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Yesso scallop Patinopecten yessoensis is an economically and ecologically important cold-water bivalve molluscs. Elucidating the molecular mechanism regulating its early larval development holds great significance in aquaculture. This study performed comparative transcriptomic analysis across nine developmental stages from fertilized eggs to spats. A variety of differentially expressed genes (DEGs) were identified to be potentially involved in larval development, including cell proliferation (cyclins, CDKs, BMPs, TGF-β), immunity (TLR7, CTLs, cathepsins, SOD, GSTs), larval settlement and metamorphosis (MHC, MELC, paramyosin, DβH, GABA receptor), shell formation (iMSP5, MSP1, CHS1, CHI3, CAM, CAML5) as well as energy metabolism (glycolysis, TCA cycle and oxidative phosphorylation components). Additionally, weighted gene co-expression network analysis (WGCNA) identified the key indianred4 module, which may play vital roles in body axis formation, neurogenesis and myogenesis in scallop larvae. An integrative framework was established delineating molecular drivers of embryogenesis, larval growth, immune defense, metamorphosis, shell production and bioenergetics throughout larval development in scallops. These findings will help understand the molecular strategies governing larval developmental process, yielding great insights to inform ecological conservation and aquaculture practices.

To understand the seasonal variations in shellfish community structure, the composition and diversity of shellfish in the intertidal zone of the Changshan Archipelago, China, were investigated. We investigated the composition and diversity of shellfish species in the intertidal zone (including NCD1, NCD2, BCD1, BCD2, TJD1, TJD2, DQD1, DQD2, NHD1, and NHD2) of five representative islands and 10 survey stations in the Changshan Archipelago during the low tide period in July and October 2021 and February and May 2022, and the water quality parameters of point water and interstitial water were analyzed. The results showed that the bottom material of the Changshan Archipelago was generally rock or gravel and the salinity fluctuated with the seasons. The salinity was high in summer and fall while low in spring and winter, with an average of 30.92±0.84. Compared with spring, summer, and fall, the temperature changed significantly in winter, with an average of (4.51±0.32) ℃ and the highest temperature being 23.48 ℃ during spring, summer, and fall. In general, the dissolved oxygen in the main islands of Changshan Archipelago (North and South Changshan Islands) was relatively low, with an average of (8.59±0.38) mg/L, while that in Tuoji Island, Daqin Island, and Nanhuangcheng Island was relatively high, with an average of (9.95±0.51) mg/L. A total of 12 species of shellfish were collected in this survey, including Crassostrea sp., Monodonta labio Linnaeus, Littorina brevicula, Mytilus galloprovincialis, Patelloida pygmaea, Chlorostoma rustica, Reishia clavigera, Thais luteostoma, Ocinebrellus inornata, Cellana toreuma, Ruditapes philippinarum, and Rapana venosa. The number of shellfish species in each season was the highest in spring, with an average of eight species, followed by in fall, with an average of six species. Winter had the least number of shellfish species collected, with an average of four species. In addition, the North and South Changshan Islands presented the most shellfish species at eight and nine species, respectively. The number of shellfish collected in DQD was the least (six species). There were differences in shellfish density at different survey sites, among which DQD2 had the highest density, with an average density of 41.26 ind./m2. The lowest density was in NCD2, and the average density was 13.71 ind./m2. In the same season, the shellfish density at different survey sites was different, the proportion of dominant species at different survey sites was also different. In spring, the density of Crassostrea sp., Cellana toreuma, and Chlorostoma rustica was high, while in summer, the density of Crassostrea sp., Mytilus galloprovincialis, Littorina brevicula, and Cellana toreuma was high. In fall, the density of Crassostrea sp., Littorina brevicula, and Mytilus galloprovincialis was the highest, while in winter, the density of Crassostrea sp., Patelloida pygmaea, and Cellana toreuma was the highest. The species diversity (H´) of shellfish in each tidal area of the survey site is shown as middle tidal zone (1.44) > low tidal zone (1.40) > high tidal zone (0.44). Overall, the average shellfish species diversity in the 10 survey sites was spring (1.26) > winter (1.21) > fall (1.11) > summer (0.95). The average evenness index of species (J´) in the 10 survey stations was 0.55, among which the evenness index of DQD2, NCD2, NHD2, and TJD1 shellfish was 0.67, 0.64, 0.64, and 0.55, respectively. The evenness index of shellfish in each tidal area of the survey site was in order of middle tidal zone (0.67) > low tidal zone (0.59) > high tidal zone (0.29). The seasonal change was not obvious. The average shellfish abundance at the survey site was 0.533, including 0.82, 0.68, 0.60, and 0.53 shellfish abundance at NCD2, NHD2, BCD2, and NCD1, respectively. The abundance index of shellfish in each tidal area of the survey site was in order of middle tidal zone (0.56) > low tidal zone (0.52) > high tidal zone (0.17). Overall, the average shellfish abundance in the 10 survey sites was spring (0.681) > fall (0.573) > summer (0.458) > winter (0.418). Seasons (temperatures) have the most obvious impact on the diversity and abundance of intertidal shellfish resources. Anthropogenic activities, such as aquaculture and tourism, also affect the distribution and quantity of shellfish species. The results of this study not only enrich the data of intertidal shellfish resources on islands in China but also provide basic information and reference for biodiversity and environmental protection of intertidal shellfish on the Changshan Islands.

Glycogen, a highly branched polysaccharide of essential energy and carbon resource, is an important flavor quality trait of oysters, and its content is closely linked to the reproductive cycle of these mollusks. However, there is a significant lack of research on the regulatory mechanisms governing glycogen in oysters. Here, we investigated the variations in glycogen levels during the reproductive cycle of Jinjiang oyster Crassostrea (Magallana) ariakensis. It revealed that glycogen content was highest during the formative stage and lowest during the mature stage in gonadal tissues. Subsequently, transcriptome and metabolome analyses were conducted, revealing 3016 differentially expressed genes (DEGs) and 162 differentially accumulated metabolites (DAMs). Comprehensive analysis indicated that glycogenesis, glycogenolysis, glycolysis, and tricarboxylic acid (TCA) cycle played crucial roles in energy supply during the formative stage. Gluconeogenesis was more important during the mature stage as it facilitated glycogen storage for reproduction preparation. These findings provide valuable insights into the mechanisms underlying gonad development-related glycogen metabolism and offer a theoretical foundation for enhancing oyster flavor.

