Methods and Protocols

The initial molecular events mediating mammalian sperm binding to the zona pellucida (ZP) of the oocyte are highly complex and still not fully elucidated. Recent advances have identified multiple candidate sperm surface proteins, often functioning as part of high-molecular-weight complexes that mediate this critical fertilization event in a species-specific and coordinated manner. To address a significant gap in the literature, we provide an in-depth overview of the functional assays employed to investigate sperm–ZP interactions, emphasizing their underlying principles, potential applications, and key methodological strengths and limitations. The techniques discussed range from classical in vitro sperm–oocyte and hemizona binding assays, including antibody-blocking and competitive strategies, to cutting-edge in vivo genetic models, each contributing unique insights into the physiological relevance of the proposed ZP receptors. Robust experimental design, including the use of appropriate controls and validation strategies, is essential for accurately interpreting the role of candidate sperm receptors. This review provides a structured overview of current methodologies to support researchers in critically evaluating and applying functional assays in future studies. Full article

Data on the genetic and environmental factors underlying the co-occurrence of Cognitive Disengagement Syndrome (CDS), Attention Deficit Hyperactivity Disorder (ADHD), and Emotional Dysregulation (ED) are limited. This study aimed to explore the nature of the associations between CDS, ADHD with ED, and to assess the role of shared etiological factors in explaining their comorbidity. We analyzed a sample of 400 Italian twin pairs aged 8–18, from Northern Italy and enrolled in the Italian Twin Registry. Bivariate genetic analyses were conducted using parent-rated CBCL scores for CDS, ADHD, and ED. For both CDS–ED and ADHD–ED associations, the best-fitting models were Cholesky AE models (−2LL = −849.167 and −339.030, respectively; p > 0.05), suggesting that the covariation was mainly due to additive genetic factors (CDS–ED—A = 0.81, 95% CI [0.66–0.95]; ADHD–ED—A = 0.86, 95% CI [0.75–0.95]). More than half of the genes were shown to be shared among the phenotypes. Non-shared environmental contributions were smaller (CDS–ED—E = 0.19, 95% CI [0.05–0.34]; ADHD–ED—E = 0.14, 95% CI [0.05–0.25]), indicating interrelated but distinct constructs. Despite some limitations, particularly the exclusive use of the CBCL, findings highlight the importance of monitoring ED symptoms in individuals with CDS or ADHD, and vice versa. Full article

Background: Accurate assessment of drug cytotoxicity in vitro is essential for preclinical evaluation of anticancer agents. Methodological parameters such as cell density and solvent concentrations can significantly influence the reproducibility and reliability of cell-based assay results. Objective: This study aims to optimize cell seeding density and evaluate the cytotoxic effects of common solvents (DMSO and ethanol) on different cancer cell lines, complemented by in silico analysis to elucidate underlying mechanisms. Materials and Methods: Six cancer cell lines (HepG2, Huh7, HT29, SW480, MCF-7, and MDA-MB-231) were seeded at different densities to determine the optimal cell seeding number ideal for cell viability assay at 24, 48, and 72 h. The cytotoxicity of DMSO and ethanol was assessed in these cell lines using an MTT assay at multiple time points. In silico docking studies were conducted to investigate the interactions between solvents and key proteins involved in apoptosis, membrane function, and metabolism. Results: A cell density of 2000 cells per well yielded consistent linear viability across cell lines and time points. DMSO at 0.3125% showed minimal cytotoxicity across all cell lines (except MCF-7) and time points; the cytotoxic effect at higher concentrations is variable depending on cell type and exposure duration. Ethanol exhibited rapid and concentration-dependent cytotoxicity, reducing viability by more than 30% at as low as 0.3125% concentration after 24 h. Docking analyses revealed that DMSO binds specifically to apoptotic and membrane proteins, suggesting a role in inducing apoptosis. In contrast, ethanol primarily interacts with metabolic proteins, consistent with its effect on membrane disruption and rapid cell death. Conclusion: DMSO at 0.3125% is a good choice as a solvent since it has low toxicity in most tested cell lines; however, the safe concentration limit is dependent on cell type and exposure duration. Ethanol exhibited higher cytotoxicity, necessitating careful concentration management. The in silico analysis supports these findings, indicating that DMSO interacts with apoptosis-related proteins, whereas ethanol primarily affects metabolic processes. These results highlight the importance of precise cell density optimization and solvents for reliable cytotoxicity assessment in cell-based assays. Full article

