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Methods and Protocols, Volume 9, Issue 2

2026 April - 36 articles

Cover Story: DNA double-strand breaks (DSBs) are highly cytotoxic lesions, and the chromatin environment around a break shapes its repair. In engineered budding yeast strains, expression of the site-specific HO endonuclease can be regulated to generate a single, unrepairable DSB at the MATa locus. We couple micrococcal nuclease digestion with chromatin immunoprecipitation and sequencing (MNase-ChIP-seq) to map histone post-translational modifications genome-wide at nucleosome-level resolution and to follow their changes over time. The workflow is validated by detecting changes in histone H3K79 methylation upon HO induction and DSB formation, providing a reliable framework to study chromatin dynamics across genetic backgrounds or stress conditions in yeast. View this paper
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Articles (36)

  • Article
  • Open Access
1 Citations
1,333 Views
20 Pages

Portable devices are powered in direct current (DC) or by batteries (primary battery), accumulators (secondary battery), and now supercapacitors, which can also be used for energy storage. The European Portable Battery Association states that approxi...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Protocol
  • Open Access
2,198 Views
24 Pages

Optimized Protocols to Extract Total Transcripts and Proteins from Lipid-Rich Tissues

  • Nicolas De Azevedo,
  • Anthony Lozano,
  • Ramon E. Parsons and
  • Tiphaine C. Martin

Background: Highly lipidic tissues (e.g., adipose tissue, brain, and liver) are challenging for transcript and protein extraction and for next-generation sequencing. Lipids can clog filters, columns, and pipettes; cause autofluorescence and quenching...

(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
  • Protocol
  • Open Access
1,350 Views
11 Pages

Stereological Assessment of Locus Coeruleus in the Mouse: A Methodological Study in Pups and Adult Animals

  • Marco Scotto,
  • Alessandro Galgani,
  • Marina Boido,
  • Nooria Mohammady,
  • Alessandro Vercelli and
  • Filippo S. Giorgi

Unbiased stereology represents the most accurate approach for estimating the total number of neurons of specific brain regions; however, its reliability critically depends on the use of rigorously defined and anatomically appropriate sampling paramet...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Article
  • Open Access
1,941 Views
14 Pages

Analytical Characterization of Pneumococcal Vaccine Conjugates Using SEC-MALS Technique

  • Chloe Wright,
  • Gowri Chellappan,
  • Abigail Mydland,
  • Gowthami Jagruthi Penumaka,
  • Geetha Karengil,
  • Harshita Seth,
  • Anup Datta and
  • Subhash V. Kapre

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 path...

(This article belongs to the Collection Analytical Chemistry Methods and Protocols: From Standard Practices to New Sustainable Approaches)
  • Article
  • Open Access
938 Views
32 Pages

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-con...

(This article belongs to the Special Issue Methods on Sport Biomechanics—2nd Edition)
  • Protocol
  • Open Access
1 Citations
2,973 Views
13 Pages

Standardized Workflow for the Generation of Patient-Derived Glioblastoma Spheroids

  • Giuseppa D’Amico,
  • Alessandra Maria Vitale,
  • Martina Di Marco,
  • Alessandro Lo Giudice,
  • Francesca Chiara Cecala,
  • Francesco Cappello and
  • Celeste Caruso Bavisotto

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...

(This article belongs to the Section Molecular and Cellular Biology)
  • Review
  • Open Access
17 Citations
4,413 Views
18 Pages

Phenolic Compounds and Antioxidant Activity: Analytical Methods and Current Knowledge—A Review

  • Miroslav Lisjak,
  • Marija Špoljarević,
  • Jelena Ravlić,
  • Zdenko Lončarić and
  • Lucija Galić

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, pharmace...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Protocol
  • Open Access
911 Views
16 Pages

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

  • 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

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 fi...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
1 Citations
1,334 Views
16 Pages

Effect of Loading Strategy on Methylene Blue Encapsulation in Ethosomes: A Comparative Study of Aqueous and Ethanol Phases

  • Dmitry Yakovlev,
  • Kanamat Efendiev,
  • Polina Alekseeva,
  • Vladimir Makarov,
  • Kirill Linkov,
  • Anna Lukianova,
  • Vladimir Oleinikov and
  • Victor Loschenov

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...

(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
  • Review
  • Open Access
1 Citations
1,252 Views
14 Pages

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...

