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Methods and Protocols, Volume 9, Issue 1

2026 February - 30 articles

Cover Story: Liquid–liquid phase separation (LLPS) drives the formation of biomolecular condensates, yet it remains difficult to link macroscopic droplet behavior to residue-level molecular features. This article presents an integrated workflow that combines quantitative, microplate-based LLPS assays and microscopy with NMR spectroscopy and structure-guided mutagenesis. Using the VAPB MSP domain as a validation system, we show how temperature-dependent HSQC changes identify candidate interface residues and how targeted substitutions can reproducibly suppress or enhance LLPS. The protocol is designed to be readily transferable to other LLPS-prone proteins. View this paper
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Articles (30)

  • Study Protocol
  • Open Access
1 Citations
1,422 Views
16 Pages

Conventional Versus Underwater Endoscopic Mucosal Resection for Superficial Non-Ampullary Duodenal Epithelial Tumors ≤ 20 mm: Study Protocol for a Multicenter Randomized Controlled Trial (D-CURE Trial)

  • Masao Yoshida,
  • Waku Hatta,
  • Tomohiro Nakamura,
  • Naoki Nakaya and ,
  • Satoki Shichijo,
  • Yasuyuki Tanaka,
  • Hiromitsu Kanzaki,
  • Kingo Hirasawa,
  • Ichiro Oda and
  • Tomonori Yano
  • + 15 authors+ 10 authors

23 February 2026

Background: Underwater endoscopic mucosal resection (UEMR) is a relatively new treatment method for sporadic non-ampullary duodenal epithelial tumors (SNADETs), and its usefulness has been reported for SNADETs ≤ 20 mm. However, its effectiveness a...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Article
  • Open Access
1,300 Views
18 Pages

Optimisation of a Caprylic Acid-Based Protocol for IgG Purification from Baboon (Papio anubis) Serum

  • Wathuto Ogopotse,
  • Valentine Musabyimana,
  • Pamela M. Khasandi,
  • Dennis Kotti and ,
  • Maina Ngotho,
  • John M. Kagira and
  • George O. Oluoch
  • + 2 authors+ 0 author

22 February 2026

Caprylic acid (CA) fractionation of serum is a simple and cost-effective method of producing high-quality immunoglobulins. While standardised procedures exist for CA purification of IgG for various animals, no published protocol exists for baboon IgG...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Tutorial
  • Open Access
2 Citations
3,046 Views
41 Pages

19 February 2026

High-throughput sequencing generally results in a list of genes. Which functional groups of genes among the DEGs are meaningful underlying factors to the differential biological/biomedical conditions under investigation? The process to find answers t...

(This article belongs to the Section Synthetic and Systems Biology)
  • Article
  • Open Access
3,114 Views
14 Pages

In Vitro 3D Model of Human Endometrial Stromal and Trophoblast Cells: Techniques for an Optimized Formation and Cryopreservation of Spheroids

  • Karthika Muthuraj,
  • Iwona Scheliga,
  • Dunja M. Baston-Buest,
  • Jana Bender-Liebenthron and ,
  • Jan-Steffen Kruessel and
  • Alexandra P. Bielfeld
  • + 1 author+ 0 author

13 February 2026

Three-dimensional (3D) cell culture models provide physiologically relevant systems that mimic the native endometrial environment better than 2D models and offer reliable platforms to study embryo implantation and maternal–embryo interactions....

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
1,700 Views
10 Pages

A Protocol for Regulating Protein Liquid–Liquid Phase Separation Using NMR-Guided Mutagenesis

  • Mayu Enomoto-Kusano,
  • Kyoko Furuita,
  • Takashi S. Kodama and
  • Chojiro Kojima

12 February 2026

Liquid–liquid phase separation (LLPS) underlies the formation of membraneless cellular compartments, yet experimental strategies that directly connect quantitative LLPS behavior with residue-level structural information remain limited. Here, we...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
1,025 Views
16 Pages

Enhancing Omics Analyses Through Coalitional Games and Shapley Values

  • Eva Vargas,
  • Inés de la Torre and
  • Francisco J. Esteban

12 February 2026

We describe a comprehensive methodology for the application of game theory to omics data analysis, with a particular focus on coalitional games and Shapley values. This approach evaluates the cooperative distribution of genes within high-dimensional...

