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This study examined the effect of the synbiotic product (PoultryStar®me) on Fayoumi and Cobb chickens upon exposure to Salmonella typhimurium (ST) infection and compared the responses of Fayoumi and Cobb chickens to ST infection. Fayoumi and Cobb chicks were fed synbiotic 1 g/kg feed from the first day. At 21 days of age, the chicks were orally challenged with 3 × 1012 cfu ST. At 72 h post-infection (pi), Fayoumi chickens showed significantly lower bacterial loads in their livers than Cobb chickens (p

Introduction: Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems. Object: Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood. Method: We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping and the Mendelian randomization was applied. Result: We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes. Conclusion: Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory target (SOX6–MYH1s axis) for breast muscle yield and myopathy, which could aid in the development of genome-scale selective breeding aimed at high meat yield in broiler chickens.

Study region: The Chaohe watershed is Beijing's primary potable water source. Study focus: The initiation of ecological restoration (ER), combined with the rapid acceleration of climate change (CC), has precipitated severe water shortages in North China. The seasonal responses of baseflow (BF), pivotal for sustaining rivers' fundamental flow and ecological equilibrium, to ER and CC are poorly understood. This study provides a precise depiction of the seasonal variations in BF by leveraging multiple separation methodologies. By applying the BFAST algorithm and a comprehensive sensitivity analysis, we unveil the nuanced seasonal patterns of BF adjustments in reaction to ER and CC. New hydrological insights for the region: Baseflow, primarily influenced by the wet season, constituted 64.21% of the annual aggregate. Considerable decreases in BF during the dry (−32.61%) and wet (−68.21%) seasons pose increasing threats to available water resources. The decrease in sub-surface runoff (−1.91 mm per decade) dominated the reduction of dry season BF. Indeed, vegetation regulated seasonal water distribution, maintaining the essential flow throughout the dry season. In the wet season, the reduction in BF acts as a supplemental water source to fulfill the escalating evapotranspiration needs due to afforestation and a drying climate. This study highlights the persistent hydrological consequences of ER and CC on water resources, emphasizing the crucial function of vegetation in baseflow, a key component for ecological restoration and water resource management in water-limited areas.

AimsProstate cancer patients face impaired body image and psychological distress during the diagnosis and treatment of the disease, which leads to changes in mood, cognition and behavior. Psychological resilience has been shown to buffer shocks and stresses from the disease. Therefore, this study investigates the relationship between family functioning and psychological resilience in prostate cancer patients and the mediating role of self-efficacy between family functioning and psychological resilience to provide a relevant theoretical basis for improving patients' psychological status by providing relevant theoretical basis.MethodUsing a cross-sectional design, participants were 215 patients with prostate cancer admitted to and treated in a tertiary hospital in Jiangsu province, China. Questionnaires were administered using the general information questionnaire, the Connor-Davidson Resilience Scale (CD-RISC), the Family Adaptation, Partnership, Growth, Affection, and Resolution Index (APGAR), and the General Self-efficacy Scale (GSES). Data were analyzed using descriptive and correlational analyses and the bootstrap mediation test was used to test the effect relationship between the variables.ResultsFamily functioning, self-efficacy and psychological resilience were significantly and positively correlated (r = 0.526, P < 0.01; r = 0.378, P < 0.01; r = 0.358, P < 0.01). The mediating effect of psychological resilience between family functioning and psychological resilience was significant, accounting for 42.56%.ConclusionFamily function and self-efficacy have been shown to increase the level of psychological resilience in prostate cancer patients. Attention should be paid to the mental health problems of prostate cancer patients, early screening and intervention, and the use of patients' family resources to improve their confidence in recovering from the disease, thus increasing their psychological resilience and improving their mental health.

ABSTRACT: Semen volume is an important economic trait of broilers and one of the important indices for continuous breeding. The objective of this study was to identify genes related to semen volume through transcriptome analysis of the testis tissue of white feather broilers. The testis samples with the highest semen volume (H group, n = 5) and lowest semen volume (L group, n = 5) were selected from 400-day-old roosters for transcriptome analysis by RNA sequencing. During the screening of differentially expressed genes (DEGs) between the H and L groups, a total of 386 DEGs were identified, among which 348 were upregulated and 38 were downregulated. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune response, leukocyte differentiation, cell adhesion molecules and collagen binding played vital roles in spermatogenesis. The results showed that 4 genes related to spermatogenesis, namely, COL1A1, CD74, ARPC1B and APOA1, were significantly expressed in Group H, which was consistent with the phenotype results. Our findings may provide a basis for further research on the genetic mechanism of semen volume in white feather broilers.

Salmonella has been one of the most important factors restricting the development of the poultry industry and also poses great threat to public health. To get insight into molecular alterations that occur during bacterial infection, we sequenced the cecal tonsil transcriptome in 2 chicken breeds (Beijing-You and Cobb) known to have differing resistance to Salmonella. The 28-day-old chickens were orally challenged by 1.83 × 1011 CFU Salmonella Typhimurium, and the cecal tonsil transcriptome was sequenced 3 d postinfection. Analysis identified 201 and 170 differentially expressed genes response to Salmonella in 2 chicken breeds, respectively. They were involved in the Toll-like receptor signaling pathway and activated the production of pro-inflammatory cytokines and chemokines. The protein–protein interaction (PPI) network suggested MMP9 as a crucial protein that may be involved in extracellular matrix breakdown and leukocyte migration in the resistant breed (Beijing-You). Meanwhile, in susceptible chickens (Cobb), ACOD1 was the key gene in the PPI network and might promote the expression of genes related to oxidative stress response and gastrointestinal tract function. These findings provide insight into the differing resistance of these 2 chicken breeds.

