Improve Research Reproducibility A Bio-protocol resource
- Submit a Protocol
- Receive Our Alerts
- EN
- Protocols
- Articles and Issues
- For Authors
- About
- Become a Reviewer
Past Issue in 2021
Volume: 11, Issue: 11
Biophysics
Preparation of Doublet Microtubule Fraction for Single Particle Cryo-electron Microscopy
Over the years, studying the ultrastructure of the eukaryotic cilia/flagella using electron microscopy (EM) has contributed significantly toward our understanding of ciliary function. Major complexes in the cilia, such as inner and outer dynein arms, radial spokes, and dynein regulatory complexes, were originally discovered by EM. Classical resin-embedding EM or cryo-electron tomography can be performed directly on the isolated cilia or in some cases, cilia directly attached to the cell body. Recently, single particle cryo-EM has emerged as a powerful structural technique to elucidate high-resolution structures of macromolecular complexes; however, single particle cryo-EM requires non-overlapping complexes, i.e., the doublet microtubule of the cilia. Here, we present a protocol to separate the doublet microtubule from the isolated cilia bundle of two species, Tetrahymena thermophila and Chlamydomonas reinhardtii, using ATP reactivation and sonication. Our approach produces good distribution and random orientation of the doublet microtubule fragments, which is suitable for single particle cryo-EM analysis.
Cell Biology
Isolation of First-Trimester and Full-term Human Placental Hofbauer Cells
The placenta is the crucial organ that regulates the health of both mother and fetus during pregnancy. The human placenta is composed of villous tree-like structures that embed into the maternal decidua. Within the stroma of the villi resides a population of fetally-derived macrophages, the Hofbauer cells (HBC). HBC are the only fetal immune cells found within the placenta in the steady-state and are thought to play a crucial role in placental function. From the 10th week of gestation, maternal blood flow into the intervillous space begins, resulting in the placental villi becoming bathed in maternal blood. To study HBC it is necessary to develop techniques that allow for their specific isolation and distinction from maternal blood monocytes and decidual macrophages. Here, we describe a protocol that explains step-by-step the strategy we have developed that allows the specific isolation of HBC.
Visualization and Quantitation of Wg Trafficking in the Drosophila Wing Imaginal Epithelium
Secretory Wnt trafficking can be studied in the polarized epithelial monolayer of Drosophila wing imaginal discs (WID). In this tissue, Wg (Drosophila Wnt-I) is presented on the apical surface of its source cells before being internalized into the endosomal pathway. Long-range Wg secretion and spread depend on secondary secretion from endosomal compartments, but the exact post-endocytic fate of Wg is poorly understood. Here, we summarize and present three protocols for the immunofluorescence-based visualization and quantitation of different pools of intracellular and extracellular Wg in WID: (1) steady-state extracellular Wg; (2) dynamic Wg trafficking inside endosomal compartments; and (3) dynamic Wg release to the cell surface. Using a genetic driver system for gene manipulation specifically at the posterior part of the WID (EnGal4) provides a robust internal control that allows for direct comparison of signal intensities of control and manipulated compartments of the same WID. Therefore, it also circumvents the high degree of staining variability usually associated with whole-tissue samples. In combination with the genetic manipulation of Wg pathway components that is easily feasible in Drosophila, these methods provide a tool-set for the dissection of secretory Wg trafficking and can help us to understand how Wnt proteins travel along endosomal compartments for short- and long-range signal secretion.Graphic abstract:Figure 1. Visualization of extracellular and intracellular Wg trafficking in Drosophila wing imaginal discs. While staining of extracellular Wg without permeabilization exclusively visualizes Wg bound to the extracellular surface (left), Wg uptake and endosomal trafficking can be visualized using an antibody uptake assay (middle). Dynamic Wg release can be visualized by performing a non-permeabilizing staining at a permissive temperature that sustains secretory Wg transport (right).
