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Methods and Protocols, Volume 5, Issue 4

2022 August - 15 articles

Cover Story: The molecular analysis of small patient tissues is often challenging. Here, we describe the workflow for two complimentary mass spectrometry approaches, which provide comprehensive analysis of the molecular features in the tissue of interest. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) generates spatial intensity maps of molecular features, and liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify and quantify proteins of interest from a consecutive section of the same tissue. Using these complimentary approaches, we monitored the abundance of hundreds of proteins within the precancerous, and neighboring healthy regions, of small precancerous tissue from a single patient. This method represents a useful tool to maximize the amount of molecular data acquired from small samples. View this paper
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Articles (15)

  • Protocol
  • Open Access
2 Citations
4,425 Views
12 Pages

The assignment of specific patterns of gene expression to specific cells in a complex tissue facilitates the connection between genotype and phenotype. Single-cell sequencing of whole tissues produces single-cell transcript resolution but lacks the s...

  • Protocol
  • Open Access
5 Citations
5,419 Views
11 Pages

A co-culture of neurons and Schwann cells has frequently been used to investigate myelin sheath formation. However, this approach is restricted to myelin-related diseases of the peripheral nervous system. This study introduces and compares an ex vivo...

  • Protocol
  • Open Access
1 Citations
2,651 Views
7 Pages

With the plethora of commercially available UV-C devices exhibiting different intensity and lifespans, it is critical to consumer safety that companies verify and clearly communicate the efficacy of their devices as per the intended use. The purpose...

  • Article
  • Open Access
2 Citations
5,983 Views
15 Pages

Comparison of Different Fixation Methods for Combined Histological and Biomolecular Analysis of Fixed and Decalcified Bone Samples

  • Sarah Al-Maawi,
  • Priscilia Valenzuela,
  • Eva Dohle,
  • Anja Heselich,
  • Robert Sader and
  • Shahram Ghanaati

The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially wh...

  • Article
  • Open Access
5 Citations
4,531 Views
8 Pages

For-profit donor human milk organizations have DNA-based proprietary methodology for testing incoming milk for adulteration with other species’ milk. However, there is currently no standardized methodology for extracting DNA from human milk. Mi...

  • Protocol
  • Open Access
4 Citations
3,938 Views
14 Pages

Measuring Electrical Responses during Acute Exposure of Roots and Rhizoids of Plants to Compounds Using a Flow-Through System

  • Robin Lewis Cooper,
  • Matthew A. Thomas,
  • Rachael M. Vascassenno,
  • Kaitlyn E. Brock and
  • David Nicholas McLetchie

Monitoring electrical signals in plants allows the examination of their acute and chronic physiological changes and responses to stimuli. Understanding how plant roots/rhizoids respond to chemical cues in their environment will provide insight into h...

  • Review
  • Open Access
24 Citations
4,345 Views
13 Pages

Analytical Methods for Nanomaterial Determination in Biological Matrices

  • Magdalini Vladitsi,
  • Charalampia Nikolaou,
  • Natasa P. Kalogiouri and
  • Victoria F. Samanidou

Nanomaterials are materials in which at least one of the three dimensions ranges from 1 to 100 nm, according to the International Organization for Standardization (ISO). Nanomaterials can be categorized according to various parameters, such as their...

  • Article
  • Open Access
16 Citations
5,504 Views
15 Pages

Performance and Information Leakage in Splitfed Learning and Multi-Head Split Learning in Healthcare Data and Beyond

  • Praveen Joshi,
  • Chandra Thapa,
  • Seyit Camtepe,
  • Mohammed Hasanuzzaman,
  • Ted Scully and
  • Haithem Afli

Machine learning (ML) in healthcare data analytics is attracting much attention because of the unprecedented power of ML to extract knowledge that improves the decision-making process. At the same time, laws and ethics codes drafted by countries to g...

  • Protocol
  • Open Access
39 Citations
5,318 Views
10 Pages

Digestibility trials need a viable rumen fluid as inoculum to degrade feeds. The variability of rumen fluid depends on the animal’s diet, while its viability is greatly influenced by the sampling and handling procedures. In this article, we pre...

  • Article
  • Open Access
29 Citations
15,454 Views
14 Pages

Streamlining Culture Conditions for the Neuroblastoma Cell Line SH-SY5Y: A Prerequisite for Functional Studies

  • Sebastian Feles,
  • Christian Overath,
  • Sina Reichardt,
  • Sebastian Diegeler,
  • Claudia Schmitz,
  • Jessica Kronenberg,
  • Christa Baumstark-Khan,
  • Ruth Hemmersbach,
  • Christine E. Hellweg and
  • Christian Liemersdorf

The neuroblastoma cell line SH-SY5Y has been a well-established and very popular in vitro model in neuroscience for decades, especially focusing on neurodevelopmental disorders, such as Parkinson’s disease. The ability of this cell type to diff...

  • Protocol
  • Open Access
3 Citations
3,350 Views
17 Pages

A Protocol for the Acquisition of Comprehensive Proteomics Data from Single Cases Using Formalin-Fixed Paraffin Embedded Sections

  • Mitchell Acland,
  • Parul Mittal,
  • Georgia Arentz,
  • Fergus Whitehead,
  • Peter Hoffmann,
  • Manuela Klingler-Hoffmann and
  • Martin K. Oehler

The molecular analysis of small or rare patient tissue samples is challenging and often limited by available technologies and resources, such as reliable antibodies against a protein of interest. Although targeted approaches provide some insight, her...

  • Protocol
  • Open Access
5 Citations
5,828 Views
19 Pages

Electrical activity is widely used for assessing a plant’s response to an injury or environmental stimulus. Commonly, a differential electrode recording between silver wire leads with the reference wire connected to the soil, or a part of the p...

  • Article
  • Open Access
7 Citations
3,656 Views
13 Pages

Development and Characterisation of a Four-Plex Assay to Measure Streptococcus pyogenes Antigen-Specific IgG in Human Sera

  • Alexander J. Keeley,
  • Martina Carducci,
  • Luisa Massai,
  • Mariagrazia Pizza,
  • Thushan I. de Silva,
  • Danilo G. Moriel and
  • Omar Rossi

The measurement of antibodies to vaccine antigens is crucial for research towards a safe and effective vaccine for Streptococcus pyogenes (Strep A). We describe the establishment and detailed characterisation of a four-plex assay to measure IgG to th...

  • Protocol
  • Open Access
3,637 Views
11 Pages

Sandwich Enzyme-Linked Immunosorbent Assay for Quantification of Callose

  • Abubakar S. Mustafa,
  • Jamilu E. Ssenku,
  • Paul Ssemanda,
  • Saidi Ntambi,
  • Savithramma P. Dinesh-Kumar and
  • Arthur K. Tugume

The existing methods of callose quantification include epifluorescence microscopy and fluorescence spectrophotometry of aniline blue-stained callose particles, immuno-fluorescence microscopy and indirect assessment of both callose synthase and β...

  • Article
  • Open Access
3 Citations
3,378 Views
16 Pages

Imaging Intron Evolution

  • Maria Antonietta Panaro,
  • Rosa Calvello,
  • Daniela Valeria Miniero,
  • Vincenzo Mitolo and
  • Antonia Cianciulli

Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Bro...

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Methods Protoc. - ISSN 2409-9279