We are looking for a postdoc to join the lab to work on the Maize NAM Ionomics project.  Here is the ad:

Postdoctoral Associate

Date Posted
11/9/2011

Description
The Baxter Lab at the Donald Danforth Plant Science Center is recruiting an enthusiastic postdoctoral associate to take a key role in an NSF funded project to combine ionomics (high-throughput elemental profiling) and genetics to identify genes and gene x environment interactions in Maize. The successful candidate will combine QTL/association/nested association mapping data with the wide variety of co-expression, comparative genomic, and other systems biology data sets that are available to create biological hypotheses and knowledge.

A Ph. D in a field related to plant bioinformatics (i.e. plant biology, genetics, bioinformatics, genomics, computer science, statistics) is required. While scripting ability is not required, candidates should be able to demonstrate familiarity with computational/bioinformatics approaches.

The interdisciplinary research environment at the Danforth Center offers an excellent opportunity for career development. Salaries are competitive and commensurate with experience, and the Danforth Center offers an excellent benefits package including medical and 403B matching.

Please send your cover letter, CV and list of 3 references to:
Ms. Billie Broeker, Director of Human Resources
REF: Baxter Lab Postdoc
Donald Danforth Plant Science Center
975 North Warson Road
St. Louis, MO 63132

or by email to bcbroeker@danforthcenter.org with Baxter Lab Postdoc in the subject line for consideration.

Job Code
9067940

The Donald Danforth Plant Science Center is an equal opportunity/affirmative action employer and encourages applications from underrepresented groups, including minorities, women, and people with disabilities.

The second of two papers in Plant Cell in the last month has just been published.  the both describe genes that we cloned from the original Lahner et al. ionomics screen.

This one is “Sphingolipids in the Root Play an Important Role in Regulating the Leaf Ionome in Arabidopsis thaliana“.  A great collaboration between our group and several groups working on sphingolipids resulted when we landed on a gene in the sphingolipid pathway. Subtly altering the sphingolipid pathway results in what appears to be two different ionomics associated phenotypes: altered suberin and Fe homeostasis.

Here is the abstract of the second paper:

Sphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10Δ mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B mutants. Although the 3-KDS reductase genes are functionally redundant and ubiquitously expressed in Arabidopsis, 3-KDS reductase activity was reduced to 10% of wild-type levels in the loss-of-function tsc10a mutant, leading to an altered sphingolipid profile. This perturbation of sphingolipid biosynthesis in the Arabidopsis tsc10a mutant leads an altered leaf ionome, including increases in Na, K, and Rb and decreases in Mg, Ca, Fe, and Mo. Reciprocal grafting revealed that these changes in the leaf ionome are driven by the root and are associated with increases in root suberin and alterations in Fe homeostasis.

And here is a summary intended for lay audiences:

Sphingolipids, a class of membrane lipids with essential functions in all Eukaryotes, are thought to make up a large percentage of some plant membranes and have specific roles in cell processes through the formation of small microdomains. Here we discuss the role of two genes in the sphigolipid biosynthesis pathway in the model plant Arabidopsis Thaliana.  When both genes are disrupted, the plants are not viable. However, when the higer expressed gene  is disrupted, the  plants look normal but elemental profiling reveals that they have significantly altered elemental accumulation in their leaves.  Several of the changes appear to be the result of altering the the amount of suberin, a polymer which forms a barrier to water and ion movement in the root, is altered.  We also observed alterations in the plants Fe homestasis mechanisms, the cause of which  is still unknown. Understanding these processes will enable the prodcution of crops that are more efficient in their water and nutrient uptake effficiency.

Anthony Becker was an undergraduate summer intern in the lab as part of the  Danforth Center NSF-REU program. He did a great job learning how to code in R and the basics of mapping genetics.  Tony worked to apply methods developed to map genes using  older microarrays to newer, high density single nucleotide polymorphism (SNP) arrays. His efforts resulted in a new paper in PLoS ONE: Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays. Tony has stayed on in the lab to help out with various and sundry R projects.

Here is the Abstract of the paper:

Bulk segregant analysis (BSA) using microarrays, and extreme array mapping (XAM) have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP) between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.

and here is a non-technical summary.

