The latest news about the ionomics project and thoughts from team members.
Tuesday, November 3, 2009
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
Thursday, September 24, 2009
Tuesday, July 21, 2009
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
Thursday, April 16, 2009
We apologize for the inconvenience.
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
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
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
- ► April (3)