Development of a Five-Chemical-Probe Method to Determine Multiple Radicals Simultaneously in Hydroxyl and Sulfate Radical-Mediated Advanced Oxidation Processes.

Advanced oxidation processes (AOPs), such as hydroxyl radical (HO•)- and sulfate radical (SO4•-)-mediated oxidation, are attractive technologies used in water and wastewater treatments. To evaluate the treatment efficiencies of AOPs, monitoring the primary radicals (HO• and SO4•-) as well as the secondary radicals generated from the reaction of HO•/SO4•- with water matrices is necessary. Therefore, we developed a novel chemical probe method to examine five key radicals simultaneously, including HO•, SO4•-, Cl•, Cl2•-, and CO3•-. Five probes, including nitrobenzene, para-chlorobenzoic acid, benzoic acid, 2,4,6-trimethylbenzoic acid, and 2,4,6-trimethylphenol, were selected in this study. Their bimolecular reaction rate constants with diverse radicals were first calibrated under the same conditions to minimize systematic errors. Three typical AOPs (UV/H2O2, UV/S2O82-, and UV/HSO5-) were tested to obtain the radical steady-state concentrations. The effects of dissolved organic matter, Br-, and the probe concentration were inspected. Our results suggest that the five-probe method can accurately measure radicals in the HO•- and SO4•--mediated AOPs when the concentration of Br- and DOM are less than 4.0 µM and 15 mgC L-1, respectively. Overall, the five-probe method is a practical and easily accessible method to determine multiple radicals simultaneously.

Detection of breakage and impurity ratios for raw sugarcane based on estimation model and MDSC-DeepLabv3.

Broken cane and impurities such as top, leaf in harvested raw sugarcane significantly influence the yield of the sugar manufacturing process. It is crucial to determine the breakage and impurity ratios for assessing the quality and price of raw sugarcane in sugar refineries. However, the traditional manual sampling approach for detecting breakage and impurity ratios suffers from subjectivity, low efficiency, and result discrepancies. To address this problem, a novel approach combining an estimation model and semantic segmentation method for breakage and impurity ratios detection was developed. A machine vision-based image acquisition platform was designed, and custom image and mass datasets of cane, broken cane, top, and leaf were created. For cane, broken cane, top, and leaf, normal fitting of mean surface densities based on pixel information and measured mass was conducted. An estimation model for the mass of each class and the breakage and impurity ratios was established using the mean surface density and pixels. Furthermore, the MDSC-DeepLabv3+ model was developed to accurately and efficiently segment pixels of the four classes of objects. This model integrates improved MobileNetv2, atrous spatial pyramid pooling with deepwise separable convolution and strip pooling module, and coordinate attention mechanism to achieve high segmentation accuracy, deployability, and efficiency simultaneously. Experimental results based on the custom image and mass datasets showed that the estimation model achieved high accuracy for breakage and impurity ratios between estimated and measured value with R2 values of 0.976 and 0.968, respectively. MDSC-DeepLabv3+ outperformed the compared models with mPA and mIoU of 97.55% and 94.84%, respectively. Compared to the baseline DeepLabv3+, MDSC-DeepLabv3+ demonstrated significant improvements in mPA and mIoU and reduced Params, FLOPs, and inference time, making it suitable for deployment on edge devices and real-time inference. The average relative errors of breakage and impurity ratios between estimated and measured values were 11.3% and 6.5%, respectively. Overall, this novel approach enables high-precision, efficient, and intelligent detection of breakage and impurity ratios for raw sugarcane.

Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis.

In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality.

Purification of aquaculture wastewater by macrophytes and biofilm systems: Efficient removal of trace antibiotics and enrichment of antibiotic resistance genes.

