Current protocols最新文献

Biochemical fractionation is a technique used to isolate and separate distinct cellular compartments, critical for dissecting cellular mechanisms and molecular pathways. Herein we outline a biochemical fraction methodology for isolation of ultra-pure nuclei and cytoplasm. This protocol utilizes hypotonic lysis buffer to suspend cells, coupled with a calibrated centrifugation strategy, for enhanced separation of cytoplasm from the nuclear fraction. Subsequent purification steps ensure the integrity of the isolated nuclear fraction. Overall, this method facilitates accurate protein localization, essential for functional studies, demonstrating its efficacy in separating cellular compartments. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Biochemical fractionation

Support Protocol 1: Protein quantification using Bradford assay

Support Protocol 2: SDS/PAGE and Western blotting

The recombinant human proteoglycan aggrecan-G1 domain (rhG1)-induced arthritis (GIA) mouse model is a complex model of rheumatoid arthritis (RA). In GIA, autoimmune arthritis is induced by repeated intraperitoneal immunization of genetically susceptible BALB/c mice with the rhG1 antigen emulsified in the adjuvant dimethyldioctadecylammonium (DDA). This article describes the steps for producing and purifying the rhG1 antigen, the immunization protocol, methods for following the clinical picture of arthritis, and the evaluation of relevant laboratory parameters. In this model, the autoimmune arthritis develops stepwise, similar to RA: First is the preclinical stage (after the first immunization, days 0-20) with no sign of inflammation but detectable T and B cell activation; next, the stage of early arthritis (after the second immunization, days 21-41), where the first definitive signs of arthritis appear together with autoantibody production; and then the severe late-stage arthritis (after the third immunization, after day 42), which presents with massive inflammation of the limbs, leading to cartilage and bone destruction and finally ankylosis. The protocols described here provide sufficient information for investigators to use the GIA model to study different aspects of autoimmune arthritis. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Induction of recombinant human proteoglycan aggrecan-G1 domain (rhG1)-induced arthritis (GIA)

Support Protocol 1: Production of rhG1-Xa-mFc2a fusion protein with CHOK1 mammalian expression system

Support Protocol 2: Purification of the rhG1-Xa-mFc2a fusion protein by affinity chromatography

Support Protocol 3: Preparation of DDA adjuvant

Support Protocol 4: Clinical assessment of arthritis

Support Protocol 5: Measurement of serum antibody levels and cytokines

Support Protocol 6: Measurement of rhG1-induced proliferation and cytokine production in spleen cell culture

Support Protocol 7: Histological assessment of arthritic limbs

Support Protocol 8: Evaluation of arthritis with micro-computed tomography

Both Ca²⁺ and protein kinase A (PKA) are multifaceted and ubiquitous signaling molecules, essential for regulating the intricate network of signaling pathways. However, their dynamics within specialized membrane regions are still not well characterized. By using genetically encoded fluorescent indicators specifically targeted to distinct plasma membrane microdomains, we have established a protocol that permits observing Ca²⁺/PKA dynamics in discrete neuronal microdomains with high spatial and temporal resolution. The approach employs a fluorescence microscope with a sensitive camera and a dedicated CFP/YFP/mCherry filter set, enabling the simultaneous detection of donor-acceptor emission and red fluorescence signal. In this detailed step-by-step guide, we outline the experimental procedure, including isolation of rat primary neurons and their transfection with biosensors targeted to lipid rafts or non-raft regions of plasma membrane. We provide information on the necessary equipment and imaging setup required for recording, along with highlighting critical parameters and troubleshooting guidelines for real-time measurements. Finally, we provide examples of the observed Ca²⁺ and PKA changes in specific cellular compartments. The application of this technique may have significant implications for studying cross-talk between second messengers and their alterations in various pathological conditions. © 2024 Wiley Periodicals LLC.

Cells continuously remodel their intracellular proteins with the monosaccharide O-linked N-acetylglucosamine (O-GlcNAc) to regulate metabolism, signaling, and stress. This protocol describes the use of GlycoID tools to capture O-GlcNAc dynamics in live cells. GlycoID constructs contain an O-GlcNAc binding domain linked to a proximity labeling domain and a subcellular localization sequence. When expressed in mammalian cells, GlycoID tracks changes in O-GlcNAc-modified proteins and their interactomes in response to chemical induction with biotin over time. Pairing the subcellular localization of GlycoID with the chemical induction of activity enables spatiotemporal studies of O-GlcNAc biology during cellular events such as insulin signaling. However, optimizing intracellular labeling experiments requires attention to several variables. Here, we describe two protocols to adapt GlycoID methods to a cell line and biological process of interest. Next, we describe how to conduct a semiquantitative proteomic analysis of O-GlcNAcylated proteins and their interactomes using insulin versus glucagon signaling as a sample application. This articles aims to establish baseline GlycoID protocols for new users and set the stage for widespread use over diverse cellular applications for the functional study of O-GlcNAc glycobiology. © 2024 Wiley Periodicals LLC.

