Improve Research Reproducibility A Bio-protocol resource
- Protocols
- Articles and Issues
- For Authors
- About
- Become a Reviewer
Volume:16 Issue: 17 | Bio-protocol
Current Issue in 2026
Volume: 16, Issue: 17
Biochemistry
ChromID: A Protocol for Mapping Protein Chromatin Interactions in Living Cells
Chromatin modifications regulate genome function by recruiting proteins that control transcription, genome organization, and DNA repair. Identifying the proteins associated with specific chromatin modifications is therefore essential for understanding how these regulatory processes operate. Traditional approaches, including chromatin immunoprecipitation and affinity purification coupled to mass spectrometry, have uncovered many chromatin-associated proteins. However, they often rely on crosslinking and chromatin fragmentation, which can disrupt native chromatin architecture and limit the detection of transient interactions. Here, we describe a proximity-labeling protocol for identifying the chromatin-dependent protein interactome associated with specific chromatin marks, termed ChromID. ChromID uses engineered chromatin readers (eCRs) fused to a promiscuous biotin ligase, which labels proteins in the immediate vicinity of the targeted chromatin mark. The protocol includes in vivo biotin labeling, nuclear extract preparation, streptavidin-based enrichment, and tryptic digestion for downstream LC-MS/MS analysis. The protocol has been validated across multiple cell types and chromatin contexts and can be extended to other chromatin-associated proteins, providing a versatile approach to profile chromatin-associated proteomes within their native cellular environment.
Bioinformatics and Computational Biology
Massively Parallel In Vitro Functional Analysis of Evolution-Derived Transcriptional Riboswitch Sequences
Riboswitches are structured non-coding RNA elements that regulate gene expression in response to small molecules; they serve as valuable systems in both public health and biophysical research by elucidating principles around RNA–ligand interactions, structure, and cellular function. Traditional approaches to studying riboswitches have relied on low-throughput techniques such as reporter assays or gel electrophoresis analysis of transcriptional products, which are limited in scalability. In this study, we present a high-throughput protocol to characterize the transcriptional activity of nearly 2,000 natural variants of the fluoride riboswitch in in vitro transcription. Starting with bioinformatics, we compiled a comprehensive dataset of riboswitch variants and then employed massive parallel oligonucleotide synthesis to generate an oligo pool of the riboswitch library. This pool was transcribed in vitro, converted into an Illumina-compatible next-generation sequencing (NGS) library, and analyzed to identify transcriptionally active riboswitch candidates. The workflow integrates natural riboswitch bioinformatic acquisition into a quantitative readout in a single streamlined pipeline, enabling large-scale exploration of transcriptional riboswitch function. This protocol offers a scalable method for mapping genotype-to-function relationships across transcriptional riboswitch families, accelerating the identification of functional variants for desired applications.
scDynaBar: A Step-By-Step Experimental and Computational Guide for Time-Resolved CRISPR Barcoding at Single-Cell Resolution
CRISPR-Cas9 barcoding technologies enable cells to record molecular events as permanent genetic changes that can be read out retrospectively. This protocol describes the implementation of a CRISPR-based recording system that gradually accumulates mutations over extended periods and is compatible with standard single-cell RNA sequencing (scRNA-seq) workflows. By temporally regulating CRISPR activity, the system generates mutational barcodes that can be captured together with individual cell transcriptomes. These barcodes are subsequently decoded using computational reconstruction approaches to infer temporal information, enabling the joint analysis of cellular states and time-resolved molecular histories. This approach provides a single-cell-compatible framework for studying dynamic biological processes in heterogeneous mouse embryonic stem cell (mESC)-derived systems, with potential extension to other biological systems.
Humanizing Antibodies and Nanobodies From Scratch With HuDiff
Antibody (Ab) and nanobody (Nb) humanization is essential for reducing immunogenicity in therapeutic applications. HuDiff is an adaptive autoregressive diffusion approach that generates humanized antibodies and nanobodies from scratch using only complementarity-determining region sequences as input, eliminating the need for preexisting human templates. The method follows a two-stage training pipeline: pretraining on human antibody sequences to learn framework region patterns, followed by fine-tuning on target-species sequences. HuDiff-Ab processes paired heavy and light chains for conventional antibodies, while HuDiff-Nb can incorporate a specialized inpainting mode to preserve critical nanobody framework residues. This protocol provides a complete step-by-step guide for implementing HuDiff, covering data preparation, model training, and sequence generation.
