Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

The phylogenetic relationships among peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothammidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Asty/ozoon, which suggested that Opisthonecta species were not the ancestors of the stalked peritrichs.

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences

The peritrichs have been recognized as a higher taxon of ciliates since 1968. However, the phylogenetic relationships among them are still unsettled, and their placement within the class Oligohymenophorea has only been supported by the analysis of the small subunit rRNA gene sequence of Opisthonecta henneguyi. DNA was isolated directly from field-sampled species for PCR, and was used to resolve relationships within the genus Epistylis and to confirm the stability of the placement of peritrichs. Small subunit rRNA gene sequences of Epistylis plicatilis, Epistylis urceolata, Epistylis chysemydis, Epistylis hentscheli, Epistylis wenrichi, and Vorticella campanula were sequenced and analyzed using both distance-matrix and maximum-parsimony methods. In phylogenetic trees, the monophyly of both the genus Epistylis and the subclass Peritrichia was strongly supported, while V. campanula clustered with Vorticella microstoma. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the peristomial area, especially the. peristomial lip, might be the important phylogenetic character within the genus Epistylis.

Systematic study of the pi(-)/pi(+) ratio in heavy-ion collisions with the same neutron/proton ratio but different masses

A systematic study of the pi(-)/pi(+) ratio in heavy-ion collisions with the same neutron/proton ratio but different masses can help single out effects of the nuclear mean field on pion production. Based on simulations using the IBUU04 transport model, it is found that the pi(-)/pi(+) ratio in head-on collisions of Ca-48 + Ca-48, Sn-124 + Sn-124, and Au-197 + Au-197 at beam energies from 0.25 to 0.6 GeV/nucleon increases with increasing the system size or decreasing the beam energies. A comprehensive analysis of the dynamical isospin fractionation and the pi(-)/pi(+) ratio as well as their time evolution and spatial distributions demonstrates clearly that the pi(-)/pi(+) ratio is an effective probe of the high-density behavior of the nuclear symmetry energy.

Study on effective masses of meson in dense nuclear matter

We introduce and summary our research progress on the effective masses of K meson in dense nuclear matter.

Effective masses of pentaquark Theta(+) in nuclear matter

The properties of baryons in nuclear matter are analysed in the relativistic mean-field theory(RMF). It is found that the scalar field sigma meson affects the properties of baryon at high density. A density dependent scalar coupling g(sigma)(N) is determined according to the idea of quark-meson coupling model and extended to RMF. It is shown that g(sigma)(N), affects the property of nuclear matter weakly at low density, but strongly at high density. The relation between the scalar density rho(S) and the nuclear density rho and the effective mass of the pentaquark circle minus(+) are studied with the density dependent coupling constant. The density dependent scalar coupling obviously affects the effective masses of baryons in nuclear matter, especially at high density.

Functional biosynthesis of an allophycocyan beta subunit in Escherichia coli

Allophycocyanin is a phycobiliprotein with various biological and pharmacological properties. An expression vector was constructed using CpeS as the bilin lyase for the allophycocyanin beta subunit, resulting in overexpression of a fluorescent allophycocyanin beta-subunit in Escherichia coli. A high-density cell culture was developed using a continuous feeding strategy. After 16 h of culture, the dry cell density reached 21.4 g 1(-1), the expression of the allophycocyanin beta-subunit was 0.86 g l(-1) broth, and the relative chromoprotein yield was 81.4%. The recombinant protein showed spectral features similar to native allophycocyanin, which provide an efficient methodology for large-scale production of this valuable fluorescent protein. (C) 2008, The Society for Biotechnology, Japan. All rights reserved.

Highly soluble and stable recombinant holo-phycocyanin alpha subunit expressed in Escherichia coli

C-phycocyanin (Cpc) is one of the phycobiliproteins with highly fluorescent and various pharmacological activities Holo-Cpc-alpha Subunit (holo-CpcA) expressed in Escherichia colt resulted in low yield and tended to aggregate after purification in this Study, we constructed a new plasmid coding holo-CpcA fused with hexahistidine and maltose-binding protein tag, which designated as HMCpcA. to Improve Its Solubility and stability without the Impairment of its spectra anti fluorescent properties HMCpcA was significantly more stable over time and a wider range of pH as compared to holo-CpcA. In addition. both the solubility and yields of HMCpcA increase significantly We here provided an example to demonstrate that MBP could also Improve the stability of the protein it fused while it has been reported as a soluble fusion partner before. This novel fluorescent protein will facilitate the large-scale production and be potentially applicable for the development Of fluorescent probes, as well as antioxidant agents (C) 2009 Elsevier B V. All rights reserved

Cloning, characterization and expression of ferritin subunit from clam Meretrix meretrix in different larval stages

