tag:blogger.com,1999:blog-13327211952268479202024-03-07T20:03:39.459-08:00Ionomics BlogThe latest news about the ionomics project and thoughts from team members.Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.comBlogger31125tag:blogger.com,1999:blog-1332721195226847920.post-26792043912100595382013-09-09T07:52:00.001-07:002013-09-09T07:52:53.658-07:00Ionomics reveals as role for dirigent proteins in lignin depositionNew research into the function of ESB1 (Enhanced Suberin 1) has revealed that this dirigent protein plays an essential role in building lignin-based Casparian strips in cell walls of endodermal cells. These discoveries recently published in PNAS start to dissect the molecular mechanisms involved in endodermal control of solute entry into plants. Further, they provide in vivo evidence for proteinsdsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-90145506047568016532013-09-09T06:32:00.001-07:002013-09-09T06:32:13.796-07:00Ionomics sheds new light on evolution
A new paper in Science from the Salt lab describes how polyploidy enhances leaf concentration
of potassium and fitness in saline soils, supporting the notion that genome duplication is
important in the evolutionary history of plants.
Chao DY, Dilkes B, Luo H, Douglas A, Yakubova E, Lahner B, Salt DE. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science. dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-36001450613524178702013-03-14T02:29:00.003-07:002013-03-14T02:29:42.057-07:00GWAS paper on Cd accumulationThe Salt lab recently published a paper in PLoS Genetics in which we describe the use of GWA mapping to identify HMA3 as the primary locus controlling natural variation in foliar accumulation of Cd in Arabidopsis thaliana. The paper can be read at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002923 and the abstract can be seen below.
Abstract: Understanding the dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-85733478853190877952012-06-28T12:12:00.001-07:002012-06-28T12:12:51.534-07:00New Perspective in ScienceBrian Dilkes and I have a perspective in the new issue of Science titled "Elemental Profiles Reflect Plant Adaptations to the Environment". The abstract is below. Science puts a very (and I mean VERY) tight word limit on the manuscript and so one of the things that we needed to cut was the acknowledgements. So we would like to take the time here to give huge thanks to all the great people who Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-9616157247236242822012-06-18T13:05:00.001-07:002012-06-18T13:05:58.710-07:00New Paper in PLoS ONEOur most recent paper was just published in PLoS ONE. "Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana" is our first installment of all the association panel data that we have generated. It looks at the corrections between elements within and between tissues in the initial 96 accession 'Nordborg' panel. It includes some very nice data on hydroponics grownIvan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-88117499932780953972012-04-27T14:17:00.000-07:002012-04-27T14:20:04.007-07:00First iHUB workshopThe first NSF sponsored iHUB workshop held 26 & 27 April, 2012 in St Louis, US was a success. New tools and features discussed at the workshop should be appearing on the iHUB soon.dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-7709955558844245872012-04-27T14:13:00.001-07:002012-04-27T14:19:21.164-07:00Aberdeen Ionomics Facility runningThe ICP-MS instruments in David Salt's Ionomics Facility at the University of Aberdeen are now up and running.dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-71499744108798773492011-11-04T01:26:00.000-07:002011-11-04T01:36:07.994-07:00PLoS one paper on CPR5 and potassiumThe Salt group has published a new paper on a novel role of CPR5 in the regulation of potassium in A. thaliana.Borghi M, Rus A, Salt DE (2011) Loss-of-Function of Constitutive Expresser of Pathogenesis Related Genes5 Affects Potassium Homeostasis in Arabidopsis thaliana. PLoS ONE 6(10): e26360. doi:10.1371/journal.pone.0026360Here is the AbstractHere, we demonstrate that thedsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-58716878708055386482011-04-26T09:05:00.001-07:002011-04-26T09:05:38.672-07:00Two new Plant Cell PapersTwo new papers have been published in Plant Cell in the last month describing genes that we cloned from the original Lahner et al. ionomics screen: The first is "Arabidopsis NPCC6/NaKR1 Is a Phloem Mobile Metal Binding Protein Necessary for Phloem Function and Root Meristem Maintenance". This paper was mainly the result of the hard work of newly minted Ph.D Hui Tian from John Ward's Lab at UMN.Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-57059181679164917212010-11-12T14:38:00.001-08:002010-11-12T14:38:44.858-08:00New paper in PLoS Genetics!Our paper "A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1" has just been published in PLoS Genetics. There is an accompanying perspective, "Beyond QTL Cloning", by Jill Anderson and Thomas Mitchell-Olds which says (among other nice things): In this issue of PLoS Genetics, Baxter et al. [9] present an elegant studyIvan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-56993509299524847722010-10-21T09:56:00.000-07:002010-10-21T10:01:35.215-07:00Prof Salt accepts new position at University of AberdeenProfessor David Salt accepts new position as 6th Century Chair in the School of Biological Sciences at the University of Aberdeen starting May 2011. Professor Salt will continue his ionomic's projects and development of the ionomicsHUB (iHUB)dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-70743104545733790212010-06-17T08:12:00.001-07:002010-06-17T08:12:58.707-07:00Arabidopsis RILs paper is publishedOur paper on "Natural Genetic Variation in Selected Populations of Arabidopsis thaliana Is Associated with Ionomic Differences" has just been published in PLoS ONE. I'm really happy that this paper is out because it demonstrates something that we have been talking about for several years now: that the ionome is dynamic and interconnected, and the relationships between elements are dependent on Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-67983956355085708012010-04-25T19:39:00.001-07:002010-04-25T19:39:28.210-07:00Arabidopsis Association Paper published in NatureThe big Nature paper, to which we contributed phenotype data, is now out. Its a great example of the power of plant genetics, many different phenotypes evaluated on a common population resulting in a wealth of really interesting associations. Its way cool, but the bigger populations that we have analyzed are even better and soon we will be submitting some really cool new results for publication.Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-34959345467330970112010-03-05T08:27:00.001-08:002010-03-05T08:27:49.683-08:00David Salt Wins McCoy AwardCongratulations to David for this well deserved honor!!!"David Salt, professor of horticulture and landscape architecture in the College of Agriculture, is the winner of the 2010 Herbert Newby McCoy Award, the most prestigious research award given by Purdue. The award is in recognition of Salt’s pioneering and innovative efforts in the use of genome-scale biological approaches and information Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-17961279785328334322009-11-03T15:05:00.001-08:002010-04-25T19:39:46.922-07:00Ferroportin Paper published in Plant CellOur 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 Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-31269718544941165202009-10-08T13:00:00.001-07:002009-10-08T13:00:38.379-07:00Review publicationsWe 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. Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-59876309484454406122009-09-24T13:26:00.000-07:002009-09-24T13:27:21.602-07:00Database repairs Oct 9The 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).dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-29028485098923554072009-09-24T09:54:00.001-07:002009-09-24T11:32:31.281-07:00Yeast database goes liveThe 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 anddsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-76526118811355626932009-07-21T10:35:00.000-07:002009-07-21T10:47:35.793-07:00iHUB proposal submitted to NSFThe 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:<!--[if gte mso 9]> Normal 0 false false false EN-US X-NONE X-NONEdsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-14020158346237006182009-06-05T12:03:00.001-07:002010-04-25T19:40:01.577-07:00esb1 paper is out!Our paper on the esb1 mutant is now available at Plos Genetics. You can find it hereIvan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-28667664201148568722009-04-16T21:48:00.003-07:002009-04-16T21:48:33.831-07:00Arabidopsis Piims data download error fixedWe 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. Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-33818899367168204152009-04-16T21:48:00.001-07:002009-04-16T21:48:19.686-07:00esb1 paper accepted at Plos GeneticsOur 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 Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-6356036428856948482009-04-03T07:55:00.001-07:002009-04-03T07:55:36.794-07:00Open 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 effectIvan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-52713054937859928382009-03-24T13:28:00.001-07:002009-03-24T13:28:48.428-07:00Rice 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:Ivan Baxterhttp://www.blogger.com/profile/17319905398505771654noreply@blogger.com0tag:blogger.com,1999:blog-1332721195226847920.post-90889294579174939112009-01-08T12:10:00.001-08:002009-01-08T12:12:53.993-08:00New seed grant to develop collaborative toolsWe 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 2009dsalthttp://www.blogger.com/profile/16083296819742643754noreply@blogger.com0