During the process of dune vegetation restoration, understanding how grazing disturbance affects the relationship between plant species is a critical issue in ecological studies. However, there is insufficient evidence on the changes in the interaction between dominant shrubs and understory vegetation under grazing behavior. We aimed to study how grazing and dune stabilization affects the relationship between Caragana microphylla and understory vegetation. We established fencing at various stages of dune stabilization and proceeded to compared the performance indicators (e.g., richness and biomass) and the relative interaction index of understory vegetation and different functional groups along the dune stability under grazing and fencing conditions. Results showed that C. microphylla had facilitation on understory plants, and increased with dune stability, while the facilitation of Caragana microphylla on understory vegetation was stronger under grazing conditions. As sand dune stabilization increases, the facilitation of C. microphylla on understory vegetation diversity decreases significantly. However, there was no significant difference in the facilitation of C. microphylla on understory vegetation biomass at different stages of sand dune stabilization. This is related to the survival strategy of perennials being less tolerant to environmental stress than annuals, because grazing increased the richness of both annuals and perennials while reducing the overall biomass, and in the later stages of sand dune stabilization, and the facilitation of C. microphylla on perennials was higher than on annuals. Our study highlights the importance of the responses of different life-form groups to environmental factors and grazing disturbance during the process of sand dune vegetation restoration, as they play a crucial role in shaping the development of the relationship between understory vegetation and dominant shrubs.

Abstract The intermittent access of renewable energy sources leads to a significant increase in fault short‐circuit currents in power grid. DC superconducting fault current limiters (SFCL) can limit short‐circuit currents in flexible DC transmission systems, which work in combination with direct current circuit breaker (DCCBs) to protect the grid system effectively. However, for the parameter design of DC superconducting fault current limiter (DCSFCL), it is difficult to balance the economics of the device and its adaptability to different fault situations. In this paper, a cross‐mapping design methodology for the DCSFCL is proposed and applied in the Nan'ao flexible DC transmission project, China. A cross‐mapping method is designed combining the critical parameters of DCSFCL and the system parameters. A three‐terminal simulation model of the flexible DC transmission system is constructed through MATLAB/Simulink and the design process of DCSFCL parameters is introduced. A cyclic calculation approach is proposed for the design of DCSFCL parameters through three fault conditions of the power system. Meanwhile, impact current short‐circuits test and artificial ground short‐circuit test were conducted on the prototype. Test results show that the designed DCSFCL meets the requirements of practical applications.

Shrubs are a key component of desert ecosystems, playing a crucial role in controlling desertification and promoting revegetation, yet their growth is often impeded by drought. Leaf hydraulic traits and economic traits are both involved in the process of water exchange for carbon dioxide. Exploring the characteristics, relationships, and anatomical basis of these two suites of traits is crucial to understanding the mechanism of desert shrubs adapting to the desert arid environment. However, the relationship between these two sets of traits currently remains ambiguous. This study explored the leaf hydraulic, economic, and anatomical traits of 19 desert shrub species. The key findings include the following: Relatively larger LT values and smaller SLA values were observed in desert shrubs, aligning with the “slow strategy” in the leaf economics spectrum. The relatively high P50leaf, low HSMleaf, negative TLPleaf, and positive HSMtlp values indicated that severe embolism occurs in the leaves during the dry season, while most species were able to maintain normal leaf expansion. This implies a “tolerance” leaf hydraulic strategy in response to arid stress. No significant relationship was observed between P50leaf and Kmax, indicating the absence of a trade-off between hydraulic efficiency and embolism resistance. Certain coupling relationships were observed between leaf hydraulic traits and economic traits, both of which were closely tied to anatomical structures. Out of all of the leaf traits, LT was the central trait of the leaf traits network. The positive correlation between C content and WPleaf and HSMleaf, as well as the positive correlation between N content and HSMtlp, suggested that the cost of leaf construction was synergistic with hydraulic safety. The negative correlation between SLA, P content, GCL, and SAI suggested a functional synergistic relationship between water use efficiency and gas exchange rate. In summary, this research revealed that the coupling relationship between leaf hydraulic traits and economic traits was one of the important physiological and ecological mechanisms of desert shrubs for adapting to desert habitats.

Genomic and transcriptomic profiling in Jingxing yellow chickens selected for a heterophil-lymphocyte ratio (H/L) provides further insight on the genetic basis of H/L and identifies PTPRJ as a relevant factor.

Abstract Background Egg production is economically important in the meat-type chicken industry. To better understand the molecular genetic mechanism of egg production in meat-type chicken, genetic parameter estimation, genome-wide association analyses combined with meta-analyses, Bayesian analyses, and selective sweep analyses were performed to screen single nucleotide polymorphisms (SNPs) and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines. Results Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age, with heritability ranging from 0.034–0.258. Based on meta-analyses and selective sweep analyses, one region (10.81–13.05 Mb) on chromosome Z was associated with egg number in all lines. Further analyses using the W2 line was also associated with the same region, and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers. The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2. There are 36 genes in the region, with glial cell derived neurotrophic factor, DAB adaptor protein 2, protein kinase AMP-activated catalytic subunit alpha 1, NAD kinase 2, mitochondrial, WD repeat domain 70, leukemia inhibitory factor receptor alpha, complement C6, and complement C7 identified as being potentially affecting to egg number. In addition, three SNPs (rs318154184, rs13769886, and rs313325646) associated with egg number were located on or near the prolactin receptor gene. Conclusion Our study used genomic information from different chicken lines and populations to identify a genomic region (spanning 2.24 Mb) associated with egg number. Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production. These results contribute to the identification of candidate genes and variants for egg traits in poultry.

Semi-hydrogenation of acetylene in excess ethylene is a key industrial process for ethylene purification. Here the authors develop highly stable Pd1/TiO2 single-atom catalyst for photo-thermo semi-hydrogenation of acetylene.

The recent oscillation events in offshore wind farms (OWFs) connected via a modular multilevel-converter-based HVDC (MMC-HVDC) system are developing towards a wider frequency band, which causes complex a small-signal interaction phenomenon and difficulties in the stability analysis and control. In this paper, the wideband dynamic interaction mechanism is investigated based on the impedance analysis method and an improved control strategy using an optimization algorithm is proposed to improve the small-signal stability and reduce the oscillation risks. First, the detailed impedance models of the grid-connected system are established considering the distribution characteristics of the submarine cable, control delay and frequency coupling effect. Then, combined with the active damping control method, the wideband resonance mechanism is analyzed, and the stability constraints of controller parameters are obtained using the impedance stability criterion. Finally, an improved multi-objective slime mold algorithm (MOSMA)-based coordinated optimization control strategy is proposed to enhance the adaptability of the controller parameters and the wideband damping ability of a grid-connected system, which can improve the wideband stability of the system. The simulation and experimental results verify the proposed control strategy.

