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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.

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All Articles (828)

The process of developing a drug is complex and involves many steps, from basic research (bench) to patient applications (bedside), which are conducted to ensure the drug is both safe and effective. In cancer research, the failure rate is high when translating basic findings to clinical trials. One of the main factors probably contributing to high failure rates is the basic quality of in vitro and in vivo study designs. Advanced basic cancer research techniques, including various types of 3D cell culture, the use of valuable organoids, organs, or tumors on chips, traditional or automated Western blots, omics research, advanced imaging techniques, usage of cutting-edge preclinical models and others, may produce inaccurate results for translational research if the basic study design is not carefully planned, especially when drugs or compounds are involved. In this manuscript, the author discussed (i) the importance of understanding and applying pharmacokinetic data in basic research, (ii) a proper comparison of the efficacy and safety of investigational drugs with the standard of care, (iii) the importance of following the actual route of drug administration as experienced by patients, the cruciality of human-to-animal dose conversion, and dose frequencies in animal models, (iv) significance of the age, gender, and strain of mice, along with adherence to the ARRIVE guidelines for ensuring transparency in conducting and reporting preclinical research, (v) benefits of having both subcutaneous and metastasis models in preclinical studies, (vi) the impact of comorbidities and related cancer drug studies in animal models and (vii) the importance of testing drug candidate/s in model mimicking acidic tumor microenvironment.

3 March 2026

A simple and cost-effective model for testing the suitability of investigational drugs/compounds for neoadjuvant, adjuvant, and combination drug settings. In this model, the C666-1 cells were seeded, and once 80% of cell confluency was achieved, the treatment was started simultaneously for all 3 settings for 6 days. In all settings, 5 wells known as (i) control, (ii) drug Y, (iii) CIS, (iv) GEM, and (v) CIS + GEM are non-modifiable for 6 days. Only the 6th well is modifiable except for the combination setting. In the neoadjuvant setting, the drug Y was first added in the 6th well, and the treatment was carried out for 3 days. Then, the old media was discarded, and new media with CIS + GEM was added and incubated for another 3 days. In an adjuvant setting, the cells were treated with CIS + GEM for 3 days, then the old media was discarded and new media with drug Y was added and incubated for another 3 days. In a combination setting, CIS + GEM + Y was added and incubated for 6 days. For all settings, on day 3 or at 72 h, the media was changed in all wells with respective treatments/controls. The final volume was 2 mL. After the experiment was terminated, the cells were fixed and stained with crystal violet. Based on this representative figure, drug Y is probably not suitable to be given as a neoadjuvant or adjuvant. It is only suitable for combination work. The work requires further preclinical validation which is planned. * Each asterisk represents cancer cells.
  • Study Protocol
  • Open Access

Recreational dance offers significant psychological well-being potential. However, traditional instruction emphasizes technique while limiting attention to nervous system development and embodied meaning-making. Despite empirical support for polyvagal theory, motor learning science, somatic education, and phenomenology, their systematic integration into unified structures is not clearly established in recreational dance contexts. This protocol integrates nervous system regulation, motor learning, and creative expression within structured Imperial Society of Teachers of Dancing (ISTD) modern dance syllabus for recreational adults. It presents a 12-week integrated dance-mindfulness intervention addressing this gap through a three-phase structure grounded in neuroscience and embodied pedagogy. The intervention comprises eight standardized components delivered weekly. The randomized controlled trial evaluates intervention effects using the Satisfaction With Life Scale (SWLS), Depression Anxiety Stress Scales-21 (DASS-21), the Mindful Attention Awareness Scale (MAAS), the Subjective Happiness Scale (SHS), and the Leisure Involvement Scale (LIS). Qualitative assessment via semi-structured phenomenological interviews (Weeks 8 and 12) and weekly journaling captures somatic awareness, nervous system resilience, technical confidence, creative expression, relational and social belonging, and embodied meaning-making. Intervention participants are expected to show significantly greater improvements compared to controls. Results will establish evidence-based practice standards for recreational dance and demonstrate neuroscience integration’s efficacy for psychological wellbeing and embodied meaning-making.

3 March 2026

Study workflow: participant enrollment, randomization, intervention delivery, data collection timeline, and follow-up across the 12–week trial.

This study aimed to establish an indirect ELISA for detecting the avian reovirus (ARV) epidemic strain xj-1.1 by using the purified recombinant protein pET-σC as the coating antigen. To optimize assay performance, key parameters were systematically evaluated, including antigen-coating concentration, serum dilution, blocking reagent and duration, serum incubation time, and the dilution and reaction time of the HRP-conjugated secondary antibody. The optimized conditions identified were a coating antigen dilution of 1:100, serum dilution of 1:1600, coating at 37 °C for 1 h followed by overnight incubation at 4 °C, and blocking with 5% skim milk for 2 h. The optimal serum incubation time was 1.5 h, with the secondary antibody diluted 1:1000 and incubated for 2 h, followed by a 20-min color development step. The cut-off value for distinguishing positive and negative samples was determined to be 0.121. Validation of the assay demonstrated favorable specificity, sensitivity, and repeatability, indicating that the developed indirect ELISA provides a reliable method for detecting ARV xj-1.1 infection.

2 March 2026

Construction of the recombinant plasmid pET-σC (A) and confirmation by double-enzyme digestion (B). Note: M: Trans8k DNA marker; lane 1: pET-σC recombinant plasmid; lane 2: pET-σC.

Generation of Primordial Germ Cell-like Cells from hESCs Using BMP4 and hAFSC-Conditioned Medium

  • Borislav Arabadjiev,
  • Ivelina Vassileva and
  • Roumen Pankov
  • + 1 author

The differentiation of human embryonic stem cells (hESCs) into primordial germ cell-like cells (PGC-LCs) provides a robust in vitro model to study human germline specification. Here, we present a simple, reproducible, and cost-effective protocol for generating DEAD-box helicase 4 (DDX4)/VASA and Deleted in Azoospermia-Like (DAZL)-positive PGC-LCs from hESCs using a combination of bone morphogenetic protein 4 (BMP4) and conditioned medium (CM) derived from Stage-Specific Embryonic Antigen-4 (SSEA4)-positive human amniotic fluid stem cells (hAFSC-4). Importantly, unlike conventional protocols that rely on embryoid body formation, our method employs adherent cultures for germ cell differentiation. This approach enhances reproducibility by avoiding the spontaneous and stochastic variability inherent to embryoid body formation. This protocol provides a reproducible and physiologically relevant platform for studying human germ cell development in vitro.

28 February 2026

Schematic overview of the protocol. Two preparatory phases (1 and 2) precede phase 3, which details the steps culminating in PGS-LC formation. Black arrows indicate the addition of factors that trigger differentiation. Small gray arrows indicate cell culture progression steps and time intervals. Cell states are color-coded: undifferentiated stem cells in purple, differentiating ES cells in yellow, and PGS-LC in green.

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Methods Protoc. - ISSN 2409-9279