Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

A passive acoustic monitoring method applied to observation and group size estimation of finless porpoises

The present study aimed at determining the detection capabilities of an acoustic observation system to recognize porpoises under local riverine conditions and compare the results with sighting observations. Arrays of three to five acoustic data loggers were stationed across the main channel of the Tian-e-zhou Oxbow of China's Yangtze River at intervals of 100-150 m to record sonar. signals of free-ranging finless porpoises (Neophocaena phocaenoides). Acoustic observations, concurrent with visual observations, were conducted at two occasions on 20-22 October 2003 and 17-19 October 2004. During a total of 42 h of observation, 316 finless porpoises were sighted and 7041 sonar signals were recorded by loggers. The acoustic data loggers recorded ultrasonic signals of porpoises clearly, and detected the presence of porpoises with a correct detection level of 77.6% and a false alarm level of 5.8% within an effective distance of 150 m. Results indicated that the stationed passive acoustic observation method was effective in detecting the presence of porpoises and showed potential in estimating the group size. A positive linear correlation between the number of recorded signals and the group size of sighted porpoises was indicated, although it is faced with some uncertainty and requires further investigation. (C) 2005 Acoustical Society of America.

Phylogenetic relationships of labeonine cyprinids of the disc-bearing group (Pisces : Teleostei)

Phylogenetic relationships of labeonine cyprinids of the disc-bearing group (Pisces. Teleostei). Zoological Studies 44 (1): 130-143. The disc-bearing group is composed of 4 currently recognized cyprinid genera: Discocheilus, Discogobio, Garra, and Placocheilus. This group is defined as having a lower lip modified to form a mental adhesive disc whose posterior margin is not continuous with the mental region, and includes 91 widely distributed species in tropical Africa and Asia. So far, it is represented in China by 28 species (about 1/3 of the total number) of all 4 genera. A phylogenetic analysis, based on 29 morphological characters scored from first-hand observations of 23 of the Chinese species examined, revealed that the disc-bearing group forms a monophyletic clade in which Garra is the basal lineage, and Placocheilus constitutes a subclade with the sister pair of Discocheilus and Discogobio. In such a phylogenetic framework, the validity of each genus of the disc-bearing group was evaluated. It was confirmed that Discocheilus, Discogobio and Placocheilus represent 3 valid cyprinid genera. Evidence provided in this phylogenetic analysis, incorporated with conclusions reached in the known literature, reveals that the monophyly and validity of Garra need to be further studied using observations of more Garra species. Additional characters should also be examined, as the characters utilized in this study and in Abebe's with Getahun's (1999) study are insufficient to resolve the monophyly of Garra.

Sequence analysis of cytochrome b gene indicates that East Asian group of cyprinid subfamily Leuciscinae (Teleostei : Cyprinidae) evolved independently

The sequences of mitochondrial cytochrome b gene of cyprinid subfamily Leuciscinae are analyzed. Phylogenetic trees generated with methods of neighbor-joining, maximum likelihood and maximum parsimony with Phenacogrammus as an outgroup indicate that Leuciscinae is not a monophyletic group but includes two discrete subgroups. The East Asian group of the subfamily Leuciscinae, including the genera Ctenopharyngodon, Elopichthys, Luciobrama, Mylopharyngodon, Ochetobius, and Squaliobarbus, is close to Aristichthys and Hypophthalmichthys, and they form a monophyletic group which is distant from the leuciscine genera in Europe, Siberia and North America, such as Phoxinus, Leuciscus, Abramis, Rutilus, Chondrostoma, Alburnus, Opsopoedus, Lythrurus, and Pimephales. Our study suggests that the diversified East Asian group of the subfamily Leuciscinae should have an independent origination.

Observations on behavior and ecology of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) group at Tian-e-Zhou Oxbow of the Yangtze River

The authors made 39 surveys (a total of 161 days) in the Tian-e-Zhou Oxbow of the Yangtze River, China, for observing 13 Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) captured from the main stream of the Yangtze River and 7 juveniles born in the oxbow from January 1997 to July 2000. The animals were usually divided into several "core" groups and moved around in shallow, muddy-bottom areas with the largest individual in the lead. Each core group was composed of 2-3 animals (either 2 adults, 1 adult and 1 juvenile, 2 adults and 1 juvenile, or 2 adults and 1 calf). Newly-released animals joined the other animals first, and then reorganized their own groups one or two days later. Average breath interval was 34.4 s (+/- s.d. 4.39) for individuals in the group. The animals mated from May through June and gave birth during the second and last ten days of April of the next year. The gestation period was estimated as 310 - 320 days. Calves over 5 months old began to eat small fish. The distance of calves swimming apart from their suspected mothers increased each month. These findings will help in the management of the reserve to protect this unique freshwater porpoise.

