Journal Description
Methods and Protocols
Methods and Protocols
is an international, peer-reviewed, open access journal aiming to establish and describe new experimental techniques in the fields of Life Sciences, Chemistry, and Biomedical Sciences, published bimonthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), PubMed, PMC, CAPlus / SciFinder, and other databases.
- Journal Rank: CiteScore - Q2 (Biochemistry, Genetics and Molecular Biology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 22.6 days after submission; acceptance to publication is undertaken in 4.9 days (median values for papers published in this journal in the second half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.0 (2024);
5-Year Impact Factor:
2.2 (2024)
Latest Articles
Analytical Characterization of Pneumococcal Vaccine Conjugates Using SEC-MALS Technique
Methods Protoc. 2026, 9(2), 63; https://doi.org/10.3390/mps9020063 - 7 Apr 2026
Abstract
Background/Objectives: Infection from Streptococcus pneumoniae can lead to serious complications, such as meningitis and pneumonia, in children under 2 years of age, older adults, and immunocompromised populations. Conjugate vaccines against the pathogen have been licensed for the prevention of invasive pneumococcal disease. Conjugate
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Background/Objectives: Infection from Streptococcus pneumoniae can lead to serious complications, such as meningitis and pneumonia, in children under 2 years of age, older adults, and immunocompromised populations. Conjugate vaccines against the pathogen have been licensed for the prevention of invasive pneumococcal disease. Conjugate vaccine development is an involved process demanding extensive characterization of both the polysaccharide (PS) and protein (Pr) moieties in complex structures. One powerful tool in our analytical tool kit that can shed light on various analytical attributes of conjugate vaccines, such as molecular weight and composition and conjugation efficiency, is the size-exclusion chromatography-multi-angle light scattering detector (SEC-MALS) technique. Herein, we demonstrate the applicability of the SEC-MALS approach for pneumococcal conjugate vaccine product characterization. Methods: Capsular polysaccharides for serotypes (STs) 1, 3, 5, 10 A, 18 C, 24 F, and 33 F conjugated to rCRM197 carrier protein were chosen for this study. Results: The technique was very straightforward, with a high degree of accuracy (>90% based on standards) and repeatability (<2% RSD) for conjugate molar mass measurements. In addition, leveraging the capability of SEC-MALS for compositional analysis, we were able to get detailed information on the molecular assembly and conformation of the conjugates and further tweak the conjugation process to yield conjugates of a desired molar mass. Conclusions: Thus, this study highlights the usefulness of the SEC-MALS technique for in-depth conjugate vaccine biophysical characterization, which is critical for achieving optimal product attributes, driving manufacturing consistency and vaccine potency.
Full article
(This article belongs to the Collection Analytical Chemistry Methods and Protocols: From Standard Practices to New Sustainable Approaches)
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Open AccessArticle
Secondary Analysis to Evaluate Performance Expression Stability of Alternative Complex–Contrast Training Set Strategies
by
Liam J. Houlton, Jeremy A. Moody, Theodoros M. Bampouras and Joseph I. Esformes
Methods Protoc. 2026, 9(2), 62; https://doi.org/10.3390/mps9020062 - 3 Apr 2026
Abstract
This study aimed to evaluate the performance expression stability (PES) of sixteen alternative complex–contrast training (CCT) set strategies. Three separate cross-sectional studies (n = 14–17) evaluated the effects of different intra-contrast rest periods (ICRP; ≤300 s) and rest redistribution (RR) strategies (≤60
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This study aimed to evaluate the performance expression stability (PES) of sixteen alternative complex–contrast training (CCT) set strategies. Three separate cross-sectional studies (n = 14–17) evaluated the effects of different intra-contrast rest periods (ICRP; ≤300 s) and rest redistribution (RR) strategies (≤60 s) within CCT sets on the application of vertical jump propulsive force were examined using dual force platforms. To establish PES for propulsive force–time variables, repetitions one and two of the baseline set were analyzed using within-participant (coefficient of variation, CV; standard error of measurement; smallest worthwhile change; relative mean bias) and between-participant (intra-class correlation coefficient, ICC3,1; Pearson’s correlation coefficient, r) stability metrics. Results showed that all CCT set strategies facilitate stable performance expression between participants and facilitated the detection of practically meaningful changes for propulsive impulse, peak force, mean force, and propulsion time (ICC3,1 = 0.64–0.99, r = 0.80–0.99, CV = 1.12–9.98%), while rate of force development metrics demonstrated less consistent between- and within-participant stability (ICC3,1 = 0.55–0.97, r = 0.46–0.96, CV = 7.52–27.66%). The findings indicate that alternative CCT set strategies facilitate the stable expression of propulsive force–time performance in vertical jumps, although individualized prescriptions are essential for optimizing rate of force development outcomes. Performance expression stability insights provide a practical tool for balancing the effectiveness and potential for performance enhancement of vertical jump propulsion across alternative CCT set strategies. Practitioners may use these results to improve the prescription and monitoring of CCT-based strength and power mesocycles.
