Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals.

Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

Bacterial growth efficiency in a partly eutrophicated bay of South China Sea: Implication for anthropogenic impacts and potential hypoxia events.

Bacterial metabolism plays a dual role [bacterial production (BP) and bacterial respiration (BR)] in the aquatic ecosystem and potentially leads to hypoxia in the coastal eutrophic area. Bacterial growth efficiency (BGE) is an important index showing the contribution of bacterial metabolism to marine biological production and carbon budget in the pelagic ecosystem. In this study, the spatial and seasonal variety as well as diurnal variation dynamics of BGE and associated ecological characteristics were investigated in a partly eutrophicated subtropical bay (the Daya Bay) located in the northern South China Sea. Furthermore, the relationship between bacterial metabolism and potential hypoxia event was analyzed. The average BGE was 0.14 and 0.22 in summer and winter, respectively, which was lower than the mean value ever reported in other coastal and estuarine waters. The diurnal variations of BGE and BP were widely fluctuated in the Daya Bay, with approximately 3-8 fold variation of BP and 2-3 fold variation of BR in different seasons, suggesting the importance of short-term ecological dynamics on evaluating the long-term ecological processes in the coastal waters. BR was the predominant contributor to the bacterial carbon demand; however, the variation of BGE was controlled by BP in both seasons. BGE was always high in the near-shore waters with higher eutrophic level and more active BP and BR. The bacterial metabolism could deplete dissolved oxygen (DO) in the Daya bay within about 9 days when the water body was enclosed and photosynthesis was prohibited. Therefore, low DO concentration and potential hypoxia was more likely to be found in the near-shore waters of the Daya Bay in summer, since the water was stratified and enclosed with poor water exchange capacity in this area. While in winter, hypoxia seldom occurred due to vertical mixing throughout the water column. Further biological-physical coupling research is recommended to find out the detailed formation mechanism of hypoxia in the bay, and to predict the potential hypoxia events and their environmental impacts in the future.

[Inner- and inter-species differences of mercury concentration in common fishes from the Yellow Sea].

Mercury concentration in marine fishes and its influencing factors are the key problems in the study of mercury biomagnification in marine ecosystems. In order to understand the inner- and inter-species differences of mercury concentration in fishes from the Yellow Sea, a total of 164 marine wild fishes covering nine different species were collected from the area from August to October, 2012. Mercury (total mercury) concentration in fish muscle tissue was measured by a direct mercury analyzer. Body length and wet weight of each sample were also determined. Moreover, feeding habit and trophic level of different species were examined. Hg concentrations (dry weight) in the muscle tissues of the 164 individuals ranged from 0.025 micro x g(-1) to 0.526 microg x g(-1), with an average of (0.124 +/- 0.096) microg x g(-1). By an inner-species analysis, log10 Hg concentration was significantly correlated to their body length and wet weight. Predator fishes with trophic level > 2.8 were more readily to be contaminated by Hg than the filter feeder with trophic level < 2.8. Furthermore, species with higher increasing rate of weight had lower Hg concentration in the muscle due to growth dilution. The results suggest that length and weight are the main factors affecting the inner- species difference of mercury concentration in common fishes from the Yellow Sea, while dietary preference, trophic level and increasing rate of weight are the main factors affecting the inter-species difference from the Yellow Sea.

The complete mitochondrial genome of a striped sole Zebrias zebrinus (Pleuronectiformes: Soleidae).

Zebrias zebrinus belongs in the family Soleidae of Pleuronectiformes. There are overlaps in the ranges of identification characters between Z. zebrinus and another striped sole Z. fasciatus. In this study, the complete mitochondrial genome of Z. zebrinus was first determined. The total length was 16,758 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (O(L)). Gene contents, locations, and arrangements were identical to those of typical bony fishes. The overall base composition of the mitogenome was 28.7%, 30.0%, 15.2%, and 26.1% for A, C, G, and T, respectively, with an A + T content of 54.8%. This result would expect the contribution to the molecular identification of this species and further phylogenetic study of Soleidae and Pleuronectiformes.

Occurrence of brackish water phytoplankton species at a closed coral reef in Nansha Islands, South China Sea.

The phytoplankton assemblage of Zhubi Reef, a closed coral reef in Nansha Islands (South China Sea, SCS) was studied in June 2007. A total of 92 species belonging to 53 genera and four phyla have been identified. The dominant taxa in the lagoon were the diatom Chaetoceros and cyanobacteria Nostoc and Microcystis, while in reef flats were cyanobacteria Trichodesmium erythraeum, dinoflagellates Gymnodinium and Prorocentrum. The species richness and diversity were consistently lower in the lagoon than in reef flats. Classification and nMDS ordination also revealed significant dissimilarity in phytoplankton community structure between the reef flat and lagoon, with statistical difference in species composition and abundance between them (ANOSIM, p=0.025). Nutrient concentrations also spatially varied, with ammonium-enrichment in the lagoon, while high Si-concentration existed in reef flat areas. Both nutrient levels and currents in SCS may play important roles in determining the composition and distribution of microalgae in Zhubi Reef and SCS.

Secretion of biologically active human epidermal growth factor from Escherichia coli using Yersinia pestis Caf1 signal peptide.

BACKGROUND AND PURPOSE: The Caf1 secretion pathway of Yersinia pestis is one of the most well-characterized export machineries. To facilitate the secretion of human epidermal growth factor (hEGF) in Escherichia coli, a DNA fragment containing the synthetic gene for hEGF was joined to a sequence encoding the signal peptide of Yersinia pestis Caf1 protein. METHODS: The gene for hEGF was synthesized by overlapping polymerase chain reaction technique and was placed under the control of the caf1 gene promoter in the recombinant plasmid pHL401 which was used to transfect E. coli BL-21 for production of hEGF. The biological function of recombinant hEGF was measured by estimating its ability to stimulate the proliferation of human embryonic kidney-293 cells. RESULTS: The results indicated that the expressed hybrid protein was processed during the secretion process. The majority of the mature hEGF was recovered from the periplasm and medium fractions, with a small amount of the expressed hEGF deposited in the cytoplasm. Furthermore, it was found that the cell proliferation was enhanced by the recombinant hEGF. CONCLUSION: These results suggested that the recombinant hEGF was successfully secreted through the inner membrane of cells into the periplasm and then through the outer membrane into the medium via the action of the signal peptide of Y. pestis Caf1 in E. coli. The mitogenic activity of hEGF in cells was demonstrated.