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Methods and Protocols, Volume 6, Issue 2

2023 April - 23 articles

Cover Story: Increasing evidence strongly supports the key role of the tumour microenvironment in response to systemic therapy, particularly immune checkpoint inhibitors (ICIs). The tumour microenvironment is a complex tapestry of immune cells, some of which can suppress T-cell immunity to negatively impact ICI therapy. In this paper, we describe a protocol built upon Visium (10x Genomics) spatial transcriptomics to map and characterise the tumour-infiltrating immune microenvironment in malignant pleural mesothelioma. The preservation of tissue architecture and alignment with gene expression data allowed us to determine the number and location of tumour-infiltrating immune cells and the upregulation of genes that are potentially responsible for better/lower therapeutic outcomes in examined patients. View this paper
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Articles (23)

  • Brief Report
  • Open Access
26 Citations
10,709 Views
10 Pages

Comparison of Automated and Traditional Western Blotting Methods

  • Aino Sormunen,
  • Emma Koivulehto,
  • Kari Alitalo,
  • Kalle Saksela,
  • Nihay Laham-Karam and
  • Seppo Ylä-Herttuala

Traditional Western blotting is one of the most used analytical techniques in biological research. However, it can be time-consuming and suffer from a lack of reproducibility. Consequently, devices with different degrees of automation have been devel...

  • Protocol
  • Open Access
3 Citations
4,072 Views
10 Pages

Outer membrane vesicles (OMVs) are lipid structures containing various biomolecules in their native environment and are spontaneously shed by gram-negative bacteria. OMVs perform several biological functions critical to both bacterial physiology and...

  • Article
  • Open Access
17 Citations
7,661 Views
8 Pages

Intrarater Reliability and Analysis of Learning Effects in the Y Balance Test

  • Olli Kattilakoski,
  • Noora Kauranen,
  • Mari Leppänen,
  • Pekka Kannus,
  • Kati Pasanen,
  • Tommi Vasankari and
  • Jari Parkkari

While the general reliability of the Y balance test has been previously found to be excellent, earlier reviews highlighted a need for a more consistent methodology between studies. The purpose of this test–retest intrarater reliability study wa...

  • Protocol
  • Open Access
1 Citations
4,225 Views
13 Pages

Medicinal and herbal plants are abundant sources of phytochemicals, which are biologically active compounds with potential health benefits. The characterisation of phytochemicals has been the subject of many studies, but there is a lack of comprehens...

  • Article
  • Open Access
3 Citations
3,815 Views
12 Pages

Acceleration of CRISPR/Cas9-Mediated Editing at Multiple Sites in the Saccharomyces cerevisiae Genome

  • Alexey D. Karpukhin,
  • Fanis A. Sabirzyanov and
  • Vsevolod A. Serebrianyi

The application of the CRISPR/Cas9-based genome editing technique to the yeast Saccharomyces cerevisiae has made it possible to simultaneously modify several sites, particularly to integrate several expression cassettes. The existing methods provide...

  • Article
  • Open Access
4 Citations
7,109 Views
20 Pages

Critical Evaluation of Embedding Media for Histological Studies of Early Stages of Chick Embryo Development

  • Melyssa Kmecick,
  • Mariliza Cristine Vieira da Costa,
  • Eduardo da Costa Ferreira,
  • Maritana Mela Prodocimo and
  • Claudia Feijó Ortolani-Machado

A histological examination is an important tool in embryology, developmental biology, and correlated areas. Despite the amount of information available about tissue embedding and different media, there is a lack of information regarding best practice...

  • Article
  • Open Access
3 Citations
2,886 Views
13 Pages

Serological Cross-Reaction between Six Thiadiazine by Indirect ELISA Test and Their Antimicrobial Activity

  • Mishell Ortiz,
  • Hortensia Rodríguez,
  • Elisabetta Lucci,
  • Julieta Coro,
  • Beatriz Pernía,
  • Abigail Montero-Calderon,
  • Francisco Javier Tingo-Jácome,
  • Leslie Espinoza and
  • Lilian M. Spencer

Malaria is a parasitic infection caused by a protozoon of the genus Plasmodium, transmitted to humans by female biting mosquitoes of the genus Anopheles. Chloroquine and its derivates have caused the parasite to develop drug resistance in endemic are...

