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

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.

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.

Liquid phase epitaxy of Al0.3Ga0.7As islands

Self-organized Al0.3Ga0.7As islands generated on the (100) facet are achieved by liquid phase epitaxy. Three particularly designed experimental conditions-partial oxidation, deficient solute and air quenching-result in defect-free nucleation. Micron-sized frustums and pyramids are observed by a scanning electron microscope. The sharp end of the tip has a radius of curvature less than 50 nm. It is proposed that such Al0.3Ga0.7As islands may be potentially serviceable in microscale and nanoscale fabrication and related spheres. (C) 2004 Elsevier B.V. All rights reserved.

The fabrication and properties of InAs/GaAs columnal islands

A columnal islands system, which was composed of three layers of self-assembled InAs/GaAs quantum dots (QDs), has been fabricated by solid-source molecular beam epitaxy (MBE) through S-K mode on a (100) semi-insulating GaAs substrate. The effects of the thickness of GaAs space layer, the growth interruption time and the amount of InAs deposition on the emission wavelength of columnal islands were presented. The image of atomic force microscopy (AFM) indicated the columnal islands with high uniformity in size and shape. At room temperature, the emission wavelength of columnal islands with different effective heights was achieved 1.32 and 1.4 mum; however, the emission wavelength of single-layer QDs with normal height was just 1. l mum. It provides a useful and intuitive approach to artificially control the emission wavelength of a QD material system.

Cleaved-edge overgrowth of aligned InAs islands on GaAs(110)

A novel approach for positioning InAs islands on GaAs(110) by cleaved-edge overgrowth is reported. The first growth sample contains a strained InxGa1-xAs/GaAs superlattice of varying indium fraction and thickness, which acts as a strain nanopattern for the cleaved edge overgrowth. The formation of aligned islands is observed by means of atomic force microscopy. The ordering of the aligned islands and the structure of a single InAs island are found to depend on the properties of the underlying InxGa1-xAs/GaAs superlattice and molecular beam epitaxy growth conditions.

A novel method for positioning of InAs islands on GaAs(110)

A novel method for positioning of InAs islands on GaAs (110) by cleaved edge overgrowth is reported. The first growth sample contains strained InxGa1-xAs/GaAs superlattice (SL) of varying indium fraction, which acts as a strain nanopattern for the cleaved-edge overgrowth. Atoms incident on the cleaved edge will preferentially migrate to InGaAs regions where favorable bonding sites are available. By this method InAs island chains with lateral periodicity defined by the thickness of InGaAs and GaAs of SL have been realized by molecular beam epitaxy (MBE). They are observed by means of atomic force microscopy (AFM). The strain nanopattern's effect is studied by the different indium fraction of SL and MBE growth conditions. (c) 2005 Elsevier B.V. All rights reserved.

Evolution of InAs/GaAs(001) islands during the two- to three-dimensional growth mode transition in molecular-beam epitaxy

A detailed observation was made using atomic force microscopy on the two- to three-dimensional (2D-3D) growth mode transition in the molecular-beam epitaxy of InAs/GaAs(001). The evolution of the 3D InAs islands during the 2D-3D mode transition was divided into two successive phases. The first phase may be explained in terms of a critical phenomenon of the second-order phase transition.

Selective growth of InAs islands on patterned GaAs (100) substrate

By a combination of prepatterned substrate and self-organized growth, InAs islands are grown on the stripe-patterned GaAs (100) substrate by solid-source molecular beam epitaxy. It is found that the InAs quantum dots can be formed either on the ridge or on the sidewall of the stripes near the bottom, depending on the structure of the stripes on the patterned substrate or molecular beam epitaxy growth conditions. When a InxGa(1-x)As strained layer is grown first before InAs deposition, almost all the InAs quantum dots are deposited at the edges of the top ridge. And when the InAs deposition amount is larger, a quasi-quantum wire structure is found. The optical properties of the InAs dots on the patterned substrate are also investigated by photoluminescence. (c) 2005 Elsevier Ltd. All rights reserved.