Journal: Journal of Biological Chemistry

Article Title: Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis

doi: 10.1074/jbc.m309338200

Figure Lengend Snippet: FIG. 6. Functional characterization of AtOPT3. A, hybridization of an 600-bp AtOPT3 cDNA probe, corresponding to the 3-terminal exon, to RNA extracted from Arabidopsis roots of plants grown in control conditions (Ctl), copper (-Cu), manganese (-Mn), zinc (-Zn), and iron (-Fe) deficiency. The ethidium bromide-stained RNA gel is shown for quantification. B, growth of ctr1 expressing AtOPT3 on YPG-Ura plates supplemented with 10 M CuSO4 compared with the mutant transformed with the vector alone. C, growth of smf1 expressing AtOPT3 on manganese-limited medium, with and without 1 mM EGTA compared with the growth of the mutant transformed with the vector alone.

Article Snippet: Genome-wide Analysis Provides Insight into Metal Transport—We have used Affymetrix Arabidopsis DNA chips containing 8,300 genes (which cover about one-third of the ge- FIG. 7.

Techniques: Functional Assay, Hybridization, Control, Staining, Expressing, Mutagenesis, Transformation Assay, Plasmid Preparation

Journal:

Article Title: Genomic Analysis of a Nutrient Response in Arabidopsis Reveals Diverse Expression Patterns and Novel Metabolic and Potential Regulatory Genes Induced by Nitrate

doi:

Figure Lengend Snippet: Arabidopsis Genes That Respond to Low Nitrate Concentrations (20 Min)

Article Snippet: This approach should detect nitrate-induced genes expressed in roots or shoots, or both, if the extent of expression is great enough for detection. mRNA was measured by using Arabidopsis GEM1 microarrays (Incyte Corp., Palo Alto, CA) containing 7942 cDNA clones corresponding to 5524 unique genes/clusters—or approximately one-quarter of the Arabidopsis genes (estimated to be ∼25,000 [ Meyerowitz, 1999 ]).

Techniques:

Journal:

Article Title: Genomic Analysis of a Nutrient Response in Arabidopsis Reveals Diverse Expression Patterns and Novel Metabolic and Potential Regulatory Genes Induced by Nitrate

doi:

Figure Lengend Snippet: Arabidopsis Genes That Respond to High Nitrate Concentrations (2 Hr)

Article Snippet: This approach should detect nitrate-induced genes expressed in roots or shoots, or both, if the extent of expression is great enough for detection. mRNA was measured by using Arabidopsis GEM1 microarrays (Incyte Corp., Palo Alto, CA) containing 7942 cDNA clones corresponding to 5524 unique genes/clusters—or approximately one-quarter of the Arabidopsis genes (estimated to be ∼25,000 [ Meyerowitz, 1999 ]).

Techniques:

Journal: BMC Plant Biology

Article Title: The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist

doi: 10.1186/s12870-019-1943-3

Figure Lengend Snippet: Experimental setup. Seven-week-old Arabidopsis thaliana Col-0 plants were subjected to either cold stress as primary (P) stimulus (4 °C, 5 days) or control (C) conditions (20 °C, 6 days). Plants treated with the primary stimulus were then retransferred to control conditions for 1 day (deacclimation phase). Subsequently plants were treated with a further triggering stimulus (T), i.e. with either larval feeding or artificial wounding. Plants which received both the P and T stimulus are here referred to as P + T plants. Plants, which were not exposed to cold and received only the T stimulus, are labelled as T plants. With respect to the T stimulus, we differentiate between T P (feeding damage by Pieris brassicae ) , T M (feeding damage by Mamestra brassicae ), and T W (artificial wounding). Untreated control plants (C1, C2) remained at control conditions at 20 °C throughout the entire experiment

Article Snippet: Genome-wide expression analyses were conducted on ArrayXS Arabidopsis v2 microarrays (series XS-5010; GEO accession GPL19779; Oaklabs GmbH, Hennigsdorf, Germany).

