Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling.

BACKGROUND: Embryonic diapause (dormancy) is a state of temporary arrest of embryonic development that is triggered by unfavorable conditions and serves as an evolutionary strategy to ensure reproductive survival. Unlike maternally-controlled embryonic diapause in mammals, chicken embryonic diapause is critically dependent on the environmental temperature. However, the molecular control of diapause in avian species remains largely uncharacterized. In this study, we evaluated the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in pre-diapause, diapause, and reactivated states. RESULTS: Our data demonstrated a characteristic gene expression pattern in effects on cell survival-associated and stress response signaling pathways. Unlike mammalian diapause, mTOR signaling is not responsible for chicken diapause. However, cold stress responsive genes, such as IRF1, were identified as key regulators of diapause. Further in vitro investigation showed that cold stress-induced transcription of IRF1 was dependent on the PKC-NF-κB signaling pathway, providing a mechanism for proliferation arrest during diapause. Consistently, in vivo overexpression of IRF1 in diapause embryos blocked reactivation after restoration of developmental temperatures. CONCLUSIONS: We concluded that embryonic diapause in chicken is characterized by proliferation arrest, which is the same with other spices. However, chicken embryonic diapause is strictly correlated with the cold stress signal and mediated by PKC-NF-κB-IRF1 signaling, which distinguish chicken diapause from the mTOR based diapause in mammals.

Mechanical properties evaluation of metacarpophalangeal joint prosthesis with new titanium-nickel memory alloy: a cadaver study.

OBJECTIVE: Ni-Ti memory alloys are unusual materials for hard-tissue replacement because of their unique superelasticity, good biocompatibility, high strength, low specific gravity, low magnetism, wear resistance, corrosion resistance and fatigue resistance. The current study aims to evaluate its mechanical properties and provide biomechanical basis for the clinical application of the prosthesis. METHODS: Ten adult metacarpophalangeal joint specimens were randomly divided into a prosthesis group (n = 5, underwent metacarpophalangeal joint prosthesis) and a control group (n = 5, underwent sham operation). Firstly, the axial compression strength was tested with BOSE material testing machine to evaluate its biomechanical strength. Secondly, these specimens were tested for strain changes using BOSE material testing machine and GOM non-contact optical strain measurement system to evaluate the stress changes. Thirdly, fatigue test was performed between groups. Lastly, the mechanical wear of the metacarpophalangeal joint prosthesis was tested with ETK5510 material testing machine to study its mechanical properties. RESULTS: Axial compression stiffness in the prosthesis group was greater than that in the control group in terms of 30 ° and 60 ° flexion positions (P < 0.05). There was no statistically significant difference between two groups with regards to axial compression stiffness and stress change test (P > 0.05). In the fatigue wear test, the mean mass loss in the prosthesis group's prosthesis was 17.2 mg and 17.619 mm3, respectively. The mean volume wear rate was 0.12%. There was no statistically significant difference in the maximum pull-out force of the metacarpal, phalangeal, and polymer polyethylene pads between the prosthesis group and the control group specimens. CONCLUSIONS: Ni-Ti memory alloy metacarpophalangeal joint prosthesis conforms to the biomechanical characteristics of metacarpophalangeal joints without implants, and the fatigue strength can fully meet the needs of metacarpophalangeal joint activities after joint replacement.

Research on Performance Degradation Estimation of Key Components of High-Speed Train Bogie Based on Multi-Task Learning.