Shell morphological traits are important quantitative traits in shellfish. Shell morphology is usually affected by many factors, such as the ecological environment and shellfish genetics. It is considered the results of comprehensive actions of natural selection, micro-evolution, and heredity. Measuring shell morphological traits aids our understanding of the current situation of germplasm resources among shellfish species or intraspecific populations and also provides important breeding traits for shellfish breeding programs. For most shellfish, quality traits (eg. live weight and soft body weight) are considered the important breeding traits, but there are practical issues in using these traits, such as the inability or difficulty in measuring them in vivo. It is well known that shellfish quality traits are closely related to shell morphological traits. However, a simple correlation analysis between quality and morphological traits cannot adequately explain all the intrinsic links between these traits. In this study, Manila clams (Ruditapes philippinarum) were collected from nine geographical locations along the north and south coasts of China. The shell morphology and quality characteristics were measured and analyzed for the nine different populations of clams. Furthermore, the main factors affecting the quality traits were analyzed using cluster analysis to reveal the genetic relationships among the populations. The optimal regression equations were constructed using the morphological traits with the soft weights of these populations. For all populations, shell length, shell height, shell width, and shell thickness were measured using a vernier caliper (with an accuracy of 0.01 mm) and a thickness gauge. After wiping the surface of clams with filter paper, their live weight was measured on an electronic balance (with an accuracy of 0.01 g). A scalpel was used to sample the soft body from the clams. After drying, soft body weights were calculated using the difference between live weight and shell weight. The morphological data, including mean values, standard deviation, and coefficient of variation, were calculated using SPSS 26.0. To eliminate the effects of size differences among individuals, two morphological scale parameters (shell width/shell length and shell height/shell length) were calculated to reflect the morphological characteristics of the clams. In addition, stepwise linear regression analyses were performed to obtain the correlation coefficients, direct path coefficients, correlation indexes, indirect path coefficients, and determine the coefficients using SPSS26.0 software. The correlation coefficient and multiple regression analyses of the traits were evaluated. The multiple regression equations were established for all populations. Cluster analysis was used to assess each trait using the calibrations (to calculate the ratio of each trait to shell length). The heatmap displayed the shortest distance method for the Euclidean distance between the different populations. There were significant differences in the effects of shell length, shell height, shell width, and shell thickness on live weight and soft body weight of clams. Morphological traits were significantly correlated with body weight and soft weight (P < 0.05), except for shell thickness. The results of determination coefficient revealed shell width had the greatest impact on live weights of the Putian, Jinzhou, and Chaozhou populations, with determination coefficients of 0.277, 0.232, and 0.307, respectively. The determination coefficients of soft body weights indicated that shell width played very important roles in determining soft body weights of the Putian and Chaozhou populations, with determination coefficients of 0.249 and 0.443, respectively. By calculating the total of determination coefficients, the results are consistent with the correlation index R2 for each trait. For the total determinant effects, the sum of determination coefficients for the morphological traits with soft body weights were greater than 0.850 in most populations. In contrast, the sum of determination coefficients for the morphological traits with soft body weights were less than 0.850 in Laizhou, Zhuanghe, Donggang, and Jinzhou. Based on the path analysis and the determination coefficient analysis, shell width had the greatest impact on live weights and soft body weights in most populations. The maximum values of the two morphological proportion parameters (shell width/shell length and shell height/shell length) were found in the Laizhou population (0.49 and 0.74), while the minimum proportion parameters were detected in the Dalian Donggang population (0.42 and 0.67). Among the shell morphological traits, shell thickness had the largest coefficient of variation (22.74), while shell height had the smallest coefficient of variation (9.47). By testing for statistically significant variation in the partial regression coefficient, the optimal regression equations of the morphological traits for soft body weight were constructed for all the populations. The cluster analysis revealed that different clam populations did not have a typically regional characteristic in terms of the shell morphological traits. There was an irregular north-south alternating clustering phenomenon. According to the present findings, shell thickness and morphological ratio parameters (ratio of shell height to shell length and ratio of shell width to shell length) are important indicators for evaluating the growth potential and nutritional status of clams in aquaculture. The present results provide a scientific basis for morphological discrimination and germplasm resource evaluation for geographical populations of clams and also aid breeding strategies to predict breeding traits for aquaculture breeding programs, including guidance for the selective breeding of clams.

The manila clam Ruditapes philippinarum has become an important bivalve species in worldwide aquaculture due to its delicious taste and high commercial value. With the rapid expansion of clam farming, there is an urgent need to obtain genetic improvement by selective breeding, such as family-based selection of improved varieties. In this study, 10 microsatellite loci were selected to establish four multiplex PCR groups using four different fluorescences (FAM, ROX, HEX, TAM). The accuracy of these loci was verified by the 100% success rate of parentage assignment in a full-sib family. Parentage assignment was carried out in the mixed-mating parents and their offspring with unknown pedigree information. The genotyping of ten microsatellite loci generated 90 alleles, having the observed heterozygosity (Ho) ranging from 0.333 to 0.729. The expected heterozygosity (He) varied from 0.358 to 0.794. The PIC ranged from 0.342 to 0.763, with a mean value of 0.620. The theoretical combined parentage exclusion (cEP) power for all ten microsatellites was 97% with known genotypes of one parent (P1) and 99% for given the genotypes of both parents (P2). The actual successful assignment rate reached 98% by using all four sets of multiplex microsatellites, serving as the effective method for parentage assignment in the clams. The development and application of multiplex microsatellite genotyping methods provide a cost-effective method for pedigree reconstruction, population genetics and selective breeding of the commercially important clams.

Abstract Background Ovarian development is an important prerequisite and basis for animal reproduction. In many vertebrates, it is regulated by multiple genes and influenced by sex steroid hormones and environmental factors. However, relative information is limited in shellfish. To explore the biological functions and molecular mechanisms of mRNA and non-coding RNA that regulate ovarian development in Scapharca broughtonii, we performed whole transcriptome sequencing analysis on ovaries at three developmental stages. Furthermore, the biological processes involved in the differential expression of mRNA and ncRNA were analyzed. Results A total of 11,342 mRNAs, 6897 lncRNAs, 135 circRNAs, and 275 miRNAs were differentially expressed. By mapping the differentially expressed RNAs from the three developmental stages of Venn diagram, multiple groups of shared mRNAs and lncRNAs were found to be associated with ovarian development, with some mRNA and ncRNA functions associated with steroid hormone. In addition, we constructed and visualized the lncRNA/circRNA-miRNA-mRNA network based on ceRNA targeting relationships. Conclusions These findings may facilitate our further understanding the mRNA and ncRNAs roles in the regulation of shellfish reproduction.

