Large-scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits.

BACKGROUND: Carcass traits are crucial indicators of meat production efficiency. However, the molecular regulatory mechanisms associated with these traits remain unclear. RESULTS: In this study, we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms. Based on association analyses with the elastic net (EN) model, we identified 12 candidate genes (AMY1A, AP3B2, CEBPG, EEF2, EIF4EBP1, FGFR1, FOXD3, GOLM1, LOC107052698, PABPC1, SERPINB6 and TBC1D16) for 4 carcass-related traits, namely live weight, dressed weight, eviscerated weight, and breast muscle weight. SERPINB6 was identified as the only overlapping gene by 3 analyses, EN model analysis, weighted gene co-expression network analysis and differential expression analysis. Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts. Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression. Furthermore, a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3'UTR of SERPINB6. CONCLUSIONS: Collectively, our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation. Additionally, the downstream variant rs317934171 regulates SERPINB6 expression. These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

Genome-wide association study identifies a novel candidate gene for egg production traits in chickens.

Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome-wide significant single nucleotide polymorphism (SNP) and three chromosome-wide significant SNPs associated with egg laying rate. MTA2 is highly likely to be a functional gene for egg laying rate. Our study identifies MTA2 as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens.

Adverse effects of cigarette filter silica on lungs: Comparison with natural crystalline silica particles.

As a common additive in cigarette filters, nanosilica has been implemented to reduce the release of harmful substances in cigarette smoke. However, the potential risk of occupational exposure for cigarette factory workers is unknown. We collected physical examination data from 710 cigarette factory workers to evaluate the adverse effects of cigarette filter silica exposure. We also established mouse models induced by cigarette filter silica and crystalline silica separately to compare the lung inflammation, pulmonary function, apoptosis, and fibrosis of the two models. Workers in the rolling and packing workshop exposed to cigarette filter silica had a higher rate of abnormal lung function (17.75%) than those in the cutting workshop (0.87%). Animal experiments showed that compared with the same dose of crystalline silica, cigarette filter silica resulted in higher levels of inflammatory factors in the bronchoalveolar lavage fluid (BALF) of mice at day 7, and lower levels of total lung capacity (TLC), inspiratory capacity (IC), vital capacity (VC), and forced vital capacity (FVC) in mice at day 28. Additionally, both exposed groups of mice showed increased levels of caspase 3, collagen I (Col-Ⅰ), α-smooth muscle actin (α-SMA) and hydroxyproline (HYP) in the lungs, as well as collagen accumulation and fibrous nodules at day 28, with no significant difference between the two groups. The results suggested that cigarette filter silica caused more severe early lung inflammation and late ventilation impairment than the same dose of crystalline silica. In the future, we need to pay more attention to nanosilica protection in cigarette factories to prevent pulmonary dysfunction in workers.

Circ-POLA2-mediated miR-138-5p/SEMA4C axis affects colon cancer cell activities.

This study aimed to investigate the mechanism of circ-POLA2 in colon cancer (CC). Circ-POLA2, miR-138-5p, and SEMA4C levels in CC tissues and cells were recorded. The influences mediated by circ-POLA2, miR-138-5p or SEMA4C on cell proliferation, migration, invasion, and apoptosis were determined. The feedback loop of circ-POLA2/miR-138-5p/SEMA4C was surveyed. As measured, circ-POLA2 and SEMA4C were highly expressed, while miR-138-5p was poorly expressed. Meanwhile, circ-POLA2 could mediate SEMA4C through miR-138-5p targeting. Circ-POLA2 knockdown caused the blockade for cell activities, but this effect was alleviated by miR-138-5p inhibition or SEMA4C overexpression. Overall, circ-POLA2 is tumorigenic for CC through miR-138-5p/SEMA4C axis, which may provide a promising molecular target for CC therapy.

Solid-State NMR Double-Quantum Dipolar Recoupling Enhanced by Additional Phase Modulation.

