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Methods and Protocols, Volume 8, Issue 4

2025 August - 30 articles

Cover Story: Developing new methods to combat cancer cell adhesion-related therapy resistance is essential. Cancer cells typically express multiple redundant integrins; one hypothesis for the lack of efficacy of current antagonists is their high selectivity for a single integrin. Elsharif et al. report a functional dual-β3-expressing cell model to investigate the effects of combined αIIbβ3/αvβ3 antagonism using K562 chronic myeloid leukemia cells treated with PMA to upregulate functional αIIbβ3 and αvβ3 integrin protein levels. This optimized method provides a reliable platform for adhesion and detachment assays, establishing a reproducible approach for studying dual β3 integrin targeting. View this paper 
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Articles (30)

  • Article
  • Open Access
1,440 Views
15 Pages

Development of an Ex Vivo Platform to Model Urethral Healing

  • Christopher Foster,
  • Ryan Tran,
  • Khushi Grover,
  • Abdullah Salama and
  • Courtney K. Rowe

Background: Urethral strictures impact millions, causing significant morbidity and millions in healthcare costs. Testing new interventions is limited by the lack of inexpensive urethral healing models. We developed an ex vivo model of early urethral...

  • Review
  • Open Access
3,613 Views
29 Pages

Functional Methods for Studying Sperm–Zona Pellucida Interaction in Mammals

  • Natalie Zelenkova,
  • Veronika Kraus,
  • Alexandra Maresova,
  • Zuzana Pilsova,
  • Aneta Pilsova,
  • Barbora Klusackova,
  • Eva Chmelikova,
  • Katerina Komrskova and
  • Pavla Postlerova

The initial molecular events mediating mammalian sperm binding to the zona pellucida (ZP) of the oocyte are highly complex and still not fully elucidated. Recent advances have identified multiple candidate sperm surface proteins, often functioning as...

  • Article
  • Open Access
1 Citations
1,813 Views
17 Pages

Data on the genetic and environmental factors underlying the co-occurrence of Cognitive Disengagement Syndrome (CDS), Attention Deficit Hyperactivity Disorder (ADHD), and Emotional Dysregulation (ED) are limited. This study aimed to explore the natur...

  • Article
  • Open Access
5 Citations
5,739 Views
19 Pages

Optimizing Cell Density and Unveiling Cytotoxic Profiles of DMSO and Ethanol in Six Cancer Cell Lines: Experimental and In Silico Insights

  • Abutaleb Asiri,
  • Munazzah Tasleem,
  • Muwadah Al Said,
  • Abdulaziz Asiri,
  • Ali Ahmed Al Qarni and
  • Ahmed Bakillah

Background: Accurate assessment of drug cytotoxicity in vitro is essential for preclinical evaluation of anticancer agents. Methodological parameters such as cell density and solvent concentrations can significantly influence the reproducibility and...

  • Protocol
  • Open Access
1,530 Views
18 Pages

1H Nuclear Magnetic Resonance (NMR) Metabolomics in Rodent Plasma: A Reproducible Framework for Preclinical Biomarker Discovery

  • Mohd Naeem Mohd Nawi,
  • Ranina Radzi,
  • Azizan Ali,
  • Siti Zubaidah Che Lem,
  • Azlina Zulkapli,
  • Ezarul Faradianna Lokman,
  • Mansor Fazliana,
  • Sreelakshmi Sankara Narayanan,
  • Karuthan Chinna and
  • Tilakavati Karupaiah
  • + 2 authors

This protocol paper outlines a robust and reproducible framework for a 1H nuclear magnetic resonance (NMR) metabolomics analysis of rodent plasma, designed to facilitate preclinical biomarker discovery. The protocol details optimised steps for plasma...

  • Article
  • Open Access
1 Citations
941 Views
12 Pages

In vitro cartilage explant culture has been used to assess nutraceuticals on cartilage responses to inflammatory stimuli. However, applying extracts of nutraceuticals directly to cartilage explants does not account for effects of digestion and hepati...

