Xin Wang | Search bioRxiv

bioRxiv2016

PBrowse: A web-based platform for real-time collaborative exploration of genomic data

SummaryThe central task of a genome browser is to enable easy visual exploration of large genomic data to gain biological insight. Most existing genome browsers were designed for data exploration by individual users, while a few allow some limited forms of collaboration among multiple users, such as file sharing and wiki-style collaborative editing of gene annotations. Our works premise is that allowing sharing of genome browser views instantaneously in real-time enables the exchange of ideas and insight in a collaborative project, thus harnessing the wisdom of the crowd. PBrowse is a parallel-access real-time collaborative web-based genome browser that provides both an integrated, real-time collaborative platform and a comprehensive file sharing system. PBrowse also allows real-time track comment and has integrated group chat to facilitate interactive discussion among multiple users. Through the Distributed Annotation Server protocol, PBrowse can easily access a wide range of publicly available genomic data, such as the ENCODE data sets. We argue that PBrowse, with the re-designed user management, data management and novel collaborative layer based on Biodalliance, represents a paradigm shift from seeing genome browser merely as a tool of data visualisation to a tool that enables real-time human-human interaction and knowledge exchange in a collaborative setting.\n\nAvailabilityPBrowse is available at http://pbrowse.victorchang.edu.au, and its source code is available via the open source BSD 3 license at http://github.com/VCCRI/PBrowse.\n\nContactj.ho@victorchang.edu.au\n\nSupplementary InformationSupplementary video demonstrating collaborative feature of pbrowse is available in https://www.youtube.com/watch?v=ROvKXZoXiIc.

Bioinformatics↗

bioRxiv2016

Maintaining proton homeostasis is an essential role of glucose metabolism in cell survival

Aerobic glycolysis, termed \"the Warburg Effect\", supports cell proliferation, and glucose deprivation directly elicits necrosis or shifts stimuli-induced apoptosis to necrosis. However, how glucose metabolism regulates cell survival or death choice remains largely unclear. Here we use our recently developed method to monitor in real-time cellular apoptosis and necrosis, and uncover a metabolic homeostasis linked to cell death control. We show that glucose metabolism is the major source to maintain both intracellular and extracellular proton homeostasis. Glucose deficiency leads to lack of proton provision, which provokes a compensatory lysosomal proton efflux and resultant increased lysosomal pH. This lysosomal alkalinization can trigger necrosis. Furthermore, artificial proton supplement enables cells to survive glucose deprivation. Taken together, our results reveal a critical role of glucose metabolism in maintaining cellular microenvironment, and provide a better understanding of the essential requirement of aerobic glycolysis for proliferating cells whose active anabolism consumes a great many protons.

Cancer Biology↗