Developmental Biology
Analysis of Caenorhabditis elegans Sperm Number, Size, Activation, and Mitochondrial Content
Infertility is a widespread and often unexplained issue. Studying reproduction using C. elegans males offers insight into the influence of individual factors on male fertility in humans. We have created a collection of protocols to assess several aspects of C. elegans sperm quality, including number, size, rate of activation, and mitochondrial morphology. Studying sperm biology in a model system such as C. elegans allows access to the wealth of resources and techniques that have been optimized for that organism while providing valuable biological information that may be applicable to other systems.Graphic abstract:Flowchart depicting the preparation of C. elegans males and subsequent sperm quality assays
Quantitation of Secretory Granule Size in Drosophila Larval Salivary Glands
Maturation of secretory granules is a crucial process that ensures the bioactivity of cargo proteins undergoing regulated secretion. In Drosophila melanogaster, the larval salivary glands produce secretory granules that are up to four-fold larger in cross-sectional area after maturation. Therefore, we developed a live imaging microscopy approach to quantitate the size of secretory granules with a view to identifying genes involved in their maturation. Here, we describe the procedures of larval salivary gland dissection and sample preparation for live imaging with a fluorescence confocal microscope. Furthermore, we describe the workflow for measuring the size of secretory granules by cross-sectional surface area and statistical analysis. Our live imaging microscopy method provides a reliable read-out for the status of secretory granule maturation in Drosophila larval salivary glands.
Immunology
Multi-color Flow Cytometry for Comprehensive Analysis of the Tumor Immune Infiltrate in a Murine Model of Breast Cancer
Flow cytometry is a popular laser-based technology that allows the phenotypic and functional characterization of individual cells in a high-throughput manner. Here, we describe a detailed procedure for preparing a single-cell suspension from mammary tumors of the mouse mammary tumor virus-polyoma middle T (MMTV-PyMT) and analyzing these cells by multi-color flow cytometry. This protocol can be used to study the following tumor-infiltrating immune cell populations, defined by the expression of cell surface molecules: total leukocytes, tumor-associated macrophages (TAMs), conventional dendritic cells (DCs), CD103-expressing DCs, tumor-associated neutrophils, inflammatory monocytes, natural killer (NK) cells, CD4+ T cells, CD8+ T cells, γδT cells, and regulatory T cells.
Microbiology
Sex-specific Separation of Plasmodium falciparum Gametocyte Populations
Plasmodium falciparum is a unicellular eukaryotic parasite that causes malaria in humans. The parasite is spread by Anopheles mosquitoes after ingestion of sexual stage parasites known as gametocytes. Malaria transmission depends on parasites switching from the disease-causing asexual blood forms to male and female gametocytes. The current protocol allows the simultaneous isolation of male and female parasites from the same population to study this critical lifecycle stage in a sex-specific manner. We have generated a transgenic P. falciparum cell line that expresses a GFP-tagged parasite protein in female, but not male, parasites. Gametocyte production is stress induced and, through a series of steps, sexual stage parasites are enriched relative to uninfected red blood cells or red blood cells infected with asexual stage parasites. Finally, male and female gametocytes are separated by fluorescence-activated cell sorting. This protocol allows for the separation of up to 12 million live male and female parasites from the same population, which are amenable to further analysis.
Molecular Biology
Mechanical Fractionation of Cultured Neuronal Cells into Cell Body and Neurite Fractions
Many cells contain spatially defined subcellular regions that perform specialized tasks enabled by localized proteins. The subcellular distribution of these localized proteins is often facilitated by the subcellular localization of the RNA molecules that encode them. A key question in the study of this process of RNA localization is the characterization of the transcripts present at a given subcellular location. Historically, experiments aimed at answering this question have centered upon microscopy-based techniques that target one or a few transcripts at a time. However, more recently, the advent of high-throughput RNA sequencing has allowed the transcriptome-wide profiling of the RNA content of subcellular fractions. Here, we present a protocol for the isolation of cell body and neurite fractions from neuronal cells using mechanical fractionation and characterization of their RNA content.Graphic abstract:Fractionation of neuronal cells and analysis of subcellular RNA contents
Neuroscience
In vivo Fluorescence Imaging of Extracellular ATP in the Mouse Cerebral Cortex with a Hybrid-type Optical Sensor
Adenosine 5’-triphosphate (ATP) works as an extracellular signaling molecule for cells in the brain, such as neurons and glia. Cellular communication via release of ATP is involved in a range of processes required for normal brain functions, and aberrant communication is associated with brain disorders. To investigate the mechanisms underlying these cellular processes, various techniques have been developed for the measurement of extracellular ATP. To monitor the dynamics of extracellular ATP signaling with high spatiotemporal resolution, we recently developed a hybrid-type ATP optical sensor (ATPOS) that enables in vivo fluorescence imaging of extracellular ATP dynamics in the brain. ATPOS is synthesized by labeling an ATP-binding protein, Bacillus FoF1-ATP synthase ϵ subunit, with a small-molecular fluorescent dye Cy3. Injection of ATPOS into the cerebral cortex of living mice enables visualization of the wave-like propagation of extracellular ATP release in response to electrical stimulation. The protocol described here should be useful for visualizing ATP signaling in diverse processes involved in intercellular communication in the brain.
