Biodegradation of dibenzofuran by Janibacter terrae strain XJ-1

The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L-1 DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.

Local strain rate and curvature dependences of scalar dissipation rate transport in turbulent premixed flames: A direct numerical simulation analysis

The statistical behaviours of the instantaneous scalar dissipation rate Nc of reaction progress variable c in turbulent premixed flames have been analysed based on three-dimensional direct numerical simulation data of freely propagating statistically planar flame and V-flame configurations with different turbulent Reynolds number Ret. The statistical behaviours of N c and different terms of its transport equation for planar and V-flames are found to be qualitatively similar. The mean contribution of the density-variation term T1 is positive, whereas the molecular dissipation term (-D2) acts as a leading order sink. The mean contribution of the strain rate term T2 is predominantly negative for the cases considered here. The mean reaction rate contribution T3 is positive (negative) towards the unburned (burned) gas side of the flame, whereas the mean contribution of the diffusivity gradient term (D) assumes negative (positive) values towards the unburned (burned) gas side. The local statistical behaviours of Nc, T1, T2, T 3, (-D2), and f(D) have been analysed in terms of their marginal probability density functions (pdfs) and their joint pdfs with local tangential strain rate aT and curvature km. Detailed physical explanations have been provided for the observed behaviour. © 2014 Y. Gao et al.

Regulation by hetC of genes required for heterocyst differentiation and cell division in Anabaena sp strain PCC 7120

Unlike those of the wild-type strain, proheterocysts of the Anabaena sp. strain PCC 7120 hetC strain keep dividing. ftsZ, the most critical cell division gene, is up-regulated in hetC proheterocysts. Heterocyst differentiation genes hglD, hglE, patB, nijB, and xisA are no longer expressed in the hetC mutant. hetC also regulates the expression of patA, a pattern formation gene.

Molecular basis of transferrin polymorphism in goldfish (Carassius auratus)

Transferrin (TF) polymorphism was investigated in a color variety of goldfish (Carassius auratus), and its molecular basis analyzed. Three TF variants (A(1), A(2) and B-1) were identified from an inbred strain of the goldfish, of which A(1) and B-1 displayed a large electrophoretic difference on both native and SDS-PAGE gels. The TF cDNAs corresponding to variants A(1) and B-1 were cloned and sequenced from A(1)A(1), A(1)B(1) and B1B1 individuals, and their deduced amino acid sequences were analyzed. Substantial amino acid variation occurred between variants A(1) and B-1, with significant differences in peptide length, theoretical molecular weight (Mw) and isoelectric point (pI). No potential glycosylation sites were observed in the two amino acid sequences, which excluded the possibility that carbohydrate difference might cause electrophoretic variation among the TF variants. Further analysis suggested that the distinct electrophoretic mobility of the two variants A(1) and B-1 by SDS-PAGE resulted from their Mw difference, while the difference by the native PAGE could be explained by their pI variation. Furthermore, genomic DNA fragments containing the transferrin alleles were amplified and subjected to RFLP analysis in A(1)A(1), A(1)B(1) and B1B1 individuals. The data revealed characteristic banding patterns for each TF genotype, and demonstrated that the TF alleles A(1) and B-1 could be used as a co-dominant marker system. The initial work relating to the goldfish TF variants will benefit the understanding of the evolutionary and functional significance of TF polymorphism in fish.

Temperature- and salinity-dependent development of a Nordic strain of Ichthyophthirius multifiliis from rainbow trout

During the twentieth century evidence was presented which suggested the presence of various strains and races of the parasite Ichthyophthirius multifiliis Fouquet. However, ecological profiles of various parasite isolates from different climatic zones are sparse. Such stringent characterizations of parasite development at defined abiotic conditions could provide valuable criteria for the different races: profile comparison from various localities is one way to differentiate these strains. Baseline investigations were therefore performed on the associations between abiotic factors (temperature/salinity) and the development of theronts in tomocysts of I. multifiliis isolated from rainbow trout in a Danish trout farm. It was shown that tomocyst formation and theront development took place between 5 and 30degreesC. Development rates and sizes of theronts were clearly affected by temperature: theronts escaped tomocysts already after 16-27 h at 25degreesC and 30degreesC, whereas this process took 8-9 days at 5degreesC. Likewise, theront size decreased steadily from a maximum of 57.4 x 28.6 mum at 5degreesC to 28.6 x 20.0 mum at 30degreesC. This size variation was only partly associated with the number of theronts that appeared at different temperatures. The lowest number of theronts escaping from one tomocyst was indeed found at 5-7degreesC (mean 329-413). At 11.6, 17.0 and 21degreesC. the highest number of theronts appeared (mean 546-642). However, at 25 and 30degreesC, the number decreased (458 and 424, respectively). Additional studies on the salinity dependent development of the parasite (at 11.6degreesC) showed that salinities above 5 p.p.t. totally inhibited development. Even at 5 p.p.t. the developmental time significantly increased and the number of theronts produced from one tomocyst decreased.