  • Technical Note
  • Open Access
1,029 Views
7 Pages

An Optimized Protocol for SBEM-Based Ultrastructural Analysis of Cultured Human Cells

  • Natalia Diak,
  • Łukasz Chajec,
  • Agnieszka Fus-Kujawa and
  • Karolina Bajdak-Rusinek

Serial block-face scanning electron microscopy (SBEM) is a powerful technique for three-dimensional ultrastructural analysis of biological samples, though its application to in vitro cultured human cells remains underutilized. In this study, we prese...

  • Article
  • Open Access
3 Citations
1,972 Views
15 Pages

Expression of Recombinant Hirudin in Bacteria and Yeast: A Comparative Approach

  • Zhongjie Wang,
  • Dominique Böttcher,
  • Uwe T. Bornscheuer and
  • Christian Müller

The expression of recombinant proteins in heterologous hosts is a common strategy to obtain larger quantities of the “protein of interest” (POI) for scientific, therapeutic or commercial purposes. However, the experimental success of such...

  • Review
  • Open Access
3 Citations
10,704 Views
27 Pages

The Allium cepa Model: A Review of Its Application as a Cytogenetic Tool for Evaluating the Biosafety Potential of Plant Extracts

  • Daniela Nicuță,
  • Luminița Grosu,
  • Oana-Irina Patriciu,
  • Roxana-Elena Voicu and
  • Irina-Claudia Alexa

In establishing the safety or tolerability profile of bioactive plant extracts, it is important to perform toxicity studies using appropriate, accessible, and sustainable methods. The Allium cepa model is well known and frequently used for accurate e...

  • Protocol
  • Open Access
1,663 Views
9 Pages

Protocol for the Systematic Quantitative Ultrastructural Analysis of Mitochondria in Cardiac Tissue

  • Rebecca Schönmehl,
  • Lina Winter,
  • Daniel H. Mendelsohn,
  • Wing-Hoi Cheung,
  • Ronald Man Yeung Wong,
  • Steffen Pabel,
  • Samuel Sossalla and
  • Christoph Brochhausen

Mitochondria play a crucial role in adapting to fluctuating energy demands, particularly in various heart diseases. In addition to functional analyses such as the measurement of ROS or ATP, analysis of mitochondrial ultrastructure can be used to draw...

  • Article
  • Open Access
2 Citations
1,265 Views
19 Pages

Comparing Nanomechanical Properties and Membrane Roughness Along the Aging of Human Erythrocytes

  • Giovanni Longo,
  • Simone Dinarelli,
  • Federica Collacchi and
  • Marco Girasole

Erythrocyte (RBC) aging involves significant structural and nanomechanical alterations crucial to their function. This study aims to bridge the gap between analyses based on statistical morphometric parameters, e.g., membrane roughness, and those bas...

  • Article
  • Open Access
1 Citations
1,501 Views
11 Pages

Comparative Analysis of a Rapid Quantitative Immunoassay to the Reference Methodology for the Measurement of Blood Vitamin D Levels

  • Gary R. McLean,
  • Samson Soyemi,
  • Oluwafunmito P. Ajayi,
  • Sandra Fernando,
  • Wiktor Sowinski-Mydlarz,
  • Duncan Stewart,
  • Sarah Illingworth,
  • Matthew Atkins and
  • Dee Bhakta

Vitamin D is the only vitamin that is conditionally essential, as it is synthesized from precursors after UV light exposure, whilst also being obtained from the diet. It has numerous health benefits, with deficiency becoming a major concern globally,...

  • Study Protocol
  • Open Access
1,639 Views
11 Pages

Air pollution is linked to childhood mortality and morbidity in low- and middle-income countries globally. There is growing evidence linking air pollution to asthma and other respiratory diseases in children. Studies have shown that children are like...

