffrey Pietersz
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Burnet Institute, Melbourne, VIC, Australia.,Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Aidan Patrick Garing Walsh
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Medicine, Monash University, Melbourne, VIC, Australia
| | - Johannes Zeller
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Plastic and Hand Surgery, University of Freiburg Medical Center, Freiburg, Germany
| | | | - Xiaowei Wang
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. .,Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. .,Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia. .,Department of Medicine, Monash University, Melbourne, VIC, Australia. .,Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
| | - Karlheinz Peter
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. .,Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia. .,Department of Medicine, Monash University, Melbourne, VIC, Australia. .,Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
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13
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Intravital microscopy for real-time monitoring of drug delivery and nanobiological processes. Adv Drug Deliv Rev 2022; 189:114528. [PMID: 36067968 DOI: 10.1016/j.addr.2022.114528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/10/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023]
Abstract
Intravital microscopy (IVM) expands our understanding of cellular and molecular processes, with applications ranging from fundamental biology to (patho)physiology and immunology, as well as from drug delivery to drug processing and drug efficacy testing. In this review, we highlight modalities, methods and model organisms that make up today's IVM landscape, and we present how IVM - via its high spatiotemporal resolution - enables analysis of metabolites, small molecules, nanoparticles, immune cells, and the (tumor) tissue microenvironment. We furthermore present examples of how IVM facilitates the elucidation of nanomedicine kinetics and targeting mechanisms, as well as of biological processes such as immune cell death, host-pathogen interactions, metabolic states, and disease progression. We conclude by discussing the prospects of IVM clinical translation and examining the integration of machine learning in future IVM practice.
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14
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Barone V, Lyons DC. Live imaging of echinoderm embryos to illuminate evo-devo. Front Cell Dev Biol 2022; 10:1007775. [PMID: 36187474 PMCID: PMC9521734 DOI: 10.3389/fcell.2022.1007775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Echinoderm embryos have been model systems for cell and developmental biology for over 150 years, in good part because of their optical clarity. Discoveries that shaped our understanding of fertilization, cell division and cell differentiation were only possible because of the transparency of sea urchin eggs and embryos, which allowed direct observations of intracellular structures. More recently, live imaging of sea urchin embryos, coupled with fluorescence microscopy, has proven pivotal to uncovering mechanisms of epithelial to mesenchymal transition, cell migration and gastrulation. However, live imaging has mainly been performed on sea urchin embryos, while echinoderms include numerous experimentally tractable species that present interesting variation in key aspects of morphogenesis, including differences in embryo compaction and mechanisms of blastula formation. The study of such variation would allow us not only to understand how tissues are formed in echinoderms, but also to identify which changes in cell shape, cell-matrix and cell-cell contact formation are more likely to result in evolution of new embryonic shapes. Here we argue that adapting live imaging techniques to more echinoderm species will be fundamental to exploit such an evolutionary approach to the study of morphogenesis, as it will allow measuring differences in dynamic cellular behaviors - such as changes in cell shape and cell adhesion - between species. We briefly review existing methods for live imaging of echinoderm embryos and describe in detail how we adapted those methods to allow long-term live imaging of several species, namely the sea urchin Lytechinus pictus and the sea stars Patiria miniata and Patiriella regularis. We outline procedures to successfully label, mount and image early embryos for 10-16 h, from cleavage stages to early blastula. We show that data obtained with these methods allows 3D segmentation and tracking of individual cells over time, the first step to analyze how cell shape and cell contact differ among species. The methods presented here can be easily adopted by most cell and developmental biology laboratories and adapted to successfully image early embryos of additional species, therefore broadening our understanding of the evolution of morphogenesis.