Affected by the pressure and constraints of available resources, plant growth and development, as well as plant life history strategies, usually vary with environmental conditions. Plant buds play a crucial role in the life history of woody plants. Nitraria tangutorum is a common dominant woody species in desertified areas of northern China and its growth is critical to the desert ecosystem. Revealing the allometry of N. tangutorum aboveground bud fates and the linkage between bud traits and plant nutrient contents and stoichiometric ratios can be useful in understanding plant adaptation strategy. We applied seven nitrogen and phosphorus fertilizer addition treatments to natural N. tangutorum ramets in Ulan Buh Desert in three consecutive years. We surveyed three types of aboveground buds (dormant buds, vegetative buds, and reproductive buds) in each N. tangutorum ramet, then measured the plant carbon (C), nitrogen (N), and phosphorus (P) contents and ratios during three consecutive years. We specified that reserve growth potential (RGP), vegetative growth intensity (VGI) and sexual reproduction effort (SRE) are the three indices of bud dynamic pattern. The results showed that the bud dynamic pattern of N. tangutorum ramets differed significantly among different fertilizer addition treatments and sampling years. The allometry of RGP, VGI, and SRE was obvious, showing size dependence. The allometric growth relationship fluctuated among the sampling years. The linkage between bud traits and plant stoichiometric characteristics of N. tangutorum ramets showed close correlation with plant P content, C:P and N:P ratios, no significant correlation with plant C content, N content and C:N ratio. These results contribute to an improved understanding of the adaptive strategies of woody plants growing in desert ecosystems and provide insights for adoption of effective measures to restore and conserve plant communities in arid and semi-arid regions.

Phagocytosis of macrophages constitutes a powerful barrier to innate immunity. Differences in the phagocytic function of macrophages among chicken breeds have rarely been reported, and the molecular mechanisms underlying phagocytosis remain poorly understood. This study compared functional difference of macrophages in Dagu chickens, originated in Zhuanghe, Liaoning Province, China, and Wenchang chickens, originated from Hainan Island in the South China Sea, and explored the potential molecular mechanisms by integrated analysis of mRNA expression profiles of macrophages and whole genome sequencing. Immunological parameters in peripheral blood indicated that Dagu chickens were more resistant to Salmonella challenge at 28 days old. Phagocytosis index and phagocytosis rate of macrophages displayed Dagu chickens performed a significantly higher phagocytic ability of macrophages at 14 and 28 days old. Furthermore, comparative analysis of mRNA expression profiles of macrophages of two breeds at 28 days old revealed that 1136 differentially expressed genes (DEGs), and 22 DEGs (e.g., H2AFZ, SNRPA1, CUEDC2, S100A12) were found to be hub genes regulating phagocytosis by participating in different immunological biological signaling pathways. In addition, many DEGs and hub genes were under strong differentiation in genome between two breeds, the H2AFZ gene was an intersection of DEGs and hub genes. These results provided a comprehensive functional comparison and transcriptomic profiles of macrophages in Chinese native chicken breeds, and deepened our understanding of the genetic mechanism of innate immunity.

With the development and wider application of meta-heuristic optimization algorithms, researchers increasingly apply them to threshold optimization of multi-level image segmentation. This paper explores the performance and effects of Capuchin Search Algorithm (CAPSA) in threshold optimization. To solve problems of uneven distribution in the initial population of Capuchin Search Algorithm, low levels of global search performance and premature falling into local optima, this paper proposes an improved Capuchin Search Algorithm (ICAPSA) through a multi-strategy approach. ICAPSA uses chaotic opposite-based learning strategy to initialize the positions of individual capuchins, and improve the quality of the initial population. In the iterative position updating process, Levy Flight disturbance strategy is introduced to balance the global optimization and local exploitation of the algorithm. Finally, taking Kapur as the objective function, this paper applies ICAPSA to multi-level thresholding in the plant images, and compares its segmentation effects with the original CAPSA, the Fuzzy Artificial Bee Colony algorithm (FABC), the Differential Coyote Optimization Algorithm (DCOA), the Modified Whale Optimization Algorithm (MWOA) and Improved Satin Bowerbird Optimization Algorithm (ISBO). Through comparison, it is found that ICAPSA demonstrates superior segmentation effect, both in the visual effects of image segmentation and in data comparison.

As the dominant shrub community plant in the Mu Us Sandy Land, S. vulgaris is the key factor of ecological environment restoration in the Mu Us Sandy Land, It is of great significance to explore the estimation and inversion of content based on spectrum for ecological environment evaluation and intervention in Mu Us Sandy Land. The SVC HR-1024 portable feature spectrometer and SPAD 502 chlorophyll meter were used to study Mu Us Sandy Land of S. vulgaris. The best band is screened by correlation matrix method, the best vegetation index is screened by Structural Equation Modeling model, and then the best inversion model is established by different mathematical modeling methods. Results revealed that the vegetation indices and chlorophyll content were correlated, combining the six vegetation indices revealed that 610–690nm and 700–940 nm were the bands with the highest correlation. In the selection of optimal vegetation index, NDVI, ratio vegetation index and mNDVI perform best and are suitable for subsequent modeling. Of the four models, the partial least squares model had the best fitting effect (R2 > 0.91). The univariate linear regression model had the simplest processing procedure, but its accuracy was unstable (R2 = 0.1–0.9). multivariate stepwise regression accuracy is also appropriate (R2 > 0.8). The stability of BP neural network modeling is not high. Compare the four methods, PLS and multivariate stepwise regression have their own advantages, and the accuracy is higher, you can make a choice according to the demand as the late modeling method.