Additional phase modulation (APM) is proposed to generally enhance the theoretical efficiency of homonuclear double-quantum (DQ) recoupling in solid-state NMR. APM applies an additional phase list to DQ recoupling in steps of an entire block. The sine-based phase list can enhance the theoretical efficiency by 15-30 %, from 0.52 to 0.68 (non-γ-encoded recoupling) or from 0.73 to 0.84 (γ-encoded recoupling), with doubled recoupling time. The genetic-algorithm (GA) optimized APM can adiabatically enhance the efficiency to ∼1.0 at longer times. The concept of APM has been tested on SPR-51 , BaBa, and SPR-31 , which represent γ-encoded recoupling, non-γ-encoded recoupling, and another kind beyond the former two, respectively. Simulations reveal that enhancements from APM are due to the activation of more crystallites in the powder. Experiments on 2,3-13 C labeled alanine are used to validate the APM recoupling. This new concept shall shed light on developing more efficient homonuclear recoupling methods.

From Basic Research to Clinical Practice: Considerations for Treatment Drugs for Silicosis.

Silicosis, characterized by irreversible pulmonary fibrosis, remains a major global public health problem. Nowadays, cumulative studies are focusing on elucidating the pathogenesis of silicosis in order to identify preventive or therapeutic antifibrotic agents. However, the existing research on the mechanism of silica-dust-induced pulmonary fibrosis is only the tip of the iceberg and lags far behind clinical needs. Idiopathic pulmonary fibrosis (IPF), as a pulmonary fibrosis disease, also has the same problem. In this study, we examined the relationship between silicosis and IPF from the perspective of their pathogenesis and fibrotic characteristics, further discussing current drug research and limitations of clinical application in silicosis. Overall, this review provided novel insights for clinical treatment of silicosis with the hope of bridging the gap between research and practice in silicosis.

Atractylenolide III Ameliorated Autophagy Dysfunction via Epidermal Growth Factor Receptor-Mammalian Target of Rapamycin Signals and Alleviated Silicosis Fibrosis in Mice.

Atractylenolide III (ATL-III) is a major active constituent of the natural plant Atractylodes rhizome. Our previous study has shown that ATL-III may alleviate alveolar macrophage apoptosis via the inhibition of the mammalian target of rapamycin (mTOR)-mediated autophagy of human silicosis. Therefore, we aimed to further explore the function of ATL-III in autophagy, apoptosis, and pulmonary fibrosis by establishing the ATL-III-intervened silicosis mouse model in this study. Meanwhile, we sought and then verified potential autophagy-related signaling pathways by matching differentially expressed genes (attained by RNA sequencing) and the autophagy database. In this study, RNA-sequencing results implied that the epidermal growth factor receptor, the crucial upstream activator of mTOR, was seen as a potential autophagy-regulatory molecule in the ATL-III-intervened silicosis mouse model. The finding of this study was that ATL-III might improve the disorder of autophagic degradation via the activation of epidermal growth factor receptor-mTOR signals in the pulmonary tissue of the silicosis mouse model. ATL-III also alleviated cell apoptosis and silicotic fibrosis. Overall, we supposed that ATL-III might be a potential protective medicine, which had a regulatory effect on autophagy, for the intervention of silicotic fibrosis. In the future, the therapeutic drugs for silicosis should be further focused on the development and application of such natural autophagy agents.

Second-order nonlinear optical properties of copper-based hybrid organic-inorganic perovskites induced by chiral amines.

Recently, chiral hybrid organic-inorganic perovskites (HOIPs) are drawing wide attention due to their intrinsic noncentrosymmetric structures which result in fascinating properties such as ferroelectronics and second-order nonlinear optics (NLO). However, previous research mainly focused on chiral lead-based halide perovskites ignoring that the toxic Pb element is harmful to humans and the environment. Herein, we successfully synthesized block-like (R-/S-NEA)2CuCl4 (NEA = 1-naphthylethylamine) and needle-like (R-/S-CYHEA)6Cu3Cl12 (CYHEA = 1-cyclohexylethylamine) single crystals, which crystallize in the Sohncke P21 and I2 space group, respectively. Each pair of chiral perovskite enantiomers shows mirror circular dichroism (CD) signals. The thin films show an efficient second harmonic generation (SHG) response and the NLO coefficients of (R-NEA)2CuCl4 and (R-CYHEA)6Cu3Cl12 are 11.74 and 3.04 pm V-1, respectively, under 920 nm excitation with Y-cut quartz as a reference, which shows that the chiral amine has a significant effect on the SHG behavior. The high SHG response of (R-NEA)2CuCl4 is perhaps due to the rigidity of the aromatic amine, which leads to highly asymmetrical space groups. Our results provide guidelines for designing and tuning the SHG response in chiral HOIPs.

