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Methods and Protocols, Volume 8, Issue 2

April 2025 - 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
1,593 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
829 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
1,714 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
2 Citations
1,228 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
2,335 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
1,915 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
1 Citations
2,025 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
1,568 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
  • Giuseppe Carrieri
  • + 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
1,445 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
1,658 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...

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Methods Protoc. - ISSN 2409-9279