  • Study Protocol
  • Open Access
2,704 Views
11 Pages

Faecal microbiota transplantation (FMT) is an emerging therapy for gastrointestinal and neurological disorders, acting via the microbiota–gut–brain axis. Altering gut microbial composition may influence cognitive function, but this has no...

  • Article
  • Open Access
3 Citations
2,418 Views
25 Pages

Green Chemistry and Multivariate Optimization in the Extraction of Phenolic Compounds: The Potential of NaDES in Alternative Raw Materials for Expanded Extrudates

  • Mateus Alves Araújo,
  • Bianca Rodrigues Morais,
  • João Pedro da Silva Santos,
  • Larissa Karla de Jesus,
  • Kaliston Aurélio Lomba,
  • Gustavo Costa do Nascimento,
  • Marcus Alvarenga Soares,
  • Nathalia de Andrade Neves,
  • Irene Andressa and
  • Marcio Schmiele
  • + 1 author

Phenolic compounds are secondary metabolites widely distributed among plants, with bioactive properties, especially antioxidant activity. The search for sustainable extraction methods has driven the use of natural deep eutectic solvents (NaDESs), for...

  • Article
  • Open Access
1 Citations
1,946 Views
20 Pages

Development and Evaluation of a Nanoparticle-Based Immunoassay for Rotavirus Detection: A Suitable Alternative to ELISA and PCR in Low-Income Setting

  • Margaret Oluwatoyin Japhet,
  • Adeogo Timilehin Bankole,
  • Temiloluwa Ifeoluwa Omotade,
  • Oyelola Eyinade Adeoye,
  • Oladiran Famurewa and
  • Simeon K. Adesina

Every year, diarrhoea is responsible for >1 million deaths in children with ages from 0 to 5 years, with rotavirus as the leading cause. The regions most affected lack routine rotavirus diagnosis due to high cost, lack of necessary equipment and s...

  • Protocol
  • Open Access
1,142 Views
8 Pages

A Simple Way to Quantify Plastic in Bats (Mammalia: Chiroptera) Using an Ultraviolet Flashlight

  • Letícia Lima Correia,
  • Ariane de Sousa Brasil,
  • Thiago Bernardi Vieira,
  • Magali Gonçalves Garcia,
  • Daniela de Melo e Silva,
  • Ana Beatriz Alencastre-Santos and
  • Danielle Regina Gomes Ribeiro-Brasil

Bats, as key ecological players, interact with a diverse array of organisms and perform essential roles in ecosystems, including pollination, pest control, and seed dispersal. However, their populations face significant threats from habitat contamina...

  • Article
  • Open Access
1 Citations
1,694 Views
12 Pages

Burn wounds present a significant challenge to both the medical and scientific communities, contributing to the global economic burden on healthcare systems. Due to the complexity and highly variability of burn injuries, along with intricate pathophy...

  • Article
  • Open Access
1 Citations
1,595 Views
13 Pages

Novel DNA Barcoding and Multiplex PCR Strategy for the Molecular Identification and Mycotoxin Gene Detection of Fusarium spp. in Maize from Bulgaria

  • Daniela Stoeva,
  • Deyana Gencheva,
  • Georgi Radoslavov,
  • Peter Hristov,
  • Rozalina Yordanova and
  • Georgi Beev

Fusarium spp. represent a critical threat to maize production and food safety due to their mycotoxin production. This study introduces a refined molecular identification protocol integrating four genomic regions—ITS1, IGS, TEF-1α, and &be...

  • Study Protocol
  • Open Access
2 Citations
6,736 Views
21 Pages

Core stability is fundamental to posture, balance, and force transmission throughout the kinetic chain. Although traditionally associated with athletic performance, emerging research highlights its broader applicability to recreational fitness. This...

