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Past Issue in 2025
Volume: 15, Issue: 10
Bioinformatics and Computational Biology
From Bedside to Desktop: A Data Protocol for Normative Intracranial EEG and Abnormality Mapping
Normative mapping is a framework used to map population-level features of health-related variables. It is widely used in neuroscience research, but the literature lacks established protocols in modalities that do not support healthy control measurements, such as intracranial electroencephalograms (icEEG). An icEEG normative map would allow researchers to learn about population-level brain activity and enable the comparison of individual data against these norms to identify abnormalities. Currently, no standardised guide exists for transforming clinical data into a normative, regional icEEG map. Papers often cite different software and numerous articles to summarise the lengthy method, making it laborious for other researchers to understand or apply the process. Our protocol seeks to fill this gap by providing a dataflow guide and key decision points that summarise existing methods. This protocol was heavily used in published works from our own lab (twelve peer-reviewed journal publications). Briefly, we take as input the icEEG recordings and neuroimaging data from people with epilepsy who are undergoing evaluation for resective surgery. As final outputs, we obtain a normative icEEG map, comprising signal properties localised to brain regions. Optionally, we can also process new subjects through the same pipeline and obtain their z-scores (or centiles) in each brain region for abnormality detection and localisation. To date, a single, cohesive dataflow pipeline for generating normative icEEG maps, along with abnormality mapping, has not been created. We envisage that this dataflow guide will not only increase understanding and application of normative mapping methods but will also improve the consistency and quality of studies in the field.
Cancer Biology
Stable 13C-glutamine Tracing Resolved Metabolomics for Cancer Metabolism Study
Stable isotopes have frequently been used to study metabolic processes in live cells both in vitro and in vivo. Glutamine, the most abundant amino acid in human blood, plays multiple roles in cellular metabolism by contributing to the production of nucleotides, lipids, glutathione, and other amino acids. It also supports energy production via anaplerosis of tricarboxylic acid cycle intermediates. While 13C-glutamine has been extensively employed to study glutamine metabolism in various cell types, detailed analyses of specific lipids derived from 13C-glutamine via the reductive carboxylation pathway are limited. In this protocol, we present a detailed procedure to investigate glutamine metabolism in human glioblastoma (GBM) cells by conducting 13C-glutamine tracing coupled with untargeted metabolomics analysis using liquid chromatography–mass spectrometry (LC–MS/MS). The method includes step-by-step instructions for the extraction and detection of polar metabolites and long-chain fatty acids (LCFAs) derived from 13C-glutamine in GBM cells. Notably, this approach enables the distinction between isomers of two monounsaturated FAs with identical masses: palmitoleic acid (16:1n-7) (cis-9-hexadecenoic acid) and palmitelaidic acid (16:1n-7) (trans-9-hexadecenoic acid) derived from 13C-glutamine through the reductive carboxylation process. In addition, using this protocol, we also unveil previously unknown metabolic alterations in GBM cells following lysosome inhibition by the antipsychotic drug pimozide.
Cell Biology
Development of Polyethylene Glycol Diacrylate-Based Micropattern Substrate to Study the Interplay Between Surface Topography and Cellular Response for Tissue Engineering Applications
A key goal in the bioengineering field is the development of surface patterning of proteins that guide and control cellular organization. To this end, we developed a method to create a microstructured hydrogel based on soft-lithography techniques using polydimethylsiloxane (PDMS) and polyethylene glycol diacrylate (PEGDA). This approach involves the design of microfluidic geometries using graphical software, employing PDMS as a mold and leaving PEGDA as a substrate for the fabrication of microstructures and, thus, patterning extracellular matrix (ECM) proteins to promote cell adhesion. The combination of these techniques allows the fabrication of hydrogel microstructures without following conventional photolithography methods, such as the use of a photomask, the alignment required to produce the patterns, and the associated expenses. This study highlights the versatility and potential of PEGDA-based hydrogels as platforms to advance tissue engineering strategies.
Developmental Biology
Egg Microinjection for the Silkworm Bombyx mori
The silkworm Bombyx mori has been extensively utilized in sericulture and serves as a representative model insect of Lepidoptera in various fields of life sciences and applied research. In recent years, its significance has further increased in molecular genetics and functional genomics. Germline transformation and genome editing in B. mori require the injection of vector solutions into early embryos; however, the thick eggshell of B. mori presents a significant challenge for microinjection. Conventional methods involve arranging eggs, pre-pierced with a tungsten needle, followed by solution injection, making the process both time-consuming and technically demanding. Here, we describe a simplified and more efficient microinjection protocol. Unlike conventional approaches, our method eliminates the need for egg removal from the egg-laying sheet and egg alignment on the slide glass by allowing injections to be performed directly on eggs retained on the egg-laying sheet. A thick-walled glass capillary, capable of penetrating the rigid eggshell, is used to directly pierce the eggshell and deliver the solution. By eliminating the need for egg alignment and micromanipulator operation, this protocol significantly enhances efficiency, enabling higher-throughput embryo injections within a shorter time frame. Moreover, this approach holds potential for application to other insect species with similarly thick eggshells.
