1
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Cai X, Huang W, Huang J, Zhu X, Wang L, Xia Z, Xu L. CAPZB mRNA is a novel biomarker for cervical high-grade squamous lesions. Sci Rep 2024; 14:20047. [PMID: 39209986 PMCID: PMC11362286 DOI: 10.1038/s41598-024-71112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
This study aimed to evaluate the potential of capping protein (actin filament) muscle Z-line subunit β (CAPZB) messenger ribonucleic acid (mRNA) levels as a biomarker for distinguishing low-grade squamous intraepithelial lesions of the cervix (LSIL) from high-grade squamous intraepithelial lesions of the cervix (HSIL). We collected a total of 166 cervical exfoliated cells and divided them into five groups based on histopathological results. Each sample was divided into two portions, one for fluorescence in situ hybridization (FISH) detection and the other for bisulfite sequencing polymerase chain reaction (BSP) detection. We found that FISH detection of CAPZB mRNA mean fluorescence intensity (MFI) and BSP detection of CAPZB deoxyribonucleic acid (DNA) percentage of methylation rate (PMR) performed as biomarkers for distinguishing HSIL from LSIL, with an area under the receiver operating characteristic curve (AUC), sensitivity, specificity and cut-off value of 0.893, 81.25%, 80.39% and 0.616, 0.794, 64.06%, 81.37% and 0.454, respectively. Furthermore, FISH detection of CAPZB mRNA exhibited a greater AUC (0.893) for the detection of HSIL than the CAPZB DNA methylation method (0.794), indicating the CAPZB mRNA levels can be used as a biomarker for assessing cervical lesions.
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Affiliation(s)
- Xia Cai
- Department of Gynaecology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuxiang Zhu
- Department of Gynaecology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Lifeng Wang
- Department of Gynaecology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Ziyin Xia
- Department of Gynaecology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Ling Xu
- Department of Gynaecology, Minhang Hospital, Fudan University, Shanghai, 201199, China.
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2
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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3
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol 2024; 162:65-77. [PMID: 38724854 PMCID: PMC11227451 DOI: 10.1007/s00418-024-02289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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4
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André M, Dinvaut S, Castellani V, Falk J. 3D exploration of gene expression in chicken embryos through combined RNA fluorescence in situ hybridization, immunofluorescence, and clearing. BMC Biol 2024; 22:131. [PMID: 38831263 PMCID: PMC11149291 DOI: 10.1186/s12915-024-01922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Fine characterization of gene expression patterns is crucial to understand many aspects of embryonic development. The chicken embryo is a well-established and valuable animal model for developmental biology. The period spanning from the third to sixth embryonic days (E3 to E6) is critical for many organ developments. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA-FISH) enables multiplex RNA detection in thick samples including embryos of various animal models. However, its use is limited by tissue opacity. RESULTS We optimized HCR RNA-FISH protocol to efficiently label RNAs in whole mount chicken embryos from E3.5 to E5.5 and adapted it to ethyl cinnamate (ECi) tissue clearing. We show that light sheet imaging of HCR RNA-FISH after ECi clearing allows RNA expression analysis within embryonic tissues with good sensitivity and spatial resolution. Finally, whole mount immunofluorescence can be performed after HCR RNA-FISH enabling as exemplified to assay complex spatial relationships between axons and their environment or to monitor GFP electroporated neurons. CONCLUSIONS We could extend the use of HCR RNA-FISH to older chick embryos by optimizing HCR RNA-FISH and combining it with tissue clearing and 3D imaging. The integration of immunostaining makes possible to combine gene expression with classical cell markers, to correlate expressions with morphological differentiation and to depict gene expressions in gain or loss of function contexts. Altogether, this combined procedure further extends the potential of HCR RNA-FISH technique for chicken embryology.
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Affiliation(s)
- Maëlys André
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
| | - Sarah Dinvaut
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Valérie Castellani
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Julien Falk
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
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5
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. Genes Dev 2024; 38:294-307. [PMID: 38688681 PMCID: PMC11146593 DOI: 10.1101/gad.351557.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 using antisense oligonucleotides (ASOs) stimulates the expression of particular pre- and postsynaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized in puncta of both axons and dendrites that costain with Staufen1 protein, similar to neuronal RNA granules formed by locally translated mRNAs. Ribosome profiling of cultured mouse cortical neurons identified ribosome footprints within a 5' region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP-coding sequence in mouse embryonic stem cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wild-type neurons and showed that M1 expression was enhanced by synaptic stimulation with KCl. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA;
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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6
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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7
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. RESEARCH SQUARE 2024:rs.3.rs-3970096. [PMID: 38464289 PMCID: PMC10925428 DOI: 10.21203/rs.3.rs-3970096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
| | | | | | - Tom Misteli
- National Cancer Institute, National Institute of Health
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8
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.580973. [PMID: 38529487 PMCID: PMC10962702 DOI: 10.1101/2024.02.19.580973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
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9
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Palicz R, Pater B, Truschow P, Witte M, Staiger JF. Intersectional strategy to study cortical inhibitory parvalbumin-expressing interneurons. Sci Rep 2024; 14:2829. [PMID: 38310185 PMCID: PMC10838283 DOI: 10.1038/s41598-024-52901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/24/2024] [Indexed: 02/05/2024] Open
Abstract
Parvalbumin-expressing (PV) interneurons are key neuronal elements to a global excitatory-inhibitory balance in normal cortical functioning. To better understand the circuit functions of PV interneurons, reliable animal models are needed. This study investigated the sensitivity and specificity of the most frequently used PV-Cre/tdTomato mouse line in this regard. The colocalization of the transgene (tdTomato) with the parvalbumin protein, with GAD1 (a conclusive inhibitory cell marker) and Vglut1 (a conclusive excitatory cell marker) as well as with a marker for perineuronal nets (WFA) was assessed and a substantial proportion of layer 5 PV neurons was found to be excitatory and not inhibitory in the PV-Cre/tdTomato mouse. The intersectional transgenic mouse line Vgat-Cre/PV-Flp/tdTomato provided a solution, since no colocalization of tdTomato with the Vglut1 probe was found there. In conclusion, the Vgat-Cre/PV-Flp/tdTomato mouse line seems to be a more reliable animal model for functional studies of GABAergic PV interneurons.
