Evolutionary analysis of phycobiliproteins: Implications for their structural and functional relationships

Phycobiliproteins, together with linker polypeptides and various chromophores, are basic building blocks of phycobilisomes, a supramolecular complex with a light-harvesting function in cyanobacteria and red algae. Previous studies suggest that the different types of phycobiliproteins and the linker polypeptides originated from the same ancestor. Here we retrieve the phycobilisome-related genes from the well-annotated and even unfinished cyanobacteria genomes and find that many sites with elevated d(N)/d(S) ratios in different phycobiliprotein lineages are located in the chromophore-binding domain and the helical hairpin domains (X and Y). Covariation analyses also reveal that these sites are significantly correlated, showing strong evidence of the functional-structural importance of interactions among these residues. The potential selective pressure driving the diversification of phycobiliproteins may be related to the phycobiliprotein-chromophore microenvironment formation and the subunits interaction. Sites and genes identified here would provide targets for further research on the structural-functional role of these residues and energy transfer through the chromophores.

Genetic mapping of laminaria japonica and l. longissima using amplified fragment length polymorphism markers in a "two-way pseudo-testcross" strategy

With a "two-way pseudo-testcross" mapping strategy, we applied the amplified fragment length polymorphism (AFLP) markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F, cross family (Laminaria longissima Aresch. x L. japonica Miyabe) with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1:1 ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3:1 Mendelian segregation ratio. Among the loci with 1:1 segregating ratios, 79 loci were ordered in 14 linkage groups (648.6 cM) of the paternal map, and 72 loci were ordered in 14 linkage groups (601.9 cM) of the maternal map. The average density of loci was approximately 1 per 8 cM. To investigate the homologies between two parental maps, we used 58 loci segregated 3:1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.

Zooplankton functional groups on the continental shelf of the yellow sea

Zooplankton plays a vital role in marine ecosystems. Variations in the zooplankton species composition, biomass, and secondary production will change the structure and function of the ecosystem. How to describe this process and make it easier to be modeled in the Yellow Sea ecosystem is the main purpose of this paper. The zooplankton functional groups approach, which is considered a good method of linking the structure of food webs and the energy flow in the ecosystems, is used to describe the main contributors of secondary produciton of the Yellow Sea ecosystem. The zooplankton can be classified into six functional groups: giant crustaceans, large copepods, small copepods, chaetognaths, medusae, and salps. The giant crustaceans, large copepods, and small copepods groups, which are the main food resources for fish, are defined depending on the size spectrum. Medusae and chaetognaths are the two gelatinous carnivorous groups, which compete with fish for food. The salps group, acting as passive filter-feeders, competes with other species feeding on phytoplankton, but their energy could not be efficiently transferred to higher trophic levels. From the viewpoint of biomass, which is the basis of the food web, and feeding activities, the contributions of each functional group to the ecosystem were evaluated; the seasonal variations, geographical distribution patterns, and species composition of each functional group were analyzed. The average zooplankton biomass was 2.1 g dry wt m(-2) in spring, to which the giant crustaceans, large copepods, and small copepods contributed 19, 44, and 26%, respectively. High biomasses of the large copepods and small copepods were distributed at the coastal waters, while the giant crustaceans were mainly located at offshore area. In summer, the mean biomass was 3.1 g dry wt m(-2), which was mostly contributed by the giant crustaceans (73%), and high biomasses of the giant crustaceans, large copepods, and small copepods were all distributed in the central part of the Yellow Sea. During autumn, the mean biomass was 1.8 g dry wt m(-2), which was similarly constituted by the giant crustaceans, large copepods, and small copepods (36, 33, and 23%, respectively), and high biomasses of the giant crustaceans and large copepods occurred in the central part of the Yellow Sea, while the small copepods were mainly located at offshore stations. The giant crustaceans and large copepods dominated the zooplankton biomass (2.9 g dry wt m(-2)) in winter, contributing respectively 57 and 27%, and they, as well as the small copepods, were all mainly located in the central part of the Yellow Sea. The chaetognaths group was mainly located in the northern part of the Yellow Sea during all seasons, but contributed less to the biomass compared with the other groups. The medusae and salps groups were distributed unevenly, with sporadic dynamics, mainly along the coastline and at the northern part of the Yellow Sea. No more than 10 species belonging to the respective functional groups dominated the zooplankton biomass and controlled the dynamics of the zooplankton community. The clear picture of the seasonal and spatial variations of each zooplankton functional group makes the complicated Yellow Sea ecosystem easier to be understood and modeled. (C) 2010 Elsevier Ltd. All rights reserved.