Growth and feed utilization in two strains of gibel carp, Carassius auratus gibelio: paternal effects in a gynogenetic fish

Gibel carp (Carassius auratus gibelio Bloch) is a natural gynogenetic fish which requires sperm of the same or related species to activate egg development. The eggs of one gibel carp were divided into two batches. One batch was 'fertilized' with sperm from gibel carp (strain DD), and the other 'fertilized' with sperm from red common carp (Cyprinus carpio red variety) (strain DR). The juveniles were transferred to the laboratory 36 days post-hatch. Triplicate groups of each strain were fed a formulated diet at either 3% or satiation ration for 8 weeks. At both the restricted and satiation rations, specific growth rate was significantly higher in strain DR than in strain DD. At the 3% ration, there was no significant difference in feeding rate or feed conversion efficiency between the two strains. At the satiation ration, strain DR had a significantly lower feeding rate but higher feed conversion efficiency than strain DD. At the satiation ration, strain DR had a significantly lower intake protein, but higher recovered protein than strain DD. There was no significant difference in faecal protein loss between the two strains. At the 3% ration, strain had no significant effects on intake protein, faecal protein or recovered protein. Neither faecal energy loss nor recovered energy was affected by strain or ration. At both the 3% and satiation ration, final body contents of dry matter and lipid were significantly lower in strain DR than strain DD, while there was no significant difference in protein and energy content between the two strains at either ration level. The results suggested that gibel carp 'fertilized' with sperm of common carp grew faster than those 'fertilized' with sperm of gibel carp through increased feed conversion efficiency and protein retention.

Construction and analysis of a high-CO2-requiring mutant of the cyanobacterium Anabaena sp strain PCC7120

A mutant of Anabaena sp. strain PCC7120 requiring high CO2 was generated using Tn5 mutagenesis. This is the first data for a filamentous cyanobacterium. The mutant was capable of growing at 5% CO2, but incapable of growing at air levels of CO2. Southern hybridization analysis indicated that the Anabaena genome was inserted by the transposon at one site. The apparent photosynthetic affinity of the mutant to external dissolved inorganic carbon (DIC) was about 300 times lower that of the wild type (WT), and the medium alkalization rate as well as the carboxysomal carbonic anhydrase activity of the mutant was also lower than those of the WT. When the mutant was transferred from the culture medium bubbled with 5% CO2 to higher DIC (8.4% CO2) or 1% CO2, it showed similar responses to the WT. However, aberrant carboxysomes were found in the mutant cells through ultrastructural analysis, indicating it was most probably the wrong organization of the carboxysomes that eventually led to the inefficient operation of carboxysomal carbonic anhydrase and the subsequent defectiveness of the mutant in utilizing DIC.

An inducible CO2 concentrating mechanism in cyanobacterium Anabaena sp strain PCC7120

In order to define its characteristics of the photosynthetic utilization of CO2 and HCO3- when the ambient inorganic carbon changed, HCG (High-CO2-Growing Cells) of cyanobacterium Anabaena sp. strain PCC7120 were prepared. The growth rate of HCG was higher than that of LCG (low-CO2-growing cells, i.e. air-growing cells). When the HCG cells were transferred from 5% CO2 to air levels of CO2 , a series of changes took place: its carbonic anhydrase activity as well as its photosynthetic affinity to the external inorganic carbon significantly increased; the number of the carboxysomes, which is one of the most important components of CCM in cyanobacteria also increased. These facts indicated that the CCM activity of Anabaena PCC 7120 was induced. When the pH in the medium increased from 6 to 9, the photosynthetic affinity to external inorganic carbon of both HCG and LCG declined, while the apparent photosynthetic affinity to external CO2 increased. In the light of these findings, this inducible CCM in cyanobacteria provided a good model for the study of the photosynthetic Ci utilization in the phototrophic microoganisms.