  • Review
  • Open Access
5 Citations
7,860 Views
13 Pages

Cell-free protein synthesis (CFPS) is a method utilized for producing proteins without the limits of cell viability. The plug-and-play utility of CFPS is a key advantage over traditional plasmid-based expression systems and is foundational to the pot...

  • Protocol
  • Open Access
9 Citations
5,219 Views
13 Pages

Identification and Characterisation of Infiltrating Immune Cells in Malignant Pleural Mesothelioma Using Spatial Transcriptomics

  • Dmitrii Shek,
  • Brian Gloss,
  • Joey Lai,
  • Li Ma,
  • Hui E. Zhang,
  • Matteo S. Carlino,
  • Hema Mahajan,
  • Adnan Nagrial,
  • Bo Gao and
  • Golo Ahlenstiel
  • + 1 author

Increasing evidence strongly supports the key role of the tumour microenvironment in response to systemic therapy, particularly immune checkpoint inhibitors (ICIs). The tumour microenvironment is a complex tapestry of immune cells, some of which can...

  • Article
  • Open Access
5 Citations
6,240 Views
19 Pages

Improvement and Validation of a Genomic DNA Extraction Method for Human Breastmilk

  • Mario Iván Alemán-Duarte,
  • Blanca Rosa Aguilar-Uscanga,
  • Guadalupe García-Robles,
  • Felipe de Jesús Ramírez-Salazar,
  • Israel Benítez-García,
  • Edgar Balcázar-López and
  • Josué Raymundo Solís-Pacheco

The human milk microbiota (HMM) of healthy women can vary substantially, as demonstrated by recent advances in DNA sequencing technology. However, the method used to extract genomic DNA (gDNA) from these samples may impact the observed variations and...

  • Protocol
  • Open Access
1 Citations
5,996 Views
11 Pages

Protocol to Assess the Biological Activity of Insulin Glargine, Insulin Lispro, and Insulin Aspart In Vitro

  • Mamatha Garige,
  • Susmita Ghosh,
  • Brian Roelofs,
  • V. Ashutosh Rao and
  • Carole Sourbier

Insulin is a hormone produced by β-cells of the pancreas and controls the amount of sugar in the blood. Since its discovery over 100 years ago, insulin has been used as a life-saving treatment for people with diabetes. Historically, the biologic...

  • Protocol
  • Open Access
4 Citations
3,920 Views
22 Pages

An Experimental Approach to Address the Functional Relationship between Antioxidant Enzymes and Mitochondrial Respiratory Complexes

  • Daniela Mendes,
  • Ana Maria Silva,
  • Maria Manuel Oliveira,
  • Paula B. Andrade and
  • Romeu A. Videira

Mitochondrial dysfunction and cytosolic oxidative stress are pathological biomarkers interlinked in several chronic diseases and cellular toxicity promoted by high-energy radiation or xenobiotics. Thus, assessing the activities of the mitochondrial r...

  • Protocol
  • Open Access
1 Citations
3,588 Views
12 Pages

An Efficient Method to Prepare Barcoded cDNA Libraries from Plant Callus for Long-Read Sequencing

  • Daniela Cordeiro,
  • Alexandra Camelo,
  • Ana Carolina Pedrosa,
  • Inês Brandão,
  • Jorge Canhoto,
  • Christophe Espírito Santo and
  • Sandra Correia

Long-read sequencing methods allow a comprehensive analysis of transcriptomes in identifying full-length transcripts. This revolutionary method represents a considerable breakthrough for non-model species since it allows enhanced gene annotation and...

  • Study Protocol
  • Open Access
7 Citations
4,413 Views
14 Pages

Despite the decline in under-five mortality by over 60% in the last three decades, majority of child mortality is still attributable to communicable and infectious diseases that are not only preventable, but they are also treatable. We evaluated the...

  • Protocol
  • Open Access
2 Citations
4,424 Views
8 Pages

Interventions to Increase Physical Activity in Community-Dwelling Older Adults in Regional and Rural Areas: A Realist Synthesis Review Protocol

  • Stephen Cousins,
  • Rebecca McKechnie,
  • Patricia Jackman,
  • Geoff Middleton,
  • Tshepo Rasekaba and
  • Irene Blackberry

The importance of physical activity (PA) for the health and wellbeing of older adults is well documented, yet many older adults are insufficiently active. This issue is more salient in regional and rural areas, where evidence of the most critical com...