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Affiliation(s)
- Rebeka Palicz
- Center Anatomy, Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany.
| | - Bettina Pater
- Center Anatomy, Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
| | - Pavel Truschow
- Center Anatomy, Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
| | - Mirko Witte
- Center Anatomy, Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
| | - Jochen F Staiger
- Center Anatomy, Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
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10
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578240. [PMID: 38352368 PMCID: PMC10862813 DOI: 10.1101/2024.02.01.578240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Synaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 from neurons stimulated expression of particular pre- and post- synaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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11
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Rolph MJ, Bolfa P, Cavanaugh SM, Rolph KE. Fluorescent In Situ Hybridization for the Detection of Intracellular Bacteria in Companion Animals. Vet Sci 2024; 11:52. [PMID: 38275934 PMCID: PMC10821249 DOI: 10.3390/vetsci11010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
FISH techniques have been applied for the visualization and identification of intracellular bacteria in companion animal species. Most frequently, these techniques have focused on the identification of adhesive-invasive Escherichia coli in gastrointestinal disease, although various other organisms have been identified in inflammatory or neoplastic gastrointestinal disease. Previous studies have investigated a potential role of Helicobacter spp. in inflammatory gastrointestinal and hepatic conditions. Other studies evaluating the role of infectious organisms in hepatopathies have received some attention with mixed results. FISH techniques using both eubacterial and species-specific probes have been applied in inflammatory cardiovascular, urinary, and cutaneous diseases to screen for intracellular bacteria. This review summarizes the results of these studies.
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Affiliation(s)
| | | | | | - Kerry E. Rolph
- Center for Integrative Mammalian Research, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
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12
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Canizo J, Vandal K, Biondic S, Petropoulos S. Whole-Mount RNA, Single-Molecule RNA (smRNA), and DNA Fluorescence In Situ Hybridization (FISH) in Mammalian Embryos. Methods Mol Biol 2024; 2767:307-320. [PMID: 37261674 DOI: 10.1007/7651_2023_490] [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: 06/02/2023]
Abstract
Fluorescence in situ hybridization (FISH) provides a valuable tool for studying the spatial localization of and expression level of genes and cell function in diverse biological contexts. In this chapter, we describe a protocol for the simultaneous detection of RNA (including single-molecule (sm)RNA) and DNA in mammalian embryos using FISH. RNA FISH is a technique that enables the detection and visualization of specific RNA molecules within cells. With advancements in technology, the sensitivity and specificity of RNA FISH has been improved to allow the detection of individual mRNA molecules. Both RNA and smRNA are detected using a set of fluorescent-labeled probes, which are complementary to a specific nucleotide sequence corresponding to the gene of interest. These probes hybridize to the target RNA molecules, enabling the simultaneous detection of multiple RNAs within the same cell or tissue. DNA FISH is performed using probes directed at the DNA sequence to detect the genome region of interest. In this chapter, we provide a protocol to process mammalian embryos for FISH with probe examples specifically for studying X-Chromosome activity. By utilizing other probe designs, this protocol can be adapted for the visualization and quantification of other genes and chromosomal regions of interest.
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Affiliation(s)
- Jesica Canizo
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Katherine Vandal
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Savana Biondic
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Sophie Petropoulos
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
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13
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Salinas-Saavedra M. SABER-FISH in Hydractinia. Methods Mol Biol 2024; 2784:77-85. [PMID: 38502479 DOI: 10.1007/978-1-0716-3766-1_5] [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: 03/21/2024]
Abstract
In situ hybridization allows the detection of nucleic acid sequences in fixed cells and tissues. The gelatinous nature of cnidarians and Hydractinia demands extensive and exhausting protocols to detect RNA transcripts with traditional methods (e.g., colorimetric in situ hybridization). Signal amplification by exchange reaction (SABER) fluorescence in situ hybridization (FISH) enables simplifying and multiplex imaging of RNA targets in a rapid and cost-effective manner. In one enzymatic reaction, SABER-FISH uses a strand-displacing polymerase and catalytic DNA hairpin to generate FISH probes with adjustable signal amplification, allowing highly sensitive detection of nucleic acids and reducing the number of required probes. Here I describe the methodology to detect transcripts within the cells of Hydractinia by SABER-FISH in whole-mount samples.
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14
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Denes LT, Kelley CP, Wang ET. Multiplexed Immunofluorescence and Single-Molecule RNA Fluorescence In Situ Hybridization in Mouse Skeletal Myofibers. Methods Mol Biol 2024; 2784:163-176. [PMID: 38502485 DOI: 10.1007/978-1-0716-3766-1_11] [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: 03/21/2024]
Abstract
RNA fluorescence in situ hybridization (FISH) is a powerful method to determine the abundance and localization of mRNA molecules in cells. While modern RNA FISH techniques allow quantification at single molecule resolution, most methods are optimized for mammalian cell culture and are not easily applied to in vivo tissue settings. Single-molecule RNA detection in skeletal muscle cells has been particularly challenging due to the thickness and high autofluorescence of adult muscle tissue and a lack of in vitro models for mature muscle cells (myofibers). Here, we present a method for isolation of adult myofibers from mouse skeletal muscle and detection of single mRNA molecules and proteins using multiplexed RNA FISH and immunofluorescence.
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Affiliation(s)
- Lance T Denes
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
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15
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D'Ambra E, Vitiello E, Santini T, Bozzoni I. In Situ Hybridization of circRNAs in Cells and Tissues through BaseScope™ Strategy. Methods Mol Biol 2024; 2765:63-92. [PMID: 38381334 DOI: 10.1007/978-1-0716-3678-7_4] [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: 02/22/2024]
Abstract
Imaging-based approaches are powerful strategies that nowadays have been largely used to gain insight into the function of different types of macromolecules. As for RNA, it is becoming clear how important is its intracellular localization for the control of proper cell differentiation and development and how its perturbation can be linked to several pathological states. This aspect is even more important if one thinks of highly polarized cells such as neurons.In this chapter, we describe in detail an innovative RNA-FISH approach for the detection of circular RNAs (circRNAs), a recently discovered class of noncoding RNAs, which display different subcellular localizations and whose functions still largely remain to be elucidated. The detection of these molecules represents a great challenge, above all because they share most of their sequence with the corresponding linear counterparts, from which they differ only for the back-splicing junction (BSJ) originating from the circularization reaction. This implies the use of RNA-FISH probes capable of specifically binding the BSJ and avoiding the detection of the linear counterpart. This requirement imposes the design of probes on a very small region, which implies the risk of obtaining a low and undetectable signal. The BaseScope™ Assay RNA-FISH technology overpasses this problem since it is based on branched-DNA probes. With this approach it is possible to target a specific region of the RNA, even small such as a splicing junction, and at the same time to obtain a strong and well detectable signal. All this is possible thanks to subsequent series of probes that, starting from the first hybridization to the BSJ, build a branched tree of probes that greatly amplifies the signal. Here we provide a detailed step-by-step protocol of BaseScope™ RNA-FISH on circRNAs coupled with immunofluorescence, both in cells and tissues, and we address difficulties which may arise when using this methodology that depend on cell type, specific permeabilization, image acquisition, and post-acquisition analyses.
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Affiliation(s)
- Eleonora D'Ambra
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Erika Vitiello
- Center for Human Technology, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy.
- Center for Human Technology, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy.