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Affiliation(s)
- Vanessa Barone
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, La Jolla, CA, United States
| | - Deirdre C. Lyons
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, La Jolla, CA, United States
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15
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Super-Resolution Microscopy and Their Applications in Food Materials: Beyond the Resolution Limits of Fluorescence Microscopy. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-022-02883-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Dong Y, Liu M, Mao Y, Wu S, Wen J, Lu J, Yang Y, Ruan S, Li L, Liu X, Zhang J, Liao S, Dong L. Discovery of 2-(isoxazol-5-yl)phenyl 3,4-dihydroxybenzoate as a potential inhibitor for the Wnt/β-catenin pathway. Bioorg Chem 2022; 128:106116. [DOI: 10.1016/j.bioorg.2022.106116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
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17
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Verma MK, Roychowdhury S, Sahu BD, Mishra A, Sethi KK. CRISPR-based point-of-care diagnostics incorporating Cas9, Cas12, and Cas13 enzymes advanced for SARS-CoV-2 detection. J Biochem Mol Toxicol 2022; 36:e23113. [PMID: 35642647 PMCID: PMC9347549 DOI: 10.1002/jbt.23113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
An outbreak of the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first came to light in December 2019, which has unfolded rapidly and turned out to be a global pandemic. Early prognosis of viral contamination involves speedy intervention, disorder control, and good-sized management of the spread of disease. Reverse transcription-polymerase chain reaction, considered the gold standard test for detecting nucleic acids and pathogen diagnosis, provides high sensitivity and specificity. However, reliance on high-priced equipped kits, associated reagents, and skilled personnel slow down sickness detection. Lately, the improvement of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated protein)-based diagnostic systems has reshaped molecular diagnosis due to their low cost, simplicity, speed, efficiency, high sensitivity, specificity, and versatility, which is vital for accomplishing point-of-care diagnostics. We reviewed and summarized CRISPR-Cas-based point-of-care diagnostic strategies and research in these paintings while highlighting their characteristics and challenges for identifying SARS-CoV-2.
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Affiliation(s)
- Monika K. Verma
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Sanjana Roychowdhury
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Bidya Dhar Sahu
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Awanish Mishra
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Kalyan K. Sethi
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
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18
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Shah HP, Devergne O. Confocal and Super-Resolution Imaging of Polarized Intracellular Trafficking and Secretion of Basement Membrane Proteins During Drosophila Oogenesis. J Vis Exp 2022:10.3791/63778. [PMID: 35662240 PMCID: PMC10325488 DOI: 10.3791/63778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023] Open
Abstract
The basement membrane (BM) - a specialized sheet of extracellular matrix present at the basal side of epithelial cells - is critical for the establishment and maintenance of epithelial tissue morphology and organ morphogenesis. Moreover, the BM is essential for tissue modeling, serving as a signaling platform, and providing external forces to shape tissues and organs. Despite the many important roles that the BM plays during normal development and pathological conditions, the biological pathways controlling the intracellular trafficking of BM-containing vesicles and how basal secretion leads to the polarized deposition of BM proteins are poorly understood. The follicular epithelium of the Drosophila ovary is an excellent model system to study the basal deposition of BM membrane proteins, as it produces and secretes all major components of the BM. Confocal and super-resolution imaging combined with image processing in fixed tissues allows for the identification and characterization of cellular factors specifically involved in the intracellular trafficking and deposition of BM proteins. This article presents a detailed protocol for staining and imaging BM-containing vesicles and deposited BM using endogenously tagged proteins in the follicular epithelium of the Drosophila ovary. This protocol can be applied to address both qualitative and quantitative questions and it was developed to accommodate high-throughput screening, allowing for the rapid and efficient identification of factors involved in the polarized intracellular trafficking and secretion of vesicles during epithelial tissue development.
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Affiliation(s)
- Hemin P Shah
- Department of Biological Sciences, Northern Illinois University
| | - Olivier Devergne
- Department of Biological Sciences, Northern Illinois University;
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19
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Barral DC, Staiano L, Guimas Almeida C, Cutler DF, Eden ER, Futter CE, Galione A, Marques ARA, Medina DL, Napolitano G, Settembre C, Vieira OV, Aerts JMFG, Atakpa‐Adaji P, Bruno G, Capuozzo A, De Leonibus E, Di Malta C, Escrevente C, Esposito A, Grumati P, Hall MJ, Teodoro RO, Lopes SS, Luzio JP, Monfregola J, Montefusco S, Platt FM, Polishchuck R, De Risi M, Sambri I, Soldati C, Seabra MC. Current methods to analyze lysosome morphology, positioning, motility and function. Traffic 2022; 23:238-269. [PMID: 35343629 PMCID: PMC9323414 DOI: 10.1111/tra.12839] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has shown that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyze lysosome morphology, positioning, motility and function. We highlight the principles behind these methods, the methodological strategies and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.