Shell formation is one of the important events during larval development and metamorphosis in bivalves. However, the molecular mechanisms and environmental cues regulating shell initiation and growth are unclear. Here, we report that ferritin, a principal protein for biological iron storage and metabolism, might play a role in larval shell development of the bivalve mollusk Meretrix meretrix. A full-length ferritin subunit cDNA, named as MmeFer, was cloned and characterized. The MmeFer mRNA expression in different developmental stages, from trochophore to post larvae, was analyzed by real-time reverse transcription polymerase chain reaction (RT-PCR). MmeFer mRNA expression in larvae of later developmental stages increased at least 8-fold following trochophores. Moreover, the temporal and spatial expressions of MmeFer mRNA were examined by whole mount in situ hybridization. In the trochophore stage, MmeFer was detectable where it was supposed to be for shell initiation. In the later developmental stages, MmeFer was found near digestive glands and mantle that secret larval shell. MmeFer expression was also detected in larvae cultured in artificial seawater with different iron concentrations ranging from 0 to 100 mu M. These results suggest that ferritin may play a role in the shell formation of mollusks. (C) 2009 Elsevier Inc. All rights reserved.

Identification of an Edwardsiella tarda surface antigen and analysis of its immunoprotective potential as a purified recombinant subunit vaccine and a surface-anchored subunit vaccine expressed by a fish commensal strain

Edwardsiella tarda is the etiological agent of edwardsiellosis, a systematic disease that affects a wide range of marine and freshwater fish cultured worldwide. In order to identify E. tarda antigens with vaccine potential, we in this study conducted a systematic search for E. tarda proteins with secretion capacity. One of the proteins thus identified was Esa1, which contains 795 amino acid residues and shares extensive overall sequence identities with the D15-like surface antigens of several bacterial species. In silico analyses indicated that Esa1 localizes to outer membrane and possesses domain structures that are conserved among bacterial surface antigens. The vaccine potential of purified recombinant Esa1 was examined in a Japanese flounder (Paralichthys olivaceus) model, which showed that fish vaccinated with Esa1 exhibited a high level of survival and produced specific serum antibodies. Passive immunization of naive fish with antisera raised against Esa1 resulted in significant protection against E. tarda challenge. Taking advantage of the secretion capacity of Esa1 and the natural gut-colonization ability of a fish commensal strain, we constructed an Esa1-expressing recombinant strain, FP3/pJsa1. Western immunoblot and agglutination analyses showed that FP3/pJsa1 produces outer membrane-localized Esa1 and forms aggregates in the presence of anti-Esa1 antibodies. Vaccination analyses showed that FP3/pJsa1 as an intraperitoneal injection vaccine and an oral vaccine embedded in alginate microspheres produced relative percent survival rates of 79% and 52%, respectively, under severe challenging conditions that resulted in 92-96% mortality in control fish. Further analyses showed that following oral vaccination, FP3/pJsa1 was able to colonize in the gut but unable to disseminate into other tissues. Together these results indicate that Esa1 is a protective immunogen and an effective oral vaccine when delivered by FP3/pJsa1 as a surface-anchored antigen. (c) 2010 Elsevier Ltd. All rights reserved.

The recombination and expression of the allophycocyanin beta subunit gene in the chloroplast of Chlamydomonas reinhardtii

A Chlamydomonas reinhardtii (C. reinhardtii) chloroplast expression vector, papc-B, containing the apc-B gene that encodes the beta subunit of the light-harvesting antenna protein allophycocyanin (APC) of cyanobacteria, was constructed and transferred to the chloroplast genome of C. reinhardtii by the biolistic method. The transformants were identified by Southern blot, Western blot and ELISA assays after selection on resistant medium. The recombinant APC beta subunit was expressed in the C. reinhardtii chloroplast and accounted for up to 2-3% (w/w) of the total soluble protein (TSP), suggesting a promising prospect of using C. reinhardtii chloroplasts to produce functional plant-derived proteins.

Benthic foraminiferal distribution in surface sediments along continental slope of the southern Okinawa Trough: dependance on water masses and food supply

Benthic foraminiferal analysis of 29 samples in surface sediments from the southern Okinawa Trough is carried out. The results indicate that benthic foraminiferal abundance decreases rapidly with increasing water depth. Percentage frequencies of agglutinated foraminifera further confirm the modem shallow carbonate lysocline in the southern Okinawa Trough. From continental shelf edge to the bottom of Okinawa Trough, benthic foraminiferal fauna in the surface sediments can be divided into 5 assemblages: (1) Continental shelf break assemblage, dominated by Cibicides pseudoungerianus, corresponds to subsurface water mass of the Kuroshio Current; (2) upper continental slope assemblage, dominated by Cassidulina carinata, Globocassidulina subglobosa, corresponds to intermediate water mass of the Kuroshio Current; (3) intermediate continental slope assemblage, dominated by Uvigerina hispida, corresponds to the Okinawa Trough deep water mass above the carbonate lysocline; (4), lower continental slope - trough bottom assemblage, dominated by Pullenia bulloides, Epistominella exigua and Cibicidoides hyalinus, corresponds to deep water mass of the Okinawa Trough; and (5) trough bottom agglutinated assemblage, dominated by Rhabdammina spp., Bathysiphon flavidus, corresponds to I strongly dissolved environment of the trough bottom. The benthic foraminiferal fauna in the southern Okinawa Trough are controlled jointly by water masses and food supply. Water temperature, oxygen concentration and carbonate dissolution of the water masses are important controlling factors especially for the continental shelf break and trough bottom assemblages. The food supply also plays an important role in these benthic foraminiferal assemblages along the western slope. of the Okinawa Trough. Both the abundance and the 5 assemblages of benthic foraminifera correspond well to the organic matter supply along the continental slope and a lateral transport of TSM (total suspended matter) and POC (particulate organic carbon) from the shelf break to the deep water is also an important food supply for benthic fauna in this region.

