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Methods and Protocols, Volume 8, Issue 2

2025 April - 21 articles

Cover Story: Insects like Drosophila and butterflies display complex behaviors and cognitive abilities, which can be attributed to their small yet highly organized brain architecture. While Drosophila brains have been extensively studied, spatial gene expression data for butterfly brains remain limited. Butterfly larvae, such as Bicyclus anynana, exhibit intricate behaviors, yet how this information is processed in their brains at the molecular level is not well understood. Banerjee et. al., 2025, optimized a Hybridization Chain Reaction v3.0 (HCR v3.0) protocol—refining fixation, polyacrylamide gel embedding, and permeabilization—to visualize the spatial expression of ten genes in whole fixed larval brains at a single-cell resolution. View this paper
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Articles (21)

  • Article
  • Open Access
2 Citations
1,802 Views
16 Pages

Quantification of Circulating Cell-Free DNA as a NETosis Marker in Trauma Patients with Type 2 Diabetes Mellitus

  • Filiz Sahin,
  • Regina Breinbauer,
  • Caren Linnemann,
  • Melike Tombaz,
  • Andreas K. Nussler and
  • Sabrina Ehnert

Type 2 diabetes mellitus (T2DM) significantly impairs fracture healing, with neutrophils playing a crucial role in this process. In T2DM, these immune cells are over-activated, leading to the excessive release of neutrophil extracellular traps (NETs)...

  • Article
  • Open Access
909 Views
12 Pages

Concurrent Validity of Three Photogrammetric Methods for Assessing Knee Alignment in Sagittal Plane

  • Bruna Nichele da Rosa,
  • Paula Andryelly Gomes Giendruczak,
  • Marina Ziegler Frantz,
  • Matias Noll and
  • Cláudia Tarragô Candotti

Background: Evidence supporting the validity of photogrammetry for assessing body segment alignment remains limited, with most studies focusing on spinal evaluation. Thus, there is a lack of robust research examining its use for other body segments s...

  • Article
  • Open Access
1 Citations
1,973 Views
11 Pages

Physical Exercise and Psychophysical Learnings on Basic Strength Development

  • Gaetano Raiola,
  • Giovanni Esposito,
  • Sara Aliberti,
  • Francesca D’Elia and
  • Tiziana D’Isanto

Strength development through physical exercise enhances neuromodulator production, neural connectivity, and motor unit efficiency. Beyond physical benefits, understanding individuals’ perceptions, opinions, and knowledge can optimize engagement...

  • Article
  • Open Access
3 Citations
1,433 Views
22 Pages

Steam-assisted gravity drainage (SAGD) is a widely used thermal enhanced oil recovery (EOR) technique in North America, particularly in high-permeability oil sand reservoirs. While effective, its economic viability has declined due to low oil prices...

  • Protocol
  • Open Access
2,588 Views
19 Pages

Short hairpin RNAs (shRNAs) are potent tools for gene silencing, offering therapeutic potential for gene and cell therapy applications. However, their efficacy and safety depend on precise processing by the RNA interference machinery and the generati...

  • Article
  • Open Access
1 Citations
2,145 Views
13 Pages

Enzyme-Linked Immunosorbent Assay (ELISA) Development for Equine Serum Amyloid A (SAA) Determination Using Recombinant Proteins

  • Pollyanna C. Souto,
  • Marcus R. Santos,
  • Andrés M. Ortega Orozco,
  • Lucas D. Bento,
  • Camilo J. Ramirez-Lopez,
  • Fabrícia M. Girardi,
  • Júlia C. Assis Machado,
  • Leandro L. de Oliveira and
  • Leandro A. da Fonseca

We aimed to develop a species-specific ELISA for qualitatively and quantitatively determining serum amyloid A (SAA) in horses. Current methods for measuring SAA in horses utilize ELISA or immunoturbidimetric tests designed for human SAA, which are no...

