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Live Leaf-Section Imaging for Visualizing Intracellular Chloroplast Movement and Analyzing Cell-Cell Interactions. 活叶切片成像用于观察胞内叶绿体运动和分析细胞-细胞相互作用。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5404
Yuta Kato, Takao Oi, Yoshikatsu Sato, Mitsutaka Taniguchi
{"title":"Live Leaf-Section Imaging for Visualizing Intracellular Chloroplast Movement and Analyzing Cell-Cell Interactions.","authors":"Yuta Kato, Takao Oi, Yoshikatsu Sato, Mitsutaka Taniguchi","doi":"10.21769/BioProtoc.5404","DOIUrl":"10.21769/BioProtoc.5404","url":null,"abstract":"<p><p>In response to environmental changes, chloroplasts, the cellular organelles responsible for photosynthesis, undergo intracellular repositioning, a phenomenon known as chloroplast movement. Observing chloroplast movement within leaf tissues remains technically challenging in leaves consisting of multiple cell layers, where light scattering and absorption hinder deep tissue visualization. This limitation has been particularly problematic when analyzing chloroplast movement in the mesophyll cells of C<sub>4</sub> plants, which possess two distinct types of concentrically arranged photosynthetic cells. In response to stress stimuli, mesophyll chloroplasts aggregate toward the inner bundle sheath cells. However, conventional methods have not been able to observe these chloroplast dynamics over time in living cells, making it difficult to assess the influence of adjacent bundle sheath cells on this movement. Here, we present a protocol for live leaf section imaging that enables long-term and detailed observation of chloroplast movement in internal leaf tissues without chemical fixation. In this method, a leaf blade section prepared either using a vibratome or by hand was placed in a groove made of a silicone rubber sheet attached to a glass slide for microscopic observation. This technique allows for the quantitative tracking of chloroplast movement relative to the surrounding cells. In addition, by adjusting the sectioning angle and thickness of the unfixed leaf sections, it is possible to selectively inactivate specific cell types based on their size and shape differences. This protocol enables the investigation of the intercellular interactions involved in chloroplast dynamics in leaf tissues. Key features • Thin leaf sections prepared while still alive enable prolonged microscopic observation of chloroplast movement within the leaf tissue. • Selective cell inactivation can be achieved by adjusting the slice thickness and angle. • This method is applicable to a wide range of plant species.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5404"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Accurate Identification of Cell Cycle Stages in RPE1 Cells Using the ImmunoCellCycle-ID Method. 免疫细胞周期id法准确鉴定RPE1细胞的细胞周期阶段
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5407
Syon Reddy, Yu-Lin Chen, Aussie Suzuki
{"title":"Accurate Identification of Cell Cycle Stages in RPE1 Cells Using the ImmunoCellCycle-ID Method.","authors":"Syon Reddy, Yu-Lin Chen, Aussie Suzuki","doi":"10.21769/BioProtoc.5407","DOIUrl":"10.21769/BioProtoc.5407","url":null,"abstract":"<p><p>Accurate identification of cell cycle stages is essential for investigating fundamental biological processes such as proliferation, differentiation, and tumorigenesis. While flow cytometry remains a widely used technique for such analyses, it is limited by its lack of single-cell resolution and its requirement for large sample sizes due to its population-based approach. These limitations underscore the need for alternative or complementary methods that offer single-cell precision with compatibility for small-scale applications. We present ImmunoCellCycle-ID, an immunofluorescence-based method that leverages the spatial distribution of endogenous markers, such as DNA, proliferating cell nuclear antigen (PCNA), centromere protein F (CENP-F), and centromere protein C (CENP-C), to reliably distinguish G1, early S, late S, early G2, late G2, and all mitotic sub-stages. This technique does not rely on precise signal quantification and utilizes standard immunofluorescence protocols alongside conventional laboratory microscopes, ensuring broad accessibility. Importantly, ImmunoCellCycle-ID detects endogenous proteins without the need for genetic modification, making it readily applicable to a wide range of human cell lines. Beyond its utility for single-cell resolution, the method can be scaled for population-level analyses, similar to flow cytometry. With its precision, versatility, and ease of implementation, ImmunoCellCycle-ID offers a powerful tool for high-resolution cell cycle profiling across diverse experimental platforms. Key features • Enables high-precision identification of cell cycle stages at single-cell resolution. • Broadly applicable to diverse human cell lines without genetic modification. • Fully compatible with standard fluorescence microscopy; no specialized equipment needed. • Requires only minimal image analysis and no complex quantification.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5407"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analyzing RNA Localization Using the RNA Proximity Labeling Method OINC-seq. 利用RNA接近标记方法OINC-seq分析RNA定位。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5403