Full article
(This article belongs to the Special Issue Methods on Sport Biomechanics—2nd Edition)
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Open AccessProtocol
Standardized Workflow for the Generation of Patient-Derived Glioblastoma Spheroids
by
Giuseppa D’Amico, Alessandra Maria Vitale, Martina Di Marco, Alessandro Lo Giudice, Francesca Chiara Cecala, Francesco Cappello and Celeste Caruso Bavisotto
Methods Protoc. 2026, 9(2), 61; https://doi.org/10.3390/mps9020061 - 3 Apr 2026
Abstract
Glioblastoma (GBM) is one of the most aggressive and therapy-resistant primary brain tumors, mainly due to its pronounced intratumoral heterogeneity and highly invasive phenotype. Patient-derived three-dimensional (3D) culture models, including tumor spheroids, represent valuable tools to preserve the cellular complexity, phenotypic plasticity, and
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Glioblastoma (GBM) is one of the most aggressive and therapy-resistant primary brain tumors, mainly due to its pronounced intratumoral heterogeneity and highly invasive phenotype. Patient-derived three-dimensional (3D) culture models, including tumor spheroids, represent valuable tools to preserve the cellular complexity, phenotypic plasticity, and microenvironmental features of GBM ex vivo. However, standardized and reproducible protocols for the generation and maintenance of GBM spheroids from surgical specimens are still limited. Here, we describe a detailed and robust protocol for the isolation, 3D cultures, and expansion of primary GBM cells obtained from patient biopsies, leading to the formation of stable and morphologically consistent spheroids. The protocol provides step-by-step instructions for tissue dissociation, cell seeding under low-adhesion conditions, optimization of culture density, and long-term spheroid maintenance. In addition, we include guidelines for the morpho-phenotypical characterization of the resulting 3D structures. This methodological workflow offers a reproducible platform for modeling GBM in vitro, enabling the study of tumor biology and supporting translational applications such as drug screening, biomarker validation, and patient-specific therapeutic testing in a 3D context.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessReview
Phenolic Compounds and Antioxidant Activity: Analytical Methods and Current Knowledge—A Review
by
Miroslav Lisjak, Marija Špoljarević, Jelena Ravlić, Zdenko Lončarić and Lucija Galić
Methods Protoc. 2026, 9(2), 60; https://doi.org/10.3390/mps9020060 - 3 Apr 2026
Abstract
Phenolic compounds are plant-derived antioxidants crucial for human health and food preservation. Their bioactive potential including anti-inflammatory, antimicrobial, and anti-carcinogenic properties makes them a vital focus in nutritional, pharmaceutical, and agricultural research. This review critically evaluates the methodologies for their extraction, detection, and
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Phenolic compounds are plant-derived antioxidants crucial for human health and food preservation. Their bioactive potential including anti-inflammatory, antimicrobial, and anti-carcinogenic properties makes them a vital focus in nutritional, pharmaceutical, and agricultural research. This review critically evaluates the methodologies for their extraction, detection, and quantification to accurately assess antioxidant activity. Oxidative stress in biological systems and food matrices necessitates accurate analytical methodologies for assessing antioxidant behavior, which include both in vitro, in vivo and ex vivo approaches. Sample pretreatment and extraction techniques are critical for reliable analysis and vary depending on the matrix, compound polarity, and target phenolic subclass. We compare conventional extraction techniques (Soxhlet, maceration) with advanced methods like ultrasound-assisted, microwave-assisted, and supercritical fluid extraction. Detection methods reviewed include spectrophotometric assays (e.g., DPPH, FRAP, ORAC), electrochemical sensors, and chromatographic techniques (e.g., HPLC, HPLC−MS). While each method has distinct advantages, a lack of standardization remains the primary challenge, driven by variations in protocols and the vast chemical diversity of phenolics. This review underscores the critical need for integrated, standardized approaches to ensure the accurate and comparable evaluation of antioxidant activity in research and industry.
