Homoeolog expression bias and expression level dominance in allopolyploid cotton.

Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.

Scanning Single-Electron Transistor Microscopy: Imaging Individual Charges

A single-electron transistor scanning electrometer (SETSE)-a scanned probe microscope capable of mapping static electric fields and charges with 100-nanometer spatial resolution and a charge sensitivity of a small fraction of an electron-has been developed. The active sensing element of the SETSE, a single-electron transistor fabricated at the end of a sharp glass tip, is scanned in close proximity across the sample surface. Images of the surface electric fields of a GaAs/AlxGa1-xAs heterostructure sample show individual photo-ionized charge sites and fluctuations in the dopant and surface-charge distribution on a length scale of 100 nanometers. The SETSE has been used to image and measure depleted regions, local capacitance, band bending, and contact potentials at submicrometer length scales on the surface of this semiconductor sample.