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Summary of the March 2014 issue of BioTechniques

The March 2014 issue of BioTechniques will feature new articles and methods, including: (i) a method that uses proximity ligation to analyze chromatin at high resolution (ii) an approach for the systematic selection of aptamer pairs for sandwich assays, (iii) a novel design for glass needles to enhance insect transformation protocols, (iv) a technique for amplifying DNA templates prior to PCR that minimizes bias and (v) a computational tool designed to detect contamination in re-sequencing studies.

Selecting aptamers for biological applications requires multiple rounds of screening and optimization. In a March Report, a team of scientists describe a method for the systematic isolation of slow off-rate modified aptamers that can potentially be used in diagnostic applications. Designed to bind to different epitopes, these method can identify aptamers to be used in pair-wise screening of multiple ligands.

Small starting amounts of template can make for difficult times in genetic analysis studies using techniques like DNA sequencing or STR profiling. Such templates can be amplified prior to analysis using approaches such as MDA, but bias during amplification can lead to difficulty in interpreting data. In the March issue, Australian researchers detail a linear PCR amplification strategy that resulted in greater allele recovery in STR profiling compared to subjects that were not amplified. The new approach should introduce less bias in amplified products, enhancing researcher’s chances to work with small quantity samples.

Germline transformation is an important tool in insect genetics. However, the difficulty of injecting transposon vectors into ova, especially when working with certain species, can limit the ability of researchers to interrogate the function of insect genes. In the March 2013 issue, a team from Vanderbilt University describes an improved glass needle design for butterfly ova injection that resulted in a significant increase in transformation efficiency. This new design should be applicable to a wide-range of lepidopteran species.

In recent years, several techniques have emerged for the investigation of chromatin structure and organization. In the March issue, researchers from the Karolinska Institute in Sweden detail a new methodology, based on the proximity ligation assay, that enables researchers to assess the proximity between two different chromatin fibers at a resolution of 170 angstroms. The new technique should enable the further dissection of chromatin states and their effects on gene expression.

A major challenge in the detection of novel polymorphisms using next-generation sequencing is the ability to separate polymorphisms from contaminates or sequence artifacts. In the March issue, a team from Penn State University details their pipeline for the reliable detection of sequence contamination and it’s origin. The pipeline and associated quality control workflow should enhance researcher’s investigations into novel genetic variation.

In addition to these primary research articles, the March issue will also feature a Tech News article examining the world of antibody production and validation as well as the development of alternative binders. Other feature articles in the March issue will include our Troubleshooting Forum that answers pressing technical questions from lab scientists, the Scientist Profile that each month uncovers the person and story behind the experiments, Citations, our highlights of methods research published in different journals, and BioSpotlights.

Keywords: next-generation sequencing, chromatin, chromatin analysis cloning, aptamers, aptamer selection, ELISA assays, sandwich assays, polymorphism analysis, ChIP-Seq, chromatin immunoprecipitation, computational biology, genetic transformation, transposon, insect genetics