Identification of a novel cathelicidin gene in the rainbow trout, Oncorhynchus mykiss

We report the cloning of a novel antimicrobial peptide gene, termed rtCATH_1, found in the rainbow trout, Oncorhynchus mykiss. The predicted 216-residue rtCATH_1 prepropeptide consists of three domains: a 22-residue signal peptide, a 128-residue cathelin-like region containing two identifiable cathelicidin family signatures, and a predicted 66-residue C-terminal cationic antimicrobial peptide. This predicted mature peptide was unique in possessing features of different known (mammalian) cathelicidin subgroups, such as the cysteine-bridged family and the specific amino-acid-rich family. The rtCATH_1 gene comprises four exons, as seen in all known mammalian cathelicidin genes, and several transcription factor binding sites known to be of relevance to host defenses were identified in the 5' flanking region. By Northern blot analysis, the expression of rtCATH_1 was detected in gill, head kidney, and spleen of bacterially challenged fish. Primary cultures of head kidney leukocytes from rainbow trout stimulated with lipopolysaccharide or poly(I (.) C) also expressed riCATH_1. A 36-residue peptide corresponding to the core part of the fish cathelicidin was chemically synthesized and shown to exhibit potent antimicrobial activity and a low hemolytic effect. Thus, rtCATH_1 represents a novel antimicrobial peptide gene belonging to the cathelicidin family and may play an important role in the innate immunity of rainbow trout.

Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region

With 210 genera and 2010 species, Cyprinidae is the largest freshwater fish family in the world. Several papers, based on morphological and molecular data, have been published and have led to some solid conclusions, such as the close relationships between North American phoxinins and European leuciscins. However, the relationships among major subgroups of this family are still not well resolved, especially for those East Asian groups. In the present paper, the mitochondrial DNA (mtDNA) control region, 896-956 base pairs, of 17 representative species of East Asian cyprinids was sequenced and compared with those of 21 other cyprinids to study their phylogenetic relationships. After alignment, there were 1051 sites. The comparison between pairwise substitutions and HKY distances showed that the mtDNA control region was suitable for phylogenetic study. Phylogenetic analysis indicated that there are two principal lineages in Cyprinidae: Cyprinine and Leuciscine. In Cyprinine, the relationships could be a basal Labeoinae, an intermediate Cyprininae, and a diversified Barbinae (including Schizothroaxinae). In Leuciscine, Rasborinae is at the basal position; Gobioninae and Leuciscinae are sister groups; the East Asian cultrin-xenocyprinin taxa form a large monophyletic group with some small affiliated groups; and the positions of Acheilognathinae and Tincinae are still uncertain.

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.

Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria

A polyphasic approach was used to clarify the taxonomy of the water-bloom-forming oscillatorioid cyanobacteria. Seventy-five strains of oscillatorioid cyanobacteria were characterized by 16S rDNA sequence analysis, DNA base composition, DNA-DNA hybridization, fatty acid composition, phycobilin pigment composition, complementary chromatic adaptation, morphological characters, growth temperature and salinity tolerance. Phylogenetic analysis based on 165 rDNA sequences divided the strains into six groups, all of which were clearly separated from the type species of the genus Oscillatoria, Oscillatoria princeps Gomont NIVA CYA 150. Therefore, these strains should be classified into genera other than Oscillatoria. Groups I-III were closely related to one another and groups IV-VI were distinct from one another and from groups I to III. Group I was further divided into two subgroups, group I-pc, which includes strains containing only phycocyanin (PC), and group I-pe, which includes strains containing large amounts of phycoerythrin (PE) in addition to PC. This phenotypic distinction was supported by DNA-DNA hybridization studies. Based on the properties examined herein and data from traditional, botanical taxonomic studies, the groups and subgroups were classified into single species and we propose either emended or new taxonomic descriptions for Planktothrix agardhii (type strain NIES 204(T)), Planktothrix rubescens (type strain CCAP 1459/22(T)) Planktothrix pseudagardhii sp. nov. (type strain T1-8-4(T)), Planktothrix mougeotii (type strain TR1-5(T)), Planktothricoides raciborskii gen. nov., comb. nov. (type strain NIES 207(T)), Tychonema bourrellyi (type strain CCAP 1459/11B(T)) and Limnothrix redekei (type strain NIVA CYA 277/1(T)).

The toxic effects of microcystin-LR on embryo-larval and juvenile development of loach, Misguruns mizolepis Gunthe

Microcystin-LR, a specific and potent hepatotoxin, was tested for its effects oil loach embryo-larval and juvenile development, The results of this study showed that loach embryos were more sensitive when exposed to microcystin-LR at a later than at an earlier stage of development, Juveniles were far less sensitive to MC-LR than were embryos and larvae. Mortality and developmental abnormality were proven to be dose-dependent and to be stage-specific sensitive. Among the abnormal changes noted were: pericardial edema and tubular heart, bradycardia, homeostasis, poor yolk resumption. small head, curved body and tail, and abnormal hatching, Liver and heart were the main targets of microcystin-LR toxicity. Ultrastructural analysis documented a complex set of sublethal effects of microcystin-LR on loach hepatocytes, chiefly including morphological alteration in nuclear and RER of loach liver cells. fit addition, microcystin-LR was lethal to loach juvenile in the subacute (7 days) exposure (LC50) = 593.3 mug/l). (C) 2002 Elsevier Science Ltd. All rights reserved.