Objective Quantitation of Focal Sweating Areas Using a Mouse Sweat-assay Model
In vivo sweat quantitation assays are required for the development of drugs for the management of focal hyperhidrosis before clinical trials; however, in vivo assays, particularly mouse models, are rare. Even in sweat assays using mice, sweating is quantitated by manually counting the number of sweating spots, which can contribute to various errors owing to arbitrary judgment. In this study, we developed a mouse sweat-assay model and a method for quantitating the amount of sweating to remove possible errors. The use of the iodine–starch test in the castor oil-covered hind footpad skin of anesthetized mice resulted in the sweating area being stained blue-black. After the anesthesia and treatment with drugs (pilocarpine, glycopyrrolate, botulinum neurotoxin, myricetin, and myricetin-loaded lipid nanoparticles), the remaining area of the footpad skin was eliminated from the acquired footpad images using ImageJ. Blue pixels extracted from the footpad image are automatically adjusted using the Phansalkar method, where the percentage of the blue area was determined based on the whole hind footpad skin area, finally indicating the percentage of the sweating area. Using this mouse model and analysis for sweat assays, a clear difference between the control group and antiperspirant-administered group was observed with respect to the sweating area % with no error. In conclusion, this assay can be used as a preclinical tool to screen potential antiperspirant drugs.Graphic abstract:Overview of the mouse-model sweat assay and objective quantitation of the focal sweating area
Plant Science
Rice Root Hair Phenotypes Imaged by Cryo-SEM
Cryo-scanning electron microscopy (cryo-SEM) was first introduced for scientific use in the 1980s. Since then, cryo-SEM has become a routine technique for studying the surfaces and internal structures of biological samples with a high water content. In contrast to traditional SEM, cryo-SEM requires no sample pretreatment processes; thus, we can obtain the most authentic images of the sample shape and structure. Cryo-SEM has two main steps: cryoprocessing of samples and scanning electron microscopy (SEM) observation. The cryoprocessing step includes preparation of the cooled slushing station, cooling of the preparation chamber, sample preparation, and sputtering. The sample is then transferred to an SEM cold stage for observation. We used cryo-SEM to study rice root hair tissues, but the methods and protocols can be applied to other root systems. This protocol optimizes the two key operation steps of reducing the humidity in the growth chamber and previewing the samples before sputtering and can more quickly obtain high-quality images.