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Affiliation(s)
- Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute for Genetic and Biomedical ResearchNational Research Council (CNR)MilanItaly
| | | | - Dan F. Cutler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Emily R. Eden
- University College London (UCL) Institute of OphthalmologyLondonUK
| | - Clare E. Futter
- University College London (UCL) Institute of OphthalmologyLondonUK
| | | | | | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Clinical Medicine and Surgery DepartmentFederico II UniversityNaplesItaly
| | - Otília V. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | | | | | - Gemma Bruno
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute of Biochemistry and Cell Biology, CNRRomeItaly
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | | | | | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Michael J. Hall
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Rita O. Teodoro
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - J. Paul Luzio
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | | | | | - Maria De Risi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Chiara Soldati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Miguel C. Seabra
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
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20
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Tello JA, Williams HE, Eppler RM, Steinhilb ML, Khanna M. Animal Models of Neurodegenerative Disease: Recent Advances in Fly Highlight Innovative Approaches to Drug Discovery. Front Mol Neurosci 2022; 15:883358. [PMID: 35514431 PMCID: PMC9063566 DOI: 10.3389/fnmol.2022.883358] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases represent a formidable challenge to global health. As advances in other areas of medicine grant healthy living into later decades of life, aging diseases such as Alzheimer's disease (AD) and other neurodegenerative disorders can diminish the quality of these additional years, owed largely to the lack of efficacious treatments and the absence of durable cures. Alzheimer's disease prevalence is predicted to more than double in the next 30 years, affecting nearly 15 million Americans, with AD-associated costs exceeding $1 billion by 2050. Delaying onset of AD and other neurodegenerative diseases is critical to improving the quality of life for patients and reducing the burden of disease on caregivers and healthcare systems. Significant progress has been made to model disease pathogenesis and identify points of therapeutic intervention. While some researchers have contributed to our understanding of the proteins and pathways that drive biological dysfunction in disease using in vitro and in vivo models, others have provided mathematical, biophysical, and computational technologies to identify potential therapeutic compounds using in silico modeling. The most exciting phase of the drug discovery process is now: by applying a target-directed approach that leverages the strengths of multiple techniques and validates lead hits using Drosophila as an animal model of disease, we are on the fast-track to identifying novel therapeutics to restore health to those impacted by neurodegenerative disease.
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Affiliation(s)
- Judith A. Tello
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Haley E. Williams
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Robert M. Eppler
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - Michelle L. Steinhilb
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
- Department of Molecular Pathobiology, New York University, New York, NY, United States
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21
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Murakawa T, Nakamura T, Kawaguchi K, Murayama F, Zhao N, Stasevich TJ, Kimura H, Fujita N. A Drosophila toolkit for HA-tagged proteins unveils a block in autophagy flux in the last instar larval fat body. Development 2022; 149:274775. [DOI: 10.1242/dev.200243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/27/2022] [Indexed: 01/18/2023]
Abstract
ABSTRACT
For in vivo functional analysis of a protein of interest (POI), multiple transgenic strains with a POI that harbors different tags are needed but generation of these strains is still labor-intensive work. To overcome this, we have developed a versatile Drosophila toolkit with a genetically encoded single-chain variable fragment for the HA epitope tag: ‘HA Frankenbody’. This system allows various analyses of HA-tagged POI in live tissues by simply crossing an HA Frankenbody fly with an HA-tagged POI fly. Strikingly, the GFP-mCherry tandem fluorescent-tagged HA Frankenbody revealed a block in autophagic flux and an accumulation of enlarged autolysosomes in the last instar larval and prepupal fat body. Mechanistically, lysosomal activity was downregulated at this stage, and endocytosis, but not autophagy, was indispensable for the swelling of lysosomes. Furthermore, forced activation of lysosomes by fat body-targeted overexpression of Mitf, the single MiTF/TFE family gene in Drosophila, suppressed the lysosomal swelling and resulted in pupal lethality. Collectively, we propose that downregulated lysosomal function in the fat body plays a role in the metamorphosis of Drosophila.
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Affiliation(s)
- Tadayoshi Murakawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tsuyoshi Nakamura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Kohei Kawaguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Futoshi Murayama
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- World Research Hub Initiative, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- World Research Hub Initiative, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Naonobu Fujita
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Precursory Research for Embryonic Science & Technology (PRESTO), Japan Science & Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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22
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:1643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 75022, USA; (T.T.); (J.L.); (T.I.)