  • Protocol
  • Open Access
2 Citations
2,305 Views
14 Pages

Specific Aspects of SELEX Protocol: Different Approaches for ssDNA Generation

  • Alexandr Garanin,
  • Andrey Shalaev,
  • Lidia Zabegina,
  • Ekaterina Kadantseva,
  • Tatiana Sharonova and
  • Anastasia Malek

Background: Synthetic DNA aptamers are a class of molecules with potential applications in medicine, serving as molecular sensors or ligands for targeted drug delivery. Systematic evolution of ligands by exponential enrichment (SELEX) is a technology...

  • Review
  • Open Access
1,755 Views
11 Pages

The Handling and Sampling of Radical Cystectomy Specimens: A Standardized Approach for Pathological Evaluation

  • Francesca Sanguedolce,
  • Angelo Cormio,
  • Magda Zanelli,
  • Maurizio Zizzo,
  • Andrea Palicelli,
  • Alessandra Filosa,
  • Ugo Giovanni Falagario,
  • Andrea Benedetto Galosi,
  • Luigi Cormio and
  • Roberta Mazzucchelli
  • + 1 author

An accurate histopathological evaluation of radical cystectomy (RC) specimens is crucial for optimal tumor staging, prognosis, and therapeutic decision making. The increasing demand for precision medicine and multidisciplinary oncological management...

  • Study Protocol
  • Open Access
1,586 Views
10 Pages

(1) Background: Research has consistently demonstrated that regular physical activity (PA) is associated with several benefits among adolescents. However, PA levels among adolescents are low worldwide and tend to decrease with age. Consequently, rese...

  • Protocol
  • Open Access
1,809 Views
10 Pages

Heavy metal contamination of soil and water is a growing environmental concern, especially mercury, lead, and cadmium. Therefore, fast and reliable methodologies to assess contamination in the field are in demand. However, many methodologies require...

  • Article
  • Open Access
3 Citations
1,745 Views
13 Pages

Using the Inverse Three-Point Bending Test to Determine Mechanical Properties of Plant Stems

  • Alexander Anisimov,
  • Maksim Suslov,
  • Anna Petrova,
  • Tatyana Chernova,
  • Oleg Gorshkov and
  • Tatyana Gorshkova

Biomechanical parameters of plant tissues and organs are increasingly recognized as key factors in plant development and application, increasing the demand for convenient devices for their study. The paper presents an original device for performing a...

  • Protocol
  • Open Access
2 Citations
1,845 Views
20 Pages

Mapping Gene Expression in Whole Larval Brains of Bicyclus anynana Butterflies

  • Tirtha Das Banerjee,
  • Linwan Zhang and
  • Antónia Monteiro

Butterfly larvae display intricate cognitive capacities and behaviors, but relatively little is known about how those behaviors alter their brains at the molecular level. Here, we optimized a hybridization chain reaction 3.0 (HCR v3.0) protocol to vi...

  • Article
  • Open Access
2 Citations
1,886 Views
10 Pages

Micro-Electrometric Method for Assessing Cholinesterase Activity in Human Whole Blood

  • Nan Ei Moh Moh Kyi,
  • Muhammad Samar,
  • Surat Hongsibsong,
  • Nootchakarn Sawarng,
  • Supansa Pata and
  • Anurak Wongta

Cholinesterase (ChE) is an essential enzyme for nervous system function, and its activity in the blood serves as a biomarker for pesticide exposure, necessitating accessible assessment methods in resource-limited areas. This study focused on developi...

  • Protocol
  • Open Access
3,813 Views
22 Pages

Development of an Application Method for Volatile Compounds Derived from Mushroom Fungi Beds as Plant Growth-Promoting Biostimulants

  • Clever N. Kanga,
  • Yui Okisaka,
  • Shigeru Hanamata,
  • Daijiro Ueda,
  • Tsutomu Sato,
  • Toshiaki Mitsui and
  • Kimiko Itoh

Volatile compounds (VCs) from fungi can promote plant growth, but their application methods are limited. Edible mushroom fungi beds (FBs) provide a readily available alternative source of fungal VCs, although their biostimulatory functions remain unv...

