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Cell Volume, Self-Organisation, and Escher: the PLOS Comp Biol August Issue

bchadwick Cell biology Community Computational biology Data Molecular biology Neuroscience PLOS Computational Biology Uncategorized

Here are our highlights from August’s PLOS Computational Biology

 

The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization

K+ exchange at the blood-brain barrier. Image Credit: Ullah et al.
K+ exchange at the blood-brain barrier. Image Credit: Ullah et al.

Cell volume changes are ubiquitous in normal and pathological activity of the brain, yet we know little of how cell volume influences neuronal activity. Ghanim Ullah and colleagues perform the first detailed study of the effects of cell volume on neuronal dynamics. By combining the dynamic ion concentrations and volume, conservation of charge, and the energy requirements of the cell within a Hodgkin-Huxley type framework, the authors demonstrate the feasibility of a comprehensive framework encompassing a wide range of neuronal behaviours.

 

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses

The connectivity of mammalian brains exhibits structure at a wide variety of spatial scales, from the broad (which brain areas connect to which) to the extremely fine (where synapses form on the morphology of individual neurons). A central question in systems neuroscience is how this structure emerges. Brent Doiron and colleagues present a theory for how activity-dependent synaptic plasticity leads to the emergence of neuronal microcircuits. The authors use this theory to show how the form of the plasticity rule can govern the promotion or suppression of different connectivity patterns.

 

 

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

August Issue Image: Systematic Mapping of Protein Mutational Space. Credit: Rockah-Shmuel et al.
August Issue Image: Systematic Mapping of Protein Mutational Space. Credit: Rockah-Shmuel et al.

We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Bernhard O. Palsson and colleagues present Escher, a web application that can be used to rapidly build pathway maps. On Escher maps, diverse datasets related to genes, reactions, and metabolites can be quickly contextualized within metabolism and, increasingly, beyond metabolism. Escher is available now for free use at https://escher.github.io.

 

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