Dissolved oxygen (DO) is one of essential factor for the survival of aquatic organisms, affecting many physiological processes including growth, survival, reproduction and development. Due to the change of global environment and the influence of human activities, hypoxia often occurs in both natural and cultured water bodies. Studies showed that water is in a hypoxic state when DO is lower than 2 mg/L, and aquatic animals in this condition may often suffer from hypoxic stress. The blood clam Scapharca broughtonii is an important economic bivalve because of its delicious taste and rich protein, vitamins and hemoglobin. At present, the S. broughtonii has become an important species in Northern China, and the better economic benefit of breeding drives the rapid development of seedling production and culture. However, hypoxia often threatens the cultivation of S. broughtonii. Hypoxic preconditioning refers to the endogenous protective mechanism generated after the body is stimulated by multiple transient and non-fatal hypoxic stimuli, which can protect the body tissues and improve the tolerance of the body. To explore the effects of hypoxic preconditioning on the physiological and biochemical characteristics of S. broughtonii under hypoxia stress, the clams were divided into three groups containing H2 (hypoxic preconditioning for two times), H4 (hypoxic preconditioning for four times) and C (no hypoxic preconditioning, as control group). And then, we analyzed the feeding rate (IR), energy metabolism and three enzymes activity of three groups during the process of hypoxia stress for 48 hours with DO concentration of ~2.0 mg/L. The first item we explored was changes in feeding rates. During hypoxia stress, the IR of the three groups showed a tendency of decreasing first and then increasing. At the late stage of stress, the feeding rate of the three groups recovered to some extent, and the recovery degree of groups H4 and H2 were better than that of group C. The energy metabolism we studied contains the oxygen consumption rate (OR) and the ammonia excretion rate (NR). The results showed that the OR of the three groups increased gradually under hypoxia stress and reached the maximum value at 48 h after treatment. The OR of group C, H2 and H4 increased by 1.15, 1.08 and 0.73 times, respectively, after 48 hours of treatment. The trends in NR were that the NR in group C gradually increased during treatment, while that in group H reduced first followed by increasing and then decreased. The NR of group C, H2 and H4 showed different trends during the stress period which were 1.67, 1.30 and 0.97 times of 0 h at 48 h, respectively. And the ratio of oxygen to nitrogen in group C was relatively stable, while that in group H was relatively wide. The following are the experimental results of enzyme activity changes, which include cytochrome c oxidase (COX), lactate dehydrogenase (LDH) and glutathione (GSH). The COX of the three groups decreased gradually with the extension of hypoxia stress time. LDH activity and GSH enzyme content all showed an upward tendency. Compared with the control group C, the enzyme activity of the pre-hypoxic group H2 and H4 were relatively stable during the hypoxic stress. In total, the results showed that S. broughtonii pretreated with hypoxia had higher feeding rate, lower oxygen consumption rate and relatively stable enzyme activity compared with the control group, which revealed hypoxia pretreatment could improve its ability of hypoxia tolerance. It showed that hypoxia preconditioning had a more positive effect on the hypoxia tolerance of S. broughtonii. In this study, the effects of hypoxic preconditioning on physiological and biochemical of S. broughtonii under hypoxia stress including feeding rate, respiratory metabolism and enzyme activity were studied for the first time. It was found that hypoxic training could effectively improve the body's response to hypoxic stress, enriching the research data related to hypoxic adaptation, and providing data for exploring the stress adaptation mechanism of S. broughtonii.

Mitochondrial genomes are playing an increasingly important role in molluscan taxonomy, germplasm, and evolution studies. The first complete mitochondrial genome of the commercial big brown mactra clam, Mactra grandis, was characterized using Illumina next-generation sequencing in this study. The 17,289 bp circular genome has a typical gene organization of 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, with an obvious (A + T)-bias of 64.54%. All PCGs exhibited a homogeneous bias in nucleotide composition with a (A + T)-bias, a positive GC skew, and a negative AT skew. Results of phylogenetic analysis showed that Mactra grandis was most closely related to Mactra cygnus. The functional gene arrangement of the two species was identical but different from other Mactra species. The congeneric relationships among Mactra species were demonstrated by genetic distance analysis. Additionally, the selective pressure analysis suggested that cox1 was highly efficient for discriminating closely related species in genus Mactra, while nad2 was the most appropriate marker for population genetic analysis.

With the continuous improvement of living standards and expansion of oyster consumer groups, people are pursuing high-quality oysters, especially with fresh and sweet taste traits. At present, almost all varieties of oysters with different flavors entering the upscale oyster market in China are imported, and their prices are high. Before 2019, among the new oyster varieties approved in China, the dominant traits of most varieties were reflected in growth, shell color, etc. The oyster farming industry has also primarily focused on quantity but not quality, and the contradiction between scale and quality has become increasingly prominent. It can be predicted that with the development of the shellfish industry, the market demand for high shellfish quality will be more and diversified. In addition to pursing traditional traits such as growth rate, the demand for high-quality oysters, such as those with high glycogen, will be more urgent. Glycogen directly affects oysters´ flavor and nutritional quality and is often used as an important criterion to evaluate oyster quality. The efficient, rapid, and high-throughput method for determining glycogen content can provide technical support for cultivating new shellfish species with a high glycogen content. At present, the detection methods for glycogen content are mainly traditional chemical detection techniques and kits. Although these methods have been well developed, they are time-consuming and costly, producing a significant amount of chemical waste liquid. Therefore, they are not suitable for rapid and batch determination of glycogen content in large quantities. As a common modern, fast, and efficient analysis technology, near-infrared (NIR) technology can record the frequency doubling and frequency absorption of the main hydrogen-containing groups using an NIR spectrometer. NIR technology can determine large quantities of samples and has the advantages of being fast and efficient, time-saving, and labor-saving, with no chemical waste liquid generation in the experimental process, offering green environmental protection. After testing by NIR technology, the chemical properties of the samples do not change and do not require significant sample amounts, which can be used for subsequent recycling. The NIR scanning samples used in this experiment can be quickly recovered and stored in a refrigerator after obtaining spectral data through a short period of NIR scanning without affecting the use of subsequent samples. In general, the NIR technique has many advantages in determining glycogen content, and are applicable for improving oyster quality traits. This method has many advantages, such as a wide application range, and is fast, efficient, convenient, and accurate; it has been widely applied in aquatic science research. This is especially true in quality element detection research. NIR quantitative models of water, fat, glycogen, total protein, amino acid, taurine, zinc, selenium, and calcium in Crassostrea glomerata, C. angulate, Saccostrea glomerata, and C. virginica were established, with demonstrably high accuracy. Among them, NIR analysis technology has been successfully applied to breeding a new Crassostrea gigas species "Lu Yi 1, " significantly improving oyster breeding efficiency. Therefore, NIR assays can effectively overcome problems of chemical detection methods, which are time-consuming, laborious, and expensive; this is highly significant for breeding oysters with high-quality traits. The NIR spectroscopy model can be used to quickly and accurately predict glycogen content. Using C. ariakensis as the research object, the glycogen content of 909 samples in seven tissues including mantle, gill, adductor muscle, hepatopancreas, labial palps, gonad, and most soft oyster parts were determined by the micro-reaction system and method of oyster glycogen content. The corresponding spectral data were obtained using a Fourier NIR spectrometer. The spectral data and glycogen content data were analyzed and processed using TQ Analyst software, and NIR quantitative models of six tissues and all the soft parts of oysters near the Jiang River were established, and 1/9 samples of the total sample size were randomly selected for external validation and cross-validation of the models. The results showed that the measured glycogen content ranged from 7.11 to 602.20 mg/g, which had a wide range and was suitable to establish the model. This study aimed to establish a NIR model for the freeze-dried tissues of C. ariakensis to realize the rapid and accurate detection of glycogen content. This study obtained the glycogen content and spectral data of 909 samples using the micro-reaction system method and NIR technology. Combined with the least-squares method, the glycogen content prediction model of six tissues and the whole soft body of C. ariakensis was established and verified. Results also show that the model is optimal after the first derivative, multiplication scattering, and smoothing pretreatment of the measured spectral data. The modeling correlation coefficients (RC) of the seven models ranged from 0.971 6 to 0.996 3, indicating that the predicted values of the seven models were highly correlated with the actual chemical values. The correlation coefficients of external validation (REV) and cross-validation (RCV) were between 0.949 0~ 0.990 8 and 0.969 4~0.996 9, respectively, indicating that the established model could accurately predict the glycogen content of the corresponding tissue samples of C. ariakensis. This method rapidly and accurately determines the glycogen content of oysters and has application value in the field of improvement of oyster characteristics and quality.