  • Article
  • Open Access
1 Citations
1,338 Views
19 Pages

A Model-Based Approach to Neuronal Electrical Activity and Spatial Organization Through the Neuronal Actin Cytoskeleton

  • Ali H. Rafati,
  • Sâmia Joca,
  • Regina T. Vontell,
  • Carina Mallard,
  • Gregers Wegener and
  • Maryam Ardalan

The study of neuronal electrical activity and spatial organization is essential for uncovering the mechanisms that regulate neuronal electrophysiology and function. Mathematical models have been utilized to analyze the structural properties of neuron...

  • Article
  • Open Access
1,358 Views
15 Pages

Formation and Characterization of Two Magnetic Three-Dimensional Spheroid Models of Murine Pancreatic Adenocarcinoma

  • Magali Perier,
  • Litan Wang,
  • Marine Simonneau,
  • Jacqueline Ngo-Reymond,
  • Julie Guillermet-Guibert,
  • Maxime Lafond and
  • Cyril Lafon

Pancreatic adenocarcinoma remains one of the deadliest cancers, with limited treatment options and high chemoresistance. Traditional 2D cell cultures fail to accurately replicate the tumor architecture. Our study introduces three-dimensional (3D) pan...

  • Study Protocol
  • Open Access
2 Citations
1,353 Views
22 Pages

A Framework for Corticomuscle Control Studies Using a Serious Gaming Approach

  • Pedro Correia,
  • Carla Quintão,
  • Cláudia Quaresma and
  • Ricardo Vigário

Sophisticated voluntary movements are essential for everyday functioning, making the study of how the brain controls muscle activity a central challenge in neuroscience. Investigating corticomuscular control through non-invasive electrophysiological...

  • Article
  • Open Access
1 Citations
2,674 Views
14 Pages

Several of the integrin family of cell adhesion receptors have been popular targets for the development of anticancer agents, but with little clinical success to date. Cancer cells usually express multiple redundant integrins; one hypothesis for the...

  • Article
  • Open Access
944 Views
11 Pages

Xanthomonas phaseoli pv. dieffenbachiae (Xpd), the causal agent of bacterial blight in Anthurium within the Araceae family, is listed as an EPPO A2 quarantine organism. Although the whole genome of Xpd has been sequenced, the molecular mechanisms und...

  • Article
  • Open Access
909 Views
19 Pages

Automated Video Quality Assessment for the Edinburgh Visual Gait Score (EVGS)

  • Rajkumar Arumugam Jeeva,
  • Edward D. Lemaire,
  • Ramiro Olleac,
  • Kevin Cheung,
  • Albert Tu and
  • Natalie Baddour

This research addresses critical challenges in clinical gait analysis by developing an automated video quality assessment framework to support Edinburgh Visual Gait Score (EVGS) scoring. The proposed methodology uses the MoveNet Lightning pose estima...

  • Study Protocol
  • Open Access
1,389 Views
21 Pages

Project SWITCH Study Protocol: A Tobacco-Free Workplace Program for Dissemination and Implementation in Lung Cancer Screening Centers

  • Ammar D. Siddiqi,
  • Maggie Britton,
  • Isabel Martinez Leal,
  • Matthew Taing,
  • Tzuan A. Chen,
  • Lisa M. Lowenstein,
  • Jennifer A. Minnix and
  • Lorraine R. Reitzel

Background/Objectives: Cigarette smoking has been causally linked to 90% of all cases of lung cancer, contributing to its high mortality rate. Lung cancer screening centers offer low-dose computed tomography, the only recommended diagnostic screening...

  • Article
  • Open Access
1 Citations
2,627 Views
12 Pages

Background: This study aimed to evaluate and compare the survival rates of immediate dental implants (type 1) in patients who received different types of prophylactic antibiotics. Methods: This retrospective analysis examined data from 3351 immediate...

  • Technical Note
  • Open Access
1,010 Views
9 Pages

Understanding the motion behaviors of animals is crucial for unraveling the mechanisms underlying ethology across various domains, such as movement patterns, food detection, and defense strategies. In this study, we devised a simplified method enabli...

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Methods Protoc. - ISSN 2409-9279