The complete mitochondrial genome of the black mud crab, Scylla serrata (Crustacea: Brachyura: Portunidae) and its phylogenetic position among (pan)crustaceans

The black mud crab, Scylla serrata (Forsk?l 1775), is the most economically important edible crab in South-East Asia. In the present study, the complete mitochondrial genome of black mud crab, S.?serrata, was determined with the sequential polymerase chain reaction and primer walking sequencing. The complete mitochondrial genome was 15,721?bp in length with an A+T content of 69.2?% and contained 37 mitochondrial genes (13 protein coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR). The analysis of the CR sequence shows that it contains a multitude of repetitive fragments which can fold into hairpin-like or secondary structures and conserved elements as in other arthropods. The gene order of S. serrata mainly retains as the pancrustacean ground pattern, except for a single translocation of trnH. The gene arrangement of S. serrata appears to be a typical feature of portunid crabs. Phylogenetic analyses with concatenated amino acid sequences of 12 PCGs establishes that S. serrata in a well-supported monophyletic Portunidae and is consistent with previous morphological classification. Moreover, the phylogenomic results strongly support monophyletic Pancrustacea (Hexapoda plus “Crustaceans”). Within Pancrustacea, this study identifies Malacostraca?+?Entomostraca and Branchiopoda as the sister group to Hexapoda, which confirms that “Crustacea” is not monophyletic. Cirripedia?+?Remipedia appear to be a basal lineage of Pancrustacea. The present study also provides considerable data for the application of both population and phylogenetic studies of other crab species.     

Response to various shock loadings of the constant recycle-sludge-concentration activated-sludge process

The stability of the model of a completely mixed activated-sludge process holding the recycle sludge concentration, X_R, as a system constant subjected to pH, temperature, potassium cyanide, and phenol shock loading was investigated. Soft-drink bottling wastewater was used and maintained at 1000 mg/liter chemical oxygen demand (COD). The hydraulic ratio and recycle sludge concentration were maintained at 0.3 and 7000 mg/liter, respectively. An initial dilution rate of ¼ hr^?1 was maintained for pH and temperature shock loading, with ¼ and ? hr^?1 for KCN shock loading and ¼, ?, and \documentclass{article}\pagestyle{empty}\begin{document}$\frac{1}{16}$\end{document} hr^?1 for phenol shock loading. It was found that the present system could handle pH shock loading as low as 4.0 and as high as 10.4 without any serious disruption of biological solid concentration and filtrate COD. At pH 4.0 shock loading, filamentous organisms were predominant. Temperature shock loading could be handled from 23 to 36°C without any leakage of effluent filtrate COD. At 46°C temperature shock, a 14 hr period was required to recuperate to the new steady state and provided only 85% of COD removal efficiency. For KCN (50 mg/liger) and phenol (85 mg/liter) shock loading, the dilution rates should be lower than \documentclass{article}\pagestyle{empty}\begin{document}$\frac{1}{16}$\end{document} hr^?1 in order to shorten the transient period and improve the effluent quality. Biological kinetic constants included cell yield value, maximum growth rate, and the saturation constant, which was varied with the qualitative shock applied.     

The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes

The Mekong giant catfish (Pangasianodon gigas) is the largest scale-less freshwater fish of the world, and a critically endangered species. We determined the complete nucleotide sequence (16,533 bp) of the mitochondrial genome of the Mekong giant catfish, and conducted phylogenetic analyses based on mitochondrial protein (the combined amino acid sequences of all 13 mitochondrial protein coding genes) and rRNA (the combined nucleotide sequences of mitochondrial 12S and 16S rRNA genes) data sets in order to further clarify the relative phylogenetic position of P. gigas, and to recover phylogenetic relationships among 15 out of the 33 families of Siluriformes. Phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, Bayesian inference) of the protein data set were congruent with a basal split of the order into Loricarioidei and Siluroidei, and supported a closer relationship of the Mekong giant catfish (family Pangasiidae) to Siluridae than to Bagridae. The rRNA-based Bayesian phylogeny recovered Callichthyidae as the sister group of all other analyzed non-diplomystid catfish families, rendering Loricarioidei paraphyletic. In addition, Loricariidae were recovered as paraphyletic due to the inclusion of Astroblepidae. However, none of the two relationships received bootstrap support in the maximum parsimony, minimum evolution, and maximum likelihood analyses, and should be interpreted with caution. The derived position of Cetopsidae within Siluroidei, the sister group relationship of Pseudopimelodidae and Pimelodidae, and a close relationship of Doradidae and Auchenipteridae to the exclusion of Mochokidae were strongly supported. Pangasiidae was placed as a single lineage without clear affinities.