Temperature is an important environmental factor affecting metabolism, growth and life activities of marine bivalves. To reveal the molecular and metabolic responses to heat stress, comparative transcriptomics and metabolomics were performed in the commercially important bivalve, Manila clam Ruditapes philippinarum. Comparative transcriptomics revealed a total of 3980 differential genes (DEGs) mainly involved in energy metabolism, protein processing, glycerolphospholipid metabolism, inoxidizability and anti-apoptosis. Comparative metabolomic analysis identified 293 differential metabolites (DEMs) in the heat-stressed clams, including Acetyl-CoA, Beta-D-Glucose, phosphatidylcholine and free amino acids. For the heat-stress clams, they showed the significantly increased enzyme activities of AKP and ACP, as well as antioxidant-related enzyme activities (SOD and CAT) and oxidative damage substance (MDA). The changes in gene expression of glycolysis-related genes (GLUT1, GLK, HK1 and GPI6) and metabolites (Beta-D-Glucose and Acetyl-CoA) reflect the adjusted energy metabolism in the heat-stressed clams. The protein processing in endoplasmic reticulum may play the important roles in the stability of cell membrane structure during heat adaptation. The increased contents of glycerophospholipid (PC) may be essential to maintain the stability and permeability of cell membrane in the heat-stressed clams. Molecular chaperones (HSP70 and HSP90) may participate in the degradation of misfolded proteins to maintain cell homeostasis during the heat stress. To defense the heat stress, clams also initiate the protection and defense mechanisms by activating antioxidant system, innate immune system and anti-apoptotic system. These findings will shed new lights on molecular and metabolic adaptation to heat stress in the intertidal mollusks in a warming climate at the global scale.

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from −0.9643 to 1.0000. The global Fst value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy–Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean FST of the total population was 0.4534). Pairwise FST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.

Aminotransferases are enzymes found in living organisms that catalyze transfer reactions between amino acids and keto acids, crucial for amino acid metabolism and synthesis. Aminotransferase classes I and II play a vital role in regulating osmolarity, protecting cells, and improving metabolic homeostasis and cellular fitness. To investigate the characteristics of the aminotransferase class I and II gene family and their roles in osmotic pressure regulation in the Jinjiang oyster (Crassostrea ariakensis), the gene structure, chromosomal localization, and phylogeny were characterized and the genes’ expression in the gill under high-salt stress was analyzed. In this study, eighteen Aminotransferase class I and II genes, including SPTLCa and SPTLCb, SPTa and SPTb, ALAT2a and ALAT2b, KAT3a and KAT3b, and ASTa, ASTb and ASTc, were identified. The physicochemical properties of 11 family members were stable, with their instability factors less than 40. Subcellular localization prediction showed that aminotransferase classes I and II were localized in the cytoplasm or mitochondria. Chromosomal localization results showed that the 18 aminotransferase class I and II genes were located on eight chromosomes. All members of this gene family had the Aminotran_1_2 structural domain which is associated with osmotic pressure regulation by adjusting the conversion reaction between amino acids and keto acids. Most gene expressions showed an initial increase followed by a decrease from 0 h to 12 h when the oysters were challenged by acute stress using artificial seawater with a salinity of 40. However, the expression of CarAGT2 and CarKAT3b genes showed an increased trend with increasing stress time. This study systematically investigated the bioinformatics characteristics of the aminotransferase class I and II gene family in C. ariakensis and their role in osmotic pressure regulation, which provides scientific data for understanding the potential functions of these genes in physiological adaptation, thereby expanding the research on osmoregulation in bivalves.

Marking technology is essential to evaluate the growth performance of shellfish species in aquaculture. Some fluorochromes have been widely used in shellfish growth studies, but their marking quality remains unresolved. In order to establish an effective marking technology in bivalves, three fluorochromes are used to evaluate the suitability of in situ growth markers in spats of commercially important bivalve, Manila clam Ruditapes philippinarum. Three different concentrations of calcein (CAL; 25 mg/L, 50 mg/L and 100 mg/L), alizarin red S (ARS; 5 mg/L, 10 mg/L and 20 mg/L) and oxytetracycline hydrochloride (OTC; 250 mg/L, 500 mg/L and 750 mg/L) were used to examine their potential effects on marker quality, growth and survival of spats. In general, marking quality scores for the three fluorochromes have a positive correlation with their increased concentrations. CAL (50–100 mg/L) and ARS (10–20 mg/L) have produced healthy spats with a bright and clear fluorescent shell mark after the recovery culture for 69 days. In contrast, OTC appears to have the weak staining signals at all concentrations. The growth and survival rates affected by fluorochrome immersion are negligible at all concentrations. The present findings indicate that in situ CAL and ARS marking of spats with moderate concentrations are non-invasive and effective method for growth studies in clams. The suitability of CAL and ARS as in situ growth markers in clams will provide new marking techniques to distinguish cohorts or families in aquaculture.

Salinity is an important environmental factor affecting the growth and survival of marine organisms. Marine shellfish possess the efficient osmoregulatory mechanism to cope with either hypo- or hyperosmotic stress. However, little is known about the molecular and metabolic adaptation involved in the osmotic regulation of these intertidal habitants. The Manila clam Ruditapes philippinarum is a worldwide cultured intertidal shellfish, which usually encounters a great risk of salinity stress in its coastal habitats. In the present study, the integrated analysis of transcriptomics and metabolomics was performed to investigate the transcriptional and metabolic profiles of the clams in response to abrupt salinity decrease. The comparative transcriptome analysis uncovers the changes of genes involved in ion channel activation, amino acid metabolism, and energy metabolism in the salinity-stressed condition. The metabolomics analysis reveals that the glucose-succinate pathway may play a critical role in energy metabolism during the osmotic stress. The multi-omics analysis reveals that neural adaptation to salinity stress may be potentially regulated by arachidonic acid metabolism and glutathione metabolism. The important metabolites (12-HPETE, PGEs, and spermine) may be served as the signaling molecules in response to acute salinity stress in the intertidal shellfish. These findings suggest that clams may get through the osmotic stress by ion channel activation, neural adaptation, and anaerobic metabolism to maintain their energy homeostasis for maximum survival. The present study provides great insights into the molecular and metabolic strategies of intertidal shellfish in response to salinity stress, and uncovers the new potential signaling metabolites to assess the health states of molluscs in aquaculture.

