The latest news about the ionomics project and thoughts from team members.

Thursday, April 16, 2009

Arabidopsis Piims data download error fixed

We just fixed a bug in the csv download code of the Arabidopsis Piims which was causing incorrect data to be produced for some samples. The error was introduced around November 13th, 2008. If you downloaded a csv file during the intervening time, you should re-download the data.

We apologize for the inconvenience.

esb1 paper accepted at Plos Genetics

Our paper entitled 'Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis' has just been accepted for publication at PLoS Genetics. Here is the abstract:

Background: Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots.

Methodologies/Principle Findings: Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root, and both water movement through the plant, and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates, and increased water use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn and Zn, and increases in the accumulation of Na, S, K, As, Se and Mo in the shoot.

Conclusions/Significance: Here we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn and Zn occurs in the apoplast.

Friday, April 3, 2009

Open science helps reviewers!

We just got the reviews back from Plos Genetics for our esb1 paper. There were many constructive suggestions and helpful suggestions, which is what we have come to expect from Plos Genetics (and why we submit many of our manuscripts there).

One of the reviewers actually came to Piims and retrieved some of the data that went into the paper to make the point that we should comment on the Mg effect of the mutation. Specifically, the reviewer pointed out that the mutation doesn't affect Mg, even though it affects Ca. They even included a figure of the data! I am posting the figure here, Blue is the mutant, and pink is the wild-type.


Just another reason to put all your data out there. We thank the reviewer for the helpful suggestions.

ps: Though we are collecting data about who visits our website, we don't collect data about what they search, so the kind reviewer is still anonymous to us.