This protocol paper outlines a robust and reproducible framework for a ¹H nuclear magnetic resonance (NMR) metabolomics analysis of rodent plasma, designed to facilitate preclinical biomarker discovery. The protocol details optimised steps for plasma collection in a preclinical rodent model, sample preparation, and NMR data acquisition using presaturation Carr–Purcell–Meiboom–Gill (PRESAT-CPMG) pulse sequences, ensuring high-quality spectral data and effective suppression of macromolecule signals. Comprehensive spectral processing and metabolite assignment are described, with guidance on multivariate and univariate statistical analyses to identify metabolic changes and potential biomarkers. The framework emphasises methodological rigour and reproducibility, enabling accurate quantification and interpretation of metabolites relevant to disease mechanisms or therapeutic interventions. By providing a standardised approach, this protocol supports longitudinal and translational studies, bridging findings from rodent models to clinical applications and advancing the reliability of metabolomics-based biomarker discovery in preclinical research. Full article

In vitro cartilage explant culture has been used to assess nutraceuticals on cartilage responses to inflammatory stimuli. However, applying extracts of nutraceuticals directly to cartilage explants does not account for effects of digestion and hepatic biotransformation, or selective exclusion of product metabolites from joint fluid by the synovial membrane. The current study produced a simulated biological extract of a common nutraceutical (glucosamine; G_sim) by exposing it to a simulated upper gastrointestinal tract digestion, hepatic biotransformation by liver microsomes, and purification to a molecular weight cut-off of 50 kDa. This extract was then used to condition cartilage explants cultured for 120 h in the presence or absence of an inflammatory stimulus (lipopolysaccharide). Media samples were analyzed for prostaglandin E₂ (PGE₂), glycosaminoglycan (GAG), and nitric oxide (NO). Tissue was digested and analyzed for GAG content and stained for viability. Conditioning of explants with G_sim significantly reduced media GAG in stimulated and unstimulated explants and reduced nitric oxide production in unstimulated explants. These data provide evidence for the value of glucosamine in protecting cartilage from deterioration following an inflammatory challenge, and the model improves applicability of these in vitro data to the in vivo setting. Full article

Serial block-face scanning electron microscopy (SBEM) is a powerful technique for three-dimensional ultrastructural analysis of biological samples, though its application to in vitro cultured human cells remains underutilized. In this study, we present an optimized SBEM sample preparation protocol using human dermal fibroblasts and induced pluripotent stem cells (iPSCs). The method includes key modifications to the original protocol, such as using only glutaraldehyde for fixation and substituting the toxic cacodylate buffer with a less hazardous phosphate buffer. These adaptations result in excellent preservation of cellular ultrastructure, with high contrast and clarity, as validated by transmission electron microscopy (TEM). The loss of natural cell morphology resulted from fixation during passage, when cells formed a precipitate, rather than from fixation directly within the culture medium. The protocol is time-efficient, safe, and broadly applicable to both stem cells and differentiated cells cultured under 2D conditions, providing a valuable tool for ultrastructural analysis in diverse biomedical research settings. Full article

The expression of recombinant proteins in heterologous hosts is a common strategy to obtain larger quantities of the “protein of interest” (POI) for scientific, therapeutic or commercial purposes. However, the experimental success of such an approach critically depends on the choice of an appropriate host system to obtain biologically active forms of the POI. The correct folding of the molecule, mediated by disulfide bond formation, is one of the most critical steps in that process. Here we describe the recombinant expression of hirudin, a leech-derived anticoagulant and thrombin inhibitor, in the yeast Komagataella phaffii (formerly known and mentioned throughout this publication as Pichia pastoris) and in two different strains of Escherichia coli, one of them being especially designed for improved disulfide bond formation through expression of a protein disulfide isomerase. Cultivation of the heterologous hosts and expression of hirudin were performed at different temperatures, ranging from 22 to 42 °C for the bacterial strains and from 20 to 30 °C for the yeast strain, respectively. The thrombin-inhibitory potencies of all hirudin preparations were determined using the thrombin time coagulation assay. To our surprise, the hirudin preparations of P. pastoris were considerably less potent as thrombin inhibitors than the respective preparations of both E. coli strains, indicating that a eukaryotic background is not per se a better choice for the expression of a biologically active eukaryotic protein. The hirudin preparations of both E. coli strains exhibited comparable high thrombin-inhibitory potencies when the strains were cultivated at their respective optimal temperatures, whereas lower or higher cultivation temperatures reduced the inhibitory potencies. Full article

