Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases

Noncontingent Reinforcement for a Student Without Disabilities

The present study addresses the following research questions: (a) Can NCR be implemented with fidelity by teachers in general education classrooms?; (b) Does NCR lead to a decrease in off task behavior for a student without identified disabilities

S3 Fig -

A) Principal component analysis (PCA) of variance stabilizing transformed gene expression counts from ancestral populations. Each point represents the total gene expression of a single sample, where the shape indicates the growth condition of the sample, and the color indicates the population. B) PCA (same as in A) colored this time by biofilm wet weight. There is no clear correlation–either among biofilm samples or planktonic samples–between gene expression patterns and ancestral biofilm phenotype (as measured by wet weight). (PNG)</p

Heatmaps of variance stabilizing transformed expression counts all genes in the genome.

Each column is a single sample from an ancestral (A) or evolved (B) population, grown either as a biofilm or in a planktonic culture. Each row is a gene. Heatmap colored by expression values for each gene which are normalized to the mean across samples. Samples are clustered by Euclidean distance and plotted as a tree at the top of the heatmap. Evolved populations have much more uniform biofilm transcriptomes. (PNG)</p

S10 Fig -

A) log2 fold change (L2FC) values between evolved and ancestral biofilm populations of MT49. Shown is each gene within the region surrounding the duplication which arose in MT31 and MT55. Points are colored according to whether they lie inside of the duplicated region. B) Top: Relative coverage of DNA sequencing for the ancestral (passage 0) and evolved (passage 12) populations of MT49. Bottom: Relative coverage of RNA sequencing for ancestral and evolved populations of MT49. Two lines per genotype indicate two biological replicates. (PNG)</p

Expression of ncRNAs and sORFs mirror coding regions after passaging.

A) Volcano plot summarizing differential expression of ncRNAs and sORFs in evolved populations. Log transformed adjusted p-values plotted against the log2 fold change for each gene. Genes that did not have significant differential expression are shown in grey. B) Heatmap of normalized, variance stabilizing transformed expression counts for ncRNAs and sORFs with significant differential expression in evolved populations. Each column is a single sample from an evolved population, grown either as a biofilm or in a planktonic culture. Each row is a gene labeled either ncRNA or sORF. Expression values for each gene are normalized to the mean across samples. Samples are clustered by Euclidean distance and plotted as a tree at the top of the heatmap. C) Principal component analysis (PCA) of variance stabilizing transformed expression counts of ncRNAs and sORFs from ancestral and evolved biofilm populations. Arrows are drawn between corresponding ancestral and evolved populations, indicating the trajectory of evolution across passaging. Points are colored by sub-lineage of the ancestral population. The effects of biofilm passage on ncRNAs and sORFs mirror that of coding regions: reduced transcriptome diversity and widespread downregulation with populations converging on a sub-lineage-specific signature. N.B. While the positions of ancestral and evolved states are known (dots on the PCA), the trajectories between them are not, and connecting lines shown here are schematic.</p

No batch effects observed for library preparation or sequencing batch.

Principal component analysis (PCA) of variance stabilizing transformed gene expression counts for all samples, colored by library preparation batch (A) or sequencing batch (B). Resequencing refers to additional sequencing of some samples to achieve target sequencing depth. (PNG)</p

Most significantly downregulated (< -5 L2FC) and upregulated (> 2 L2FC) ncRNAs in evolved populations grown as biofilms (compared to planktonic cultures).

Features included in this list are significantly differentially expressed when all populations were analyzed together, as well as in at least five individual populations. Log2 fold change (L2FC) values given for analysis of all populations together.</p