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Methods and Protocols, Volume 2, Issue 1

2019 March - 25 articles

Cover Story: Single-particle tracking has been developed over the past 25 years to investigate molecular dynamics, structure, interactions, and function in the cellular context. We show how single-molecule and ensemble Förster resonance energy transfer (FRET) are used to build a model of epidermal growth factor receptor (EGFR) complexes in cells. EGFRs in cells are labelled with a mixture of donor (green) and acceptor (red) fluorophores. FRET then measures distances between EGFR in complexes. EGFRs are also liganded with EGF labelled with a green fluorescent dye, and the plasma membrane is labelled with a red dye. Ensemble FRET between the dyes measures EGFR-membrane separation, and hence the receptor’s conformation. These data are combined to produce a model for EGFR oligomerization in the cell. Data from Webb et al., Biophys. J. 94, 803 (2008) and Tynan et al., Mol. Cell. Biol. 31, 2241 (2011). View this paper.
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Articles (25)

  • Opinion
  • Open Access
17 Citations
4,642 Views
10 Pages

Size-based fungal growth studies are limited because they do not provide information about the mold’s state of maturity, and measurements such as radius and diameter are not practical if the fungus grows irregularly. Furthermore, the current me...

  • Review
  • Open Access
226 Citations
46,196 Views
34 Pages

A User’s Guide to Cell-Free Protein Synthesis

  • Nicole E. Gregorio,
  • Max Z. Levine and
  • Javin P. Oza

Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include it...

(This article belongs to the Special Issue Cell-Free Synthetic Biology)
  • Protocol
  • Open Access
22 Citations
7,090 Views
11 Pages

An Evidence-Based Objective Study Protocol for Evaluating Cardiovascular and Cerebrovascular Indices Following Concussion: The Neary Protocol

  • J. Patrick Neary,
  • Jyotpal Singh,
  • Scott A. Bishop,
  • Ryan T. Dech and ,
  • Matthew J. A. Butz and
  • Trevor K. Len
  • + 1 author+ 0 author

Introduction: The prevalence and incidence of sport-related concussion have continued to increase over the past decade, and researchers from various backgrounds strive for evidenced-based clinical assessment and management. When diagnosing and managi...

  • Protocol
  • Open Access
10 Citations
6,654 Views
13 Pages

Reverse Genetic Systems for Pseudomonas aeruginosa Leviphages

  • Jae-Yeol Lee,
  • Se-Jeong Ahn,
  • Chanseop Park,
  • Hee-Won Bae and ,
  • Eun Sook Kim and
  • You-Hee Cho
  • + 1 author+ 0 author

Reverse genetic systems for RNA viruses are the platforms to introduce mutations into the RNA genomes and thus have helped understand their life cycle and harness them for human purposes to develop vaccines and delivery systems. These systems are bas...

(This article belongs to the Special Issue 100 Years of Bacteriophage: From Basic Research to Medical Application)
  • Protocol
  • Open Access
6 Citations
9,058 Views
15 Pages

Uganda has persistently had high adolescent pregnancy prevalence; 25% for the last 10 years. This protocol presents the design of a Cluster Randomized Controlled Trial (CRCT) to investigate the effectiveness of School-Based Sexual and Reproductive He...

  • Article
  • Open Access
5 Citations
4,095 Views
8 Pages

The Inhibition of Radial and Axial Micromovement of Bone Scaffold with Gelfoam® and Titanium Mesh Fixation and Its Effects on Osteointegration

  • Jane Kwon,
  • Dong Joon Lee,
  • Mallory Kocher,
  • Yong-Il Kim and ,
  • Te-Ju Wu,
  • John Whitley and
  • Ching-Chang Ko
  • + 2 authors+ 0 author

26 February 2019

A major drawback of nanocomposite scaffolds in bone tissue engineering is dimensional shrinkage after the fabrication process. Shrinkage yields gaps between the scaffold and host bone in the defect site and eventually causes failure in osteointegrati...

  • Review
  • Open Access
32 Citations
7,737 Views
11 Pages

Campylobacter Phage Isolation and Characterization: What We Have Learned So Far

  • Claudia Jäckel,
  • Jens Andre Hammerl and
  • Stefan Hertwig

15 February 2019

Lytic Campylobacter phages, which can be used to combat this pathogen in animals and on food products, have been studied for more than 30 years. Though, due to some peculiarities of the phages, which hampered their isolation and particularly their mo...

(This article belongs to the Special Issue 100 Years of Bacteriophage: From Basic Research to Medical Application)
  • Protocol
  • Open Access
45 Citations
9,244 Views
30 Pages

Protocol for Construction of Rat Nerve Stimulation Cuff Electrodes

  • Manolo U. Rios,
  • Jesse E. Bucksot,
  • Kimiya C. Rahebi,
  • Crystal T. Engineer and ,
  • Michael P. Kilgard and
  • Seth A. Hays
  • + 1 author+ 0 author

15 February 2019

Peripheral nerve stimulation has emerged as a platform therapy to treat a wide range of disorders. Continued development and translation of these strategies requires that researchers have access to reliable, customizable electrodes for nerve stimulat...

  • Protocol
  • Open Access
18 Citations
10,254 Views
19 Pages

Efficient Construction and Effective Screening of Synthetic Domain Antibody Libraries

  • Arghavan Solemani Zadeh,
  • Alissa Grässer,
  • Heiko Dinter,
  • Maximilian Hermes and
  • Katharina Schindowski

14 February 2019

Phage display is a powerful technique for drug discovery in biomedical research in particular for antibody libraries. But, several technical challenges are associated with the selection process. For instance, during the panning step, the successful e...