In establishing the safety or tolerability profile of bioactive plant extracts, it is important to perform toxicity studies using appropriate, accessible, and sustainable methods. The Allium cepa model is well known and frequently used for accurate environmental risk assessments, as well as for evaluating the toxic potential of the bioactive compounds of plant extracts. The present review focuses on this in vivo cytogenetic model, highlighting its widespread utilization and advantages as a first assessment in monitoring the genotoxicity and cytotoxicity of herbal extracts, avoiding the use of animals for testing. This plant-based assay allows for the detection of the possible cytotoxic and genotoxic effects induced on onion meristematic cells. The outcomes of the Allium cepa assay are comparable to other tests on various organisms, making it a reliable screening test due to its simplicity in terms of implementation, as well as its high sensitivity and reproducibility. Full article

Mitochondria play a crucial role in adapting to fluctuating energy demands, particularly in various heart diseases. In addition to functional analyses such as the measurement of ROS or ATP, analysis of mitochondrial ultrastructure can be used to draw further conclusions about their functions and effects in tissue. In this protocol, we introduce a set of measurements to compare the ultrastructural and functional characteristics of human left ventricular mitochondria, using transmission electron microscopy (TEM). Measured parameters included mean size in µm², elongation, count, percental mitochondrial area in the measuring frame, and a conglomeration score. We also introduce a novel method of defining hydropic mitochondria as a comparable evaluation standard. With this cluster of measurement parameters, we aim to contribute a protocol for studying human mitochondrial morphology, distribution, and functionality. Full article

Erythrocyte (RBC) aging involves significant structural and nanomechanical alterations crucial to their function. This study aims to bridge the gap between analyses based on statistical morphometric parameters, e.g., membrane roughness, and those based on point-dependent nanomechanical properties, e.g., stiffness or Young’s modulus. Using Atomic Force Microscopy, we investigated morphology, membrane roughness, and nanomechanical properties on the very same RBCs under dehydrated (air) and hydrated (physiological buffer) conditions. The cells were studied at different stages of in vitro aging: one, seven, and 12 days. Our results quantitatively show that across dehydration, as well as along the aging pathway, RBCs become progressively more rigid while their membrane roughness decreases, a trend observed in both environments. Notably, the differences between the hydrated and dehydrated states were large in young cells but diminished when erythrocytes aged. Despite these parallel trends, high-resolution mapping on the nanoscale revealed that roughness and Young’s modulus do not correlate, indicating that these parameters are linked to different properties. In conclusion, this work provides a comprehensive protocol for a biophysical description of RBC aging and establishes that the simultaneous measurement of membrane roughness and nanomechanical properties offers a complementary approach, yielding a more complete characterization of cellular properties. Full article

Vitamin D is the only vitamin that is conditionally essential, as it is synthesized from precursors after UV light exposure, whilst also being obtained from the diet. It has numerous health benefits, with deficiency becoming a major concern globally, such that dietary supplementation has more recently achieved vital importance to maintain satisfactory levels. In recent years, measurements made from blood have, therefore, become critical to determine the status of vitamin D levels in individuals and the larger population. Tests for vitamin D have routinely relied on laboratory analysis with sophisticated equipment, often being slow and costly, whilst rapid immunoassays have suffered from poor specificity and sensitivity. Here, we have evaluated a new rapid immunoassay test on the market (Rapi-D & IgLoo) to quickly and accurately measure vitamin D levels in small capillary blood specimens and compared this to measurements made using the standard laboratory method of liquid chromatography and mass spectrometry. Our results show that vitamin D can be measured very quickly and over a broad range using the new method, as well as correlate relatively well with standard laboratory testing; however, it cannot be fully relied upon currently to accurately diagnose deficiency or sufficiency in individuals. Our statistical and comparative analyses find that the rapid immunoassay with digital quantification significantly overestimates vitamin D levels, leading to diminished diagnosis of vitamin D deficiency. The speed and simplicity of the rapid method will likely provide advantages in various healthcare settings; however, further calibration of this rapid method and testing parameters for improving quantification of vitamin D from capillary blood specimens is required before integration of it into clinical decision-making pathways. Full article