Temperature dependence of effective g factor in diluted magnetic semiconductor (Ga,Mn)As

Time resolved magneto-optic Kerr rotation measurements of optically induced spin quantum beats are performed on heavily doped bulk (Ga,Mn)As diluted magnetic semiconductors (DMS). An effective g-factor of about 0.2-0.3 over a wide range of temperature for both as-grown and annealed (Ga,Mn)As samples is obtained. A larger effective g-factor at lower temperature and an increase of the spin relaxation with increasing in-plane magnetic field are observed and attributed to the stronger p-d exchange interaction between holes and the localized magnetic ion spins, leading to a larger Zeeman splitting and heavy-hole-light-hole mixing. An abnormal dip structure of the g-factor in the vicinity of the Curie temperature suggests that the mean-field model is insufficient to describe the interactions and dynamics of spins in DMS because it neglects the short-range spin correlation effect. (c) 2008 American Institute of Physics.

Thermal annealing effect on InAs/InGaAs quantum dots grown by atomic layer molecular beam epitaxy

The effect of rapid thermal annealing on the InAs quantum dots (QDs) grown by atomic layer molecular beam epitaxy and capped with InGaAs layer has been investigated using transmission electron microscopy and photoluminescence (PL). Different from the previously reported results, no obvious blueshift of the PL emission of QDs is observed until the annealing temperature increases up to 800 degreesC. The size and shape of the QDs annealed at 750 degreesC have hardly changed indicating the relatively weak Ga/In interdiffusion, which is characterized by little blueshift of the PL peak of QDs. The QD size increases largely and a few large clusters can be observed after 800 degreesC RTA, implying the fast interdiffusion and the formation of InGaAs QDs. These results indicate that the delay of the blueshift of the PL peak of QDs is correlated with the abnormal interdiffusion process, which can be explained by two possible reasons: the reduction of excess-As-induced defects and the redistribution of In, Ga atoms around the InAs QDs resulted from the sub-monolayer deposition of InGaAs capping layer. (C) 2004 Elsevier B.V. All rights reserved.

Optical properties of GaN grown on Si(111) substrates by MOCVD

GaN epilayers were grown on Si (111) substrates by MOCVD. The optical properties of the samples under different growth conditions were characterized The abnormal peaks of excitonic emissions related to cubic-GaN were observed on the samples under improper growth conditions based on the LT PL measurements. Also the peak intensity is much higher than that of hexagonal-GaN. The higher intensity of exciton peaks is attributed to the local quantum well formed between the hexagonal- and cubic-GaN. No exciton peaks of cubic-GaN were found on the sample using the optimal growth conditions.

Optical properties of highly strained GaInAs/GaAs quantum wells grown by Sb assistance

Optical properties of highly strained GaInAs/GaAs quantum wells (QWs) grown by molecular beam epitaxy with Sb assistance are investigated. The samples grown by Sb incorporation and Sb pre-deposition methods display high room-temperature photoluminescence (PL) intensity at extended long wavelength. This result is explained by the surfactant effects of Sb during the growth of GaInAs/GaAs QW systems. An abnormal S-shaped temperature dependence of the PL peak position is found in the In0.42Ga0.58As/GaAs triple QWs sample grown with Sb pre-deposition. By investigating the transmission electron microscope images and time-resolved PL spectra, it is found that the S-shaped temperature dependence of the PL peak position originates from the exciton localization effect brought by the Sb-rich clusters on the QW interface.

Rapid thermal annealing effects on structural and optical properties of self-assembled InAs/GaAs quantum dots capped by InAlAs/InGaAs layers

Effects of rapid thermal annealing on the optical and structural properties of self-assembled InAs/GaAs quantum dots capped by the InAlAs/InGaAs combination layers are studied by photoluminescence and transmission electron microscopy. The photoluminescence measurement shows that the photoluminescence peak of the sample after 850 degrees C rapid thermal annealing is blue shifted with 370meV and the excitation peak intensity increases by a factor of about 2.7 after the rapid thermal annealing, which indicates that the InAs quantum dots have experienced an abnormal transformation during the annealing. The transmission electron microscopy shows that the quantum dots disappear and a new InAlGaAs single quantum well structure forms after the rapid thermal annealing treatment. The transformation mechanism is discussed. These abnormal optical properties are attributed to the structural transformation of these quantum dots into a single quantum well.

