OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data.

With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).

TOmicsVis: An all-in-one transcriptomic analysis and visualization R package with Shinyapp interface.

Transcriptomic analysis has been widely used in comparative experiments to uncover biological mechanisms in various species. However, a simple tool is still lacking to optimize and integrate the features from multiple R packages. In this study, we developed TOmicsVis (Transcriptomics Visualization) (CRAN: https://cran.r-project.org/package=TOmicsVis, v2.0.0), an R package that provides a comprehensive solution for transcriptomics analysis and visualization. It utilizes 46 R packages to design 40 suitable functions for the streamlined analysis of multigroup transcriptomic projects, which covers six main categories: Sample Statistics, Traits Analysis, Differential Expression, Advanced Analysis, GO and KEGG Enrichment, and Table Operation. TOmicsVis can be performed either locally or online (https://shiny.hiplot.cn/tomicsvis-shiny/), which provides significant convenience for researchers without coding training. These user-friendly visualization functions and built-in analysis capabilities enable researchers to monitor experimental data dynamics promptly and explore transcriptomics data quickly.

The Plant Alkaloid Camptothecin as a Novel Antifouling Compound for Marine Paints: Laboratory Bioassays and Field Trials.

The extensive use of copper and booster biocides in antifouling (AF) paints has raised environmental concerns and the need to develop new AF agents. In the present study, 18 alkaloids derived from terrestrial plants were initially evaluated for AF activity using laboratory bioassays with the bryozoan Bugula neritina and the barnacle Balanus albicostatus. The results showed that 4 of the 18 alkaloids were effective in inhibiting larval settlement of B. neritina, with an EC50 range of 6.18 to 43.11 µM, and 15 of the 18 alkaloids inhibited larval settlement of B. albicostatus, with EC50 values ranging from 1.18 to 67.58 µM. Field trials that incorporated five alkaloids respectively into paints with 20% w/w indicated an in situ AF efficiency of evodiamine, strychnine, camptothecin (CPT), and cepharanthine, with the most potent compound being CPT, which also exhibited stronger AF efficiency than the commercial antifoulants cuprous oxide and zinc pyrithione in the field over a period of 12 months. Further field trials with different CPT concentrations (0.1 to 20% w/w) in the paints suggested a concentration-dependent AF performance in the natural environment, and the effective concentrations to significantly inhibit settlement of biofoulers in the field were ≥ 0.5% w/w (the efficiency of 0.5% w/w lasted for 2 months). Moreover, CPT toxicity against the crustacean Artemia salina, the planktonic microalgae Phaeodactylum tricornutum and Isochrysis galbana, was examined. The results showed that 24 h LC50 of CPT against A. salina was 20.75 µM, and 96 h EC50 (growth inhibition) values of CPT to P. tricornutum and I. galbana were 55.81 and 6.29 µM, respectively, indicating that CPT was comparatively less toxic than several commercial antifoulants previously reported. Our results suggest the novel potential application of CPT as an antifoulant.

Oyster-based national mapping of trace metals pollution in the Chinese coastal waters.

To investigate the distribution and variability of trace metal pollution in the Chinese coastal waters, over 1000 adult oyster individuals were collected from 31 sites along the entire coastline, spanning from temperate to tropical regions (Bohai Sea, Yellow Sea, East China Sea and South China Sea), between August and September 2015. Concentrations of macroelements [sodium (Na), potassium (K), calcium (Ca), magnesium (Mg) and phosphorus (P)] and trace elements [cadmium (Cd), copper (Cu), zinc (Zn), nickel (Ni), lead (Pb), chromium (Cr), silver (Ag), and titanium (Ti)] in these oysters were concurrently measured and analyzed. The results showed high Ti, Zn and Cu bioaccumulation in oysters from Guangdong (South China Sea) and Zhejiang (East China Sea). Oysters at Nanji Island (Wenzhou) and Daya Bay (Huizhou) accumulated significantly high concentrations of Ni and Cr. The elements in these oysters were several times higher than the national food safety limits of China. On the other hand, the present study found that normalization of metals by salinity (Na) and nutrient (P) could reflect more details of metal pollution in the oysters. Biomonitoring of metal pollution could benefit from incorporating the macroelement calibration instead of focusing only on the total metal concentrations. Overall, simultaneous measurement of macroelements and trace metals coupled with non-linear analysis provide a new perspective for revealing the underlying mechanism of trace metal bioavailability and bioaccumulation in marine organisms.