Stem Cell
Generation and Maintenance of Homogeneous Human Midbrain Organoids
Three-dimensional cell cultures (“organoids”) promise to better recapitulate native tissue physiology than traditional 2D cultures and are becoming increasingly interesting for disease modeling and compound screening efforts. While a number of protocols for the generation of neural organoids have been published, most protocols require extensive manual handling and result in heterogeneous aggregates with high sample-to-sample variation, which can hinder screening-based strategies. We have now developed a fast and efficient protocol for the generation and maintenance of highly homogeneous and reproducible midbrain organoids. The protocol is streamlined for use in fully automated workflows but can also be performed manually without the need for highly specialized equipment. It relies on the aggregation of small molecule neural precursor cells (smNPCs) in standard 96-well V-bottomed plates under static culture conditions without cumbersome matrix embedding. The result is ready-to-assay uniform 3D human midbrain organoids available in freely scalable quantities for downstream analyses in 3D cell cultureGraphic abstract:Automated midbrain organoid generation workflow and timeline
Generation of Mouse Pluripotent Stem Cell-derived Trunk-like Structures: An in vitro Model of Post-implantation Embryogenesis
Post-implantation mammalian embryogenesis involves profound molecular, cellular, and morphogenetic changes. The study of these highly dynamic processes is complicated by the limited accessibility of in utero development. In recent years, several complementary in vitro systems comprising self-organized assemblies of mouse embryonic stem cells, such as gastruloids, have been reported. We recently demonstrated that the morphogenetic potential of gastruloids can be further unlocked by the addition of a low percentage of Matrigel as an extracellular matrix surrogate. This resulted in the formation of highly organized trunk-like structures (TLSs) with a neural tube that is frequently flanked by bilateral somites. Notably, development at the molecular and morphogenetic levels is highly reminiscent of the natural embryo. To facilitate access to this powerful model, here we provide a detailed step-by-step protocol that should allow any lab with access to standard cell culture techniques to implement the culture system. This will provide the user with a means to investigate early mid-gestational mouse embryogenesis at an unprecedented spatiotemporal resolution.
Muscle Cryoinjury and Quantification of Regenerating Myofibers in Mice
Cryoinjury, or injury due to freezing, is a method of creating reproducible, local injuries in skeletal muscle. This method allows studying the regenerative response following muscle injuries in vivo, thus enabling the evaluation of local and systemic factors that influence the processes of myofiber regeneration. Cryoinjuries are applicable to the study of various modalities of muscle injury, particularly non-traumatic and traumatic injuries, without a loss of substantial volume of muscle mass. Cryoinjury requires only simple instruments and has the advantage over other methods that the extent of the lesion can be easily adjusted and standardized according to the duration of contact with the freezing instrument. The regenerative response can be evaluated histologically by the average maturity of regenerating myofibers as indicated by the cross-sectional areas of myofibers with centrally located nuclei. Accordingly, cryoinjury is regarded as one of the most reliable and easily accessible methods for simulating muscle injuries in studies of muscle regeneration.
Systems Biology
Simplified Epigenome Profiling Using Antibody-tethered Tagmentation
We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps specific chromatin features in small samples and single cells. With CUT&Tag, intact cells or nuclei are permeabilized, followed by successive addition of a primary antibody, a secondary antibody, and a chimeric Protein A-Transposase fusion protein that binds to the antibody. Addition of Mg++ activates the transposase and inserts sequencing adapters into adjacent DNA in situ. We have since adapted CUT&Tag to also map chromatin accessibility by simply modifying the transposase activation conditions when using histone H3K4me2, H3K4me3, or Serine-5-phosphorylated RNA Polymerase II antibodies. Using these antibodies, we redirect the tagmentation of accessible DNA sites to produce chromatin accessibility maps with exceptionally high signal-to-noise and resolution. All steps from nuclei to amplified sequencing-ready libraries are performed in single PCR tubes using non-toxic reagents and inexpensive equipment, making our simplified strategy for simultaneous chromatin profiling and accessibility mapping suitable for the lab, home workbench, or classroom.
Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R
DNA methylation in gene promoters plays a major role in gene expression regulation, and alterations in methylation patterns have been associated with several diseases. In this context, different software suites and statistical methods have been proposed to analyze differentially methylated positions and regions. Among them, the novel statistical method implemented in the mCSEA R package proposed a new framework to detect subtle, but consistent, methylation differences. Here, we provide an easy-to-use pipeline covering all the necessary steps to detect differentially methylated promoters with mCSEA from Illumina 450K and EPIC methylation BeadChips data. This protocol covers the download of data from public repositories, quality control, data filtering and normalization, estimation of cell type proportions, and statistical analysis. In addition, we show the procedure to compare disease vs. normal phenotypes, obtaining differentially methylated regions including promoters or CpG Islands. The entire protocol is based on R programming language, which can be used in any operating system and does not require advanced programming skills.