Full article
(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Open AccessProtocol
A Simple and Fast Protocol to Detect Nucleophosmin 1 (NPM1) Mutation and Fms-like Tyrosine Kinase 3 Internal Tandem Duplication (FLT3/ITD): Optimizing Laboratory Routine
by
Alessandra Helena da Silva Hellwig, Gisele Menezes Ewald, Grazielle Motta Rodrigues, William Latosinski Matos, Juliana Bergmann, Viviane Horn de Melo, Rodrigo Minuto Paiva, Dariane Castro Pereira and Eduardo Wandame Gomez
Methods Protoc. 2026, 9(2), 59; https://doi.org/10.3390/mps9020059 - 3 Apr 2026
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy. AML classification is currently based on cytogenetic and molecular alterations as well as immunophenotyping, although risk stratification still relies primarily on cytogenetic findings. However, approximately 45% of AML patients present with a normal karyotype,
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Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy. AML classification is currently based on cytogenetic and molecular alterations as well as immunophenotyping, although risk stratification still relies primarily on cytogenetic findings. However, approximately 45% of AML patients present with a normal karyotype, which makes accurate risk classification and treatment stratification more challenging. Therefore, the identification of molecular prognostic markers described in the literature has become essential in routine diagnostic laboratories, enabling the more precise categorization of patients into risk groups. In this study, we present a simple, rapid, step-by-step multiplex PCR protocol combined with capillary electrophoresis for the detection of two of the most prevalent molecular alterations in AML: nucleophosmin 1 (NPM1) mutations and Fms-like tyrosine kinase 3 internal tandem duplications (FLT3/ITD). This protocol provides a practical workflow that can assist diagnostic laboratories in implementing and optimizing multiplex mutation detection in routine practice.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessReview
The Ability of Vibrational Spectroscopy to Analyze Holistically the Food Matrix-Moving Away from the Concept of Individual Compounds
by
Daniel Cozzolino
Methods Protoc. 2026, 9(2), 58; https://doi.org/10.3390/mps9020058 - 2 Apr 2026
Abstract
The concepts of food matrix and holistic analysis have been used in a wide range of scientific disciplines to describe the sum of the parts of a whole that provide a specific property or functionality to the sample. Traditional chemical and physical analysis
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The concepts of food matrix and holistic analysis have been used in a wide range of scientific disciplines to describe the sum of the parts of a whole that provide a specific property or functionality to the sample. Traditional chemical and physical analysis needs to destroy the sample (e.g., dilution, extraction, drying) before analysis. The utilization of vibrational spectroscopy techniques, like near (NIR), mid infrared (MIR) and Raman spectroscopy, allows for the non-destructive analysis of food ingredients and products. The resulting output of this analysis is based on the information provided by the vibrational modes of atoms present in the different molecules, allowing the measurement of different chemical and physical characteristics of the food. The objective of this paper is to discuss the ability of vibrational spectroscopy methods to provide robust tools to analyze the food matrix holistically, moving away from the traditional analysis of individual compounds or chemical parameters. Studies discussed and presented in this review demonstrated the ability of vibrational spectroscopy (e.g., NIR, MIR and Raman spectroscopy, hyperspectral imaging) to assess the whole food matrix beyond the traditional notion of developing a calibration model.
Full article
(This article belongs to the Special Issue Spectroscopic Methods of Analysis)
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Open AccessArticle
Effect of Loading Strategy on Methylene Blue Encapsulation in Ethosomes: A Comparative Study of Aqueous and Ethanol Phases
by
Dmitry Yakovlev, Kanamat Efendiev, Polina Alekseeva, Vladimir Makarov, Kirill Linkov, Anna Lukianova, Vladimir Oleinikov and Victor Loschenov
Methods Protoc. 2026, 9(2), 57; https://doi.org/10.3390/mps9020057 - 2 Apr 2026
Abstract
This study presents a comparative analysis of the effect of methylene blue (MB) loading strategy on the physicochemical and colloidal properties of ethosomes prepared by the cold method. Two synthesis protocols differing in the phase of introduction of the cationic hydrophilic dye were
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This study presents a comparative analysis of the effect of methylene blue (MB) loading strategy on the physicochemical and colloidal properties of ethosomes prepared by the cold method. Two synthesis protocols differing in the phase of introduction of the cationic hydrophilic dye were investigated: a classical approach with MB loading into the aqueous phase and an alternative approach involving MB incorporation into the ethanolic lipid phase. It is shown that the loading strategy is a critical technological factor determining vesicle size, encapsulation efficiency, loading capacity, and electrokinetic properties of the systems. The alternative method results in the formation of smaller ethosomes (Rh ≈ 78 nm) compared to the classical protocol (Rh ≈ 96 nm), but is accompanied by a lower encapsulation efficiency (EE ≈ 36% versus 48%). The results indicate that a reduction in vesicle size does not necessarily lead to higher encapsulation of hydrophilic cationic MB and may be associated with a decrease in the total internal aqueous volume as well as an increased contribution of a weakly bound surface-associated dye fraction. Spectral analysis indicates the preservation of a predominantly monomeric form of MB within ethosomes, while differences in ζ-potential suggest distinct localization of the dye within the vesicular systems. Overall, the results highlight the importance of optimizing the loading protocol in the development of ethosomal drug delivery systems for photodynamic therapy and topical applications.
Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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Open AccessArticle
Management of Patients with Suspected Hypersensitivity to Chemotherapy Drugs: A Practical Approach in a Tertiary Care Setting
by
Maria Bernadette Cilona, Serena Nannipieri, Arianna Ferlito, Giulia Orsi, Monica Ronzoni, Giorgia Mangili, Emanuela Rabaiotti, Fabio Ciceri, Michele Reni and Mona-Rita Yacoub
Methods Protoc. 2026, 9(2), 56; https://doi.org/10.3390/mps9020056 - 2 Apr 2026
Abstract
Background: Hypersensitivity reactions to antineoplastic agents are an increasing clinical challenge due to their rising incidence and potential severity. Early allergological assessment and tailored drug re-exposure strategies may allow continuation of essential therapies, although real-world data remain limited. Methods: We conducted a monocentric
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Background: Hypersensitivity reactions to antineoplastic agents are an increasing clinical challenge due to their rising incidence and potential severity. Early allergological assessment and tailored drug re-exposure strategies may allow continuation of essential therapies, although real-world data remain limited. Methods: We conducted a monocentric retrospective observational study including adult oncologic patients with suspected chemotherapy-induced hypersensitivity reactions. Clinical features, allergological work-up, and management strategies were analyzed. The primary outcome was the success rate of drug reintroduction using desensitization or enhanced premedication. Secondary outcomes included skin test positivity rates and the association between cumulative chemotherapy exposure and anaphylaxis. Results: Forty-two patients were included (95% female; median age 57.5 years). Re-exposure was required in 18 patients, and was successful in all patients undergoing desensitization and in 92% of those managed with enhanced premedication. Skin testing was positive in 71% of suspected platinum reactions, 30% of taxanes, and 40% of biologic agent reactions. Anaphylaxis occurred in 26.2% of patients, and a trend toward an association with cumulative chemotherapy exposure was observed; each additional cycle was associated with a 28% increase in the odds of anaphylaxis (adjusted OR 1.28; 95% CI, 1.00–1.63). Conclusions: Desensitization and enhanced premedication allow safe reintroduction of antineoplastic agents. Cumulative chemotherapy exposure is associated with an increased risk of anaphylaxis.
Full article
(This article belongs to the Section Public Health Research)
Open AccessStudy Protocol
Work at Heights Training: Conventional Approach with and Without Immersive Virtual Reality Study Protocol
by
Diana Guerrero-Jaramillo, Ricardo de la Caridad Montero and Oscar Campo
Methods Protoc. 2026, 9(2), 55; https://doi.org/10.3390/mps9020055 - 1 Apr 2026
Abstract
Background: Work at heights is a high-risk occupational activity, with falls being a leading cause of fatal accidents in construction and industrial maintenance. Conventional safety training often does not fully prepare workers for real-world hazards. Immersive virtual reality (IVR) has emerged as a
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Background: Work at heights is a high-risk occupational activity, with falls being a leading cause of fatal accidents in construction and industrial maintenance. Conventional safety training often does not fully prepare workers for real-world hazards. Immersive virtual reality (IVR) has emerged as a promising training tool, providing controlled and realistic simulations of hazardous scenarios. This hypothesis-generating pilot study evaluates the feasibility and effectiveness of IVR in enhancing practical skills, safety perception, and physiological responses during work-at-height training. Methods: This controlled trial will recruit first-time trainees from the National Learning Service (SENA) of Colombia. Participants will be assigned to an intervention group, receiving IVR training before field-based practical sessions, or a control group, receiving standard theoretical instruction. Outcomes include practical skill acquisition, ergonomic risk, cognitive performance, and physiological responses, including heart rate variability measured with validated devices. Assessments will be performed using standardized tools, and data will be analyzed with repeated-measures ANOVA and regression models to compare groups. Conclusions: By integrating practical, cognitive, ergonomic, and physiological measures, this study will provide evidence on whether IVR improves the effectiveness of work-at-height training beyond conventional methods. Findings may inform future strategies to enhance occupational safety training in high-risk work environments.
Full article
(This article belongs to the Section Public Health Research)
Open AccessReview
Click Reactions in Kinetic Target-Guided Synthesis: Progress in the Discovery of Inhibitors for Biological Targets
by
Prakash T. Parvatkar and Nishikant Satam
Methods Protoc. 2026, 9(2), 54; https://doi.org/10.3390/mps9020054 - 1 Apr 2026
Abstract
The rapid expansion of click chemistry reflects its transformative influence on contemporary drug discovery. This review highlights major advances in the application of click reactions within the kinetic target-guided synthesis (KTGS) paradigm for identifying potent inhibitors across a broad range of biological targets.
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The rapid expansion of click chemistry reflects its transformative influence on contemporary drug discovery. This review highlights major advances in the application of click reactions within the kinetic target-guided synthesis (KTGS) paradigm for identifying potent inhibitors across a broad range of biological targets. KTGS constitutes a methodological shift that leverages the inherent dynamics of biomolecular systems, enabling biological targets to direct the in situ assembly of high-affinity bidentate ligands from a diverse repertoire of reactive building blocks. The review systematically classifies the principal bond-forming reactions that underpin effective inhibitor generation via KTGS. Collectively, it provides a comprehensive and scholarly analysis of how click-chemistry-enabled KTGS is redefining drug discovery and expediting the development of next-generation therapeutics.
Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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Open AccessArticle
Detection of Certain Berries in Difficult Samples by Singleplex and Multiplex Real-Time PCR-HRM: A Case Study of Pitfalls
by
Lenka Fialova and Ivana Marova
Methods Protoc. 2026, 9(2), 53; https://doi.org/10.3390/mps9020053 - 1 Apr 2026
Abstract
Singleplex and multiplex real-time PCR-HRM (polymerase chain reaction with high resolution melting), both with specific and non-specific amplicon detection, are used for a wide range of applications, from clinical diagnostics to food authentication. However, their results can be influenced by the quality of
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Singleplex and multiplex real-time PCR-HRM (polymerase chain reaction with high resolution melting), both with specific and non-specific amplicon detection, are used for a wide range of applications, from clinical diagnostics to food authentication. However, their results can be influenced by the quality of the template DNA and composition of the reaction mixture. The methods used for the analysis of these results then influence the conclusions drawn. In this work we present an example from our laboratory practice, where the results of singleplex and multiplex real-time PCR differed, despite using the same reaction conditions, primers and analyzed plant material. We show the influence of a singleplex and multiplex PCR setup on the results, as well as the influence of template contamination on the melting behaviour of amplicons. We also discuss the usefulness of cluster analysis for the clarification of real-time PCR-HRM results which appear unclear when only melting and difference curves or similarity scores are used for the analysis of these results. We provide a discussion of problems which we encountered during an analysis of commercial teas and which should be considered by researchers new to PCR-based analysis of plant material, especially if the studied material is rich in various contaminants.
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(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Open AccessArticle
In Silico Design and Characterization of the Essential Outer-Membrane Lipoprotein LolB-Derived Multi-Epitope Vaccine Candidate Against Pseudomonas aeruginosa
by
Sinethemba H. Yakobi and Uchechukwu U. Nwodo
Methods Protoc. 2026, 9(2), 52; https://doi.org/10.3390/mps9020052 - 1 Apr 2026
Abstract
Pseudomonas aeruginosa causes severe healthcare-associated infections, yet no vaccine has been licenced. To circumvent the antigenic variability of classical surface antigens, we evaluated LolB—an essential outer-membrane lipoprotein whose periplasmic orientation favours T-cell-dominant mechanisms with potential antibody access via outer-membrane vesicles (OMVs) or bacteriolysis.
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Pseudomonas aeruginosa causes severe healthcare-associated infections, yet no vaccine has been licenced. To circumvent the antigenic variability of classical surface antigens, we evaluated LolB—an essential outer-membrane lipoprotein whose periplasmic orientation favours T-cell-dominant mechanisms with potential antibody access via outer-membrane vesicles (OMVs) or bacteriolysis. An integrative in silico pipeline combined multi-strain conservation (20 isolates), epitope discovery (B- and T-cell), safety filters, physicochemical profiling, de novo/refined 3D modelling, molecular dynamics (MD), and docking to TLR4/MD-2. LolB was highly conserved (95–100% identity) under strong purifying selection (dN/dS = 0.15). A conformational B-cell hotspot centred on Q72 mapped to a solvent-accessible flexible loop. Two class II epitopes—LAAQNSPLT and FLGSAAAVS—showed predicted high affinity (IC50 < 10 nM), non-toxicity, and broad coverage, with the pooled set achieving 98.6% global HLA coverage in silico. The final 119-aa construct (N-terminal hBD-3 adjuvant; GPGPG linkers) was compact and tractable (MW = 12.7 kDa; instability index < 40; near-neutral GRAVY) and scored higher for antigenicity than native LolB (VaxiJen 0.82 vs. 0.41). MD supported thermal stability up to 350 K, linker RMSF < 1.5 Å, and a stable 18.2 ± 2.8 Å interdomain spacing. Docking predicted a 1420 Å2 interface and ΔG = −10.2 kcal·mol−1 (Kd = 28 nM) with reproducible polar contacts, suggesting productive TLR4/MD-2 engagement. A conservative R42A/K variant is proposed to temper IFN-γ bias. This work therefore suggests an essentiality-anchored LolB-derived multi-epitope construct as a computational vaccine candidate against multidrug-resistant P. aaeruginosa and defines specific experimentally testable hypotheses for future in vitro/in vivo assessment. Essentiality-anchored epitope selection plus adjuvant-surface engineering yielded a structurally coherent, immunologically rational LolB-derived multi-epitope vaccine warranting experimental validation.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessStudy Protocol
Effect of Roxadustat on Cardiometabolism in Healthy Individuals (ROXACardioMeta): Protocol for a Double-Blind, Placebo-Controlled and Randomised Cross-Over Trial
by
Emma Klemola, Joona Tapio, Rasmus I. P. Valtonen, Mikko P. Tulppo, Janne Hukkanen and Peppi Koivunen
Methods Protoc. 2026, 9(2), 51; https://doi.org/10.3390/mps9020051 - 23 Mar 2026
Abstract
Hypoxia activates hypoxia-inducible factors (HIFs), which regulate genes involved in erythropoiesis, angiogenesis, and metabolism. HIF stability is controlled by oxygen-dependent HIF prolyl 4-hydroxylases (HIF-P4Hs). Pharmacological HIF-P4H inhibitors are approved for the treatment of anaemia in chronic kidney disease (CKD). Beyond erythropoiesis, these drugs