Bioaccessibility and Health Risk Assessment of Cu, Cd, and Zn in "Colored" Oysters.

Bioaccessibility describes the fraction of contaminants released from the food matrix into the digestive tracts of humans, which is beneficial for improving the health risk assessment of contaminants. In this study, the bioaccessibilities of cadmium (Cd), copper (Cu), and zinc (Zn) in two severely contaminated green oyster (Crassostrea angulate) and blue oyster (Crassostrea hongkongensis) populations were investigated. A human health risk assessment of these metals was then performed based on bioaccessibility measurements. Among the three metals, the bioaccessibility was the highest for Cu (42-95%), and Cd and Zn had comparable bioaccessibility (13-58%). There was no major difference in the bioaccessibility between green and blue oysters. A significant correlation between the tissue Cu and Zn concentrations was found in these highly contaminated oysters. A health risk assessment showed that all three metals in both oyster species seriously exceeded the levels recommended by the United States Environmental Protection Agency. Thus, oysters from these locations, and the metals contained therein, presented quite high risks for human consumption, which should be a great cause of concern. A significant relationship was only found between metal bioaccessibility and its tissue concentration instead of between metal bioaccessibility and subcellular distribution. In addition, a significant relationship was only observed between metal health risks and its tissue concentration. The influence of metal bioaccessibilities on the health risks was limited. This may suggest that in the case of the colored oysters examined in this study, metal concentration instead of metal subcellular distribution could be the driving factor of the metal bioaccessibility, and metal concentration, instead of metal bioaccessibility, could be the driving factor of the metal health risks.

Involvement of Antizyme Characterized from the Small Abalone Haliotis diversicolor in Gonadal Development.

The small abalone Haliotis diversicolor is an economically important mollusk that is widely cultivated in Southern China. Gonad precocity may affect the aquaculture of small abalone. Polyamines, which are small cationic molecules essential for cellular proliferation, may affect gonadal development. Ornithine decarboxylase (ODC) and antizyme (AZ) are essential elements of a feedback circuit that regulates cellular polyamines. This paper presents the molecular cloning and characterization of AZ from small abalone. Sequence analysis showed that the cDNA sequence of H. diversicolor AZ (HdiODCAZ) consisted of two overlapping open reading frames (ORFs) and conformed to the +1 frameshift property of the frame. Thin Layer chromatography (TLC) analysis suggested that the expressed protein encoded by +1 ORF2 was the functional AZ that targets ODC to 26S proteasome degradation. The result demonstrated that the expression level of AZ was higher than that of ODC in the ovary of small abalone. In addition, the expression profiles of ODC and AZ at the different development stages of the ovary indicated that these two genes might be involved in the gonadal development of small abalone.

Toxicological responses of the hard clam Meretrix meretrix exposed to excess dissolved iron or challenged by Vibrio parahaemolyticus.

The responses of genes encoding defense components such as ferritin, the lipopolysaccharide-induced tumor necrosis factor-alpha factor (LITAF), the inhibitor of nuclear factor-κB (IκB), metallothionein, and glutathione peroxidase were assessed at the transcriptional level in order to investigate the toxicological and immune mechanism of the hard clam Meretrix meretrix (HCMM) following challenge with iron or a bacterium (Vibrio parahaemolyticus). Fe dissolved in natural seawater led to an increase of Fe content in both the hepatopancreas and gill tissue of HCMM between 4 and 15 days of exposure. The ferritin gene responded both transcriptionally as indicated by real-time quantitative PCR and translationally as shown by western blotting results to iron exposure and both transcriptional and translational ferritin expression in the hepatopancreas had a positive correlation with the concentration of dissolved iron in seawater. Both iron and V. parahaemolyticus exposure triggered immune responses with similar trends in clam tissues. There was a significant post-challenge mRNA expression of LITAF and IκB at 3h, ferritin at 24h, and metallothionein and glutathione peroxidase at 48h. This behavior might be linked to their specific functions in physiological processes. These results suggested that similar signaling pathways were triggered during both iron and V. parahaemolyticus challenges. Here, we indicated that the ferritin of Meretrix meretrix was an intermediate in the pathway of iron homeostasis and in its innate immune defense mechanism.

