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.

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 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.

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.

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.

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.

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.

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

Unlabelled: 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.

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.

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.

[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.

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.

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.

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.

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.

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.

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.

Biochemical responses and DNA damage in red sea bream from coastal Fujian Province, China.

Relationships between measures of oxidative stress and adaptive antioxidant defenses were studied in red sea bream (Pagrus major, RSB) caged at eight locations along the Fujian coast, China. Oxidative damage in tissues was investigated by measuring concentrations of protein carbonyl (CP) and reactive oxygen species (ROS), lipid peroxidation (LPO), acetyl cholinesterase activity (AChE), concentration of thiol groups and activities of enzymes associated with antioxidant defense. Magnitudes of antioxidant defense parameters were significantly, positively correlated with oxidative stress.

Effects of cooking and subcellular distribution on the bioaccessibility of trace elements in two marine fish species.

In current human health risk assessment, the maximum acceptable concentrations of contaminants in food are mostly based on the total concentrations. However, the total concentration of contaminants may not always reflect the available amount. Bioaccessibility determination is thus required to improve the risk assessment of contaminants.

Modification and modificatory kinetics of the active center of prawn beta-N-acetyl-D-glucosaminidase.

Beta-N-acetyl-D-glucosaminidase (NAGase, EC3.2.1.

Isolation and characterization of microsatellite loci in Babylonia areolata and cross-species amplification in Babylonia formosae habei.

Nine novel microsatellite primer pairs were presented for Babylonia areolata, representing the first microsatellite markers available for this genus. Levels of polymorphism were variable with 2 to 11 alleles per locus and expected heterozygosities ranging from 0.073 to 0.

A new atisane-type diterpene from the bark of the mangrove plant Excoecaria agallocha.

A new atisane-type diterpene, ent-16alpha-hydroxy-atisane-3,4-lactone (4) and three known diterpenes, ent-16alpha-hydroxy-atisane-3-one (1), ent-atisane-3beta,16alpha-diol (2), ent-3,4-seco-16alpha-hydroxyatis- 4(19)-en -3-oic acid (3) were isolated from the bark of the mangrove plant Excoecaria agallocha. Their structures and relative stereochemistry were elucidated by means of extensive NMR and MS analysis. Compound 3 exhibited significant anti-microfouling activity against the adherence of Pseudomonas pseudoalcaligenes, with an EC(50) value of 0.