Wednesday, November 9, 2011

Postdoctoral position open in the Baxter lab

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

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 with Baxter Lab Postdoc in the subject line for consideration.

Job Code


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.

Tuesday, April 26, 2011

2nd Plant Cell paper published

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.


Saturday, March 5, 2011

New Paper in PLosONE

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


Friday, March 4, 2011

New paper in Plant Cell

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 specificallyexpressed in companion cells of the phloem. The nakr1-1 mutantphenotype includes high Na+, K+, Rb+, and starch accumulationin leaves, short roots, late flowering, and decreased long-distancetransport of sucrose. Using traditional and DNA microarray-baseddeletion mapping, a 7-bp deletion was found in an exon of NaKR1that introduced a premature stop codon. The mutant phenotypeswere complemented by transformation with the native gene orNaKR1-GFP (green fluorescent protein) and NaKR1-β-glucuronidasefusions driven by the native promoter. NAKR1-GFP was mobilein the phloem; it moved from companion cells into sieve elementsand into a previously undiscovered symplasmic domain in theroot meristem. Grafting experiments revealed that the high Na+accumulation was due mainly to loss of NaKR1 function in theleaves. This supports a role for the phloem in recirculatingNa+ to the roots to limit Na+ accumulation in leaves. The onsetof root phenotypes coincided with NaKR1 expression after germination.The nakr1-1 short root phenotype was due primarily to a decreasedcell division rate in the root meristem, indicating a role inroot meristem maintenance for NaKR1 expression in the phloem.

And here is a non-technical summary:

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.

Monday, February 28, 2011

New lab members


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.

Jennie Hard

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.

Greg ziegler