SARP19 and vdg3 gene families are functionally related during abalone metamorphosis.

The transcriptional activity of the SARP19-I1 and vdg3-I1 genes increases over tenfold when Haliotis diversicolor larvae shift from the pelagic to benthic lifestyle, signifying the important role of these genes during abalone metamorphosis. In this study, eight paralogous SARP19 genes and six paralogous vdg3 genes were identified from H. diversicolor transcriptomes. Phylogenetic analyses were performed, and the spatio-temporal expression patterns of these genes were separately determined by quantitative polymerase chain reaction (qPCR) and whole mount in situ hybridization (WMISH). Five SARP19 paralogs and five vdg3 paralogs showed at least a tenfold increase in expression after settlement. Among these differentially expressed genes, three SARP19 paralogs and four vdg3 paralogs were verified as being spatially expressed in the digestive glands of newly settled postlarvae. We proposed that a hypothesis of coevolution between the two gene families might explain the similarities in their expression patterns and their phylogenetics.

Differential expression profile of membrane proteins in Aplysia pleural­pedal ganglia under the stress of methyl parathion.

This study was aimed to analyze the alteration of membrane protein profiles in Aplysia juliana Quoy & Gaimard (A. juliana) pleural­pedal ganglia under MP exposure. Both the results of GC­MS analysis and the activity assay of acetylcholinesterase (AChE), superoxide dismutase (SOD), catalase (CAT) reveal that MP toxicological effects on Aplysia left and right pleural­pedal ganglia are different under 7 and 14 days of exposure. Therefore, Aplysia were subjected for exposure at two concentrations (1 and 2 mg/l) of MP for 7 and 14 days for membrane proteomic study. As a result, 19 and 14 protein spots were differentially expressed in A. juliana left pleural­pedal ganglia under 7 and 14 days treatment, and 20 and 14 protein spots found with differential expressions in their right ganglia under the same treatment, respectively. Several proteins with expression variations were detected from both the left and right pleural­pedal ganglia; however, most proteins have distinctive expressions, indicating different mechanisms might be involved in initiating MP toxicology in left and right ganglia. Among the total differential protein spots obtained, 29 proteins were classed as membrane proteins. These proteins are mainly involved in the metabolism process, cell redox homeostasis, signal transduction, immunology, intracellular transport and catalysis, indicating MP toxicity in mollusks seems to be complex and diverse. Some differentially expressed proteins were further confirmed by Western blotting and quantitative real-time PCR. These results might provide renovated insights to reveal the mechanism of MP-induced neurotoxicity, and the novel candidate biomarkers might have potential application for environmental evaluation of MP pollution level.

Proteomic approach for identifying gonad differential proteins in the oyster (Crassostrea angulata) following food-chain contamination with HgCl2.