Basic Protocol 1: Expression of targeted GlycoID constructs to verify subcellular location and labeling activity in mammalian cells

Basic Protocol 2: GlycoID labeling in live HeLa cells for O-GlcNAc proteomic comparisons

Nuclear factor-κB (NF-κB) is a crucial pro-inflammatory transcription factor whose activation is of immense interest to immunology research. Estimation of NF-κB activation through flow cytometry is not possible due to the unavailability of robust flow cytometry antibodies that can bind to its phosphorylated, active, nuclear form. In this protocol, we describe a flow cytometry assay that measures the activation of the pro-inflammatory transcription factor NF-κB in stimulated immune cells by quantifying the degradation of its upstream regulator IκBα. We demonstrate the utility of this protocol by assessment of intracellular IκBα in human primary regulatory T cells experiencing TNFR2 agonism, a process previously reported to activate NF-κB in these cells. We also show that this assay may be applied to study NF-κB activation in other cell types, such as human primary T cells and THP-1 cell-derived macrophages, when induced by their corresponding inflammatory cues. Thus, this robust and reproducible protocol will be of interest to a wide range of scientists who aim to measure NF-κB activity in medium-to-high-throughput assays. © 2024 Wiley Periodicals LLC.

Basic Protocol: Quantifying inflammatory activation by flow cytometry of IκBα degradation

Support Protocol 1: Isolating and expanding human regulatory T cells

Support Protocol 2: Calculating IC₅₀ from flow cytometry data using Excel

Nematodes are naturally infected by the fungal-related pathogen microsporidia. These ubiquitous eukaryotic parasites are poorly understood, despite infecting most types of animals. Identifying novel species of microsporidia and studying them in an animal model can expedite our understanding of their infection biology and evolution. Nematodes present an excellent avenue for pursuing such work, as they are abundant in the environment and many species are easily culturable in the laboratory. The protocols presented here describe how to isolate bacterivorous nematodes from rotting substrates, screen them for microsporidia infection, and molecularly identify the nematode and microsporidia species. Additionally, we detail how to remove environmental contaminants and generate a spore preparation of microsporidia from infected samples. We also discuss potential pitfalls and provide suggestions on how to mitigate them. These protocols allow for the identification of novel microsporidia species, which can serve as an excellent starting point for genomic analysis, determination of host specificity, and infection characterization. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Gathering samples

Support Protocol 1: Generating 10× and 40× Escherichia coli OP50 and seeding NGM plates

Basic Protocol 2: Microsporidia screening, testing for Caenorhabditis elegans susceptibility, and sample freezing

Basic Protocol 3: DNA extraction, PCR amplification, and sequencing to identify nematode and microsporidia species

Basic Protocol 4: Removal of contaminating microbes and preparation of microsporidia spores

Support Protocol 2: Bleach-synchronizing nematodes

The cell surface distribution patterns (clustering) of membrane proteins have been widely investigated in cell biology. Here we describe a novel transmission electron microscopic (TEM) protocol designed to improve the quality of information obtained about the protein distribution patterns detected. This novel method makes it possible to study the clustering of all transmembrane proteins on one half of the cytoplasmic membrane of a whole cell. To achieve better imaging, we combine various methods, including critical-point drying, fixation of gold beads with a carbon layer, and a newly developed chemical thinning method. In addition, in our image-processing algorithm, we implemented pair correlation and pair cross-correlation functions, providing more details and better quantitative accuracy in characterizing the size and numbers of possible protein clusters. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Sample preparation and transmission electron micrography

Alternate Protocol: Direct cell labeling for transmission electron micrography

Basic Protocol 2: Analysis of TEM images to detect immunogold-labeled proteins

Scanning electron microscopy (SEM) remains distinct in its ability to allow topographical visualization of structures. Key elements to consider for successful examination of biological specimens include appropriate preparative and imaging techniques. Chemical processing induces structural artifacts during specimen preparation, and several factors need to be considered when selecting fixation protocols to reduce these effects while retaining structures of interest. Particular care for proper dehydration of specimens is essential to minimize shrinkage and is necessary for placement under the high-vacuum environment required for routine operation of standard SEMs. Choice of substrate for mounting and coating specimens can reduce artifacts known as charging, and a basic understanding of microscope settings can optimize parameters to achieve desired results. This article describes fundamental techniques and tips for routine specimen preparation for a variety of biological specimens, preservation of labile or fragile structures, immune-labeling strategies, and microscope imaging parameters for optimal examination by SEM. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Chemical preparative techniques for preservation of biological specimens for examination by SEM