Immunology
PBMC-Humanized Mouse Model for Multiple Sclerosis: Studying Immune Changes and CNS Involvement
Humanized immune system (HIS) mice are powerful tools for studying human immune system function and dysfunction and developing human-specific immunotherapeutics. The availability of sophisticated super immunodeficient mouse strains has allowed immune system humanization using transplants of human peripheral blood mononuclear cells (PBMC) or hematopoietic stem cells. HIS mice are used extensively in immune-oncology, while there are fewer studies in autoimmunity, especially multiple sclerosis (MS). Using the protocol described here, we generated HIS mice that show key features of MS not represented in other widely used MS models [1]. Severely immunodeficient NOD.Cg-B2mem1Tac Prkdcscid Il2rgtm1Sug/JicTac (B2m-NOG) mice, which lack murine B, T, and NK cells and murine major histocompatibility class I molecules and have defective innate immune responses, were transplanted with PBMC from HLA-DRB1-genotyped MS patients and healthy donors. Mice were successfully engrafted with hCD4 and hCD8 T and B lymphocytes and developed both spontaneous and experimental autoimmune encephalomyelitis (EAE)-enhanced T-cell lesions in the central nervous system. B-cell engraftment was highest in mice receiving cells from MS patients with serological evidence for Epstein–Barr virus (EBV) reactivation. This humanized MS model shows advantages over EAE, particularly spontaneous hCD8 T-cell lesions in the brain and spinal cord, mixed hCD8/hCD4 T-cell lesions in EAE-immunized mice, and more severe lesions in mice engrafted with PBMC from MS donors carrying the DRB1*15 MS susceptibility allele compared to DRB1*15-positive healthy and DRB1*13-positive MS donors. MS HIS mice represent simple and rapid tools for investigating human immunopathology and the efficacy of therapeutics at a personalized level.
Tracking Oral Nanoparticle Uptake in Mouse Gastrointestinal Tract by Fluorescent Labeling and t-SNE Flow Cytometry
The growing demand for advanced analytical techniques to explore complex cellular targets of nanotherapeutics has driven the development of innovative methodologies. This protocol presents a refined approach for fluorescent labeling and flow cytometric analysis of colonic cells following oral lipid nanoparticle (LNP) treatment, focusing on LNP uptake in colonic cell subpopulations in a DSS-induced colitis mouse model. By integrating optimized fluorochrome selection and gating strategies with advanced t-distributed stochastic neighbor embedding (t-SNE) analysis, this method enables precise identification and multidimensional visualization of LNP-targeted epithelial and macrophage populations under the complex conditions of inflamed colon tissue. Building on our previous studies demonstrating the effectiveness of nanoparticles in targeted drug delivery, this approach highlights the utility of flow cytometry for assessing uptake efficiency and cellular targeting. Unlike conventional protocols, it incorporates t-SNE for enhanced multidimensional analysis, allowing for the detection of subtle cellular patterns and the delineation of intricate clusters. By addressing gaps in traditional methodologies, this protocol provides a robust and reproducible framework for investigating in vivo cellular targets and optimizing drug delivery strategies for nanomedicines.
Medicine
Quantifying Thrombogenicity: A Bioanalytical Protocol for the Absorbance-Based Assessment of Vascular Implants with Plasma
Assessing thrombogenicity is crucial for evaluating biomaterials, especially those that interface with flowing blood, such as cardiovascular implants, including vascular stents, grafts, and stent-grafts. To standardize thrombogenicity assessments, we use human plasma and quantify the light absorbance associated with the biomaterial. For this evaluation, various tubular vascular implants from leading brands—such as bare-metal stents, drug-eluting stents, vascular grafts, and stent-grafts—are longitudinally sectioned into small pieces and placed in a low-adhesion 96-well plate. Using either platelet-rich plasma (PRP) or platelet-poor plasma (PPP), we measure the absorbance of light passing through the plate over an hour and plot the resulting curve. This method quantifies the thrombogenicity of a biomaterial under controlled conditions. Key factors examined include anticoagulants, platelet presence, and surface-coating molecules to assess their impact on thrombogenicity. Using this simple, reproducible protocol, we demonstrated (a) the relative efficacy of various anticoagulants in thrombogenicity assessments, and (b) the effectiveness of vascular coating molecules in reducing thrombogenicity on stents. This streamlined approach offers valuable insights for optimizing biomaterial performance in vascular implants. Unlike conventional clotting assays, which focus on standardized blood clotting mechanisms, this assay is tailored to evaluate biomaterials and external parameters influencing thrombogenicity.
