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Simple Summary: 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. In this paper, we investigate the genetic diversity and differentiation of R. philippinarum populations. The present results not only provide the scientific basis for the phylogenetic relationship of clam resources, but also lay the foundation for natural population conservation and genetic improvement of R. philippinarum. 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. [ABSTRACT FROM AUTHOR]

The Pacific abalone is an economically important cold-water shellfish. With its widespread culture, high temperature has become a key abiotic factor for the high mortality of Pacific abalone in summer, particularly in the south of China. To understand the molecular regulatory mechanisms of thermal stress response in Pacific abalone for further analyzing its heat adaptive capacity, we subjected Pacific abalone to acute heat stress at 28°C for 6, 24, and 48 hr, respectively. A total of 2,213, 2,337, and 1,420 differentially expressed genes (DEGs) were identified in Pacific abalone after 6, 24, and 48 hr of thermal stress, respectively, as compared with the control group without heat stimulation. These DEGs were significantly enriched in protein folding and chaperone-mediated protein folding process, antigen processing and presentation, and protein processing in endoplasmic reticulum pathways. The expression of numerous molecular chaperones was significantly upregulated after thermal stress. Maintaining cellular homeostasis through the upregulated expression of molecular chaperones associated with endoplasmic reticulum-associated degradation (ERAD) pathways might be central to the defense of Pacific abalone against thermal stress. In addition, the expression of Toll-like receptor 6 (TLR6) and myeloid differentiation factor 88 (MyD88) genes of the TLR signaling pathway was also induced. Therefore, the Pacific abalone might activate the immune defense system to resist the invasion of pathogenic bacteria by upregulating immune-related genes after thermal challenges. Our results not only contribute to a deeper understanding of heat stress regulation in the Pacific abalone but also provide basic data for molecular genetic breeding of heat-resistant abalone. [ABSTRACT FROM AUTHOR]

Simple Summary: The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. The increasing expanding of clam culture may result in some serious problems. In this paper, we investigated the genetic diversity and differentiation of R. philippinarum populations and tested the hypothesis that clam population differentiation is influenced by the southern breeding and northern culture. The present findings will provide useful information for natural resource conservation and genetic breeding of the Manila clam in China. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Salinity can affect the physiological, reproductive, and developmental characteristics of marine molluscs. The Chinese razor clam (Sinonovacula constricta) is a marine bivalve that inhabits estuarine and intertidal habitats where salinity is usually lower when compared to open sea waters. The species is also an economically important subject of aquaculture in China. Here, RNA sequencing was used to study the internal mechanism of salt stress response in the Chinese razor clam. Differentially expressed RNAs were identified and lncRNA/circRNA-miRNA-mRNA regulatory networks were successfully constructed. Furthermore, the expression of four candidate genes in the Chinese razor clam subjected to different salinity stress were examined by qRT-PCR. The results of this study will improve our understanding of genetic-level responses to salinity changes in the Chinese razor clam. Moreover, the acquired information may be useful for optimization of the artificial breeding of the species under aquaculture conditions. 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. [ABSTRACT FROM AUTHOR]

Power transmission and transformation projects (PTTPs) under new energy grid connections are different from ordinary engineering construction projects. With large investment amounts, various supporting facilities, and high safety and quality requirements, PTTPs are vulnerable to the volatility of new energy power generation, climate, geological conditions, geopolitical environment, technological changes, and other kinds of uncertain factors. Therefore, the investment risk of PTTPs under new energy grid connection is particularly considerable in the project management. For the owner of PTTPs, adopting the engineering-procurement-construction (EPC) mode is an effective attempt to solve the project construction problems faced by the owners. Thus, this paper deeply excavates the key risk points of PTTPs in the initial investment phase under the EPC mode and constructs the novel risk evaluation index system from the perspectives of economy, management, policy, society, and environment. An assessment model is established based on triangle fuzzy number-hesitant fuzzy linguistic term sets (HFLTS-TFNs), the entropy method, and the fuzzy comprehensive evaluation method, which is used to evaluate the investment risk of PTTPs to provide reference for power grid corporations to control project risks. Finally, a case study in the Hexi Corridor region, Gansu Province, China, is illustrated to demonstrate the rationality of the decision model and find management risks are the most vital risk factors for PTTPs under EPC mode. [ABSTRACT FROM AUTHOR]