Microstructure and strain analysis of GaN epitaxial films using in-plane grazing incidence x-ray diffraction

This paper investigates the major structural parameters, such as crystal quality and strain state of (001)-oriented GaN thin films grown on sapphire substrates by metalorganic chemical vapour deposition, using an in-plane grazing incidence x-ray diffraction technique. The results are analysed and compared with a complementary out-of-plane x-ray diffraction technique. The twist of the GaN mosaic structure is determined through the direct grazing incidence measurement of (100) reflection which agrees well with the result obtained by extrapolation method. The method for directly determining the in-plane lattice parameters of the GaN layers is also presented. Combined with the biaxial strain model, it derives the lattice parameters corresponding to fully relaxed GaN films. The GaN epilayers show an increasing residual compressive stress with increasing layer thickness when the two dimensional growth stage is established, reaching to a maximum level of -0.89 GPa.

Quantitative strain characterization of SiGe heterostructures by high-resolution transmission electron microscopy

We report the quantitative strain characterization in semiconductor heterostructures of silicon-germaniums (Si(0.76)Geo(0.24)) grown on Si substrate by an ultra-high vacuum chemical vapor deposition system. The relaxed SiGe virtual substrate has been achieved by thermal annealing of the SiGe film with an inserted Ge layer. Strain analysis was performed using a combination of high-resolution transmission electron microscopy and geometric phase analysis.

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.

Uniaxial Strain Effects on Optical Properties of c-plane Wurtzite GaN

We investigate the uniaxial strain effect in the c-plane on optical properties of wurtzite GaN based on k center dot p theory, the spin-orbit interactions are also taken into account. The energy dispersions show that the uniaxial strain in the c-plane gives an anisotropic energy splitting in the k(x) - k(y) plane, which can reduce the density of states. The uniaxial strain also results in giant in-plane optical polarization anisotropy, hence causes the threshold carrier density reduced. We clarify the relations between the uniaxial strain and the optical polarization properties. As a result, it is suggested that the compressive uniaxial strain perpendicular to the laser cavity direction in the c-plane is one of the preferable approaches for the effcient improvement of GaN-based laser performance.

Raman scattering characterization of Mn composition and strain in Ga1-xMnxSb/GaSb epitaxial layers

Raman scattering (RS) experiments have been performed for simultaneous determination of Mn composition and strain in Ga1-xMnxSb thin films grown on GaSb substrate by liquid phase epitaxy technique. The Raman spectra obtained from various Ga1-xMnxSb samples show only GaSb-like phonon modes whose frequency positions are found to have Mn compositional dependence. With the combination of epilayer strain model, RS and energy dispersive x-ray (EDX) experiments, the compositional dependence of GaSb-like LO phonon frequency is proposed both in strained and unstrained conditions. The proposed relationships are used to evaluate Mn composition and strain from the Ga1-xMnxSb samples. The results obtained from the RS data are found to be in good agreement with those determined independently by the EDX analysis. Furthermore, the frequency positions of MnSb-like phonon modes are suggested by reduced-mass model. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Anisotropic exchange splitting of excitons in (001)GaAs/Al0.3Ga0.7As superlattice studied by reflectance difference spectroscopy

Anisotropic exchange splitting (AES) is induced by the joint effects of the electron-hole exchange interaction and the symmetry reduction in quantum wells and quantum dots. A model has been developed to quantitatively obtain the electron-hole exchange energy and the hole-mixing energy of quantum wells and superlattices. In this model, the AES and the degree of polarization can both be obtained from the reflectance difference spectroscopy. Thus the electron-hole exchange energy and the hole-mixing energy can be completely separated and quantitatively deduced. By using this model, a (001)5 nm GaAs/7 nm Al0.3Ga0.7As superlattice sample subjected to [110] uniaxial strains has been investigated in detail. The n=1 heavy-hole (1H1E) exciton can be analyzed by this model. We find that the AES of quantum wells can be linearly tuned by the [110] uniaxial strains. The small uniaxial strains can only influence the hole-mixing interaction of quantum wells, but have almost no contribution to the electron-hole exchange interaction. (c) 2008 American Institute of Physics.

Effects of accumulated strain on the surface and optical properties of stacked 1.3 mu m InAs/GaAs quantum dot structures

We report the effects of accumulated strain by stacking on the surface and optical properties of stacked 1.3 mu m InAs/GaAs quantum dot (QD) structures grown by MOCVD. It is found that the surface of the stacked QD structures becomes more and more undulated with stacking, due to the increased strain in the stacked QD structures with stacking. The photoluminescence intensity from the QD structures first increases as the stacking number increases from 1 to 3 and then dramatically decreases as it further increases, implying a significant increase in the density of crystal defects in the stacked QD structures due to the accumulated strain. Furthermore, we demonstrate that the strain can be reduced by simply introducing annealing steps just after growing the GaAs spacers during the deposition of the stacked QD structures, leading to significant improvement in the surface and optical properties of the structures. (C) 2007 Elsevier B.V. All rights reserved.