Expressed sequence tags from the zhikong scallop (Chlamys farreri): Discovery and annotation of host-defense genes

A high-quality cDNA library was constructed from whole body tissues of the zhikong scallop, Chlamys farreri, challenged by Listonella anguillarum. A total of 5720 clones were sequenced, yielding 5123 expressed sequence tags (ESTs). Among the 3326 unique genes identified, 2289 (69%) genes had no significant (E-value < 1e-5) matches to known sequences in public databases and 194 (6%) matched proteins of unknown functions. The remaining 843 (25%) genes that exhibited homology with genes of known functions, showed broad involvement in metabolic processes (31%), cell structure and motility (20%), gene and protein expression (12%), cell signaling and cell communication (8%), cell division (4%), and notably, 25% of those genes were related to immune function. They included stress response genes, complement-like genes, proteinase and proteinase inhibitors, immune recognition receptors and immune effectors. The EST collection obtained in this study provides a useful resource for gene discovery and especially for the identification of host-defense genes and systems in scallops and other molluscs. (C) 2009 Elsevier Ltd. All rights reserved.

The cDNA cloning and mRNA expression of cytoplasmic Cu, Zn superoxide dismutase (SOD) gene in scallop Chlamys farreri

Cu, Zn superoxide dismutases (SODs) are rnetalloenzymes that represent one important line of defence against reactive oxygen species (ROS). A cytoplasmic Cu. Zn SOD cDNA sequence was cloned from scallop Chlamys farreri by the homology-based cloning technique. The full-length cDNA of scallop cytoplasmic Cu, Zn SOD (designated CfSOD) was 1022 bp with a 459 bp open reading frame encoding a polypeptide of 153 amino acids. The predicted amino acid sequence of CfSOD shared high identity with cytoplasmic Cu. Zn SOD in molluscs, insects, mammals and other animals, such as cytoplasmic Cu, Zn SOD in oyster Crassostrea sostrea gigas (CAD42722), mosquito Aedes aegypti (ABF18094), and cow Bos taurus (XP_584414). A quantitative reverse transcriptase real-time PCR (qRT-PCR) assay was developed to assess the mRNA expression of CfSOD in different tissues and the temporal expression of CfSOD in scallop challenged with Listonella anguillarum, Micrococcus luteus and Candida lipolytica respectively. Higher-level mRNA expression of CfSOD was detected in the tissues of haemocytes, gill filaments and kidney. The expression of CfSOD dropped in the first 8-16 h and then recovered after challenge with L. anguillarum and M. litteus, but no change was induced by the C. lipolytica challenge. The results indicated that CfSOD was a constitutive and inducible acute-phase protein, and could play an important role in the immune responses against L. anguillarum and M. luteus infection. (C) 2007 Elsevier Ltd. All rights reserved.

Development of expressed sequence tags from the bay scallop, Argopecten irradians irradians

The bay scallop, Argopecten irradians irradians, introduced from North America, has become one of the most important aquaculture species in China. Inan effort to identify scallop genes involved in host defense, a high-quality cDNA library was constructed from whole body tissues of the bay scallop. A total of 5828 successful sequencing reactions yielded 4995 expressed sequence tags (ESTs) longer than 100 bp. Cluster and assembly analyses of the ESTs identified 637 contigs (consisting of 2853 sequences) and 2142 singletons, totaling 2779 unique sequences. Basic Local Alignment Search Tool (BLAST) analysis showed that the majority (73%) of the unique sequences had no significant homology (E-value >= 0.005) to sequences in GenBank. Among the 748 sequences with significant GenBank matches, 160 (21.4%) were for genes related to metabolism, 131 (17.5%) for cell/organism defense, 124 (16.6%) for gene/protein expression, 83 (11.1%) for cell structure/motility, 70 (9.4%) for cell signaling/communication, 17 (2.3%) for cell division, and 163 (21.8%) matched to genes of unknown functions. The list of host-defense genes included many genes with known and important roles in innate defense such as lectins, defensins, proteases, protease inhibitors, heat shock proteins, antioxidants, and Toll-like receptors. The study provides a significant number of ESTs for gene discovery and candidate genes for studying host defense in scallops and other molluscs.