Hg discharged into the environmental waters can generally be bioaccumulated, transformed and transmited by living organisms, thus resulting in the formation of Hg-toxicity food chains. The pathway and toxicology of food chain contaminated with environmental Hg are rarely revealed by proteomics. Here, we showed that differential proteomics had the potential to understand reproduction toxicity mechanism in marine molluscs through the Hg-contaminated food chain. Hg bioaccumulation was found in every link of the HgCl2-Chlorella vulgaris-oyster-mice food chain. Morphological observations identified the lesions in both the oyster gonad and the mice ovary. Differential proteomics was used to study the mechanisms of Hg toxicity in the oyster gonad and to find some biomarkers of Hg contamination in food chain. Using 2-DE and MALDI-TOF/TOF MS, we identified 13 differential protein spots, of which six were up-regulated, six were down-regulated, while one was undecided. A portion of these differential proteins was further confirmed using real-time PCR and western blotting methods. Their major functions involved binding, protein translocation, catalysis, regulation of energy metabolism, reproductive functioning and structural molecular activity. Among these proteins, 14-3-3 protein, GTP binding protein, arginine kinase (AK) and 71kDa heat shock connate protein (HSCP 71) are considered to be suitable biomarkers of environmental Hg contamination. Furthermore, we established the gene correspondence, responding to Hg reproductive toxicity, between mouse and oyster, and then used real-time PCR to analyze mRNA differential expression of the corresponding genes in mice. The results indicated that the mechanism of Hg reproductive toxicity in mouse was similar to that in oyster. We suggest that the proteomics would be further developed in application research of food safety including toxicological mechanism. BIOLOGICAL SIGNIFICANCE: It is well known that mercury (Hg) is one of the best toxic metal elements in nature. The research reports as previously described indicated that multiple mercury compounds can directly contaminate the aquatic animals by flowing of water body and through the diffusion of air. The pollution sources of the mercury compounds in marine water were mainly found from the pathways such as steam power plant and mineral exploitation which are located on the inshore. Of note, after being released into environmental waters, mercury compounds undergo the processes of bioaccumulation, transformation and transmission in living organisms, thus resulting in the multiple forms of Hg found in Hg-toxicity food chains, and among them, methyl mercury (MeHg) showing the high toxic characteristics is the main form of Hg. The abundant reports indicated that the metal salts were easily found within the various organs of the animals, but it is difficult to judge the level of its perniciousness according to its content only in vivo. Here, the algae to have been contaminated by the mercury compounds have the ability for contaminating both the fish and shellfish as food pathway quickly. If these fish and shellfish edible as food will be taken by human, they will further affect the human health badly. However, studies about their perniciousness are rarely reported, especially in using proteomics. The oysters as normal food are largely consumed in Southern China, especially in Xiamen City. Similarly, a pathway question that the contaminated oysters can effect on the human health such as cancer is unclear or poorly understood. Here, we showed that an analytical technology such as differential proteomics has potential to understand toxicity mechanism induced by Hg-contamination through the food pathway. It is for reason that the oyster proteomics including relative analytical methods have been used to reveal the contaminant level and to determine its perniciousness using toxic algae as food. Here, we also indicated that the research here shows great significance for both analysis of food safety and toxicology of the metal compounds. In addition, a few biomarkers have shown their strong potential for monitoring the level of Hg pollution in sea in the manuscript and gene correspondence between mouse and oyster, the two contiguous links of the Hg-contaminated food chain, was further investigated to better illustrate our finding in the analysis of food chain proteomics. Moreover, similar research work is rarely reported compared to the current proteomic development, showing that a lot of novel results by proteomic methods in the manuscript have strong potential for developing the new area of food chain proteomics.

Metabolic energy sensors (AMPK and SIRT1), protein carbonylation and cardiac failure as biomarkers of thermal stress in an intertidal limpet: linking energetic allocation with environmental temperature during aerial emersion.

The effects of heat stress on organisms are manifested at the levels of organ function, metabolic activity, protein stability and gene expression. Here, we examined effects of high temperature on the intertidal limpet Cellana toreuma to determine how the temperatures at which (1) organ failure (cardiac function), (2) irreversible protein damage (carbonylation) and (3) expression of genes encoding proteins involved in molecular chaperoning (hsp70 and hsp90) and metabolic regulation (ampk and sirt1) occur compare with field temperatures, which commonly exceed 30°C and can reach 46°C. Heart failure, indexed by the Arrhenius break temperature, occurred at 34.3°C. Protein carbonylation rose significantly at 38°C. Genes for heat shock proteins HSP70 (hsp70) and HSP90 (hsp90), for two subunits of AMP-activated protein kinase (AMPK) (ampkα and ampkß) and for histone/protein deacetylase SIRT1 (sirt1) all showed increased expression at 30°C. Temperatures of maximal expression differed among genes, as did temperatures at which upregulation ceased. Expression patterns for ampk and sirt1 indicate that heat stress influenced cellular energy homeostasis; above ~30°C, upregulation of ATP-generating pathways is suggested by elevated expression of genes for ampk; an altered balance between reliance on carbohydrate and lipid fuels is indicated by changes in expression of sirt1. These results show that C. toreuma commonly experiences temperatures that induce expression of genes associated with the stress response (hsp70 and hsp90) and regulation of energy metabolism (ampk and sirt1). At high temperatures, there is likely to be a shift away from anabolic processes such as growth to catabolic processes, to provide energy for coping with stress-induced damage, notably to proteins.