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structure of lineages. We sequenced 1140 bp of cytochrome b from 30 individuals of Xenocyprinae and one putative outgroup (Myxocypris asiaticus) and also sequenced 297 bp of ND4L, 1380 bp of ND4, 68 bp of tRNA(His), and 69 bp of tRNA(Ser) from 17 individuals of Xenocyprinae and the outgroup (M. asiaticus). We detected high levels of nucleotide variation among populations, species, and genera. The phylogenetic analysis suggested that Distoechodon hupeinensis might be transferred to the genus Xenocypris, the taxonomic status of the genus Plagiognathops might be preserved, and species of Xenocypris and Plagiognathops form a monophyletic group that is sister to the genus Distoechodon and Pseudobrama. The introgressive hybridization might occur among the populations of X. argentea and X. davidi, causing the two species to not be separated by mtDNA patterns according to their species identification, and the process and direction of hybridization are discussed. The spatial distributions of mtDNA lineages among populations of Xenocypris were compatible with the major geographic region, which indicated that the relationship between Hubei + Hunan and Fujian is closer than that between Hubei + Hunan and Sichuan, From a perspective of parasite investigation, our data suggested that the fauna of Hexamita in Xenocyprinae could be used to infer the phylogeny of their hosts. (C) 2001 Academic Press.

Coherence loss and recovery of an electron spin coupled inhomogeneously to a one-dimensional interacting spin bath: An adaptive time-dependent density-matrix renormalization group study

Coherence evolution and echo effect of an electron spin, which is coupled inhomogeneously to an interacting one-dimensional finite spin bath via hyperfine-type interaction, are studied using the adaptive time-dependent density-matrix renormalization group method. It is found that the interplay of the coupling inhomogeneity and the transverse intrabath interactions results in two qualitatively different coherence evolutions, namely, a coherence-preserving evolution characterized by periodic oscillation and a complete decoherence evolution. Correspondingly, the echo effects induced by an electron-spin flip at time tau exhibit stable recoherence pulse sequence for the periodic evolution and a single peak at root 2 tau for the decoherence evolution, respectively. With the diagonal intrabath interaction included, the specific feature of the periodic regime is kept, while the root 2 tau-type echo effect in the decoherence regime is significantly affected. To render the experimental verifications possible, the Hahn echo envelope as a function of tau is calculated, which eliminates the inhomogeneous broadening effect and serves for the identification of the different status of the dynamic coherence evolution, periodic versus decoherence.

Revised ab initio natural band offsets of all group IV, II-VI, and III-V semiconductors

Using an all-electron band structure approach, we have systematically calculated the natural band offsets between all group IV, III-V, and II-VI semiconductor compounds, taking into account the deformation potential of the core states. This revised approach removes assumptions regarding the reference level volume deformation and offers a more reliable prediction of the "natural" unstrained offsets. Comparison is made to experimental work, where a noticeable improvement is found compared to previous methodologies.

Effect of the ratio of TMIn flow to group III flow on the properties of InGaN/GaN multiple quantum wells

Triple-axis x-ray diffraction (TXRD) and photoluminescence (PL) spectra are used to assess the influence of the ratio of TMIn flow to group III flow on structural defects, such as dislocations and interface roughness, and optical properties of multiple quantum wells(MQWs). In this paper the mean densities of edge and screw dislocations in InGaN/GaN MQWs are obtained by W scan of every satellite peak of (0002) symmetric and (1012) asymmetric diffractions. At the same time, the interface roughness is measured by the radio of the full width at half maximum of satellite peaks to the peak orders. The experimental results showed that the density of dislocation, especially of edge dislocation, and interface roughness increase with the increase of the ratio, which leads to the decrease of PL properties. It also can be concluded that the edge dislocation acts as nonradiative recombination centers in InGaN/GaN MQWs. Also noticed is that the variation of the ratio has more influence on edge dislocation than on screw dislocation.

Characterization of entanglement transformation via group representation theory

Entanglement transformation of composite quantum systems is investigated in the context of group representation theory. Representation of the direct product group SL(2, C) circle times SL(2, C), composed of local operators acting on the binary composite system, is realized in the four-dimensional complex space in terms of a set of novel bases that are pseudo-orthonormalized. The two-to-one homomorphism is then established for the group SL(2, C) circle times SL(2, C) onto the SO(4, C). It is shown that the resulting representation theory leads to the complete characterization for the entanglement transformation of the binary composite system.

Chemical trends of defect formation in Si quantum dots: The case of group-III and group-V dopants

Using first-principles methods, we have systematically calculated the defect formation energies and transition energy levels of group-III and group-V impurities doped in H passivated Si quantum dots (QDs) as functions of the QD size. The general chemical trends found in the QDs are similar to that found in bulk Si. We show that defect formation energy and transition energy level increase when the size of the QD decreases; thus, doping in small Si QDs becomes more difficult. B-Si has the lowest acceptor transition energy level, and it is more stable near the surface than at the center of the H passivated Si QD. On the other hand, P-Si has the smallest donor ionization energy, and it prefers to stay at the interior of the H passivated Si QD. We explained the general chemical trends and the dependence on the QD size in terms of the atomic chemical potentials and quantum confinement effects.

Correlation effects for semiconducting single-wall carbon nanotubes: A density matrix renormalization group study

In this paper we report the applicability of the density matrix renormalization group (DMRG) approach to the cylindrical single wall carbon nanotube (SWCN) for the purpose of its correlation effect. By applying the DMRG approach to the t+U+V model, with t and V being the hopping and Coulomb energies between the nearest neighboring sites, respectively, and U the on-site Coulomb energy, we calculate the phase diagram for the SWCN with chiral numbers (n(1)=3, n(2)=2), which reflects the competition between the correlation energy U and V. Within reasonable parameter ranges, we investigate possible correlated ground states, the lowest excitations, and the corresponding correlation functions in which the connection with the excitonic insulator is particularly addressed.