Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer

<p>Abstract</p> <p>Background</p> <p>Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging.</p> <p>Methods</p> <p>We describe a method to identify the <it>trans-</it>acting drivers of multiple gene co-expression, which reflects the action of regulatory molecules. This method-termed <it>co-regulatory expression quantitative trait locus </it>(creQTL) <it>mapping</it>-allows for evaluation of a more focused set of phenotypes within a clear biological context than conventional eQTL mapping.</p> <p>Results</p> <p>Applying this method to a study of endometrial cancer revealed regulatory mechanisms supported by the literature: a creQTL between a locus upstream of STARD13/DLC2 and a group of seven IFNβ-induced genes. This suggests that the Rho-GTPase encoded by STARD13 regulates IFNβ-induced genes and the DNA damage response.</p> <p>Conclusions</p> <p>Because of the importance of IFNβ in cancer, our results suggest that creQTL may provide a finer picture of gene regulation and may reveal additional molecular targets for intervention. An open source R implementation of the method is available at <url>http://sites.google.com/site/kenkompass/</url>.</p

Bioreactor technology for sustainable production of plant cell-derived products

The successful cultivation of plant cell and tissue cultures for the production of valuable chemical components requires the selection of an appropriate bioreactor. Selection criteria are determined based on a number of factors that are intrinsic to particular plant cell or tissue cultures and are influenced by the process objectives. Due to the specific properties of plant cell and tissue cultures, bioreactor systems may differ significantly from those used for microorganism or animal cell cultures. Furthermore, the differences from one plant culture to another can be immense; it is obvious that the optimal bioreactor system for a plant suspension cell culture is different to one for a plant tissue culture in many ways. General considerations are presented, and based on these key points, selection criteria are used to establish a “bioreactor chooser” tool. The particular details of the most relevant bioreactor types for plant cell and tissue cultures are listed and described. To produce valuable products, the process also needs to be scaled up to an economically justifiable size, which is usually done either by scaling up the size of the bioreactor itself or by bioreactor parallelization. Therefore, the most significant influencing factors are also discussed