Megan C Pockalny, Hei-Yong G Lo, Raeann Goering, J Matthew Taliaferro
{"title":"Analyzing RNA Localization Using the RNA Proximity Labeling Method OINC-seq.","authors":"Megan C Pockalny, Hei-Yong G Lo, Raeann Goering, J Matthew Taliaferro","doi":"10.21769/BioProtoc.5403","DOIUrl":"10.21769/BioProtoc.5403","url":null,"abstract":"<p><p>Thousands of RNAs are localized to specific subcellular locations, and these localization patterns are often required for optimal cell function. However, the sequences within RNAs that direct their transport are unknown for almost all localized transcripts. Similarly, the RNA content of most subcellular locations remains unknown. To facilitate the study of subcellular transcriptomes, we developed the RNA proximity labeling method OINC-seq. OINC-seq utilizes photoactivatable, spatially restricted RNA oxidation to specifically label RNA in proximity to a subcellularly localized bait protein. After labeling, these oxidative RNA marks are then read out via high-throughput sequencing due to their ability to induce predictable misincorporation events by reverse transcriptase. These induced mutations are then quantitatively assessed for each gene using our software package PIGPEN. The observed mutation rate for a given RNA species is therefore related to its proximity to the localized bait protein. This protocol describes procedures for assaying RNA localization via OINC-seq experiments as well as computational procedures for analyzing the resulting data using PIGPEN. Key features • OINC-seq assays the RNA content of a variety of subcellular locations. • OINC-seq utilizes a photoactivatable, proximity-dependent RNA oxidation reaction to label RNAs. • Oxidative RNA marks are read using high-throughput sequencing without the need for enrichment. • Oxidative RNA marks are identified and quantified using the associated PIGPEN software.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5403"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reliable and Sensitive Detection of Carbonylated Proteins by Oxime Blot. 肟印迹法可靠灵敏地检测羰基化蛋白。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5401
Filip Luka Mikulić, Viktor Merćep, Marcela Finek, Mladen Merćep
{"title":"Reliable and Sensitive Detection of Carbonylated Proteins by Oxime Blot.","authors":"Filip Luka Mikulić, Viktor Merćep, Marcela Finek, Mladen Merćep","doi":"10.21769/BioProtoc.5401","DOIUrl":"10.21769/BioProtoc.5401","url":null,"abstract":"<p><p>Oxidative protein damage is important in various biological processes and age-related diseases. Protein carbonylation is the predominant and most frequently studied form of protein oxidation. It is most frequently detected following its derivatization with 2,4-dinitrophenylhydrazine (DNPH) hapten, followed by its detection with an anti-DNP antibody. However, when used to detect protein carbonylation by western blotting, this method suffers from diminished sensitivity, distortion of protein migration patterns, and unsatisfactory representation of low-abundance proteins. This is due to the poor solubility of DNPH in typical buffer solutions, the acidic protein precipitation due to the use of strong acid for its dissolution, the instability in solution, and the distorted protein migration patterns introduced by an additional salt content generated by the required pH adjustment prior to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). To address the DNPH method limitations, a new Oxime blot technique was developed. This method is based on forming the stable oxime bonds between the protein carbonyl groups and biotin-aminooxy probe in the presence of a p-phenylenediamine (pPDA) catalyst at neutral pH conditions. The derivatization reaction reaches a plateau within 3 h. It ensures efficient and complete derivatization of carbonylated proteins, which are separated by SDS-PAGE without additional manipulation and detected with avidin-HRP and enhanced chemiluminescence (ECL) in western blotting. The Oxime blot protocol allows researchers to reliably and sensitively detect carbonylated proteins and provides a valuable tool for studying oxidative stress in diverse biological settings. Key features • This method enables the sensitive and reliable detection of protein carbonylation in various biological samples. • The chemically stable oxime bond forms quickly and efficiently, reaching its plateau level after 3 h, enabling relative carbonylation quantification. • Carbonylation derivatization at low salt content and neutral pH ensures good SDS-PAGE protein migration without any protein loss. • This method integrates well with detecting specific protein carbonylation following its immunoprecipitation.