The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.

Salinity can affect the physiological and productive characteristics of bivalves. The razor clam Sinonovacula constricta naturally distributing in intertidal zones and estuarine waters is extensively cultured in China. High-salinity is a serious threat to its culture, especially in pond culture model. Here, we investigated the effects of high-salinity on the survival, gill tissue, enzyme activity and free amino acid content of S. constricta. Individuals were randomly divided into six groups treated with different salinities of 20, 25, 30, 35, 40, and 45 ppt. The median lethal salinity calculated by linear regression and probit analysis methods were similar, with 46.61, 43.17, 36.99, 35.99, and 34.99 ppt by linear regression, while 44.63, 42.87, 38.45, 37.32, and 36.17 ppt by probit analysis at 72, 96, 120, 144, and 168 h, respectively. Furthermore, paraffin section revealed that the gill of razor clam shrunk quickly under high-salinity and dissolved at 48 h under salinity of 40 ppt, but not under 30 ppt. In addition, the activities of three enzymes including Na+-K+-ATPase, acid phosphatase and alkaline phosphatase changed significantly under high-salinity. Besides, the contents of total free amino acids (TFAAs) in the gill tissues were 61.25 ± 1.58, 89.36 ± 4.18, and 111.98 ± 1.46 mg⋅g–1 at salinity of 20, 30, and 40 ppt, respectively, indicating increasing TFAA contents with salinity. Notably, several amino acid species including taurine, alanine, proline, glycine and glutamic showed significantly changed contents in response to salinity variation, suggesting these amino acids might play an important role in razor clam’s adaptation to salinity stress. Combining all these results, it was referred that razor clams may adapt to moderately high-salinity of 30 ppt in a short time through osmotic adjustment. Although a small proportion of individuals could survive under the salinity of 35 ppt, the death of most individuals still suggested it can hardly be accepted in aquacultural production. Notably, living under a salinity of 40 ppt for more than 48 h could cause great damage to razor clams. Therefore, the seawater salinity is recommended to be lower than 30 ppt for S. constricta aquaculture. Overall, this study provides guidance for the culture and breeding of high-salinity tolerant razor clams.

Glycogen, a stored form of glucose, is an important form of energy for aquatic shellfish, contributing to the flavor and quality of the oyster. The glycogen synthase (GYS) and glycogen synthase kinase 3β (GSK3β) are two major enzymes in the glycogenesis. However, the information of the two genes in the Jinjiang oyster Crassostrea ariakensis remains limited. In this study, we identified the genes of GYS and GSK3β and further explored their function in the glycogen synthesis of C. ariakensis. The GYS and GSK3β were distributed in all tested tissues, and high expression of GYS and glycogen content were detected in the gonad, labial palp, hepatopancreas, and mantle, while the high expression of GSK3β was observed in the gill and adductor muscle. The expression of GYS was positively correlated with the glycogen content, while GSK3β was negatively correlated. Additionally, knockdown of GSK3β using RNAi decreased the GYS expression, revealing the negative regulatory effect of GSK3β on GYS. These findings enrich the research data of GSK3β and GYS involved in glycogen synthesis, providing valuable information for further research on the function of GSK3β and GYS in the glycogen synthesis process of oyster.

The Chinese razor clam (Sinonovacula constricta) is an important for Chinese aquaculture marine bivalve that naturally occurs across intertidal and estuarine areas subjected to significant changes in salinity level. However, the information on the molecular mechanisms related to high salinity stress in the species remain limited. In this study, nine gill samples of S. constricta treated with 20, 30, and 40 ppt salinity for 24 h were used for whole-transcriptome RNA sequencing, and a regulatory network of competing endogenous RNAs (ceRNAs) was constructed to better understand the mechanisms responsible for adaptation of the species to high salinity. A total of 83,262 lncRNAs, 52,422 mRNAs, 2890 circRNAs, and 498 miRNAs were identified, and 4175 of them displayed differential expression pattern among the three groups examined. The KEGG analyses of differentially expressed RNAs evidenced that amino acid synthesis and membrane transport were the dominant factors involved in the adaptation of the Chinese razor clam to acute salinity increase, while lipid metabolism and signaling played only a supporting role. In addition, lncRNA/circRNA-miRNA-mRNA regulatory networks (ceRNA network) showed clearly regulatory relationships among different RNAs. Moreover, the expression of four candidate genes, including tyrosine aminotransferase (TAT), hyaluronidase 4 (HYAL4), cysteine sulfinic acid decarboxylase (CSAD), and ∆1-pyrroline-5-carboxylate synthase (P5CS) at different challenge time were detected by qRT-PCR. The expression trend of TAT and HYAL4 was consistent with that of the ceRNA network, supporting the reliability of established network. The expression of TAT, CSAD, and P5CS were upregulated in response to increased salinity. This might be associated with increased amino acid synthesis rate, which seems to play an essential role in adaptation of the species to high salinity stress. In contrast, the expression level of HYAL4 gene decreased in response to elevated salinity level, which is associated with reduction Hyaluronan hydrolysis to help maintain water in the cell. Our findings provide a very rich reference for understanding the important role of ncRNAs in the salinity adaptation of shellfish. Moreover, the acquired information may be useful for optimization of the artificial breeding of the Chinese razor clam under aquaculture conditions.

A tropical cyclone (TC) usually induces strong sea-surface cooling due to vertical mixing. In turn, surface cooling influences the intensities and tracks of TCs. Therefore, the relationship between sea-surface temperature (SST) and TC is one of the important components of air-sea interaction. Sea-surface cooling associated with three TCs (Bailu, Lingling, and Mitag) was investigated based on wave-glider observations, satellite altimetry, and Massachusetts Institute of Technology General Circulation Model (MITgcm) numerical experiments from August 3rd to October 10th, 2019. Surface cooling varied among the three TCs. TC Lingling had the nearest distance to the wave-glider position, the slowest translation speed, and the strongest intensity of three TCs, but extreme cooling (1.4) occurred during TC Bailu. Although MITgcm underestimated the extreme cooling, the SST trend driven by the net heat flux, advection, and vertical mixing within the mixed layer was greater during TC Bailu than during other TCs. Advection was the largest of the three heat balance terms during TC Bailu, while it was quite small during the other two TCs. Interestingly, the extreme cooling occurred at the position of preexisting warm eddy. Based on heat balance analysis, we found that the eddy-induced heat advection transport reached −0.4/day, contributing 60% of the heat balance; this was attributed to extreme cooling via eddy disturbance. We suggest TC Bailu leads to the decrease in SST and increase in the area of the cold eddy, and then, the cooled-enlarged eddy is advected to the neighbored position of wave glider, which observes the extreme cooling. These findings provide the utilization of wave gliders and help improve air-sea coupled models during TCs.