The safe and comfortable operation of high-speed trains has attracted extensive attention. With the operation of the train, the performance of high-speed train bogie components inevitably degrades and eventually leads to failures. At present, it is a common method to achieve performance degradation estimation of bogie components by processing high-speed train vibration signals and analyzing the information contained in the signals. In the face of complex signals, the usage of information theory, such as information entropy, to achieve performance degradation estimations is not satisfactory, and recent studies have more often used deep learning methods instead of traditional methods, such as information theory or signal processing, to obtain higher estimation accuracy. However, current research is more focused on the estimation for a certain component of the bogie and does not consider the bogie as a whole system to accomplish the performance degradation estimation task for several key components at the same time. In this paper, based on soft parameter sharing multi-task deep learning, a multi-task and multi-scale convolutional neural network is proposed to realize performance degradation state estimations of key components of a high-speed train bogie. Firstly, the structure takes into account the multi-scale characteristics of high-speed train vibration signals and uses a multi-scale convolution structure to better extract the key features of the signal. Secondly, considering that the vibration signal of high-speed trains contains the information of all components, the soft parameter sharing method is adopted to realize feature sharing in the depth structure and improve the utilization of information. The effectiveness and superiority of the structure proposed by the experiment is a feasible scheme for improving the performance degradation estimation of a high-speed train bogie.

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens.

BACKGROUND: Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken liver is poorly understood. To identify estrogen-responsive genes and estrogen functional sites on a genome-wide scale, we determined expression profiles of mRNAs, lncRNAs, and miRNAs in estrogen-treated ((17ß-estradiol)) and control chicken livers using RNA-Sequencing (RNA-Seq) and studied the estrogen receptor α binding sites by ChIP-Sequencing (ChIP-Seq). RESULTS: We identified a total of 990 estrogen-responsive genes, including 962 protein-coding genes, 11 miRNAs, and 17 lncRNAs. Functional enrichment analyses showed that the estrogen-responsive genes were highly enriched in lipid metabolism and biological processes. Integrated analysis of the data of RNA-Seq and ChIP-Seq, identified 191 genes directly targeted by estrogen, including 185 protein-coding genes, 4 miRNAs, and 2 lncRNAs. In vivo and in vitro experiments showed that estrogen decreased the mRNA expression of PPARGC1B, which had been reported to be linked with lipid metabolism, by directly increasing the expression of miR-144-3p. CONCLUSIONS: These results increase our understanding of the functional network of estrogen in chicken liver and also reveal aspects of the molecular mechanism of estrogen-related lipid metabolism.

Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells.

BACKGROUND: Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowledge of PEDV-induced transcriptomic responses in host cells is imperative to understanding the molecular mechanisms involved in the immune response. Here, we analyzed the transcriptomic profile of intestinal porcine epithelial cell line J2 (IPEC-J2) after infection with a classical strain of PEDV to explore the host response. RESULTS: In total, 854 genes were significantly differentially expressed after PEDV infection, including 716 upregulated and 138 downregulated genes. Functional annotation analysis revealed that the differentially expressed genes were mainly enriched in the influenza A, TNF signaling, inflammatory response, cytokine receptor interaction, and other immune-related pathways. Next, the putative promoter regions of the 854 differentially expressed genes were examined for the presence of transcription factor binding sites using the MEME tool. As a result, 504 sequences (59.02%) were identified as possessing at least one binding site of signal transducer and activator of transcription (STAT), and five STAT transcription factors were significantly induced by PEDV infection. Furthermore, we revealed the regulatory network induced by STAT members in the process of PEDV infection. CONCLUSION: Our transcriptomic analysis described the host genetic response to PEDV infection in detail in IPEC-J2 cells, and suggested that STAT transcription factors may serve as key regulators in the response to PEDV infection. These results further our understanding of the pathogenesis of PEDV.

Characteristics of expression and regulation of sirtuins in chicken (Gallus gallus).

Sirtuins (SIRT1-SIRT7) are a family of NAD+-dependent protein deacetylases that are linked to post-translational regulation of many metabolic processes. There are few reports available for chicken sirtuins (designated cSIRT1-cSIRT7), whose expression and regulation in the liver have yet to be explored. In the present study, we characterized the expression and regulation of sirtuin family members in chicken liver. The results showed that the sirtuin family members in chicken share the same conserved functional SIR2 domains. All the sirtuin family members were expressed extensively in all tissues examined, and the expression levels of cSIRT1, cSIRT2, cSIRT4, cSIRT6, and cSIRT7 in the liver increased significantly with sexual maturity. However, all sirtuin family members were downregulated (P < 0.05) in chicken livers and cultured primary hepatocytes treated with 17ß-estradiol. We concluded that the expression levels of some chicken sirtuin family members in the liver were upregulated with sexual maturation, but might not be regulated directly by estrogen. Whereas estrogen could be used as an inhibitor of all sirtuins, both in vivo and in vitro.