Estimation of genetic parameters for important traits using a multi-trait model in late-feathering Qingyuan partridge hens in China.

Qingyuan partridge chicken is one of the most well-known Chinese indigenous yellow broilers. In breeding programmes, five traits are usually selected when the chickens are 105 days old, namely body weight (BW), comb height (CH), shank length (SL), shank girth (SG) and feather maturity (FM). The objective of this study was to estimate the genetic parameters of these five traits, especially direct additive genetic correlations, to lay the foundation for balanced selection of Qingyuan partridge chickens. Approximately 9600 records were used for estimation. Variance components for these five traits were estimated using three multi-trait models incorporating different effects via Gibbs sampling. Based on model 1 in which the random effects included direct additive genetic effects and residuals, the estimated direct heritabilities for BW, CH, SL, SG and FM were 0.29 ± 0.04, 0.53 ± 0.04, 0.47 ± 0.04, 0.43 ± 0.05 and 0.18 ± 0.03, respectively. The direct genetic correlations ranged from -0.08 to 0.46. When additionally considering maternal additive genetic effects (model 2), the estimates of direct heritabilities and absolute values of direct additive genetic correlations were smaller. The heritabilities were 0.14 ± 0.04, 0.40 ± 0.02, 0.34 ± 0.05, 0.27 ± 0.05 and 0.12 ± 0.03 for BW, CH, SL, SG and FM, respectively. The direct additive genetic correlations ranged from -0.33 to 0.36. More specifically, the direct additive genetic correlations between BW and CH, SL, SG and FM were 0.19 ± 0.13, 0.15 ± 0.15, 0.36 ± 0.15 and - 0.33 ± 0.21, respectively. The genetic correlations of FM with SL, SG and CH were - 0.15 ± 0.15, -0.08 ± 0.17 and 0.18 ± 0.15, respectively. The direct genetic correlations between CH and SG and SL were - 0.02 ± 0.11 and - 0.20 ± 0.11, respectively, and that between SL and SG was 0.19 ± 0.11. The total heritabilities and maternal additive genetic correlations ranged from 0.16 to 0.44 and from -0.13 to 0.61, respectively. The third model also included the maternal permanent environmental effect for BW. The estimates of direct heritability, direct additive genetic correlation, total heritability and maternal additive genetic correlation were only slightly different from those based on the second model. Therefore, the maternal additive genetic effect has a large effect on the estimation of genetic parameters, and it is better to consider this effect in the genetic evaluation of these five traits. Relatively high direct and maternal additive genetic correlations for most trait pairs suggested that it is better to jointly evaluate these five traits in breeding programmes.

[Kinesio Taping combined with electroacupuncture for the treatment of Bigliani typeâ subacromial impingement syndrome].