Abstract Background The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. Results In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1, which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway. Conclusions The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis. Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function.

The wave glider is an ocean-wave-propelled autonomous marine vehicle with unique dual-body architecture, which can converse the energy obtained from the ocean wave into the forward thrust. In this paper, the dynamic models of the submerged glider based on dynamic characteristics of tandem hydrofoils and the surface float were separately established. The pitching angles of the hydrofoils and the submerged glider and the angle of attack between hydrofoils and relative current were considered for dynamic models and hydrodynamic coefficients. The translational hydrodynamic coefficient term for high-angle-of-attack passive motion of the submerged glider was calculated from static test simulations by using Computational Fluid Dynamics (CFD). Moreover, the rotational damping coefficients and added mass coefficients varying with the pitching angle of hydrofoils were analyzed by the simulation of the vertical planar motion mechanism (VPMM) tests. Furthermore, the numerical simulation of longitudinal motion with the computed hydrodynamic coefficients was performed, and the simulation results were compared with the sea trial data. The analysis was performed, and conclusions were drawn, which would provide a theoretical reference for the design of the wave glider.

Paramyosin is an important myofibrillar protein in molluscan smooth muscle. The full-length cDNA encoding paramyosin has been identified from Yesso scallop Patinopecten yessoensis. The length of paramyosin molecule has been found to be 3715 bp, which contains an open reading frame (ORF) of 2805 bp for 934 amino acid residues. Characterization of P. yessoensis paramyosin reveals the typical structural feature of coiled-coil protein, including six α-helix (α1-α6) and one coil (η) structures. Multiple phosphorylation sites have been predicted at the N-terminus of paramyosin, representing the unique phosphorylation sites in scallops. The highest levels of mRNA and protein expression of paramyosin have been found in foot and the smooth adductor muscle. According to whole-mount in situ hybridization (WISH), strong paramyosin mRNA signals were detected in the symmetric positions of anterior and posterior adductor muscles at late larval stages. These findings support that paramyosin may serve as the most important components for myogenesis and catch regulation in scallops. The present findings will not only help uncover the potential function of myofibrillar proteins in molluscs but also provide molecular evidence to infer evolutionary relationships among invertebrates.

A wave glider can convert vertical wave motion into its forward propulsion. There are many factors affecting the propulsion performance of a wave glider. The swing amplitude of hydrofoil can affect the efficiency of hydrofoil to capture wave energy, and the pull direction of an umbilical cable can affect the transmission efficiency of wave energy. In this paper, an optimized hydrofoil mechanism with a self-adjusting lower limit (SALL) was proposed by analyzing the un- synchronized movement between the submerged glider and the surface float. This mechanism was able to transfer the movement of umbilical cable to the hydrofoil swing mechanism through the linkage to control the lower limit of hydrofoil swing (maximum swing angle of hydrofoil in a counterclockwise direction). Firstly, the user-defined function (UDF) was written to control the motion of hydrofoil in the fluid domain. The lower limit swing angle and the heave direction of the hydrofoil were both set in the UDF, and the forward thrust generated by the passive swing of the hydrofoil in the fluid domain was able to be obtained by the simulation. Secondly, the prototype was designed by introducing a parallelogram mechanism on a conventional submerged glider, and a wave simulation test platform was built to verify the propulsive performance of the prototype. The results showed that, in comparison with the conventional submerged glider, the forward thrust of the SALL submerged glider was able to be improved by 1.50%, 17.78%, 7.42%, and 20.70% under the stiffness coefficients of torsion spring set to K = 2, K = 4, K = 6, and K = 8 in the simulation experiment, respectively. The forward thrust of the SALL submerged glider was able to be elevated by 9.99% with torsion spring K = 8 in the tank experiment. The advantage of the SALL mechanism was verified by comparing the results of the simulation and the tank experiment. Finally, the feasibility of the SALL submerged glider was verified in actual sea conditions by a sea trial.

To understand the molecular mechanism associated with growth variability in bivalves, we employed Illumina RNA-seq technology to analyze the transcriptomic profiles from fast- and slow-growing individuals in one full-sib family of the ark shell, Scapharca kagoshimensis. De novo assembly of S. kagoshimensis transcriptome yielded 276,082,016 raw reads, which were assembled into 98,502 unique transcripts using the Trinity strategy. A total of 6357 differentially expressed genes (DEGs) were obtained between fast- and slow-growing individuals, with 68 up-regulated genes and 846 down-regulated genes. Functional annotation revealed that most of the DEGs were classified to subunits of the large or small ribosomal protein, all of which showed significantly lower expression levels in the fast-growing group than those in the slow-growing group. Gene Ontology (GO) enrichment analysis indicated that most of the DEGs were involved in biological processes, followed by molecular functions and cellular components. The most Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enriched genes were related to energy metabolism, protein synthesis and degradation. These findings presented the potential links between genes expression and contrasting phenotypes in the ark shell, suggesting that the fast-growing phenotype might be attributed to lower energy demands for metabolism maintenance, and more effective protein biosynthesis and degradation in bivalves.

Abstract Background Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis. Results Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle. For the same comparison, iTRAQ-based proteomics reveals 474 differentially expressed proteins (DEPs), 198 up- and 276 downregulated. These DEPs mainly comprise muscle-specific proteins of the sarcoplasmic reticulum, extracellular matrix, and metabolic pathways. A group of conventional muscle proteins—myosin heavy chain, myosin regulatory light chain, myosin essential light chain, and troponin—are enriched in fast muscle. In contrast, paramyosin, twitchin, and catchin are preferentially expressed in slow muscle. The association analysis of proteomic and transcriptomic data provides the evidences of regulatory events at the transcriptional and posttranscriptional levels in fast and slow muscles. Among 1236 differentially expressed unigenes, 22.7% show a similar regulation of mRNA levels and protein abundances. In contrast, more unigenes (53.2%) exhibit striking differences between gene expression and protein abundances in the two muscles, which indicates the existence of fiber-type specific, posttranscriptional regulatory events in most of myofibrillar proteins, such as myosin heavy chain, titin, troponin, and twitchin. Conclusions This first, global view of protein and mRNA expression levels in scallop fast and slow muscles reveal that regulatory mechanisms at the transcriptional and posttranscriptional levels are essential in the maintenance of muscle structure and function. The existence of fiber-type specific, posttranscriptional regulatory mechanisms in myofibrillar proteins will greatly improve our understanding of the molecular basis of muscle contraction and its regulation in non-model invertebrates.