Association of estradiol on expression of melanocortin receptors and their accessory proteins in the liver of chicken (Gallus gallus).

The melanocortin receptor accessory proteins (MRAP and MRAP2) are small single-pass transmembrane proteins that regulate the biological functions of the melanocortin receptor (MCR) family. MCRs comprise five receptors (MC1R-MC5R) with diverse physiological roles in mammals. Five MCR members and two MRAPs were also predicted in the chicken (Gallus gallus) genome. However, little is known about their expression, regulation and biological functions. In this study, we cloned the MRAP and MRAP2 genes. Sequencing analysis revealed that the functional domains of MRAP and MRAP2 were conserved among species, suggesting that the physiological roles of chicken MRAP and MRAP2 could be similar to their mammalian counterparts. Tissue expression analysis demonstrated that MRAP was expressed in the adrenal gland, liver, spleen, glandular stomach and lungs, while MRAP2 is predominantly expressed in the adrenal gland. All five MCRs were present in the adrenal gland, but showed different expression patterns in other tissues. The MC5R was the only MCR member that was expressed in the chicken liver. The expression levels of MRAP in chicken liver were significantly increased at sexual maturity stage, and were significantly up-regulated (P<0.05) when chickens and chicken primary hepatocytes were treated with 17ß-estradiol in vivo and in vitro, respectively; however, expression levels of PPARγ were down-regulated, and no effect on MC5R was observed. Our results suggested that estrogen could stimulate the expression of MRAP in the liver of chicken through inhibiting the expression of transcription regulation factor PPARγ, and MRAP might play its biological role in a different way rather than forming an MRAP/MC2R complex in chicken liver during the egg-laying period.

Multifunctional hyaluronic acid modified graphene oxide loaded with mitoxantrone for overcoming drug resistance in cancer.

Multifunctional nanosheets (HA-GO/Pluronic) with targeted chemo-photothermal properties were successfully developed for controlled delivery of mitoxantrone (MIT) to overcome multidrug resistance (MDR). In vitro release profiles displayed that both an acidic environment and a NIR laser could trigger and accelerate the release of a drug, which ensured nanosheets were stable in blood circulation and released MIT within tumor cells under laser irradiation. HA-GO/Pluronic nanosheets were taken up into MCF-7/ADR cells via receptor-mediated endocytosis, which further facilitated escapement of P-gp efflux. Compared with MIT solution, MIT/HA-GO/Pluronic showed greater cytotoxicity and increase in cellular MIT accumulation in MCF-7/ADR cells. Cell apoptosis and cell cycle arrest studies also revealed that MIT/HA-GO/Pluronic was more potent than MIT/GO/Pluronic and MIT solution. The anticancer efficacy in vivo was evaluated in MCF-7 and MCF-7/ADR-bearing mice, and inhibition of tumors by MIT/HA-GO/Pluronic with NIR laser irradiation was the most effective among all MIT formulations. In summary, the MIT/HA-GO/Pluronic system had striking functions such as P-gp reversible inhibitor and anticancer efficacy, and could present a promising platform for drug-resistant cancer treatment.

Smart nanocomposite hydrogels based on azo crosslinked graphene oxide for oral colon-specific drug delivery.