(This article belongs to the Special Issue Spectroscopic Methods of Analysis)
  • Article
  • Open Access
2 Citations
1,444 Views
11 Pages

Management of Patients with Suspected Hypersensitivity to Chemotherapy Drugs: A Practical Approach in a Tertiary Care Setting

  • Maria Bernadette Cilona,
  • Serena Nannipieri,
  • Arianna Ferlito,
  • Giulia Orsi,
  • Monica Ronzoni,
  • Giorgia Mangili,
  • Emanuela Rabaiotti,
  • Fabio Ciceri,
  • Michele Reni and
  • Mona-Rita Yacoub

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...

(This article belongs to the Section Public Health Research)
  • Study Protocol
  • Open Access
1 Citations
908 Views
13 Pages

Work at Heights Training: Conventional Approach with and Without Immersive Virtual Reality Study Protocol

  • Diana Guerrero-Jaramillo,
  • Ricardo de la Caridad Montero and
  • Oscar Campo

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...

(This article belongs to the Section Public Health Research)
  • Review
  • Open Access
2,795 Views
36 Pages

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 id...

(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
  • Article
  • Open Access
790 Views
19 Pages

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....

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
3 Citations
1,474 Views
23 Pages

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 peri...

(This article belongs to the Section Molecular and Cellular Biology)
  • Study Protocol
  • Open Access
1,723 Views
14 Pages

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 inhibitor...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
1,583 Views
14 Pages

Fluorescence Quantification of Silicone Oil Release upon Contact with Liquid Therapeutic Formulations

  • Mathilde Rodriguez,
  • Claire Brunet,
  • Franz Bruckert and
  • Marianne Weidenhaupt

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...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
1,842 Views
16 Pages

Establishment of a Sensitized 3D Spheroid Cancer Cell Model for Enhanced Anti-Cancer Drug Discovery

  • Ee Wern Tan,
  • Tien Yang Goh,
  • Shi Hui Law,
  • Kuan Onn Tan and
  • Bey Hing Goh

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...

(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
  • Article
  • Open Access
1,848 Views
11 Pages

Surface Plasmon Resonance Analysis for Evaluating ASO Targeting Structured RNA

  • Tomohiro Shinozaki,
  • Takuya Hasegawa,
  • MST Tahmina Akter,
  • Kazuyuki Kumagai,
  • Youichi Suzuki and
  • Taiichi Sakamoto

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...

(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
  • Article
  • Open Access
1,347 Views
11 Pages

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 l...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Article
  • Open Access
1,718 Views
27 Pages

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 gai...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
1,781 Views
18 Pages

Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements

  • Marc Follmer,
  • Korbinian Pürckhauer and
  • Klaus Neuhaus

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 bi...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
1,409 Views
23 Pages

Development of an Efficient In Vitro Propagation Method for Acmella oleracea (L.) R.K. Jansen

  • Pál Szarvas,
  • Judit Csabai,
  • Anzhela Kolesnyk and
  • Judit Dobránszki

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...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Study Protocol
  • Open Access
1,036 Views
14 Pages

A Study Protocol for a Randomized, Controlled Trial: Improving Glucose Time-in-Range in Diabetes in African Youth (DAYTime)

  • Thereza Piloya-Were,
  • Catherine Nyangabyaki,
  • Elizabeth Pappenfus,
  • Expeditus Ahimbisibwe,
  • Ezrah Trevor Rwakinanga,
  • Lin Zhang,
  • Silver Bahendeka and
  • Antoinette Moran

Metabolic control is poor in East Africa for youth with type1 diabetes (T1D). Self-monitoring of blood glucose (SMBG) by fingerstick 2–3 times daily is routine care. This randomized controlled trial (RCT) will test the hypothesis that providing...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
2,005 Views
25 Pages

An MNase-ChIP-Seq Protocol to Profile Histone Modifications at a DNA Break in Yeast

  • Elena Di Nisio,
  • Chiara Frigerio,
  • Valerio Licursi,
  • Sara Castelli,
  • Benedetta Caraba,
  • Rodolfo Negri and
  • Michela Clerici

Eukaryotic DNA is wrapped around octamers of four core histones, forming nucleosomes. Histone post-translational modifications (PTMs) influence chromatin structure and the recruitment of regulatory factors, thereby affecting gene expression and DNA r...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
1 Citations
1,045 Views
25 Pages

Searching for Mechanisms of Analgesic Activity in the Group of 1H-Pyrrolo[3,4-c]pyridine-1,3(2H)-dione Derivatives—In Vitro and In Vivo Studies

  • Anna Dziubina,
  • Dominika Szkatuła,
  • Małgorzata Szafarz,
  • Agata Siwek,
  • Marek Kowalski and
  • Joanna Gdula-Argasińska

