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Methods and Protocols, Volume 3, Issue 2

June 2020 - 21 articles

Cover Story: The analysis of glycosylphosphatidylinositol (GPI)-anchored receptor distribution and dynamics in live cells is challenging because their clusters exhibit subdiffraction-limited sizes and are highly dynamic. We compared three approaches to receptor labeling and found that the enzyme-mediated site-specific fluorescence labeling of receptor modified with a short peptide tag has several advantages over labeling by fluorescent proteins or antibodies. We successfully detected the Förster resonance energy transfer (FRET) of GPI-anchored receptors, T-cadherin, and ephrin-A1 without ligands and showed in real time that adiponectin induces stable T-cadherin cluster formation. Here, we present the practical aspects of labeling and the heteroFRET measurements of GPI-anchored receptors to study their dynamics on a plasma membrane in live cells. View this paper.
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Articles (21)

  • Article
  • Open Access
16 Citations
4,902 Views
12 Pages

Optimization of a Digestion Method to Determine Total Mercury in Fish Tissue by Cold Vapor Atomic Fluorescence Spectrophotometry

  • Gabriela S. Yánez-Jácome,
  • David Romero-Estévez,
  • Hugo Navarrete,
  • Karina Simbaña-Farinango and
  • Pamela Y Vélez-Terreros

Several microwave-assisted digestion methods were tested at the Centro de Estudios Aplicados en Química laboratory in Quito, Ecuador, to determine the accuracy and performance efficiency of the mineralization process for the determination of t...

  • Benchmark
  • Open Access
1 Citations
2,849 Views
12 Pages

Precise creation, maintenance, and monitoring of neuronal circuits would facilitate the investigation of subjects such as neuronal development or synaptic plasticity, or assist in the development of neuronal prosthetics. Here we present a method to p...

  • Article
  • Open Access
7 Citations
5,139 Views
15 Pages

Synthesis of Quenchbodies for One-Pot Detection of Stimulant Drug Methamphetamine

  • Hee-Jin Jeong,
  • Jinhua Dong,
  • Chang-Hun Yeom and
  • Hiroshi Ueda

The problem of illicit drug use and addiction is an escalating issue worldwide. As such, fast and precise detection methods are needed to help combat the problem. Herein, the synthesis method for an anti-methamphetamine Quenchbody (Q-body), a promisi...

  • Feature Paper
  • Protocol
  • Open Access
31 Citations
8,144 Views
13 Pages

Characterized by their covalently closed structure and thus an elevated stability compared to linear RNA molecules, circular RNAs (circRNAs) form a novel class of mainly non-coding RNAs. Although the biological functions of naturally occurring circRN...

  • Technical Note
  • Open Access
2 Citations
16,460 Views
7 Pages

A simple and fast manual centrifuge was developed to spin down solutions in 96-well polymerase chain reaction (PCR) plates. A commercially available salad spinner was utilized for this purpose. Acceleration and deceleration of the centrifuge were fas...

  • Protocol
  • Open Access
4 Citations
4,823 Views
12 Pages

In transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were t...

  • Article
  • Open Access
23 Citations
7,139 Views
17 Pages

The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

  • Anna Ojo-Okunola,
  • Shantelle Claassen-Weitz,
  • Kilaza S. Mwaikono,
  • Sugnet Gardner-Lubbe,
  • Heather J. Zar,
  • Mark P. Nicol and
  • Elloise du Toit

Culture-independent molecular techniques have advanced the characterization of environmental and human samples including the human milk (HM) bacteriome. However, extraction of high-quality genomic DNA that is representative of the bacterial populatio...

  • Article
  • Open Access
36 Citations
3,854 Views
12 Pages

Preconditioning of Bioactive Glasses before Introduction to Static Cell Culture: What Is Really Necessary?

  • Frederike Hohenbild,
  • Marcela Arango-Ospina,
  • Arash Moghaddam,
  • Aldo R. Boccaccini and
  • Fabian Westhauser

Due to their high bioreactivity, the in-vitro analysis of bioactive glasses (BGs) can be challenging when it comes to maintaining a physiological pH. To improve BG biocompatibility, a heterogenic spectrum of preconditioning approaches, such as &ldquo...

  • Letter
  • Open Access
3,428 Views
10 Pages

Positive Selection of Specific Antibodies Produced against Fusion Proteins

  • Lukas Kramberger-Kaplan,
  • Tina Austerlitz and
  • Holger Bohlmann

A method for the positive selection of specific antibodies for target proteins expressed as fusion proteins for the production of antiserum is presented. As proof of concept, the fusion protein FLAG::His::GFP::His::FLAG was expressed in Escherichia c...

  • Protocol
  • Open Access
4 Citations
4,198 Views
17 Pages

High-Throughput Fingerprinting of Rhizobial Free Fatty Acids by Chemical Thin-Film Deposition and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

  • Aleksey Gladchuk,
  • Julia Shumilina,
  • Alena Kusnetsova,
  • Ksenia Bureiko,
  • Susan Billig,
  • Alexander Tsarev,
  • Irina Alexandrova,
  • Larisa Leonova,
  • Vladimir A. Zhukov and
  • Igor A. Tikhonovich
  • + 3 authors

Fatty acids (FAs) represent an important class of metabolites, impacting on membrane building blocks and signaling compounds in cellular regulatory networks. In nature, prokaryotes are characterized with the most impressing FA structural diversity an...

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Methods Protoc. - ISSN 2409-9279