(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
  • Protocol
  • Open Access
2 Citations
2,508 Views
13 Pages

Optimized Method for Efficient DNA Extraction from Agricultural Soils

  • Elías Hernández-Cruz,
  • Lorena Jacqueline Gómez-Godínez,
  • José Martín Ruvalcaba-Gómez and
  • Ramón Ignacio Arteaga-Garibay

9 February 2026

Soil harbors the highest concentration of microorganisms in ecosystems, and their molecular characterization through high-throughput sequencing is essential for metagenomic studies. However, obtaining high-quality, high-concentration DNA is limited b...

(This article belongs to the Section Molecular and Cellular Biology)
  • Technical Note
  • Open Access
1,070 Views
7 Pages

Development of an In Vitro Whole Blood Model to Study Anti-Inflammatory Effects of Strawberry Polyphenolic Compounds and Postprandial Inflammation

  • Skyelar Reuter,
  • Peter Geevarghese Alex,
  • Casey Weisfuss,
  • Britt Burton-Freeman and
  • Indika Edirisinghe

7 February 2026

Postprandial inflammation, characterized by elevated cytokines, is linked to metabolic diseases. Polyphenol-rich fruits like strawberries possess anti-inflammatory properties that may help reduce this response. Because clinical studies are often cost...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
2,533 Views
16 Pages

Improved Step-by-Step qPCR Method for Absolute Telomere Length Measurement

  • Ekaterina Sergeevna Arshinova,
  • Nataliia Sergeevna Karpova,
  • Olga Leonidovna Terekhina,
  • Malik Nurbekov and
  • Maria Ivanovna Burtovskaya

5 February 2026

Telomere length is a crucial marker of cellular aging and genomic stability, with significant implications for age-related diseases and cancers. This study introduces an improved quantitative PCR (qPCR) method for measuring absolute telomere length,...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
1,938 Views
13 Pages

2 February 2026

Three-dimensional (3D) culture systems that recapitulate the tumor microenvironment are essential for studying cancer cell behavior, drug response, and cell–matrix interactions. Here, we present a detailed protocol for generating 3D spheroid cu...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Article
  • Open Access
1 Citations
1,281 Views
14 Pages

Comprehensive Analytical Profiling for Sustainable Jewelry: A Multi-Technique Characterization of Essential Oil-Modified Rosin

  • Dantong Huang,
  • Kaewbucha Manus,
  • Apiwathnasorn Chalisa,
  • Tianyi Liu and ,
  • Chuyun Yan and
  • Yumeng Gu
  • + 1 author+ 0 author

2 February 2026

Rosin, a renewable natural resin derived from pine trees, is a promising biomass material for sustainable product development, though its distinct intrinsic odor limits broader use. This study implemented a comprehensive analytical strategy to mitiga...

(This article belongs to the Special Issue Analytical Methods in Natural Sciences and Archaeometry)
  • Article
  • Open Access
1,348 Views
10 Pages

28 January 2026

Introduction: Management of trochanteric fractures in revision hip surgery has a high incidence of non-union and complications. Fixation devices are often bulky, prone to breakage, and necessitate reoperation. This study describes a novel soft tissue...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Study Protocol
  • Open Access
1 Citations
2,472 Views
26 Pages

An Integrated Monitoring Protocol to Study the Effects of Management on the C Sequestration Potential of Mediterranean Pine Ecosystems

  • Nikoleta Eleftheriadou,
  • Efstathia D. Mantzari,
  • Natasa Kiorapostolou,
  • Christodoulos I. Sazeides and ,
  • Georgios Xanthopoulos,
  • Nikos Markos,
  • Gavriil Spyroglou,
  • Evdoxia Bintsi-Frantzi,
  • Alexandros Gouvas and
  • Nikolaos M. Fyllas
  • + 8 authors+ 3 authors

26 January 2026

This article describes a field- and laboratory-based framework that can be used to monitor the C balance in Mediterranean pine forest ecosystems under different management practices that determine their structure and function. By jointly monitoring s...