Origins and pathways of the subsurface and intermediate water masses of the Indonesian Throughflow derived from historical and Argo data

On the basis of Argo data and historic temperature/salinity data from the World Ocean Database 2001 (WOD01 origins and spreading pathways of the subsurface and intermediate water masses in the Indonesian Throughflow (ITF) region were discussed by analyzing distributions of salinity on representative isopycnal layers. Results were shown that, Subsurface water mostly comes from the North Pacific Ocean while the intermediate water originates from both the North and South Pacific Ocean, even possibly from the Indian Ocean. Spreading through tire Sulawesi Sea, the Makassar Strait, and the Flores Sea, the North Pacific subsurface water and the North Pacific Intermediate water dominate the western part of the Indonesian Archipelago. Furthermore its the depth increases, the features of the North Pacific sourced water masses become more obvious. In the eastern part of the waters, high salinity South Pacific subsurface water is blocked by a strong salinity front between Halmahera and New Guinea. Intermediate water in the eastern interior region owns salinity higher than the North Pacific intermediate water and the antarctic intermediate water (AAIW), possibly coming from the vertical mixing between subsurface water and the AAIW from the Pacific Ocean, and possibly coming front the northward extending of the AAIW front the Indian Ocean as well.

Autumn net copepod abundance and assemblages in relation to water masses on the continental shelf of the Yellow Sea and East China Sea

Copepod species diversity, abundance and assemblages in relation to water masses over the continental shelf of the Yellow Sea (YS) and East China Sea (ECS) were studied extensively based on the net plankton samples in autumn 2000. Multivariate analysis based on copepod assemblage resulted in recognition of five groups (Groups 1-5) corresponding to the water masses. Groups 1 and 2 delineated from inshore stations with low salinity YS Surface Water, and offshore stations with YS Cold Water in the YS. Group 3 located in the joint area of YS and ECS mainly with Mixed Water. Groups 4 and 5 in the ECS delineated two assemblages mainly from inshore and shallow stations with ECS Mixed Water in the southeastern ECS, and offshore stations along the ECS shelf edge controlled by saline Kuroshio Water. Salinity and temperature were more important in characterizing copepod assemblage of the continental shelf than chlorophyll a. (c) 2005 Elsevier B.V. All rights reserved.

Isolation and characterization of a novel variant of HMW glutenin subunit gene from the St genome of Pseudoroegneria stipifolia

The x- and y-type high molecular weight (HMW) glutenin subunits are conserved seed storage proteins in wheat and related species. Here we describe investigations on the HMW glutenin subunits from several Pseudoroegneria accessions. The electrophoretic mobilities of the HMW glutenin subunits from Pd. stipifolia, Pd tauri and Pd strigosa were much faster than those of orthologous wheat subunits, indicating that their protein size may be smaller than that of wheat subunits. The coding sequence of the Glu-1St1 subunit (encoded by the Pseudoroegneria stipifolia accession PI325181) was isolated, and found to represent the native open reading frame (ORF) by in vitro expression. The deduced amino acid sequence of Glu-1St1 matched with that determined from the native subunit by mass spectrometric analysis. The domain organization in Glu-1St1 showed high similarity with that of typical HMW glutenin subunits. However, Glu-1St1 exhibited several distinct characteristics. First, the length of its repetitive domain was substantially smaller than that of conventional subunits, which explains its much faster electrophoretic mobility in SDS-PAGE. Second, although the N-terminal domain of Glu-1St1 resembled that of y-type subunit, its C-terminal domain was more similar to that of x-type subunit. Third, the N- and C-terminat domains of Glu-1St1 shared conserved features with those of barley D-hordein, but the repeat motifs and the organization of its repetitive domain were more similar to those of HMW glutenin subunits than to D-hordein. We conclude that Glu-1St1 is a novel variant of HMW glutenin subunits. The analysis of Glu-1St1 may provide new insight into the evolution of HMW glutenin subunits in Triticeae species. (C) 2007 Elsevier Ltd. All rights reserved.