The complete mitochondrial genome of Takydromus septentrionalis (Reptilia: Lacertidae).

The complete mitochondrial genome sequence of Takydromus septentrionalis was determined by shotgun sequencing. The total length of mitogenome is 18,304 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. Most of the genes of T. septentrionalis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of T. septentrionalis and 8 other closely related species was reconstructed. The phylogenetic analyses based on these mitogenomes presented here will be useful for further insights on the evolutionary relationships of Takydromus.

The complete mitochondrial genome of Sphenomorphus indicus (Reptilia: Scincidae).

The complete mitochondrial genome (mitogenome) sequence of Sphenomorphus indicus was sequenced and characterized by next-generation sequencing technology. The total length of mitogenome is 17,027 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 non-coding regions (the control region and the putative L-strand replication origin). Most of the genes of S. indicus are encoded on the H-strand, except for the ND6 subunit gene and 8 tRNA genes which is distributed on the L-strand. Phylogenetic reconstruction suggested that S. indicus is the sister group of the S. incognitus within the genus Sphenomorphus. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of S. indicus.

Huangshan population of Chinese Zacco platypus (Teleostei, Cyprinidae) harbors diverse matrilines and high genetic diversity.

Six main mitochondrial DNA (mtDNA) lineages have been described in minnow (Zacco platypus) samples obtained from northern, western and southern China. Perdices et al. (2004) predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b (cytb) sequence variations. Combined with reported data in GenBank, we identified ten matrilines (Zacco A-J) in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.

Development and characterization of polymorphic microsatellite markers (SSRs) for an endemic plant, Pseudolarix amabilis (Nelson) Rehd. (Pinaceae).

Pseudolarix (Pinaceae) is a vulnerable (sensu IUCN) monotypic genus restricted to southeastern China. To better understand levels of genetic diversity, population structure and gene flow among populations of P. amabilis, we developed five compound SSR markers and ten novel polymorphic expressed sequence tags (EST) derived microsatellites. The results showed that all 15 loci were polymorphic with the number of alleles per locus ranging from two to seven. The expected and observed heterozygosities varied from 0.169 to 0.752, and 0.000 to 1.000, respectively. The inbreeding coefficient ranged from -0.833 to 1.000. These markers will contribute to research on genetic diversity and population genetic structure of P. amabilis, which in turn will contribute to the species conservation.

Mitochondrial genome of the Chung-an ground lizard Takydromus sylvaticus (Reptilia: Lacertidae).

The Chung-an ground lizard Takydromus sylvaticus is an endemic and long-lost reptile species in China. In this study, its mitochondrial genome (mitogenome) sequence was firstly determined by long PCR and primer walking methods. The genome is 17,838 bp long and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 main noncoding regions (the control region and the putative L-strand replication origin). The gene order and contents in the T. sylvaticus mitogenome is identical to that found in typical vertebrates, suggesting that it represents an ancestral arrangement. Within the control region, typical conserved domains and distinct repeat regions were identified.

Characteristic Analysis from Excessive to Deficient Syndromes in Hepatocarcinoma Underlying miRNA Array Data.

Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for many diseases. In this study, the characteristics among excessive, excessive-deficient, and deficient syndromes of Hepatocellular carcinoma (HCC) were studied using miRNA array data. We first calculated the differentially expressed miRNAs based on random module t-test and classified three TCM syndromes of HCC using SVM method. Then, the weighted miRNA-target networks were constructed for different TCM syndromes using predicted miRNA targets. Subsequently, the prioritized target genes of upexpression network of TCM syndromes were analyzed using DAVID online analysis. The results showed that there are distinctly different hierarchical cluster and network structure of TCM syndromes in HCC, but the excessive-deficient combination syndrome is extrinsically close to deficient syndrome. GO and pathway analysis revealed that the molecular mechanisms of excessive-deficient and deficient syndromes of HCC are more complex than excessive syndrome. Furthermore, although excessive-deficient and deficient syndromes have similar complex mechanisms, excessive-deficient syndrome is more involved than deficient syndrome in development of cancer process. This study suggested that miRNAs might be important mediators involved in the changing process from excessive to deficient syndromes and could be potential molecular markers for the diagnosis of TCM syndromes in HCC.

Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.

Cytochrome b (cyt b) gene complete sequences (1143bp) of Takydromus sylvaticus were sequenced. In order to clarify the phylogenetic position of the Takydromus sylvaticus, we investigated the phylogeny of 15 Takydromus spp. distributed in East-Asia by Maximum Parsimony (MP), Bayesian Inference (BI), and Maximum Likelihood (ML) methods using DNA fragments of cyt b genes. The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus. Furthermore, the prediction of tertiary structures of cyt b exhibited the CD loop region contain two short helices forming a hairpin arrangement, namely cd1 and cd2. Thermostability analysis shows that the CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme, and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. It suggested that the two short helices of CD loop region of cyt b was a dominating portion for ISP binding site.

Description of male Takydromus sylvaticus (Squamata: Lacertidae) from China, with notes on sexual dimorphism and a revision of the morphological diagnosis of the species.

The Chungan ground lizard, Takydromus sylvaticus, long known only from five females collected in Fujian Province of China, was recently found in Anhui Province of the country. The newly collected specimens included the first male specimens (n=7), in which the tail bases were stouter than in conspecific females. Ventral scales in these males were invariably keeled, whereas in females those forming the four median rows were smooth. Females had more dorsal scales (47-48) than males (42-43) in the median longitudinal row between axilla and groin. Takydromus sylvaticus differed from the closely related T. dorsalis in having more dorsal scales in the median longitudinal row between axilla and groin (42-48 versus 32-40, respectively), more rows of large dorsal scales between the hind legs (10 versus 7-8, respectively), shorter hind legs, two distinct white longitudinal stripes on each side of the body, and no black stripe in the preocular and postocular regions. The number of transverse rows of ventral scales between collar and femoral pores in T. sylvaticus (26-28) was larger, but with a slight overlap, than that in T. dorsalis (22-26). Ecological observations on T. sylvaticus were also documented.