OBJECTIVE: To investigate the clinical effect of Kinesio Taping combined with electroacupuncture in the treatment of Bigliani typeⅠsubacromial impingement syndrome. METHODS: From January 2019 to June 2021, 82 cases with Bigliani typeⅠsubacromial impingement syndrome were selected and divided into treatment group and control group. Treatment group included 41 cases, 23 males and 18 females, aged from 20 to 52 years old, with an average of (39.31±5.80)years old. There were 12 cases on left shoulder and 29 cases on right shoulder. The course of disease was from 3.2 to 35.4 months. The treatment group was treated with Kinesio Taping and electroacupuncture. In control group, there were 41 cases, including 22 males and 19 females, aged from 19 to 53 years old with an average of (40.67±6.13) years old, 30 cases on right shoulder, 11 cases on left shoulder. The courses of disease was from 3.0 to 36.0 months. The control group was treated with simple shoulder electroacupuncture. Patients in both groups were treated with electroacupuncture 3 times a week for 3 weeks. After each electroacupuncture treatment in the treatment group, the Kinesio Taping was applied immediately and kept for 2 days. Before treatment, immediately after treatment, and after 1, 3, 8 weeks, the shoulder joint Constant-Murley score, pain visual analogue scale (VAS), and shoulder joint range of motion were used to evaluate the treatment effect. RESULTS: After 1 week of treatment, there was 1 patient in treatment group refused treatment due to hypersensitivity to Kinesio Taping, 1 patient in control group was allergic to the metal needle and refused treatment. And the other 80 patients completed all treatment. Immediately after treatment, and 1, 3, and 8 weeks after treatment, VAS of treatment group were (2.06±1.03), (2.74±1.66), (3.28±1.04), and (3.90±0.12) points, respectively. The Constant-Murley scores of shoulder joint were(86.41±3.52), (82.44±3.14), (80.46±2.54), (76.97±2.01) points. VAS of control group were(3.35±0.41), (3.08±0.92), (3.77±0.67), (3.96±1.04) points, and the Constant-Murley scores of the shoulder joint were(75.82±2.73), (74.72±1.53), (73.66±1.53), (70.68±1.95) points respectively. Immediately after treatment, VAS, Constant-Murley score, and shoulder range of motion between two groups were better than those of before treatment (P<0.05), and the difference was statistically significant between two groups after treatment (P<0.05). One week after treatment, VAS, Constant-Murley score, and shoulder joint range of motion between two groups were better than those of before treatment (P<0.05), but there was no significant difference in VAS between two groups (P>0.05). There were significant differences in the Constant-Murley score and shoulder range of motion between two groups (P<0.05). At 3 and 8 weeks after treatment, VAS, Constant-Murley score, and the range of motion of shoulder joints between two groups were better than those of before treatment (P<0.05), but there was no significant difference between two groups(P>0.05). CONCLUSION: The treatment for bigliani typeⅠsubacromial impingement syndrome with Kinesio Taping combined with electroacupuncture can reduce pain, effectively improve the function of shoulder joint. In addition, with Kinesio Taping protection when motion, the patients sports ability can be improved obviously, with good immediate effect, and no trauma. If the patients are willing to accept it, it would be an immediate and effective treatment.

circ_0052184 Promotes Colorectal Cancer Progression via Targeting miR-604/HOXA9 Axis.

Background: The mortality rate of colorectal cancer (CRC) ranks second. circRNAs are abnormal expression in some diseases, and their dysregulation is associated with cancer progression. Recent studies have shown that the malignant progression of colorectal cancer is inseparable from the abnormal expression of circRNAs. Methods: First, the circ_0052184 expression in clinical tissue and cell samples was analyzed by qRT-PCR. Then, we constructed circ_0052184-silenced CRC cells and detected by qRT-PCR. Furthermore, the proliferation ability of cells was detected by colony formation assay. Cell migration ability was tested by wound healing assay and transwell assay. Cell invasion ability was detected by transwell assay. Results: Expression of circ_0052184 was significantly increased in colorectal cancer cell lines and tissues. Silencing circ_0052184 affected the proliferation, migration, and invasion of colorectal cancer cells. miR-604 was targeted by circ_0052184. The downstream target of miR-604 was HOXA9, and silencing circ_0052184 inhibited HOXA9 expression. The existence of the circ_0052184/miR-604/HOXA9 regulatory network in colorectal cancer was validated. circ_0052184 promoted the occurrence and development of colorectal cancer by targeting the miR-604/HOXA9 axis. Conclusions: Our study revealed that the molecular mechanism of circ_0052184 regulated the miR-604/HOXA9 axis, which might promote the malignant progression of colorectal cancer cells.

Genomic Selection in Chinese Holsteins Using Regularized Regression Models for Feature Selection of Whole Genome Sequencing Data.

Genomic selection (GS) is an efficient method to improve genetically economic traits. Feature selection is an important method for GS based on whole-genome sequencing (WGS) data. We investigated the prediction performance of GS of milk production traits using imputed WGS data on 7957 Chinese Holsteins. We used two regularized regression models, least absolute shrinkage and selection operator (LASSO) and elastic net (EN) for feature selection. For comparison, we performed genome-wide association studies based on a linear mixed model (LMM), and the N single nucleotide polymorphisms (SNPs) with the lowest p-values were selected (LMMLASSO and LMMEN), where N was the number of non-zero effect SNPs selected by LASSO or EN. GS was conducted using a genomic best linear unbiased prediction (GBLUP) model and several sets of SNPs: (1) selected WGS SNPs; (2) 50K SNP chip data; (3) WGS data; and (4) a combined set of selected WGS SNPs and 50K SNP chip data. The results showed that the prediction accuracies of GS with features selected using LASSO or EN were comparable to those using features selected with LMMLASSO or LMMEN. For milk and protein yields, GS using a combination of SNPs selected with LASSO and 50K SNP chip data achieved the best prediction performance, and GS using SNPs selected with LMMLASSO combined with 50K SNP chip data performed best for fat yield. The proposed method, feature selection using regularization regression models, provides a valuable novel strategy for WGS-based GS.