Toll-like receptors (TLRs) are involved in the sensing of pathogen-associated molecular patterns (PAMPs) such as lipopolysaccharide (LPS), flagellin, unmethylated double-stranded DNA (CpG), single-stranded RNA (ssRNA) and lipoproteins. Myeloid differentiation primary response protein 88 (MyD88) is a canonical adaptor for the Toll-like receptor family which has crucial roles in host defense against infection by microbial pathogens. The dysregulation of MyD88 may also induce autoimmune diseases. Here, we demonstrate that the deubiquitinase USP7 interacts with MyD88 in chicken, with knockdown or overexpression of USP7 leading to the regulation of MyD88 protein in a positive manner. Consequently, USP7 positively regulates the expression of proinflammatory factors upon LPS challenge. Furthermore, we observed USP7-deficient mice to be more susceptible to infection by Salmonella typhimurium. Collectively, our findings demonstrate MyD88 as a bona fide substrate of USP7 and uncover a mechanism by which USP7 regulates innate immune signaling.

Abstract Background Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. Results Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34–2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27–92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. Conclusions We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

ABSTRACT: Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (

The gastrointestinal microbiota plays a vital role in ensuring the maintenance of host health through interactions with the immune system. The Heterophil/Lymphocyte (H/L) ratio reflects poultry’s robustness and immune system status. Chickens with low H/L ratio are superior to the chickens with high H/L ratio in survival, immune response, and resistance to Salmonella infection, but the underlying mechanisms remain unclear. This study aimed to identify microorganisms associated with resistance to Salmonella Enteritidis infection in chickens based on the H/L ratio. The 16S rRNA and metagenomic analysis were conducted to examine microbiome and functional capacity between the 2 groups, and Short Chain Fatty Acids (SCFAs) and histopathology were conducted to explore the potential difference between susceptible and resistant groups at 7 and 21 days post-infection (dpi). The microbiome exploration revealed that low H/L ratio chickens, compared to high H/L ratio chickens, displayed a significantly higher abundance of Proteobacteria (Escherichia coli) and Bacteroidetes (Bacteroides plebeius) at 7 and 21 dpi, respectively. Anaerostipes (r = 0.63) and Lachnoclostridium (r = 0.63) were identified as bacterial genus significantly correlated with H/L (P < 0.001). Interestingly, Bacteroides was significantly and positively correlated with bodyweight post-infection (r = 0.72), propionate (r = 0.78) and valerate (r = 0.82) contents, while Salmonella was significantly and negatively correlated with bodyweight post-infection (r = − 0.67), propionate (r = − 0.61) and valerate (r = − 0.65) contents (P < 0.001). Furthermore, the comparative analysis of the functional capacity of cecal microbiota of the chickens with high and low H/L ratio revealed that the chickens with low H/L ratio possess more enriched immune pathways, lower antibiotic resistance genes and virulence factors compared to the chickens with high H/L ratio. These results suggest that the chickens with low H/L ratio are more resistant to Salmonella Enteritidis, and it is possible that the commensal Proteobacteria and Bacteroidetes are involved in this resistance against Salmonella infection. These findings provide valuable resources for selecting and breeding disease-resistant chickens.

H5N1 avian influenza virus (AIV) is a highly pathogenic influenza virus that poses a substantial threat to poultry production and public health. A comprehensive understanding of host–pathogen interactions for AIV requires knowledge of gene expression changes in both the pathogen and the host upon infection. We report the use of dual RNA sequencing technology to uncover trends in gene expression in H5N1 AIV and chickens (DF1 cells) during the course of infection. The expression of all viral genes increased continuously from 0 to 20 h post infection. We also identified 2,762 differentially expressed host genes during infection. Pathway analysis found that genes related to the signaling pathways of DNA replication, T cell activation, NF-kappa B signaling pathway, and RNA degradation were significantly enriched. We demonstrated that the cis-acting lncRNA MSTRG.14019.1 targeted CSE1L and may affect virus replication. This study provides a more comprehensive and detailed understanding of host-virus interactions at the RNA level during the course of H5N1 AIV infection.

Abstract Intraductal papillary mucinous neoplasm (IPMN) is an intraepithelial precancerous lesion of pancreatic ductal adenocarcinoma (PDAC) that progresses from adenoma to carcinoma, and long noncoding RNAs (lncRNA) might be involved in the tumorigenesis. In this study, we obtained the expression profiles of more than 4000 lncRNAs by probe reannotation of a microarray dataset. As a correlation network‐based systems biology method, weighted gene coexpression network analysis (WGCNA) was used to find clusters of highly correlated lncRNAs in the tumorigenesis of IPMN, which covered four stepwise stages from normal main pancreatic duct to invasive IPMN. In the most relevant module (R2 = −0.75 and P = 5E‐05), three hub lncRNAs were identified (HAND2‐AS1, CTD‐2033D15.2, and lncRNA‐TFG). HAND2‐AS1 and CTD‐2033D15.2 were negatively correlated with the tumorigenesis (P in one‐way ANOVA test = 1.45E‐07 and 1.39E‐0.5), while lncRNA‐TFG were positively correlated with the tumorigenesis (P = 3.99E‐08). The validation set reached consistent results (P = 2.66E‐03 in HAND2‐AS1, 1.47E‐04 in CTD‐2033D15.2 and 6.23E‐08 in lncRNA‐TFG). In functional enrichment analysis, the target genes of microRNAs targeting also these lncRNAs were overlapped in multiple biological processes, pathways and malignant diseases including pancreatic cancer. In survival analysis, patients with higher expression of HAND2‐AS1‐targeted and CTD‐2033D15.2‐targeted microRNAs showed a significantly poorer prognosis in PDAC, while high expression of lncRNA‐TFG‐targeted microRNAs demonstrated an obviously better prognosis (log‐rank P