Air pollution is linked to childhood mortality and morbidity in low- and middle-income countries globally. There is growing evidence linking air pollution to asthma and other respiratory diseases in children. Studies have shown that children are likely to experience asthma due to their narrow airways and their heightened sensitivity to environmental irritants. This study aims to investigate the relationship between ambient air pollution and respiratory diseases in children under the age of 5. The study will be conducted in the informal township of Alexandra, north of Johannesburg, South Africa. A quantitative approach will be used in this cross-sectional analytical study. Data will be collected using different tools that include a questionnaire to determine the prevalence of asthma and respiratory disease and potential risk factors. While environmental air pollution will be measured using Radiello passive samplers and Gillian pumps. Data will be analyzed using the latest version of the STATANow/MP 19.5 software. Furthermore, health risk assessment will be conducted for lifetime non-carcinogenic and carcinogenic risk estimation following the USEPA framework. The study will identify environmental triggers that exacerbate asthma and other respiratory conditions in other similar community settings and will contribute to the body of knowledge in public health. Ethical approval was obtained from the Research Ethics Committee, Faculty of Health Sciences at the University of Johannesburg. Full article

Faecal microbiota transplantation (FMT) is an emerging therapy for gastrointestinal and neurological disorders, acting via the microbiota–gut–brain axis. Altering gut microbial composition may influence cognitive function, but this has not been tested in cognitively healthy adults. This randomised, double-blinded, placebo-controlled pilot trial investigates whether FMT is feasible and improves cognition in adults with irritable bowel syndrome (IBS). Participants receive a single dose of FMT or placebo via rectal retention enema. Cognitive performance is the primary outcome, assessed using the Cambridge Neuropsychological Test Automated Battery (CANTAB). Secondary outcomes include IBS symptom severity and mood. Tertiary outcomes include microbiome composition and plasma biomarkers related to inflammation, short-chain fatty acids, and tryptophan metabolism. Outcomes are assessed at baseline and at one, three, six, and twelve months following treatment. We hypothesise that FMT will lead to greater improvements in cognitive performance than placebo, with benefits extending beyond practice effects, emerging at one month and persisting in the long term. The findings will contribute to evaluating the safety and efficacy of FMT and enhance our understanding of gut–brain interactions. Full article

Phenolic compounds are secondary metabolites widely distributed among plants, with bioactive properties, especially antioxidant activity. The search for sustainable extraction methods has driven the use of natural deep eutectic solvents (NaDESs), formed by combinations of natural compounds, such as organic acids, sugars, alcohols, and amino acids. This study optimized NaDES (sorbitol, citric acid, and glycine) efficiency and compared it to that of 70% methanol solution in extracting total soluble phenolic compounds (TSPCs) from six flours matrices—corn, buckwheat, biofortified orange sweet potato, red lentil, Sudan grass, and chickpea—before and after thermoplastic extrusion cooking. Quantification was performed using the Folin–Ciocalteu method, with statistical analysis at the 10% significance level. In general, the methanolic extracts showed higher TSPC levels in the raw materials, whereas the levels were higher in NaDESs for legumes. After extrusion, a reduction in the TSPC levels was observed, except in the sweet potato. Multivariate analysis (PLS-DA and heatmap) distinguished the raw and extruded samples, revealing structural and chemical changes from thermal processing. The AGREE scores were 0.7 (NaDES) and 0.54 (methanol), favoring NaDES. The BAGI score (75.0) confirmed the method’s robustness and suitability for sustainable analytical applications. Full article

Every year, diarrhoea is responsible for >1 million deaths in children with ages from 0 to 5 years, with rotavirus as the leading cause. The regions most affected lack routine rotavirus diagnosis due to high cost, lack of necessary equipment and shortage of trained-personnel for Enzyme-Link-Immunosorbent-Assay (ELISA) and molecular methods. We report the development and evaluation of a cheap, nanoparticle-based immunoassay for routine machine-free rotavirus diagnosis. In this work, optimal conditions for oxidation of cotton swabs and aldehyde production for kit development was confirmed by Fourier-Transform Infrared Spectroscopy (FTIR). Lactoferrin (LF) needed to bind the virus to the cotton swab was immobilised on activated cotton swabs, followed by the capture of commercial rotavirus antigen on LF-immobilised swabs. This was dipped in coloured nanobeads covalently coupled to rotavirus-group-specific monoclonal antibody for visual rotavirus detection. Subsequently, rotavirus detection by nanoassay, commercial ELISA and quantitative reverse transcription PCR were compared using same set of 186 stool samples and subjected to statistical analyses. Optimal oxidisation condition was observed using 48 mg/mL NaIO₄ in 0.1 M sodium acetate buffer at 35 °C for 9 h. Rotavirus detection was confirmed visually by blue colour retention on swabs after several washings. Sensitivity, specificity, positive-predictive-value and negative-predictive-value of ELISA in rotavirus detection were 60%, 84%, 53% and 88%, respectively, while our immunoassay showed performance at 88%, 94%, 82% and 96%. This immunoassay will provide effective rotavirus public health interventions in low-and-middle-income countries with high morbidity/mortality. Full article

