Building flexible and robust analysis frameworks for molecular subtyping of cancers

Molecular subtyping is essential to infer tumor aggressiveness and predict prognosis. In practice, tumor profiling requires in-depth knowledge of bioinformatics tools involved in the processing and analysis of the generated data. Additionally, data incompatibility (e.g., microarray versus RNA sequencing data) and technical and uncharacterized biological variance between training and test data can pose challenges in classifying individual samples. In this article, we provide a roadmap for implementing bioinformatics frameworks for molecular profiling of human cancers in a clinical diagnostic setting. We describe a framework for integrating several methods for quality control, normalization, batch correction, classification and reporting, and develop a use case of the framework in breast cancer.

Extracellular polymeric substances are transient media for microbial extracellular electron transfer

Microorganisms exploit extracellular electron transfer (EET) in growth and information exchange with external environments or with other cells. Every microbial cell is surrounded by extracellular polymeric substances (EPS). Understanding the roles of three-dimensional (3D) EPS in EET is essential in microbiology and microbial exploitation for mineral bio-respiration, pollutant conversion, and bioenergy production. We have addressed these challenges by comparing pure and EPS-depleted samples of three representative electrochemically active strains viz Gram-negative Shewanella oneidensis MR-1, Gram-positive Bacillus sp. WS-XY1, and yeast Pichia stipites using technology from electrochemistry, spectroscopy, atomic force microscopy, and microbiology. Voltammetry discloses redox signals from cytochromes and flavins in intact MR-1 cells, whereas stronger signals from cytochromes and additional signals from both flavins and cytochromes are found after EPS depletion. Flow cytometry and fluorescence microscopy substantiated by N-acetylglucosamine and electron transport system activity data showed less than 1.5% cell damage after EPS extraction. The electrochemical differences between normal and EPS-depleted cells therefore originate from electrochemical species in cell walls and EPS. The 35 ± 15-nm MR-1 EPS layer is also electrochemically active itself, with cytochrome electron transfer rate constants of 0.026 and 0.056 s-1 for intact MR-1 and EPS-depleted cells, respectively. This surprisingly small rate difference suggests that molecular redox species at the core of EPS assist EET. The combination of all the data with electron transfer analysis suggests that electron "hopping" is the most likely molecular mechanism for electrochemical electron transfer through EPS.