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23
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Avellaneda J, Schnorrer F. Tagging Drosophila Proteins with Genetically Encoded Fluorophores. Methods Mol Biol 2022; 2540:251-268. [PMID: 35980582 DOI: 10.1007/978-1-0716-2541-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins are typically not expressed homogeneously in all cells of a complex organism. Within cells, proteins can dynamically change locations, be transported to their destinations, or be degraded upon external signals. Thus, revealing the cellular and subcellular localizations as well as the temporal dynamics of a protein provides important insights into the possible function of the studied protein. Tagging a protein of interest with a genetically encoded fluorophore enables us to follow its expression dynamics in the living organism. Here, we summarize the genetic resources available for tagged Drosophila proteins that assist in studying protein expression and dynamics. We also review the various techniques used in the past and at present to tag a protein of interest with a genetically encoded fluorophore. Comparing the pros and cons of the various techniques guides the reader to judge the suitable applications possible with these tagged proteins in Drosophila.
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Affiliation(s)
- Jerome Avellaneda
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Frank Schnorrer
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France.
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24
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Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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25
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Zhu T, Cao L, Zhou Z, Guo H, Ge M, Dong WF, Li L. Ultra-bright carbon quantum dots for rapid cell staining. Analyst 2022; 147:2558-2566. [DOI: 10.1039/d2an00325b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A schematic illustration of the synthesis of G-CDs and cell imaging under one-photon and two-photon conditions.
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Affiliation(s)
- Tongtong Zhu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
| | - Lei Cao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
| | - Zhenqiao Zhou
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
| | - Hanzhou Guo
- Changchun Guoke Medical Engineer and Technology Development Co., Ltd, Changchun 13003, China
| | - Mingfeng Ge
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
| | - Wen-Fei Dong
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
| | - Li Li
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, P. R. China
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26
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Xia F, Gao X, Shen X, Xu H, Zhong S. Preparation of a gold@europium-based coordination polymer nanocomposite with excellent photothermal properties and its potential for four-mode imaging. NEW J CHEM 2022. [DOI: 10.1039/d2nj01021f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nanocomposite was synthesized by replacing the toxic CTAB on the surface of GNRs with a europium-based hyaluronic acid coordination polymer. The nanocomposite exhibits excellent photothermal performance and also has potential for four-mode imaging.
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Affiliation(s)
- Faming Xia
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Xuejiao Gao
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiaomei Shen
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Hualan Xu
- Analytical and Testing Center, Jiangxi Normal University, Nanchang 330022, China
| | - Shengliang Zhong
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
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27
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Hickey SM, Ung B, Bader C, Brooks R, Lazniewska J, Johnson IRD, Sorvina A, Logan J, Martini C, Moore CR, Karageorgos L, Sweetman MJ, Brooks DA. Fluorescence Microscopy-An Outline of Hardware, Biological Handling, and Fluorophore Considerations. Cells 2021; 11:35. [PMID: 35011596 PMCID: PMC8750338 DOI: 10.3390/cells11010035] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.
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Affiliation(s)
- Shane M. Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | - Ben Ung
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
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28
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S. Bell H, Tower J. In vivo assay and modelling of protein and mitochondrial turnover during aging. Fly (Austin) 2021; 15:60-72. [PMID: 34002678 PMCID: PMC8143256 DOI: 10.1080/19336934.2021.1911286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022] Open
Abstract
To maintain homoeostasis, cells must degrade damaged or misfolded proteins and synthesize functional replacements. Maintaining a balance between these processes, known as protein turnover, is necessary for stress response and cellular adaptation to a changing environment. Damaged mitochondria must also be removed and replaced. Changes in protein and mitochondrial turnover are associated with aging and neurodegenerative disease, making it important to understand how these processes occur and are regulated in cells. To achieve this, reliable assays of turnover must be developed. Several methods exist, including pulse-labelling with radioactive or stable isotopes and strategies making use of fluorescent proteins, each with their own advantages and limitations. Both cell culture and live animals have been used for these studies, in systems ranging from yeast to mammals. In vivo assays are especially useful for connecting turnover to aging and disease. With its short life cycle, suitability for fluorescent imaging, and availability of genetic tools, Drosophila melanogaster is particularly well suited for this kind of analysis.