In order to understand all of life, it is necessary to identify the genes underlying all facets of an organism. The process of mapping to a gene has historically been a time and resource intensive endevour. One of the limiting steps was the identification of DNA differences that can be used for mapping (markers) between two lines that have differences in a given trait. Significant advances in sequencing and microarray technologies have enabled the creation of silicon arrays with hundreds of thousands of features for assaying single DNA base changes (single nucleotide polymorphisms, SNP). For any given pair of crop lines, the arrays will have tens of thousands of features that  can be used as markers. In this paper, we show that a SNP array designed for the model plant Arabidopsis can be used  for several established mapping techniques with improved speed and cost.  Large sequencing resources are available for many crop plants which would allow these approaches to be used in economically important crops, such as Maize, Soybean and Cotton. These resources will enable plant breeders and producers to make rapid strides in crop improvement

Our paper “Arabidopsis NPCC6/NaKR1 Is a Phloem Mobile Metal Binding Protein Necessary for Phloem Function and Root Meristem Maintenance” was just published in Plant Cell.  This paper was mainly the result of the hard work of newly minted Ph.D Hui Tian from John Ward’s Lab at UMN.  She worked with me to clone the gene, finally finding it when the causal deletion of only 7 bp disrupted a single oligo on the Arabidopsis tiling array. It’s a fascinating gene, encoding a protein that moves through the phloem, the part of the plants vasculature responsible for moving solutes away from leaves.

Here is the abstract:

SODIUM POTASSIUM ROOT DEFECTIVE1 (NaKR1; previously called NPCC6) encodes a soluble metal binding protein that is specifically expressed in companion cells of the phloem. The nakr1-1 mutant phenotype includes high Na⁺, K⁺, Rb⁺, and starch accumulation in leaves, short roots, late flowering, and decreased long-distance transport of sucrose. Using traditional and DNA microarray-based deletion mapping, a 7-bp deletion was found in an exon of NaKR1 that introduced a premature stop codon. The mutant phenotypes were complemented by transformation with the native gene or NaKR1-GFP (green fluorescent protein) and NaKR1-β-glucuronidase fusions driven by the native promoter. NAKR1-GFP was mobile in the phloem; it moved from companion cells into sieve elements and into a previously undiscovered symplasmic domain in the root meristem. Grafting experiments revealed that the high Na⁺ accumulation was due mainly to loss of NaKR1 function in the leaves. This supports a role for the phloem in recirculating Na⁺ to the roots to limit Na⁺ accumulation in leaves. The onset of root phenotypes coincided with NaKR1 expression after germination. The nakr1-1 short root phenotype was due primarily to a decreased cell division rate in the root meristem, indicating a role in root meristem maintenance for NaKR1 expression in the phloem.

And here is a summary intended for lay audiences:

A major problem for world agriculture is the growing decrease in avaialable arable land. More and more we are working in solils that impart a stress on the plants that make up the crops we depend on. In order for plants to survive without being able to move out of unfavorable soil environments, they adjust the biochemical composition of their tissues through a wide variety of mechanisms.  One of these mechanisms is to move  elements such as sodium (Na) and potassium (K) from tissue to tissue, including from the root to the shoot and back again.  Understanding the molecular basis of these mechanisms will enable the production of crops that are better able to respond to the changing environment  and increase yields with fewer inputs.  In this study, we identified and characterized a gene which is important for loading Na  into the phloem, the ‘veins’ of the plant responsible for moving molecules out of the leaves to the seeds and roots. The protein also moves into the  phloem. Plants without a functional form of this gene, called NAKR1, have altered levels of Na, K and starch in the leaves, have shorter roots and flower later than plants with a functional copy of NAKR1.  These results will lead to a better understanding of how plants distribute elements between tissues and ultimately will allow for crop improvement strategies that deal with poor soil quality.

A belated welcome to our new lab members:

Jennie Hard is working on the algae project, and has already made a great impact. Appropriately for a member of an ionomics lab, in her spare time, Jennie plays in a (folk) Metal band.