Microbiology
I-PREFR: Inverse PCR-Based Restriction Enzyme FRee Unidirectional Strategy for Rapid Markerless Chromosomal Gene Deletion and Reconstitution in Bacteria Using Suicide Vectors
The standard protocols for allelic exchange using homologous recombination deploy suicide vectors with negative selection markers. However, the use of multiple restriction enzymes to generate sticky ends in the vector and the insert for cloning is time-consuming, resource-intensive, and challenging. The advent of next-generation proofreading enzymes is enabling researchers to routinely carry out long-range PCR. Hence, amplifying 5–6 kb of complete low-complex DNA cloning vectors and 2–3 kb of complex genomic regions is much easier. Here, we report a simple, accurate, rapid, and unidirectional approach for chromosomal in-frame gene deletion and complementation by reconstitution of the full-length gene without using any restriction enzymes. The method requires long-range PCR using Phusion polymerase to linearize the vector and amplify the target gene to create a recombinant vector (pRM1) and further inverse PCR amplification of pRM1 to create a recombinant vector (pRM4) with a deleted version of the gene. The cloning steps involve the use of kinase and ligase for phosphorylation and ligation steps, respectively. The recombinant plasmid, pRM4, is finally transformed into electrocompetent cells of Xanthomonas sontii, a gram-negative phytobacterium, for final genomic integration/excision to obtain an in-frame gene deletion mutant (PPL1RM15). Gene reconstitution for complementation is carried out by electroporating the deletion mutant with the recombinant plasmid (pRM1) carrying the wild-type allele. Clean gene mutation, allele restoration, and plasmid excision are confirmed using whole-genome sequencing.
Synchronized Visualization and Analysis of Intracellular Trafficking and Maturation of Orthoflavivirus Subviral Particles
Orthoflavivirus is an enveloped, positive-stranded RNA virus that buds into the endoplasmic reticulum (ER) lumen. The budded virus particles are subsequently transported to the Golgi apparatus and secreted into the extracellular environment via the conventional secretion pathway. In this protocol, we describe a method for monitoring the secretion of Orthoflavivirus particles from the ER. To visualize intracellular membrane trafficking, we combine two distinct imaging techniques: the retention using selective hooks (RUSH) system and the split green fluorescent protein (GFP) system. In this approach, GFP11, a peptide tag fused to prME, the outer coat structural protein of Japanese encephalitis virus particles, was co-expressed in HeLa cells along with two additional components: GFP1-10 fused to a streptavidin-binding peptide and a hook construct consisting of streptavidin fused to the ER retention sequence KDEL. Time-lapse imaging was performed after the addition of biotin, which releases the captured GFP-labeled subviral particles from the ER. This method enables synchronized visualization of intracellular subviral particle trafficking and serves as a valuable tool for analyzing the maturation process of Orthoflavivirus particles within cells.
Mycobacterium smegmatis Ribosome Purification, Co-sedimentation, and Subunit Association Assay
The ribosome, a complex macromolecular machine, plays a vital role in cellular translation. To investigate its structure and conduct in vitro experiments, isolating the ribosomes from cells is the first step. While isolating ribosomes from bacterial cells is routine, obtaining them from mycobacteria proves challenging due to the protective mycolic acid layer, which hinders cell lysis. In this study, we present a straightforward and efficient protocol for isolating ribosomes from Mycobacterium smegmatis. Additionally, we introduce a co-sedimentation assay using density gradient ultracentrifugation, providing a simple yet powerful method for studying ribosome–protein interactions. The re-association assay also offers a practical approach for obtaining tRNA-free 70S ribosomes and evaluating the anti-association properties of potential ligands. While these assays are commonly used, our protocol stands out for its simplicity, requiring limited specialized instruments. These methods can also be scaled up or down per requirement. By employing sonication for cell rupture and utilizing basic lab equipment for ultracentrifugation-based assays, our method greatly simplifies ribosome isolation and related research.