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16
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Reißing J, Berres M, Strnad P, Wree A, Inzaugarat ME, Trautwein C, Bruns T, Zimmermann HW. Th2 Cell Activation in Chronic Liver Disease Is Driven by Local IL33 and Contributes to IL13-Dependent Fibrogenesis. Cell Mol Gastroenterol Hepatol 2023; 17:517-538. [PMID: 38158122 PMCID: PMC10882164 DOI: 10.1016/j.jcmgh.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND & AIMS Type 2 immune responses contribute to liver fibrosis in parasite infections, but their role in other liver diseases is less well understood. Here, we aimed at unravelling mechanisms involved in T helper 2 (Th2) T-cell polarization, activation, and recruitment in human liver fibrosis and cirrhosis. METHODS Tissues, cells, and serum from human livers were analyzed using quantitative reverse-transcription polymerase chain reaction, enzyme-linked immunosorbent assay, fluorescence in situ hybridization, immunostaining, flow cytometry, and various functional in vitro assays. Cellular interactions and soluble mediators involved in T-cell polarization and recruitment were studied, as well as their effect on hepatic stellate cell (HSC) activation, proliferation, and extracellular matrix synthesis. RESULTS In human liver fibrosis, a stage-dependent increase in Th2-related transcription factors, Th2 cytokines, and trans-acting T-cell-specific transcription factor-expressing T cells was observed, and was highest in cirrhotic livers. The alarmin interleukin (IL)33 was found to be increased in livers and sera from patients with cirrhosis, to act as a chemotactic agent for Th2 cells, and to induce type 2 polarization of CD4+ T cells. Oval cells, liver sinusoidal endothelial cells, intrahepatic macrophages, and migrating monocytes were identified as sources of IL33. IL33-activated T cells, but not IL33 alone, induced HSC activation, as shown by Ki67 and α-smooth muscle actin staining, increased collagen type I alpha 1 chain messenger RNA expression, and wound healing assays. The profibrotic effect of IL33-activated T cells was contact-independent and could be antagonized using monoclonal antibodies against IL13. CONCLUSION In patients with chronic liver disease, the alarmin IL33 promotes the recruitment and activation of CD4+ T cells with Th2-like properties, which activate paracrine HSC in an IL13-dependent manner and promotes fibrogenesis.
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Affiliation(s)
- Johanna Reißing
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Marie Berres
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Pavel Strnad
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Alexander Wree
- Department of Gastroenterology/Hepatology, Campus Virchow Klinikum, Charité Campus Mitte, Charité University Medicine Berlin, Berlin, Germany
| | - Maria Eugenia Inzaugarat
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Christian Trautwein
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Tony Bruns
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Henning Wolfgang Zimmermann
- Department of Internal Medicine III, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany.
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17
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Huang T, Guillotin B, Rahni R, Birnbaum KD, Wagner D. A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol. PLANT METHODS 2023; 19:131. [PMID: 37993896 PMCID: PMC10666358 DOI: 10.1186/s13007-023-01108-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. RESULTS We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. CONCLUSIONS The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.
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Affiliation(s)
- Tian Huang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bruno Guillotin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Ramin Rahni
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kenneth D Birnbaum
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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18
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Raji JI, Potter CJ. Hybridization Chain Reaction RNA Whole-Mount Fluorescence In situ Hybridization of Chemosensory Genes in Mosquito Olfactory Appendages. J Vis Exp 2023:10.3791/65933. [PMID: 38047558 PMCID: PMC11099874 DOI: 10.3791/65933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Mosquitoes are effective vectors of deadly diseases and can navigate their chemical environment using chemosensory receptors expressed in their olfactory appendages. Understanding how chemosensory receptors are spatially organized in the peripheral olfactory appendages can offer insights into how odor is encoded in the mosquito olfactory system and inform new ways to combat the spread of mosquito-borne diseases. The emergence of third-generation hybridization chain reaction RNA whole-mount fluorescence in situ hybridization (HCR RNA WM-FISH) allows for spatial mapping and simultaneous expression profiling of multiple chemosensory genes. Here, we describe a stepwise approach for performing HCR RNA WM-FISH on the Anopheles mosquito antenna and maxillary palp. We investigated the sensitivity of this technique by examining the expression profile of ionotropic olfactory receptors. We asked if the HCR WM-FISH technique described was suitable for multiplexed studies by tethering RNA probes to three spectrally distinct fluorophores. Results provided evidence that HCR RNA WM-FISH is robustly sensitive to simultaneously detect multiple chemosensory genes in the antenna and maxillary palp olfactory appendages. Further investigations attest to the suitability of HCR WM-FISH for co-expression profiling of double and triple RNA targets. This technique, when applied with modifications, could be adaptable to localize genes of interest in the olfactory tissues of other insect species or in other appendages.
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Affiliation(s)
- Joshua I Raji
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine;
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19
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Yang X, Poelmans W, Grones C, Lakehal A, Pevernagie J, Van Bel M, Njo M, Xu L, Nelissen H, De Rybel B, Motte H, Beeckman T. Spatial transcriptomics of a lycophyte root sheds light on root evolution. Curr Biol 2023; 33:4069-4084.e8. [PMID: 37683643 DOI: 10.1016/j.cub.2023.08.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/15/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.
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Affiliation(s)
- Xilan Yang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ward Poelmans
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Carolin Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Abdellah Lakehal
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Julie Pevernagie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Maria Njo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lin Xu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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20
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Graham G, Chimenti MS, Knudtson KL, Grenard DN, Co L, Sumner M, Tchou T, Bieszczad KM. Learning induces unique transcriptional landscapes in the auditory cortex. Hear Res 2023; 438:108878. [PMID: 37659220 PMCID: PMC10529106 DOI: 10.1016/j.heares.2023.108878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023]
Abstract
Learning can induce neurophysiological plasticity in the auditory cortex at multiple timescales. Lasting changes to auditory cortical function that persist over days, weeks, or even a lifetime, require learning to induce de novo gene expression. Indeed, transcription is the molecular determinant for long-term memories to form with a lasting impact on sound-related behavior. However, auditory cortical genes that support auditory learning, memory, and acquired sound-specific behavior are largely unknown. Using an animal model of adult, male Sprague-Dawley rats, this report is the first to identify genome-wide changes in learning-induced gene expression within the auditory cortex that may underlie long-lasting discriminative memory formation of acoustic frequency cues. Auditory cortical samples were collected from animals in the initial learning phase of a two-tone discrimination sound-reward task known to induce sound-specific neurophysiological and behavioral effects. Bioinformatic analyses on gene enrichment profiles from bulk RNA sequencing identified cholinergic synapse (KEGG rno04725), extra-cellular matrix receptor interaction (KEGG rno04512), and neuroactive receptor interaction (KEGG rno04080) among the top biological pathways are likely to be important for auditory discrimination learning. The findings characterize candidate effectors underlying the early stages of changes in cortical and behavioral function to ultimately support the formation of long-term discriminative auditory memory in the adult brain. The molecules and mechanisms identified are potential therapeutic targets to facilitate experiences that induce long-lasting changes to sound-specific auditory function in adulthood and prime for future gene-targeted investigations.