Greg Ziegler has joined the ionomics team as a jack of all trades. A recent St. Louis transplant, Greg is working with us while finishing up his Ph.D in Computational Biology from Purdue.

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 study of the geographic variation in salinity tolerance, and allelic variation at the sodium transport gene AtHKT1;1 in European populations of A. thaliana.

As always, it was great team effort and many thanks go out to my collaborators at Purdue, UChicago, and USC. Here is the non-technical summary of the paper:

The unusual geographical distribution of certain animal and plant species has provided puzzling questions to the scientific community regarding the interrelationship of evolutionary and geographic histories for generations. With DNA sequencing, such puzzles have now extended to the geographical distribution of genetic variation within a species. Here, we explain one such puzzle in the European population of Arabidopsis thaliana, where we find that a version of a gene encoding for a sodium-transporter with reduced function is almost uniquely found in populations of this plant growing close to the coast or on known saline soils. This version of the gene has previously been linked with elevated salinity tolerance, and its unusual distribution in populations of plants growing in coastal regions and on saline soils suggests that it is playing a role in adapting these plants to the elevated salinity of their local environment.

and here is the technical abstract:

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na+) transporter, as being a major factor controlling natural variation in leaf Na+ accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na+ in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.

I am happy to introduce the labs newest researcher, Aimee Terauchi. Aimee got
her BA from UC-Berkeley and her Ph.D from UCLA. As you can see from the picture, she is a Californian at heart, but she is really looking forward to her first midwestern winter.

For her Ph.D Aimee did some fantastic work on Fe homeostasis and it’s relation to phonotsynthesis in Chlamydomonas. She will continue her work in the Baxter lab as part of the NAABB project.

Welcome Aimee!

there is a technician position available in the lab as part of the NAABB project. The announcement is below, please spread the word to all interested parties…..

The USDA, ARS, Plant Genetics Research Unit in St. Louis, MO, is seeking applications for a Biological Science Laboratory Technician, GS-0404-4/5, to work on an algal biofuels project. Salary range is $27,990 to $40,706 per annum, plus benefits. This is a Term appointment NTE 13 months which may be extended up to 4 years without further competition. U.S Citizenship is required. For information on application procedures visit full vacancy announcement ARS-D10W-0255R at http://www.afm.ars.usda.gov/divisions/hrd/vacancy/VAC2.HTM. Candidates must submit specific information as outlined in the vacancy announcement. Applications must be received by September 24, 2010. Contact JoAnne Kniptash at 573-875-5293 with questions on application process. USDA/ARS is an equal opportunity provider and employer.

What you are looking at are individual soybeans digesting in Nitric acid. This process breaks down almost every molecule in the bean to its elemental components, which allows us to quantify the levels of each element within the sample using ICP-MS. The renovations to the lab are finally complete and we are starting to work out the kinks in the process. Pretty soon we will be able to start working our way through the backlog of samples that have accumulated in our lab.

The 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.

How cool is Ionomics? So cool that we are able to recruit beer scientists to the cause! Introducing Walter Iverson, the newest member of the Baxter lab.

Walter has years of analytical chemistry expirience and will be running the ICPs and the elemental profiling facility. Welcome Walter!

We are getting really close to having a functional ionomics lab. Yesterday, the last major piece of equipment, the fan for the top of the exhaust system was installed on the roof. As you can see, it was quite a production….

Almost all the internal construction is finished and we are on schedule for the ICPs to be installed at the beginning of March.

In other news, the weighing robot is almost finished. This week I visited Paul Armstrong at the USDAs Engineering and Wind Erosion Research Unit in Manhattan Kansas. Paul has built a robot that can take single corn and soybean seeds from a 48 well plate, weigh them and then put them in a specified digestion tube. This turns out to be one of the bottleneck steps in our sample prep, so the robot will save us hours every day. Here is a photo of the robot with Paul in the background….

and here is a front view……

Before you know it, we will be cranking through samples.