Coumarins from the Herb Cnidium monnieri and chemically modified derivatives as antifoulants against Balanus albicostatus and Bugula neritina larvae.

In the search for new environmental friendly antifouling (AF) agents, four coumarins were isolated from the herbal plant Cnidium monnieri, known as osthole (1), imperatorin (2), isopimpinellin (3) and auraptenol (4). Furthermore, five coumarin derivatives, namely 8-epoxypentylcoumarin (5), meranzin hydrate (6), 2'-deoxymetranzin hydrate (7), 8-methylbutenalcoumarin (8), and micromarin-F (9) were synthesized from osthole. Compounds 1, 2, 4, 7 showed high inhibitory activities against larval settlement of Balanus albicostatus with EC(50) values of 4.64, 3.39, 3.38, 4.67 µg mL-1. Compound 8 could significantly inhibit larval settlement of Bugula neritina with an EC(50) value of 3.87 µg mL-1. The impact of functional groups on anti-larval settlement activities suggested that the groups on C-5' and C-2'/C-3' of isoamylene chian could affect the AF activities.

Pyrosequencing of Haliotis diversicolor transcriptomes: insights into early developmental molluscan gene expression.

BACKGROUND: The abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking. METHODOLOGY/PRINCIPAL FINDINGS: In this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the 'lock system' in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae. CONCLUSION: This study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.

[Cadmium bioaccumulation and its toxicity in Babylonia areolata under different nutritional status].

An indoor exposure experiment with juvenile Babylonia areolata was conducted to study its survival, growth, cadmium (Cd) accumulation, metallothionein (MT) induction, and glycogen content as well as the DNA integrity of hepatopancreas tissue. The juveniles were starved or fed with mussel (Perna viridis) or clamworm (Perinereis aibuhitensis), and exposed to 50 microg x L(-1) of Cd2+ for 10 weeks. Prolonged starvation and simultaneous exposure to Cd reduced the survival rate of B. areolata, and its glycogen was mobilized in great extent. Feeding with P. viridis or P. aibuhitensis helped the B. areolata to combat Cd toxicity and lessen mortality. After exposed to Cd, the damage of the DNA integrity of hepatopancreas tissue for the B. areolata fed with P. viridis or P. aibuhitensis could be recovered with time, but not for the starved B. areolata. Prolonged starvation caused tissue atrophy and led to Cd accumulation and MT increase, while feeding with P. viridis or P. aibuhitensis increased the B. areolata mass and lowered the Cd accumulation and MT level because of the tissue dilution effect. The B. areolata fed with P. viridis had better growth and lower Cd content than that fed with P. aibuhitensis. This study indicated that starvation intensified the toxicity of Cd to B. areolata, while prey type had significant effects on the growth rate of the B. areolata and indirectly affected its Cd accumulation, MT induction, and glycogen consumption. It was suggested that when using gastropods such as B. areolata as the indicator species to monitor marine environmental pollution, it would be necessary to consider the effects of habitat ecological data including food richness and prey type. Moreover, in the high-density cultivation of B. areolata in factory, rational feeding and periodic measurement of Cd concentration in seawater should be made.

Stable expression of Y-box protein 1 gene in early development of the abalone Haliotis diversicolor.

Abalone animals are import models for the study of the early development of marine invertebrates. However, systematical evaluations of internal control genes (ICG) have seldomly been performed. In this study, ten candidate genes were cloned and surveyed for their stability throughout the early developmental period of H. diversicolor using qPCR. In a period from fertilized egg to postlarva, three genes, Y-box protein 1 (YB1), ornithine decarboxylase antizyme 1 (OAZ1) and eukaryotic translation initiation factor 5A (EIF5A), were found to be the most stable and could be used as ICGs. It is suggested that using two genes jointly, such as YB1 and OAZ1, could be sufficiently reliable to normalize the temporal dynamics of other genes. Normalized by YB1/OAZ1, some rough features of early development of a small abalone were characterized. This is the first report of the temporal dynamics of metabolic activities and overall mRNA abundance of abalone animals in early stages. It is also the first time the multi-functional gene YB1 has been described as an internal control for early developmental biology studies. Phylogeny and function of YB1 are further discussed.

