CpG island density and its correlations with genomic features in mammalian genomes

Background: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one geno

Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia : Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis

With modified DNA extraction and Purification protocols, the complete cytochrome b gene sequences (1140 bp) were determined from degraded museum specimens. Molecular analysis and morphological examination of cranial characteristics of the giant flying squirrels of Petaurista philippensis complex (P. grandis, P. hainana, and P. yunanensis) and other Petaurista species yielded new insights into long-standing controversies in the Petaurista systematics. Patterns of genetic variations and morphological differences observed in this study indicate that P. hainana, P. albiventer, and P. yunanensis can be recognized as distinct species, and P. grandis and P. petaurista are conspecific populations. Phylogenetic relationships reconstructed by using parsimony, likelihood, and Bayesian methods reveal that, with P. leucogenys as the basal branch, all Petaurista groups formed two distinct clades. Petaurista philippensis, P. hainana, P. yunanensis, and P. albiventer are clustered in the same clade, while P. grandis shows a close relationship to P. petaurista. Deduced divergence times based on Bayesian analysis and the transversional substitution at the third codon suggest that the retreating of glaciers and upheavals or movements of tectonic plates in the Pliocene-Pleistocene were the major factors responsible for the present geographical distributions of Petaurista groups. (c) 2005 Elsevier Inc. All rights reserved.

Rhinopithecus bieti at Tacheng, Yunnan: Diet and daytime activities

We collected data on diet and activity budget in a group of Rhinopithecus bieti at Tacheng (99degrees 18'E, 27degrees 36' N, between 2,700 - 3,700 m asl), Yunnan, from March 1999 to December 2000. We mainly recorded species-parts eaten with feeding scores from scanning state behaviors of one-male units in tree-crowns. We also conducted microscopic analysis of feces collected monthly. The subjects consumed 59 plant species, belonging to 42 genera in 28 families, of which 90 species-parts were distributed as follows: 21 in Winter, 38 in spring, 39 in Summer, 47 in autumn. Conversely, the group annually spent, on average, 35% of daytime feeding, 33% resting, 15% moving, and 13% in social activities. Seasonal changes are apparent in daytime budget and food item-related feeding time in tree-crowns, food remains in feces, and the number of species-parts eaten. Correlations within and between food items and time budget clearly indicate maximization of foraging effectiveness and minimization of energy expenditure. In consideration of reports from northern and southern groups, that which underlay the specific adaptation to the habitat appeared to be similar to those of other colobines. Thus, the ultimate factors for survival of the species are more hopeful than expected.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Correlations between electronic energy bands spin splitting and magnetic profile symmetry of magnetic superlattice

We have theoretically investigated the energy band structures of two typical magnetic superlattices formed by perpendicular or parallel magnetization ferromagnetic stripes periodically deposited on a two-dimensional electron gas (2DEG), where the magnetic profile in the perpendicular magnetization is of inversion anti-symmetry, but of inversion symmetry in parallel magnetization, respectively. We have shown that the energy bands of perpendicular magnetization display the spin-splitting and transverse wave-vector symmetry, while the energy bands of the parallel magnetization exhibit spin degeneration and transverse wave-vector asymmetry. These distinguishing spin-dependent and transverse wave-vector asymmetry features are essential for future spintronics devices applications. (c) 2008 Elsevier B.V. All rights reserved.

Circular photogalvanic effect at inter-band excitation in InN

The circular photogalvanic effect (CPGE) is observed in InN at inter-band excitation. The function of the CPGE induced current on laser helicity is experimentally demonstrated and illustrated with the microscopic model. A spin-dependent current obtained in InN is one order larger than in the AlGaN/GaN heterostructures at inter-band excitation. The dependence of CPGE current amplitude on light power and incident angle can be well evaluated with phenomenological theory. This sizeable spin-dependent current not only provides an opportunity to realize spin polarized current at room temperature, but also can be utilized as a reliable tool of spin splitting investigation in semiconductors. (c) 2007 Published by Elsevier Ltd.

Correlations between antibunching and blinking of photoluminescence from a single CdSe quantum dot

The antibunching and blinking from a single CdSe/ZnS nanocrystal with an emission wavelength of 655 nm were investigated under different excitation powers. The decay process of the photoluminescence from nanocrystal was fitted into a stretched exponential, and the small lifetime and the small stretching exponent under a high excitation power were explained by using nonradiative multi-channel model. The probability of distributions for off-times from photoluminescence intermittence was fitted into the power law, and the power exponents were explained by using a tunneling model. For higher excitation power, the Auger-assisted tunneling model takes effect, where the tunneling rate increases and the observed lifetime decreases. For weak excitation power, the electron directly tunnels between the nanocrystal and trapping state without Auger assistance. The correlation between antibunching and blinking from the same nanocrystal was analyzed.

Effect of inter-level relaxation and cavity length on double-state lasing performance of quantum dot lasers

Double-state lasing phenomena are easily observed in self-assembled quantum dot (QD) lasers. The effect of inter-level relaxation rate and cavity length on the double-state lasing performance of QD lasers is investigated on the basis of a rate equation model. Calculated results show that, for a certain cavity length, the ground state (GS) lasing threshold current increases almost linearly with the inter-level relaxation lifetime. However, as the relaxation rate becomes slower, the ratio of excited state (ES) lasing threshold current over the GS one decreases, showing an evident exponential behavior. A relatively feasible method to estimate the inter-level relaxation lifetime, which is difficult to measure directly, is provided. In addition, fast inter-level relaxation is favorable for the GS single-mode lasing, and leads to lower wetting layer (WL) carrier occupation probability and higher QD GS capture efficiency and external differential quantum efficiency. Besides, the double-state lasing effect strongly depends on the cavity length. (c) 2007 Elsevier B.V. All rights reserved.

Temperature and power-density-dependent inter-shell energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling in InAs/GaAs quantum dot (QD) structures as a function of the excitation power density by using rnicro-photoluminescence spectroscopy at different temperatures. In addition to the emission bands of exciton recombination corresponding to the atom-like S, P and D, etc. shells of QDs, it was observed that some extra states V between the S and P shells, and D' between the P and D shells appear in the spectra with increasing number of excitons occupying the QDs at a certain temperature. The emergence of these inter-shell excitonic levels is power density and temperature dependent, which is an experimental demonstration of strong exciton-exciton exchange interaction, state hybridization, and coupling of a multi-exciton system in QDs. (c) 2006 Elsevier B.V. All rights reserved.

Temperature and power-density-dependent inter-shell energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling in InAs/GaAs quantum dot (QD) structures as a function of the excitation power density by using rnicro-photoluminescence spectroscopy at different temperatures. In addition to the emission bands of exciton recombination corresponding to the atom-like S, P and D, etc. shells of QDs, it was observed that some extra states V between the S and P shells, and D' between the P and D shells appear in the spectra with increasing number of excitons occupying the QDs at a certain temperature. The emergence of these inter-shell excitonic levels is power density and temperature dependent, which is an experimental demonstration of strong exciton-exciton exchange interaction, state hybridization, and coupling of a multi-exciton system in QDs. (c) 2006 Elsevier B.V. All rights reserved.