Biological Engineering
Engineering MRI-Based Programmable Genetic Sensors Using the MAPPER Platform
Genetically encodable reporters that produce signals detectable in deep tissues offer a powerful tool for noninvasive monitoring of molecular events in vivo. Although magnetic resonance imaging (MRI) is a standard technique for noninvasive clinical imaging, its wider application in detecting molecular activities has been constrained by the lack of programmable sensors. This limitation is in stark contrast to the widespread use of fluorescent reporter–derived sensors in cultured cells and in transparent specimens. To overcome this limitation, we recently developed the modular aquaporin-based protease-activatable probe for enhanced reporting (MAPPER) platform. This sensor engineering framework integrates a metal-free MRI reporter derived from human aquaporin-1 (hAqp1) with synthetic protease-based circuits. This integration facilitates the modular and scalable creation of a wide range of sensors by regulating protease activity through precise molecular events, such as protein–protein interactions, pharmacological inhibition, and second messenger signaling. In this paper, we present a detailed protocol for constructing and deploying sensors using the MAPPER paradigm. The protocol encompasses genetic design, lentiviral production, stable cell line generation, biochemical and microscopic validation of sensor function, diffusion-weighted MRI, and MR image analysis to quantify sensor signals in terms of the apparent diffusion coefficient. We describe two distinct MAPPER architectures: DD-MAPPER, which leverages protease-controlled protein degradation, and ER-MAPPER, which utilizes protease-controlled, subcellular trafficking. The MAPPER framework allows adaptation to various molecular targets without the need to redesign the core MRI reporter mechanism, making MAPPER a versatile platform for noninvasive biosensing in living cells and tissues.
From Bacterial Cellulose Production by Komagataeibacter xylinus to Bacterial Cellulose Nanoparticles: A Standardized Enzymatic Approach
Bacterial cellulose (BC) is a renewable biopolymer valued for its exceptional purity, biocompatibility, and mechanical strength, with broad applications in biomedicine and sustainable materials. However, achieving reproducible BC production and downstream processing remains a major challenge. Inoculum preparation is particularly difficult to standardize because cellulose-producing strains form pellicles that sequester cells, making optical density measurements unreliable. In addition, recovery and drying procedures can alter fiber accessibility, and enzymatic hydrolysis conditions are often inconsistently defined and lack proper enzyme activity assessment. These issues contribute to substantial variability in BC-derived nanoparticle yields. This protocol describes the production of BC from Komagataeibacter xylinus DSMZ 6513, including culture medium preparation, inoculum generation, and scaling up under static cultivation conditions. It further details BC pellicle purification using NaOH, followed by pulping, freeze-drying, and milling to ensure material stability during storage and use. BC hydrolysis is performed with commercially available cellulase from Trichoderma reesei, with enzyme activity quantified prior to each reaction to ensure reproducibility. This standardized approach enables the reproducible production of bacterial cellulose nanoparticles (BCNPs). The protocol also includes minimal morphological characterization methods. By standardizing culture, recovery, and hydrolysis steps, the workflow reduces experimental variability and improves comparability across laboratories. Overall, it provides an accessible and reproducible method for generating BC and BCNPs of consistent quality without the need for specialized instrumentation.
Biophysics
Cryo-EM Pipeline for Actin Filament End Structures
Actin filaments undergo dynamic growth and disassembly at their ends, regulated by many actin-binding proteins. However, structural analysis of filament end dynamics has been challenging due to the low abundance of filament ends in cryo-electron microscopy (cryo-EM) micrographs, their intrinsic polymorphisms, and the diversity and flexibility of end-binding proteins. Here, we describe a standardized cryo-EM protocol for determining actin filament end structures. First, short actin filaments are generated either biochemically using capping or severing proteins or mechanically through shearing. Filaments are then vitrified under conditions optimized for each specific end-binding protein. We describe data collection parameters using a 300 kV Titan Krios G3i microscope, including optimized grid preparation and imaging settings. Finally, we present a data processing pipeline for filament end structure determination based on machine learning–based particle picking, masking, and sorting strategies. This protocol has enabled the determination of multiple high-resolution structures of free, capped, elongating, and depolymerizing actin filament ends, and we further discuss considerations for extending this approach to other end-binding proteins.
Cancer Biology
Endoscopic Collection and Analysis of Gastric Fluid DNA: A Liquid Biopsy Methodology for Tumor Biomarker Discovery
Gastric cancer remains a major global health challenge, and reliable prognostic biomarkers are urgently needed to guide treatment decisions. Here, we present a simple and efficient protocol for a novel liquid biopsy approach based on quantifying gastric fluid DNA (gfDNA) collected during routine esophagogastroduodenoscopy (EGD). We have previously shown that gfDNA carries gastric cancer–derived mutations; moreover, its concentration increases with tumor progression and varies according to cancer prognosis. This empirically observed increase in gfDNA may mechanistically stem from enhanced cellular turnover, tissue disorganization, dysbiosis of the local microbiota, and/or fluctuations in immune cell infiltrates. Surprisingly, however, in patients diagnosed with gastric cancer, elevated gfDNA levels were also associated with improved survival. This paradoxical finding may be reconciled by an increased anti-tumor immune cell response in treatment-responsive gastric cancers, as well as by the contribution of non-tumoral DNA from inflammatory processes within the microenvironment of the stomach. Here, we detail a standardized protocol for gastric fluid collection and processing, designed to support downstream gfDNA quantification among other potential molecular applications.