The purification performance of aquaculture wastewater and the risk of antibiotic resistance genes (ARGs) dissemination in wetlands dominated by macrophytes remain unclear. Here, the purification effects of different macrophytes and biofilm systems on real aquaculture wastewater were investigated, as well as the distribution and abundance of ARGs. Compared to the submerged macrophytes, artificial macrophytes exhibited higher removal rates of TOC (58.80 ± 5.04 %), TN (74.50 ± 2.50 %), and TP (77.33 ± 11.66 %), and achieved approximately 79.92 % removal of accumulated trace antibiotics in the surrounding water. Additionally, the biofilm microbial communities on the surface of artificial macrophytes exhibited higher microbial diversity with fewer antibiotic-resistant bacteria (ARB) enrichment from the surrounding water. The absolute abundance of ARGs (sul1, sul2, and intI1) in the mature biofilm to be one to two orders of magnitude higher than that in the water. Although biofilms could decrease ARGs in the surrounding water by enriching ARB, the intricate network structure of biofilms further facilitated the proliferation of ARB and the dissemination of ARGs in water. Network analysis suggested that Proteobacteria and Firmicutes phyla were dominant and potential carriers of ARGs, contributing 69.00 % and 16.70 %, respectively. Our findings highlight that macrophytes and biofilm systems have great performance on aquaculture wastewater purification, but with high risk of ARGs.

Role of COL6A2 in malignant progression and temozolomide resistance of glioma.

BACKGROUND: Gliomas are one of the most common primary malignant tumors of the central nervous system, and have an unfavorable prognosis. Even combining precise surgery, chemotherapy and radiotherapy, the survival rate is still unsatisfactory. Chemotherapy resistance is one of main reasons for its adverse prognosis. As shown by several studies, glioma stem cells (GSCs) were correlated with radiotherapy/chemotherapy resistance and high relapse rate. This study aimed to find a new biomarker related to GSCs and chemotherapy resistance. METHODS: TCGA, CGGA, GSE16011, GSE23806 and GDSC datasets were used to screen the genes related to GSCs, Temozolomide (TMZ) resistance, and survival. In the TCGA, GTEx, GSE16011 and CGGA datasets, mRNA level, prognostic value, and correlation with immune infiltration in the selected genes were analyzed through methods including Kaplan-Meier analysis, Cox analysis, the ESTIMATE algorithm, and the CIBERSORT algorithm. The expression of COL6A2 mRNA and protein in different groups was detected by RT-qPCR and western blot. A MTT assay and flow cytometry were used to measure the effect of COL6A2 on proliferation and apoptosis of glioma cells. RESULTS: COL6A2 was positively correlated with glioma stemness and TMZ resistance. Its expression was up-regulated in GBM, and high expression was correlated with adverse prognosis. As shown by Cox analysis, COL6A2 was an independent prognostic factor for glioma. COL6A2 mRNA was increased with the glioma grade. It was over-expressed in MGMT non-methylation and IDH wild-type specimens. The results of in vitro experiments showed that COL6A2 promots proliferation of glioma cells and inhibits their apoptosis. Meanwhile, the expression of COL6A2 in TMZ-resistant glioma cells was significantly higher than that in ordinary glioma cells. As shown by GO and KEGG pathway analysis, COL6A2 was correlated with glioma proliferation, migration, invasion, and immunity. In particular, it was significantly positively correlated with PD-1, PD-L2, PD-L1, B7-H3, CTLA-4, IDO1 and TIM-3 expression, further verifying that it may play an important role in immune response. In addition, COL6A2 might influence immune cell infiltration in the glioma microenvironment. CONCLUSION: COL6A2 high-expression is an indicator for adverse glioma prognosis, and is correlated with TMZ-resistant and immune response. Meanwhile, it may be a prospective biomarker for treatment.

Transcriptome sequencing analysis of the role of miR-499-5p and SOX6 in chicken skeletal myofiber specification.

