The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Silurifonnes : Cranoglanididae) and the phylogeny of otophysan fishes

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characifonnes, Gymnotiformes), Siluriformes), Cyprinifionnes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed. (c) 2006 Elsevier B.V. All rights reserved.

Probing lanthanide ions binding on tRNA(Phe) by H-1 NMR

The structure of phenylalanine transfer ribonucleic acid (tRNA(Phe)) in solution was explored by H-1 NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It was found that La3+ ions possess specific effects on the imino proton region of the H-1 NMR spectra for yeast tRNA(Phe). The dependence of the imino proton spectra of yeast tRNA(Phe) as a function of La3+ concentration was examined, and the results suggest that the tertiary base pair G(15). C-48, which is located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by La3+ (shifted to downfield by as much as 0.35). Base pair U-8. A(14) in yeast tRNA(Phe), which are stacked on G(15). C-48, was also affected by added La3+ when 1 similar to 2 Mg2+ were also present. Another imino proton that may be affected by La3+ in yeast tRNA(Phe) is that of the tertiary base pair G(19). C-56. The assignment of this resonance in yeast tRNA(Phe) is tentative since it is located in the region of highly overlapping resonances beween 12.6 and 12.2. This base pair helps to anchor the D-loop to the T Psi C loop. The binding of La3+ caused conformational change of tRNA, which is responsible for shifts to upfield or downfield in H-1 NMR spectra.

Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern

Complete mitochondrial genome plays an important role in the accurate revelation of phylogenetic relationships among metazoans. Here we present the complete mitochondrial genome sequence from a sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea), which is the first representative from the subclass Aspidochirotacea. The mitochondrial genome of A. japonicus is 16,096 bp in length. The heavy strand consists of 31.8% A, 20.2% C, 17.9% G, and 30.1% T bases (AT skew = 0.027: GC skew = 0.062). It contains thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes, and two ribosomal RNA genes. There are a total of 3793 codons in all thirteen mitochondrial PCGs, excluding incomplete termination codons. The most frequently used amino acid is Leu (15.77%), followed by Set (9.73%), Met (8.62%), Phe (7.94%), and Ala (7.28%). Intergenetic regions in the mitochondrial genome of A. japonicus are 839 bp in total, with three relatively large regions of Unassigned Sequences (UAS) greater than 100 bp. The gene order of A. japonicus is identical to that observed in the five studied sea urchins, which confirms that the gene order shared by the two classes (Holothuroidea and Echinoidea) is a ground pattern of echinoderm mitochondrial genomes. Bayesian tree based on the cob gene supports the following relationship: (outgroup, (Crinoids, (Asteroids, Ophiuroids, (Echinoids, Holothuroids)))). (C) 2009 Elsevier B.V. All rights reserved.

The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations

Complete mitochondrial genomes have proven extremely valuable in helping to understand the evolutionary relationships among metazoans. However, uneven taxon sampling may lead to unclear or even erroneous phylogenetic topologies. The decapod crustaceans are relatively well-sampled, but sampling is still uneven within this group. We have sequenced the mitochondrial genomes of two shrimps Litopenaeus vannamei and Fenneropenaeus chinensis. As seen in other metazoans, the genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. The gene arrangements are consistent with the pancrustacean ground pattern. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial protein-coding genes strengthened the support that Caridea and Palinura are primitive members of Pleocyemata. These sequences, in combination with two previously published penaeid mitochondrial genomes, suggest that genera within the family Penaeidae have the following relationship: (((Penaeits + Fenneropenaett.) + Litopeiiaelts) + Marsupenaeus). The analyses of nucleic acid and amino acid sequences of the mitochondrial genomes also strongly support the monophyly of Penaeidae, Brachyura and Pleocyemata. In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group.

Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results: The mitochondrial genome of P. esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

The complete mitochondrial (mt) DNA sequence was determined for a ridgetail white prawn, Exopalaemon carinicauda Holthuis, 1950 (Crustacea: Decopoda: Palaemonidae). The mt genome is 15,730 bp in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which is typical for metazoans. The majority-strand consists of 33.6% A, 23.0% C, 13.4% G, and 30.0% T bases (AT skew = 0.057: GC skew = -0.264). A total of 1045 bp of non-coding nucleotides were observed in 16 intergenic regions,,including a major A+ T rich (79.7%) noncoding region (886 bp). A novel translocation of tRNA(Pro) and tRNA(Thr) was found when comparing this genome with the pancrustacean ground pattern indicating that gene order is not conserved among caridean mitochondria. Furthermore, the rate of Ka/Ks in 13 protein-coding genes between three caridean species is Much less than 1, which indicates a strong Purifying selection within this group. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based oil Currently available malacostracan complete mitochondrial sequences were built with the maximum likelihood and Bayesian models. All analyses based oil nucleotide and amino acid data strongly support the monophyly of Decapoda. The Penaeidae, Reptantia, Caridea, and Meiura clades were also recovered as monophyletic groups with Strong Statistical Support. However, the phylogenetic relationships within Pleocyemata are unstable, as represented by the inclusion or exclusion of Caridea. (C) 2009 Elsevier B.V. All rights reserved.

Heat-Transfer Study of External Superheater of CFB Incinerator

The heat transfer coefficients for horizontally immersed tubes have been studied in model internally circulating fluidized bed (ICFB) and pilot ICFB incinerators. The characteristics in the ICFB were found to be significantly different from those in a bubbling bed. In ICFB, there is a flowing zone with high velocity, a heat exchange zone, and a moving zone with low velocity. The controllable heat transfer coefficients in ICFB strongly depend on the fluidized velocity in the flowing zone, and also the flow condition in the moving zone. The heat exchange process and suitable bed temperature can be well controlled according to this feature. Based on the results of experiments, a formulation for heat transfer coefficient has been developed. These results were applied to an external superheater of a CFB incinerator with a 450 degreesC steam outlet in a waste-to-energy pilot cogeneration plant of 12 MW in Jiaxing City, China.

Three-Dimensional Modeling of Heat Transfer and Fluid Flow in Laminar-Plasma Material Re-Melting Processing

Modeling study is performed concerning the heat transfer and fluid flow for a laminar argon plasma jet impinging normally upon a flat workpiece exposed to the ambient air. The diffusion of the air into the plasma jet is handled by using the combined-diffusion-coefficient approach. The heat flux density and jet shear stress distributions at the workpiece surface obtained from the plasma jet modeling are then used to study the re-melting process of a carbon steel workpiece. Besides the heat conduction within the workpiece, the effects of the plasma-jet inlet parameters (temperature and velocity), workpiece moving speed, Marangoni convection, natural convection etc. on the re-melting process are considered. The modeling results demonstrate that the shapes and sizes of the molten pool in the workpiece are influenced appreciably by the plasma-jet inlet parameters, workpiece moving speed and Marangoni convection. The jet shear stress manifests its effect at higher plasma-jet inlet velocities, while the natural convection effect can be ignored. The modeling results of the molten pool sizes agree reasonably with available experimental data.

Conjugate Model for Heat and Mass Transfer of Porous Wall in the High Temperature Gas Flow

Heat and mass transfer of a porous permeable wall in a high temperature gas dynamical flow is considered. Numerical simulation is conducted on the ground of the conjugate mathematical model which includes filtration and heat transfer equations in a porous body and boundary layer equations on its surface. Such an approach enables one to take into account complex interaction between heat and mass transfer in the gasdynamical flow and in the structure subjected to this flow. The main attention is given to the impact of the intraporous heat transfer intensity on the transpiration cooling efficiency.

Effects of Baffle Design on Fluid Flow and Heat Transfer in Ammonothermal Growth System of Nitrides

Efforts have been made in growing bulk single crystals of GaN front supercritical fluids using the ammonothermal method, which utilizes ammonia as fluid rather than water as in the hydrothermal process. Different mineralizers such as amide or azide and temperatures in the range of 200-600degreesC have been used to increase the solubility. The pressure is from 1 to 4 kbar. Modeling of the ammonothermal growth process has been used to identify factors which may affect the temperature distribution, fluid flow and nutrient transport. The GaN charge is considered as a porous media bed and the flow in the charge is simulated using the Darcy-Brinkman-Forchheimer model. The resulting governing equations are solved using the finite volume method. The effects of baffle design and opening on flow pattern and temperature distribution in an autoclave are analyzed. Two cases are considered with baffle openings of 15% and 20% in cross-sectional area, respectively.