Alternate Protocol 1: Practical considerations for the preparation of soft tissues

Alternate Protocol 2: Removal of debris from the exoskeleton of invertebrates

Alternate Protocol 3: Fixation of colonies grown on agar plates

Alternate Protocol 4: Stabilization of polysaccharide structures with alcian blue and lysine

Alternate Protocol 5: Preparation of non-adherent particulates in solution for SEM

Support Protocol 1: Application of thin layer of adhesive on substrate to improve adherence

Support Protocol 2: Poly-L-lysine coating specimen substrates for improved adherence

Support Protocol 3: Microwave processing of biological specimens for examination by SEM

Basic Protocol 2: Critical point drying of specimens

Alternate Protocol 6: Chemical alternative to critical point drying

Basic Protocol 3: Sputter coating

Alternate Protocol 7: Improved bulk conductivity through “OTOTO”

Basic Protocol 4: Immune-labeling strategies

Alternate Protocol 8: Immune-labeling internal antigens with small gold probes

Alternate protocol 9: Quantum dot or fluoronanogold preparations for correlative techniques

Basic Protocol 5: Exposure of internal structures by mechanical fracturing

Basic Protocol 6: Exposure of internal structures of tissues by fracturing with liquid nitrogen

Basic Protocol 7: Anaglyph production from stereo pairs to produce 3D images

Whole-genome sequencing is widely used to investigate population genomic variation in organisms of interest. Assorted tools have been independently developed to call variants from short-read sequencing data aligned to a reference genome, including single nucleotide polymorphisms (SNPs) and structural variations (SVs). We developed SNP-SVant, an integrated, flexible, and computationally efficient bioinformatic workflow that predicts high-confidence SNPs and SVs in organisms without benchmarked variants, which are traditionally used for distinguishing sequencing errors from real variants. In the absence of these benchmarked datasets, we leverage multiple rounds of statistical recalibration to increase the precision of variant prediction. The SNP-SVant workflow is flexible, with user options to tradeoff accuracy for sensitivity. The workflow predicts SNPs and small insertions and deletions using the Genome Analysis ToolKit (GATK) and predicts SVs using the Genome Rearrangement IDentification Software Suite (GRIDSS), and it culminates in variant annotation using custom scripts. A key utility of SNP-SVant is its scalability. Variant calling is a computationally expensive procedure, and thus, SNP-SVant uses a workflow management system with intermediary checkpoint steps to ensure efficient use of resources by minimizing redundant computations and omitting steps where dependent files are available. SNP-SVant also provides metrics to assess the quality of called variants and converts between VCF and aligned FASTA format outputs to ensure compatibility with downstream tools to calculate selection statistics, which are commonplace in population genomics studies. By accounting for both small and large structural variants, users of this workflow can obtain a wide-ranging view of genomic alterations in an organism of interest. Overall, this workflow advances our capabilities in assessing the functional consequences of different types of genomic alterations, ultimately improving our ability to associate genotypes with phenotypes. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Predicting single nucleotide polymorphisms and structural variations

Support Protocol 1: Downloading publicly available sequencing data

Support Protocol 2: Visualizing variant loci using Integrated Genome Viewer

Support Protocol 3: Converting between VCF and aligned FASTA formats

Recent advancements in protein structure determination and especially in protein structure prediction techniques have led to the availability of vast amounts of macromolecular structures. However, the accessibility and integration of these structures into scientific workflows are hindered by the lack of standardization among publicly available data resources. To address this issue, we introduced the 3D-Beacons Network, a unified platform that aims to establish a standardized framework for accessing and displaying protein structure data. In this article, we highlight the importance of standardized approaches for accessing protein structure data and showcase the capabilities of 3D-Beacons. We describe four protocols for finding and accessing macromolecular structures from various specialist data resources via 3D-Beacons. First, we describe three scenarios for programmatically accessing and retrieving data using the 3D-Beacons API. Next, we show how to perform sequence-based searches to find structures from model providers. Then, we demonstrate how to search for structures and fetch them directly into a workflow using JalView. Finally, we outline the process of facilitating access to data from providers interested in contributing their structures to the 3D-Beacons Network. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Programmatic access to the 3D-Beacons API

Basic Protocol 2: Sequence-based search using the 3D-Beacons API

Basic Protocol 3: Accessing macromolecules from 3D-Beacons with JalView

Basic Protocol 4: Enhancing data accessibility through 3D-Beacons