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Summary of the March 2013 issue of BioTechniques

The March 2013 issue of BioTechniques will feature peer-reviewed research articles describing methods for determining both membrane protein stoichiometry and insertion patterns, a new phase changing peptide for bioseparations, a novel analysis tool to deal with missing data associated with ‘omics studies and an integrated computational platform to identify transcription factor binding site. In addition to these research articles, the March issue will also contain the first in a series of special 30th Anniversary Focus Sections celebrating the launch of BioTechniques in 1983. Our first section will examine the best biochemical methods articles published in the pages of BioTechniques over the past 30 years. In addition to this, March will also have a Tech News feature examining the latest developments in the field of in vivo imaging methods and applications.

Analysis of membrane proteins is critical since these biomolecules enable a cell to communicate and interpret their external environment. In this issue of BioTechniques, a group of researchers describe a new technique aimed at understanding the distribution, localization and trafficking of membrane proteins. The researchers from Helsinki detail a biochemical technique that takes advantage of a cold-adapted trypsin enzyme and a fluorescent dye to label intracellular pools of proteins prior to incorporation in the membrane. In this way, researchers can study trafficking of proteins to the cell membrane in response to chemical signals or other extracellular cues.

Chromatography can be an important step in the purification of proteins, including those found on the membrane. One approach advanced to improve protein purification is the creation of stimulus-responsive protein tags. These tags become active under specific conditions and then can then be used to precipitate the target protein. In a Report slated for the March issue, a team of researchers describes a new calcium-responsive precipitation tag that can be easily cleaved following protein isolation. The value of this new tag is that by being calcium-responsive it will enable bioseparations under more gentle conditions than previously possible using other stimulus-responsive tag approaches.

With the recent publications from the ENCODE consortium describing various regulatory elements within the genome, interest in understanding gene regulation and transcription factor binding is very high at the moment. One issue for researchers curious to predict where within a particular sequence a transcription factor might bind prior to an experiment is the lack of integrated computational tools to make such binding site predictions. In the March issue of BioTechniques, a team of researchers describes an integrated computer platform for the analysis of transcription factor binding sites and tools to visualize those sites within sequences of interest. This new suite of applications provides a “one-stop” location for computational analysis of transcription factor binding.

‘Omics datasets (think transcriptomics, proteomics, metabolomics, ect), especially those generated by approach such as mass spectrometry and NMR, tend to be both large and complex, but also often missing values or datapoints. This large number of non-random missing values can often make data analysis methods, such as the commonly used principal component analysis (PCA) technique, less effective when it comes to pattern visualization. To overcome this limitation and extend analysis/interpretation of these large-scale datasets, researchers at the Pacific Northwest National Laboratory describe the use of sequential projection pursuit PCA as an alternative to PCA that works even in the presence of missing data without the need for imputation.

Something special is starting in the March issue of BioTechniques – we will be celebrating our 30th anniversary as a publication with a unique series of four special sections containing articles published in the pages of this journal that have truly shaped the way research is done in the lab. We are calling these articles “BioTechniques Gems”, and eight will be highlighted in 2013 in celebration of 30 years of BioTechniques. In March, our first two Gem articles in the category of biochemical methods will be revealed. Both articles will be reprinted in full, as they appeared originally, along with a special commentary on each article, its history and significance within the field of biochemical methods. Look for future Gem sections on PCR, imaging and DNA sequencing in the months to come.

Keywords: chromatography, sequencing, mass spectrometry, network analysis, , diagnostics, GFP, protein purification and separation, fluorescence microscopy, membrane proteins, membrane trafficking, data analysis, ‘omics approaches and technologies, protein tag, in vivo imaging, DNA/RNA/protein isolation, fluorescent probes