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Affiliation(s)
- Hans S. Bell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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29
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Saini A, Singh J, Kumar S. Optically superior fluorescent probes for selective imaging of cells, tumors, and reactive chemical species. Org Biomol Chem 2021; 19:5208-5236. [PMID: 34037048 DOI: 10.1039/d1ob00509j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fluorescent chemical probes have become powerful tools to study biological events in living cells. They provide a great opportunity to quantitatively and qualitatively analyze the physiological and biochemical properties of living cells in real time. The ability of researchers to manipulate these probes for a desired specific purpose has turned many heads in the scientific community. Despite a slow start, fluorescent probe research has seen exponential growth over the last decade in the world. This change required some adventurous and creative scientists from different fields-like biology, medicine, and chemistry-to come together to facilitate the constant expansion of this field. This review article introduces some fundamental concepts related to fluorescent probe designing and development. It also summarizes various fluorescent probes with superior optical properties used in fields like cell biology, cellular imaging, medical research, and cancer diagnosis. It is hoped that this article will encourage more young and creative scientists to contribute their talents to this field.
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Affiliation(s)
- Abhishek Saini
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
| | - Jyoti Singh
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
| | - Sonu Kumar
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
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30
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Velasco MGM, Zhang M, Antonello J, Yuan P, Allgeyer ES, May D, M’Saad O, Kidd P, Barentine AES, Greco V, Grutzendler J, Booth MJ, Bewersdorf J. 3D super-resolution deep-tissue imaging in living mice. OPTICA 2021; 8:442-450. [PMID: 34239948 PMCID: PMC8243577 DOI: 10.1364/optica.416841] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 05/08/2023]
Abstract
Stimulated emission depletion (STED) microscopy enables the three-dimensional (3D) visualization of dynamic nanoscale structures in living cells, offering unique insights into their organization. However, 3D-STED imaging deep inside biological tissue is obstructed by optical aberrations and light scattering. We present a STED system that overcomes these challenges. Through the combination of two-photon excitation, adaptive optics, red-emitting organic dyes, and a long-working-distance water-immersion objective lens, our system achieves aberration-corrected 3D super-resolution imaging, which we demonstrate 164 µm deep in fixed mouse brain tissue and 76 µm deep in the brain of a living mouse.
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Affiliation(s)
- Mary Grace M. Velasco
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Mengyang Zhang
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jacopo Antonello
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Peng Yuan
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: Department of Biology, Stanford University, Stanford, California 94304, USA
| | - Edward S. Allgeyer
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: The Gurdon Institute, University of Cambridge, Cambridge CB21QN, UK
| | - Dennis May
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ons M’Saad
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Andrew E. S. Barentine
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Valentina Greco
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jaime Grutzendler
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Joerg Bewersdorf
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Corresponding author:
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31
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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32
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An insight on Drosophila myogenesis and its assessment techniques. Mol Biol Rep 2020; 47:9849-9863. [PMID: 33263930 DOI: 10.1007/s11033-020-06006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Movement assisted by muscles forms the basis of various behavioural traits seen in Drosophila. Myogenesis involves developmental processes like cellular specification, differentiation, migration, fusion, adherence to tendons and neuronal innervation in a series of coordinated event well defined in body space and time. Gene regulatory networks are switched on-off, fine tuning at the right developmental stage to assist each cellular event. Drosophila is a holometabolous organism that undergoes myogenesis waves at two developmental stages, and is ideal for comparative analysis of the role of genes and genetic pathways conserved across phyla. In this review we have summarized myogenic events from the embryo to adult focussing on the somatic muscle development during the early embryonic stage and then on indirect flight muscles (IFM) formation required for adult life, emphasizing on recent trends of analysing muscle mutants and advances in Drosophila muscle biology.