MicroRNAs (miRNAs) might play critical roles in skeletal myofiber specification. In a previous study, we found that chicken miR-499-5p is specifically expressed in slow-twitch muscle and that its potential target gene is SOX6. In this study, we performed RNA sequencing to investigate the effects of SOX6 and miR-499-5p on the modulation and regulation of chicken muscle fiber type and its regulatory mechanism. The expression levels of miR-499-5p and SOX6 demonstrated opposing trends in different skeletal muscles and were associated with muscle fiber type composition. Differential expression analysis revealed that miR-499-5p overexpression led to significant changes in the expression of 297 genes in chicken primary myoblasts (CPMs). Myofiber type-related genes, including MYH7B and CSRP3, showed expression patterns similar to those in slow-twitch muscle. According to functional enrichment analysis, differentially expressed genes were mostly associated with muscle development and muscle fiber-related processes. SOX6 was identified as the target gene of miR-499-5p in CPM using target gene mining and luciferase reporter assays. SOX6 knockdown resulted in upregulation of the slow myosin genes and downregulation of fast myosin genes. Furthermore, protein-protein interaction network analysis revealed that MYH7B and RUNX2 may be the direct targets of SOX6. These results indicated that chicken miR-499-5p may promote slow-twitch muscle fiber formation by repressing SOX6 expression. Our study provides a dataset that can be used as a reference for animal meat quality and human muscle disease studies.

Risk and benefit assessment of potential neurodevelopment effect resulting from consumption of cultured largemouth bass (Micropterus salmoides) in China.

The aim of this study was to evaluate the net effects of dietary consumption on the potential neurodevelopmental effects of largemouth bass (Micropterus Salmoides, simplify as bass) cultured in China, especially when the bait of largemouth bass is changed from iced trash fish to formulated feed. A total of three bait group bass samples were collected from main producing areas during harvest period, including formulated feed group, iced trash fish group, and both group (converting from iced trash fish to formulated feed). Net neurodevelopment value (expressed as intelligence quotient or IQ) was calculated using FAO/WHO deterministic methods and probabilistic assessment model. The results showed net IQ of largemouth bass fed by the three baits groups all showed positive or beneficial neurodevelopmental effects, with the values of 1.55 ± 0.97 (formulated feed group), 3.17 ± 1.76 (iced trash fish group), and 2.65 ± 1.29 (both group) respectively. Bass samples fed with ice trash fish showed the highest neurodevelopmental effect. The present study suggested that more valuable formulated feed should be developed to improve the quality of cultured largemouth bass.

Determination of trace organic contaminants by a novel mixed-mode online solid-phase extraction coupled to liquid chromatography-tandem mass spectrometry.

In this study, a novel mixed-mode online solid-phase extraction (SPE) method was developed to recover miscellaneous trace organic contaminants (TrOCs) from environmental water samples. Six kinds of sorbents, including C18 substances, hypercross-linked polymers (2), cation-exchange resins, anion-exchange resins, and graphitized nonporous carbons, were packed into a single online SPE cartridge. Furthermore, a fully automated analytic method was established by coupling this mixed-mode online SPE with liquid chromatography tandem mass spectrometry (online SPE-LC-MS/MS). Sixty-nine TrOCs with diverse properties were selected to examine the performance of this mixed-mode SPE cartridge in comparison with solo-mode online SPE cartridges. The method quantification limit (MQL) and the relative recovery coefficient of TrOCs in diverse water matrices, including groundwater, surface water and sewage effluent were evaluated. The MQL of most TrOCs was lower than 10 ng L-1. The relative recovery coefficients for most TrOCs in the groundwater (50/69) and surface water (38/69) matrix fit in the satisfactory range. Moreover, mixed-mode online SPE coupled with LC-high-resolution MS was applied for a suspect screening of TrOCs in sewage effluents. A series of highly polar TrOCs that had scarcely been reported by previous studies were identified by this practical and easily accessible method. Finally, this novel mixed-mode online SPE with LC-MS/MS method was applied to quantify the TrOCs in the environmental water samples.

Photosensitized Transformation of Peroxymonosulfate in Dissolved Organic Matter Solutions under Simulated Solar Irradiation.