PurposeTo develop and validate a radiomics nomogram for the prediction of clinically significant prostate cancer (CsPCa) in Prostate Imaging-Reporting and Data System (PI-RADS) category 3 lesions.MethodsWe retrospectively enrolled 306 patients within PI-RADS 3 lesion from January 2015 to July 2020 in institution 1; the enrolled patients were randomly divided into the training group (n = 199) and test group (n = 107). Radiomics features were extracted from T2-weighted imaging (T2WI), apparent diffusion coefficient (ADC) imaging, and dynamic contrast-enhanced (DCE) imaging. Synthetic minority oversampling technique (SMOTE) was used to address the class imbalance. The ANOVA and least absolute shrinkage and selection operator (LASSO) regression model were used for feature selection and radiomics signature building. Then, a radiomics score (Rad-score) was acquired. Combined with serum prostate-specific antigen density (PSAD) level, a multivariate logistic regression analysis was used to construct a radiomics nomogram. Receiver operating characteristic (ROC) curve analysis was used to evaluate radiomics signature and nomogram. The radiomics nomogram calibration and clinical usefulness were estimated through calibration curve and decision curve analysis (DCA). External validation was assessed, and the independent validation cohort contained 65 patients within PI-RADS 3 lesion from January 2020 to July 2021 in institution 2.ResultsA total of 75 (24.5%) and 16 (24.6%) patients had CsPCa in institution 1 and 2, respectively. The radiomics signature with SMOTE augmentation method had a higher area under the ROC curve (AUC) [0.840 (95% CI, 0.776–0.904)] than that without SMOTE method [0.730 (95% CI, 0.624–0.836), p = 0.08] in the test group and significantly increased in the external validation group [0.834 (95% CI, 0.709–0.959) vs. 0.718 (95% CI, 0.562–0.874), p = 0.017]. The radiomics nomogram showed good discrimination and calibration, with an AUC of 0.939 (95% CI, 0.913–0.965), 0.884 (95% CI, 0.831–0.937), and 0.907 (95% CI, 0.814–1) in the training, test, and external validation groups, respectively. The DCA demonstrated the clinical usefulness of radiomics nomogram.ConclusionThe radiomics nomogram that incorporates the MRI-based radiomics signature and PSAD can be conveniently used to individually predict CsPCa in patients within PI-RADS 3 lesion.

To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L−1 nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes’ responses to increased nitrogen in the future.

Salmonella enterica serovar Typhimurium (ST) is a food-borne pathogen that can infect animals and humans. It is currently the most common bacterial pathogen that negatively affects the poultry industry. Although different chicken breeds have been observed to exhibit diverse resistance to ST infection, the underlying genetic mechanisms remain unclear and the genes involved in this differential disease resistance need to be identified. To overcome this knowledge gap, we used a liver transcriptome analysis to screen differentially expressed genes (DEGs) in two different chicken breeds (local Beijing You (BY) and commercial Guang Ming No. 2 broiler line B (GM)) before and after ST infection. We also performed weighted gene co-expression network analysis (WGCNA) to detect hub genes, and employed selection signal analysis of candidate genes. Three promising genes (EGR1, JUN and FOS) were eventually identified, and were significantly and differentially expressed in the same breed under different conditions, and in the two breeds after ST infection. Hub genes, such as PPFIA4 and ZNF395, were identified using WGCNA, and were associated with the ratio of heterophils to lymphocytes (H/L), an indicator of disease resistance. the present study identified several genes and pathways associated with resistance to ST infection, and found that BY had greater resistance to ST infection than GM. The results obtained provide valuable resources for investigating the mechanisms of resistance to ST infection in different chicken breeds.

Abstract Background Increasing evidence indicates that microRNAs (miRNAs) are involved in inflammatory response and immune regulation following pathogen invasion. The purpose of this study was to elucidate the roles played by Gallus gallus microRNA-1306-5p (gga-miR-1306-5p) in host responses against potential invasion by Salmonella enteritidis (SE) in chickens and the underlying mechanisms. Results In present study, the expression levels of gga-miR-1306-5p were determined in both tissues and HD11 cells. The results showed that gga-miR-1306-5p was significantly increased following SE infection or lipopolysaccharide (LPS) stimulation. The dual luciferase reporter assay further validated that gga-miR-1306-5p targeted the Toll-interacting protein (Tollip), and thereby participated in the regulation of immune response against SE or LPS stimulation through binding with the 3′-untranslated region (3’UTR) of Tollip. Additionally, the expression of Tollip was significantly blocked by over-expressed gga-miR-1306-5p. The underlying mechanisms by which gga-miR-1306-5p modulated the production of pro-inflammatory cytokines were also investigated. Molecular biological assays demonstrated that overexpression of gga-miR-1306-5p promoted the production of pro-inflammatory mediators, including NF-κB, TNF-α, IL-6, and IL-1β, which produced effects similar to those of Tollip knockdown. Conclusions Taken together, gga-miR-1306-5p induced by SE or LPS, regulates the immune response by inhibiting Tollip, which activates the production of inflammatory cytokines. This study has provided the first direct evidence that gga-miR-1306-5p targets Tollip, and is involved in the host response against SE.

Abstract Background China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. Results Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. Conclusions We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.

As a highly pathogenic influenza virus, H5N1 avian influenza virus (AIV) poses a great threat to poultry production and public health. H5N1 AIV has a small genome and, therefore, relies heavily on its host cellular machinery to replicate. To develop a comprehensive understanding of how H5N1 AIV rewires host cellular machinery during the course of infection, it is crucial to identify which host proteins and complexes come into physical contact with the viral proteins. Here, we utilized affinity purification mass spectrometry (AP-MS) to systematically determine the physical interactions of 11 H5N1 AIV proteins with host proteins in chicken DF1 cells. We identified with high confidence 1,043 H5N1 AIV–chicken interactions involving 621 individual chicken proteins and uncovered a number of host proteins and complexes that were targeted by the viral proteins. Specifically, we revealed that chicken Staufen double-stranded RNA-binding protein 2 interacts with AIV non-structural protein 1 (NS1) and promotes the replication of the virus by enhancing the nuclear export of NS1 mRNA. This dataset facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of H5N1 AIV infection.