In collaboration with Owen Hoekenga (Boyce Thompson Institute/USDA-ARS/Cornell University), Mourad Ouzzani (Purdue University), Margaret Smith (Cornell University), and Paul Anderson (Danforth Center) I just submitted a grant to the NSF-Plant Genome Research Program entitled “Mineral Nutrient Gene Discovery and Gene X Environment Interactions Using the Nested Association Mapping Population in Maize”.

Here is the abstract:

Maize is the most widely adapted and adopted crop on the planet. This is largely due to the amazing degree of genetic and phenotypic diversity that can be harnessed into adaptation to local conditions. While progress has been made in some aspects of adaptation, e.g. flowering time, little progress has been made with respect to adaptation to soil conditions at the molecular and genetic levels. This is ironic given the importance of plant-soil interactions as they relate to agricultural efficiency, sustainability and productivity. We will utilize the Nested Association Mapping (NAM) population, a unique and powerful genetic resource, to identify genes controlling the elemental composition (the ionome) of maize grain. We will measure the levels of 20 different elements: P, Ca, S, K, Mg, Sr, Rb (macronutrients or their chemical analogs); B, Cu, Fe, Zn, Mn, Co, Ni, Mo (micronutrients of significance to plant and human health); Na, Al, As, Se and Cd (minerals causing agricultural or environmental problems). We will leverage grain samples from the 5,000 recombinant inbred lines that constitute the NAM population, which have already been grown at four different locations with widely different soils. One expected outcome of our project is the identification, at single gene resolution, of loci and alleles that alter the accumulation of the mineral nutrients and toxic elements from different soil conditions. We will confirm these results and identify potential causative polymorphisms by association analysis. For 20 selected loci, we will create Heterogeneous Inbred Families (HIFs) that an extended team of collaborators will help us to evaluate in multiple soil environments, which we will select based upon screening soil samples provided by our extended team. The HIFs will confirm the predicted allelic affects and allow us investigate the interactions between genetic and environmental factors to determine grain quality. Additional outcomes for our project will be the identification of hundreds of genetic loci and dozens of nucleotide polymorphisms that determine the mineral nutritional content of maize grain. We will also gain a better understanding of how many of these genes interact with environmental factors.

Here is a non-technical summary of our recent Ferroportin paper in Plant Cell.

Iron (Fe) is an essential element for both plants and animals, with insufficient Fe causing reduced plant growth and severe human health effects including anemia. While the basic mechanisms that plants use to take up Fe from the soil is known, relatively little is known about how the Fe is moved through the root to the vasculature, which takes it up to the shoot. Here we characterize two genes related to the mammalian Fe transporter, Ferrroportin, FPN1 and FPN2, in the model plant Arabidopsis Thaliana. The two proteins are expressed in different cell layers and go to two different cellular locations. FPN1 is localized to the plasma membrane (the cells outer layer) and is expressed around the vasculature, suggesting that it is involved in loading Fe into the vasculature. FPN2 is localized to the vacuole, an internal storage compartment that performs a variety of functions, and is expressed in the outer root layers. This suggests that FPN2 is working to buffer the levels of Fe in these cells by sequestering Fe in the vacuole. Consistent with these roles, we show that lines where these genes are disrupted have altered responses to Fe deficient conditions. We also show that these genes are involved in the homeostasis of Co, which is chemically similar to Fe but can be toxic to plants.

you can find the paper here (also available from our publications page)

I am looking to hire the first member of the Baxter lab, the technician who will run the ionomics facility. Here is the ad:

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetics Research Unit in St. Louis, Missouri is seeking applications for a permanent, full-time PHYSICAL SCIENCE TECHNICIAN, GS-07/08/09 to provide support with the operation of a high-throughput elemental profiling facility centered around inductively coupled plasma spectrophotometers. Salary is commensurate with experience (38,117 – 60,612 per year), plus benefits. US Citizenship is required. Candidates must request a copy of the vacancy announcement (ARS-X10W-0048) by either calling 301-504-1583 or by copying the full text announcement from the http://www.afm.ars.usda.gov/divisions/hrd/vacancy/VAC2.HTM website. Candidates must submit specific information as outlined in the vacancy announcement. Applications must be received by the closing date of January 11, 2010. The USDA-ARS is an equal opportunity provider and employer.

