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Summary of the September 2014 issue of BioTechniques

The September 2014 issue of BioTechniques will feature new research articles on:

  • CRISPR/Cas9 gene deletion
  • analysis and visualization of reverse phase protein array data
  • stabilization of primers and fluorogenic probes for long-term storage
  • a stain for improved visualization of cells on polymer scaffolds by electron microscopy
  • the influence of clotting duration on the concentration of brain-derived neutrophic factor (BDNF) in serum

In addition to these articles, September will also feature a Practical Guide article devoted to the development of scaffolds and media for cell culture applications, and a Tech News article examining the latest developments and methods for cataloguing and studying epigenetic modifications.

 Stabilization of primers and fluorogenic

Imagine being able to do a real-time PCR assay in the middle of the field – in a jungle, or some other truly remote locale? Aside from the cycler equipment, the other challenge is keeping reaction components – primers, probes, fluorophores, all stable and cold. Wouldn’t it be prove easier if those primers and probes could be stored at ambient temperatures? In the September issue, a team from Germany describe how two stabilizing agents, trehalose and xanthan, can enable the storage of fluorogenic hydrolysis probes (TaqMan) at room temperature. The authors provide data showing that room temperature storage did not impede primers, even after one year of storage, if the proper stabilizing reagents are used.

 CRISPR/Cas9 gene deletion

Genome modification is a critical technique in modern molecular biology. While a number of approaches have been described (including zinc finger nucleases, TALENs, and retroviral vectors), the CRISPR-Cas9 system is proving to be one of the more efficient techniques, possessing high accuracy with little off-target effects. In September, a group of scientists from Fudan University detail their methodology for accurate gene deletion or replacement using CRISPR-Cas9. The authors demonstrate the effectiveness of the technique in human cells, paving the way for more in-depth analysis of the genetics and structure-function relationship within human cells.

 A stain for improved visualization of cells on polymer scaffolds by electron microscopy

Of late, culturing cells on polymer scaffolds (and other systems) has become more common as researchers seek out laboratory environments that more closely mimic in vivo conditions. A challenge when examining cells cultured on these scaffolds is to distinguish the cells as they grow from the scaffold in the background. In September, an article from a team in England describes the use of platinum blue to stain cells prior to scanning electron microscopy analysis. The authors show that platinum blue clearly allows the discrimination of cells and scaffolds, enabling better visualization of development, migration and differentiation of cells in these environments.

 Analysis and visualization of reverse phase protein array data

In proteomics, reverse phase protein arrays (RPPA) can be used to quantify protein levels or test for post-translational modifications. Although increasing in use and application, bioinformatic tools to analyze RPPA data are still limited to a few possible solutions. In September, researchers from Germany describe the development of an expanded RPPA analysis computational toolkit that incorporates new correction algorithms and visualization tools with simple interface in an open source format. This new platform should further expand the usage of RPPA amongst proteomic researchers.

 The influence of clotting duration on the concentration of brain-derived neutrophic factor (BDNF) in serum

BDNF, the most abundant neurotrophin in the central nervous system, has been suggested as a potential biomarker for several psychiatric and neurodegenerative diseases. The challenge in applying BDNF as a biomarker is that the concentration of this neurotrophin varies considerably in human serum. In September, a team of researchers tackles the impact of clotting time on BDNF levels in serum. The team found that BDNF concentration rises for the first hour in clotted serum, but then plateaus after 60 minutes. The authors therefore suggest that BDNF measurements should be made after 60 minutes of clotting to get a accurate dosage measurement.

The September issue will also feature the latest installment of our new, and popular, Practical Guide article series. This month, authors look at the development and application of cell culture scaffolds and defined media formulations in understand cell biology and how these innovations have led to more advanced three-dimensional cell culture platforms and systems. The Guide will supply insights into the design and analysis of cells cultured on various scaffolds, and provide tips and instruction on media preparation and the application of cell culture systems for downstream cell analysis assays.

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