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Affiliation(s)
- G Graham
- Neuroscience Graduate Program, Rutgers Univ., Piscataway, NJ, USA; Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA
| | - M S Chimenti
- Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - K L Knudtson
- Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - D N Grenard
- Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA
| | - L Co
- Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA
| | - M Sumner
- Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA
| | - T Tchou
- Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA
| | - K M Bieszczad
- Neuroscience Graduate Program, Rutgers Univ., Piscataway, NJ, USA; Behavioral and Systems Neuroscience, Dept. of Psychology, Rutgers Univ., Piscataway, NJ, USA; Rutgers Center for Cognitive Science, Rutgers Univ., Piscataway, NJ, USA; Dept. of Otolaryngology-Head and Neck Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
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21
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Dörrenhaus R, Wagner PK, Kath-Schorr S. Two are not enough: synthetic strategies and applications of unnatural base pairs. Biol Chem 2023; 404:883-896. [PMID: 37354104 DOI: 10.1515/hsz-2023-0169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 06/26/2023]
Abstract
Nucleic acid chemistry is a rapidly evolving field, and the need for novel nucleotide modifications and artificial nucleotide building blocks for diagnostic and therapeutic use, material science or for studying cellular processes continues unabated. This review focusses on the development and application of unnatural base pairs as part of an expanded genetic alphabet. Not only recent developments in "nature-like" artificial base pairs are presented, but also current synthetic methods to get access to C-glycosidic nucleotides. Wide-ranging viability in synthesis is a prerequisite for the successful use of unnatural base pairs in a broader spectrum and will be discussed.
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22
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Gilbonio HE, Puckett GL, Nguyen E, Rieder LE. A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes. BMC Res Notes 2023; 16:197. [PMID: 37679799 PMCID: PMC10486132 DOI: 10.1186/s13104-023-06482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
OBJECTIVES Investigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF. RESULTS We developed a hybrid RNA FISH-IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.
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Affiliation(s)
| | - Gwyn L Puckett
- Piedmont Virginia Community College, Charlottesville, VA, USA
| | - Erica Nguyen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA, USA.
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23
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Ball JB, McNulty CJ, Green-Fulgham SM, Dragavon JM, Correia Rocha IR, Finch MR, Prévost ED, Siddique II, Woodall BJ, Watkins LR, Baratta MV, Root DH. Combining RNAscope and immunohistochemistry to visualize inflammatory gene products in neurons and microglia. Front Mol Neurosci 2023; 16:1225847. [PMID: 37664240 PMCID: PMC10470653 DOI: 10.3389/fnmol.2023.1225847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
A challenge for central nervous system (CNS) tissue analysis in neuroscience research has been the difficulty to codetect and colocalize gene and protein expression in the same tissue. Given the importance of identifying gene expression relative to proteins of interest, for example, cell-type specific markers, we aimed to develop a protocol to optimize their codetection. RNAscope fluorescent in situ hybridization (FISH) combined with immunohistochemistry (IHC) in fixed (CNS) tissue sections allows for reliable quantification of gene transcripts of interest within IHC-labeled cells. This paper describes a new method for simultaneous visualization of FISH and IHC in thicker (14-μm), fixed tissue samples, using spinal cord sections. This method's effectiveness is shown by the cell-type-specific quantification of two genes, namely the proinflammatory cytokine interleukin-1beta (IL-1b) and the inflammasome NLR family pyrin domain containing 3 (NLRP3). These genes are challenging to measure accurately using immunohistochemistry (IHC) due to the nonspecificity of available antibodies and the hard-to-distinguish, dot-like visualizations of the labeled proteins within the tissue. These measurements were carried out in spinal cord sections after unilateral chronic constriction injury of the sciatic nerve to induce neuroinflammation in the spinal cord. RNAscope is used to label transcripts of genes of interest and IHC is used to label cell-type specific antigens (IBA1 for microglia, NeuN for neurons). This combination allowed for labeled RNA transcripts to be quantified within cell-type specific boundaries using confocal microscopy and standard image analysis methods. This method makes it easy to answer empirical questions that are intractable with standard IHC or in situ hybridization alone. The method, which has been optimized for spinal cord tissue and to minimize tissue preparation time and costs, is described in detail from tissue collection to image analysis. Further, the relative expression changes in inflammatory genes NLRP3 and IL-1b in spinal cord microglia vs. neurons of somatotopically relevant laminae are described for the first time.
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Affiliation(s)
- Jayson B. Ball
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Connor J. McNulty
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Suzanne M. Green-Fulgham
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph M. Dragavon
- Advanced Light Microscopy Core, Biofrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Igor R. Correia Rocha
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Maggie R. Finch
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Emily D. Prévost
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Imaad I. Siddique
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Brodie J. Woodall
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Linda R. Watkins
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Michael V. Baratta
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - David H. Root
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
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24
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Xiao W, Yeom KH, Lin CH, Black DL. Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells. RNA (NEW YORK, N.Y.) 2023; 29:1274-1287. [PMID: 37130703 PMCID: PMC10351894 DOI: 10.1261/rna.079591.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/31/2023] [Indexed: 05/04/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a widely used tool for quantifying gene expression and determining the location of RNA molecules in cells. We present an improved method for FISH probe production that yields high-purity probes with a wide range of fluorophores using standard laboratory equipment at low cost. The method modifies an earlier protocol that uses terminal deoxynucleotidyl transferase to add fluorescently labeled nucleotides to synthetic deoxyoligonucleotides. In our protocol, amino-11-ddUTP is joined to an oligonucleotide pool prior to its conjugation to a fluorescent dye, thereby generating pools of probes ready for a variety of modifications. This order of reaction steps allows for high labeling efficiencies regardless of the GC content or terminal base of the oligonucleotides. The degree of labeling (DOL) for spectrally distinct fluorophores (Quasar, ATTO, and Alexa dyes) was mostly >90%, comparable with commercial probes. The ease and low cost of production allowed the generation of probe sets targeting a wide variety of RNA molecules. Using these probes, FISH assays in C2C12 cells showed the expected subcellular localization of mRNAs and pre-mRNAs for Polr2a (RNA polymerase II subunit 2a) and Gapdh, and of the long noncoding RNAs Malat1 and Neat1 Developing FISH probe sets for several transcripts containing retained introns, we found that retained introns in the Gabbr1 and Noc2l transcripts are present in subnuclear foci separate from their sites of synthesis and partially coincident with nuclear speckles. This labeling protocol should have many applications in RNA biology.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
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25
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Zhu N, Ahmed M, Li Y, Liao JC, Wong PK. Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion. Proc Natl Acad Sci U S A 2023; 120:e2305410120. [PMID: 37364126 PMCID: PMC10319025 DOI: 10.1073/pnas.2305410120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
Cancer cells collectively invade using a leader-follower organization, but the regulation of leader cells during this dynamic process is poorly understood. Using a dual double-stranded locked nucleic acid (LNA) nanobiosensor that tracks long noncoding RNA (lncRNA) dynamics in live single cells, we monitored the spatiotemporal distribution of lncRNA during collective cancer invasion. We show that the lncRNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is dynamically regulated in the invading fronts of cancer cells and patient-derived spheroids. MALAT1 transcripts exhibit distinct abundance, diffusivity, and distribution between leader and follower cells. MALAT1 expression increases when a cancer cell becomes a leader and decreases when the collective migration process stops. Transient knockdown of MALAT1 prevents the formation of leader cells and abolishes the invasion of cancer cells. Taken together, our single-cell analysis suggests that MALAT1 is dynamically regulated in leader cells during collective cancer invasion.