Immunology
An Automated, Ventana Discovery Platform-based Imaging Workflow for Simultaneous Quantification of B Cells, Plasma Cells, and Plasmablasts in FFPE Human Tissues
Accurate, sensitive quantification of B-lineage cells is critical for pharmacodynamic evaluation of B cell–targeted therapies in lupus nephritis (LN) clinical trials. While high-dimensional discovery platforms offer broad profiling, they often lack the sensitivity, quantitative rigor, and throughput needed for precise cell enumeration in renal trial needle biopsies. Traditional immunostaining is hampered by CD20-directed therapeutic masking or downregulation, inadequate sensitivity of CD19 in FFPE tissue, and confounding renal tubular CD138 expression. This protocol details an automated, fit-for-purpose, 5-plex sequential tyramide signal amplification (TSA)-based immunofluorescence assay (CD38, CD79a, CD19, Ki-67, CD138) developed on the Ventana Discovery Ultra platform for deployment on single tissue sections. The workflow anchors B-cell detection on CD79a to ensure sensitivity and utilizes CD38 as an obligate co-marker for CD138+ antibody-secreting cells (ASCs) to definitively exclude the CD138+ epithelial background. Following acquisition via fluorescence whole-slide imaging, a digital analysis pipeline utilizing InstanSeg-based automated segmentation rigorously classifies cell phenotypes to generate precise spatial densities (cells/mm2). This validated protocol maximizes data yield from scarce clinical biopsies while providing high-precision quantitative monitoring of longitudinal therapeutic depletion in the renal microenvironment.
Microbiology
A Modified Slide-Embedded Scanning Electron Microscopy Preparation Method to Visualize Antagonistic Interactions Between Trichoderma viride and Fusarium sp.
Mycoparasitism is an important mechanism of fungal antagonism in which one fungus parasitizes another. This type of interaction plays a major role in the biocontrol activity of Trichoderma spp. against phytopathogenic fungi. Detailed visualization of these interactions is essential for understanding the structural mechanisms involved in fungal antagonism, including hyphal attachment, coiling, penetration, and cellular distortion. Scanning electron microscopy (SEM) is widely used for structural examination of fungal interactions; however, conventional preparation methods such as filter paper systems, membrane overlays, and agar block techniques often result in structural distortion, fragile sample handling, and difficulty in locating defined interaction zones. Here, we describe a modified slide-embedded technique for SEM visualization of mycoparasitic interactions between filamentous fungi. The protocol is adapted from previously reported slide culture approaches and involves embedding pre-cut sterile glass slide fragments directly into potato dextrose agar (PDA), followed by sequential inoculation of Fusarium sp. and Trichoderma viride. Fungal interactions occurring directly on the glass surface are subsequently subjected to fixation with 2.5% glutaraldehyde, graded ethanol dehydration, sputter coating, and SEM observation. Compared with conventional methods, the present approach provides improved handling stability, better preservation of native hyphal architecture, reduced deformation during processing, and easier localization of interaction zones during microscopy. The protocol also enables clear visualization of early antagonistic events such as hyphal coiling, penetration, and surface colonization. Due to its simplicity, reproducibility, and minimal technical complexity, this method serves as a practical and efficient approach for SEM-based investigation of fungal–fungal interactions and can be readily adapted for studying diverse mycoparasitic systems.
Determining the Age of Every Cell Within Each Budding Yeast Microcolony Combining Single-Cell Microencapsulation With Confocal Microscopy
Isogenic populations of Saccharomyces cerevisiae exhibit significant proliferative heterogeneity, with individual cells within a clonal culture displaying divergent growth rates and metabolic states. Investigating the origins of this variation requires a method to reconstruct the individual histories of cells within the population. This protocol describes a method for single-cell microencapsulation in alginate microspheres to create a physically stable, traceable, three-dimensional genealogical environment. By utilizing the alginate matrix to prevent daughter cell migration, the replicative history of a founder cell can be mathematically reconstructed. This is achieved by correlating the total cell count (N) within a developed microcolony with the total number of accumulated bud scars (n) visualized via confocal microscopy.
