You are currently viewing a new version of our website. To view the old version click .

Methods and Protocols, Volume 1, Issue 3

September 2018 - 12 articles

Cover Story: Generation of locus-specific genomic editing using CRISPR/Cas9 in cell lines and primary cells is becoming routine lab practice. However, identification of specifically induced mutations and sequence changes can require laborious screening of hundreds of clones. This protocol permits high-throughput genotyping of edited cells using next generation sequencing. In addition to allowing for the screening of hundreds of clones simultaneously, this approach provides the edited sequence of each allele and can be applied to multiple loci in a single sequencing run. View this paper.
  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list .
  • You may sign up for email alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.

Articles (12)

  • Protocol
  • Open Access
23 Citations
7,351 Views
6 Pages

Two-Step Concentration of Complex Water Samples for the Detection of Viruses

  • Kata Farkas,
  • James E. McDonald,
  • Shelagh K. Malham and
  • Davey L. Jones

10 September 2018

The accurate detection and quantification of pathogenic viruses in water is essential to understand and reduce the risk of human infection. This paper describes a two-step method suitable for concentrating viruses in water and wastewater samples. The...

  • Benchmark
  • Open Access
1 Citations
5,889 Views
10 Pages

5 September 2018

Several studies have shown the potential of using Ectomycorrhizal (ECM) fungi in conifer micropropagation to overcome the cessation of adventitious root development. In vitro inoculation promotes the re-growth of the root system induced previously by...

  • Technical Note
  • Open Access
1 Citations
4,004 Views
11 Pages

Improved Detection and Fragmentation of Disulphide-Linked Peptides

  • Evelyne Maes,
  • Stefan Clerens,
  • Jolon M. Dyer and
  • Santanu Deb-Choudhury

3 September 2018

Characterisation of peptides containing intact disulphide bonds (DSBs) via mass spectrometry is challenging. Our study demonstrates that the addition of aniline to alpha-cyano-4-hydroxycinnamic acid improves detection and fragmentation of complex DSB...

  • Technical Note
  • Open Access
1 Citations
3,521 Views
7 Pages

“Mirror” Method to Estimate Mutagenic Activity of DNA Lesions

  • Leonid V. Gening,
  • Oleg V. Shevchenko,
  • Konstantin Y. Kazachenko and
  • Vyacheslav Z. Tarantul

We propose an improved method for detecting mutations that arise in DNA due to misincorporations of deoxyadenosine-5′-monophosphate (dAMP) opposite 7,8-dihydro-8-oxoguanine (8-oxoG). The method is based on the synthesis of complementary chains...

  • Benchmark
  • Open Access
14 Citations
6,155 Views
14 Pages

Validation of Total Mercury in Marine Sediment and Biological Samples, Using Cold Vapour Atomic Absorption Spectrometry

  • Ahmed Abou Elezz,
  • Hassan Mustafa Hassan,
  • Hamood Abdulla Alsaadi,
  • Ahmed Easa,
  • Saeed Al-Meer,
  • Khaled Elsaid,
  • Zafar Khan Ghouri and
  • Ahmed Abdala

A method for the measurement of total mercury (T-Hg) in environmental samples using cold vapour atomic absorption spectrometry (CV AAS) has been validated yielding a dynamic range (0.04–10.00 μg/kg) and high certified reference material (CRM...

  • Technical Note
  • Open Access
5 Citations
6,218 Views
12 Pages

Molecular Analysis of PKU-Associated PAH Mutations: A Fast and Simple Genotyping Test

  • Manuela Tolve,
  • Cristiana Artiola,
  • Amelia Pasquali,
  • Teresa Giovanniello,
  • Sirio D’Amici,
  • Antonio Angeloni,
  • Antonio Pizzuti,
  • Claudia Carducci,
  • Vincenzo Leuzzi and
  • Carla Carducci

Neonatal screening for phenylketonuria (PKU, OMIM: 261600) was introduced at the end of the 1960s. We developed a rapid and simple molecular test for the most frequent phenylalanine hydroxylase (PAH, Gene ID: 5053) mutations. Using this method to det...

  • Protocol
  • Open Access
5 Citations
9,386 Views
14 Pages

High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates

  • Lea Nussbaum,
  • Jelena M. Telenius,
  • Stephanie Hill,
  • Priscila P. Hirschfeld,
  • Maria C. Suciu,
  • The WIGWAM Consortium,
  • Damien J. Downes and
  • Jim R. Hughes

The emergence in recent years of DNA editing technologies—Zinc finger nucleases (ZFNs), transcription activator-like effector (TALE) guided nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/Cas family enzyme...

  • Protocol
  • Open Access
19 Citations
11,329 Views
17 Pages

Robust CRISPR/Cas9 Genome Editing of the HUDEP-2 Erythroid Precursor Line Using Plasmids and Single-Stranded Oligonucleotide Donors

  • Gemma Moir-Meyer,
  • Pak Leng Cheong,
  • Aude-Anais Olijnik,
  • Jill Brown,
  • Samantha Knight,
  • Andrew King,
  • Ryo Kurita,
  • Yukio Nakamura,
  • Richard J. Gibbons and
  • Douglas R. Higgs
  • + 2 authors

The study of cellular processes and gene regulation in terminal erythroid development has been greatly facilitated by the generation of an immortalised erythroid cell line derived from Human Umbilical Derived Erythroid Precursors, termed HUDEP-2 cell...

  • Protocol
  • Open Access
92 Citations
13,910 Views
5 Pages

A Rapid Bacteriophage DNA Extraction Method

  • Džiuginta Jakočiūnė and
  • Arshnee Moodley

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understand...

  • Article
  • Open Access
9 Citations
6,217 Views
16 Pages

Bisphenol A (BPA) is a widely used chemical in several consumer products and a well-studied environmental toxicant, and therefore, its accurate measurement is highly demanded. However, the co-presence of nanoparticles as an emerging class of contamin...

of 2

Get Alerted

Add your email address to receive forthcoming issues of this journal.

XFacebookLinkedIn
Methods Protoc. - ISSN 2409-9279