The current study investigated the effects of inulin on the gut microbiota, microbiome functions, and short-chain fatty acids (SCFAs) levels in specific pathogen-free (SPF) chickens infected with Salmonella enteritidis (SE). SPF Arbor Acres chickens (n = 240, 1-day-old) were divided into four groups: a control group (CON) fed a basal diet without inulin supplementation or SE infection, and three groups fed a basal diet supplemented with inulin 0, 0.5, and 1% (SE, 0.5%InSE, 1%InSE, respectively) up to 28-days-old, followed by SE challenge at 28 days of age. Cecal SCFA contents and microbiome composition and function were analyzed at 1-day post-infection. The results showed that SE infection significantly decreased cecal butyrate concentrations compared with the CON group (p < 0.05), while inulin supplementation reversed these changes compared with the SE group (p < 0.05). Inulin supplementation at 1% significantly increased the abundances of Lactobacillus and Streptococcus, and significantly decreased the abundances of Subdoligranulum and Sellimonas compared with the SE group (p < 0.05). The functional profiles of microbial communities based on metagenomic sequencing analysis showed that SE infection significantly increased the abundances of pathways related to carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, and glycan biosynthesis and metabolism (p < 0.05), and significantly decreased the abundances of pathways related to nucleotide metabolism, translation, and replication and repair compared with the CON group (p < 0.05), and these effects were reversed by inulin supplementation (0.5 and 1%) (p < 0.05). In conclusion, inulin modulated the dysbiosis induced by SE infection via affecting SCFA metabolism and microbial functional profiles.

As a canonical adaptor for the Toll-like receptor (TLR) family, myeloid differentiation primary response protein 88 (MyD88) has crucial roles in host defense against infection by microbial pathogens, and its dysregulation might induce autoimmune diseases. Here, we demonstrate that the chicken Cullin 3-based ubiquitin ligase adaptor Speckle-type BTB-POZ protein (chSPOP) recognizes the intermediate domain of chicken MyD88 (chMyD88) and degrades it through the proteasome pathway. Knockdown or genetic ablation of chSPOP leads to aberrant elevation of chMyD88 protein. Through this interaction, chSPOP negatively regulates NF-κB pathway activity and thus the production of IL-1β upon LPS challenge in chicken macrophages. Furthermore, Spop-deficient mice are more susceptible to infection with Salmonella typhimurium. Collectively, these findings demonstrate MyD88 as a bona fide substrate of SPOP and uncover a mechanism by which SPOP regulates MyD88 abundance and disease susceptibility.

Abstract Background Skeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to investigate the effects of IMPA on MSC in chickens and unveil the molecular mechanisms by transcriptome analysis. Results Primary MSC and IMPA were isolated from the pectoralis major muscle of 7-day-old chickens. After both cell types reached confluence, MSC were cultured alone or co-cultured with IMPA for 2 or 4 d. MSC treated for 2 d were subjected to RNA-seq. A total of 1653 known differentially expressed genes (DEG) were identified between co-cultured and mono-cultured MSC (|log2 FC| ≥ 1, FDR

With the aim of studying the molecular mechanisms underlying lipid deposition in chickens, the expression profiles of eight novel candidate genes and miRNA involved in lipid deposition were examined in the undifferentiated and differentiated adipocyte at 3d, 5d and 10d after inducing differentiation. The level of expression of gga-miR-30 cluster (gga-miR-30a-5p, miR-30c-5p and miR-30e-5p) and miR-17-92 cluster (gga-miR-17-5p, miR-19a-3b and miR-20a-5p), compared to undifferentiated adipocyte, was significantly up-regulated with differentiated adipocyte; expression of miR-103-3p and miR-92-5p was significantly up-regulated with differentiated adipocyte. Seven genes, ACSL1, CYB5A, SEC23A, BRP44L, PLTP, MGLL and GART, compared to undifferentiated adipocyte, were significantly down-regulated with differentiated adipocyte. Correlation analysis of the detected genes and miRNAs indicated BRP44L may be a target of miR-103-3p and it was negatively correlated with miR-103-3p. CYB5A may be a target of miR-30a-5p and it was negatively correlated with miR-30a-5p. SEC23A may be a target of miR-19a-3p and it was negatively correlated with miR-19a-3p. MGLL may be a target of miR-19a-3p and it was negatively correlated with miR-19a-3p. These findings will improve more integrated information of the miRNA and genes in regulating the quantity of lipid deposition in chicken adipocyte.

Abstract Background Caponization results in reduced androgen levels, which leads to abdominal fat accumulation in capons. In this study, we sought to understand the molecular mechanisms behind this fat accumulation. Results Abdominal fat (AF) content increased significantly (P

Abstract Background Skeletal muscle development is closely linked to meat production and its quality. This study is the first to quantify the proteomes and metabolomes of breast muscle in two distinct chicken breeds at embryonic day 12 (ED 12), ED 17, post-hatch D 1 and D 14 using mass spectrometry-based approaches. Results Results found that intramuscular fat (IMF) accumulation increased from ED 17 to D 1 and that was exactly the opposite of when most obvious growth of muscle occurred (ED 12 - ED 17 and D 1 - D 14). For slow-growing Beijing-You chickens, Ingenuity Pathway Analysis of 77–99 differential abundance (DA) proteins and 63–72 metabolites, indicated significant enrichment of molecules and pathways related to protein processing and PPAR signaling. For fast-growing Cobb chickens, analysis of 68–95 DA proteins and 56–59 metabolites demonstrated that molecules and pathways related to ATP production were significantly enriched after ED12. For IMF, several rate-limiting enzymes for beta-oxidation of fatty acid (ACADL, ACAD9, HADHA and HADHB) were identified as candidate biomarkers for IMF deposition in both breeds. Conclusions This study found that ED 17 - D 1 was the earliest period for IMF accumulation. Pathways related to protein processing and PPAR signaling were enriched to support high capacity of embryonic IMF accumulation in Beijing-You. Pathways related to ATP production were enriched to support the fast muscle growth in Cobb. The beta-oxidation of fatty acid is identified as the key pathway regulating chicken IMF deposition at early stages.

Chickens are bred all over the world and have significant economic value as one of the major agricultural animals. The growth rate of commercial broiler chickens is several times higher than its Red Jungle fowl (RJF) ancestor. To further improve the meat production of commercial chickens, it is quite important to decipher the genetic mechanism of chicken growth traits. In this study, we found that broiler chickens exhibited lower levels of E3 ubiquitin ligase muscle atrophy F-box (MAFbx or Atrogin-1) relative to its RJF ancestor. As a ubiquitin ligase, Atrogin-1 plays a crucial role in muscle development in which its up-regulation often indicates the activation of muscle atrophic pathways. Here, we showed that the Atrogin-1 expression variance partly affects chicken muscle growth rates among different breeds. Furthermore, we demonstrated that the reduced expression of Atrogin-1 in broiler chickens was ascribed to a single nucleotide polymorphism (SNP), which inhibited the binding of transcription regulators and attenuated the enhancer activity. The decreased Atrogin-1 in broiler chickens suppresses the catabolism of muscle protein and preserves muscle mass. Our study facilitates the understanding of the molecular mechanism of chicken muscle development and has a high translational impact in chicken breeding.