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Hypoxia activates hypoxia-inducible factors (HIFs), which regulate genes involved in erythropoiesis, angiogenesis, and metabolism. HIF stability is controlled by oxygen-dependent HIF prolyl 4-hydroxylases (HIF-P4Hs). Pharmacological HIF-P4H inhibitors are approved for the treatment of anaemia in chronic kidney disease (CKD). Beyond erythropoiesis, these drugs have been linked to improved lipid profiles in CKD, and preclinical studies suggest benefits for glucose tolerance and cardiovascular protection. However, cardiometabolic effects of HIF-P4H inhibitors have not been systematically examined in healthy or non-anaemic individuals. This investigator-initiated, double-blind, placebo-controlled, randomised crossover trial evaluates the systemic effects of roxadustat, an orally administered pan-HIF-P4H inhibitor. The study consists of two 10-day study arms separated by a minimum 4-week washout. Participants receive 70 mg of roxadustat or a placebo thrice a week. The primary hypothesis is that roxadustat lowers plasma total cholesterol. Secondary outcomes include changes in LDL cholesterol, triglycerides, insulin sensitivity, glucose tolerance, body composition, 24 h blood pressure, exercise capacity, autonomic cardiovascular regulation, and skeletal muscle microcirculation. Healthy volunteers (n = 24) aged 18–40 years will be enrolled. This study will provide insights into the potential of HIF-P4H inhibitors for obesity, dyslipidaemia, insulin resistance, and hypertension, and may inform future therapeutic strategies for metabolic syndrome, type 2 diabetes, and cardiovascular disease.
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(This article belongs to the Section Public Health Research)
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Open AccessArticle
Fluorescence Quantification of Silicone Oil Release upon Contact with Liquid Therapeutic Formulations
by
Mathilde Rodriguez, Claire Brunet, Franz Bruckert and Marianne Weidenhaupt
Methods Protoc. 2026, 9(2), 50; https://doi.org/10.3390/mps9020050 - 16 Mar 2026
Abstract
Prefilled syringes are valuable drug delivery systems, offering convenience and precision dosing. Among the critical factors influencing their performance is the stability of the silicone oil layer, which acts as a lubricant, guaranteeing the gliding properties of the plunger. The silicone oil, if
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Prefilled syringes are valuable drug delivery systems, offering convenience and precision dosing. Among the critical factors influencing their performance is the stability of the silicone oil layer, which acts as a lubricant, guaranteeing the gliding properties of the plunger. The silicone oil, if it comes in contact with therapeutic formulations, can be subject to drug–container interactions, potentially leading to silicone oil release into the solution, thereby altering the gliding properties of the syringe and leading to unwanted particle formation, compromising drug efficacy and safety. Different measurement techniques, such as visual inspection, dynamic light scattering and spectroscopic analysis, are used to assess silicone oil layer stability in prefilled syringes. However, a quantitative, rapid and low-volume screening method to rapidly evaluate container compatibility for therapeutic formulations is not available. Here, we present a multi-well-based screening protocol allowing users to quantify, through fluorescence, the silicone oil released into a solution upon contact with liquid formulations. Fluorescently labeled uniform silicone oil layers of the desired thickness are deposited in glass-bottom wells and exposed to typical formulations, containing surfactants and monoclonal antibodies. The release of silicon oil as a function of contact time is quantified using fluorescence calibration. Beyond its use as a screening tool to evaluate drug–container compatibility, our protocol can contribute to the fundamental understanding of the factors and mechanisms influencing silicone oil layer stability and, furthermore, to the optimization of drug delivery systems.
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(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Open AccessArticle
Establishment of a Sensitized 3D Spheroid Cancer Cell Model for Enhanced Anti-Cancer Drug Discovery
by
Ee Wern Tan, Tien Yang Goh, Shi Hui Law, Kuan Onn Tan and Bey Hing Goh
Methods Protoc. 2026, 9(2), 49; https://doi.org/10.3390/mps9020049 - 16 Mar 2026
Abstract
Three-dimensional (3D) spheroid cancer models provide enhanced physiological relevance relative to traditional monolayer cultures but often demonstrate restricted drug responsiveness due to their dense architecture, hypoxic gradients, and diminished therapeutic penetrance. This study overcomes these limitations by establishing a sensitized 3D spheroid cancer
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Three-dimensional (3D) spheroid cancer models provide enhanced physiological relevance relative to traditional monolayer cultures but often demonstrate restricted drug responsiveness due to their dense architecture, hypoxic gradients, and diminished therapeutic penetrance. This study overcomes these limitations by establishing a sensitized 3D spheroid cancer cell model that employs the adenovirus-mediated gene expressions of tumor-suppressor and pro-apoptotic genes consisting of MOAP-1, BAX, and RASSF1A. The optimization of adenoviral infectivity led to the discovery of an intermediate multiplicity of infection (MOI) that facilitated effective and uniform transduction while reducing cytotoxicity. Adenovirus-infected 3D spheroid cells demonstrated enhanced apoptotic activities, evidenced by increased cell death relative to untreated spheroids. When exposed to the anti-cancer compound such as piperonal and pyrazole, the sensitized spheroids exhibited significantly enhanced drug responsiveness and synergistic effects over a five-day treatment period, surpassing the effects of adenovirus or anti-cancer drug treatment alone. Notably, similar responses were noted between low- and high drug doses, suggesting an enhancement of therapeutic efficacy at lower concentrations. This sensitized 3D spheroid model constitutes a more predictive in vitro system for anti-cancer drug discovery, facilitating enhanced mechanistic evaluation and the identification of potent drug candidates with greater translational significance.