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Affiliation(s)
- Ninghao Zhu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA16802
| | - Mona Ahmed
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA16802
| | - Yanlin Li
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA16802
| | - Joseph C. Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA94305
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA16802
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA16802
- Department of Surgery, The Pennsylvania State University, University Park, PA17033
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26
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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27
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Gilbonio HE, Puckett GL, Nguyen E, Rieder LE. A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544616. [PMID: 37398336 PMCID: PMC10312655 DOI: 10.1101/2023.06.12.544616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Objectives Investigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF. Results We developed a hybrid RNA FISH and IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi-sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.
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Affiliation(s)
| | - Gwyn L. Puckett
- Piedmont Virginia Community College, Charlottesville, VA, USA
| | - Erica Nguyen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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28
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Han X, Pan Y, Fan J, Wang M, Wang L, Wang J, Afedo SY, Zhao L, Wang Y, Zhao T, Zhang T, Zhang R, Cui Y, Yu S. LncRNA MEG3 regulates ASK1/JNK axis-mediated apoptosis and autophagy via sponging miR-23a in granulosa cells of yak tertiary follicles. Cell Signal 2023; 107:110680. [PMID: 37086956 DOI: 10.1016/j.cellsig.2023.110680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Apoptosis and autophagy in granulosa cells (GCs) are highly related to follicular development and atresia. It has also been reported that they are related to LncRNA MEG3, miR-23a and apoptosis signal-regulating kinase 1 (ASK-1). However, their relationship to follicular development and the extent to which follicle stimulating hormone (FSH) or luteinizing hormone (LH) can regulate this process remain unknown. Here, we found that ASK1 and JNK were expressed in the GCs of gonadotropin-dependent follicles, and those levels were significantly higher (p < 0.05) in yak Tertiary follicles compared to that of Secondary follicles and Graafian follicles. Then, the effect of LncRNA MEG3 / miR-23a on apoptosis and autophagy via ASK1/JNK (c-Jun N-terminal kinase) in yak GCs was studied. Overexpressing LncRNA MEG3 reduced miR-23a levels and p-967 protein expression, but enhanced ASK1 and JNK mRNA levels as well as t-ASK1, p-845, t-JNK, and p-JNK proteins levels. And Up-regulation of LncRNA MEG3 promoted apoptosis while attenuating autophagy. The targeting relationship between miR-23a and the binding sites of LncRNA MEG3 and ASK1 was also confirmed with the dual luciferase reporter assay. And, the relationship between LncRNA MEG3 and miR-23a was observed as a negative feedback regulation, and changes in LncRNA MEG3 and miR-23a levels can alter the expression of ASK1/JNK axis in yaks GCs. In addition, FSH (10 μg/mL) or LH (100 μg/mL) ability to reverse the effects of LncRNA MEG3 on miR-23a levels and ASK1/JNK axis-mediated apoptosis and autophagy was verified in yak GCs. This is significantly beneficial for decreasing abnormal follicular atresia for yaks tertiary follicles.
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Affiliation(s)
- Xiaohong Han
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yangyang Pan
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangfeng Fan
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Meng Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Libin Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinglei Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Seth Yaw Afedo
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Ling Zhao
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaying Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Tian Zhao
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Tongxiang Zhang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Rui Zhang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yan Cui
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Sijiu Yu
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.
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29
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Monné Rodríguez JM, Frisk AL, Kreutzer R, Lemarchand T, Lezmi S, Saravanan C, Stierstorfer B, Thuilliez C, Vezzali E, Wieczorek G, Yun SW, Schaudien D. European Society of Toxicologic Pathology (Pathology 2.0 Molecular Pathology Special Interest Group): Review of In Situ Hybridization Techniques for Drug Research and Development. Toxicol Pathol 2023; 51:92-111. [PMID: 37449403 PMCID: PMC10467011 DOI: 10.1177/01926233231178282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In situ hybridization (ISH) is used for the localization of specific nucleic acid sequences in cells or tissues by complementary binding of a nucleotide probe to a specific target nucleic acid sequence. In the last years, the specificity and sensitivity of ISH assays were improved by innovative techniques like synthetic nucleic acids and tandem oligonucleotide probes combined with signal amplification methods like branched DNA, hybridization chain reaction and tyramide signal amplification. These improvements increased the application spectrum for ISH on formalin-fixed paraffin-embedded tissues. ISH is a powerful tool to investigate DNA, mRNA transcripts, regulatory noncoding RNA, and therapeutic oligonucleotides. ISH can be used to obtain spatial information of a cell type, subcellular localization, or expression levels of targets. Since immunohistochemistry and ISH share similar workflows, their combination can address simultaneous transcriptomics and proteomics questions. The goal of this review paper is to revisit the current state of the scientific approaches in ISH and its application in drug research and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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30
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Dumigan A, Gonzalez RC, Morris B, Sá-Pessoa J. Visualisation of Host-Pathogen Communication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1406:19-39. [PMID: 37016109 DOI: 10.1007/978-3-031-26462-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The core of biomedical science is the use of laboratory techniques to support the diagnosis and treatment of disease in clinical settings. Despite tremendous advancement in our understanding of medicine in recent years, we are still far from having a complete understanding of human physiology in homeostasis, let alone the pathology of disease states. Indeed medical advances over the last two hundred years would not have been possible without the invention of and continuous development of visualisation techniques available to research scientists and clinicians. As we have all learned from the recent COVID pandemic, despite advances in modern medicine we still have much to learn regarding infection biology. Indeed antimicrobial resistant (AMR) bacteria are a global threat to human health, meaning research into bacterial pathogenesis is vital. In this chapter, we will briefly describe the nature of microbes and host immune responses before delving into some of the visualisation techniques utilised in the field of biomedical research with a focus on host-pathogen interactions. We will give a brief overview of commonly used techniques from gold standard staining methods, in situ hybridisation, microscopy, western blotting, microbial characterisation, to cutting-edge image flow cytometry and mass spectrometry. Specifically, we will focus on techniques utilised to visualise interactions between the host, our own bodies, and invading organisms including bacteria. We will touch on in vitro and ex vivo modelling methodology with examples utilised to delineate pathogenicity in disease. A better understanding of bacterial biology, immunology and how these fields interact (host-pathogen communications) in biomedical research is integral to developing novel therapeutic approaches which circumvent the need for antibiotics, an important issue as we enter a post-antibiotic era.