Poultry diseases pose a large threat to poultry production. Selection to improve immune traits is a feasible way to prevent and control avian diseases. The objective of this study was to investigate the efficiency of estimation of genetic parameters for antibody response to avian influenza virus (Ab-AIV), antibody response to Newcastle disease virus (Ab-NDV), sheep red blood cell antibody titer (SRBC), the ratio of heterophils to lymphocytes (H/L), immunoglobulin G (IgG), the spleen immune index (SII), thymus immune index (TII), thymus weight at 100 d (TW) and the spleen weight at 100 d (SW) in Beijing oil chickens, by using the best linear unbiased prediction (BLUP) method and genomic best linear unbiased prediction (GBLUP) method. The phenotypic data used in the two methods were the same and were from 519 individuals. With the BLUP model, Ab-AIV, Ab-NDV, SRBC, H/L, IgG, TII, and TW had low heritability ranging from 0.000 to 0.281, whereas SII and SW had high heritability of 0.631 and 0.573. With the GBLUP model, all individuals were genotyped with Illumina 60K SNP chips, and Ab-AIV, Ab-NDV, SRBC, H/L and IgG had low heritability ranging from 0.000 to 0.266, whereas SII, TII, TW and SW had moderate heritability ranging from 0.300 to 0.472. We compared the prediction accuracy obtained from BLUP and GBLUP through 50 time 5-fold cross-validation (CV), and the results indicated that BLUP provided a slightly higher accuracy of prediction than GBLUP in this population.

Salmonellosis is a zoonosis that is not only harmful to the health of poultry but also poses a threat to human health. Although many measures have been put in place to reduce morbidity, they have not provided satisfactory results. Therefore, it is necessary to clarify the immune mechanisms involved in improving the resistance of chickens against Salmonella. BTB (Broad-complex Tramtrack and Bric-a-brac) Speckle-type POZ (poxvirus and zinc finger) protein (SPOP) regulates protein expression by promoting substrate ubiquitination and degradation. The correlation between SPOP expression and the immune response has not been fully described. Therefore, the aim of this study was to clarify this relationship. In vitro, we stimulated chicken macrophage cells (HD11) with lipopolysaccharide, then analyzed the correlation between SPOP and IL1β or IL8 expression using quantitative real-time polymerase chain reaction (qRT-PCR). In vivo, we infected 7-days-old chickens with Salmonella Typhimurium, then analyzed the association between SPOP expression and the immune response, including IL1β and IL8 expression, IgA production, and bacterial loads. We found that SPOP may participate in the regulation of the immune response in macrophage cells. SPOP expression was negatively correlated with IL-1β and IL-8 expression both in vivo and in vitro. SPOP expression was also negatively related to bacterial loads and immunoglobulin (Ig) A production. These results indicate that SPOP may have important functions in the response to Salmonella infection.

Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Controlling poultry SE infection will have great practical significance for human public health, as poultry are considered to be important sources and carriers of the disease. In this study, the splenic transcriptomes of challenged-susceptible (S), challenged-resistant (R) and non-challenged (C) chicks (3-days old, specific-pathogen-free White Leghorn) were characterized in order to identify the immune-related gene markers and pathways. A total of 934 significant differentially expressed genes (DEGs) were identified in comparisons among the C, R and S birds. First reported here, the DEGs involved in the Forkhead box O (FoxO) signaling pathway, especially FoxO3, were identified as potential markers for host resistance to SE infection. The challenged-susceptible birds exhibited strong activation of the FoxO signaling pathway, which may be a major defect causing immune cell apoptosis as part of SE-induced pathology; these S birds also showed weak activation of mitogen-activated protein kinase (MAPK)-related genes, contrasting with strong splenic activation in the R birds. Interestingly, suppression of several pathways in the immune response against Salmonella, including cytokine-cytokine receptor interaction and Jak-STAT, was only found in S birds and there was evidence of cross-talk among these pathways, perhaps contributing to susceptibility to Salmonella infection. These findings will help facilitate understanding resistance and susceptibility to SE infection in the earliest phases of the host immune response through Salmonella-induced pathways, provide new approaches to develop strategies for SE prevention and treatment, and may enhance innate resistance by genetic selection in animals.

PA-N155 and PA-N182 proteins were translated from the 11th and 13th start codon AUG of the RNA polymerase acidic protein (PA) mRNA of H5N1 influenza A virus (IAV), which plays an important role in viral replication. Little is known about the interactions between PA-N155 and PA-N182 and the host proteins. This study investigated the interaction landscape of PA-N155 and PA-N182 of H5N1 IAV in chicken cells while their interacting complexes were captured by immunoprecipitation and analyzed by mass spectrometry. A total of 491 (PA-N155) and 302 (PA-N182) interacting proteins were identified. Gene ontology and pathway enrichment analyses showed that proteins of the two interactomes were enriched in RNA processing, viral processing and protein transport, and proteins related to signaling pathways of proteasome, ribosome, and aminoacy1-tRNA biosynthesis were significantly enriched, suggesting their potential roles in H5N1 IAV infection. Comparative analysis of the interactome of PA, PA-N155, and PA-N182 identified UBA52 as a conserved host factor that interacted with all three viral proteins. UBA52 is a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein L40 at the C terminus. Knockdown of UBA52 significantly decreased the titer of H5N1 IAV in chicken cells and was accompanied with attenuated production of proinflammatory cytokines. Our analyses of the influenza–host protein interactomes identified UBA52 as a PA interaction protein for virus replication.

