Molecular phylogeny of Stentor (Ciliophora : Heterotrichea) based on small subunit ribosomal RNA sequences

To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally.

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei : Cypriniformes)

It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenctic relationship of the Cobitoidea was ((Catostomidae + Gyrinocheilidae) + (Botiinae + (Balitorinae + (Cobitinae + Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae. (c) 2005 Elsevier Inc. All rights reserved.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Evolution of surface morphology and photoluminescence characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots grown by molecular beam epitaxy

Evolution of surface morphology and optical characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots (QDs) grown by molecular beam epitaxy (MBE) are investigated by atomic force microscopy (AFM) and photoluminescence (PL). After deposition of 16 monolayers (ML) of In0.5Ga0.5As, QDs are formed and elongated along the [110] direction when using sub-ML depositions, while large size InGaAs QDs with better uniformity are formed when using ML or super-ML depositions. It is also found that the larger size QDs show enhanced PL efficiency without optical nonlinearity, which is in contrast to the elongated QDs.

Annealing effect on the surface morphology and photoluminescence of InGaAs/GaAs quantum dots grown by molecular beam epitaxy

Postgrowth rapid thermal annealing was performed on InGaAs/GaAs quantum dots grown by molecular beam epitaxy. The blue shift of the emission peak and the narrowing of the luminescence line width are observed at lower annealing temperature. However, when the annealing temperature is increased to 850 degrees C, the emission line width becomes larger. The TEM image of this sample shows that the surface becomes rough, and some large clusters are formed, which is due to the interdiffusion of In, Ga atoms at the InGaAs/GaAs interface and to the strain relaxation. The material is found to degrade dramatically when the annealing temperature is further increased to 900 degrees C, while emission from quantum dots can still be detected, along with the appearance of the emission from excited state. (C) 2000 Elsevier Science B.V. All rights reserved.

Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates

Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemosensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantly with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolutionary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among primates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.

Morphology Evolution of (331)A High-Index Surfaces During Atomic Hydrogen Assisted Molecular Beam Epitaxy (MBE)

Step like morphology of (331)A high-index surfaces during atomic hydrogen assisted molecular beam epitaxy (MBE) growth has been investigated. Atomic Force Microscope (AFM) measurements show that in conventional MBE, the step heights and terrace widths of GaAs layers increase monotonically with increasing substrate temperatures. The terrace widths and step densities increase with increasing the GaAs layer thickness and then saturates. And, in atomic hydrogen assisted MBE, the terrace width reduces and density increases when depositing the same amount of GaAs. It attributes this to the reduced surface migration length of Ga adatoms with atomic hydrogen. Laterally ordered InAs self-aligned nano-wires were grown on GaAs (331)A surfaces and its optical polarization properties were revealed by photoluminescence measurements.

Film Morphology and Molecular Orientation in Oligothiophene-fluorene Films

The effects of processing conditions on film morphology and molecular orientation were studied for a novel conjugated fluorene-bithiophene oligomer, oligo(9,9-dioctylfluorene-alt-bithiophene) (OF8T2). Depending on the method of film preparation, OF8T2 molecules adopt different orientations in the films. X-ray diffraction peak at 4.9 degrees of the OF8T2 film deposited from petroleum ether/dichloromethane mixture is attributed to a layering distance between sheets of OF8T2 chains, which are separated by the octyl side chains. Preferred orientation is clearly inferred through the absence of peaks corresponding to pi-pi stacking.

Effects of molecular weight, solvent and substrate on the dewetting morphology of polystyrene films

Surface morphology of polystyrene (PS) films on different substrates by spin-coating before and after annealing was observed using atomic force microscopy (AFM). The effects of polymer molecular weight, substrates, solvents, and annealing conditions on the morphology of the films were investigated. Before annealing, the grain height decreases, and simultaneously the grain diameter increases with molecular weight (M-w) within the measured molecular weight. After annealing. the situation is opposite, i.e., the grain height increases while the grain diameter decreases with M-w. Furthermore, after annealing the smaller surface roughness (Ra) was obtained. It was also found that film surface roughness (Ra) depends on the vapor pressure and dipole moment of different used solvents as well as the substrates. The experimental results show that when the used solvents have similar dipole moment but different vapor pressure, the Ra of PS film decreased with the decreasing vapor pressure of solvents whether on silicon or on mica. And when the used solvents have close vapor pressure but different dipole moment, the Ra decreased with the increasing of solvent dipole moments on both substrates.

Molecular weight effects on the phase morphology of PS/P4VP blend films on homogeneous SAM and heterogeneous SAM/Au substrates

The effects of the molecular weight of polystyrene (PS) component on the phase separation of PS/poly(4-vinylpyridine) (PS/P4VP) blend films on homogeneous alkanethiol self-assembled monolayer (SAM) and heterogeneous SAM/Au substrates have been investigated by means of atomic force microscopy (AFM). For the PS (22.4k)/P4VP (60k) system, owing to the molecular weight of PS component is relatively small, the well-aligned PS and P4VP stripes with good thermal stability are directed by the patterned SAM/Au surfaces. With the increase of the molecular weight of PS component (for the PS (582k)/P4VP (60k) system), the diffusion of P4VP is hindered by the high viscosity of PS during the fast spin-coating process. The phase separation behavior of PS/P4VP on the SAM/Au patterned substrates is similar to that on the homoueneous SAM and cannot be easily directed by the patterned SAM surfaces even though the characteristic length of the lateral domain morphology is commensurate with the stripe width.

Molecular heterogeneity and crystal morphology in metallocene short chain branch polyethylene (SCBPE)

Metallocene, a newer generation of commercial polymerization catalysts for polyolefins, is best known for its "single sitednss", and the intermolecular structural homogeneity of metallocene polyethylene copolymer is a very interesting research issue. The molecular segregation effects on the crystallization, melting and crystal morphologies of metallocene SCBPE have been investigated with DSC and TEM. The multiple endothermic peaks were observed in the DSC thermograms during heating experiments. The heterogeneity increases as branching content increases, the lamellae becomes thinner, and lamellae distribution becomes broader. Both macroscopic segregation (between two crystal aggregates) and microscopic segreation (between two lamellae) have been observed when SCBPE crystallized from phase separated melt.