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5401"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reprogramming White Fat Cells for Adipose Manipulation Transplantation (AMT) Therapy. 重编程白色脂肪细胞用于脂肪操作移植(AMT)治疗。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5405
Kelly An, Yusuke Ito, Nadav Ahituv
{"title":"Reprogramming White Fat Cells for Adipose Manipulation Transplantation (AMT) Therapy.","authors":"Kelly An, Yusuke Ito, Nadav Ahituv","doi":"10.21769/BioProtoc.5405","DOIUrl":"10.21769/BioProtoc.5405","url":null,"abstract":"<p><p>Adipocytes are endocrine cells that function as the main energy storage in our body. They are commonly used in clinical procedures, including their removal via liposuction and transplantation in plastic surgery. Building on this, adipocytes can be used for ex vivo cellular manipulations, enabling therapeutic modifications that can provide beneficial clinical outcomes after transplantation. Here, we provide a detailed protocol on how to modify adipocytes and adipose organoids using CRISPR activation (CRISPRa), a technology termed adipose manipulation transplantation (AMT). Key features • This protocol is used to generate adipocytes and adipose organoids from human preadipocytes that can be genetically engineered for therapeutic purposes, including cancer metabolic therapy.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5405"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Luminal Cerebrovascular Proteomics. 脑血管蛋白质组学。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5411
Sophia M Shi, Carolyn R Bertozzi, Tony Wyss-Coray
{"title":"Luminal Cerebrovascular Proteomics.","authors":"Sophia M Shi, Carolyn R Bertozzi, Tony Wyss-Coray","doi":"10.21769/BioProtoc.5411","DOIUrl":"10.21769/BioProtoc.5411","url":null,"abstract":"<p><p>Brain endothelial cells, which constitute the cerebrovasculature, form the first interface between the blood and brain and play essential roles in maintaining central nervous system (CNS) homeostasis. These cells exhibit strong apicobasal polarity, with distinct luminal and abluminal membrane compositions that crucially mediate compartmentalized functions of the vasculature. Existing transcriptomic and proteomic profiling techniques often lack the spatial resolution to discriminate between these membrane compartments, limiting insights into their distinct molecular compositions and functions. To overcome these limitations, we developed an in vivo proteomic strategy to selectively label and enrich luminal cerebrovascular proteins. In this approach, we perfuse a membrane-impermeable biotinylation reagent into the vasculature to covalently tag cell surface proteins exposed on the luminal side. This is followed by microvessel isolation and streptavidin-based enrichment of biotinylated proteins for downstream mass spectrometry analysis. Using this method, we robustly identified over 1,000 luminally localized proteins via standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques, achieving substantially improved enrichment of canonical luminal markers compared with conventional vascular proteomic approaches. Our method enables the generation of a high-confidence, compartment-resolved atlas of the luminal cerebrovascular proteome and offers a scalable platform for investigating endothelial surface biology in both healthy and disease contexts. Key features • Enables high-resolution proteomic profiling of the luminal surface of the brain vasculature in vivo. • Improves signal-to-noise ratio through an added microvessel isolation step, reducing nonspecific background. • Applied to uncover aging-related changes in luminal endothelial surface protein composition. • Adaptable for identifying therapeutic targets, transporters, signaling pathways, and disease-associated alterations in the luminal vascular environment across diverse biological contexts.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5411"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Direct Activity Measurement of Heterotrimeric Gi Proteins and Gq Protein By Effector Pulldown. 利用效应下拉法直接测定异三聚体Gi蛋白和Gq蛋白的活性。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5406
