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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
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Zhang L, Meng X, Zhu XW, Yang DC, Chen R, Jiang Y, Xu T. Long non-coding RNAs in Oral squamous cell carcinoma: biologic function, mechanisms and clinical implications. Mol Cancer 2019; 18:102. [PMID: 31133028 PMCID: PMC6535863 DOI: 10.1186/s12943-019-1021-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/22/2019] [Indexed: 01/17/2023] Open
Abstract
There is growing evidence that regions of the genome that cannot encode proteins play an important role in diseases. These regions are usually transcribed into long non-coding RNAs (lncRNAs). LncRNAs, little or no coding potential, are defined as capped transcripts longer than 200 nucleotides. New sequencing technologies have shown that a large number of aberrantly expressed lncRNAs are associated with multiple cancer types and indicated they have emerged as an important class of pervasive genes during the development and progression of cancer. However, the underlying mechanism in cancer is still unknown. Therefore, it is necessary to elucidate the lncRNA function. Notably, many lncRNAs dysregulation are associated with Oral squamous cell carcinoma (OSCC) and affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review expounds the up- or down-regulation of lncRNAs in OSCC and the molecular mechanisms by which lncRNAs perform their function in the malignant cell. Finally, the potential of lncRNAs as non-invasive biomarkers for OSCC diagnosis are also described. LncRNAs hold promise as prospective novel therapeutic targets, but more research is needed to gain a better understanding of their biologic function.
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Affiliation(s)
- Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Department of Periodontology, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xiang Meng
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xin-Wei Zhu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Outpatient Department of Binhu District, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230601, Anhui Province, China
| | - Deng-Cheng Yang
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Ran Chen
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Yong Jiang
- Department of Stomatology, The Fourth Affiliated Hospital of Anhui Medical University, 372 Tunxi Road, Hefei, 230000, Anhui Province, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China. .,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China.
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Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization. Methods Mol Biol 2017; 1616:137-146. [PMID: 28600766 DOI: 10.1007/978-1-4939-7037-7_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this chapter, we describe a fluorescence in vivo hybridization (FIVH) protocol, using nucleic acid probes, for the detection of the bacterium Helicobacter pylori in the gastric mucosa of an infected C57BL/6 mouse model. This protocol should be easily extended to other microorganisms not only as a way to identify in vivo important microorganisms and their patterns of distribution within specific or at different anatomic sites, but also to better understand interaction mechanisms involving the microbiome and the human body.
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Exploring the dark matter of the human genome using oligonucleotide-based molecules. Future Med Chem 2015; 7:1627-30. [PMID: 26381721 DOI: 10.4155/fmc.15.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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X-FISH: Analysis of cellular RNA expression patterns using flow cytometry. J Immunol Methods 2015; 423:111-9. [PMID: 25997675 DOI: 10.1016/j.jim.2015.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful technique for the detection of RNA or DNA within cells and tissues, which provides a unique link between molecular and cell biology. This technique is broadly applicable across a range of biological systems. While FISH has been previously adapted to flow-based platforms, their use remains limited because of procedural challenges and costs associated with commercial kits. Herein we present a protocol that modifies existing techniques to sensitively and specifically detect and examine RNA expression patterns in primary cells and cell lines using flow cytometry (expression-FISH; X-FISH). As relevant examples, we show how this technique can be used to monitor changes in mRNA expression following activation, how it can be combined with antibody staining to study RNA and protein in the same sample, and how it can help distinguish among subsets in a mixed cell population. X-FISH can integrate multiple probes and can be performed in conjunction with other assays, allowing for informative multiparametric analyses and increased statistical robustness. For non-classical comparative animal models this procedure provides a time saving alternative to de novo production of antibody-based markers. Finally, X-FISH provides an economical solution that is applicable to conventional as well as multi-spectral imaging flow cytometry platforms.
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Fontenete S, Guimarães N, Wengel J, Azevedo NF. Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models. Crit Rev Biotechnol 2015; 36:566-77. [PMID: 25586037 DOI: 10.3109/07388551.2014.993589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The thermodynamics and kinetics of DNA hybridization, i.e. the process of self-assembly of one, two or more complementary nucleic acid strands, has been studied for many years. The appearance of the nearest-neighbor model led to several theoretical and experimental papers on DNA thermodynamics that provide reasonably accurate thermodynamic information on nucleic acid duplexes and allow estimation of the melting temperature. Because there are no thermodynamic models specifically developed to predict the hybridization temperature of a probe used in a fluorescence in situ hybridization (FISH) procedure, the melting temperature is used as a reference, together with corrections for certain compounds that are used during FISH. However, the quantitative relation between melting and experimental FISH temperatures is poorly described. In this review, various models used to predict the melting temperature for rRNA targets, for DNA oligonucleotides and for nucleic acid mimics (chemically modified oligonucleotides), will be addressed in detail, together with a critical assessment of how this information should be used in FISH.
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Affiliation(s)
- Sílvia Fontenete
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.,d ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal
| | - Nuno Guimarães
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Jesper Wengel
- c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Nuno Filipe Azevedo
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal
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Wu M, Piccini ME, Singh AK. MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. Methods Mol Biol 2014; 1211:245-260. [PMID: 25218391 DOI: 10.1007/978-1-4939-1459-3_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155 and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. We also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.
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Affiliation(s)
- Meiye Wu
- Biological Science and Technology, Sandia National Laboratories, MS 9292, 969, Livermore, CA, 94551-0969, USA
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Liu Y, Döring J, Hurek T. Bias in topoisomerase (TOPO)-cloning of multitemplate PCR products using locked nucleic acid (LNA)-substituted primers. J Microbiol Methods 2012; 91:483-6. [PMID: 23064262 DOI: 10.1016/j.mimet.2012.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 11/15/2022]
Abstract
Locked nucleic acid (LNA) modifications help to improve nucleic acid recognition in molecular biology applications. We report that LNA-substituted primers in PCR reactions may cause considerable cloning bias when the widely used topoisomerase-based ligation is used for cloning of multitemplate PCR products.
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Affiliation(s)
- Yuan Liu
- University of Bremen, Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), 28359 Bremen, Germany
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