The present study was to evaluate the analgesic activity of two newly synthesized 1H-pyrrolo[3,4-c]pyridine-1,3(2H)-dione derivatives, designated DSZ-13 and DSZ-19. To achieve the desired result, the in vitro XTT cell proliferation assay, serotonin 5...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
1,344 Views
15 Pages

Comparative Analysis of Cardiac Puncture and Perfusate Blood Collection for Murine Extracellular Vesicle Isolation

  • Jamie Cooper,
  • Scott Tait Airey,
  • Eric Patino,
  • Theo Andriot,
  • Mousumi Ghosh and
  • Damien D. Pearse

Reliable characterization of circulating extracellular vesicles (EVs) in rodents may be significantly influenced by how blood is collected, yet systematic comparisons of commonly used sampling methods remain limited. Here, we directly evaluate the ef...

(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
  • Article
  • Open Access
983 Views
16 Pages

A GasPak-Based Ischemia Model for Studying ER Stress–Ischemia Interactions in Human Endothelial Cells

  • Mathilde Hoareau,
  • Grégorie Lebeau,
  • Luce Muzi,
  • Jérémy Fontaine,
  • Pascale Krejbich-Trotot,
  • Olivier Meilhac,
  • Christine Robert-Da Silva and
  • Wildriss Viranaicken

During ischemia, endothelial cell integrity is compromised, as a consequence, blood barrier homeostasis is disrupted. Therefore, the structural and functional preservation of endothelial cells is paramount when trying to improve outcomes after ischem...

(This article belongs to the Section Molecular and Cellular Biology)
  • Review
  • Open Access
1 Citations
2,040 Views
24 Pages

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 t...

(This article belongs to the Special Issue Advanced Methods and Technologies in Drug Discovery)
  • Study Protocol
  • Open Access
2,157 Views
33 Pages

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 polyvaga...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
917 Views
16 Pages

Development of an Indirect ELISA for the Detection of ARV Epidemic Strain xj-1.1

  • Weiqi Li,
  • Yongjie Wang,
  • Borui Qi,
  • Lin Yang,
  • Xin Ma,
  • Xinyu Dang,
  • Yayin Qi and
  • Shilei Zhang

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 systematic...

(This article belongs to the Section Omics and High Throughput)
  • Protocol
  • Open Access
2 Citations
1,228 Views
12 Pages

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

  • Borislav Arabadjiev,
  • Ivelina Vassileva,
  • Georgi Nikolaev and
  • Roumen Pankov

28 February 2026

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...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
1 Citations
1,376 Views
14 Pages

Detached Twig Assay to Evaluate Bacterial Canker on Peaches

  • Bilgehan A. Geylani,
  • Stephen M. Parris,
  • Jhulia Gelain,
  • Guido Schnabel and
  • Ksenija Gasic

28 February 2026

Pseudomonas syringae pv. syringae (Pss) is the causal agent of bacterial canker, a disease that can result in yield losses, aerial tissue damage, and tree mortality in stone fruits worldwide. Peach, one of the major stone fruit crops, experiences sig...

(This article belongs to the Section Omics and High Throughput)
  • Review
  • Open Access
3 Citations
3,870 Views
31 Pages

A Review of Multi-Agent AI Systems for Biological and Clinical Data Analysis

  • Jackson Spieser,
  • Ali Balapour,
  • Jarek Meller,
  • Krushna C. Patra and
  • Behrouz Shamsaei

28 February 2026

This review evaluates the emerging paradigm of multi-agent systems (MASs) for biomedical and clinical data analysis, focusing on their ability to overcome the reasoning and reliability limitations of standalone large language models (LLMs). We synthe...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Study Protocol
  • Open Access
1,714 Views
11 Pages

27 February 2026

Gastroesophageal reflux disease (GERD) is a common chronic condition mainly caused by the dysfunction of the antireflux mechanism at the gastroesophageal junction. This is composed of the lower esophageal sphincter and the crural diaphragm. Increasin...

(This article belongs to the Section Public Health Research)
  • Study Protocol
  • Open Access
1,553 Views
16 Pages

26 February 2026

Robot-assisted therapy (RT) is increasingly implemented in rehabilitation, yet evidence on its effectiveness in improving upper extremity function after cervical spinal cord injury (cSCI) remains limited. Therefore, this randomised crossover study ai...

(This article belongs to the Section Biomedical Sciences and Physiology)
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Methods Protoc. - ISSN 2409-9279