  • Article
  • Open Access
1 Citations
1,165 Views
14 Pages

Measurement of Wheel Skidding on Racing Wheelchairs

  • Nolwenn Poquerusse,
  • Arnaud Hays,
  • Aurélie Cortial,
  • Opale Vigié,
  • Ilona Alberca,
  • Mathieu Deves,
  • Lorian Honnorat,
  • Safiya Noury,
  • Bruno Watier and
  • Arnaud Faupin

In the context of wheelchair racing, research primarily focuses on studying wheelchair ergonomics and determining kinematic, kinetic, and rolling resistance variables. One factor identified as influencing athletes’ performance is wheel skidding...

  • Article
  • Open Access
2 Citations
2,016 Views
15 Pages

Whole-Exome Sequencing Followed by dPCR-Based Personalized Genetic Approach in Solid Organ Transplantation: A Study Protocol and Preliminary Results

  • Mirgul Bayanova,
  • Aidos Bolatov,
  • Dias Malik,
  • Aida Zhenissova,
  • Aizhan Abdikadirova,
  • Malika Sapargaliyeva,
  • Lyazzat Nazarova,
  • Gulzhan Myrzakhmetova,
  • Svetlana Novikova and
  • Yuriy Pya
  • + 1 author

Genetic profiling and molecular biology methods have made it possible to study the etiology of the end-stage organ disease that led to transplantation, the genetic factors of compatibility and tolerance of the transplant, and the pharmacogenetics of...

  • Study Protocol
  • Open Access
2,052 Views
9 Pages

Background and aim: The use of mHealth, especially short-message text (SMS), has proven to be an effective intervention in promoting behavioral health outcomes in populations across different contexts and settings. While MomConnect, an mHealth techno...

  • Protocol
  • Open Access
1,052 Views
12 Pages

A Validation Protocol for an Instrumented Wheel: A Comparison with a Dual-Roller Handrim Wheelchair Ergometer

  • Safiya Noury,
  • Arnaud Hays,
  • Nolwenn Poquerusse,
  • Opale Vigié,
  • Lorian Honnorat,
  • Ilona Alberca,
  • Mathieu Deves,
  • Justin Regnaud and
  • Arnaud Faupin

Measuring the propulsion performance of sport wheelchairs in ecological conditions remains complex due to variations inherent in real-world practice. This study aims to develop a validation protocol for an instrumented wheel designed to measure propu...

  • Article
  • Open Access
2,244 Views
14 Pages

Reporting guidelines are created with the intention to enhance the quality and transparency of reporting different research methods. Trochim’s concept mapping (often referred to as group concept mapping) is a six-phase, participatory mixed-meth...

  • Article
  • Open Access
2 Citations
3,763 Views
14 Pages

Comparative Analysis of Methods for Assessing On-Target Gene Editing Efficiencies

  • Bing Yao,
  • Qiangbing Yang,
  • Manuel A. F. V. Gonçalves,
  • Raymond Schiffelers,
  • Joost P. G. Sluijter and
  • Zhiyong Lei

Genome editing based on CRISPR-derived technologies has become a cornerstone in both fundamental research and clinical applications. Accurately measuring editing efficiency is crucial for developing and applying genome editing strategies. This study...

  • Study Protocol
  • Open Access
1 Citations
2,157 Views
12 Pages

A Randomized, Double-Blind, Controlled Trial Protocol for Therapeutic Neuroscience Education in Chronic Migraine Patients: A Clinical–Neurophysiological Combined Study Design

  • Matteo Castaldo,
  • Tiziana Atzori,
  • Angela Comanducci,
  • Giacomo Querzola,
  • Chiara-Camilla Derchi,
  • Daniele Lovattini,
  • Carlo Manzoni,
  • Carlo Lovati,
  • Francesca Baglio and
  • Alessandro Viganò
  • + 3 authors

20 February 2025

Chronic migraine (CM) is a highly disabling condition, affecting about 2% of the global population. Non-pharmacological treatments can be optimal for their non-invasive nature. This prospective, randomized, double-blind, controlled trial aimed to tes...

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Methods Protoc. - ISSN 2409-9279