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Methods and Protocols, Volume 7, Issue 6

2024 December - 22 articles

Cover Story: With the growing interest in malaria-derived extracellular vesicles (EVs), standardizing the isolation protocols is essential for ensuring reproducibility and enabling inter-study comparisons. This article provides a detailed, reproducible differential centrifugation (DC) protocol for isolating EVs from Plasmodium falciparum-infected red blood cell cultures at various asexual blood stages. The method yields two EV subtypes from high-parasitemia, synchronized cultures, characterized by the Western blot analysis of human and parasite proteins, and identifies the potential protein markers for malaria EV subpopulations. Researchers can use this protocol to facilitate downstream applications for further characterisation, such as proteomics and functional studies, advancing our understanding of malaria biology. View this paper
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Articles (22)

  • Article
  • Open Access
2,642 Views
9 Pages

Evaluation of Protocols for DNA Extraction from Individual Culex pipiens to Assess Pyrethroid Resistance Using Genotyping Real-Time Polymerase Chain Reaction

  • Ilaria Congiu,
  • Elisa Cugini,
  • Daniele Smedile,
  • Federico Romiti,
  • Manuela Iurescia,
  • Valentina Donati,
  • Claudio De Liberato and
  • Antonio Battisti

23 December 2024

Culex pipiens is a major vector of pathogens, including West Nile and Usutu viruses, that poses a significant public health risk. Monitoring pyrethroid resistance in mosquito populations is essential for effective vector control. This study aims to e...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
2,908 Views
17 Pages

21 December 2024

Recommendations released by the CDC in 2023 address the need to demonstrate that the RNA genome of positive-strand RNA viruses is inactivated in addition to viral particles. This recommendation is in response to the similarities between host mRNA and...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
1 Citations
2,942 Views
12 Pages

Establishment of Stable Knockdown of MACC1 Oncogene in Patient-Derived Ovarian Cancer Organoids

  • Sophia Hierlmayer,
  • Liliia Hladchenko,
  • Juliane Reichenbach,
  • Christoph Klein,
  • Sven Mahner,
  • Fabian Trillsch,
  • Mirjana Kessler and
  • Anca Chelariu-Raicu

20 December 2024

High-grade serous ovarian cancer (HGSOC) remains the most lethal gynecological malignancy, and there is still an unmet medical need to deepen basic research on its origins and mechanisms of progression. Patient-derived organoids of high-grade serous...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Article
  • Open Access
1 Citations
2,245 Views
10 Pages

20 December 2024

The accurate measurement of spatiotemporal parameters, such as step length and step frequency, is crucial for analyzing running and sprinting performance. Traditional methods like video analysis and force platforms are either time consuming or limite...

(This article belongs to the Special Issue Methods on Sport Biomechanics)
  • Article
  • Open Access
1 Citations
2,447 Views
13 Pages

20 December 2024

An electrochemical investigation of 1,2- and 1,4-dihydroxybenzenes was carried out with platinum macro- and microelectrodes using square wave and cyclic voltammetry techniques. Furthermore, the effect of the two solvents—acetic acid and ethyl a...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
3 Citations
4,411 Views
13 Pages

Proof of Concept Study: Comparison of Semi-Automated RNA Isolation Methods from Archived Formalin-Fixed, Paraffin-Embedded Tissues with Clinical Routine RNA Isolation Methods

  • Patrick Hannibal Dalsbo Petersen,
  • Jaslin Pallikkunnath James,
  • Lene Buhl Riis,
  • Claus Kim Høgdall and
  • Estrid Vilma Høgdall

19 December 2024

High-quality RNA is crucial in clinical diagnostics and precision medicine. Formalin-fixed and paraffin-embedded (FFPE) tissues pose a challenge due to nucleic acid fragmentation and crosslinking. In this pilot study, various commercially available t...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
3,091 Views
26 Pages

The Multifunctional Catalytic Hemoglobin from Amphitrite ornata: Protocols on Isolation, Taxonomic Identification, Protein Extraction, Purification, and Characterization

  • Anna L. Husted,
  • Victoria R. Sutton,
  • Lauren A. Presnar,
  • R. Kevin Blackburn,
  • Joseph L. Staton,
  • Stephen A. Borgianini and
  • Edward L. D’Antonio

11 December 2024

The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. Th...