The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species in China. However, studies on its genomics and population genetics remain lacking. Here, we assembled the chromosome‐level genome of a female C. ariakensis and re‐sequenced 261 individuals from five locations in China representing three typical habitats. The C. ariakensis genome was 662.9 Mb with contig N50 length of 5.9 Mb using PacBio HiFi‐CCS long reads, and 99.83% sequences were anchored onto 10 pseudochromosomes using Hi‐C data. A total of 26,354 protein‐coding genes were predicted. We identified three significantly expanded gene families which are closely associated with osmotic pressure regulation, including CDO, SLC13 and SDR. Population structure analysis revealed that the C. ariakensis from five locations were clustered into three typical groups (northern, southern and Shanghai) (K = 3) and their phylogenetic relationship was consistently correlated to their geographical distribution. Furtherly, the differentiation between northern and southern groups was clearly demonstrated by estimated population differentiation coefficient (FST = 0.1154), and the PSMC distribution showed the two groups of effective population size separated at 0.1 Ma. Meanwhile gene flow from southern to Shanghai was detected. Selective sweep analysis between northern and southern group detected genes associated with heat response and salinity adaptation. This study could provide valuable genomic resources and information for further research on the molecular evolution, genetic breeding, biological function and evolutionary adaptation of C. ariakensis. [ABSTRACT FROM AUTHOR]

Recent reports have shown that wild crabs may be important hosts involved in the transmission and spread of the parasitic Hematodinium in cultured marine crustaceans. Therefore, monitoring the prevalence of Hematodinium infections in wild crabs is necessary to develop effective strategies for the prevention and control of Hematodinium disease. Here we report a wild crab species, Macrophthalmus ( Macrophthalmus ) abbreviatus Manning & Holthuis, 1981, as a new natural host for Hematodinium sp. infection. It is one of the common wild crab species dwelling in the ponds or waterways connected to the polyculture ponds located on the coast of Rizhao or Weifang, Shandong Peninsula, China. According to the results of PCR detection and phylogenetic analysis targeting the internal transcribed spacer 1 (ITS 1) region, these Hematodinium sp. isolates were identified as H. perezi and fell into the genotype II category within H. perezi . A high monthly prevalence of H. perezi infection was observed during the 2021-2022 field survey, ranging from 33.3% to 90.6% in M. abbreviatus originating from Weifang (n=304 wild crabs) and from 53.6% to 92.9% in those from Rizhao (n=42 wild crabs). Artificial inoculation infection experiments demonstrated that M. abbreviatus could be infected by H. perezi , and massive Hematodinium cells and typical histopathological changes were observed in the hepatopancreas and gill tissues of the infected crabs. To our knowledge, this is the first report of M. abbreviatus as a new natural host for H. perezi infection. Results in the present study extend the known host spectrum for this emerging parasite pathogen, and also provide valuable information for epidemic surveillance of the Hematodinium disease as well., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liu, Xie, Wang, Li, Wan, Li, Zhou, Shi, Zhang and Huang.)

Background: The ark shell (Scapharca broughtonii) is one of the most economically important mollusks in the Bohai Sea and Yellow Sea of China. In recent years, ark shells from the Korean population were introduced to China for seed propagation and culture., Objective: To explore the impact of the introduction of Korean ark shell on the genetic diversity of native population in China., Methods: Simple sequence repeat (SSR) is effective and widely used tool for genetic analysis. In this study, 180 EST-SSRs were selected and verified by polymerase chain reaction and polyacrylamide gel electrophoresis. Subsequently, five polymorphic EST-SSRs were screened and their primers were modified by fluorescein for use in the genetic analysis of four populations., Results: Genetic analysis showed that 361 alleles amplified by five SSR loci were detected in the four populations. The number of alleles for the five SSRs ranged from 8 to 30, with a mean of 18.05 (standard deviation, SD = 6.492). The effective number of alleles varied from 2.253 to 22.222, with a mean of 10.596 (SD = 4.713). Observed heterozygosity and expected heterozygosity were 0.167-0.833 and 0.566-0.971, with average values of 0.520 (SD = 0.177) and 0.891 (SD = 0.062), respectively. Polymorphic information content ranged from 0.521 to 0.953, with a mean of 0.865 (SD = 0.070). The pairwise genetic differentiation coefficient (F ST ) of the four populations ranged from 0.0267 to 0.0477, showing low genetic differentiation. The phylogenetic tree constructed by neighbor-joining method showed that the genetic distance between the Chinese Dalian native population and three Korean populations was relatively more far than that among those Korean populations., Conclusion: The results indicated that the genetic structure of the Dalian wild population was less affected by the introduced Korean wild populations.

Genome-wide association studies (GWASs) have provided many insights into cancer genetics. However, the molecular mechanisms of many susceptibility SNPs defined by GWASs in cancer heritability and in promoting cancer risk remain elusive. New research strategies, including functional evaluations, are warranted to systematically explore truly causal genetic variants. In this study, we developed an integrative functional genomics methodology to identify cancer susceptibility SNPs in transcription factor-binding sites across the whole genome. Employing integration of functional genomic data from c-Myc cistromics, 1000 Genomes, and the TRANSFAC matrix, we successfully annotated 12 SNPs present in the c-Myc cistrome with properties consistent with modulating c-Myc binding affinity in hepatocellular carcinoma (HCC). After genotyping these 12 SNPs in 1,806 HBV-related HCC case subjects and 1,708 control subjects, we identified a HCC susceptibility SNP, rs157224G>T, in Chinese populations (T allele: odds ratio = 1.64, 95% confidence interval = 1.32-2.02; p = 5.2 × 10(-6)). This polymorphism leads to HCC predisposition through modifying c-Myc-mediated transcriptional regulation of EPB41, with the risk rs157224T allele showing significantly decreased gene expression. Based on cell proliferation, wound healing, and transwell assays as well as the mouse xenograft model, we identify EPB41 as a HCC susceptibility gene in vitro and in vivo. Consistent with this notion, we note that EPB41 expression is significantly decreased in HCC tissue specimens, especially in portal vein metastasis or intrahepatic metastasis, compared to normal tissues. Our results highlight the involvement of regulatory genetic variants in HCC and provide pathogenic insights of this malignancy via a genome-wide approach., (Copyright © 2016 American Society of Human Genetics. All rights reserved.)

As an important member in homologous recombination repair, RAD52 plays a crucial part in maintaining genomic stability and prevent carcinogenesis. Several cancer susceptibility RAD52 single nucleotide polymorphisms (SNPs) have been identified previously. However, little or nothing has been known about the RAD52 SNPs and their functional significance in hepatitis B viruses (HBV)-related hepatocellular carcinoma (HCC). Therefore, we investigated the association between five RAD52 SNPs (rs1051669, rs10774474, rs11571378, rs7963551, and rs6489769) and HBV-related HCC risk as well as its biological function in vivo. Genotypes were determined in two independent case-control sets from two regions of China. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. The allele-specific regulation on RAD52 expression by the functional genetic variant was examined with normal liver tissues. We found that only the RAD52 rs7963551 SNP was significantly associated with HCC risk, with the odds of having the rs7963551 CC genotype in patients was 0.59 (95% CI = 0.45-0.78, P = 1.5 × 10(-4), HCC cases versus chronic HBV carriers) or 0.65 (95% CI = 0.52-0.81, P = 1.1 × 10(-4), HCC cases versus healthy controls) compared with the AA genotype. In the genotype-phenotype correlation analyses of 44 human liver tissue samples, rs7963551 CC or AC was associated with a statistically significant increase of RAD52 mRNA expression, which are consistent to functional relevance of allelic regulation of RAD52 expression by rs7963551 SNP and miRNA let-7 in cancer cells. Our data demonstrated that RAD52 functional rs7963551 SNP contributes to susceptibility to developing HCC., (© 2014 Wiley Periodicals, Inc.)

Most acculturation research throughout the world has been conducted in immigrant settings. In order to examine the generalizability of the previous conclusions in immigrant settings, the present study tried to explore the relationship between cultural identity and self-esteem and the mediating role of acculturation attitudes in China. Using the cross-sectional design, a total number of 342 Uyghur college students were asked to complete a survey comprising the Multi-Group Ethnic/National Identity Measure-Revised Scale, the Acculturation Attitudes Scale, and the Rosenberg Self-Esteem Scale. Using hierarchical multiple regression, the results indicated that cultural identity was positively correlated with self-esteem. A significant mediation of acculturation was observed between cultural identity and self-esteem. These findings demonstrated the significance of cultural identity and acculturation attitudes in the adaptation of Chinese Uyghur college students, in which integration is an optimal acculturation attitude.

