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Methods and Protocols, Volume 8, Issue 3

2025 June - 24 articles

Cover Story: Major Histocompatibility Complex (MHC) molecules are a central puzzle piece in the initiation of immune responses. Although outbred Swiss mice are widely used in biomedical research, there is a paucity of information on the sequences of antigenic peptides presented by MHC molecules. To facilitate immunological studies involving these mice, we present an array of validated antibodies suitable as capture reagents for the study of peptide–MHC complexes in the outbred Swiss albino mouse strain. Using antibodies that capture MHC class I and MHC class II complexes, we present the thymic and splenic immunopeptidomes in this highly genetically diverse mouse strain. View this paper
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Articles (24)

  • Protocol
  • Open Access
1 Citations
1,258 Views
21 Pages

Expression and Site-Specific Biotinylation of Human Cytosolic 5′-Nucleotidase 1A in Escherichia coli

  • Nataliya Slater,
  • Anuradha Sooda,
  • Frank L. Mastaglia,
  • Sue Fletcher,
  • Mark Watson,
  • Merrilee Needham and
  • Jerome D. Coudert

Autoantibodies targeting cytosolic 5′-nucleotidase 1A (cN1A) are found in several autoimmune diseases, including inclusion body myositis (IBM), Sjögren’s syndrome, and systemic lupus erythematosus. While they have diagnostic relevanc...

  • Feature Paper
  • Article
  • Open Access
1,669 Views
20 Pages

DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) pr...

  • Protocol
  • Open Access
1,948 Views
16 Pages

Oligodendrocytes form myelin in the central nervous system, and their dysfunction can cause severe neurological symptoms, as large-scale analyses have highlighted numerous gene expression alterations in pathological conditions. Although in vivo funct...

  • Communication
  • Open Access
784 Views
8 Pages

Cystic Lung Phantom to Validate Clinical CT Protocols

  • Shefra Shah,
  • Farah Hussaini,
  • Dumitru Mazilu,
  • Eric E. Bennett and
  • Han Wen

In computed tomography (CT)-based evaluation of the extent of cystic changes in the lungs of patients with cystic lung diseases, such as Lymphangioleiomyomatosis (LAM), there is a lack of a lung phantom containing air-filled cavities that mimic pulmo...

  • Study Protocol
  • Open Access
2,505 Views
15 Pages

Background: Pressure injuries (PIs) and shoulder pain (SP) are frequent problems in individuals with spinal cord injury (SCI), affecting both quality of life and healthcare use. Although pressure relief (PR) is recommended to prevent PIs, it is often...

  • Article
  • Open Access
1,526 Views
19 Pages

A Refined Approach to Isolate Interneurons for High-Validity Epigenetic Studies in Human Brain Tissue

  • Ariel Cariaga-Martínez,
  • Kilian Jesús Gutierrez,
  • Ignacio Regidor,
  • Marta Del Álamo,
  • Jerónimo Saiz-Ruiz and
  • Raúl Alelú-Paz

Epigenetic research has made notable progress in recent years, yet our ability to explore the human brain at a cellular level remains limited. One of the main obstacles has been the difficulty of isolating specific neuronal populations from postmorte...

  • Article
  • Open Access
1 Citations
2,060 Views
10 Pages

Improved RSV Neutralization Assay Using Recombinant RSV Expressing Reporter Fluorescent Protein

  • Yutaro Yamagata,
  • Michiko Toizumi,
  • Jean-Francois Eleouet,
  • Marie-Anne Rameix-Welti,
  • Makoto Takeda and
  • Lay-Myint Yoshida

Human respiratory syncytial virus (RSV) causes acute respiratory illness, attributing to deaths among young children and older adults worldwide. RSV neutralization assay is an important tool to measure RSV neutralization antibody that can prevent inf...

  • Protocol
  • Open Access
1,451 Views
17 Pages

Single-cell adhesion assays can be divided into studies on attachment and detachment events, and several methods that enable the characterization of both processes have been established in the past. Due to their low invasiveness, label-free principle...

  • Protocol
  • Open Access
2,121 Views
26 Pages

Synthesis of DOTA-Based 43Sc Radiopharmaceuticals Using Cyclotron-Produced 43Sc as Exemplified by [43Sc]Sc-PSMA-617 for PSMA PET Imaging

  • Jason P. Meier,
  • Mohammed Bhuiyan,
  • Richard Freifelder,
  • Hannah J. Zhang,
  • Lucas Gonzalez,
  • Antonino Pusateri,
  • Hsiu-Ming Tsai,
  • Lara Leoni,
  • Kaustab Ghosh and
  • Satish K. Chitneni
  • + 9 authors

The implementation of theranostics in oncologic nuclear medicine has exhibited immense potential in improving patient outcomes in prostate cancer with the implementation of [68Ga]Ga-PSMA-11 PET and [177Lu]Lu-PSMA-617 into clinical practice. However,...