(This article belongs to the Topic Recent Advances in Oxidoreductases Biochemistry and Biotechnology)
  • Protocol
  • Open Access
3 Citations
3,991 Views
13 Pages

Liver Cancer Neuroscience: Regulating Liver Tumors via Selective Hepatic Vagotomy

  • Kylynda C. Bauer,
  • Shadin Ghabra,
  • Chi Ma,
  • Lee Chedester and
  • Tim F. Greten

11 December 2024

Both the prevalence and mortality of liver cancers continue to rise. Early surgical interventions, including liver transplantation or resection, remain the only curative treatment. Nerves in the periphery influence tumor growth within visceral organs...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Study Protocol
  • Open Access
2 Citations
2,855 Views
13 Pages

10 December 2024

Background: About 287,000 women died globally during their pregnancy journey in 2020, yet most of these deaths could have been prevented. In Uganda, studies show that using Community Health Worker (CHW) visits to households with a pregnant woman can...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
3 Citations
1,891 Views
14 Pages

2 December 2024

Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from t...

(This article belongs to the Collection Analytical Chemistry Methods and Protocols: From Standard Practices to New Sustainable Approaches)
  • Article
  • Open Access
2 Citations
4,013 Views
17 Pages

AI-Assisted High-Throughput Tissue Microarray Workflow

  • Konrad Kurowski,
  • Sylvia Timme,
  • Melanie Christine Föll,
  • Clara Backhaus,
  • Philipp Anton Holzner,
  • Bertram Bengsch,
  • Oliver Schilling,
  • Martin Werner and
  • Peter Bronsert

25 November 2024

Immunohistochemical (IHC) studies of formalin-fixed paraffin-embedded (FFPE) samples are a gold standard in oncology for tumor characterization, and the identification of prognostic and predictive markers. However, despite the abundance of archived F...

(This article belongs to the Section Omics and High Throughput)
  • Article
  • Open Access
25 Citations
15,690 Views
17 Pages

A Critical Exploration of the Total Flavonoid Content Assay for Honey

  • Sharmin Sultana,
  • Ivan Lozada Lawag,
  • Lee Yong Lim,
  • Kevin J. Foster and
  • Cornelia Locher

21 November 2024

This study critically investigates the aluminium chloride–based colorimetric determination of the total flavonoid content (TFC) of honey. Following a comprehensive review of the recent literature reporting the use of the assay in the determinat...

(This article belongs to the Collection Analytical Chemistry Methods and Protocols: From Standard Practices to New Sustainable Approaches)
  • Article
  • Open Access
4 Citations
4,711 Views
18 Pages

Digital PCR Validation for Characterization of Quantitative Reference Material of Escherichia coli O157:H7 Genomic DNA

  • Claudia Patricia Tere-Peña,
  • Martha Nancy Calderon-Ozuna and
  • John Emerson Leguizamón Guerrero

15 November 2024

Escherichia coli O157:H7, a Shiga-toxin-producing E. coli (STEC), is an important pathogen related to foodborne disease that is responsible for a growing number of outbreaks worldwide and has been detected in processed meats, dairy, and fresh vegetab...

(This article belongs to the Section Molecular and Cellular Biology)
  • Study Protocol
  • Open Access
6 Citations
3,119 Views
10 Pages

Identifying and Removing Fraudulent Attempts to Enroll in a Human Health Improvement Intervention Trial in Rural Communities

  • Karla L. Hanson,
  • Grace A. Marshall,
  • Meredith L. Graham,
  • Deyaun L. Villarreal,
  • Leah C. Volpe and
  • Rebecca A. Seguin-Fowler

9 November 2024

Using the internet to recruit participants into research trials is effective but can attract high numbers of fraudulent attempts, particularly via social media. We drew upon the previous literature to rigorously identify and remove fraudulent attempt...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
1 Citations
5,575 Views
33 Pages