Identification and mapping of amplified fragment length polymorphism markers linked to shell color in bay scallop, Argopecten irradians irradians (Lamarck, 1819)

Amplified fragment length polymorphisms (AFLP) were used to study the inheritance of shell color in Argopecten irradians. Two scallops, one with orange and the other with white shells, were used as parents to produce four F-1 families by selfing and outcrossing. Eighty-eight progeny, 37 orange and 51 white, were randomly selected from one of the families for segregation and mapping analysis with AFLP and microsatellite markers. Twenty-five AFLP primer pairs were screened, yielding 1138 fragments, among which 148 (13.0%) were polymorphic in two parents and segregated in progeny. Six AFLP markers showed significant (P < 0.05) association with shell color. All six loci were mapped to one linkage group. One of the markers, F1f335, is completely linked to the gene for orange shell, which we designated as Orange1, without any recombination in the progeny we sampled. The marker was amplified in the orange parent and all orange progeny, but absent in the white parent and all the white progeny. The close linkage between F1f335 and Orange1 was validated using bulk segregation analysis in two natural populations, and all our data indicate that F1f335 is specific for the shell color gene, Orange1. The genomic mapping of a shell color gene in bay scallop improves our understanding of shell color inheritance and may contribute to the breeding of molluscs with desired shell colors.

Its length polymorphism in oysters and its use in species identification

In an effort to develop genetic markers for oyster identification, we studied length polymorphism in internal transcribed spacers (ITS) between major ribosomal RNA genes in 12 common species of Ostreidae: Crassostrea virginica, C. rhizophorae, C. gigas, C. angulata, C. sikamea, C. ariakensis, C. hongkongensis, Saccostrea echinata, S. glomerata, Ostrea angasi, O. edulis, and O. conchaphila. We designed two pairs of primers and optimized PCR conditions for simultaneous amplification of ITS 1 and ITS2 in a single PCR. Amplification was successful in all 12 species, and PCR products were visualized on high-resolution agarose gels. ITS2 was longer than ITS 1 in all Crassostrea and Saccostrea species, whereas they were about the same size in the three Ostrea species. No intraspecific variation in ITS length was detected. Among species, the length of ITS I and ITS2 was polymorphic and provided unique identification of 8 species or species pairs: C. ariakensis, C. hongkongensis, C. sikamea, O. conchaphila, C. virginica/C. rhizophorae, C. gigas/C. angulata, S. echinata/S. glonzerata, and O. angasi/O. edulis. The ITS assay provides simple, rapid and effective identification of C. ariakensis and several other oyster species. Because the primer sequences are conserved, the ITS assay may be useful in the identification of other bivalve species.

High performance cocktail functional monomer for making molecule imprinting polymer

In order to make a molecule imprinting polymer (MIP) with highly chiral selectivity against N-t-Boc-L-Trp, a new kind of "cocktail" functional monomer: acrylamide+2-vinylpyridine was investigated. The MIP showed impressive chiral selectivity (alpha=3.23). With the increasing of water content in the mobile phase, ionic and hydrophobic interaction were found to be responsible for the chiral recognition process instead of the hydrogen bond. Tailing and peak asymmetry problems were overcome by using linear gradient elution. Physical properties such as thermal stability and pore structure for the MIP were also investigated.

New cocktail functional monomers in making molecule imprinting polymer with high chiral selectivity

in order td produce molecule imprinting polymer (MIP) with high chiral selectivity against N-c-protected amino acid, new cocktail functional monomers acrylamide (AM) + 2-vinylpyridine (2-VP) and AM + methacrylic acid (MAA) were investigated. AM + 2-VP was found to be more efficient in improving the selectivity and resolution of the molecule imprinting polymer.