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Affiliation(s)
- Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
| | | | - Brenda Morris
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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31
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Nagai MH, Matsunami H. Activity-Dependent Labeling of Olfactory Sensory Neurons Using RNA Fluorescence In Situ Hybridization Followed by Phospho-S6 Immunofluorescence. Methods Mol Biol 2023; 2710:83-97. [PMID: 37688726 DOI: 10.1007/978-1-0716-3425-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
This microscope-based method allows demonstrating that an odorant receptor responded to an odorant in vivo. In sections of olfactory epithelium from odorant-exposed mice, the subpopulation of olfactory sensory neurons expressing a particular odorant receptor type is labeled using RNA fluorescence in situ hybridization. Sequential immunofluorescence against the phosphorylated S6 ribosomal subunit reveals the activated olfactory sensory neurons. The presence of double-labeled cells confirms that the particular odorant receptor type was activated by the odorant stimulation.
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Affiliation(s)
- Maira Harume Nagai
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
- Department of Neurobiology, Duke Institute for Brain Sciences, Durham, NC, USA.
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32
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [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: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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33
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O’Toole AD, Zhang J, Williams LBA, Brown CC. Viral replication site distribution for rabbit hemorrhagic disease virus 2 in formalin-fixed, paraffin-embedded tissues via in situ hybridization. J Vet Diagn Invest 2022; 34:1023-1026. [PMID: 36171733 PMCID: PMC9597347 DOI: 10.1177/10406387221126999] [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: 11/16/2022] Open
Abstract
We made 2 Z-based in situ hybridization (ISH) probes for the detection of rabbit hemorrhagic disease virus 2 (RHDV2; Lagovirus GI.2) nucleic acid in formalin-fixed, paraffin-embedded tissues from European rabbits (Oryctolagus cuniculus) that had died during an outbreak of RHD in Washington, USA. One probe system was made for detection of negative-sense RNA (i.e., the replicative intermediate RNA for the virus), and the other probe system was constructed for detection of genomic and mRNA of the virus (viral mRNA). Tissue sets were tested separately, and the viral mRNA probe system highlighted much broader tissue distribution than that of the replicative intermediate RNA probe system. The latter was limited to liver, lung, kidney, spleen, myocardium, and occasional endothelial staining, whereas signal for the viral mRNA was seen in many more tissues. The difference in distribution suggests that innate phagocytic activity of various cell types may cause overestimation of viral replication sites when utilizing ISH of single-stranded, positive-sense viruses.
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Affiliation(s)
- Alicia D. O’Toole
- Department of Pathology, College of Veterinary Medicine,
University of Georgia, Athens, GA, USA
| | - Jian Zhang
- Department of Pathology, College of Veterinary Medicine,
University of Georgia, Athens, GA, USA
| | - Laura B. A. Williams
- Department of Veterinary Microbiology & Pathology,
Washington State University, Pullman, WA, USA
| | - Corrie C. Brown
- Department of Pathology, College of Veterinary Medicine,
University of Georgia, Athens, GA, USA
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34
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Chiriboga L, Callis GM, Wang Y, Chlipala E. Guide for collecting and reporting metadata on protocol variables and parameters from slide-based histotechnology assays to enhance reproducibility. J Histotechnol 2022; 45:132-147. [DOI: 10.1080/01478885.2022.2134022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- NYULH Center for Biospecimen Research and Development, New York, NY, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas, MO, USA
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35
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Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, Patel D, Alkurdi AA, Yang W. Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA. Cells 2022; 11:3079. [PMID: 36231040 PMCID: PMC9564294 DOI: 10.3390/cells11193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.
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Affiliation(s)
| | | | | | | | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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36
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Horn T, Narov KD, Panfilio KA. Persistent Parental RNAi in the Beetle Tribolium castaneum Involves Maternal Transmission of Long Double-Stranded RNA. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100064. [PMID: 36620196 PMCID: PMC9744488 DOI: 10.1002/ggn2.202100064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 01/11/2023]
Abstract
Parental RNA interference (pRNAi) is a powerful and widely used method for gene-specific knockdown. Yet in insects its efficacy varies between species, and how the systemic response is transmitted from mother to offspring remains elusive. Using the beetle Tribolium castaneum, an RT-qPCR strategy to distinguish the presence of double-stranded RNA (dsRNA) from endogenous mRNA is reported. It is found that injected dsRNA is directly transmitted into the egg and persists throughout embryogenesis. Despite this depletion of dsRNA from the mother, it is shown that strong pRNAi can persist for months before waning at strain-specific rates. In seeking the receptor proteins for cellular uptake of long dsRNA into the egg, a phylogenomics profiling approach of candidate proteins is also presented. A visualization strategy based on taxonomically hierarchical assessment of orthology clustering data to rapidly assess gene age and copy number changes, refined by sequence-based evidence, is demonstrated. Repeated losses of SID-1-like channel proteins in the arthropods, including wholesale loss in the Heteroptera (true bugs), which are nonetheless highly sensitive to pRNAi, are thereby documented. Overall, practical considerations for insect pRNAi against a backdrop of outstanding questions on the molecular mechanism of dsRNA transmission for long-term, systemic knockdown are elucidated.
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Affiliation(s)
- Thorsten Horn
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany
| | - Kalin D. Narov
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
| | - Kristen A. Panfilio
- Institute for Zoology: Developmental BiologyUniversity of CologneZülpicher Straße 47b50674CologneGermany
- School of Life SciencesUniversity of WarwickGibbet Hill CampusCoventryCV4 7ALUK
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37
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Wu HF, Kailasa SK. Recent advances in nanomaterials-based optical sensors for detection of various biomarkers (inorganic species, organic and biomolecules). LUMINESCENCE 2022. [PMID: 35929140 DOI: 10.1002/bio.4353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022]
Abstract
This review briefly emphasizes the different detection approaches (electrochemical sensors, chemiluminescence, surface-enhanced Raman scattering), functional nanostructure materials (quantum dots, metal nanoparticles, metal nanoclusters, magnetic nanomaterials, metal oxide nanoparticles, polymer-based nanomaterials, and carbonaceous nanomaterials) and detection mechanisms. Further, this review emphasis on the integration of functional nanomaterials with optical spectroscopic techniques for the identification of various biomarkers (nucleic acids, glucose, uric acid, oxytocin, dopamine, ascorbic acid, bilirubin, spermine, serotonin, thiocyanate, Pb2+ , Cu2+ , Hg2+ , F- , peptides, and cancer biomarkers (mucin 1, prostate specific antigen, carcinoembryonic antigen, CA15-3, human epidermal growth factor receptor 2, C-reactive protein, and interleukin-6). Analytical characteristics of nanomaterials-based optical sensors are summarized in Tables, providing the insights of nanomaterials-based optical sensors for biomarkers detection. Finally, the opportunities and challenges of nanomaterials-based optical analytical approaches for the detection of various biomarkers (inorganic, organic, biomolecules, peptides and proteins) are discussed.
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Affiliation(s)
- Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan
- International PhD Program for Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Suresh Kumar Kailasa
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, Gujarat, India
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Du J, Dartawan R, Rice W, Gao F, Zhou JH, Sheng J. Fluorescent Platforms for RNA Chemical Biology Research. Genes (Basel) 2022; 13:1348. [PMID: 36011259 PMCID: PMC9407474 DOI: 10.3390/genes13081348] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating.
