Jove-Journal of Visualized Experiments最新文献_第4页

A Comprehensive Pipeline to Assess the Efficiency of Human Erythropoiesis In Vitro and Ex Vivo.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67123

Céline Philippe, Shoshana Burke, Kevin Rouault-Pierre

引用次数: 0

In Vitro Culturing Technique for Studying Cellular Dynamics in Zebrafish Scales.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/66619

Juan D Carvajal-Agudelo, Tamara A Franz-Odendaal

{"title":"In Vitro Culturing Technique for Studying Cellular Dynamics in Zebrafish Scales.","authors":"Juan D Carvajal-Agudelo, Tamara A Franz-Odendaal","doi":"10.3791/66619","DOIUrl":"10.3791/66619","url":null,"abstract":"Zebrafish scales offer a variety of advantages for use in standard laboratories for teaching and research purposes. Scales are easily collected without the need for euthanasia, regenerate within a couple of weeks, and are translucent and small, allowing them to be viewed using a standard microscope. Zebrafish scales are especially useful in educational environments, as they provide a unique opportunity for students to engage in hands-on learning experiences, particularly in understanding cellular dynamics and in vitro culturing methods. The main objective of this protocol is to describe a method for collecting and maintaining zebrafish scales in culture for use in a variety of biological studies using basic laboratory equipment. Additionally, the protocol details their use in understanding bone homeostasis by examining the activity of bone cells involved in bone resorption and deposition. It also includes additional protocols for general techniques, such as the visualization of nuclei and apoptotic cells. The in vitro culturing protocol produces reliable results with minimal reagents and equipment. This article discusses the benefits of using in vitro cultures of zebrafish scales to foster scientific inquiry and outlines the resources needed to support their integration into educational settings.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Laboratory-Engineered Glioblastoma Organoid Culture and Drug Screening.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67593

Changwen Wang, Nadja Stöffler, Hai-Kun Liu

{"title":"Laboratory-Engineered Glioblastoma Organoid Culture and Drug Screening.","authors":"Changwen Wang, Nadja Stöffler, Hai-Kun Liu","doi":"10.3791/67593","DOIUrl":"https://doi.org/10.3791/67593","url":null,"abstract":"Glioblastoma (GBM) is described as a group of highly malignant primary brain tumors and stands as one of the most lethal malignancies. The genetic and cellular characteristics of GBM have been a focal point of ongoing research, revealing that it is a group of heterogeneous diseases with variations in RNA expression, DNA methylation, or cellular composition. Despite the wealth of molecular data available, the lack of transferable pre-clinic models has limited the application of this information to disease classification rather than treatment stratification. Transferring the patients' genetic information into clinical benefits and bridging the gap between detailed descriptions of GBM, genotype-phenotype associations, and treatment advancements remain significant challenges. In this context, we present an advanced human GBM organoid model, the Laboratory Engineered Glioblastoma Organoid (LEGO), and illustrate its use in studying the genotype-phenotype dependencies and screening potential drugs for GBM. Utilizing this model, we have identified lipid metabolism dysregulation as a critical milestone in GBM progression and discovered that the microsomal triglyceride transfer protein inhibitor Lomitapide shows promise as a potential treatment for GBM.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Roughness Impact of Piezoelectric Dental Scaler on Two Distinct Flowable Composite Filling Materials.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67446

Omer Birkan Agrali

{"title":"Roughness Impact of Piezoelectric Dental Scaler on Two Distinct Flowable Composite Filling Materials.","authors":"Omer Birkan Agrali","doi":"10.3791/67446","DOIUrl":"https://doi.org/10.3791/67446","url":null,"abstract":"Dental ultrasonic scalers are commonly employed in periodontal treatment; however, their ability to roughen tooth surfaces is a worry since roughness may increase plaque production, a key cause of periodontal disease. This research studied the influence of a piezoelectric ultrasonic scaler on the roughness of two distinct flowable composite filling materials. To do this, 10 disc-shaped samples were generated from each of the two flowable composite materials. After standardized polishing, samples were submerged in water for 24 h before the first surface examination using electron microscopy and profilometry. The ultrasonic scaler was applied to a specified location of each sample for 60 s under water cooling and regulated force. Post-scaler surface parameters were again examined. Following the application of the scaler, both composite materials exhibited a notable increase in surface roughness, as determined by profilometry (p < 0.01). Additionally, the observed surface roughness was also qualitatively visualized with scanning electron microscopy. While initial roughness levels were comparable across the two composites (p = 0.143) after scaler application, no substantial discrepancy in surface texture was noticed between them (p = 0.684). The use of a high-power piezoelectric ultrasonic scaler on routinely used flowable composite restorations might generate considerable surface roughness, possibly leading to increased plaque accumulation. Nevertheless, it might be postulated that nanohybrid flowable composite materials having conventional monomer ingredients may demonstrate comparable surface alterations within the limitations of this experiment.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67581