The impact of Yangtze River discharge, ocean currents and historical events on the biogeographic pattern of Cellana toreuma along the China coast.

AIM: Genetic data were used to measure the phylogeographic distribution of the limpet, Cellana toreuma along the China coast in order to acsertain impacts of historic events, ocean currents and especially freshwater discharge from the Yangtze River on the connectivity of intertidal species with limited larval dispersal capability. METHODOLOGY/PRINCIPAL FINDINGS: Genetic variation in 15 populations of C. toreuma (n = 418), ranging from the Yellow Sea (YS), East China Sea (ECS) and South China Sea (SCS), were determined from partial mitochondrial cytochrome c oxidase subunit I gene. Genetic diversity and divergence based on haplotype frequencies were analyzed using CONTRIB, and AMOVA was used to examine genetic population structure. Historic demographic expansions were evaluated from both neutrality tests and mismatch distribution tests. Among the 30 haplotypes identified, a dominant haplotype No. 1 (H1) existed in all the populations, and a relatively abundant private haplotype (H2) in YS. Pairwise F(ST) values between YS and the other two groups were relatively high and the percentage of variation among groups was 10.9%. CONCLUSIONS: The high nucleotide and gene diversity in the YS, with large pairwise genetic distances and relatively high percentages of variation among groups, suggests that this group was relatively isolated from ECS and SCS. This is likely driven by historic events, ocean currents, and demographic expansion. We propose that freshwater discharge from the Yangtze River, which may act as physical barrier limiting the southward dispersal of larvae from northern populations, is especially important in determining the separation of the YS group from the rest of the Chinese populations of C. toreuma.

Gonad differential proteins revealed with proteomics in oyster (Saccostrea cucullata) using alga as food contaminated with cadmium.

As mercury and lead, cadmium (Cd) is one of the highly toxic metals in both the ocean and land environments, but its toxicological mechanism in organisms including human is still unclear because of the complex toxicological pathways in vivo. Here, the alga Chlorella vulgaris were cultivated at room temperature under the stress of cadmium (1 mg L(-1)) to obtain a toxic food, and then the contaminated food were directly supplied to oyster (Saccostrea cucullata) in seawater. After feeding with C. vulgaris contaminated with Cd (C. vulgaris-Cd), the differential proteins in the oyster gonad (OG) were effectively separated and identified with proteomic approaches. Eleven protein spots were observed to be significantly changed in the OG feeding with C. vulgaris-Cd, which seven spots of these differential proteins were down-regulated while four spots were up-regulated. These altered spots were further excised in gels and identified by a combined technique of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and database searching. A portion of these differential proteins were further proofed by real-time PCR and Western blotting. The results indicate that the major functions of these differential proteins were described as follows: binding, protein translocation, catalysis, regulation of energy metabolism, reproductive function and skeleton structure. These differential proteins in part may effectively provide a few novel biomarkers for the evaluation of Cd pollution level via a food pathway for harming halobios, mammal and human health, and for understanding the complex mechanisms of Cd toxicity in vivo.

Proteomic analysis of dimethoate-responsive proteins in the oyster (Saccostrea cucullata) gonad.