Keiichiro Tanaka, Martin A Schwartz
{"title":"Direct Activity Measurement of Heterotrimeric Gi Proteins and Gq Protein By Effector Pulldown.","authors":"Keiichiro Tanaka, Martin A Schwartz","doi":"10.21769/BioProtoc.5406","DOIUrl":"10.21769/BioProtoc.5406","url":null,"abstract":"<p><p>Studying G protein-coupled receptor (GPCR) activation of heterotrimeric G proteins is crucial for understanding diverse physiological processes and developing novel therapeutics. Traditional methods to assay GPCR activation of G proteins, including assays of second messengers and biosensors, involve complex or indirect procedures. However, second messengers like cAMP and calcium are not direct readouts of GPCR activity due to signaling crosstalk, while biosensors can have undesired consequences due to structural alteration caused by fluorescent protein insertion. Here, we present a streamlined protocol employing GST-tagged bait proteins and epitope-embedded Gα subunits to achieve direct monitoring of Gα activity within cells. This method involves purification of GST-tagged bait constructs from bacteria and subsequent direct interaction studies with GluGlu-tagged Gα proteins expressed in any human cells of interest by including GST-tagged bait proteins in the cell lysis buffer. The approach enables sensitive detection of activated Gα within cells following extracellular stimulation. Advantages of this protocol include high sensitivity, enhanced monitoring of GPCR signaling dynamics under physiologically relevant conditions with minimum alteration in Gα, and the ability to distinguish between highly homologous isoforms within the same Gα family. Key features • Improved analysis of GPCR-Gα signaling: Establishes a novel effector pulldown method to monitor Gα activation within cells. • Endogenous GPCR activity measurement with increased sensitivity: Enables assays of endogenous physiological GPCR activities with improved sensitivity by increasing sample sizes. • Epitope Incorporation without affecting functions: Uses epitope tag sequence with a few amino acid substitutions functioning like wild-type proteins, adaptable for any endogenous Gα assay if suitable antibodies are available. • Isoform distinction: Distinguishes Gα isoforms by using embedded epitope.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5406"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Step-By-Step Protocol for Correlative Light and Electron Microscopy Imaging of Proteinaceous Deposits in Cultured Cells and Human Brain Tissues. 在培养细胞和人脑组织中蛋白质沉积物的相关光学和电子显微镜成像的一步一步的协议。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5402
Peizhou Jiang, Dennis W Dickson
{"title":"A Step-By-Step Protocol for Correlative Light and Electron Microscopy Imaging of Proteinaceous Deposits in Cultured Cells and Human Brain Tissues.","authors":"Peizhou Jiang, Dennis W Dickson","doi":"10.21769/BioProtoc.5402","DOIUrl":"10.21769/BioProtoc.5402","url":null,"abstract":"<p><p>An improved correlative light and electron microscopy (CLEM) method has recently been introduced and successfully employed to identify and analyze protein inclusions in cultured cells as well as pathological proteinaceous deposits in postmortem human brain tissues from individuals with diverse neurodegenerative diseases. This method significantly enhances antigen preservation and target registration by replacing conventional dehydration and embedding reagents. It achieves an optimal balance of sensitivity, accuracy, efficiency, and cost-effectiveness compared to other current CLEM approaches. However, due to space constraints, only a brief overview of this method was provided in the initial publication. To ensure reproducibility and facilitate widespread adoption, the author now presents a detailed, step-by-step protocol of this optimized CLEM technique. By enhancing usability and accessibility, this protocol aims to promote broader application of CLEM in neurodegenerative disease research. Key features • This protocol incorporates optimized sample processing and innovative fiducial marking techniques that enhance antigen preservation and improve target registration, respectively. • By utilizing serial ultrathin sections for CLEM, this protocol significantly increases correlation accuracy. • A novel \"sandwich method\" is introduced, which enables simultaneous detection of multiple proteinopathies through immunofluorescence staining or precise localization of pathological targets using immunogold labeling. • Overall, this protocol offers an effective balance of sensitivity, accuracy, efficiency, and cost-effectiveness compared to existing CLEM methodologies.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5402"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fertility test of mice (Mus musculus). 小鼠(小家鼠)生育能力试验。
