Biomedical subjects

Ivan Baxter

Publications and source records attributed to Ivan Baxter.

5 recordsLinked to original sources

PubMed2006

Purdue ionomics information management system. An integrated functional genomics platform.

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

Arabidopsis↗

PubMed2006

Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis.

Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomic strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here, we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na(+) from the soil. Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that two coastal populations of Arabidopsis collected from Tossa del Mar, Spain, and Tsu, Japan (Ts-1 and Tsu-1, respectively), accumulate higher shoot levels of Na(+) than do Col-0 and other accessions. We identify AtHKT1, known to encode a Na(+) transporter, as being the causal locus driving elevated shoot Na(+) in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence approximately 5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na(+). Interestingly, and in contrast to the hkt1-1 null mutant, under NaCl stress conditions, this novel AtHKT1 allele not only does not confer NaCl sensitivity but also cosegregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; http://www.purdue.edu/dp/ionomics). Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the casual locus driving the natural variation in shoot Na(+) accumulation we observed in Ts-1 and Tsu-1. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes.

Alleles↗

PubMed2004

Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array.

Plants alter their gene expression patterns in response to drought. Sometimes these transcriptional changes are successful adaptations leading to tolerance, while in other instances the plant ultimately fails to adapt to the stress and is labeled as sensitive to that condition. We measured the expression of approximately half of the genes in rice ( approximately 21,000) in phenotypically divergent accessions and their transgressive segregants to associate stress-regulated gene expression changes with quantitative trait loci (QTLs) for osmotic adjustment (OA, a trait associated with drought tolerance). Among the parental lines, a total of 662 transcripts were differentially expressed. Only 12 genes were induced in the low OA parent, CT9993, at moderate dehydration stress levels while over 200 genes were induced in the high OA parent, IR62266. The high and low OA parents had almost entirely different transcriptional responses to dehydration stress suggesting a complete absence of an appropriate response rather than a slower response in CT9993. Sixty-nine genes were up-regulated in all the high OA lines and nine of those genes were not induced in any of the low OA lines. The annotation of four of those genes, sucrose synthase, a pore protein, a heat shock and an LEA protein, suggests a role in maintaining high OA and membrane stability. Of the 3,954-probe sets that correspond to the QTL intervals, very few had a differential expression pattern between the high OA and low OA lines that suggest a role leading to the phenotypic variation. However, several promising candidates were identified for each of the five QTL including a snRNP auxiliary factor, a LEA protein, a protein phosphatase 2C and a Sar1 homolog.

Disasters↗

PubMed2003

Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice.

Members of the P-type ATPase ion pump superfamily are found in all three branches of life. Forty-six P-type ATPase genes were identified in Arabidopsis, the largest number yet identified in any organism. The recent completion of two draft sequences of the rice (Oryza sativa) genome allows for comparison of the full complement of P-type ATPases in two different plant species. Here, we identify a similar number (43) in rice, despite the rice genome being more than three times the size of Arabidopsis. The similarly large families suggest that both dicots and monocots have evolved with a large preexisting repertoire of P-type ATPases. Both Arabidopsis and rice have representative members in all five major subfamilies of P-type ATPases: heavy-metal ATPases (P1B), Ca2+-ATPases (endoplasmic reticulum-type Ca2+-ATPase and autoinhibited Ca2+-ATPase, P2A and P2B), H+-ATPases (autoinhibited H+-ATPase, P3A), putative aminophospholipid ATPases (ALA, P4), and a branch with unknown specificity (P5). The close pairing of similar isoforms in rice and Arabidopsis suggests potential orthologous relationships for all 43 rice P-type ATPases. A phylogenetic comparison of protein sequences and intron positions indicates that the common angiosperm ancestor had at least 23 P-type ATPases. Although little is known about unique and common features of related pumps, clear differences between some members of the calcium pumps indicate that evolutionarily conserved clusters may distinguish pumps with either different subcellular locations or biochemical functions.

Adenosine Triphosphatases↗

PubMed1998

Synthetic Ways to Tris(nucleobase) Complexes Derived from cis-Diammineplatinum(II) and a Platinum(II) Complex Containing Four Different Ligands, Three of Which Are Nucleobases.

Reactions of cis-[PtCl(L-N7)(NH(3))(2)]Cl (L = 9-ethylguanine, 9-EtGH, or 9-methyladenine, 9-MeA) with excess KI leads in slightly acidic solution to trans-PtI(2)(L)(NH(3)). Partial or complete substitution of the iodo ligands by aqua, chloro, or nucleobase ligands can be achieved and gives a series of neutral or cationic complexes. Among others, tris(nucleobase) complexes containing three different nucleobases (9-EtGH, 9-MeA, and 1-methylcytosine, 1-MeC), [Pt(1-MeC)(9-EtGH)(9-MeA)(NH(3))](2+) with SP-4-3 and SP-4-4 configuration numbers have been prepared and the deprotonated form SP-4-4-[Pt(1-MeC-N3)(9-EtG-N7)(9-MeA-N7)(NH(3))]NO(3).2H(2)O (7b) has been X-ray structurally characterized: monoclinic system, space group C2/c, a = 23.817(5) Å, b = 10.992(2) Å, c = 21.647(4) Å, beta = 112.07(3) degrees, V = 5251.9 Å(3), Z = 8. Moreover, the X-ray crystal structure analyses of trans-PtCl(2)(9-EtGH-N7)(NH(3)).0.5H(2)O (4) and trans-[Pt(1-MeC-N3)(2)(9-EtG-N7)(NH(3))]NO(3).3H(2)O (6b) are reported. 4: triclinic system, space group P&onemacr; (No. 2), a = 11.557(3) Å, b = 12.742(2) Å, c = 8.880(2) Å, alpha = 96.95(1) degrees, beta = 94.91(2) degrees, gamma = 88.32(2) degrees, V = 1293.1(5) Å(3), Z = 4. 6b: triclinic system, space group P&onemacr; (No. 2), a = 10.957(2) Å, b = 11.022(2) Å, c = 12.916(2) Å, alpha = 81.18(3) degrees, beta = 89.93(3) degrees, gamma = 64.22(3) degrees, V = 1384.2(5) Å(3), Z = 2. Relative orientations of the nucleobases in these compounds appear to be dictated by intranucleobase H bond formation.

Journal Article↗