Food utilization of adult flatfishes co-occurring in the Bohai Sea of China

Stomach contents were examined of 4527 adult individuals of 12 flatfish species collected during the 1982 - 1983 Bohai Sea Fisheries Resources Investigation. Their food habits, diet diversity, similarity of prey taxa, trophic niche breadth and diet overlap were systematically analysed. Ninety-seven prey species belonging to the Coelenterata, Nemertinea, Polychaeta, Mollusca, Crustacea, Echinodermata, Hemichordata and fish were found and five of them were considered to be principal prey for flatfishes: Alpheus japonicus, Oratosquilla oratoria, Alpheus distinguendus, Loligo japonicus and Crangon affinis. Among the flatfishes, Paralichthys olivaceus was piscivorous, whereas Pseodopleuronectes yokohamae and Pseudopleuronectes herzensteini both had polychaetes and molluscs as their main prey groups. Pleuronichthys cornutus was classified as a polychaete-mollusc eater, with a strong preference for crustaceans. Verasper variegatus, Cynoglossus semilaevis, Eopsetta grigorjewi and Cleisthenes herzensteini ate crustaceans. Kareius bicoloratus was classified as a mollusc-crustacean eater: Cynoglossus abbreviatus, Cynoglossus joyneri and Zebrias zebra were grouped as crustacean-fish eaters. However, Z. zebra also took polychaetes and C. abbreviatus and C. joyneri preyed on some molluscs. Trophic relationships among the flatfishes were complicated, but they occupied distinctive microhabitats in different seasons and selected their specific prey items, which was favourable to the stability of the flatfish community in the Bohai Sea.

Feeding and growth on bivalve biodeposits by the deposit feeder Stichopus japonicus Selenka (Echinodennata : Holothuroidea) co-cultured in lantern nets

Suspension aquaculture of filter-feeding bivalves has been developing rapidly in coastal waters in the world, especially in China. Previous studies have demonstrated that dense populations of filter-feeding bivalves in shallow water can produce a large amount of faeces and pseudofaeces (biodeposits) that may lead to negative impacts on the benthic environment. To determine whether the deposit feeder Stichopus (Apostichopus) japonicus Selenka can feed on bivalve biodeposits and whether the sea cucumber can be co-cultured with bivalves in suspended lantern nets, three experiments were conducted, two in tanks in the laboratory and one in the field. In a 3-month flow-through experiment, results showed that sea cucumbers grew well with specific growth rate (SGR) reaching 1.38% d(-1), when cultured in the bottom of tanks (10 m(3) water volume) where scallops were cultured in suspension in lantern nets. Moreover, results of another laboratory experiment demonstrated that sea cucumbers could survive well on bivalve biodeposits, with a feeding rate of 1.82 +/- 0.13 g dry biodeposits ind(-1) d(-1), absorption efficiency of organic matter in biodeposits of 17.2% +/- 5.5%, and average SGR of 1.60% d(-1). Our longer-term field experiments in two coastal bays (Sishili Bay and Jiaozhou Bay, northern China) showed that S. japonicus co-cultured with bivalves also grew well at growth rates (0.09-0.31 g wet weight ind(-1) d(-1)) depending on individual size. The results suggest that bivalve lantern nets can provide a good habitat for sea cucumbers; and the co-culture of bivalve molluscs with sea cucumbers may provide an additional valuable crop with no additional inputs. (c) 2006 Elsevier B.V. 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.

Early-Holocene environments in the Wadi Faynan, Jordan

Hunt, C. Elrishi, H. Gilbertson, D. Grattan, J. McLaren, S. Pyatt, B. Rushworth, G. Barker, G. Early-Holocene environments in the Wadi Faynan, Jordan. The Holocene. 2004. 14,6 pp 921-930

Protein kinase C regulation of cell spreading in the molluscan Biomphalaria glabrata embryonic (Bge) cell line

Judith E. Humphries, Leah Elizondo and Timothy P. Yoshino (2001). Protein kinase C regulation of cell spreading in the molluscan Biomphalaria glabrata embryonic (Bge) cell line. Biochimica et Biophysica Acta - Molecular Cell Research, 1540(3), 243-252. Sponsorship: National Institutes of Health AI 15503 RAE2008

Synecology in soft sediment bivalves: the influence of parasites, physiological processes, and environmental stressors on health and disease