Ligand Exchange Strategy to Achieve Chiral Perovskite Nanocrystals with a High Photoluminescence Quantum Yield and Regulation of the Chiroptical Property.

Chiral nanomaterials have drawn extensive attention on account of numerous application prospects in optoelectronics, asymmetric catalysis, chiral recognition, and three-dimensional (3D) display. Thereinto, chiral perovskite has been a hotspot due to brilliant optoelectronic properties, but some problems limit the development, including low quantum yield, low chiral intensity, and the lack of facile regulation. To overcome these issues, an effective ligand exchange strategy, i.e. the interface modification has been proposed for chiral perovskite nanocrystals (PNCs). With the surface modification of CsPbBr3 PNCs with chiral organic ammonium in methyl acetate in the typical purification process, excellent circular dichroism (CD) signals were obtained and defects were eliminated, leading to an increase in the photoluminescence quantum yield (PLQY) from 50% to nearly 100%. The CD signal can be regulated through a ligand exchange strategy in the longitudinal dimension, the chiral intensity, and the transverse dimension, the wavelength range. Here, the proper addition of R-α-PEAI into the R-α-PEABr-capped CsPbBr3 PNCs can produce a superstrong CD signal with the highest anisotropy factor (g-factor) of 0.0026 in the visible region among reported chiral colloidal PNCs. Simultaneously, the luminescence emission can be tuned from the green to red region with boosted PLQY through the approach. The density functional theory (DFT) calculation result supports that chirality comes from the hybridization between the energy level of a perovskite structure and that of chiral organic molecules. These properties can be used in the structural engineering of high-performance chiral optical materials, spin-polarized light-emitting devices, and polarized optoelectronic devices.

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content.

BACKGROUND: In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. RESULTS: First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. CONCLUSIONS: Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.

A Novel Diarylethene-rhodamine Unit Based Chemosensor for Fluorimetric and Colorimetric Detection of Hg2.

A novel fluorimetric and colorimetric chemosensor (1O) was synthesized with diarylethene-rhodamine unit and characterized by ESI-MS, 1H NMR, and 13C NMR. The chemosensor can selectively recognize extremely low concentrations of Hg2+ over a variety of metal ions with remarkable colorimetric and fluorescent responses. The colorimetric and fluorescent changes were ascribed the reaction between 1O and Hg2+ destructed the rhodamine hydrazide into open-ring form which was proved by mass spectrometry and nuclear magnetic titration analyses. The detection limits of the UV absorption and fluorescence methods for Hg2+ were found to be 0.708 µM and 24.6 nM, respectively. Moreover, the chemosensor exhibited excellent photochromism and outstanding fatigue resistance property under alternating UV and visible light irradiation. The application potential of the chemosensor was demonstrated with the qualitative detection of Hg2+ in real water samples.

Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues.

BACKGROUND: A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. The transcriptome analysis performed in this study of intramuscular preadipocytes (DIMFPs) and adipose tissue-derived preadipocytes (DAFPs) aimed to explore the characteristics of lipid deposition in different chicken preadipocytes by dedifferentiation in vitro. RESULTS: Compared with DAFPs, the total lipid content in DIMFPs was reduced (P < 0.05). Moreover, 72 DEGs related to lipid metabolism were screened, which were involved in adipocyte differentiation, fatty acid transport and fatty acid synthesis, lipid stabilization, and lipolysis. Among the 72 DEGs, 19 DEGs were enriched in the PPAR signaling pathway, indicating its main contribution to the regulation of the difference in lipid deposition between DAFPs and DIMFPs. Among these 19 genes, the representative APOA1, ADIPOQ, FABP3, FABP4, FABP7, HMGCS2, LPL and RXRG genes were downregulated, but the ACSL1, FABP5, PCK2, PDPK1, PPARG, SCD, SCD5, and SLC27A6 genes were upregulated (P < 0.05 or P < 0.01) in the DIMFPs. In addition, the well-known pathways affecting lipid metabolism (MAPK, TGF-beta and calcium) and the pathways related to cell communication were enriched, which may also contribute to the regulation of lipid deposition. Finally, the regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs was proposed based on the above information. CONCLUSIONS: Our data suggested a difference in lipid deposition between DIMFPs and DAFPs of chickens in vitro and proposed a molecular regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs. The lipid content was significantly increased in DAFPs by the direct mediation of PPAR signaling pathways. These findings provide new insights into the regulation of tissue-specific fat deposition and the optimization of body fat distribution in broilers.

Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation.

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellularlocations and potential functions for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.

A Random Regression Model Based on a Single-Step Method for Improving the Genomic Prediction Accuracy of Residual Feed Intake in Pigs.

Residual feed intake (RFI) is considered as a measurement of feed efficiency, which is greatly related to the growth performance in pigs. Daily feeding records can be obtained from automatic feeders. In general, RFI is usually calculated from the total measurement records during the whole test period. This measurement cannot reflect genetic changes in different growth periods during the test. A random regression model (RRM) provides a method to model such type of longitudinal data. To improve the accuracy of genetic prediction for RFI, the RRM and regular animal models were applied in this study, and their prediction performances were compared. Both traditional pedigree-based relationship matrix (A matrix) and pedigree and genomic information-based relationship matrix (H matrix) were applied for these two models. The results showed that, the prediction accuracy of the RRM was higher than that of the animal model, increasing 24.2% with A matrix and 40.9% with H matrix. Furthermore, genomic information constantly improved the accuracy of evaluation under each evaluation model. In conclusion, longitudinal traits such as RFI can describe feed efficiency better, and the RRM with both pedigree and genetic information was superior to the animal model. These results provide a feasible method of genomic prediction using longitudinal data in animal breeding.

Genetic parameters and direct and maternal effects for important traits in late-feathering Qingyuan partridge hens in China.

Qingyuan partridge chicken is an important indigenous chicken in China. In its breeding schemes, chickens are usually selected at the age of 105-day-old for five traits, including body weight (BW), shank length (SL), shank girth (SG), comb height (CH) and feather maturity (FM). At present, genetic parameters of the aforementioned traits have still not been studied in Qingyuan partridge chickens. The objectives of this study were the following: (1) to investigate whether the optimal statistical models of these traits need to consider maternal genetic and permanent environmental effects in late-feathering Qingyuan partridge hens, and (2) to estimate genetic parameters for these traits based on the optimal models. The numbers of records for BW, SL, SG, CH and FM were 13,721, 13,671, 13,670, 13,669 and 13,672, respectively. Variance components were estimated using average information-restricted maximum likelihood method, and the optimal model was determined based on Bayesian information criterion. More specifically, the optimal model for BW considered maternal genetic and permanent environmental effects in addition to direct additive genetic effect; SL, SG and FM considered direct and maternal genetic effects; and CH considered direct and maternal genetic effects, and the covariance between them. The direct heritabilities of these traits estimated using the optimal models were 0.21 ± 0.04, 0.30 ± 0.05, 0.40 ± 0.05, 0.59 ± 0.09 and 0.09 ± 0.04, respectively; the maternal heritabilities were 0.01 ± 0.04, 0.05 ± 0.05, 0.04 ± 0.05, 0.09 ± 0.09 and 0.03 ± 0.04, respectively. Maternal genetic effect evidently played an important part in FM and maternal heritability accounted for 30 per cent of total heritability. Furthermore, the direct and maternal genetic effects for CH were estimated to be negatively and moderately correlated (-0.51 ± 0.11). For all traits, neglecting existent maternal effects biased the estimation of direct heritability. Therefore, to implement optimum breeding strategies for improvement of these traits in Qingyuan partridge hens, maternal effects should be taken into consideration.

[Analysis of INS gene variant in a juvenile with maturity-onset diabetes of the young type 10].

OBJECTIVE: To analyze INS gene variant in a patient with maturity-onset diabetes of the young type 10. METHODS: High-throughput sequencing was used to screen for the variants. Suspected variant was verified by Sanger sequencing. RESULTS: Genetic testing indicated that the patient and his mother have both carried a heterozygous c.130G>A (p.Gly44Arg) variant in exon 1 of the INS gene. Prediction of protein structure suggested the variant to be pathogenic. CONCLUSION: The c.130G>A (p.Gly44Arg) variant of the INS gene probably underlies the disease in this patient.