A safe and efficient nanocomposite hydrogel for colon cancer drug delivery was synthesized using pH-sensitive and biocompatible graphene oxide (GO) containing azoaromatic crosslinks as well as poly (vinyl alcohol) (PVA) (GO-N=N-GO/PVA composite hydrogels). Curcumin (CUR), an anti-cancer drug, was encapsulated successfully into the hydrogel through a freezing and thawing process. Fourier transform infrared spectroscopy, scanning electron microscopy and Raman spectroscopy were performed to confirm the formation and morphological properties of the nanocomposite hydrogel. The hydrogels exhibited good swelling properties in a pH-sensitive manner. Drug release studies under conditions mimicking stomach to colon transit have shown that the drug was protected from being released completely into the physiological environment of the stomach and small intestine. In vivo imaging analysis, pharmacokinetics and a distribution of the gastrointestinal tract experiment were systematically studied and evaluated as colon-specific drug delivery systems. All the results demonstrated that GO-N=N-GO/PVA composite hydrogels could protect CUR well while passing through the stomach and small intestine to the proximal colon, and enhance the colon-targeting ability and residence time in the colon site. Therefore, CUR loaded GO-N=N-GO/PVA composite hydrogels might potentially provide a theoretical basis for the treatment of colon cancer with high efficiency and low toxicity.

Discovery and functional characterization of leptin and its receptors in Japanese quail (Coturnix japonica).

Leptin is an important endocrine regulation factor of food intake and energy homeostasis in mammals; however, the existence of a poultry leptin gene (LEP) is still debated. Here, for the first time, we report the cloning of a partial exon 3 sequence of LEP (qLEP) and four different leptin receptor splicing variants, including a long receptor (qLEPRl) and three soluble receptors (qLEPR-a, qLEPR-b and qLEPR-c) in Japanese quail (Coturnix japonica). The qLEP gene had high GC content (64%), which is similar to other reported avian leptin genes. The encoded qLEP protein possessed the conserved pair of cysteine residues that are required to form a lasso knot for full biological activity, but shared relatively low identities with LEPs of other vertebrates. The translated qLEPRl protein contained 1143 amino acids and shared high amino acid sequence identity with a chicken homolog (89% identity). qLEPRl also contained all the motifs, domains, and basic tyrosine residues that are conserved in the LEPRl proteins of other vertebrates. qRT-PCR analysis showed that LEP and the four LEPR variants were expressed extensively in all tissues examined; the expression levels of LEP were relatively high in hypothalamus, skeletal muscle, and pancreas, while the expression levels of the LEPRs were highest in the pituitary. Compared with the expression levels of juvenile qLEP and total qLEPR (including all LEPR variants), the expression levels of mature qLEP and total qLEPR were up-regulated in the hypothalamus and pituitary, and down-regulated in the ovary. The expressions of LEP/LEPR increased when fasting and decreased when refeeding in the brain and peripheral tissues of juvenile quail, which suggested that the LEP/LEPR system modulated food intake and energy expenditure, although, unlike in mammals, LEP may actually act to inhibit food intake during fasting, at least in juvenile quail. The results indicate that qLEP and qLEPR have unique expression patterns and that the encoded proteins play important roles in the regulation of reproduction and energy status in Japanese quail.

Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens.

BACKGROUND: Liver is an important metabolic organ that plays a critical role in lipid synthesis, degradation, and transport; however, the molecular regulatory mechanisms of lipid metabolism remain unclear in chicken. In this study, RNA-Seq technology was used to investigate differences in expression profiles of hepatic lipid metabolism-related genes and associated pathways between juvenile and laying hens. The study aimed to broaden the understanding of liver lipid metabolism in chicken, and thereby to help improve laying performance in the poultry industry. RESULTS: RNA-Seq analysis was carried out on total RNA harvested from the liver of juvenile (n = 3) and laying (n = 3) hens. Compared with juvenile hens, 2567 differentially expressed genes (1082 up-regulated and 1485 down-regulated) with P ≤ 0.05 were obtained in laying hens, and 960 of these genes were significantly differentially expressed (SDE) at a false discovery rate (FDR) of ≤0.05 and fold-change ≥2 or ≤0.5. In addition, most of the 198 SDE novel genes (91 up-regulated and 107 down-regulated) were discovered highly expressed, and 332 SDE isoforms were identified. Gene ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the SDE genes were most enrichment in steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms among the SDE genes included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction, indicating that principal lipogenesis occurred in the liver of laying hens. CONCLUSIONS: This study suggests that the majority of changes at the transcriptome level in laying hen liver were closely related to fat metabolism. Some of the SDE uncharacterized novel genes and alternative splicing isoforms that were detected might also take part in lipid metabolism, although this needs further investigation. This study provides valuable information about the expression profiles of mRNAs from chicken liver, and in-depth functional investigations of these mRNAs could provide new insights into the molecular networks of lipid metabolism in chicken liver.

