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

Journal: Human Molecular Genetics

Article Title: PITX2 deficiency and associated human disease: insights from the zebrafish model

doi: 10.1093/hmg/ddy074

Figure Lengend Snippet: Microarray target analysis. (A) Heatmap of selected transcripts identified by microarray as potential downstream targets of pitx2. (B) Down-regulation of eleven selected transcripts was independently confirmed by quantitative RT-PCR at 24, 48 and 72-hpf. dkk2 , a previously reported downstream target of Pitx2 during mouse eye development , was included for comparison. Statistical significance is indicated by asterisks (compared with wild-type values) as follows: a single asterisk corresponds to P < 0.05; two asterisks to P < 0.01; three asterisks to P < 0.001.

Article Snippet: RNA from three independent pitx2 M64 * homozygous eye collections with RNA Integrity Numbers (RINs) of 8.9, 8.6 and 9.0 and three independent wild-type collections with RINs 8.7, 8.9, and 8.7 was submitted to OakLabs (Hennigsdorf, Germany) for transcriptome analysis using an ArrayXS Zebrafish v1 microarray containing 60 023 target IDs.

Techniques: Microarray, Quantitative RT-PCR, Comparison