Techniques: Control

Journal: BMC Plant Biology

Article Title: The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist

doi: 10.1186/s12870-019-1943-3

Figure Lengend Snippet: Regulation of gene expression in response to herbivory or artificial wounding in Arabidopsis thaliana leaves compared to untreated control leaves. Plants were exposed to feeding by P. brassicae larvae (T p ), M. brassicae larvae (T M ), artificial wounding (T W ) or were left untreated (C2). Here, the T P , T M and T W treatments were adjusted in such a way that we obtained comparable extent of leaf damage (about 60 mm 2 per plant; see Additional file : Figure S4). Plant material for microarray analysis was collected 2 days later. N = 3 biological replicates of each sample type. a Principle component analysis (PCA) of transcriptomic patterns of individual samples collected for microarray analysis. Samples originated from untreated control plants (C2, purple), feeding-damaged plants by either P. brassicae (T P , red) or M. brassicae (T M , blue) or artificially wounded plants (T W , green). The first two principal components, which explain most of the changes, are depicted (explained variances are shown at the axes). Ellipses indicate the 95% confidence interval. b The Venn diagram shows the number of genes, which were upregulated (upwards pointing arrows) or downregulated (downwards pointing arrows) in T p , T M and T W samples compared to C2 samples. c Heatmap depicting genes, which show opposed regulation in at least two treatments. Yellow = upregulated, blue = downregulated, grey = not regulated (log 2 fold changes). d Gene Ontology terms associated with commonly or uniquely up- and downregulated genes

Article Snippet: Genome-wide expression analyses were conducted on ArrayXS Arabidopsis v2 microarrays (series XS-5010; GEO accession GPL19779; Oaklabs GmbH, Hennigsdorf, Germany).

Techniques: Gene Expression, Control, Microarray

Journal: BMC Plant Biology

Article Title: The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist

doi: 10.1186/s12870-019-1943-3

Figure Lengend Snippet: Previous cold treatment alters the transcriptional response to herbivory and artificial wounding. Leaves of A. thaliana were untreated (C2), cold-treated (P2), damaged by Pieris brassicae (T P ) or Mamestra brassicae feeding (T M ) or artificial wounding (T W ), or cold-treated followed by feeding/wounding damage (P + T P , P + T M and P + T W ). N = 3 biological replicates of each sample type. a Principle component analysis (PCA) of the normalized gene expression of individual experimental leaf samples. The first two components, which explain most of the changes, are depicted (explained variances are shown at the axes). Ellipses indicate the 95% confidence interval. b Venn diagrams of genes regulated in response to larval feeding or artificial wounding with and without prior cold treatment. Blue characters, genes specifically regulated upon cold treatment; green characters, genes specifically regulated upon damage; red characters, genes regulated upon both cold per se and damage per se; orange characters, genes regulated only when the plant had been exposed to the combination of prior cold and subsequent damage; colored intersections, genes that were differentially regulated in P + T plants relative to T plants (P + T vs T) and also in untreated (T vs C2) or cold-treated, damaged plants (P + T vs C2) relative to control plants. c Venn diagram with the genes in the colored sectors in panel ( b ). d Numbers of differentially expressed genes (DEGs) in cold-treated and herbivore- or wounding-damaged plants compared to untreated plants (P + T vs C2; left panel) and in cold-treated herbivore- or wounding-damaged plants compared to untreated, damaged plants (P + T vs T; right panel). e Genes responsive to herbivory or artificial wounding with enhanced or attenuated expression changes in cold-treated relative to untreated plants

Article Snippet: Genome-wide expression analyses were conducted on ArrayXS Arabidopsis v2 microarrays (series XS-5010; GEO accession GPL19779; Oaklabs GmbH, Hennigsdorf, Germany).

Techniques: Gene Expression, Control, Expressing