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Methods and Protocols, Volume 8, Issue 3

June 2025 - 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
1,110 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
1,388 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
1,628 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
713 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
2,220 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
1,291 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
1,755 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
1,267 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
1,786 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
  • Erica Markiewicz
  • + 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
6,398 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...

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Methods Protoc. - ISSN 2409-9279