Molecular Biology
RNA PolyA Tailing Assay to Qualitatively Analyze Circular RNA Manufacturing
A covalently closed loop structure provides circular RNA (circRNA) with more stability than conventional RNAs in linear form, making circRNA an emerging tool in RNA therapeutics. The qualification and quantification of circRNA after production is critical for its design and effectiveness assessments, particularly when the following applications could be affected by byproduct RNAs. Despite PCR-based methods effectively detecting low-abundance circRNA, they are unsuitable for assessing uncircularized RNA in a mass production fraction to maintain quality control. Here, we present a straightforward protocol for evaluating uncircularized byproduct RNAs from circRNA production. This method enrolls the template-independent RNA polymerase activity to add adenine tails (polyA) to the 3' ends of a linear RNA, making it easy to distinguish trace byproducts or uncircularized RNA from a pool of mass circRNA products. With conventional linear RNA and RNase R-treated circRNA as the positive and negative controls, the purity of a circRNA preparation could be readily resolved. Regardless of circRNA production strategies, this protocol provides a reliable and practical way to ensure the consistent quality of homemade circRNAs or to recheck circRNA quality from commercial manufacturing.
Neuroscience
Dissection and Whole-Mount Immunofluorescent Staining of Mouse Hind Paw Muscles for Neuromuscular Junction Analysis
The neuromuscular junction (NMJ) is a peripheral synaptic connection between a lower motor neuron and skeletal muscle fibre that enables muscle contraction in response to neuronal stimulation. NMJ dysfunction and morphological abnormalities are commonly observed in neurological conditions, including amyotrophic lateral sclerosis, Charcot–Marie–Tooth disease, and spinal muscular atrophy. Employing precise and reproducible techniques to visualise NMJs in mouse models of neuromuscular disorders is crucial for uncovering aspects of neuropathology, revealing disease mechanisms, and evaluating therapeutic approaches. Here, we present a method for dissecting the deep lumbrical and flexor digitorum brevis (FDB) muscles of the mouse hind paw and describe the process of whole-mount immunofluorescent staining for morphological analysis of NMJs. Similar whole-mount techniques have been applied to other muscles, such as the diaphragm; however, dense connective tissue in adult samples often impedes antibody penetration. Moreover, large hind limb muscles, including the gastrocnemius and tibialis anterior, are commonly used to examine NMJs but require embedding and cryosectioning. These additional steps increase the complexity and duration of the protocol and can introduce sectioning artefacts, including transection of NMJs and disruption of morphology. Using small hind paw muscles enables whole-mounting, which completely eliminates the requirement for embedding and cryosectioning. As a result, the entire neuromuscular innervation pattern can be visualised, allowing a more accurate assessment of NMJ development, denervation, and regeneration in mouse models of neurological disease and nerve injury, which can be applied across all postnatal ages.
Electrophysiological Evaluation of a Sciatic Nerve Degree III Injury Model in Rats
Sciatic nerve injury is a prevalent traumatic condition that significantly impacts a patient's quality of life. The sciatic nerve compression injury model is among the most commonly utilized models for investigating nerve repair and regeneration. Within this context, the degree III sciatic nerve injury model is frequently employed in scientific research due to its clinical relevance and its suitability for studies focused on functional recovery. However, a standardized approach for accurately assessing the success of constructing the degree III sciatic nerve injury model remains lacking. Traditional macroscopic observation methods exhibit limitations, whereas neurophysiological testing serves as a highly sensitive and objective evaluation technique that can directly reflect changes in nerve conduction function, thus providing reliable quantitative evidence for the successful establishment of the model. This study aims to offer a comprehensive description of the application of neurophysiological techniques in evaluating the construction of the degree III sciatic nerve injury model, thereby ensuring the success of model preparation.
Plant Science
Rapid Miniprep of Intact Chloroplasts from Arabidopsis thaliana Leaves
Cell subfractionation is a common technique employed in many research laboratories to isolate organelles or intracellular compartments for the study of metabolism or biomolecule purification. While numerous protocols exist for isolating organelles, few are specifically designed for starting materials in the milligram range. Here, we present a detailed milligram-scale miniprep protocol for purifying intact chloroplasts from Arabidopsis thaliana leaves. This chloroplast miniprep procedure is suitable for applications such as confocal microscopy, western blotting, enzymatic assays, and other downstream analyses.
High-Throughput Screening Identification of Chemical Compounds That Affect Cold-Regulated Gene Expression in Arabidopsis thaliana Using an Excised Single Leaf
The identification of chemical compounds that affect intracellular processes has greatly contributed to the understanding of developmental regulation in plants. In this protocol, we describe a method for identifying chemical compounds that affect cold-regulated gene expression in Arabidopsis thaliana. Specifically, we generated Arabidopsis plants harboring a COLD-REGULATED 15A (COR15A) promoter::luciferase (COR15Apro::LUC) construct and grew them in a submerged liquid culture. Using a single true leaf excised from COR15Apro::LUC plants and 96-well culture plates, we performed high-throughput screening of chemical compounds that inhibit cold-induction of COR15Apro::LUC. Luciferase activity was detected using a microplate reader and a chemiluminescence imaging device. This protocol can be easily used for the identification of chemical compounds that regulate other processes, being versatile with respect to equipment.