  • Protocol
  • Open Access
2 Citations
2,937 Views
15 Pages

Patient-Reported Quality of Care for Osteoarthritis in General Practice in South Tyrol, Italy: Protocol for Translation, Validation and Assessment of the OsteoArthritis Quality Indicator Questionnaire (OA-QI)

  • Christian J. Wiedermann,
  • Pasqualina Marino,
  • Antje van der Zee-Neuen,
  • Isabella Mastrobuono,
  • Angelika Mahlknecht,
  • Verena Barbieri,
  • Sonja Wildburger,
  • Julia Fuchs,
  • Alessandra Capici and
  • Markus Ritter
  • + 3 authors

Background: Evidence-based recommendations for the treatment of knee and hip osteoarthritis are similar internationally. Nevertheless, clinical practice varies across countries. Instruments for measuring quality have been developed to improve health...

  • Protocol
  • Open Access
7 Citations
3,752 Views
8 Pages

Assessing the Effectiveness of Tobacco 21 Laws to Reduce Underage Access to Tobacco: Protocol for a Repeated Multi-Site Study

  • Mary Hrywna,
  • Amanda Y. Kong,
  • Christopher Ackerman,
  • Daniel P. Giovenco,
  • Torra E. Spillane,
  • Joseph G. L. Lee,
  • Shawna V. Hudson and
  • Cristine D. Delnevo

Prior to the federal law passed in December 2019, many states passed an increased age of sale law prohibiting youth under age 21 (or Tobacco 21) from purchasing tobacco products, including e-cigarettes. Although previous research has documented tobac...

  • Article
  • Open Access
39 Citations
9,801 Views
10 Pages

Test−Retest Reliability of Isokinetic Ankle, Knee and Hip Strength in Physically Active Adults Using Biodex System 4 Pro

  • Juho Tuominen,
  • Mari Leppänen,
  • Heidi Jarske,
  • Kati Pasanen,
  • Tommi Vasankari and
  • Jari Parkkari

Background: The isokinetic dynamometry is considered a gold standard in muscle strength testing. The reliability of lower limb isokinetic strength measurements has not been thoroughly evaluated. Objective: To examine the test−retest reliability...

  • Technical Note
  • Open Access
1 Citations
6,136 Views
15 Pages

Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids

  • Nadeem Asad,
  • Emily Smith,
  • Sudeep Shakya,
  • Sutton Stegman and
  • Lisa Timmons

We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive screening of difficult-t...

  • Review
  • Open Access
10 Citations
15,256 Views
14 Pages

Tn5 DNA Transposase in Multi-Omics Research

  • Dmitry Penkov,
  • Ekaterina Zubkova and
  • Yelena Parfyonova

28 February 2023

Tn5 transposase use in biotechnology has substantially advanced the sequencing applications of genome-wide analysis of cells. This is mainly due to the ability of Tn5 transposase to efficiently transpose DNA essentially randomly into any target DNA w...

  • Protocol
  • Open Access
1 Citations
2,342 Views
11 Pages

A Simple Radioassay to Detect Nanoscale Membrane Disruption

  • Neha Nanajkar,
  • Lekhana S. Mruthyunjaya and
  • Deepesh Nagarajan

25 February 2023

Understanding the mechanisms and kinetics of membrane damage is of interest to researchers in several overlapping fields of biology. In this study, we describe the development and validation of a simple 32PO43 release radioassay used to track...

  • Article
  • Open Access
15 Citations
5,156 Views
16 Pages

23 February 2023

Trauma triggers critical molecular and cellular signaling cascades that drive biological outcomes and recovery. Variations in the gene expression of common endogenous reference housekeeping genes (HKGs) used in data normalization differ between tissu...

  • Technical Note
  • Open Access
1 Citations
4,840 Views
10 Pages

Sustainable and Cost-Effective Gel Documentation

  • Nadeem Asad,
  • Scott Cregg,
  • Sudeep Shakya,
  • Sutton Stegman and
  • Lisa Timmons

21 February 2023

A common laboratory method involves gel electrophoresis followed by photographic documentation of the results, a procedure which is performed worldwide by students and experienced scientists alike. Proprietary Gel Documentation Systems are convenient...

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Methods Protoc. - ISSN 2409-9279