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Affiliation(s)
| | | | | | | | | | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (J.D.); (R.D.); (W.R.); (F.G.); (J.H.Z.)
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Zhao Y, Deng H, Chen Y, Li J, Chen S, Li C, Mu X, Hu Z, Li K, Wang W. Establishment and Optimization of Molecular Cytogenetic Techniques (45S rDNA-FISH, GISH, and Fiber-FISH) in Kiwifruit ( Actinidia Lindl.). FRONTIERS IN PLANT SCIENCE 2022; 13:906168. [PMID: 35734244 PMCID: PMC9208197 DOI: 10.3389/fpls.2022.906168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The kiwifruit (Actinidia chinensis) has long been regarded as "the king of fruits" for its nutritional importance. However, the molecular cytogenetics of kiwifruit has long been hampered because of the large number of basic chromosome (x = 29), the inherent small size and highly similar morphology of metaphase chromosomes. Fluorescence in situ hybridization (FISH) is an indispensable molecular cytogenetic technique widely used in many plant species. Herein, the effects of post-hybridization washing temperature on FISH, blocking DNA concentration on genomic in situ hybridization (GISH), extraction method on nuclei isolation and the incubation time on the DNA fiber quality in kiwifruit were evaluated. The post-hybridization washing in 2 × saline sodium citrate (SSC) solution for 3 × 5 min at 37°C ensured high stringency and distinct specific FISH signals in kiwifruit somatic chromosomes. The use of 50 × blocking DNA provided an efficient and reliable means of discriminating between chromosomes derived from in the hybrids of A. chinensis var. chinensis (2n = 2x = 58) × A. eriantha (2n = 2x = 58), and inferring the participation of parental genitors. The chopping method established in the present study were found to be very suitable for preparation of leaf nuclei in kiwifruit. A high-quality linear DNA fiber was achieved by an incubation of 20 min. The physical size of 45S rDNA signals was approximately 0.35-0.40 μm revealed by the highly reproducible fiber-FISH procedures established and optimized in this study. The molecular cytogenetic techniques (45S rDNA-FISH, GISH, and high-resolution fiber-FISH) for kiwifruit was for the first time established and optimized in the present study, which is the foundation for the future genomic and evolutionary studies and provides chromosomal characterization for kiwifruit breeding programs.
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Affiliation(s)
- Yang Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Xinxiang Academy of Agricultural Sciences, Xinxiang, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yao Chen
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jihan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Silei Chen
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chunyan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xue Mu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Horticultural Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zhongrong Hu
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Kunming Li
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Conrad T, Altmüller J. Single cell- and spatial 'Omics revolutionize physiology. Acta Physiol (Oxf) 2022; 235:e13848. [PMID: 35656634 DOI: 10.1111/apha.13848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/24/2022] [Accepted: 05/27/2022] [Indexed: 11/29/2022]
Abstract
Single cell multi- 'Omics and Spatial Transcriptomics are prominent technological highlights of recent years, and both fields still witness a ceaseless firework of novel approaches for high resolution profiling of additional omics layers. As all life processes in organs and organisms are based on the functions of their fundamental building blocks, the individual cells and their interactions, these methods are of utmost worth for the study of physiology in health and disease. Recent discoveries on embryonic development, tumor immunology, the detailed cellular composition and function of complex tissues like for example the kidney or the brain, different roles of the same cell type in different organs, the oncogenic program of individual tumor entities, or the architecture of immunopathology in infected tissue are based on single cell and spatial transcriptomics experiments. In this review, we will give a broad overview of technological concepts for single cell and spatial analysis, showing both advantages and limitations, and illustrate their impact with some particularly impressive case studies.
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Affiliation(s)
- Thomas Conrad
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
| | - Janine Altmüller
- Genomics Technology Platform Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany
- Core Facility Genomics Berlin Institute of Health at Charité ‐ Universitätsmedizin Berlin Berlin Germany
- Center for Molecular Medicine Cologne (CMMC) Cologne Germany
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41
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Nilsson OR, Kari L, Rosenke R, Steele-Mortimer O. Protocol for RNA fluorescence in situ hybridization in mouse meningeal whole mounts. STAR Protoc 2022; 3:101256. [PMID: 35345596 PMCID: PMC8956821 DOI: 10.1016/j.xpro.2022.101256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Olof Rickard Nilsson
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840-2932, USA
- Corresponding author
| | - Laszlo Kari
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840-2932, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840-2932, USA
| | - Olivia Steele-Mortimer
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840-2932, USA
- Corresponding author
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Vervaeke P, Borgos SE, Sanders NN, Combes F. Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics. Adv Drug Deliv Rev 2022; 184:114236. [PMID: 35351470 PMCID: PMC8957368 DOI: 10.1016/j.addr.2022.114236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
The success of the messenger RNA-based COVID-19 vaccines of Moderna and Pfizer/BioNTech marks the beginning of a new chapter in modern medicine. However, the rapid rise of mRNA therapeutics has resulted in a regulatory framework that is somewhat lagging. The current guidelines either do not apply, do not mention RNA therapeutics, or do not have widely accepted definitions. This review describes the guidelines for preclinical biodistribution studies of mRNA/siRNA therapeutics and highlights the relevant differences for mRNA vaccines. We also discuss the role of in vivo RNA imaging techniques and other assays to fulfill and/or complement the regulatory requirements. Specifically, quantitative whole-body autoradiography, microautoradiography, mass spectrometry-based assays, hybridization techniques (FISH, bDNA), PCR-based methods, in vivo fluorescence imaging, and in vivo bioluminescence imaging, are discussed. We conclude that this new and rapidly evolving class of medicines demands a multi-layered approach to fully understand its biodistribution and in vivo characteristics.
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Affiliation(s)
- P Vervaeke
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - S E Borgos
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway
| | - N N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - F Combes
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway.
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Hwang J, Rick J, Hsiao J, Hamzavi IH, Shi VY. Microbiome in Hidradenitis Suppurativa: Current Evidence and Practice. CURRENT DERMATOLOGY REPORTS 2022. [DOI: 10.1007/s13671-021-00349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Liu D, Bi X, Yang Y. Circular RNA hsa_circ_0011324 is involved in endometrial cancer progression and the evolution of its mechanism. Bioengineered 2022; 13:7485-7499. [PMID: 35259044 PMCID: PMC8973664 DOI: 10.1080/21655979.2022.2049026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common gynecological tumors with an increasing incidence. CircRNA plays an essential regulatory role in EC. Our objective was to investigate the potential mechanism of circRNAs derived SPOC Domain Containing 1 (SPOCD1) in EC progression. Seven circRNAs from SPOCD1 were analyzed by circBase and their expression was verified by quantitative real-time polymerase chain reaction. Only the expression of hsa_circ_0011324 was significantly increased in cancer tissues. The cell lines Ishikawa and RL95-2 which interfered with or overexpressed hsa_circ_0011324 were constructed and cell functions were tested. Results revealed hsa_circ_0011324 overexpression promoted cell proliferation, migration, and invasion; while silence of hsa_circ_0011324 had opposite effect on cell functions. RNA22 website and Targetscan website were applied to analyze downstream genes regulated by hsa_circ_0011324. Then, the expression of downstream genes was detected in EC tissues. Results indicated hsa-miR-497/16-5p expression were down-regulated, and mechanistic target of rapamycin kinase (mTOR) was up-regulated in EC. Furthermore, hsa_circ_0011324 regulated mTOR expression and cell functions by affecting hsa-miR-497/16-5p. And the potential mechanism was hsa_circ_0011324 competes with mTOR to directly bind to hsa-miR-497/16-5p. In conclusion, hsa_circ_0011324 could sponge hsa-miR-497/16-5p targeted mTOR to participate in EC progress. Our study may provide a new therapeutic target for EC.