Application of rapid thermal annealing on 1.3-1.55 mu m GaInNAs(Sb) lasers grown by molecular beam epitaxy

Rapid thermal annealing (RTA) has been demonstrated as an effective way to improve the crystal quality of GaInNAs(Sb) quantum wells (QWs). However, few investigations have been made into its application in laser growth and fabrication. We have fabricated 1.3 mu m GaInNAs lasers, both as -grown and with post-growth RTA. Enhanced photoluminescence (PL) intensity and decreased threshold current are obtained with RTA, but the characteristic temperature T-o and slope efficiency deteriorate. Furthermore, T-o has an abnormal dependence on the cavity length. We attribute these problems to the deterioration of the wafer's surface. RTA with deposition Of SiO2 was performed to avoid this deterioration, T-o was improved over the samples that underwent RTA without SiO2. Post-growth and in situ annealing were also investigated in a 1.55 mu m GaInNAsSb system. Finally, continuous operation at room temperature of a GaAs-based dilute nitride laser with a wavelength over 1.55 mu m was realized by introducing an in situ annealing process. (c) 2007 Elsevier B.V. All rights reserved.

Temperature-dependent bimodal size evolution of InAs quantum dots on vicinal GaAs(100) substrates

The effects of growth temperature on the bimodal size distribution of InAs quantum dots on vicinal GaAs(100) substrates grown by metal organic chemical vapor deposition are studied. An abnormal trend of the bimodal size evolution on temperature is observed. With the increase of the growth temperature, while the density of the large dots decreases continually, that of the small dots first grows larger when temperature was below 520 degrees C, and then exhibits a sudden decrease at 535 degrees C. The trend is explained by taking into account the presence of multiatomic steps on the substrates. Photoluminescence (PL) studies show that quantum dots on vicinal substrates have a narrower PL linewidth, a longer emission wavelength, and a larger PL intensity than those of the dots with exact substrates. (c) 2006 American Institute of Physics.

Semiconductor-metal transition in InSb nanowires and nanofilms under external electric field

The electronic structures, Rashba spin-orbit couplings, and transport properties of InSb nanowires and nanofilms are investigated theoretically. When both the radius of the wire (or the thickness of the film) and the electric field are large, the electron bands and hole bands overlap, and the Fermi level crosses with some bands, which means that the semiconductors transit into metals. Meanwhile, the Rashba coefficients behave in an abnormal way. The conductivities increase dramatically when the electric field is larger than a critical value. This semiconductor-metal transition is observable at the room temperature. (c) 2006 American Institute of Physics.

Electronic structure and g factors of narrow-gap zinc-blende nanowires and nanorods

The Hamiltonian in the framework of eight-band effective-mass approximation of the zinc-blende nanowires and nanorods in the presence of external homogeneous magnetic field is given in the cylindrical coordinate. The electronic structure, optical properties, magnetic energy levels, and g factors of the nanowires and nanorods are calculated. It is found that the electron states consist of many hole-state components, due to the coupling of the conduction band and valence band. For the normal bands which are monotone functions of |k(z)|, long nanorods can be modeled by the nanowires, the energy levels of the nanorods approximately equal the values of the energy band E(k(z)) of the nanowires with the same radius at a special k(z), where k(z) is the wave vector in the wire direction. Due to the coupling of the states, some of the hole energy bands of the nanowires have their highest points at k(z)=0. Especially, the highest hole state of the InSb nanowires is not at the k(z)=0 point. It is an indirect band gap. For these abnormal bands, nanorods can not be modeled by the nanowires. The energy levels of the nanorods show an interesting plait-like pattern. The linear polarization factor is zero, when the aspect ratio L/2R is smaller than 1, and increases as the length increases. The g(z) and g(x) factors as functions of the k(z), radius R and length L are calculated for the wires and rods, respectively. For the wires, the g(z) of the electron ground state increases, and the g(z) of the hole ground state decreases first, then increases with the k(z) increasing. For the rods, the g(z) and g(x) of the electron ground state decrease as the R or the L increases. The g(x) of the hole ground state decreases, the g(z) of the hole ground state increases with the L increasing. The variation of the g(z) of the wires with the k(z) is in agreement with the variation of the g(z) of the rods with the L.

Dependence of bimodal size distribution on temperature and optical properties of InAs quantum dots grown on vicinal GaAs (1-00) substrates by using MOCVD

Self-assembled InAs quantum dots (QDs) are grown on vicinal GaAs (100) substrates by using metal-organic chemical vapour deposition (MOCVD). An abnormal temperature dependence of bimodal size distribution of InAs quantum dots is found. As the temperature increases, the density of the small dots grows larger while the density of the large dots turns smaller, which is contrary to the evolution of QDs on exact GaAs (100) substrates. This trend is explained by taking into account the presence of multiatomic steps on the substrates. The optical properties of InAs QDs on vicinal GaAs(100) substrates are also studied by photoluminescence (PL). It is found that dots on a vicinal substrate have a longer emission wavelength, a narrower PL line width and a much larger PL intensity.