  • Protocol
  • Open Access
1 Citations
6,856 Views
8 Pages

Optimization of Nile Tilapia Artificial Breeding Using Human Chorionic Gonadotropin (hCG) Hormone

  • Golam Rbbani,
  • Prabhugouda Siriyappagouder,
  • Riaz Murshed,
  • Rajesh Joshi,
  • Artem Nedoluzhko,
  • Jorge Galindo-Villegas and
  • Jorge M. O. Fernandes

Nile tilapia (Oreochromis niloticus) is the most widely farmed tilapia species globally, making it one of the most important aquaculture species. To meet increasing demand, hatcheries occasionally use artificial breeding techniques such as hormonal i...

  • Article
  • Open Access
1 Citations
1,893 Views
22 Pages

Towards Automated Testing of Kynurenine for Point-of-Care Metabolomics

  • Dipanjan Bhattacharyya,
  • Marcia A. LeVatte and
  • David S. Wishart

Our objective was to develop a simple, low-cost colorimetric assay to detect kynurenine (L-Kyn) in human biofluids, that would be compatible with a point-of-care (POC) system being developed in our lab. Elevated L-Kyn is associated with many patholog...

  • Protocol
  • Open Access
1,658 Views
13 Pages

A Minimally Invasive Transthoracic Injection Technique for Reproducible Intrapleural Delivery in Mice

  • Sophie Rovers,
  • Pooyeh Farahmand,
  • Dana Liu,
  • Louize Brants,
  • Christophe Hermans,
  • Dieter Peeters,
  • Danielle McKinven,
  • Jennifer Doig,
  • Filip Lardon and
  • Evelien Smits
  • + 3 authors

The development of standardised, reproducible preclinical models is essential for advancing pleural mesothelioma (PM) research. Here, we present a simple and reliable minimally invasive transthoracic intrapleural injection technique that could improv...

  • Protocol
  • Open Access
1,843 Views
10 Pages

Well-spread pachytene chromosomes are critical for studying the location of meiotic proteins along individual chromosomes. However, producing good spreads in species with large genomes is challenging due to the tangling of pachytene chromosomes. Exis...

  • Article
  • Open Access
2 Citations
3,626 Views
13 Pages

New Bioelectrical Impedance-Based Equations to Estimate Resting Metabolic Rate in Young Athletes

  • Theodoros Stampoulis,
  • Alexandra Avloniti,
  • Dimitrios Draganidis,
  • Dimitrios Balampanos,
  • Polyxeni Efthimia Chalastra,
  • Anastasia Gkachtsou,
  • Dimitrios Pantazis,
  • Nikolaos-Orestis Retzepis,
  • Maria Protopapa and
  • Athanasios Chatzinikolaou
  • + 4 authors

Resting metabolic rate (RMR) significantly impacts total daily energy expenditure, particularly on training days, and varies among trained individuals. Studies estimating RMR in this population show notable discrepancies. This study aimed to develop...

  • Protocol
  • Open Access
1 Citations
1,592 Views
17 Pages

Development and Characterization of a Ten-Plex Assay to Measure Klebsiella pneumoniae Antigen-Specific IgG in Human Sera

  • Luca Rovetini,
  • Gianina Florentina Belciug,
  • Luisa Massai,
  • Francesca Nonne,
  • Renzo Alfini,
  • Heena Ranchod,
  • Denasha L. Reddy,
  • Mariagrazia Molfetta,
  • Davide Oldrini and
  • Omar Rossi
  • + 7 authors

Klebsiella pneumoniae is a leading cause of nosocomial infections, neonatal sepsis, and childhood mortality worldwide. A drastic rise in antibiotic-resistant isolates poses an urgent threat to humanity, and the World Health Organization (WHO) has cla...

  • Article
  • Open Access
2 Citations
1,614 Views
12 Pages

Safety and Efficacy of Pressurized Intra-Thoracic Aerosol Chemotherapy in Non-Small Cell Lung Cancer Pleural Carcinomatosis: Preliminary Results of a Pilot Study

  • Maria Giovanna Mastromarino,
  • Vittorio Aprile,
  • Gianmarco Elia,
  • Diana Bacchin,
  • Alessandra Lenzini,
  • Stylianos Korasidis,
  • Marcello Carlo Ambrogi,
  • Silvia Martina Ferrari,
  • Poupak Fallahi and
  • Marco Lucchi

Pleural carcinomatosis (PC) and malignant pleural effusion (MPE) affect up to 20% of patients with non-small cell lung cancer (NSCLC) and are usually synonymous with poor prognosis. Pressurized Intra-Thoracic Aerosol Chemotherapy (PITAC) is a novel a...