Quercetin relieves compression-induced cell death and lumbar disc degeneration by stabilizing HIF1A protein.

Background: Lumbar disc degeneration (LDD) is a prevalent condition characterized by the decreased viability and functional impairment of nucleus pulposus mesenchymal stem cells (NPMSCs). Shaoyao-Gancao decoction (SGD), a traditional Chinese medicine formula, has been used to treat LDD, but its active components and mechanisms are unclear. Methods: An integrative network pharmacology and transcriptome analysis were conducted to identify bioactive compounds in SGD that could target LDD. NPMSCs were cultured under mechanical compression as a cellular model of LDD. A rat model of annulus fibrosus needle-puncture was established to induce intervertebral disc degeneration. The effects of quercetin, a predicted active component, on alleviating compression-induced NPMSC death and LDD were evaluated in vitro and in vivo. Results: The analysis identified hypoxia-inducible factor 1-alpha (HIF1A) as a potential target of quercetin in LDD. HIF1A was upregulated in degenerated human disc samples and compression-treated NPMSCs. Quercetin treatment alleviated compression-induced oxidative stress, apoptosis, and loss of viability in NPMSCs by stabilizing HIF1A. The protective effects of quercetin were abrogated by HIF1A inhibition. In the rat model, quercetin ameliorated intervertebral disc degeneration. Conclusion: Our study identified HIF1A as a protective factor against compression-induced cell death in NPMSCs. Quercetin, a bioactive compound found in the traditional Chinese medicine formula SGD, improved the survival of NPMSCs and alleviated LDD progression by stabilizing HIF1A. Targeting the HIF1A pathway through natural compounds like quercetin could represent a promising strategy for the clinical management of LDD and potentially other degenerative disc diseases.

Association between genetically plasma proteins and osteonecrosis: a proteome-wide Mendelian randomization analysis.

Background: Previous studies have explored the role of plasma proteins on osteonecrosis. This Mendelian randomization (MR) study further assessed plasma proteins on osteonecrosis whether a causal relationship exists and provides some evidence of causality. Methods: Summary-level data of 4,907 circulating protein levels were extracted from a large-scale protein quantitative trait loci study including 35,559 individuals by the deCODE Genetics Consortium. The outcome data for osteonecrosis were sourced from the FinnGen study, comprising 1,543 cases and 391,037 controls. MR analysis was conducted to estimate the associations between protein and osteonecrosis risk. Additionally, Phenome-wide MR analysis, and candidate drug prediction were employed to identify potential causal circulating proteins and novel drug targets. Results: We totally assessed the effect of 1,676 plasma proteins on osteonecrosis risk, of which 71 plasma proteins had a suggestive association with outcome risk (P < 0.05). Notably, Heme-binding protein 1 (HEBP1) was significant positively associated with osteonecrosis risk with convening evidence (OR, 1.40, 95% CI, 1.19 to 1.65, P = 3.96 × 10-5, P FDR = 0.044). This association was further confirmed in other MR analysis methods and did not detect heterogeneity and pleiotropy (all P > 0.05). To comprehensively explore the health effect of HEBP1, the phenome-wide MR analysis found it was associated with 136 phenotypes excluding osteonecrosis (P < 0.05). However, no significant association was observed after the false discovery rate adjustment. Conclusion: This comprehensive MR study identifies 71 plasma proteins associated with osteonecrosis, with HEBP1, ITIH1, SMOC1, and CREG1 showing potential as biomarkers of osteonecrosis. Nonetheless, further studies are needed to validate this candidate plasma protein.

Exploring the genetic association between immune cells and susceptibility to osteonecrosis using large-scale population data.