IF 1.1
Bio-protocol Pub Date : 2025-08-05 DOI: 10.21769/BioProtoc.5408
Menglei Yang, Mengmeng Ming, Botao Yuan, Qinghua Shi, Baolu Shi
{"title":"Fertility test of mice (<i>Mus musculus</i>).","authors":"Menglei Yang, Mengmeng Ming, Botao Yuan, Qinghua Shi, Baolu Shi","doi":"10.21769/BioProtoc.5408","DOIUrl":"10.21769/BioProtoc.5408","url":null,"abstract":"<p><p>Infertility has emerged as a global health concern, impacting around 8%-12% of couples during their reproductive years. Due to limitations in obtaining human biological samples, mouse models have been widely used for investigating gene functions. Fertility assessment in mouse models is a critical component in reproductive biology for studying gene function and elucidating mechanisms of reproductive disorders. However, natural mating observation of mice may yield inconsistent results, especially in the absence of standard guidelines, prolonged experimental cycles, and operational complexity. This protocol establishes a comprehensive breeding strategy for evaluating murine fertility through systematic vaginal plug monitoring and litter size quantification within defined timeframes. Key steps include (1) standardized male-female pairing protocols, (2) daily vaginal plug inspection, and (3) longitudinal tracking of pregnancy outcomes. This protocol presents a straightforward and easily implementable protocol for mouse mating cage setup and statistical analysis, enabling reliable fertility assessment under natural breeding conditions. Key features • Standardized natural mating protocol combining vaginal plug monitoring (daily) and litter size tracking. • Time-optimized workflow completes fertility phenotyping in 2 months. • An easy and custom-constructed vaginal plug inspection tool for optimized vaginal plug inspection.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 15","pages":"e5408"},"PeriodicalIF":1.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12336854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Flow Cytometric Quantification of HIV-1-Infected Cells Expressing Either Abortive or Elongated HIV-1 Transcripts Using Flow-FISH. 使用Flow- fish对表达流产或延长的HIV-1转录物的HIV-1感染细胞进行流式细胞术定量
IF 1.1
Bio-protocol Pub Date : 2025-07-20 DOI: 10.21769/BioProtoc.5392
Shirley Man, Teunis B H Geijtenbeek, Neeltje A Kootstra
{"title":"Flow Cytometric Quantification of HIV-1-Infected Cells Expressing Either Abortive or Elongated HIV-1 Transcripts Using Flow-FISH.","authors":"Shirley Man, Teunis B H Geijtenbeek, Neeltje A Kootstra","doi":"10.21769/BioProtoc.5392","DOIUrl":"10.21769/BioProtoc.5392","url":null,"abstract":"<p><p>The persistence of the HIV-1 reservoir remains the ultimate obstacle in achieving a cure. Cure strategies targeting the HIV-1 reservoir are under development, and therefore, finding ways to improve the detection of the reservoir is crucial. Several reservoir detection techniques exist to assess different markers of the HIV-1 reservoir, such as PCR-based assays and protein-based flow cytometric methods. We developed a flow cytometry-fluorescent in situ hybridization (flow-FISH) approach that assesses HIV-1 at the transcriptional level. Using a combination of probes that target either the HIV-1 trans-activation response (TAR) region and 5' long terminal repeat (LTR) or the Gag sequence, our assay distinguishes between infected cells expressing abortive or elongated HIV-1 RNAs. This assay utilizes the branched-DNA method to amplify the fluorescent signal of the hybridized RNA probes and can be used directly for thawed or cultured cells, with the option to include surface antibody staining. Cellular expression of abortive and/or Gag HIV-1 RNAs is measured by flow cytometry. Our flow-FISH approach gives insight into the transcriptional dynamics of the HIV-1 reservoir and allows for the characterization of latently infected cells. Key features • Detection of latently HIV-1-infected cells identified by the expression of abortive HIV-1 TAR transcripts. • Cell activation is not required for HIV-1 detection; therefore, the cellular phenotypic landscape remains preserved. • Can be used for direct ex vivo measurements in isolated cells, such as PBMCs, from untreated and antiretroviral therapy (ART)-treated people with HIV-1 (PWH).</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":"15 14","pages":"e5392"},"PeriodicalIF":1.1,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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