Not too long after publishing version 1 of the SmartFlare paper at Science Open, we received a couple of very helpful reviews. We’ve been working on the points made by the reviewers to improve the manuscript for version 2 (coming very shortly!). Below are some thoughts on a couple of the comments and a quick update on some new data in the works.
The Uptake Control SmartFlare was opened first to help us to establish a loading protocol. As such, the physical characterisation of that SmartFlare was performed in an earlier post. Thanks once again go to Joan Comenge for taking the VEGF and Scrambled control SmartFlare to the Transmission Electron Microscope (TEM).
The SmartFlare that we have chosen for this project is specific to vascular endothelial growth factor (VEGF) mRNA.
VEGF was selected as the target because it’s transcript becomes increased in a cell as part of a characterized response to hypoxia with the aid of hypoxia inducible factor-1 (HIF-1). Active HIF-1 is a heterodimer of α and β subunits, levels of HIF-1α are kept low by oxygen-dependent prolyl hydroxylases (PHDs). When a cell becomes hypoxic, PHD levels are reduced so more HIF-1α is present to dimerise with HIF-1β forming the active heterodimer that can act as the VEGF transcription factor.
From the start of the Open Notebook, we have wanted to provide readers with access to the full data generated as part of the project. In order to do this, we have had to address the two issues of where to host the data and how to make the original data easily readable.
Way back in the mists of time (…ok in 1989), Tim Berners-Lee, at the time working at CERN, proposed a way to share experimental results and ideas among colleagues. Tired of seeing information and knowledge lost to the aether when Scientists left the facility, he proposed ENQUIRE, a way to share information by allowing computers (and the humans controlling them) to talk to each other using a text-based mark-up language.