Journal: PLoS Genetics

Article Title: Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter ( MOT1 )

doi: 10.1371/journal.pgen.1000004

Figure Lengend Snippet: A: Shoot Mo content across 98 accessions. Histogram of shoot Mo content in 98 Arabidopsis accessions which include 94 from Nordborg et al. (2005). Black bars indicate the distribution of lines having the mot1 Ler-0 deletion. Grey lines denote the low and high accessions, as detailed in the text. The black arrow denotes Col-0 Mo content. Shoot Mo concentrations are normalized so that the average of the Col-0 and Cvi-0 means included in each growth tray are equivalent across all trays. Plants were grown in soil for 5 weeks. Data represents median values (average n = 11.6) for each accession. B: Mo accumulation of Col-0, Ler-0, Van-0, mot1-1 , st5.1-1 and the mot1-1st5.1-1 double mutant. Data is shown as a five number summary (the minimum, 1 st quartile, median, 3 rd quartile and maximum) for each line, and is summarized from an average of 10 replicate plants for each line. Lower case letters denote groups that are not significantly different from each other at P<0.01 with the Holm correction. Plants were grown in soil for 5 weeks. C: Shoot Mo accumulation in Arabidopsis in response to increasing levels of Mo in the nutrient solution. Mo accumulation in Col-0 (Black) and Ler-0 (Red) after 5 weeks of growth in soil at varying concentrations of Mo in the watering solution. Data is shown as a five number summary for each line, and is summarized from 6 replicate plants for each treatment.

Article Snippet: Plants with the lowest shoot Mo contents (n = 40) and plants with Mo shoot contents similar to Col-0 (n = 40) were pooled separately, and genomic DNA from each pool hybridized to the Affymetrix Arabidopsis ATH1 DNA microarray.

Techniques: Mutagenesis

Journal: PLoS Genetics

Article Title: Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter ( MOT1 )

doi: 10.1371/journal.pgen.1000004

Figure Lengend Snippet: Mo contents in Arabidopsis plants grafted at 5 days after germination and transferred to soil for growth were determined in self grafted plants of Col-0 (n = 32) and Ler-0 (n = 11), Col-0 shoot grafted onto Ler-0 root (n = 22), and Ler-0 shoot grafted onto Col-0 root (n = 15). Data is shown as a five number summary (the minimum, 1 st quartile, median, 3 rd quartile and maximum) for each line with outliers denoted by small circles.

Article Snippet: Plants with the lowest shoot Mo contents (n = 40) and plants with Mo shoot contents similar to Col-0 (n = 40) were pooled separately, and genomic DNA from each pool hybridized to the Affymetrix Arabidopsis ATH1 DNA microarray.

Techniques:

Journal: PLoS Genetics

Article Title: Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter ( MOT1 )

doi: 10.1371/journal.pgen.1000004

Figure Lengend Snippet: A: Bulk Segregant analysis of the low shoot Mo content in an F2 population from a Col-0×Ler-0 cross.Data are presented as a scaled pool hybridization difference (SPHD), representing the difference between the hybridization of the two pools at the SFPs, scaled so that a pure Col-0 pool would be at −1 and a pure Ler-0 pool would be at 1. The pools were prepared from F2 plants with a low Mo content (n = 40) and F2 plants with a high Mo content (n = 40). SFPs were scored after hybridization of genomic DNA prepared from these pools to Affymetrix ATH1 DNA microarrays. Dotted lines denote likely location of the causal loci. B: Shoot Mo content and genotype on chromosome II of selected Col-0×Ler-0 RILs. The genotype of each of the 106 markers determined by Singer et al. (2006) for chromosome II are shown; Col-0 alleles are denoted in black, Ler-0 in white. The average shoot Mo content (n = 12) for each line is shown, and, those with Col-0 shoot levels of Mo are underlined. Blue lines indicate the narrowed mapping interval on chromosome II (10.771 to 11.056 Mb). C: Structure of the MOT1 gene. The DNA sequence of MOT1 showing location of the T-DNA insert in mot1-1 , and the 50 base pair deletion in the 5′ UTR in the seven accessions with low shoot Mo content aligned with the Col-0 DNA sequence, with the TATA box underlined.