Molecular Biology
R-Loop Modification and Quantification by Dot Blot
RNA modifications and their “writer,” “eraser,” and “reader” proteins are emerging as key regulators of gene expression and DNA repair through dynamically regulating RNA:DNA hybrids, or R-loops, during transcription. Therefore, it is paramount to develop rigorous techniques for accurate analysis of R-loop modifications. A convenient method for analyzing RNA modifications within total RNA is by dot blot with specific RNA modification antibodies; however, analysis of the modification of the RNA moiety within R-loops presents specific challenges. Here, we provide a detailed protocol for the production or purification of DNA containing R-loops in vitro and from cells, and the analysis of the RNA moiety modifications by dot blot. The DNA containing R-loops is treated with either mock or RNase H, which specifically degrades the RNA within RNA:DNA hybrids, to control for the specificity of the signal as originating from R-loops. Known quantities of the mock or RNase H–treated DNA are then spotted on three membranes, each blotted with antibodies that recognize double-stranded DNA, RNA:DNA hybrids, or the specific RNA modification antibodies of interest, such as m6A or ac4C. Thus, this protocol is useful to both biochemists and cell biologists with scientific interests at the intersection of R-loops and epitranscriptomics.
Neuroscience
Quantitative Analysis of Axonal Degeneration and TDP-43 Aggregation in Compartmentalized Human iPSC-Derived Motor Neuron–Myotube Co-cultures
Amyotrophic lateral sclerosis (ALS) is characterized by early and spatially restricted pathology in motor axons, including distal degeneration and accumulation of aggregation-prone proteins such as TDP-43. However, a major limitation in the field has been the lack of approaches that enable robust, quantitative, and compartment-specific analysis of these early axonal events, particularly in human-relevant systems. Here, we describe an integrated experimental and analytical framework that enables quantitative dissection of axonal degeneration and protein aggregation, specifically within distal motor axons. By combining compartmentalized human co-cultures with a dedicated image analysis strategy, this approach enables selective and quantitative analysis of pathological processes specifically within axons, independent of surrounding tissues such as muscle and other cellular compartments. This framework captures both structural degeneration and protein aggregation dynamics at subcellular resolution, enabling spatially resolved quantitative analysis of disease-relevant changes along axons. Importantly, the analytical framework is not limited to TDP-43 but is broadly applicable to diverse aggregation-prone proteins, thereby providing a generalizable platform to study axonal pathology across neurodegenerative diseases. Together, this work provides a scalable approach for investigating axonal pathology as an early and measurable feature of neurodegeneration, with potential applications in mechanistic studies and therapeutic targeting in ALS and related disorders.
Plant Science
Identifying D-Group Mitogen-Activated Protein Kinases as Substrates of Arabidopsis Tyrosine Phosphatase RLPH2 Using Phospho-Tyrosine Peptide Enrichment
Identifying substrates of protein phosphatases has been technically challenging and has hampered progress in the field of plant sciences. Small molecule inhibitors of protein phosphatases have aided in uncovering classes of phosphatases that target substrates, but that too has severe limitations. Here, we describe a method that enriches phosphorylated substrates using TiO2 and phospho-tyrosine antibodies in phosphatase knockout lines of Arabidopsis thaliana. When compared to wild-type plants, this approach permits identification of putative substrates and specific phosphorylation sites by mass spectrometry, allowing for further in vitro or functional validation. The key to the approach described here is the use of phosphatase knockout lines to maintain substrates in a phosphorylated state and using phospho-tyrosine antibodies to enrich for tyrosine phosphorylated peptides.
Stem Cell
Generation of Budoids: 3D Multilineage Limb Models From Mouse Embryonic Stem Cells
Limb development requires the coordination of multiple cell types, including the limb bud mesoderm and surface ectoderm, by the apical ectodermal ridge (AER), a specialized signaling center secreting numerous morphogens. Characterizing these cell–cell interactions is crucial for understanding limb morphogenesis, but they are challenging to study in vivo. Furthermore, existing in vitro models do not capture the multilineage complexity of the limb. We recently developed a robust 7-day differentiation protocol using mouse embryonic stem cells (mESCs) to generate heterogeneous cultures containing cells with characteristics of the limb bud mesoderm, surface ectoderm, and AER. Dissociating and reaggregating these cultures in low attachment 96-well plates forms budoids, organoids that display certain limb bud–like features. Budoids undergo chondrogenesis-mediated symmetry breaking and elongation within 5 days of culture. Altogether, our protocols have enabled the study of cell–cell interactions in limb development and provide an easily scalable model adaptable for various applications, including drug testing and congenital disorder modeling.