Bats, as key ecological players, interact with a diverse array of organisms and perform essential roles in ecosystems, including pollination, pest control, and seed dispersal. However, their populations face significant threats from habitat contamination, particularly from microplastics (MPs). This study introduces a novel, efficient, and cost-effective method for visualizing transparent microplastics using ultraviolet (UV) light. By employing handheld UV flashlights with a wavelength range of 312 to 400 nm, we enhance the detection of MPs that may otherwise go unnoticed due to color overlap with filtration membranes. All necessary precautions were taken during sampling and analysis to minimize the risk of contamination and ensure the reliability of the results. Our findings demonstrate that the application of UV light significantly improves the visualization and identification of MPs, particularly transparent fibers. This innovative approach contributes to our understanding of plastic contamination in bat habitats and underscores the importance of monitoring environmental pollutants to protect bat populations and maintain ecosystem health. Full article

Burn wounds present a significant challenge to both the medical and scientific communities, contributing to the global economic burden on healthcare systems. Due to the complexity and highly variability of burn injuries, along with intricate pathophysiological mechanisms, the development of appropriate and effective treatment strategies remains particularly demanding. The development of robust pre-clinical models that recapitulate specific molecular and cellular events underlying burn injury are essential to advance the understanding of associated biological mechanisms and facilitate the screening of innovative therapeutic interventions. While conventional in vivo models can replicate the key aspects of human burn wound pathology, they are often associated with ethical, logistical, and cost-related limitations. In this context, this study aims to explore the potential of the chicken chorioallantoic membrane (CAM) as an alternative model for burn wound research. Thus, we describe a reproducible and ethically favorable protocol for establishing standardized burn injuries on the CAM and provide a comprehensive evaluation of tissue responses through macroscopic, morphometric, and histological analyses. Our findings support the CAM as a viable pre-clinical platform for the study of burn wound healing and for the early-stage screening of candidate therapeutic agents. Full article

Fusarium spp. represent a critical threat to maize production and food safety due to their mycotoxin production. This study introduces a refined molecular identification protocol integrating four genomic regions—ITS1, IGS, TEF-1α, and β-TUB—for robust species differentiation of Fusarium spp. isolates from post-harvest maize in Bulgaria. The protocol enhances species resolution, especially for closely related taxa within the Fusarium fujikuroi species complex (FFSC). A newly optimized multiplex PCR strategy was developed using three primer sets, each designed to co-amplify a specific pair of toxigenic genes: fum6/fum8, tri5/tri6, and tri5/zea2. Although all five genes were analyzed, they were detected through separate two-target reactions, not in a single multiplex tube. Among 17 identified isolates, F. proliferatum (52.9%) dominated, followed by F. verticillioides, F. oxysporum, F. fujikuroi, and F. subglutinans. All isolates harbored at least one toxin biosynthesis gene, with 18% co-harboring genes for both fumonisins and zearalenone. This dual-protocol approach enhances diagnostic precision and supports targeted mycotoxin risk management strategies. Full article

Core stability is fundamental to posture, balance, and force transmission throughout the kinetic chain. Although traditionally associated with athletic performance, emerging research highlights its broader applicability to recreational fitness. This study investigates the effects of an eight-week core training program on muscle hypertrophy, static balance, and neuromuscular control in recreationally active, non-athletic adults. Participants will undertake a structured intervention comprising progressive triads targeting core stability, strength, and power. Assessment methods include surface electromyography (EMG), ultrasound imaging, three-dimensional force plates, Kinovea motion analysis, and the Satisfaction With Life Scale (SWLS) questionnaire. Expected outcomes include enhanced core muscle activation, improved static balance, and increased core-generated force during overhead medicine ball slam trials. Additionally, the intervention aims to facilitate hypertrophy of the transverse abdominis, internal oblique, and lumbar multifidus muscles, contributing to spinal resilience and motor control. This protocol bridges gaps in core training methodologies and advances their scalability for recreational populations. The proposed model offers a structured, evidence-informed framework for improving core activation, postural stability, muscle adaptation, movement efficiency, and perceived quality of life in recreationally active individuals. Full article