(This article belongs to the Section Synthetic and Systems Biology)
  • Protocol
  • Open Access
1,809 Views
19 Pages

Workflow for Gene Overexpression and Phenotypic Characterisation in Taraxacum kok-saghyz

  • Loredana Lopez,
  • Michele Antonio Savoia,
  • Loretta Daddiego,
  • Paolo Facella and ,
  • Elio Fantini,
  • Linda Bianco,
  • Simone Maci and
  • Francesco Panara
  • + 3 authors+ 0 author

24 January 2026

Taraxacum kok-saghyz (Tks) is a promising plant species for natural rubber (NR) production and represents a model for studying NR biosynthesis in the Asteraceae family. The generation of transgenic plants overexpressing a gene of interest is a well-e...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
2 Citations
1,747 Views
23 Pages

21 January 2026

Reversed-phase high-performance liquid chromatography (RP-HPLC) remains one of the most widely applied analytical techniques in the development and quality control testing of finished pharmaceutical products. The combination of gradient chromatograph...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
1 Citations
1,619 Views
21 Pages

Multimodal Wearable Monitoring of Exercise in Isolated, Confined, and Extreme Environments: A Standardized Method

  • Jan Hejda,
  • Marek Sokol,
  • Lydie Leová,
  • Petr Volf and ,
  • Jan Tonner,
  • Wei-Chun Hsu,
  • Yi-Jia Lin,
  • Tommy Sugiarto,
  • Miroslav Rozložník and
  • Patrik Kutílek
  • + 5 authors+ 0 author

21 January 2026

This study presents a standardized method for multimodal monitoring of exercise execution in isolated, confined, and extreme (ICE) environments, addressing the need for reproducible assessment of neuromuscular and cardiovascular responses under space...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Study Protocol
  • Open Access
1 Citations
1,993 Views
12 Pages

Probiotic and Prebiotic Supplementation for Gastrointestinal Discomfort in Chronic Spinal Cord Injury (PRO-GIDSCI): A Randomized Controlled Crossover Trial Protocol

  • Julia Trunz,
  • Cyra Schmandt,
  • Anneke Hertig-Godeschalk,
  • Marija Glisic and ,
  • Jivko Stoyanov and
  • Claudio Perret
  • + 1 author+ 0 author

17 January 2026

Background: Gastrointestinal discomfort affects up to 70% of individuals with spinal cord injury (SCI), largely due to gut dysbiosis caused by altered transit time and reduced gastrointestinal motility from autonomic disruption. Emerging evidence lin...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
3 Citations
1,345 Views
15 Pages

16 January 2026

Although sample matrices are available for assessing cortisol output over hours/days (serum, saliva, or urine) or months (hair or nails), there is no current method for measuring integrated cortisol output over a period of 1 week. Therefore, the prim...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Study Protocol
  • Open Access
1,570 Views
16 Pages

A Study Protocol for Developing a Pragmatic Aetiology-Based Silicosis Prevention and Elimination Approach in Southern Africa

  • Norman Nkuzi Khoza,
  • Thokozani Patrick Mbonane,
  • Phoka C. Rathebe and
  • Masilu Daniel Masekameni

14 January 2026

Workers’ exposure to silica dust is a global occupational and public health concern and is particularly prevalent in Southern Africa, mainly because of inadequate dust control measures. It is worsened by the high prevalence of HIV/AIDS, which e...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
2 Citations
1,520 Views
26 Pages

Methodologies of Care: A Multimodal, Participatory Research Approach with Vulnerable Families Among South African Communities

  • James Reid,
  • Chanté Johannes,
  • Shenaaz Wareley,
  • Collen Ngadhi and ,
  • Avukonke Nginase,
  • Katerina Demetriou and
  • Nicolette V. Roman
  • + 2 authors+ 0 author

13 January 2026

Multimodal methods provide valuable opportunities within Participatory Action Research (PAR), to foster meaningful participation, and amplify marginalized voices. However, conventional research approaches have not always adequately captured the compl...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
1,588 Views
15 Pages

11 January 2026

Background: Effective cetylpyridinium chloride (CPC)-based mouthwashes critically depend on maintaining maximum levels of bioavailable CPC to deliver optimum antimicrobial benefits. While this is traditionally assessed using cellulose-based methods,...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
1 Citations
3,428 Views
10 Pages

Accurate quantification of iron is essential in biological, chemical, and nanomaterial research, yet commonly used ferrozine-based assays suffer from safety hazards, inconsistent reduction efficiency, and unstable absorbance readings. To address thes...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Protocol
  • Open Access
2,069 Views
19 Pages

Decoding Cerebrospinal Fluid: Integrative Metabolomics Across Multiple Platforms

  • Antoine Presset,
  • Sylvie Bodard,
  • Antoine Lefèvre,
  • Edward Oujagir and ,
  • Camille Dupuy,
  • Jean-Michel Escoffre and
  • Lydie Nadal-Desbarats
  • + 2 authors+ 0 author

Cerebrospinal fluid (CSF) is a key biological matrix that reflects the physiological and pathological states of the central nervous system (CNS). It supports brain function by regulating ionic balance, facilitating molecular transport, and clearing m...

