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Bio-Protocol
Scopus
ISSN 2331-8325 · Bio-protocol LLC · 4.982 artikel di indeks
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Artikel Jurnal
Orthogonal Temperature-Related Intensity Change and Time-Resolved Förster Resonance Energy Transfer High-Throughput Screening Platform for the Discovery of SLIT2 Binders
SLIT2 is a secreted glycoprotein implicated in axon guidance, immune modulation, and tumor biology, whose extracellular and glycosylated nature can complicate conventional biophysical screening workflows. Here, we provide a complete, step-by-step protocol for an orthogonal high-throughput discovery…
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Artikel Jurnal
Optimized Mechanical Isolation of Mitochondria From Saccharomyces cerevisiae Preserving Atg32 for Quantitative Analysis
Mitophagy is a highly conserved process among eukaryotic cells, playing a primordial role in mitochondrial quality control and overall cellular homeostasis. In Saccharomyces cerevisiae, Atg32 is the only identified mitophagy receptor localized to the mitochondrial outer membrane, making this yeast…
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Quick and Cheap: Optimized Purification and Concentration of Bacteriophages Produced in Rich Culture Media
This protocol describes an easy, quick, cheap, and effective method for the purification and concentration of bacteriophages (phages) produced in rich culture media, meeting the quality criteria required for structural analyses. It is based on a tube dialysis system that replaces the classical but…
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sc3D: A Comprehensive Tool for 3D Spatial Transcriptomic Analysis
Serial spatial omics technologies capture genome-wide gene expression patterns in thin tissue sections but lose spatial continuity along the third dimension. Reconstructing these two-dimensional measurements into coherent three-dimensional volumes is necessary to relate molecular domains…
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Artikel Jurnal
Step-by-Step Protocol for In Situ Profiling of RNA Subcellular Localization Using TATA-seq
Membrane-less organelles play essential roles in both physiological and pathological processes by compartmentalizing biomolecules through phase separation to form dynamic hubs. These hubs enable rapid responses to cellular stress and help maintain cellular homeostasis. However, a straightforward…
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Artikel Jurnal
How to Train Custom Cell Segmentation Models Using Cell-APP
The deep learning revolution has accelerated discovery in cell biology by allowing researchers to outsource their microscopy analyses to a new class of tools called cell segmentation models. The performance of these models, however, is often constrained by the limited availability of annotated data…
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Identification of the Subcompartment-Specific Mitochondrial Proteome by APEX2 Proximity Labeling in Saccharomyces cerevisiae
The cellular compartments of eukaryotic cells are defined by their specific protein compositions. Different strategies are used for the identification of the subcellular proteomes, such as fractionation by differential centrifugation of cellular extracts. The localization of mitochondrial proteins…
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Artikel Jurnal
Introducing Exogenous DNA Vectors Directly into Trypoxylus dichotomus Larvae Via In Vivo Electroporation
In the Japanese rhinoceros beetle Trypoxylus dichotomus, gene function studies have relied mainly on systemic larval RNA interference (RNAi), as gain-of-function techniques remain underdeveloped and germline transgenesis is impractical given the species’ approximately one-year generation time. In…
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In Vitro Model of Cytokine-Induced Inflammatory 3T3-L1 Adipocytes Mimicking Obesity
Obesity is a risk factor for many diseases. The 3T3-L1 cell line is often used to obtain mature adipocytes, but these lack the inflammatory phenotype observed in obesity. Using a cocktail of cytokines that mimics the secretome of macrophages found in the inflammatory adipose tissue, we developed a…
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Time-Lapse Into Immunofluorescence Imaging Using a Gridded Dish
Time-lapse into immunofluorescence (TL into IF) imaging combines the wealth of information acquired during live-cell imaging with ease of access for static immunofluorescence markers. In the field of mechanobiology, connecting live and static imaging to visualize cell biology dynamics is often…
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Artikel Jurnal
In Ovo CAM-Based Xenograft Model for Investigating Tumor Developmental Biology in Breast Cancer
Breast cancer remains one of the most prevalent and deadly malignancies affecting women worldwide. Its progression and metastatic behavior are driven by complex mechanisms. To develop more effective therapeutic strategies, it is crucial to understand tumor growth, angiogenesis, and…
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Artikel Jurnal
Deaminase-Assisted Sequencing for the Identification of 5-glyceryl-methylcytosine
DNA epigenetic modifications play crucial roles in regulating gene expression and cellular function across diverse organisms. Among them, 5-glyceryl-methylcytosine (5gmC), a unique DNA modification first discovered in Chlamydomonas reinhardtii, represents a novel link between redox metabolism and…
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Simple and Rapid Model to Generate Differentiated Endometrial Floating Organoids
Nowadays, the use of 3D cultures (organoids) is considered a valuable experimental tool to model physiological and pathological conditions of organs and tissues. Organoids, retaining cellular heterogeneity with the presence of stem, progenitor, and differentiated cells, allow the faithful in vitro…
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Advancing EAE Modeling: Establishment of a Non-Pertussis Immunization Protocol for Multiple Sclerosis
Experimental autoimmune encephalomyelitis (EAE) is a widely used rodent model of multiple sclerosis (MS), typically induced with pertussis toxin (PTX) to achieve robust disease onset. However, PTX has been shown to exert broad immunomodulatory effects that include disruption of G protein-coupled…
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On-Column Dual-Gradient Refolding for Efficient Recovery of Insoluble Affinity-Tagged Recombinant Proteins
This article presents an efficient protocol for refolding recombinant proteins that are prone to aggregation and form inclusion bodies during expression in Escherichia coli. As a model system, the homolog of CRISPR-associated effector protein CasV-M was investigated. The key element of the…
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Qualitative Detection of Lipid Peroxidation in Mosquito Larvae Using Schiff’s Reaction: A Simple Histochemical Tool for In Situ Assessment of Oxidative Damage
Lipid peroxidation (LPO) is a major indicator of oxidative stress and cellular damage, frequently associated with environmental and toxicological stressors and mechanistically linked to ferroptotic regulated cell death (RCD). This protocol describes a simple and reproducible method for the…
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Artikel Jurnal
Monitoring of Sperm-Independent Calcium Oscillations in Immature Oocytes of Mice
Repetitive increases of intracellular calcium ions (Ca2+ oscillations) control cellular functions in various biological events, including meiotic resumption after fertilization. Sperm-derived substances enter the cytoplasm of mature oocytes by sperm fusion, causing Ca2+ oscillations…
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Detailed Method for the Purification of Rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana
The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and…
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Artikel Jurnal
Biochemical Reconstitution and FRAP Analysis of Membrane-Associated Condensates on Supported Lipid Bilayers
Plasma membrane–associated condensates driven by liquid–liquid phase separation represent a novel mechanism of receptor-mediated signaling transduction, serving as mesoscale platforms that concentrate signaling molecules and modulate reaction kinetics. Condensate formation is a highly dynamic…
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