Sulfate radical (SO4•-)-mediated advanced oxidation processes via peroxymonosulfate (PMS) activation have been extensively investigated. However, the phototransformation of PMS in sunlit dissolved organic matter (DOM) solution has not been previously examined. For the first time, the photosensitized transformation of PMS in DOM-enriched solutions under simulated solar irradiation was observed. The generation of reactive species, including 1O2, SO4•-, and •OH, was confirmed by electron paramagnetic resonance and quantified by chemical probes. SO4•- was the primary reactive species generated via the reaction of excited triplet DOM (3DOM*) with PMS. 3DOM* acted as a reactive reductant and was quickly oxidized by PMS, with an estimated reaction rate constant of (4.09 ± 0.21) × 108 M-1 s-1. Compared to 3DOM*, one-electron-reducing DOM (DOM•-) was a minor contributor to the photosensitized transformation of PMS, and the contribution of DOM•- relied on the phenolic constituents. In addition, a series of different types of DOM, including terrestrial DOM, autochthonous DOM, and effluent organic matter and its fractions, were employed to examine the photosensitized transformation kinetics of PMS. Overall, the photosensitized transformation of PMS by irradiated DOM could be a useful and economical approach to generate SO4•- under environmentally relevant conditions.

From pond to table: Differences in breeding and consumption affect the balance between dietary risk of residual cadmium and uptake benefits of nutrients in Chinese mitten crab (Eriocheir sinensis).

We used a risk-benefit model to evaluate the effects of different farming methods and consumption habits on dietary risk of Chinese mitten crab. In this study, we found that cadmium levels in the total edible parts and brown meat were 0.029-0.462 mg/kg and 0.017-1.694 mg/kg, respectively. Cadmium exposure experiment showed that brown meat was the main enrichment site of cadmium. Fatty acid test found that the EPA + DHA content in total edible parts fed with formulated feed and iced trash fish was 19.64 ± 3.62 mg/g and 28.72 ± 2.30 mg/g (p > 0.05), respectively, and that in brown meat was 27.66 ± 5.16 mg/g and 40.15 ± 3.50 mg/g (p > 0.05), respectively. According to the risk-benefit model analysis, the dietary risk of brown meat under the two breeding methods is relatively high, but the risk quotient is less than 1.

Population Structure and Genetic Diversity of Seven Chinese Indigenous Chicken Populations in Guizhou Province.

To investigate the population structure and genetic diversity of indigenous chicken breeds in Guizhou, a total of 150 individual samples were collected from 12 breeds, including seven local chicken breeds in Guizhou Province, three Chinese native breeds found in other provinces, and two commercial breeds. The genotype datasets were obtained using a 50K single nucleotide polymorphism array method, and then a series of population analyses were performed. The obtained population parameters and linkage disequilibrium decay indicated a higher degree of genetic diversity in Guizhou chickens than in commercial breeds. Two Guizhou local breeds, Wumeng black-bone and Weining, were clustered with a breed from a neighboring province, Xinwen black-bone, which exhibited similar ancestral composition patterns. A newly found breed, Wumeng crested, had high genetic diversity and displayed genetic differences from other Guizhou breeds. These findings provide insight into the establishment of efficient conservation and utilization programs for Guizhou chicken breeds.

Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens.

SART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.

Deep sequencing microRNA profiles associated with wooden breast in commercial broilers.

Wooden breast (WB) is a muscle disorder affecting modern commercial broiler chickens that leads to a palpable firm pectoralis major muscle and causes severe reduction in meat quality, resulting in substantial economic losses for the poultry industry. Most studies have focused on the regulatory mechanisms underlying this defect with respect to the gene and protein expression levels as well as the levels of metabolites. MicroRNAs (miRNAs) play critical roles in human muscular disorders, such as the Duchenne muscular dystrophy, by regulating the muscle regeneration or fibrosis processes. In this study, we investigated the miRNAs and related pathways that play important roles in the development of WB. We generated the miRNA expression profiles of the pectoralis major muscle samples from 3 WB-affected and 3 nonaffected chickens selected from a commercial broiler population via small RNA sequencing. A total of 578 miRNAs were identified in the chicken breast muscles from the initial analysis of the sequencing data. Of these, 23 miRNAs were significantly differentially expressed (false discovery rate [FDR] <0.05, log2|Foldchange| >1), including 20 upregulated and 3 downregulated miRNAs in the WB group compared to the normal group. Moreover, functional enrichment of the predicted target genes of differential miRNAs indicated that these miRNAs were involved in biological processes and pathways related to energy metabolism, apoptosis, focal adhesion, and development of blood vessels. Four differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). We also highlighted several differentially expressed miRNAs, such as gga-miR-155, gga-miR-29c, and gga-miR-133, for their potential roles in the regulation of the development of WB. To the best of our knowledge, this is the first study investigating the miRNA expression profile of the breast muscle associated with WB. The findings of this study can be used to explore the potential molecular mechanisms of other muscle disorders in broilers and provide valuable information for chicken breeding.