  • Protocol
  • Open Access
21 Citations
8,559 Views
12 Pages

12 February 2019

Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatu...

(This article belongs to the Special Issue Cell-Free Synthetic Biology)
  • Protocol
  • Open Access
5 Citations
6,607 Views
7 Pages

5 February 2019

The application of high-throughput nucleic acid and protein sequencing technologies is transforming our understanding of plant microbiomes and their interactions with their hosts in health and disease. However, progress in studying host-microbiome in...

  • Technical Note
  • Open Access
5 Citations
5,403 Views
13 Pages

2 February 2019

Air puff systems are at once trivially straightforward and dauntingly complex. On the one hand, they are little but a pressure source, valve, and tube connected together. On the other, the air passing through them is a compressible medium, expanding...

  • Protocol
  • Open Access
3 Citations
6,454 Views
14 Pages

Novel Applications of Lead Acetate and Flow Cytometry Methods for Detection of Sulfur-Containing Molecules

  • Evgeniya Anishchenko,
  • Carmela Vigorito,
  • Luigi Mele,
  • Patrizia Lombari and ,
  • Alessandra F. Perna and
  • Diego Ingrosso
  • + 1 author+ 0 author

1 February 2019

Hydrogen sulfide (H2S) is the most recently established gaseous vasodilator, enzymatically produced from cysteine metabolism, involved in a number of pathophysiological processes. However, its accurate detection in vivo is critical due to its volatil...

  • Review
  • Open Access
24 Citations
6,773 Views
30 Pages

30 January 2019

Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecu...

(This article belongs to the Special Issue Single-Molecule Techniques)
  • Letter
  • Open Access
13 Citations
5,083 Views
11 Pages

29 January 2019

Recent improvements in optical tools that can perturb brain activity and simultaneously reveal the elicited alterations in the associated regions offer an exceptional means to understand and map the connectivity of the brain. In this work, we exploit...

  • Protocol
  • Open Access
21 Citations
11,343 Views
17 Pages

The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of t...

  • Benchmark
  • Open Access
5 Citations
4,935 Views
11 Pages

Preparing pioloform/formvar support films on transmission electron microscopy (TEM) grids is a routine laboratory procedure in practically all electron microscopy units. In current practice, these grids are manually placed on the support film one by...

  • Protocol
  • Open Access
16 Citations
5,777 Views
18 Pages

Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate recepto...

(This article belongs to the Special Issue Single-Molecule Techniques)
  • Technical Note
  • Open Access
7 Citations
4,125 Views
9 Pages

A Software Architecture to Mimic a Ventricular Tachycardia in Intact Murine Hearts by Means of an All-Optical Platform

  • Francesco Giardini,
  • Valentina Biasci,
  • Marina Scardigli,
  • Francesco S. Pavone and ,
  • Gil Bub and
  • Leonardo Sacconi
  • + 1 author+ 0 author

Optogenetics is an emerging method that uses light to manipulate electrical activity in excitable cells exploiting the interaction between light and light-sensitive depolarizing ion channels, such as channelrhodopsin-2 (ChR2). Initially used in the n...

  • Article
  • Open Access
3 Citations
5,500 Views
12 Pages

Metagenomic techniques, notably the cloning of environmental DNA (eDNA) into surrogate hosts, have given access to the genome of uncultured bacteria. However, the determination of gene functions based on DNA sequences alone remains a significant chal...

  • Patent Summary
  • Open Access
1 Citations
3,209 Views
4 Pages

A Novelty System for Biotization of Plant Microshoots and Collection of Natural Compounds

  • Mário Rui da Costa Basílio e Castro,
  • Carla Ragonezi,
  • Paulo Guilherme Leandro de Oliveira and
  • Maria Amely Zavattieri

An in vitro plant microshoot culture system composed of two phases; a liquid phase overlaid by a floating solid phase, which is described in detail herein. This system is designed to enable the extraction of natural compounds released/disseminated in...

  • Protocol
  • Open Access
43 Citations
12,862 Views
5 Pages

Synthesis of Highly Concentrated Suspensions of Silver Nanoparticles by Two Versions of the Chemical Reduction Method

  • Miguel Gakiya-Teruya,
  • Luis Palomino-Marcelo and
  • Juan Carlos F. Rodriguez-Reyes

24 December 2018

In spite of the widespread use of the chemical reduction method to obtain silver nanoparticles, the nanoparticle yield is often low due to a required addition of small volumes of diluted metal ions to a solution containing a reducer. Higher yields ca...

  • Technical Note
  • Open Access
5 Citations
3,956 Views
10 Pages

20 December 2018

Compared to previously tested fumigants such as methyl bromide, sulfuryl fluoride and phosphine; ethanedinitrile (EDN) is a new fumigant which is being trialled around the world as a pre-plant soil treatment and as a quarantine and pre-shipment (QPS)...

  • Article
  • Open Access
42 Citations
10,175 Views
11 Pages

Fast Calculation of Computer Generated Holograms for 3D Photostimulation through Compressive-Sensing Gerchberg–Saxton Algorithm

  • Paolo Pozzi,
  • Laura Maddalena,
  • Nicolò Ceffa,
  • Oleg Soloviev and ,
  • Gleb Vdovin,
  • Elizabeth Carroll and
  • Michel Verhaegen
  • + 2 authors+ 0 author

20 December 2018

The use of spatial light modulators to project computer generated holograms is a common strategy for optogenetic stimulation of multiple structures of interest within a three-dimensional volume. A common requirement when addressing multiple targets s...

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Methods Protoc. - ISSN 2409-9279