Objectives: Research shows a close association between aberrant immune reactions in osteonecrotic tissues and immune cell infiltration. However, due to limitations in sample size and dataset comprehensiveness, the causal relationship between them is not fully established. This study aims to determine whether there is a causal relationship using a larger and more diverse dataset. Methods: We conducted a comprehensive Mendelian Randomization (MR) analysis to investigate the causal relationship between immune cell characteristics and osteonecrosis. Utilizing publicly available genetic data, we explored the causal relationships between 731 immune cell features and 604 cases from the FinnGen Finnish database, as well as 257 cases from the UK Biobank database with osteonecrosis data. The inverse-variance weighted (IVW) method was used for the primary analysis, and we employed sensitivity analyses to assess the robustness of the main results. In addition, considering data from the two databases used in this study, a meta-analysis was conducted on the significant immune cells associated with osteonecrosis (FDR <0.05). Results: our findings suggested that specific immune cell signatures, such as CD20- % lymphocytes, CD62L-monocytes, and CD33br HLA DR+ CD14-cells were associated with increased odds of osteonecrosis. In contrast, EM CD4+ activated cells and DP (CD4+ CD8+) T cells were associated with decreased odds. Notably, osteonecrosis was associated with a potential decrease in CD45 on immature MDSC cell content. Conclusion: From a genetic perspective, we demonstrated a close association between immune cells and osteonecrosis. These findings significantly enhance our understanding of the interplay between immune cell infiltration and the risk of osteonecrosis, contributing to the potential design of therapeutic strategies from an immunological standpoint.

Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment.

OBJECTIVE: Dysregulated lipid metabolism enhances the development and advancement of many cancers, including osteosarcoma (OS); however, the underlying mechanisms are still largely unknown. Therefore, this investigation aimed to elucidate novel potential lipid metabolism-related long non-coding RNAs (lncRNAs) that regulate OS development and provide novel signatures for its prognosis and precise treatment. MATERIALS AND METHODS: The GEO datasets (GSE12865 and GSE16091) were downloaded and analyzed using R software packages. Immunohistochemistry (IHC) was used to evaluate protein levels in OS tissues while real-time qPCR was used to measure lncRNA levels, and MTT assays were used to assess OS cell viability. RESULTS: Two lipid metabolism-associated lncRNAs (LM-lncRNAs), small nucleolar RNA host gene 17 (SNHG17) and LINC00837, were identified as efficient and independent prognostic indicators for OS. In addition, further experiments confirmed that SNHG17 and LINC00837 were significantly elevated in OS tissues and cells than para-cancerous counterparts. Knockdown of SNHG17 and LINC00837 synergistically suppressed the viability of OS cells, whereas overexpression of the two lncRNAs promoted OS cell proliferation. Moreover, bioinformatics analysis was conducted to construct six novel SNHG17-microRNA-mRNA competing endogenous RNA (ceRNA) networks, and three lipid metabolism-associated genes (MIF, VDAC2, and CSNK2A2) were found to be abnormally upregulated in OS tissues, suggesting that they were potential effector genes of SNHG17. CONCLUSION: In summary, SNHG17 and LINC00837 were found to promote OS cell malignancy, suggesting their use as ideal biomarkers for OS prognosis and treatment.

Performance Degradation Estimation of High-Speed Train Bogie Based on 1D-ConvLSTM Time-Distributed Convolutional Neural Network.

High-speed train bogies are essential for the safety and comfort of train operation. The performance of the bogie usually degrades before it fails, so it is necessary to detect the performance degradation of a high-speed train bogie in advance. In this paper, with two key dampers on the bogie taken as experimental objects (lateral damper and yaw damper), a novel 1D-ConvLSTM time-distributed convolutional neural network (CLTD-CNN) is proposed to estimate the performance degradation of a high-speed train bogie. The proposed CLTD-CNN is an encoder-decoder structure. Specifically, the encoder part of the proposed structure consists of a time-distributed 1D-CNN module and a 1D-ConvLSTM. The decoder part consists of a 1D-ConvLSTM and a simple time-CNN with residual connections. In addition, an auxiliary training part is introduced into the structure to support CLTD-CNN in learning the performance degradation trend characteristic, and a special input format is designed for this structure. The whole structure is end-to-end and does not require expert knowledge or engineering experience. The effectiveness of the proposed CLTD-CNN is tested by the high-speed train CRH380A under different performance states. The experimental results demonstrate the superiority of CLTD-CNN. Compared to other methods, the estimation error of CLTD-CNN is the smallest.