Full article
(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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Open AccessArticle
Surface Plasmon Resonance Analysis for Evaluating ASO Targeting Structured RNA
by
Tomohiro Shinozaki, Takuya Hasegawa, MST Tahmina Akter, Kazuyuki Kumagai, Youichi Suzuki and Taiichi Sakamoto
Methods Protoc. 2026, 9(2), 48; https://doi.org/10.3390/mps9020048 - 15 Mar 2026
Abstract
Antisense oligonucleotides (ASOs) are nucleic acid therapeutics that regulate gene expression through sequence-specific hybridization with target RNA. Under physiological conditions, many target RNAs adopt higher-order structures, which can strongly influence ASO accessibility and binding behavior. Although UV melting analysis is widely used to
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Antisense oligonucleotides (ASOs) are nucleic acid therapeutics that regulate gene expression through sequence-specific hybridization with target RNA. Under physiological conditions, many target RNAs adopt higher-order structures, which can strongly influence ASO accessibility and binding behavior. Although UV melting analysis is widely used to evaluate the thermal stability of ASO/RNA duplexes, this approach does not adequately account for the structural features of target RNAs. In this study, we investigated the utility of surface plasmon resonance (SPR) analysis as an in vitro method to evaluate ASO binding while considering RNA structural constraints. Multiple ASOs were designed to target PRF84, an 84-nucleotide RNA motif that induces −1 programmed ribosomal frameshifting in HIV-1 gag-pol expression. SPR analyses were performed to compare ASO interactions with complementary RNA fragments and with structurally folded PRF84. The results demonstrated that identical ASOs exhibited distinct binding behaviors depending on whether the target was a complementary RNA or PRF84, indicating that RNA structure significantly affects ASO binding. These findings suggest that SPR analysis enables the evaluation of ASO–RNA interactions taking structure into account, and may be a useful alternative approach to conventional UV melting analysis-based ASO screening.
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(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
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Open AccessArticle
Examining Epigenetic Age in Women with Different Obesity Conditions Using DNA Methylation at the FHL2 Gene
by
Licínio Manco, Helena Correia Dias and Lara Palmeira
Methods Protoc. 2026, 9(2), 47; https://doi.org/10.3390/mps9020047 - 12 Mar 2026
Abstract
DNA methylation (DNAm) age estimation is one of the hottest topics in forensic contexts. However, there is growing evidence that DNAm can be affected by several factors, including many clinical conditions. In this study, we analyzed the methylation levels within the FHL2 gene
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DNA methylation (DNAm) age estimation is one of the hottest topics in forensic contexts. However, there is growing evidence that DNAm can be affected by several factors, including many clinical conditions. In this study, we analyzed the methylation levels within the FHL2 gene in Portuguese women using the droplet digital PCR (ddPCR) methodology to develop age prediction models (APMs). We hypothesized that obesity could affect the accuracy of APMs and would be associated with the advancement in epigenetic aging. We collected blood samples from 62 women (aged 21–58 years old) with overweight and obesity. DNA extracts were subjected to bisulfite conversion followed by ddPCR using dual-labeled probes targeting the methylated and unmethylated FHL2 CpG site cg06639320. The developed APM yielded a mean absolute deviation (MAD) of 4.72 years between predicted and chronological ages in the total sample. When applying the developed APM to women classified as overweight, the MAD was 3.64 years, while, for those with obesity class 1, it was 3.93 years, and, for those with obesity class 2, 6.29 years. The same pattern of accuracy was observed when we developed APMs specifically for the groups categorized by overweight and obesity, obtaining MAD values of 3.75 years (overweight), 3.69 years (obesity class 1) and 6.24 years (obesity class 2). Our study indicates that severe obesity may impact the accuracy of DNA methylation-based age estimators. We did not find evidence of an association between BMI and accelerated epigenetic aging. However, we found signals of epigenetic age acceleration in younger subjects and epigenetic age deceleration in the older participants.
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(This article belongs to the Section Biomedical Sciences and Physiology)
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Open AccessArticle
Investigating Metabolically Altered Pathways in Small Cell Lung Cancer: From RNA Sequencing Analysis to Seahorse-Based Functional Validation
by
Subhadeep Das, Sagar M. Utturkar, Roshnee Bose and Elizabeth J. Tran
Methods Protoc. 2026, 9(2), 46; https://doi.org/10.3390/mps9020046 - 10 Mar 2026
Abstract
Small cell lung cancer (SCLC) is an aggressive malignancy characterized by rapid progression, early metastasis, and high relapse rates due to acquired chemoresistance. The human DEAD-box RNA helicase DDX5 is overexpressed in SCLC and has recently gained attention as a viable therapeutic target.