(This article belongs to the Section Omics and High Throughput)
  • Article
  • Open Access
3 Citations
4,548 Views
22 Pages

Repeatability and Variability of a High-Fat High-Fructose Diet-Induced Metabolic Syndrome Model in Young Adult Male Wistar Rats

  • Danail Pavlov,
  • Silvia Gancheva,
  • Klementina Moneva-Marinova,
  • Antoaneta Georgieva and ,
  • Milena Todorova,
  • Nadezhda Stefanova,
  • Mehmed Reyzov,
  • Elis Rafailova,
  • Miroslav Eftimov and
  • Maria Zhelyazkova-Savova
  • + 7 authors+ 2 authors

Metabolic syndrome is a disorder of energy metabolism characterized by persistently high prevalence and significant medical and economic burden on society. An effective animal model that closely replicates the key features of the syndrome in humans i...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
1 Citations
2,710 Views
25 Pages

Setting is a fundamental movement in volleyball. While there are several optimal interpreters of the role in professional play, there is a surprising lack of advanced measurement techniques for the evaluation of the movement from a biomechanical pers...

  • Protocol
  • Open Access
2 Citations
2,648 Views
16 Pages

Human Amniotic Membrane Procurement Protocol and Evaluation of a Simplified Alkaline Decellularization Method

  • David A. de la Garza Kalife,
  • Antonio Rojas Murillo,
  • Rodolfo Franco Marquez,
  • Diana Laura Morales Wong and ,
  • Jorge Lara Arias,
  • José Felix Vilchez Cavazos,
  • Hector Leija Gutierrez,
  • Mario A. Simental Mendía and
  • Elsa Nancy Garza Treviño
  • + 4 authors+ 0 author

Amniotic membrane (AM) has gained wide application in regenerative medicine due to its biocompatibility and extracellular matrix (ECM) composition. Effective decellularization is essential to minimize immunogenicity while preserving tissue architectu...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Article
  • Open Access
2,107 Views
14 Pages

Development of an ELISA Using Recombinant Chimeric SM Protein for Serological Detection of SARS-CoV-2 Antibodies

  • Gulnur Nakhanova,
  • Olga Chervyakova,
  • Kamshat Shorayeva,
  • Aisha Issabek and ,
  • Sabina Moldagulova,
  • Asankadyr Zhunushov,
  • Aknur Ulankyzy,
  • Aigerim Zhakypbek,
  • Alisher Omurtay and
  • Aslan Kerimbayev
  • + 10 authors+ 5 authors

22 December 2025

The emergence and spread of coronavirus infections have created a necessity to develop serological methods for assessing population immunity. The enzyme-linked immunosorbent assay (ELISA) remains one of the most accessible and informative approaches...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
1,692 Views
12 Pages

Raman Spectroscopy for Testing Wood Pellets

  • Tereza Zemánková,
  • Martin Kizovský,
  • Zdeněk Pilát,
  • Pavlína Modlitbová and ,
  • Jan Ježek,
  • Martin Šiler and
  • Ota Samek
  • + 2 authors+ 0 author

21 December 2025

The creation of bioenergy based on the biomass wood pellet industry, which accounts for the majority of the global biomass supply, is one of the most common and important ways to utilize waste wood, wood dust, and other byproducts of wood manufacturi...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
5 Citations
2,511 Views
13 Pages

21 December 2025

Ordinary linear regression is the most common approach for modeling relationships between continuous outcomes and explanatory variables in epidemiological research. However, this method relies on restrictive assumptions—normality, homoscedastic...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
1,695 Views
8 Pages

Imaging Cell Competition in Ex-Vivo Drosophila Adult Brains

  • Andrés Gutiérrez-García,
  • Mariana Marques-Reis and
  • Eduardo Moreno

20 December 2025

Live imaging has been instrumental in understanding cellular dynamics in Drosophila tissues, but technical limitations have prevented the long-term visualization of cell competition in adult brains. Here, we describe a simple ex vivo protocol that en...

(This article belongs to the Section Molecular and Cellular Biology)
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Methods Protoc. - ISSN 2409-9279