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Affiliation(s)
- Dajiang Liu
- Department of Obstetrics and Gynecology, The first Hospital of Lanzhou University, Gansu, Lanzhou, China
| | - Xuehan Bi
- Department of Obstetrics and Gynecology, The first Hospital of Lanzhou University, Gansu, Lanzhou, China
| | - Yongxiu Yang
- Department of Obstetrics and Gynecology, The first Hospital of Lanzhou University, Gansu, Lanzhou, China
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Comprehensive Assessment of the Virulence Factors sub 3, sub 6 and mcpA in the Zoonotic Dermatophyte Trichophyton benhamiae Using FISH and qPCR. J Fungi (Basel) 2021; 8:jof8010024. [PMID: 35049964 PMCID: PMC8778074 DOI: 10.3390/jof8010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Skin infections by keratinophilic fungi are commonly referred to as dermatophytosis and represent a major health burden worldwide. Although patient numbers are on the rise, data on virulence factors, their function and kinetics are scarce. We employed an ex vivo infection model based on guinea pig skin explants (GPSE) for the zoonotic dermatophyte Trichophyton (T.) benhamiae to investigate kinetics of the virulence factors subtilisin (sub) 3, sub 6, metallocarboxypeptidase A (mcpA) and isocitrate lyase (isol) at gene level for ten days. Fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR) were used to detect and quantify the transcripts, respectively. Kingdom-spanning, species-specific and virulence factor-specific probes were successfully applied to isolated fungal elements showing inhomogeneous fluorescence signals along hyphae. Staining results for inoculated GPSE remained inconsistent despite thorough optimization. qPCR revealed a significant increase of sub 3- and mcpA-transcripts toward the end of culture, sub 6 and isol remained at a low level throughout the entire culture period. Sub 3 is tightly connected to the de novo formation of conidia during culture. Since sub 6 is considered an in vivo disease marker. However, the presented findings urgently call for further research on the role of certain virulence factors during infection and disease.
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46
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Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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47
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Parker DM, Winkenbach LP, Parker A, Boyson S, Nishimura EO. Improved Methods for Single-Molecule Fluorescence In Situ Hybridization and Immunofluorescence in Caenorhabditis elegans Embryos. Curr Protoc 2021; 1:e299. [PMID: 34826343 PMCID: PMC9020185 DOI: 10.1002/cpz1.299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule fluorescence in situ hybridization (smFISH) and immunofluorescence (IF) enable the visualization of the abundance and localization of mRNAs and proteins, respectively, allowing researchers to ultimately elucidate the localization, dynamics, and functions of the corresponding genes. Whereas both smFISH and immunofluorescence have been foundational techniques in molecular biology, each protocol poses challenges for use in the C. elegans embryo. smFISH protocols suffer from high initial costs and can photobleach rapidly, and immunofluorescence requires technically challenging permeabilization steps and slide preparation. Most importantly, published smFISH and IF protocols have predominantly been mutually exclusive, preventing the exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we describe protocols to perform immunofluorescence and smFISH in C. elegans embryos either in sequence or simultaneously. We also outline the steps to perform smFISH or immunofluorescence alone, including several improvements and optimizations to existing approaches. These protocols feature improved fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility in the embryo, a streamlined, in-tube approach for antibody staining that negates freeze-cracking, a validated method to perform the cost-reducing single molecule inexpensive FISH (smiFISH) adaptation, slide preparation using empirically determined optimal antifade products, and straightforward quantification and data analysis methods. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol. Together, these protocols simplify existing workflows for single-molecule RNA and protein detection. Moreover, simultaneous, high-resolution imaging of proteins and RNAs of interest will permit analysis, quantification, and comparison of protein and RNA distributions, furthering our understanding of the relationship between RNAs and their protein products or cellular markers in early development. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Sequential immunofluorescence and single-molecule fluorescence in situ hybridization Alternate Protocol: Abbreviated protocol for simultaneous immunofluorescence and single-molecule fluorescence in situ hybridization Basic Protocol 2: Simplified immunofluorescence in C. elegans embryos Basic Protocol 3: Single-molecule fluorescence in situ hybridization or single-molecule inexpensive fluorescence in situ hybridization.
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Affiliation(s)
- Dylan M Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Lindsay P Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Annemarie Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Sam Boyson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
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Hepp C, Shiaelis N, Robb NC, Vaughan A, Matthews PC, Stoesser N, Crook D, Kapanidis AN. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Sci Rep 2021; 11:19579. [PMID: 34599242 PMCID: PMC8486776 DOI: 10.1038/s41598-021-98972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.
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Affiliation(s)
- Christof Hepp
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| | - Nicolas Shiaelis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Nicole C Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Vaughan
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicole Stoesser
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Veselinyová D, Mašlanková J, Kalinová K, Mičková H, Mareková M, Rabajdová M. Selected In Situ Hybridization Methods: Principles and Application. Molecules 2021; 26:molecules26133874. [PMID: 34202914 PMCID: PMC8270300 DOI: 10.3390/molecules26133874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
We are experiencing rapid progress in all types of imaging techniques used in the detection of various numbers and types of mutation. In situ hybridization (ISH) is the primary technique for the discovery of mutation agents, which are presented in a variety of cells. The ability of DNA to complementary bind is one of the main principles in every method used in ISH. From the first use of in situ techniques, scientists paid attention to the improvement of the probe design and detection, to enhance the fluorescent signal intensity and inhibition of cross-hybrid presence. This article discusses the individual types and modifications, and is focused on explaining the principles and limitations of ISH division on different types of probes. The article describes a design of probes for individual types of in situ hybridization (ISH), as well as the gradual combination of several laboratory procedures to achieve the highest possible sensitivity and to prevent undesirable events accompanying hybridization. The article also informs about applications of the methodology, in practice and in research, to detect cell to cell communication and principles of gene silencing, process of oncogenesis, and many other unknown processes taking place in organisms at the DNA/RNA level.
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Affiliation(s)
- Dominika Veselinyová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Jana Mašlanková
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
- Correspondence:
| | - Katarina Kalinová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Helena Mičková
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia;
| | - Mária Mareková
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Miroslava Rabajdová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
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