9 November 2024

Over the last few decades, malaria-derived extracellular vesicles (EVs) have gained increasing interest due to their role in disease pathophysiology and parasite biology. Unlike other EV research fields, the isolation of malaria EVs is not standardiz...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
6 Citations
5,168 Views
13 Pages

Near-Infrared Spectroscopy for Growth Estimation of Spirulina platensis Cultures

  • Lamprini Malletzidou,
  • Eleni Kyratzopoulou,
  • Nikoletta Kyzaki,
  • Evangelos Nerantzis and
  • Nikolaos A. Kazakis

3 November 2024

The present study proposes the use of Near-Infrared (NIR) spectroscopy as a rapid method for estimating the growth of Spirulina platensis cultures, avoiding any sample manipulation or pretreatment. NIR spectroscopy in diffuse reflectance mode was use...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Communication
  • Open Access
2 Citations
3,896 Views
9 Pages

Optimizing Arterial Tissue Thickness Measurement Protocols: Digital Vernier Caliper Versus Digital Thickness Gauge

  • Alexandru Petru Ion,
  • Alexandra Asztalos,
  • Claudiu Constantin Ciucanu,
  • Eliza Russu,
  • Adrian Vasile Mureșan,
  • Eliza-Mihaela Arbănași,
  • Traian V. Chirilă,
  • Gabriela Strnad and
  • Emil-Marian Arbănași

2 November 2024

Background: The aim of this study is to analyze the reproducibility of sample thickness measurements taken by a non-experienced user by comparing a standard digital vernier caliper, with four different protocols, to a specialized thickness gauge. Met...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Protocol
  • Open Access
8 Citations
5,348 Views
18 Pages

Effect of Biomass Drying Protocols on Bioactive Compounds and Antioxidant and Enzymatic Activities of Red Macroalga Kappaphycus alvarezii

  • Aline Nunes,
  • Felipe de Souza Dutra,
  • Sinara de Nazaré Santana Brito,
  • Milene Stefani Pereira-Vasques,
  • Gadiel Zilto Azevedo,
  • Alex Ricardo Schneider,
  • Eva Regina Oliveira,
  • Alex Alves dos Santos,
  • Marcelo Maraschin and
  • Giuseppina Pace Pereira Lima
  • + 1 author

1 November 2024

Kappaphycus alvarezii is a red seaweed used globally in various biotechnological processes. To ensure the content and stability of its bioactive compounds postharvest, suitable drying protocols must be adopted to provide high-quality raw materials fo...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Study Protocol
  • Open Access
2 Citations
2,929 Views
9 Pages

1 November 2024

South Africa developed the differentiated service delivery (DSD) model to improve access to healthcare for people living with HIV (PLHIV), especially key populations (KPs) including female sex workers (FSWs) who often face barriers in accessing HIV s...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
4 Citations
2,804 Views
16 Pages

Method for Valorization of Coffee Cherry Waste via Hydrothermal Valorization Using Organic and Inorganic Acids as Catalysts

  • Alejandra Sophia Lozano Pérez,
  • Valentina Romero Mahecha and
  • Carlos Alberto Guerrero Fajardo

29 October 2024

The valorization of coffee cherry waste through hydrothermal carbonization (HTC) was investigated using various organic and inorganic acid catalysts to produce platform chemicals. This study aimed to evaluate the effectiveness of these catalysts for...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Review
  • Open Access
3,134 Views
16 Pages

Methodology for Studying Hypothalamic Regulation of Feeding Behaviors

  • Julia B. Davenport,
  • Ali D. Güler and
  • Qi Zhang

24 October 2024

Continuous advances in neurological research techniques are enabling researchers to further understand the neural mechanisms that regulate energy balance. In this review, we specifically highlight key tools and techniques and explore how they have be...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Communication
  • Open Access
8 Citations
3,482 Views
9 Pages

23 October 2024

The monitoring of species in a habitat is important to ensure biological diversity. Environmental DNA (eDNA) can infer the presence–absence of species and enable rapid action to avoid threatening factors in ecosystems in the case of non-indigen...

(This article belongs to the Section Molecular and Cellular Biology)
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Methods Protoc. - ISSN 2409-9279