Katherine Do, Subina Mehta, Reid Wagner, Timothy J Griffin, Pratik D Jagtap

{"title":"A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease.","authors":"Katherine Do, Subina Mehta, Reid Wagner, Timothy J Griffin, Pratik D Jagtap","doi":"10.3791/67581","DOIUrl":"https://doi.org/10.3791/67581","url":null,"abstract":"Clinical metaproteomics reveals host-microbiome interactions underlying diseases. However, challenges to this approach exist. In particular, the characterization of microbial proteins present in low abundance relative to host proteins is difficult. Other significant challenges are attributed to using very large protein sequence databases, which impedes sensitivity and accuracy during peptide and protein identification from mass spectrometry data in addition to retrieving taxonomy and functional annotations and performing statistical analysis. To address these problems, we present an integrated bioinformatics workflow for mass spectrometry-based metaproteomics that combines custom protein sequence database generation, peptide-spectrum match generation and verification, quantification, taxonomic and functional annotations, and statistical analysis. This workflow also offers characterization of human proteins (while prioritizing microbial proteins), thus offering insights into host-microbe dynamics in disease. The tools and workflow are deployed in the Galaxy ecosystem, enabling the development, optimization, and dissemination of these computational resources. We have applied this workflow for metaproteomic analysis of numerous clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its utility via the analysis of residual fluid from cervical swabs. The complete workflow and accompanying training resources are accessible on the Galaxy Training Network to equip non-experts and experienced researchers with the necessary knowledge and tools to analyze their data.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multifractal Spectrum Analysis for Assessing Pulmonary Nodule Malignancy.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67990

Baixin Wang, YaWen Xu, Fangliang Xing, Tengxiao Liang

{"title":"Multifractal Spectrum Analysis for Assessing Pulmonary Nodule Malignancy.","authors":"Baixin Wang, YaWen Xu, Fangliang Xing, Tengxiao Liang","doi":"10.3791/67990","DOIUrl":"https://doi.org/10.3791/67990","url":null,"abstract":"Non-invasive assessment of pulmonary nodule malignancy remains a critical challenge in lung cancer diagnosis. Traditional methods often lack precision in differentiating benign from malignant nodules, particularly in the early stages. This study introduces an approach using multifractal spectrum analysis to quantitatively evaluate pulmonary nodule characteristics. A fractal-based protocol was developed to process computed tomography (CT)-digital imaging and communications in medicine (DICOM) data, enabling three-dimensional (3D) visualization and analysis of pulmonary nodule's multifractal spectrum. The method involves 3D volume reconstruction, precise ROI delineation, and calculation of fractal dimensions across multiple scales. Multifractal spectra were computed for both early-stage and late-stage lung adenocarcinoma nodules, with comparative analysis performed using data tip tool quantification. Analysis revealed that the fractal dimension of a pulmonary nodule's 3D digital matrix varies continuously with different voxel scales, forming a distinctive multifractal spectrum. Significant differences were observed between early-stage and late-stage nodules. Late-stage nodules demonstrated a wider scale range (longer X-axis) and higher extreme points in their multifractal spectra. These distinctions were quantitatively confirmed, indicating the method's potential for precise staging. The multifractal spectrum analysis provides a highly significant and precise quantitative method for staging pulmonary nodules, effectively differentiating between benign and malignant cases. This non-invasive technique shows promise for improving early diagnosis and accurate staging of lung cancer, potentially enhancing clinical decision-making in pulmonary oncology.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Analysis of Mitochondria-Associated Endoplasmic Reticulum Membrane (MAM) Stabilization in a Neural Model of Alzheimer's Disease (AD).

