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Summary of the August 2013 issue of BioTechniques

The August 2013 issue of BioTechniques will feature articles describing: (i) method for high-plex PCR to enable massively parallel sequencing, (ii) a technique to inhibit differentiation of stem cells by inducing hypothermia, (iii) an approach for characterizing sequencing libraries through the use of digital PCR, (iv) a low cost media formulation for maintenance of brain tumor spheroids, and (v) a novel design for an osmotic minipump to deliver compounds to the mouse brain. The August issue will also contain a Tech News article examining the story behind the discovery of circular RNAs, as well as our regular monthly features and columns.

Maintaining cultures of embryonic or induced pluripotent stem cells in an undifferentiated state can be a challenge for researchers. In August, a team of researchers from the University of Connecticut suggest a simply approach to inhibiting stem cell differentiation by reducing the temperature of incubation. With a very small temperature shift, the researchers found significantly lower rates of differentiation without any adverse effects on the cells. This simple modification can reduce the effort and expense needed for researchers working with stem cells.

The ability to sequence specific sections of genomes using next-generation sequencing platforms remains an important technique for researchers. Enhancing approaches for the design of targeted baits or capture probes could further assist researchers in these efforts. In a Report in August, a team of researchers from the University of Melbourne detail their new platform, called Hi-Plex, which provides a pipeline that facilitates the design and use of primers and probes for targeted massively parallel sequencing experiments. This new set of tools should further enhance the use of next-generation sequencing for scientists.

In next-generation sequencing, characterizing the DNA sequencing library is a critical final step prior to instrument loading. Current library quality control methods, which are laborious and limited, commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. In a Report, researchers describe the use of droplet digital PCR to both quantify and size target DNA in a single assay. This new approach should both speed and enhance the characterization of sequencing libraries prior to sequence analysis.

Osmotic minipumps provide a convenient method for the delivery of compounds into the brains of small rodents. Current pumps have limited reservoirs, providing for an infusion time that last only 4-6 weeks. A new pump design detailed in the August issue of BioTechniques that takes advantage of a Y-shaped connector allows for the repeated infusion of compounds into the mouse brain. Experimental evaluation showed the new pump design did not cause any tissue irritation or damage, thus validating the use of this new osmotic minipump system.

A significant drawback for the culture of primary tumors as spheroids has been the cost of custom-formulated media. In a Benchmark article slated for August, researchers describe a cost-effective, serum-free media for culturing tumor spheroids. This new media should enable a greater range of experiments for scientists at lower costs.

Keywords:  drug delivery, infusion, next-generation sequencing, targeted resequencing, real-time PCR, qPCR, transcriptomics, stem cells, cell culture, transcriptional analysis, single cell analysis, digital PCR, NGS library characterization, multiplex-PCR, neurosphere culturing, cell culture media formulations