Microheterogeneous Distribution of Hydroxyl Radicals in Illuminated Dissolved Organic Matter Solutions.

Hydroxyl radicals (•OH) are important reactive species that are photochemically generated through solar irradiation of chromophoric dissolved organic matter (CDOM) in surface waters. However, the spatial distribution within the complex three-dimensional structure of CDOM has not been examined. In this study, we used a series of hydrophobic chlorinated paraffins as chemical probes to elucidate the microheterogeneous distribution of •OH in illuminated CDOM solutions. The steady-state concentration of •OH inside the CDOM microphase is 210 ± 31-fold higher than the concentration in the aqueous phase. Our results suggest that the most photochemically generated •OH are confined into the CDOM microphase. Thus, illuminated CDOM behaves as a natural microreactor for •OH-based oxidations. By including intra-CDOM •OH, the quantum yield of •OH for CDOM solutions was estimated to be 2.2 ± 0.5 × 10-3, which is 2 orders of magnitude greater than previously thought. The elevated concentrations of photogenerated •OH within the CDOM microphase may improve the understanding of hydrophobic pollutant degradation in aqueous environments. Moreover, our results also suggest that •OH oxidation may play more important roles in the phototransformation of CDOM than previously expected.

Identifying Signatures of Selection Related to Comb Development.

The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens' comb formation. Fixation index (FST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger FST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, FST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.

Identification of genes involved in inbreeding depression of reproduction in Langshan chickens.

OBJECTIVE: Inbreeding depression of reproduction is a major concern in the conservation of native chicken genetic resources. Here, based on the successful development of strongly inbred (Sinb) and weakly inbred (Winb) Langshan chickens, we aimed to evaluate inbreeding effects on reproductive traits and identify candidate genes involved in inbreeding depression of reproduction in Langshan chickens. METHODS: A two-sample t-test was performed to estimate the differences in phenotypic values of reproductive traits between Sinb and Winb chicken groups. Three healthy chickens with reproductive trait values around the group mean values were selected from each of the groups. Differences in ovarian and hypothalamus transcriptomes between the two groups of chickens were analyzed by RNA sequencing (RNA-Seq). RESULTS: The Sinb chicken group showed an obvious inbreeding depression in reproduction, especially for traits of age at the first egg and egg number at 300 days (p<0.01). Furthermore, 68 and 618 differentially expressed genes (DEGs) were obtained in the hypothalamus and ovary between the two chicken groups, respectively. In the hypothalamus, DEGs were mainly enriched in the pathways related to vitamin metabolism, signal transduction and development of the reproductive system, such as the riboflavin metabolism, Wnt signaling pathway, extracellular matrix-receptor interaction and focal adhesion pathways, including stimulated by retinoic acid 6, serpin family F member 1, secreted frizzled related protein 2, Wnt family member 6, and frizzled class receptor 4 genes. In the ovary, DEGs were significantly enriched in pathways associated with basic metabolism, including amino acid metabolism, oxidative phosphorylation, and glycosaminoglycan degradation. A series of key DEGs involved in folate biosynthesis (gamma-glutamyl hydrolase, guanosine triphosphate cyclohydrolase 1), oocyte meiosis and ovarian function (cytoplasmic polyadenylation element binding protein 1, structural maintenance of chromosomes 1B, and speedy/RINGO cell cycle regulator family member A), spermatogenesis and male fertility (prostaglandin D2 synthase 21 kDa), Mov10 RISC complex RNA helicase like 1, and deuterosome assembly protein 1) were identified, and these may play important roles in inbreeding depression in reproduction. CONCLUSION: The results improve our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction and provide a theoretical basis for the conservation of species resources.