Although the entire etiology of esophageal squamous cell carcinoma (ESCC) is still unclear, alcohol drinking has been identified as a major environmental risk factor. The aldehyde dehydrogenase (ALDH) superfamily members are major enzymes involved in the alcohol-metabolizing pathways. Accumulating evidences demonstrated that ALDH7A1, one of ALDH superfamily members, degrades and detoxifies acetaldehyde generated by alcohol metabolism and have been associated with development and prognosis of multiple cancers. However, it is still unknown if ALDH7A1 single nucleotide polymorphisms (SNPs) contribute to ESCC susceptibility. In this study, we examined the association between sixteen ALDH7A1 SNPs and risk of developing ESCC. Genotypes were determined in 2,098 ESCC patients and 2,150 controls (three independent hospital-based case-control sets from different regions of China). Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated by logistic regression. Our data demonstrated that only the ALDH7A1 rs13182402 SNP confer susceptibility to ESCC (For AG genotype, OR = 0.75, 95 % CI = 0.66-0.91, P = 4.8 × 10(-6); for GG genotype, OR = 0.59, 95 % CI = 0.41-0.88, P = 0.003). These results are consistent to the biological functions of ALDH7A1 during alcohol metabolism and carcinogenesis.

The oncoprotein MDM4 plays an essential role in P53 tumor suppressor pathway through negative regulation of P53 function. It has been reported that the rs4245739 A > C polymorphism located in the MDM4 3'-untranslated region creates a miR-191 target site and results in decreased MDM4 expression. Therefore, we investigated the association of the MDM4 rs4245739 polymorphism as well as the P53 Arg72Pro genetic variant with the breast cancer risk. Genotypes were determined in two independent case-control sets consisting of 1100 breast cancer cases and 1400 controls from two regions of China. Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated by logistic regression. Our results demonstrated that the MDM4 rs4245739 AC and CC genotypes were significantly associated with decreased breast cancer risk compared to the AA genotype in both the case-control sets (Jinan set: OR = 0.55, 95 % CI 0.40-0.76, P = 2.3 × 10(-4); Huaian set: OR = 0.41, 95 % CI 0.25-0.67, P = 3.1 × 10(-4)). The P53 Arg/Pro genotype or Pro/Pro genotype was significantly associated with an increased risk of developing breast cancer, compared to the P53 Arg/Arg genotype in both the case-control sets (all P < 0.05). Interestingly, we observed a combinational effect between MDM4 rs4245739 and P53 Arg72Pro variants in attenuating breast cancer risk, highlighting the importance of the P53 tumor suppressor pathway genes during malignant transformation. Our results also support the hypothesis that genetic variants interrupting miRNA-mediated gene regulation might be important genetic modifiers of breast cancer risk.

Aim: P53 plays a critical role in the maintenance of genomic stability as well as the control of cell growth and apoptosis. Recently, an uncommon P53 genetic variant (rs78378222) was reported to be significantly associated with multiple cancers in Caucasians in a genome-wide association study. rs78378222 locates in the 3'-untranslated region of the P53 gene, and this A-to-C polymorphism results in changes of the AATAAA polyadenylation signal to AATACA, which leads to impaired 3'-end processing of P53 mRNA and decreased P53 expression., Methods: We evaluated the association between this polymorphism and esophageal squamous cell carcinoma (ESCC) risk in a case-control cohort consisting of 405 ESCC patients and 810 healthy controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression., Results: We did observe this polymorphism with low minor allele frequency in Chinese Han population. Additionally, significantly increased ESCC risk was associated with P53 rs78378222 A>C polymorphism. Compared with rs78378222AA carriers, the OR of developing ESCC for AC carriers was 3.22 (95% CI=1.71-6.33, P=1.34×10(-4))., Conclusion: These results suggest that this functional uncommon P53 rs78378222 variant is associated with ESCC risk in the current Han Chinese population., (Copyright © 2012 Elsevier B.V. All rights reserved.)