Article Snippet: Plants with the lowest shoot Mo contents (n = 40) and plants with Mo shoot contents similar to Col-0 (n = 40) were pooled separately, and genomic DNA from each pool hybridized to the Affymetrix Arabidopsis ATH1 DNA microarray.

Techniques: Hybridization, Sequencing

Journal: PLoS Genetics

Article Title: Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter ( MOT1 )

doi: 10.1371/journal.pgen.1000004

Figure Lengend Snippet: Pictures represent histochemical analysis of GUS activity in Arabidopsis plants stably transformed with a MOT1 -promoter-GUS construct. A: Primary root shown from root tip to the beginning of the lateral root development. Boxes denote close-ups shown in B,C and D; B: Root tip and cross section shown in insert panel B2. C: Root elongation zone with a cross section shown in insert panel C2; D: Root shown from between the elongation zone and the start of the lateral root production zone; E: Hypocotyl; F: Fully expanded leaves. Pd – protoderm; co – cortex; vb vascular bundle; ep – epidermis.

Article Snippet: Plants with the lowest shoot Mo contents (n = 40) and plants with Mo shoot contents similar to Col-0 (n = 40) were pooled separately, and genomic DNA from each pool hybridized to the Affymetrix Arabidopsis ATH1 DNA microarray.

Techniques: Activity Assay, Stable Transfection, Transformation Assay, Construct

Journal: PLoS Genetics

Article Title: Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter ( MOT1 )

doi: 10.1371/journal.pgen.1000004

Figure Lengend Snippet: MOT1::GFP was transiently expressed in Arabidopsis leaf protoplasts co transformed with F1-ATPase::RFP: (A) DIC (B) GFP filter (C) RFP filter and (D) merged image. Roots of Arabidopsis stably transformed with MOT1::GFP and stained with Mitotracker Red: (E) Red Filter (F) GFP Filter (G) Merged.

Article Snippet: Plants with the lowest shoot Mo contents (n = 40) and plants with Mo shoot contents similar to Col-0 (n = 40) were pooled separately, and genomic DNA from each pool hybridized to the Affymetrix Arabidopsis ATH1 DNA microarray.

Techniques: Transformation Assay, Stable Transfection, Staining

Journal: PLoS Computational Biology

Article Title: Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

doi: 10.1371/journal.pcbi.1002962

Figure Lengend Snippet: We consider as performance measures the number of predicted targets consistent with up-regulation in gene expression microarrays for different rank cutoffs and thresholds of 1 and 0.5 on the log-fold changes (left panel), and the precision-recall (PR) curve (right panel) using a threshold of 1 on the log-fold changes.

Article Snippet: The expression levels of A. thaliana genes are measured by Affymetrix Ath1 microarrays (imaGenes GmbH, Berlin, Germany), RMA normalized, and fold changes are determined for each of the 3 transgenic lines compared to 3 non-transgenic lines independently.

Techniques: Expressing

Journal: PLoS ONE

Article Title: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

doi: 10.1371/journal.pone.0025279

Figure Lengend Snippet: ( A ) Comparison of estimated log 2 -fold changes from analysis of microarrays (x-axis) and RNA-Seq using GENE-counter running NBPSeq (y-axis). Only induced genes measurable by both platforms are presented. Differentially induced genes are colored to highlight genes uniquely identified using microarrays (open red down triangles) or RNA-Seq (open blue up triangles) and found common between the two methods (purple crosses). ( B ) Three-way Venn comparing differentially expressed genes identified from GENE-counter's assessment of RNA-Seq data and analysis of microarrays. Only genes measurable using both methods were included in the comparison.

Article Snippet: The mRNA labeling, hybridization, and scanning of Affymetrix ATH1 microarrays were done by the CGRB core facility at OSU.

Techniques: Comparison, RNA Sequencing