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33
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Keegan SE, Hughes SC. Role of nuclear-cytoplasmic protein localization during Drosophila neuroblast development. Genome 2020; 64:75-85. [PMID: 32526151 DOI: 10.1139/gen-2020-0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear-cytoplasmic localization is an efficient way to regulate transcription factors and chromatin remodelers. Altering the location of existing protein pools also facilitates a more rapid response to changes in cell activity or extracellular signals. There are several examples of proteins that are regulated by nucleo-cytoplasmic shuttling, which are required for Drosophila neuroblast development. Disruption of the localization of homologs of these proteins has also been linked to several neurodegenerative disorders in humans. Drosophila has been used extensively to model the neurodegenerative disorders caused by aberrant nucleo-cytoplasmic localization. Here, we focus on the role of alternative nucleo-cytoplasmic protein localization in regulating proliferation and cell fate decisions in the Drosophila neuroblast and in neurodegenerative disorders. We also explore the analogous role of RNA binding proteins and mRNA localization in the context of regulation of nucleo-cytoplasmic localization during neural development and a role in neurodegenerative disorders.
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Affiliation(s)
- Sophie E Keegan
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Sarah C Hughes
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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34
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Corliss BA, Doty RW, Mathews C, Yates PA, Zhang T, Peirce SM. REAVER: A program for improved analysis of high-resolution vascular network images. Microcirculation 2020; 27:e12618. [PMID: 32173962 PMCID: PMC7507177 DOI: 10.1111/micc.12618] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/17/2022]
Abstract
Alterations in vascular networks, including angiogenesis and capillary regression, play key roles in disease, wound healing, and development. The spatial structures of blood vessels can be captured through imaging, but effective characterization of network architecture requires both metrics for quantification and software to carry out the analysis in a high‐throughput and unbiased fashion. We present Rapid Editable Analysis of Vessel Elements Routine (REAVER), an open‐source tool that researchers can use to analyze high‐resolution 2D fluorescent images of blood vessel networks, and assess its performance compared to alternative image analysis programs. Using a dataset of manually analyzed images from a variety of murine tissues as a ground‐truth, REAVER exhibited high accuracy and precision for all vessel architecture metrics quantified, including vessel length density, vessel area fraction, mean vessel diameter, and branchpoint count, along with the highest pixel‐by‐pixel accuracy for the segmentation of the blood vessel network. In instances where REAVER's automated segmentation is inaccurate, we show that combining manual curation with automated analysis improves the accuracy of vessel architecture metrics. REAVER can be used to quantify differences in blood vessel architectures, making it useful in experiments designed to evaluate the effects of different external perturbations (eg, drugs or disease states).
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Affiliation(s)
- Bruce A Corliss
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Richard W Doty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Corbin Mathews
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Paul A Yates
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Tingting Zhang
- Department of Statistics, University of Virginia, Charlottesville, Virginia
| | - Shayn M Peirce
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia
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35
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Matthews BJ, Vosshall LB. How to turn an organism into a model organism in 10 'easy' steps. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb218198. [PMID: 32034051 DOI: 10.1242/jeb.218198] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many of the major biological discoveries of the 20th century were made using just six species: Escherichia coli bacteria, Saccharomyces cerevisiae and Schizosaccharomyces pombe yeast, Caenorhabditis elegans nematodes, Drosophila melanogaster flies and Mus musculus mice. Our molecular understanding of the cell division cycle, embryonic development, biological clocks and metabolism were all obtained through genetic analysis using these species. Yet the 'big 6' did not start out as genetic model organisms (hereafter 'model organisms'), so how did they mature into such powerful systems? First, these model organisms are abundant human commensals: they are the bacteria in our gut, the yeast in our beer and bread, the nematodes in our compost pile, the flies in our kitchen and the mice in our walls. Because of this, they are cheaply, easily and rapidly bred in the laboratory and in addition were amenable to genetic analysis. How and why should we add additional species to this roster? We argue that specialist species will reveal new secrets in important areas of biology and that with modern technological innovations like next-generation sequencing and CRISPR-Cas9 genome editing, the time is ripe to move beyond the big 6. In this review, we chart a 10-step path to this goal, using our own experience with the Aedes aegypti mosquito, which we built into a model organism for neurobiology in one decade. Insights into the biology of this deadly disease vector require that we work with the mosquito itself rather than modeling its biology in another species.