INTRODUCTION: The organophosphorus pesticide dimethoate (DM) has been widely used in agriculture, and its extensive use could still have left many environmental problems. METHODS: In the present study, the oyster (Saccostrea cucullata) was subjected to acute DM toxicity (2 mg/L), and gas chromatographic analysis revealed and quantified residues of DM in the oyster gonad. RESULTS: Two-dimensional gel electrophoresis showed 12 differentially expressed proteins in the DM-exposed oyster gonad in comparison to the control. Among these 12 protein spots, nine were down-regulated, and three were up-regulated. Both matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry and database searching were utilized to identify these differential proteins, and revealed five proteins previously described as being related to DM toxicity. In addition, the levels of mRNA expression corresponding to these differential proteins were further proved in part by real-time PCR. The functions of these proteins were summarized as: carrying out energy metabolism, DNA repair, DNA transcriptional regulation, and oxidative protection. The remaining seven protein spots were of particular interest in terms of their responses to DM, which have seldom been reported. CONCLUSION: These data might point to a number of novel and significant biomarkers for evaluating the contamination levels of DM and provide useful insight into the mechanisms of DM toxicity in vivo.

Mass spectrometric characteristics and kinetics of iron release in visceral mass of Saccostrea cucullata.

Ferritins with electrophoretic homogeneity were prepared from the visceral mass of Saccostrea cucullata in batch. The native PAGE approach showed similar electrophoretic mobility among pig pancreatic ferritin, liver ferritin of Dasyatis akajei, and visceral mass ferritin of Saccostrea cucullata. SDS-PAGE indicated that the Saccostrea cucullata visceral ferritin (SCVF) consisted of a single subunit type and had a molecular weight (MW) of approximately 20 kDa, suggesting that the protein shell in SCVF was composed of a single subunit. In addition, peptide mass fingerprinting and transmission electron microscopy were used to identify SCVF further, and to observe its molecular structure. We found that the molecular structure in SCVF was similar to that of most mammalian ferritins, which are composed of a protein shell and an iron core. The results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry under the assistance of an acidic matrix, sinapic acid, also showed that SCVF was composed of a single subunit type and its subunit MW was calculated to be 19871.042 Da in the absence of heme. Kinetics analysis revealed that the complete process of iron release fitted the law of a first-order reaction, which is similar to that of most ferritins in mammals. Similar to bacterial ferritin, studies indicated that the shell consisted of a single subunit type and showed similar kinetics of iron release, suggesting that this subunit plays two important roles in iron release and storage, and that it shows different stability and intensity of interaction in carrying out its physiological functions in SCVF.

Single subunit type of ferritin from visceral mass of Saccostrea cucullata: cloning, expression and cisplatin-subunit analysis.

Ferritin, the iron storage protein, plays a key role in iron metabolism. Here, we have cloned an inducible ferritin cDNA with 516 bp within the open reading frame fragment from the visceral mass of Saccostrea cucullata. The subunit sequence of the ferritin was predicted to be a polypeptide of 171 amino acids with a molecular weight (MW) of 19.9182 kDa and an isoelectric point of 5.24. The cDNA sequence of S. cucullata ferritin was constructed into a pET-32a expression system for expressing its relative protein efficiently in the Escherichia coli BL21 strain under isopropyl-ß-D-thiogalactoside (IPTG) induction. The recombinant ferritin, which was further purified on a Ni-NTA resin column and digested with enterokinase, was detected as a single subunit of approximately MW 20 kDa using both SDS-PAGE and mass spectrometry. S. cucullata ferritin (ScFer) showed 98% identity with Crassostrea gigas ferritin at the amino acid level. The secondary structure and phosphorylation sites of deduced amino acids were predicted with ExPASy proteomics tools and the NetPhos 2.0 server, respectively, and the subunit space structure of recombinant S. cucullata ferritin (rScFer) was built using the molecular operating environmental software system. The results of both in-gel digestion and identification using MALDI-TOF MS/MS showed that the recombinant protein was ScFer. ICP-MS indicated that rScFer subunit can directly bind to cisplatin[cis-Diaminedichloroplatinum(CDDP)], giving approximately 22.9 CDDP/ferritin subunit for forming a novel complex of CDDP-subunit, which suggests that it constructs a nanometer CDDP core-ferritin for developing a new drug of anti-cancer. The results of both the real-time PCR and Western blotting showed that the expression of ScFer mRNA was up-regulated in the oyster under the stress of Cd(2+). In addition, the expression increment of ScFer mRNA under bacterial challenge indicated that ferritin participated in the immune response of S. cucullata. The recombinant ScFer should prove to be useful for further study of the structure and function of ferritin in S. cucullata.