Experimental Study on Convective Boiling Heat Transfer in Narrow-Gap Annulus Tubes

Since convective boiling or highly subcooled single-phase forced convection in micro-channels is an effective cooling mechanism with a wide range of applications, more experimental and theoretical studies are required to explain and verify the forced convection heat transfer phenomenon in narrow channels. In this experimental study, we model the convective boiling behavior of water with low latent heat substance Freon 113 (R-113), with the purpose of saving power consumption and visualizing experiments. Both heat transfer and pressure drop characteristics were measured in subcooled and saturated concentric narrow gap forced convection boiling. Data were obtained to qualitatively identify the effects of gap size, pressure, flow rate and wall superheat on boiling regimes and the transition between various regimes. Some significant differences from unconfined forced convection boiling were found,and also, the flow patterns in narrow vertical annulus tubes have been studied quantitatively.

Numerical Study Of Heat Transfer Mechanism In Turbulent Supercritical Co2 Channel Flow

Direct numerical simulation (DNS) of supercritical CO2 turbulent channel flow has been performed to investigate the heat transfer mechanism of supercritical fluid. In the present DNS, full compressible Navier-Stokes equations and Peng-Robison state equation are solved. Due to effects of the mean density variation in the wall normal direction, mean velocity in the cooling region becomes high compared with that in the heating region. The mean width between high-and low-speed streaks near the wall decreases in the cooling region, which means that turbulence in the cooling region is enhanced and lots of fine scale eddies are created due to the local high Reynolds number effects. From the turbulent kinetic energy budget, it is found that compressibility effects related with pressure fluctuation and dilatation of velocity fluctuation can be ignored even for supercritical condition. However, the effect of density fluctuation on turbulent kinetic energy cannot be ignored. In the cooling region, low kinematic viscosity and high thermal conductivity in the low speed streaks modify fine scale structure and turbulent transport of temperature, which results in high Nusselt number in the cooling condition of the supercritical CO2.

A note on the heat-transfer to nonspherical particles from plasma

Heat transfer from plasma to a nonspherical partical in the free-molecular regime is studied in the present paper under thin plasma sheath condition. Analytical expressions for the floating potential charge and heat fluxes of an ellipsoid particle of revolution are derived and curves are given for key parameters for arbitrary plasma flow direction. On the basis of these results, an equivalent sphere with the same surface area as the nonspherical particle is suggested to be used for calculating the total heat flux of nonspherical particle in engineering application with acceptable accuracy. Furthermore, the effects of particle rotation, which occurs in most aerosol systems, on the heat transfer are also discussed.

Basic equations for suspension flows with interphase mass-transfer

In the case of suspension flows, the rate of interphase momentum transfer M(k) and that of interphase energy transfer E(k), which were expressed as a sum of infinite discontinuities by Ishii, have been reduced to the sum of several terms which have concise physical significance. M(k) is composed of the following terms: (i) the momentum carried by the interphase mass transfer; (ii) the interphase drag force due to the relative motion between phases; (iii) the interphase force produced by the concentration gradient of the dispersed phase in a pressure field. And E(k) is composed of the following four terms, that is, the energy carried by the interphase mass transfer, the work produced by the interphase forces of the second and third parts above, and the heat transfer between phases. It is concluded from the results that (i) the term, (-alpha-k-nabla-p), which is related to the pressure gradient in the momentum equation, can be derived from the basic conservation laws without introducing the "shared-pressure presumption"; (ii) the mean velocity of the action point of the interphase drag is the mean velocity of the interface displacement, upsilonBAR-i. It is approximately equal to the mean velocity of the dispersed phase, upsilonBAR-d. Hence the work terms produced by the drag forces are f(dc) . upsilonBAR-d, and f(cd) . upsilonBAR-d, respectively, with upsilonBAR-i not being replaced by the mean velocity of the continuous phase, upsilonBAR-c; (iii) by analogy, the terms of the momentum transfer due to phase change are upsilonBAR-d-GAMMA-c, and upsilonBAR-d-GAMMA-d, respectively; (iv) since the transformation between explicit heat and latent heat occurs in the process of phase change, the algebraic sum of the heat transfer between phases is not equal to zero. Q(ic) and Q(id) are composed of the explicit heat and latent heat, so that the sum Q(ic) + Q(id)) is equal to zero.