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Affiliation(s)
- Benjamin J Matthews
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, New York, NY 10065, USA.,Kavli Neural Systems Institute, New York, NY 10065, USA
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36
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Norouz Dizaji A, Ding D, Kutsal T, Turk M, Kong D, Piskin E. In vivo imaging/detection of MRSA bacterial infections in mice using fluorescence labelled polymeric nanoparticles carrying vancomycin as the targeting agent. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2019; 31:293-309. [PMID: 31762403 DOI: 10.1080/09205063.2019.1692631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This study aims to develop fluorescence labelled polymeric nanoparticle (NP) carrying vancomycin as the targeting agent for in vivo imaging of Methicillin-resistant Staphylococcus aureus bacterial infections in animal models. Maleimide functionalized 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[maleimide (polyethylene glycol)-2000] as the main was carrier matrix to prepare the NPs. A fluorescence probe, namely, poly[9,9'-bis (6″-N,N,N-trimethylammonium) hexyl) fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] was encapsulated within these NPs by ultrasonication successfully. UV-Vis spectro- photometry of the NPs showed the characteristic shifting on the peak of conjugated polymers indicating successful packaging of this compound with lipid bilayers in nanoscales. Zeta-sizer and TEM analysis showed that the prepared NPs have a diameter of 80-100 nm in a narrow size distribution. Thiolated vancomycin was synthesized and attached to the NPs as the targeting agent. FTIR and MALDI-TOF spectroscopy analysis confirmed the immobilization. The specific targeting properties of the vancomycin conjugated NPs to the target bacteria were first confirmed in in vitro bacterial cultures in which Escherichia coli was the non-target bacteria - using confocal microscopy and TEM. Imaging of bacterial infections in vivo was investigated in mice model using a non-invasive live animal fluorescence imaging technique. The results confirmed that bacterial infections can be detected using these novel polymeric NPs carrying fluorescence probes for imaging and vancomycin as the targeting agent - in vivo successfully.
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Affiliation(s)
- Araz Norouz Dizaji
- Bioengineering Division, Institute of Graduate Studies, Hacettepe University, Beytepe, Ankara, Turkey
| | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences, Nankai University, Tianjin, China
| | - Tulin Kutsal
- Faculty of Engineering, Chemical Engineering Department, Hacettepe University, Beytepe, Ankara, Turkey
| | - Mustafa Turk
- Faculty of Engineering, Department of Bioengineering, Kirikkale University, Yahsihan, Kirikkale, Turkey
| | - Deling Kong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences, Nankai University, Tianjin, China
| | - Erhan Piskin
- Bioengineering Division, Institute of Graduate Studies, Hacettepe University, Beytepe, Ankara, Turkey.,NanoBMT: Nanobiyomedtek Biyomedikal ve Biyoteknoloji San.Tic.Ltd.Şti, Bilkent, Ankara, Turkey
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37
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Shetty HS, Suryanarayan SM, Jogaiah S, Janakirama ARS, Hansen M, Jørgensen HJL, Tran LSP. Bioimaging structural signatures of the oomycete pathogen Sclerospora graminicola in pearl millet using different microscopic techniques. Sci Rep 2019; 9:15175. [PMID: 31645602 PMCID: PMC6811540 DOI: 10.1038/s41598-019-51477-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022] Open
Abstract
In this case study, the mycelium growth of Sclerospora graminicola in the infected tissues of pearl millet and the process of sporulation and liberation of sporangia and zoospores were observed using four different microscopic techniques. The cotton blue-stained samples observed under light microscope revealed the formation of zoospores with germ tubes, appressoria and initiation of haustorium into the host cells, while the environmental scanning electron microscopy showed the rapid emergence of sporangiophores with dispersed sporangia around the stomata. For fluorescence microscopy, the infected leaf samples were stained with Fluorescent Brightener 28 and Calcofluor White, which react with β-glucans present in the mycelial walls, sporangiophores and sporangia. Calcoflour White was found to be the most suitable for studying the structural morphology of the pathogen. Therefore, samples observed by confocal laser scanning microscopy (CLSM) were pre-treated with Calcofluor White, as well as with Syto-13 that can stain the cell nuclei. Among the four microscopic techniques, CLSM is ideal for observing live host-pathogen interaction and studying the developmental processes of the pathogen in the host tissues. The use of different microscopic bioimaging techniques to study pathogenesis will enhance our understanding of the morphological features and development of the infectious propagules in the host.
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Affiliation(s)
| | | | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Biotechnology and Microbiology, Karnatak University, Dharvad, Karnataka, India.
| | | | - Michael Hansen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 QuangTrung, Da Nang, Vietnam. .,Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurmi-ku, Yokohama, 230-0045, Japan.
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