Ecosystem goods and services provided by estuarine and near coastal regions are being increasingly recognised for their immense value, as is the biodiversity in these areas and these near coastal communities have been identified as sentinels of climate change also. Population structure and reproductive biology of two bivalve molluscs, Cerastoderma edule and, Mytilus edulis were assessed at two study sites over a 16-month study period. Following an anomalously harsh winter, advancement of spawning time was observed in both species. Throughout Ireland and Europe the cockle has experienced mass surfacings in geographically distinct regions, and a concurrent study of cockles was undertaken to explore this phenomenon. Surfaced and buried cockles were collected on a monthly basis and their health compared. Age was highlighted as a source of variation between dying and healthy animals with a parasite threshold being reached possibly around age three. Local factors dominated when looking at the cause of surfacing at each site. The health of mussels was explored too on a temporal and seasonal basis in an attempt to assess what constitutes a healthy organism. In essence external drivers can tip the balance between “acceptable” levels of infection where the mussel can still function physiologically and “unacceptable” where prevalence and intensity of infection can result in physiological impairment at the individual and population level. Synecological studies of intertidal ecosystems are lacking, so all bivalves encountered during the sampling were assessed in terms of population structure, reproduction, and health. It became clear, that some parasites might specialize on one host species while others are not so specific in host choice. Furthermore the population genetics of the cockle, its parasite Meiogymnophallus minutus, and its hyperparasite Unikaryon legeri were examined too. A small nucleotide polymorphism was detected upon comparison of Ireland and Morocco.

The use of biological indicators of heavy metal contamination in estuaries. Occasional Publication of the Marine Biological Association 1

The use of the deposit-feeding molluscs Scrobicularia plana and Macoma balthica and the burrowing polychaete Nereis diversicolor as indicators of the biological availability of heavy metals in sediments has been evaluated. Concentrations of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sn and Zn have been measured in organisms and sediments from more than 30 estuaries in south west England and South Wales and indicate that the biological availability of most metals varies by order of magnitude between uncontaminated and contaminated sites. The results have been compared with those obtained with the use of other species of indicator organisms in estuaries.

Structural and functional vulnerability to elevated pCO2 in marine benthic communities

The effect of elevated pCO(2)/low pH on marine invertebrate benthic biodiversity, community structure and selected functional responses which underpin ecosystem services (such as community production and calcification) was tested in a medium-term (30 days) mesocosm experiment in June 2010. Standardised intertidal macrobenthic communities, collected (50.3567A degrees N, 4.1277A degrees W) using artificial substrate units (ASUs), were exposed to one of seven pH treatments (8.05, 7.8. 7.6, 7.4, 7.2, 6.8 and 6.0). Community net calcification/dissolution rates, as well as changes in biomass, community structure and diversity, were measured at the end of the experimental period. Communities showed significant changes in structure and reduced diversity in response to reduced pH: shifting from a community dominated by calcareous organisms to one dominated by non-calcareous organisms around either pH 7.2 (number of individuals and species) or pH 7.8 (biomass). These results were supported by a reduced total weight of CaCO3 structures in all major taxa at lowered pH and a switch from net calcification to net dissolution around pH 7.4 (a"broken vertical bar(calc) = 0.78, a"broken vertical bar(ara) = 0.5). Overall community soft tissue biomass did not change with pH and high mortality was observed only at pH 6.0, although molluscs and arthropods showed significant decreases in soft tissue. This study supports and refines previous findings on how elevated pCO(2) can induce changes in marine biodiversity, underlined by differential vulnerability of different phyla. In addition, it shows significant elevated pCO(2)-/low pH-dependent changes in fundamental community functional responses underpinning changes in ecosystem services.

Aspects Of Gametogenesis In The Marine Mussel Mytilus-Edulis-L

Marine bivalve molluscs have in recent years attracted considerable attention for a variety of reasons, not least of which is their importance as a source of food for man. Much of this research has concentrated on studies of reproduction; Mytilus viridis (India: Nagabhushanam & Mane, 1975), M. edulis aoteanus and Aulacomya maoriana (New Zealand: Kennedy, 1977);Choromytilus meridionalis and Aulacomya ater (South Africa: Berry, 1978); Mytilus (= Perna) perna (Brazil: Lunetta, 1969); M. edulis planulatus (Australia: Wilson & Hodgkin, 1967); Mytilus californianus and M. edulis (U.S.A.: Hines, 1979); Mytilus galloprovincialis (France: Lubet, 1959) and M. edulis (U.K.: Chipperfield, 1953; Seed, 1975; Bayne et al. 1978). A review of the literature revealed that in the majority of studies cytology was used as a descriptive tool for the ‘staging’ (Chipperfield, 1953; Lubet, 1957; Seed, 1975, 1976) of the developing gametes and certain anomalies were apparent with regard to the nomenclature of the connective tissue matrix of the mantle lobes.

