Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes

CpG islands (CGIs) are often considered as gene markers, but the number of CGIs varies among mammalian genomes that have similar numbers of genes. In this study, we investigated the distribution of CGIs in the promoter regions of 3,197 human-mouse ortholo

Contrast features of CpG islands in the promoter and other regions in the dog genome

The recent release of the domestic dog genome provides us with an ideal opportunity to investigate dog-specific genomic features. In this study, we performed a systematic analysis of CpG islands (CGIs), which are often considered gene markers, in the dog

CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?

Background: CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. ( 2006) recently developed a new algorithm, CpGcluster, which uses a completely diffe

Evolution and biogeography of talpid moles from continental East Asia and the Japanese islands inferred from mitochondrial and nuclear gene sequences

We sequenced the cytochrome b gene from two little-studied mammal species from the highlands of Southwest China, the long-tailed mole Scaptonyx fusicaudus and the gracile shrew-like mole Uropsilus gracilis. This data was used to examine the phylogenetic r

Comparative analysis of CpG islands in four fish genomes

There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We

Promoting strain relaxation of Si0.72Ge0.28 film on Si (100) substrate by inserting a low-temperature Ge islands layer in UHVCVD

A flat, fully strain-relaxed Si0.72Ge0.28 thin film was grown on Si (1 0 0) substrate with a combination of thin low-temperature (LT) Ge and LT-Si0.72Ge0.28 buffer layers by ultrahigh vacuum chemical vapor deposition. The strain relaxation ratio in the Si0.72Ge0.28 film was enhanced up to 99% with the assistance of three-dimensional Ge islands and point defects introduced in the layers, which furthermore facilitated an ultra-low threading dislocation density of 5 x 10(4) cm (2) for the top SiGe film. More interestingly, no cross-hatch pattern was observed on the SiGe surface and the surface root-mean-square roughness was less than 2 nm. The temperature for the growth of LT-Ge layer was optimized to be 300 degrees C. (C) 2008 Elsevier B.V. All rights reserved.

Shape stability of InAs self-assembled islands on vicinal GaAs(001) substrates

We have grown InAs self-assembled islands on vicinal GaAs( 001) substrates. Atomic force microscopy and photoluminescence studies show that the islands have a clear bimodal size distribution. While most of the small islands whose growth is limited by the width of one multi-atomic step have compact symmetric shapes, a large fraction of the large islands limited by the width of one step plus one terrace have asymmetric shapes which are elongated along the multi-atomic step lines. These results can be attributed to the shape-related energy of the islands at different states of their growth. (C) 2008 Elsevier B. V. All rights reserved.

Size distributions of quantum islands on stepped substrates

The size distributions of self-assembled quantum islands on stepped substrates are studied using kinetic Monte Carlo simulations. It is found that the energy barrier E-SW between the step and the terrace region is the key factor in affecting the size distribution of islands. With small E-SW (<= 0.1 eV), lines of uniform islands can be obtained at relative low surface coverage. As the surface coverage is increased, wirelike islands can be obtained. Scaling behavior is obeyed for the size distributions of the wirelike islands. When the size distributions are separated into their width and length components, however, scaling is only observed in the length distribution of the wirelike islands. With larger E-SW, the size distribution of islands shows a clear bimodal size distribution and anomalous growth temperature dependent island size evolutions are observed. The simulation results reproduce qualitatively the phenomena observed in the cases of InAs islands grown on stepped GaAs substrates. (c) 2009 American Institute of Physics. [doi:10.1063/1.3248367]

1.55 mu m Ge islands resonant-cavity-enhanced detector with high-reflectivity bottom mirror

A 1.55 mum Ge islands resonant-cavity-enhanced (RCE) detector with high-reflectivity bottom mirror was fabricated by a simple method. The bottom mirror was deposited in the hole formed by anisotropically etching in a basic solution from the back side of the sample with the buried SiO2 layer in silicon-on-insulator substrate as the etch-stop layer. Reflectivity spectrum indicates that the mirror deposited in the hole has a reflectivity as high as 99% in the range of 1.2-1.65 mum. The peak responsivity of the RCE detector at 1543.8 nm is 0.028 mA/W and a full width at half maximum of 5 nm is obtained. Compared with the conventional p-i-n photodetector, the responsivity of RCE detector has a nearly threefold enhancement. (C) 2004 American Institute of Physics.

Novel room temperature photoluminescence of Ge/Si islands in multilayer structure grown on silicon-on-insulator substrate

Novel room temperature photoluminescence (PL) of the Ge/Si islands in multilayer structure grown on silicon-on-insulator substrates is investigated. The cavity formed by the mirrors at the surface and the buried SiO2 interface has a strong effect on the PL emission. The peak position is consistent with the theoretical calculation and independent of the exciting power, which is the evidence of cavity effect on the room temperature photoluminescence. (C) 2004 Elsevier B.V. All rights reserved.