  • Protocol
  • Open Access
2,786 Views
13 Pages

Rapid and Efficient DNA Extraction Protocol from Peruvian Native Cotton (Gossypium barbadense L.) Lambayeque, Peru

  • Luis Miguel Serquén Lopez,
  • Herry Lloclla Gonzales,
  • Wilmer Enrique Vidaurre Garcia,
  • Ricardo Leonidas de Jesus Velez Chicoma and
  • Mendoza Cornejo Greta

Efficient extraction of high-quality DNA from plants is a critical challenge in molecular research, especially in species such as Gossypium barbadense L., native to Peru, due to the presence of inhibitors such as polysaccharides and phenolic compound...

  • Study Protocol
  • Open Access
2,608 Views
17 Pages

SmilebrightRO—Study Protocol for a Randomized Clinical Trial to Evaluate Oral Health Interventions in Children

  • Ruxandra Sava-Rosianu,
  • Guglielmo Campus,
  • Vlad Tiberiu Alexa,
  • Octavia Balean,
  • Ruxandra Sfeatcu,
  • Alice Murariu,
  • Alexandrina Muntean,
  • Daniela Esian,
  • Constantin Daguci and
  • Atena Galuscan
  • + 9 authors

Background: Oral diseases represent a constant burden for health care and socio-economic systems as they are correlated to other non-communicable diseases. The aim of the proposed intervention is to test the effect of daily tooth brushing and oral he...

  • Study Protocol
  • Open Access
1 Citations
2,035 Views
13 Pages

Empagliflozin Repurposing for Lafora Disease: A Pilot Clinical Trial and Preclinical Investigation of Novel Therapeutic Targets

  • Giuseppe d’Orsi,
  • Antonella Liantonio,
  • Paola Imbrici,
  • Nicola Gambacorta,
  • Giorgia Dinoi,
  • Cosimo Damiano Altomare,
  • DEFEAT-LD Study Group and
  • Massimo Carella

Background: Lafora disease (LD) is an ultra-rare and fatal neurodegenerative disorder with limited therapeutic options. Current treatments primarily address symptoms, with modest efficacy in halting disease progression, thus highlighting the urgent n...

  • Article
  • Open Access
2 Citations
1,313 Views
14 Pages

The Eurasian lynx (Lynx lynx) is listed in CITES Appendix II and is protected under the Bern Convention and the EU Habitats Directive, yet it remains a frequent target of wildlife crime, highlighting the urgent need for reliable identification method...

  • Protocol
  • Open Access
3 Citations
1,512 Views
15 Pages

Replicating in vivo conditions is essential for understanding immune responses and measuring immune biomarkers in blood. Sampling immune biomarkers in plasma or serum often fails to detect disease-relevant signals, possibly because these markers are...

  • Study Protocol
  • Open Access
1 Citations
2,611 Views
11 Pages

External Validation of the NECPAL CCOMS-ICO Prognostic Tool for Early Palliative Care and Mortality Prediction in Patients with Advanced Chronic Conditions: A Prospective Observational Study Protocol

  • Ana Bustamante-Fermosel,
  • Elena Díaz-Sánchez,
  • Natalia Pavón-Muñoz,
  • Laetitia Hennekinne,
  • Fuensanta Gil-Gil,
  • Helena Notario-Leo,
  • Alicia Sánchez-Pizarro,
  • Marta Bustamante-Vega,
  • Juan Torres-Macho and
  • on behalf of the COMPASS Research Group
  • + 1 author

Early initiation of palliative care in patients with advanced chronic conditions significantly improves their quality of care; however, variability in disease trajectories complicates such interventions’ timing. The NECPAL CCOMS-ICO prognostic...

  • Review
  • Open Access
1 Citations
2,031 Views
11 Pages

The PROMISE of Precision Medicine in Myocardial Infarction with Non-Obstructive Coronary Arteries

  • Giulia La Vecchia,
  • Vincenzo Scarica,
  • Ludovica Leo and
  • Rocco A. Montone

Myocardial infarction with non-obstructive coronary arteries (MINOCA) is a working diagnosis encompassing several pathophysiological mechanisms with specific treatments and different prognoses. Despite the absence of obstructive coronary artery disea...

  • Article
  • Open Access
2,658 Views
14 Pages

The Validation of Antibodies Suitable for Flow Cytometric Analysis and Immunopeptidomics of Peptide–MHC Complexes in the Outbred Swiss Albino Mouse Strain

  • Shanzou Chung,
  • Isambard G. Knox-Johnson,
  • Sarah E. Gazzard,
  • Runqiu Song,
  • Ngoc H. Le,
  • Luise A. Cullen-McEwen,
  • John F. Bertram,
  • Anthony W. Purcell and
  • Asolina Braun

Antigen presentation on major histocompatibility complex (MHC) molecules is central to the initiation of immune responses, and a lot of our understanding about the antigen processing and presentation pathway has been gained through studies in mice. M...

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Methods Protoc. - ISSN 2409-9279