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Small cell lung cancer (SCLC) is an aggressive malignancy characterized by rapid progression, early metastasis, and high relapse rates due to acquired chemoresistance. The human DEAD-box RNA helicase DDX5 is overexpressed in SCLC and has recently gained attention as a viable therapeutic target. Supinoxin (RX-5902), a selective small-molecule inhibitor of DDX5, exhibits strong anti-tumor activity. Recent evidence suggests that its cytotoxic effects are mediated through the disruption of mitochondrial respiration. In this study, transcriptomic profiling via RNA sequencing (RNA-seq) revealed significant downregulation of genes involved in cellular respiration following Supinoxin treatment and DDX5 knockdown in chemoresistant H69AR cells. To functionally validate these findings, we employed the Seahorse XF Cell Mito Stress Test, which measures key parameters of mitochondrial bioenergetics through oxygen consumption rate (OCR) analysis. Supinoxin-treated cells exhibited marked mitochondrial dysfunction, supporting the hypothesis that DDX5 inhibition disrupts cellular energy metabolism. These findings illuminate a previously underappreciated role of DDX5 in mitochondrial regulation and offer mechanistic insights into Supinoxin’s cytotoxic effects, underscoring its potential as a targeted therapy in SCLC.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessArticle
Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements
by
Marc Follmer, Korbinian Pürckhauer and Klaus Neuhaus
Methods Protoc. 2026, 9(2), 45; https://doi.org/10.3390/mps9020045 - 10 Mar 2026
Abstract
Ribosome profiling, or Ribo-Seq, is a powerful tool for studying translation. It maps the positions of translating ribosomes on mRNAs, providing insights into actively expressed genes. Unlike mass spectrometry, Ribo-Seq is not affected by the same biases that limit mass spectrometry, such as
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Ribosome profiling, or Ribo-Seq, is a powerful tool for studying translation. It maps the positions of translating ribosomes on mRNAs, providing insights into actively expressed genes. Unlike mass spectrometry, Ribo-Seq is not affected by the same biases that limit mass spectrometry, such as protein size, concentration, trypsin digestibility, or hydrophobicity. Thus, the translatome has previously been used to discover unannotated genes, including small and overlapping ones that were missed by mass spectrometry or gene prediction models. However, a major limitation of classical ribosome profiling is its complexity, involving multiple steps such as sucrose density gradient centrifugation and gel electrophoresis. These make the method costly, time-consuming, and limit its throughput. Here, we compared the classical method using gradient centrifugation and size exclusion by gel electrophoresis with shortened versions to evaluate experimental performance and achieved reductions. Our results show that the sucrose density gradient centrifugation is essential for obtaining accurate Ribo-Seq data, whereas gel electrophoresis for size selection can be omitted (although this requires increased sequencing depth). Thus, future experiments can be conducted with reduced sample input and hands-on time while still achieving a reliable quantification of translation.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessArticle
Development of an Efficient In Vitro Propagation Method for Acmella oleracea (L.) R.K. Jansen
by
Pál Szarvas, Judit Csabai, Anzhela Kolesnyk and Judit Dobránszki
Methods Protoc. 2026, 9(2), 44; https://doi.org/10.3390/mps9020044 - 8 Mar 2026
Abstract
Acmella oleracea (L.) R.K. Jansen is an herbaceous plant cultivated globally as an annual ornamental species. While conventional propagation methods exist, the lack of a standardized in vitro protocol limits research and industrial applications that require genetically and morphologically uniform plant material. In
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Acmella oleracea (L.) R.K. Jansen is an herbaceous plant cultivated globally as an annual ornamental species. While conventional propagation methods exist, the lack of a standardized in vitro protocol limits research and industrial applications that require genetically and morphologically uniform plant material. In this study, in vitro cultures of A. oleracea were established via seed germination. Well-developed in vitro shoots were dissected into individual nodal segments to serve as explants. Multiple media were evaluated for regeneration and growth, including full-, half, and quarter-strength Murashige and Skoog (MS) media, as well as full- and half-strength McCown Woody Plant media. Two carbohydrate sources, saccharose and glucose, were tested at concentrations of 1%, 2%, and 3% (w/v) in the multiplication medium. Subsequently, the effects of different cytokinins were assessed at concentrations of 4.4 µM and 13.2 µM. The findings demonstrated that 13.2 µM meta-Topolin with 3% saccharose, or 13.2 µM Benzyladenine with 2% glucose was most beneficial for shoot multiplication of A. oleracea. The multiplied shoots were rooted in vitro within 13 days, then potted and acclimatized within 8 days. This protocol facilitates future industrial applications of A. oleracea, particularly in the cosmetics sector, where the use of standardized biomass is essential.
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(This article belongs to the Section Biomedical Sciences and Physiology)
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