Please spread the word!

A short feature on me in the Danforth newsletter (see page 3). Bonus action shot of me actually working in the lab!

The Baxter Lab now has a Facebook group!

Join us for links, news and discussions.

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.

I will be giving 3 public talks in October:

1. Tuesday, October 20th, Plant Lunch Seminar.
Rm 212 McDonnell Hall, Washington University.
How Plants Alter their Elemental Composition to Adapt to Different Soil Environments

2. Integrating Web 2.0 Tools Into the Lab
A workshop as part of the IPMB meeting.
Wednesday, Oct 28th, 6pm. Location:TBD

3. As part of the Thursday, Oct. 29th morning IPMB session on Abiotic Stress I “water, salts, minerals”, I will be giving a talk on combining association mapping with ionomics to identify genes important for stress tolerance.

We just found out that our paper “The ferroportin metal efflux proteins function in iron and cobalt homeostasis” has been accepted in Plant Cell!

The full Author list is……

Joe Morrissey, Ivan R. Baxter, Joohyun Lee, Liangtao Li, Brett Lahner, Natasha Grotz, Jerry Kaplan, David E. Salt and Mary Lou Guerinota

I am looking to hire the first member of the Baxter lab, the technician who will run the ionomics facility. Here is the ad:

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetics Research Unit in St. Louis, Missouri is seeking applications for a permanent, full-time PHYSICAL SCIENCE TECHNICIAN, GS-07 to provide support with the operation of a high-throughput elemental profiling facility centered around inductively coupled plasma spectrophotometers. Salary is commensurate with experience (38,117 – 49,553 per year), plus benefits. US Citizenship is required. Candidates must request a copy of the vacancy announcement (ARS-X9W-0265) by either calling 301-504-1583 or by copying the full text announcement from the http://www.ars.usda.gov/Careers/Careers.htm website. Candidates must submit specific information as outlined in the vacancy announcement. Applications must be received by the closing date of September 24, 2009. The USDA/ARS is an equal opportunity provider and employer.

In collaboration with Olga Vitek, David Salt and Mourad Ouzzani at Purdue University, we just submitted a grant to the NSF Advances in Bioinformatics Infrastructure program. The title of the grant was “Connecting ionome and deletome: a computational and statistical approach”.

In this grant, we propose to use the Yeast ionomics datasets as a model to:

1. Develop statistical methods to deal with large screens of high-dimensional phenotyping data.

2. Develop workflows to integrate multiple data types to generate knowledge using these datasets and other publicly available datasets.

3. Incorporate tools into Piims to facilitate these types of projects.

Dr. Baxter just published a review on ionomics in Current Opinions in Plant Biology titled “Ionomics: Studying the Social Network of Mineral Nutrients”. Contact Dr. Baxter for a PDF.

You can find a full list of Dr. Baxters papers here.

Dr. Baxters paper describing an ionomics mutant (enhanced suberin 1 (esb1)) is now available at Plos Genetics. You can find it here

You can find a full list of Dr. Baxters papers here

We are in the middle of reviewing the designs for the lab renovations of the space that will house our prep lab and the instrument room.

The prep lab will have two digestion hoods and a weighing robot that will allow us to get the individual kernel/bean weights for the thousands of corn and soybean samples that we will be running. When we analyze arabidopsis, we can calculate the weights for the samples better than we can actually measure them with a 5 place balance (you can read about the weight calculation and see a powerpoint presentation of how it works here). Due to the much higher starch, oil or protein content of agricultural seeds, the proportion of the seed containing most of the elements is a much small proportion of the total seed. This would throw off the weight calculation so we are going to actually weigh each seed individually. Hence the need for the robot.

The Instrument lab will have two Perkin Elmer inductively coupled plasma (ICP) spectrometers: An Optima 7300DV optical emission spectrometer (OES) and an Elan DRC-e.

The Baxter lab is open for business. We are part of the USDA-ARS Plant Genetics Research Unit (HQ is Columbia, MO) but we are housed at the Donald Danforth Plant Sciences Center in St. Louis, MO. Here is our Danforth website.