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

Tuesday, November 3, 2009

Ferroportin Paper published in Plant Cell

Our paper describing the function of the two Ferroportin genes in Arabidopsis has just been published in the early access feed of Plant Cell!

The pdf is here (also available from our publications page)

here is the abstract......

Relatively little is known about how metals such as iron are effluxed from cells, a necessary step for transport from the root to the shoot. Ferroportin (FPN) is the sole iron efflux transporter identified to date in animals, and there are two closely related orthologs in Arabidopsis thaliana, IRON REGULATED1 (IREG1/FPN1) and IREG2/FPN2. FPN1 localizes to the plasma membrane and is expressed in the stele, suggesting a role in vascular loading; FPN2 localizes to the vacuole and is expressed in the two outermost layers of the root in response to iron deficiency, suggesting a role in buffering metal influx. Consistent with these roles, fpn2 has a diminished iron deficiency response, whereas fpn1 fpn2 has an elevated iron deficiency response. Ferroportins also play a role in cobalt homeostasis; a survey of Arabidopsis accessions for ionomic phenotypes showed that truncation of FPN2 results in elevated shoot cobalt levels and leads to increased sensitivity to the metal. Conversely, loss of FPN1 abolishes shoot cobalt accumulation, even in the cobalt accumulating mutant frd3. Consequently, in the fpn1 fpn2 double mutant, cobalt cannot move to the shoot via FPN1 and is not sequestered in the root vacuoles via FPN2; instead, cobalt likely accumulates in the root cytoplasm causing fpn1 fpn2 to be even more sensitive to cobalt than fpn2 mutants.

Thursday, October 8, 2009

Review publications

We have added a new publications page to hold review papers produced by the ionomics team. You can find it here or follow the link from the top of the main publications page.

Thursday, September 24, 2009

Database repairs Oct 9

The ionomicshub will be down for a few essential security patches on Friday, October 9th. These updates will start at 11:00am and be complete by 1:00pm (ET) (may be before).

Yeast database goes live

The Beta version of our yeast database is now live. This database holds over 50,000 samples worth of ionomic data on all viable yeast strains from both the full genome knockout and over expression collections. A description of how the data was collected has been published in Danku et al., J Anal. At. Spectrom. 2009, 24, 103-107. The database supports searches for specific genes, data display and download. We have also included features that allow the re-upload of downloaded data sets after user-defined manipulations have been performed. These new up-loaded user-defined data sets then become searchable by the community. We are currently working on a paper in which we describe the statistical analysis of the data and its biological implications. Please report bugs or suggestions to or

Tuesday, July 21, 2009

iHUB proposal submitted to NSF

The Salt lab has just submitted a proposal to the US NSF Research Coorodination Network in Biological Science (RCN) program titled "The iHUB: A Collaborative International Network for Ionomics". If funded we will add various new tools to the ionomicsHUB including:

1. Tools to allow the easy sharing and annotation of data.

2. Literature Cloud: A tool to allow the easy filtering and sharing of literature.

3. Tools to allow the coordinated collection of ICP data from distributed sites.

4. Tools to allow the easy sharing of presentations and lectures.

5. Tools to allow the self formation of online work groups and online communication.

6. iHUB interaction map – The iHUB interactome.

7. On-line Help tools.

8. iHUB Annual Meeting.

9. Student and facility scientific exchange between collaborating laboratories.

Friday, June 5, 2009

esb1 paper is out!

Our paper on the esb1 mutant is now available at Plos Genetics. You can find it here

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.

Tuesday, March 24, 2009

Rice Piims is up and running!

We have now deployed a working prototype of Piims to manage the pipeline and data for our NSF funded Rice project. This represents a substantial redesign of the Piims system. Some of the major changes are listed below. We are releasing the data as soon as it enters the database. We are in the process of uploading all of the ~7000 samples that we have already run into the database.

New features:
The biggest change is that for Rice, we have incorporated features allowing us to track samples that were grown in fields by collaborators. Piims will now allow us to keep track of Packets of seed that get sent to us.

Piims will track information like field location and weather data for fields.

Piims will now allow for the flexible construction of analysis runs, so packets from different fields and years can be analyzed to together.

Thursday, January 8, 2009

New seed grant to develop collaborative tools

We are please to announce that along with our support from NSF and NIH for ionomicsHUB, we have recently been awarded a seed grant from the Purdue University Cyber center to develop collaborative work space and literature sharing tools for the ionomicsHUB. Look out for these new tools in 2009