A gene co-expression network analysis of the candidate genes and molecular pathways associated with feather follicle traits of chicken skin.

Back and thigh skin of chickens showed significant differences in the thickness and the feather follicle density and size, which are important traits for slaughtered chickens' appearance. In the present study, global gene expression profiling was conducted in the back and thigh skin of chickens using Microarray technology. The results showed that 676 genes were differentially expressed between back and thigh skin. The expression of the differentially expressed genes (DEGs), including PPP1R3C, IGF1, PTCHD1, HOXB6, FGF9, CAMK4, SHH, BMP8B, FOXN1 and PTGER2, was validated by real-time quantitative polymerase chain reaction (RT-qPCR), and the results were consistent with microarray results. Functional analysis revealed that the DEGs were significantly involved in cell proliferation, differentiation, apoptosis, adhesion and transport process, and the pathways were significantly mapped into the ECM-receptor interaction, peroxisome, focal adhesion, Hedgehog and PPAR signalling pathways. Protein-protein interaction network analysis suggested that signalling pathways related to feathers morphogenesis and development, such as Wnt, FGF, MAPK, SHH and BMP signalling pathways, occupied important positions in the network. Genes involved in these signalling pathways and adhesion molecules might play a vital role in skin and feather follicle development. Further single nucleotide polymorphism (SNP) association analysis of Wnt3A showed that the AC genotype of SNP g.255361 C>A significantly increased the feather follicle density of thigh skin. Our findings may provide new insights on candidate genes and pathways related to skin and feather follicle formation of chickens.

Quantitative benefit and risk assessment of cadmium and nutrient levels in Chinese mitten crab (Eriocheir sinensis).

The use of Chinese mitten crabs for human consumption is controversial due to their uptake of heavy metals, such as cadmium (Cd). We developed a formula for quantification of benefit and risk assessment (hazard quotient) for the intake of a product containing essential polyunsaturated fatty acids versus heavy metals. A total of 70 samples (2100 individuals) of crabs were collected from 6 representative basins in Jiangsu province to determine Cd levels. Cd levels ranged from 0.028 to 5.015 mg kg-1, and the levels among the basin regions were similar (p > 0.05). To determine the nutritional differences between crabs fed with iced trash fish and formulated feed, we conducted a comparative aquaculture experiment. We simulated the cultivation conditions of crabs in China and found that the nutritional content in the trash fish group (28.724 ± 2.301 mg kg-1) was significantly higher than in the formulated food group (19.278 ± 3.556 mg kg-1; p < 0.05). The differences in the hazard quotient of benefit and risk balance between these two diets were not significant (p > 0.05). The average hazard quotient of iced trash fish feed culture was 0.023 ± 0.019, compared with the formulated feed culture (0.034 ± 0.028). Formulated feed and iced trash fish produce similar results as culture food for the Chinese mitten crab. In terms of cadmium exposure risk, the appropriate daily consumption of crabs is less than eight. These data can help justify culture using formulated food and the sustainable development of the Chinese mitten crab industry.

miRNA-mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome.

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.

Genome-wide analysis of the role of DNA methylation in inbreeding depression of reproduction in Langshan chicken.

Inbreeding depression of chicken reproduction is a major concern in the conservation of chicken genetic resources. To investigate the potential DNA methylation sites involved in the inbreeding depression of chicken reproduction, we carried out whole-genome bisulfite sequencing (WGBS) of hypothalamus and ovary tissues from the strongly and weakly inbred Langshan chickens, respectively. 5948 and 4593 differentially methylated regions (DMRs) were identified in the hypothalamus and ovary between the strongly and weakly inbred Langshan chickens, respectively. Large numbers of DMR-related genes (DMGs) were enriched in reproduction-related pathways. By combining the WGBS and transcriptome data, two DMRs in SRD5A1 and CDC27 genes were inferred as the most likely biomarkers of inbreeding depression of reproduction in Langshan chicken. Our study provides the first systematic investigation of the DNA methylation changes in strongly inbred chickens, and extends our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction.