Risk management of agricultural supply chain in China with weather compensatory contract

This paper is based on some situations in China that agricultural products are transported directly to distribution centers and / or super markets. The retailer supplies an additional weather compensatory contract to the farmer before the planting time, in which the compensatory parameters are designed according to the forecast of temperature of the forthcoming demanding season. Such kind of contract can induce farmer to plant more properly to meet the market demands and increase the farmer's profits at the same time control market risk. This contract also helps the retailer as well as the farmer to reduce their weather risks

Transcriptome Analysis Reveals the Immunosuppression in Tiger Pufferfish (Takifugu rubripes) under Cryptocaryon irritans Infection

The tiger pufferfish (Takifugu rubripes), also known as fugu, has recently suffered from severe C. irritans infections under aquaculture environment, yet the underlying immune mechanisms against the parasite remain poorly understood. In this study, we conducted a comprehensive transcriptome analysis of the gill tissue from infected and uninfected fish using PacBio long-read (one pooled sample each for seriously infected and healthy individuals, respectively) and Illumina short-read (three pools for mildly infected, seriously infected, and healthy individuals, respectively) RNA sequencing technologies. After aligning sequence data to fugu's reference genome, 47,307 and 34,413 known full-length transcripts were identified and profiled in healthy and infected fish, respectively. Similarly, we identified and profiled 1126 and 803 novel genes that were obtained from healthy and infected fish, respectively. Interestingly, we found a decrease in the number of alternative splicing (AS) events and long non-coding RNAs (lncRNAs) after infection with C. irritans, suggesting that they may be involved in the regulation of the immune response in fugu. There were 687 and 1535 differentially expressed genes (DEGs) in moderately and heavily infected fish, respectively, compared to uninfected fish. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that immune-related DEGs in the two comparison groups were mainly enriched in cytokine-cytokine receptor interactions, ECM-receptor interactions, T-cell receptor signaling pathways, Th1 and Th2 cell differentiation, and Th17 cell differentiation pathways. Further analysis revealed that a large number of immune-related genes were downregulated in infected fish relative to uninfected ones, such as CCR7, IL7R, TNFRSF21, CD4, COL2A1, FOXP3B, and ITGA8. Our study suggests that C. irritans is potentially a highly efficient parasite that may disrupt the defense mechanisms of fugu against it. In addition, in combination of short-read RNA sequencing and previous genome-wide association analyses, we identified five key genes (NDUFB6, PRELID1, SMOX, SLC25A4, and DENND1B) that might be closely associated with C. irritans resistance. This study not only provides valuable resources of novel genic transcripts for further research, but also provides new insights into the immune mechanisms underlying C. irritans infection response in farmed fugu.</p

A newly developed 20K SNP array reveals QTLs for disease resistance to Cryptocaryon irritans in tiger pufferfish (Takifugu rubripes)

This study describes the development and application of a 20 K single nucleotide polymorphism (SNP) array in fugu (Takifugu rubripes). The main goal of this newly developed SNP array is to enhance selective breeding practice via the incorporation of genomic information. Fugu is one of the economic aquaculture species and mainly threatened by parasite disease. The performance of the array was evaluated in a farmed pufferfish population challenged with Cryptocaryon irritans and benchmarked against whole-genome sequencing of a subset of the animals. The array showed very high call rates, consistency between technical replicates, and concordance with genome-resequencing data. Heritability estimates using pedigree and SNP datasets demonstrated a significant genetic component of resistance to C. irritans, with heritability estimates ranging from 0.53 to 0.67, and prediction accuracies were significantly improved with the use of genomic data. Genome-wide association study identified two putative quantitative trait loci (QTLs) on chromosomes 3 and 17. Our findings suggest resistance to C. irritans can be rapidly increased in fugu populations by selective breeding, further expedited via the application of genetic markers. Therefore, they represent a valuable resource for selective breeding programmes aimed at enhancing disease resistance in fugu aquacultur

Epigenetic modification and inheritance in sexual reversal of fish

Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species, co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model—a marine fish that has both ZW chromosomal GSD and temperature-dependent ESD—we investigated the role of DNA methylation in transition from GSD to ESD. Comparative analysis of the gonadal DNA methylomes of pseudomale, female, and normal male fish revealed that genes in the sex determination pathways are the major targets of substantial methylation modification during sexual reversal. Methylation modification in pseudomales is globally inherited in their ZW offspring, which can naturally develop into pseudomales without temperature incubation. Transcriptome analysis revealed that dosage compensation occurs in a restricted, methylated cytosine enriched Z chromosomal region in pseudomale testes, achieving equal expression level in normal male testes. In contrast, female-specific W chromosomal genes are suppressed in pseudomales by methylation regulation. We conclude that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish. We also offer the first clues on the mechanisms behind gene dosage balancing in an organism that undergoes sexual reversal. Finally, we suggest a causal link between the bias sex chromosome assortment in the offspring of a pseudomale family and the transgenerational epigenetic inheritance of sexual reversal in tongue sole fish

Sophora moocroftiana seeds ethanol extract regulates NLRP3 inflammasome activation and pyroptosis via ROS/TXNIP pathway to amelioration of NAFLD in vitro and in vivo

BackgroundSophora moorcroftiana (Benth.) Baker is a perennial shrub endemic to the Tibetan Plateau. Its seeds are traditional Tibetan medicine for treating jaundice, hepatitis, purulent tonsillitis, diphtheria, and parasitosis.Aim of the studyThe aim of this research is to explore the possible processes by which the 70% ethanol extract of S. moocroftiana seeds (SMS) imparts healing effects in NAFLD what is done by simulating the disease state of NAFLD via the creation of a lipid accumulation model in HepG2 cells induced by FFA, and a NAFLD model in C57BL/6J mice induced by HFD.Materials and methodsThe experiment used HFD fed C57BL/6J mice to establish a NAFLD model, which was divided into a control group, HFD model group, different doses of SMS groups, and a Silymarin group. Were used in the experiment. SMS could improve lipid accumulation, reduce oxidative stress and inflammatory response, which confirmed the improvement effect of SMS on NAFLD. The protective mechanism of SMS on HepG2 cell lipid accumulation model was further verified by qRT-PCR, WB, ELISA, and other methods.ResultsIn vitro and in vivo experiments showed that SMS could inhibit ROS and TXNIP dissociation, regulate NLRP3/caspase 1/GSDMD pathway to inhibit pyroptosis, and reduce the release of inflammatory factors such as TNF-α, IL-6, IL-18, and IL-1β, thereby improving the symptoms of lipid accumulation and oxidative stress. These results suggest that SMS can improve NAFLD via regulating pyroptosis.ConclusionSMS has promising therapeutic potential in NAFLD management by inhibiting the activation of the NLRP3 inflammasome and pyroptosis via ROS/TXNIP pathway in hepatocytes

Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis)

Chinese tongue sole is a marine fish with ZW sex determination. Genome sequencing suggested that the Z-linked dmrt1 is a putative male determination gene, but direct genetic evidence is still lacking. Here we show that TALEN of dmrt1 efficiently induced mutations of this gene. The ZZ dmrt1 mutant fish developed ovary-like testis, and the spermatogenesis was disrupted. The female-related genes foxl2 and cyp19a1a were significantly increased in the gonad of the ZZ dmrt1 mutant. Conversely, the male-related genes Sox9a and Amh were significantly decreased. The dmrt1 deficient ZZ fish grew much faster than ZZ male control. Notably, we obtained an intersex ZW fish with a testis on one side and an ovary on the other side. This fish was chimeric for a dmrt1 mutation in the ovary, and wild-type dmrt1 in the testis. Our data provide the first functional evidence that dmrt1 is a male determining gene in tongue sole

The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation(1-5). The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways. We demonstrate that retinoic acid is critical in establishing asymmetric pigmentation and, via cross-talk with thyroid hormones, in modulating eye migration. The unexpected expression of the visual opsins from the phototransduction pathway in the skin translates illumination differences and generates retinoic acid gradients that underlie the generation of asymmetry. Identifying the genetic underpinning of this unique developmental process answers long-standing questions about the evolutionary origin of asymmetry, but it also provides insight into the mechanisms that control body shape in vertebrates.National Natural Science Foundation of China [31130057, 31461163005, 31530078, 31472269, 31472262, 31472273]; State 863 High Technology R&D Project of China [2012AA092203, 2012AA10A408, 2012AA10A403-2]; Education and Research of Guangdong Province [2013B090800017]; Taishan Scholar Climb Project Fund of Shandong of China; Taishan Scholar Project Fund of Shandong of China for Young Scientists; Shanghai Universities First-class Disciplines Project of Fisheries; Program for Professor of Special Appointment (Eastern Scholar) at the Shanghai Institutions of Higher Learning; Shanghai Municipal Science, Special Project on the Integration of Industryinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/publishedVersio