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/66129

Jacob C Zellmer, Selene Lomoio, Rudolph E Tanzi, Raja Bhattacharyya

{"title":"Quantitative Analysis of Mitochondria-Associated Endoplasmic Reticulum Membrane (MAM) Stabilization in a Neural Model of Alzheimer's Disease (AD).","authors":"Jacob C Zellmer, Selene Lomoio, Rudolph E Tanzi, Raja Bhattacharyya","doi":"10.3791/66129","DOIUrl":"https://doi.org/10.3791/66129","url":null,"abstract":"A method to quantitate the stabilization of Mitochondria-Associated endoplasmic reticulum Membranes (MAMs) in a 3-dimensional (3D) neural model of Alzheimer's disease (AD) is presented here. To begin, fresh human neuro progenitor ReN cells expressing β-amyloid precursor protein (APP) containing familial Alzheimer's disease (FAD) or naïve ReN cells are grown in thin (1:100) Matrigel-coated tissue culture plates. After the cells reach confluency, these are electroporated with expression plasmids encoding red fluorescence protein (RFP)-conjugated mitochondria-binding sequence of AKAP1(34-63) (Mito-RFP) that detects mitochondria or constitutive MAM stabilizers MAM 1X or MAM 9X that stabilize tight (6 nm ± 1 nm gap width) or loose (24 nm ± 3 nm gap width) MAMs, respectively. After 16-24 h, the cells are harvested and enriched by a fluorescence-activated cell sorter (FACS). An equal number of FACS-enriched cells are seeded in the 3-dimensional matrix (1:1 Matrigel) and allowed to differentiate into mature neurons for 10 days. Live cell images of the 10-day differentiated cells expressing the RFP-conjugated MAM stabilizers are captured under a fluorescent microscope equipped with a live-cell imaging culture chamber maintaining the CO2 (5%), temperature (37 °C), and humidity (~90%). Toward this end, we performed live-cell imaging and kymographic analyses to measure the motility of free mitochondria labeled with Mito-RFP or ER-bound mitochondria of tight or loose gap widths stabilized by MAM 1X or MAM 9X, respectively, in the most extended neuronal process of each ReN GA neuron which is at least 500 nm long, considering these as axons.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Establishment of a Mouse Model with Cough Hypersensitivity via Inhalation of Citric Acid.

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-10 DOI: 10.3791/67462

Mingtong Lin, Chen Zhan, Tingting Xu, Jinlan Gu, Chuqin Huang

{"title":"Establishment of a Mouse Model with Cough Hypersensitivity via Inhalation of Citric Acid.","authors":"Mingtong Lin, Chen Zhan, Tingting Xu, Jinlan Gu, Chuqin Huang","doi":"10.3791/67462","DOIUrl":"https://doi.org/10.3791/67462","url":null,"abstract":"Cough is one of the most common symptoms of many respiratory diseases. Chronic cough significantly impacts quality of life and imposes a considerable economic burden. Increased cough sensitivity is a pathophysiological hallmark of chronic cough. It has been observed that cough hypersensitivity is related to airway inflammation, remodeling of airway sensory nerves, and alterations in the central nervous system. However, the precise molecular mechanisms remain unclear and require further elucidation using suitable animal models. Previous studies have utilized guinea pigs as models for studying cough, but these models present several experimental limitations, including high costs, a lack of transgenic tools, and a scarcity of commercial reagents. In addition, guinea pigs typically exhibit poor environmental tolerance and high mortality when exposed to stimuli. In contrast, mice are smaller, easier to maintain, more cost-effective, and amenable to genetic manipulation, making them more suitable for mechanistic investigations. In this study, we established a mouse model with cough hypersensitivity via continuous inhalation of citric acid (CA). This model is straightforward to operate and yields reproducible results, making it a valuable tool for further studies on the mechanisms and potential novel treatments for chronic cough.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Erratum: A Mouse Model of Hemorrhagic Transformation Induced by Acute Hyperglycemia Combined with Transient Focal Ischemia. 更正：急性高血糖合并短暂局灶性缺血致出血转化的小鼠模型。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-06 DOI: 10.3791/6615

Yaojian Sun, Changlong Leng, Kang Ma, Wei Liu

引用次数: 0

ATAC-Seq Library Preparation of Murine Bone Marrow-Derived Neutrophils. 小鼠骨髓中性粒细胞的ATAC-Seq文库制备。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-01-03 DOI: 10.3791/67490

Ju Zhang, Shuai Tong, Siyuan Liang, Fangyuan Li, Can Zhang, Nan Ding, Yu Hao

{"title":"ATAC-Seq Library Preparation of Murine Bone Marrow-Derived Neutrophils.","authors":"Ju Zhang, Shuai Tong, Siyuan Liang, Fangyuan Li, Can Zhang, Nan Ding, Yu Hao","doi":"10.3791/67490","DOIUrl":"https://doi.org/10.3791/67490","url":null,"abstract":"Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) is a powerful, high-throughput technique for assessing chromatin accessibility and understanding epigenomic regulation. Neutrophils, as a crucial leukocyte type in immune responses, undergo substantial chromatin architectural changes during differentiation and activation, which significantly impact the gene expression necessary for their functions. ATAC-seq has been instrumental in uncovering key transcription factors in neutrophil maturation, revealing pathogen-specific epigenomic signatures, and identifying therapeutic targets for autoimmune diseases. However, neutrophils' sensitivity to the external milieu complicates high-quality ATAC-seq data production. Here, we propose a scalable protocol for preparing ATAC-seq libraries from rodent bone marrow-derived neutrophils, featuring improved immunomagnetic separation to ensure optimal cell viability and high-quality libraries. The vital elements impacting the library quality and optimization principles for methodological extension are discussed in detail. This protocol will support the researchers who are willing to study the chromatin architecture and epigenomic reprogramming of neutrophils, advancing studies in basic and clinical immunology.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 215","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0