Aiming at the problems of difficult attitude stabilization, low landing accuracy, large external disturbance and slow dynamic response during the quadrotor dynamic landing on the wave glider, an improved series active disturbance rejection control method for the quadrotor is proposed. The quadrotor controller with inner-loop attitude angular velocity control and outer-loop position control based on the active disturbance rejection controller (ADRC) is designed by analyzing the dynamic model of the quadrotor. A tracking differentiator (TD) is adopted to track the input signal, and an expansive state observer (ESO) is used to estimate the total disturbance. Moreover, a nonlinear law state error feedback (NLSEF) is used to generate the virtual control volume of the system to realize the control of the quadrotor, and the stability of the cascaded self-turbulent controller is verified by Lyapunov’s theory. The simulation verifies that the proposed controller can accurately control the attitude and the position with better anti-interference capability and faster tracking speed. According to the final sea trial, a combination of an active disturbance rejection controller optimized with improved crow search algorithm (ICADRC) and April Tag visual reference system is used to land the quadrotor efficiently and successfully even under the surface float attitude uncertainty.

The air–sea interface is a key gateway in the Earth system. It is where the atmosphere sets the ocean in motion, climate/weather-relevant air–sea processes occur, and pollutants (i.e., plastic, anthropogenic carbon dioxide, radioactive/chemical waste) enter the sea. Hence, accurate estimates and forecasts of physical and biogeochemical processes at this interface are critical for sustainable blue economy planning, growth, and disaster mitigation. Such estimates and forecasts rely on accurate and integrated in situ and satellite surface observations. High-impact uses of ocean surface observations of essential ocean/climate variables (EOVs/ECVs) include (1) assimilation into/validation of weather, ocean, and climate forecast models to improve their skill, impact, and value; (2) ocean physics studies (i.e., heat, momentum, freshwater, and biogeochemical air–sea fluxes) to further our understanding and parameterization of air–sea processes; and (3) calibration and validation of satellite ocean products (i.e., currents, temperature, salinity, sea level, ocean color, wind, and waves). We review strengths and limitations, impacts, and sustainability of in situ ocean surface observations of several ECVs and EOVs. We draw a 10-year vision of the global ocean surface observing network for improved synergy and integration with other observing systems (e.g., satellites), for modeling/forecast efforts, and for a better ocean observing governance. The context is both the applications listed above and the guidelines of frameworks such as the Global Ocean Observing System (GOOS) and Global Climate Observing System (GCOS) (both co-sponsored by the Intergovernmental Oceanographic Commission of UNESCO, IOC–UNESCO; the World Meteorological Organization, WMO; the United Nations Environment Programme, UNEP; and the International Science Council, ISC). Networks of multiparametric platforms, such as the global drifter array, offer opportunities for new and improved in situ observations. Advances in sensor technology (e.g., low-cost wave sensors), high-throughput communications, evolving cyberinfrastructures, and data information systems with potential to improve the scope, efficiency, integration, and sustainability of the ocean surface observing system are explored.

Surface waves induced by tropical cyclones (TCs) play an important role in the air–sea interaction, yet are seldom observed. In the 2017 summer, a wave glider in the northern South China Sea successfully acquired the surface wave parameters when three TCs (Hato, Pakhar, and Mawar) passed though successively. During the three TCs, surface wave period increased from 4–6 s to ~8–10 s and surface wave height increased from 0–1 m to 3–8 m. The number of wave crests observed in a time interval of 1024 s decreased from 100–150 to 60–75. The sea surface roughness, a key factor in determining the momentum transfer between air and sea, increased rapidly during Hato, Pakhar, and Mawar. Surface waves rotated clockwise (anti-clockwise) on the right (left) side of the TC track, and generally propagated to the right side of the local cyclonic tangential direction relative to the TC center. The azimuthal dependence of the wave propagation direction is close to sinusoidal in a region within 50–600 km. The intersection angle between surface wave direction and the local cyclonic tangential direction is generally smallest in the right-rear quadrant of the TC and tends to be largest in the left-rear quadrant. This new set of glider wave observational data proves to be useful for assessing wave forecast products and for improvements in corresponding parameterization schemes.

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture.

The Yesso scallop Patinopecten yessoensis is an economically important marine bivalve species in aquaculture and fishery in Asian countries. However, limited genomic resources are available for this scallop, which hampers investigations into molecular mechanisms underlying their unique biological characteristics, such as shell formation and pigmentation. Mantle is the special tissue of P. yessoensis that secretes biomineralization proteins inducing shell deposition as well as pigmentation on the shells. However, a current deficiency of transcriptome information limits insight into mechanisms of shell formation and pigmentation in this species. In this study, the transcriptome of the mantle of P. yessoensis was deeply sequenced and characterized using Illumina RNA-seq technology. A total of 86,521 unique transcripts are assembled from 55,884,122 reads that passed quality filters, and annotated, using Gene Ontology classification. A total of 259 pathways are identified in the mantle transcriptome, including the calcium signaling and melanogenesis pathways. A total of 237 unigenes that are homologous to 102 reported biomineralization genes are identified, and 121 unigenes that are homologous to 93 known proteins related to melanin biosynthesis are found. Twenty-three annotated unigenes, which are mainly homologous to calmodulin and related proteins, Ca2+/calmodulin-dependent protein kinase, adenylate/guanylate cyclase, and tyrosinase family are potentially involved in both biomineralization and melanin biosynthesis. It is suggested that these genes are probably not limited in function to induce shell deposition by calcium metabolism, but may also be involved in pigmentation of the shells of the scallop. This potentially supports the idea that there might be a link between calcium metabolism and melanin biosynthesis, which was previously found in vertebrates. The findings presented here will notably advance the understanding of the sophisticated processes of shell formation as well as shell pigmentation in P. yessoensis and other bivalve species, and also provide new evidence on gene expression for the understanding of pigmentation and biomineralization not only in invertebrates but also probably in vertebrates.

Hypoxia tolerance and adaptive regulation are important for aquatic animals, especially for species with poor mobility, such as most bivalves. Previous studies have confirmed that the blood clam Scapharca broughtonii has strong hypoxia resistance. However, the molecular mechanism supporting its hypoxic tolerance is still largely limited. To further screen the genes and their potential regulation of hypoxia tolerance, the transcriptome changes of S. broughtonii after acute hypoxic stress were explored by RNA sequencing. In this study, the average value of Q30 is 92.89%, indicating that the quality of sequencing is relatively high. The Unigenes obtained were annotated using four databases, namely Interpo, KEGG, Swisspro and TrEMBL. The annotation rates in these four databases were 71.82%, 75.95%, 92.98%, and 79.26%, respectively. And also, there were 649 DEGs in group B (dissolved oxygen (DO) of 2.5 mg/L) compared with group D (DO of 7.5 mg/L), among which 252 were up-regulated, and 397 were down-regulated. There were 965 DEGs in group A (DO of 0.5 mg/L), 2.5 mg/L, and 7.5 mg/L, compared with group B, among which 530 were up-regulated, and 435 were down-regulated. Meanwhile, there were 2,040 DEGs in group A compared with group D, among which 901 were up-regulated, and 1,139 were down-regulated. The main metabolic-related pathways of KEGG enriched in this study included Insulin secretion, Insulin signaling pathway, MAPK signal transduction pathway, and PPAR signaling pathway. These pathways may be critical metabolic pathways to solve energy demand and rebuild energy balance in S. broughtonii under hypoxic conditions. This study preliminarily clarified the response of S. broughtonii to hypoxia stress on the molecular levels, providing a reference for the following study on the response laws of related genes and pathways under environmental stress of S. broughtonii. [ABSTRACT FROM AUTHOR]

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Exposure to low Ca2+ and/or Mg2+ is tolerated by cardiac myocytes, astrocytes, and neurons, but restoration to normal divalent cation levels paradoxically causes Ca2+ overload and cell death. This phenomenon has been called the ‘Ca2+ paradox’ of ischemia-reperfusion. The mechanism by which a decrease in extracellular Ca2+ and Mg2+ is ‘detected’ and triggers subsequent cell death is unknown. Transient periods of brain ischemia are characterized by substantial decreases in extracellular Ca2+ and Mg2+ that mimic the initial condition of the Ca2+ paradox. In CA1 hippocampal neurons, lowering extracellular divalents stimulates a nonselective cation current. We show that this current resembles TRPM7 currents in several ways. Both (i) respond to transient decreases in extracellular divalents with inward currents and cell excitation, (ii) demonstrate outward rectification that depends on the presence of extracellular divalents, (iii) are inhibited by physiological concentrations of intracellular Mg2+, (iv) are enhanced by intracellular phosphatidylinositol 4,5-bisphosphate (PIP2), and (v) can be inhibited by Gaq-linked G protein-coupled receptors linked to phospholipase C β-induced hydrolysis of PIP2. Furthermore, suppression of TRPM7 expression in hippocampal neurons strongly depressed the inward currents evoked by lowering extracellular divalents. Finally, we show that activation of TRPM7 channels by lowering divalents significantly contributes to cell death. Together, the results demonstrate that TRPM7 contributes to the mechanism by which hippocampal neurons ‘detect’ reductions in extracellular divalents and provide a means by which TRPM7 contributes to neuronal death during transient brain ischemia. [ABSTRACT FROM AUTHOR]

Objective: Morphometric studies of postmortem brains from subjects with mood disorders have reported altered density of glial cells in the amygdala; however, the nuclear regions have not been examined individually. Methods: We assessed the size and density of both neuronal and glial cells in discrete amygdalar nuclei in postmortem sections from subjects with major depressive disorder, bipolar disorder (BD) and schizophrenia and from nonpsychiatric control subjects. Three adjacent Nissl-stained sections were examined from each individual. Results: We report significantly decreased neuron somal size in the lateral amygdalar nucleus (LAN) and the accessory basal parvocellular nucleus (ABPC) in subjects with BD, relative to control subjects. These changes in cellular morphology were most prominent in the LAN in sections obtained from the left hemisphere. Conclusions: These findings add to increasing evidence for neuropathological changes in the amygdala of subjects with BD and specifically implicate the LAN and ABPC in this disorder. [ABSTRACT FROM AUTHOR]

Objective: Many studies indicate a genetic predisposition to bipolar disorder (BD) and suggest that a number of abnormal genes are involved in its development. In this study, we used DNA microarray technology to analyze gene-expression profiles in the postmortem frontal cortex of subjects with BD. Methods: Microarray hybridization was performed using human 19K microarray with universal human reference RNA in each hybridization. The reference cDNA was labelled with Cy3 and experimental cDNA, with Cy5. Glass array slides were cohybridized with equal amounts of mixed reference and experimental cDNA. Selected gene targets were further verified using real-time polymerase chain reaction (PCR). Results: We found that 831 genes were differentially expressed in subjects with BD, including a number of genes in the mitochondrial electron transport chain (ETC), phosphatidylinositol-signalling system and glycolysis/gluconeogenesis. Eight genes coding for the components of the mitochondrial ETC were identified along with 15 others related to mitochondrial function. Downregulation of NADH-ubiquinone oxidoreductase 20-kd subunit (ETC complex I), cytochrome c oxidase polypeptide Vic (ETC complex IV) and ATP synthase lipid-binding protein (ETC complex V) were further verified by real-time PCR. We also found that the expression of the NADH-ubiquinone oxidoreductase 20-kd subunit was increased in subjects with BD who were receiving mood-stabilizing treatment with lithium at the time of death, when compared with subjects with BD who were not being treated with lithium. Conclusions: Because the mitochondrial ETC is a major source for the generation of reactive oxygen species, these findings suggest that oxidative damage may play an important role in the pathophysiology of BD and that neuroprotection against this damage may be involved in the effect of lithium treatment. [ABSTRACT FROM AUTHOR]

Lithium, a common drug for the treatment of bipolar disorder (BD), requires chronic administration to prevent recurrences of the illness. The necessity for long-term treatment suggests that changes in genes expression are involved in the mechanism of its action. We studied effects of lithium on gene expression in lymphoblasts from BD patients, all excellent responders to lithium prophylaxis. Gene expression was analyzed using cDNA arrays that included a total of 2400 cDNAs. We found that chronic lithium treatment at a therapeutically relevant concentration decreased the expression of seven genes in lymphoblasts from lithium responders. Five of these, candidate lithiumregulated genes, including alpha | B-adrenoceptor (α | B-AR), acetylcholine receptor protein alpha chain precursor (ACHR), cAMPdependent 3′,5′-cyclic phosphodiesterase 4D (PDE4D), substance-P receptor (SPR), and ras-related protein RAB7, were verified by Northem blotting analysis in lithium responders. None of these genes were regulated by lithium in healthy control subjects. When we compared the expression of these five genes between bipolar subjects and healthy control subjects at baseline, prior to lithium administration, we found that α | B-AR gene expression was higher in bipolar subjects than in healthy control subjects. Our findings indicate that α | B-AR may play an important role in the mechanism of action of lithium treatment. [ABSTRACT FROM AUTHOR]

Oligonucleotide microarray technology was used to analyze gene expression profiles after chronic treatment with the mood stabilizing drug valproate at a therapeutically relevant concentration in primary cultured rat cerebral cortical cells. We discovered that valproate regulates expression of 28 genes, including three isoenzymes (M1, A3 and A4) of glutathione S-transferase (GST), an important protective factor against oxidative stress. Because previous studies in our laboratory found that chronic valproate treatment protected cultured neurons against oxidative stress, further experiments on the regulation of GST were performed. Regulation of GST M1, GST A3 and GST A4 was verified using northern blotting hybridization. Chronic valproate treatment increased mRNA levels of M1 and A4, but decreased the A3 mRNA level dose-dependently, indicating further complexities in the regulation of GST by valproate. The level of GST M1 protein and GST activity were also increased by chronic valproate treatment. In addition, chronic treatment with lithium, another commonly prescribed mood stabilizer, also increased levels of GST M1 mRNA and protein. The present findings suggest that regulation of GST M1, and possibly GST A4, may mediate the anti-oxidative effects of valproate treatment, and regulation of GST may be involved in the mood stabilizing effect of valproate and lithium. [ABSTRACT FROM AUTHOR]