To understand the role of miRNAs in regulating genes involved in the host response to Salmonella enteritidis (SE) infection, next generation sequencing was applied to explore the altered splenic expression of microRNAs (miRNAs) and deregulated genes in specific-pathogen-free chickens. Birds were either infected or not (controls, C) and those challenged with SE were evaluated 24 h later and separated into two groups on the basis of the severity of clinical symptoms and blood load of SE: resistant (R, SE challenged-slight clinical symptoms and 107 cfu/10 μL). Thirty-two differentially expressed (DE) miRNAs were identified in spleen, including 16 miRNAs between S and C, 13 between R and C, and 13 between S and R. Through integration analysis of DE miRNAs and mRNA, a total of 273 miRNA-target genes were identified. Functional annotation analysis showed that Apoptosis and NOD-like receptor signaling pathway and adaptive immune response were significantly enriched (P < 0.05). Interestingly, apoptosis pathway was significantly enriched in S vs. C, while NOD-like receptor pathway was enriched in R vs. C (P < 0.05). Two miRNAs, gga-miR-101-3p and gga-miR-155, in the hub positions of the miRNA-mRNA regulatory network, were identified as candidates potentially associated with SE infection. These 2 miRNAs directly repressed luciferase reporter gene activity via binding to 3′-untranslated regions of immune-related genes IRF4 and LRRC59; over-expressed gga-miR-155 and interference gga-miR-101-3p in chicken HD11 macrophage cells significantly altered expression of their target genes and decreased the production of pro-inflammatory cytokines. These findings facilitate better understanding of the mechanisms of host resistance and susceptibility to SE infection in chickens.

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and low IgY chickens showed substantial genetic variations. In total, more than 30,000 SNPs were found in all four chicken groups, among which 1045 were non-synonymous mutations resulting in amino acids alterations. In total, 23,309 Indels were identified. Among the 1169 Indels that were found only in Beijing-You chickens, 702 were shared between high and low IgY chickens compared with the reference genome. There were 1016 Indels specific to the White Leghorn chickens, among which 188 were high IgY-specific, 134 were low IgY-specific and 694 were shared between the high and low IgY chicken lines. Many genetic mutations were located in the regulatory regions of important immunomodulatory genes, including TAP1, TAP2 and BF1. Our findings provide an in-depth understanding of genetic mutations in chicken microchromosomes.

Muscle development and growth influences the efficiency of poultry meat production, and is closely related to deposition of intramuscular fat (IMF), which is crucial in meat quality. To clarify the molecular mechanisms underlying muscle development and IMF deposition in chickens, protein expression profiles were examined in the breast muscle of Beijing-You chickens at ages 1, 56, 98 and 140 days, using isobaric tags for relative and absolute quantification (iTRAQ). Two hundred and four of 494 proteins were expressed differentially. The expression profile at day 1 differed greatly from those at day 56, 98 and 140. KEGG pathway analysis of differential protein expression from pair-wise comparisons (day 1 vs. 56; 56 vs. 98; 98 vs. 140), showed that the fatty acid degradation pathway was more active during the stage from day 1 to 56 than at other periods. This was consistent with the change in IMF content, which was highest at day 1 and declined dramatically thereafter. When muscle growth was most rapid (days 56-98), pathways involved in muscle development were dominant, including hypertrophic cardiomyopathy, dilated cardiomyopathy, cardiac muscle contraction, tight junctions and focal adhesion. In contrast with hatchlings, the fatty acid degradation pathway was downregulated from day 98 to 140, which was consistent with the period for IMF deposition following rapid muscle growth. Changes in some key specific proteins, including fast skeletal muscle troponin T isoform, aldehyde dehydrogenase 1A1 and apolipoprotein A1, were verified by Western blotting, and could be potential biomarkers for IMF deposition in chickens. Protein-protein interaction networks showed that ribosome-related functional modules were clustered in all three stages. However, the functional module involved in the metabolic pathway was only clustered in the first stage (day 1 vs. 56). This study improves our understanding of the molecular mechanisms underlying muscle development and IMF deposition in chickens.

The formation of many nebkha dunes relies on the layering of clonal plants. The microenvironmental conditions of such phytogenic nebkha are heterogeneous depending on the aspect and slope. Exploring the effects of aspect on clonal reproduction and biomass allocation can be useful in understanding the ecological adaptation of species. We hypothesized that on the windward side layering propagation would be promoted, that biomass allocation to leaves and stems of ramets would increase, and that the effects of aspect would be greater in the layering with larger biomass. To test these hypotheses, we surveyed the depth of germination points of axillary buds, the rate of ramet sprouting, the density of adventitious root formation points, and the biomass of modules sprouting from layering located on the NE, SE, SW and NW, aspects of Nitraria tangutorum nebkhas. The windward side was located on the NW and SW aspects. The results indicated that conditions of the NW aspect were more conducive to clonal reproduction and had the highest rate of ramet sprouting and the highest density of adventitious formation points. For the modules sprouting from layering on the SW aspect, biomass allocation to leaves and stems was greatest with biomass allocation to adventitious roots being lowest. This result supported our hypothesis. Contrary to our hypothesis, the effects of aspect were greater in layering of smaller biomass. These results support the hypothesis that aspect does affect layering propagation capacity and biomass allocation in this species. Additionally, clonal reproduction and biomass allocation of modules sprouting from layering with smaller biomass was more affected by aspect. These results suggest that the clonal growth of N. tangutorum responses to the microenvironmental heterogeneity that results from aspect of the nebkha.

Cytosine DNA methylation is an important epigenetic modification termed as the fifth base that functions in diverse processes. Till now, the genome-wide DNA methylation maps of many organisms has been reported, such as human, Arabidopsis, rice and silkworm, but the methylation pattern of bird remains rarely studied. Here we show the genome-wide DNA methylation map of bird, using the chicken as a model organism and an immunocapturing approach followed by high-throughput sequencing. In both of the red jungle fowl and the avian broiler, DNA methylation was described separately for the liver and muscle tissue. Generally, chicken displays analogous methylation pattern with that of animals and plants. DNA methylation is enriched in the gene body regions and the repetitive sequences, and depleted in the transcription start site (TSS) and the transcription termination site (TTS). Most of the CpG islands in the chicken genome are kept in unmethylated state. Promoter methylation is negatively correlated with the gene expression level, indicating its suppressive role in regulating gene transcription. This work contributes to our understanding of epigenetics in birds.