Some Ecological Consequences Of The Physiological And Biochemical Effects Of Petroleum Compounds On Marine Mollusks

The problems of relating the results of experiments in the laboratory to events in nature are twofold: to equate the response to a single variable (hydrocarbons) with the natural variability in the biological material in a multivariate environment, and to consider whether the response established experimentally has any relevance to the animal's chances of survival and reproduction (i.e. its fitness) in the natural population. Recent studies of the effects of petroleum hydrocarbons on marine invertebrates are reviewed, with an emphasis on the physiological and cytochemical responses by bivalve molluscs. The dose-response relations that emerge suggest the intensity of the 'signal' that must be detected in nature if the chronic, sublethal effects of petroleum pollution are to be measured. The natural variability in these physiological and cytochemical processes are then reviewed and the main causes of variability in natural populations, both endogenous and exogenous, discussed. These results indicate the extent of the `noise' above which the signal from possible pollution effects must be detected. The results from recent field studies on the common mussel, Mytilus edulis, are discussed. The results are as complex as expected, but it proves possible to reduce the variance in the measured responses so that pollution effects, including those due to hydrocarbons, can be detected. The ecological consequences of the observed effects of petroleum hydrocarbons are then discussed in terms of reproductive effort and reproductive value. Considerable variation between populations exists here also and this can be used to help in the interpretation of the extent of the impact of the environment on the ecology of the population. The result is to place the findings of the laboratory experiments in an ecological context of natural variability and of the physiological costs of adaptation.

Some Practical Considerations In The Measurement Of Pollution Effects On Bivalve Mollusks And Some Possible Ecological Consequences

A consideration of some physiological (rates of oxygen consumption, the scope for growth) and cellular (the cytochemical latency of a lysosomal enzyme) processes in bivalve molluscs suggests that animal size and seasonal changes related to the gametogenic cycle are important sources of natural variability. Correcting for size using regression techniques, and limiting measurements to one part of the gametogenic cycle, reduces observed natural variability considerably. Differences between populations are then still apparent, but the results of laboratory experiments with hydrocarbons from crude oil suggest that it should be possible to detect sub-lethal effects due to pollution (the ‘signal’) in the presence of the remaining natural variability (the ‘noise’). Statistical considerations, taken together with results from current studies on Mytilus edulis and Scobicularia plana, indicate that sample sizes of 10–15 individuals should suffice for the detection of possible pollution effects. The physiological effects to be expected in the presence of sub-lethal levels of polluting hydrocarbons are on a scaie that can cause significant ecological damage to a population through a reduction in fecundity and the residual reproductive value of the individuals.

Mixed-Function Oxygenases And Xenobiotic Detoxication-Toxication Systems In Bivalve Mollusks

Components of a xenobiotic detoxication/toxication system involving mixed function oxygenases are present inMytilus edulis. Our paper critically reviews the recent literature on this topic which reported the apparent absence of such a system in bivalve molluscs and attempts to reconcile this viewpoint with our own findings on NADPH neotetrazolium reductase, glucose-6-phosphate dehydrogenase, aldrin epoxidation and other reports of the presence of mixed function oxygenases. New experimental data are presented which indicate that some elements of the detoxication/toxication system inM. edulis can be induced by aromatic hydrocarbons derived from crude oil. This includes a brief review of the results of long-term experiments in which mussels were exposed to low concentrations of the water accommodated fraction of North Sea crude oil (7.7–68 µg 1−1) in which general stress responses such as reduced physiological scope for growth, cytotoxic damage to lysosomal integrity and cellular damage are considered as characteristics of the general stress syndrome induced by the toxic action of the xenobiotics. In addition, induction in the blood cells of microsomal NADPH neotetrazolium reductase (associated with mixed function oxygenases) and the NADPH generating enzyme glucose-6-phosphate dehydrogenase are considered to be specific biological responses to the presence of aromatic hydrocarbons. The consequences of this detoxication/toxication system forMytilus edulis are discussed in terms of the formation of toxic electrophilic intermediate metabolites which are highly reactive and can combine with DNA, RNA and proteins with subsequent damage to these cellular constituents. Implications for neoplasms associated with the blood cells are also discussed. Finally, in view of the increased use of mussel species in pollutant monitoring programmes, the induction phenomenon which is associated with microsomal enzymes in the blood cells is considered as a possible tool for the detection of the biological effects of environmental contamination by low concentrations of certain groups of organic xenobiotics.