Systematic screening of long intergenic noncoding RNAs expressed during chicken embryogenesis.

Long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes, including embryogenesis and development. To provide a systematic analysis of lncRNAs expressed during chicken embryogenesis, we used Iso-Seq and RNA-Seq to identify potential lncRNAs at embryonic stages from d 1 to d 8 of incubation: sequential stages covering gastrulation, somitogenesis, and organogenesis. The data characterized an expanded landscape of lncRNAs, yielding 45,410 distinct lncRNAs (31,282 genes). Amongst these, a set of 13,141 filtered intergenic lncRNAs (lincRNAs) transcribed from 9803 lincRNA gene loci, of which, 66.5% were novel, were further analyzed. These lincRNAs were found to share many characteristics with mammalian lincRNAs, including relatively short lengths, fewer exons, lower expression levels, and stage-specific expression patterns. Functional studies motivated by "guilt-by-association" associated individual lincRNAs with specific GO functions, providing an important resource for future studies of lincRNA function. Most importantly, a weighted gene co-expression network analysis suggested that genes of the brown module were specifically associated with the day 2 stage. LincRNAs within this module were co-expressed with proteins involved in hematopoiesis and lipid metabolism. This study presents the systematic identification of lincRNAs in developing chicken embryos and will serve as a powerful resource for the study of lincRNA functions.

The effect of breed and age on the gloss of chicken eggshells.

The monitoring of eggshell quality is important mainly in terms of production economy. Eggshell appearance is one of the most characteristics, influencing the purchasing behavior of consumers. Besides numerous eggshell appearance quality (color, shape, etc.), gloss is an important trait to reflect the eggshell appearance. In this study, 2 experiments were conducted to investigate the effect of breed and age on the gloss of eggshells. In experiment 1, we compared the eggshell gloss of 7 chicken breeds. In experiment 2, 105 Wanan (WA) chickens were raised, and 1 egg was collected from each individual at 26, 32, 40, and 50 wks of age. Eggshell gloss, color (L*, a*, b*), cuticle coverage (ΔE*ab), and thickness were measured. The results of experiment 1 showed that the average gloss values were highly variable among different breeds, and the highest was found in WA (gloss unit [GU] = 8.12), almost 2.5 folds as many as the lowest in Rhode Island Red (GU = 3.23). Also, the eggshell gloss of the local chicken breeds was significantly higher than the highly selected lines of egg-type chicken breeds (P < 0.001). In experiment 2, the results showed that gloss ranged from 9.08 GU to 12.12 GU with a variation of 28.38 to 39.71%. It fluctuated with the increasing age of hens and had the peak value at 26 wk. But, the correlation analysis between eggshell gloss and other eggshell quality traits were very low (-0.07 to 0.25). This study laid a foundation for improving the uniformity and intensity of eggshell gloss for breeders.

Dynamic Transcriptional Landscape of the Early Chick Embryo.

Defining the dynamic transcriptome of the early embryo at high resolution would assist greatly in understanding vertebrate development. Here, we describe the dynamic transcription landscape of early chick embryo development using advanced single-molecule long-read isoform sequencing (Iso-Seq) and RNA-Seq technology. Our transcriptomic profiling reflected the time course of chicken embryonic development from day 1 to day 8 of incubation, a period encompassing gastrulation, somitogenesis, and organogenesis. This analysis identified transcriptional isoforms, alternative splicing (AS) events, fusion transcripts, alternative polyadenylation (APA) sites, and novel genes. Our results showed that intron retention (IR) represented the most abundant AS type and displayed distinct features and dynamic modulation during development. Moreover, we constructed a high-resolution expression profile across embryonic development. Our combined expression dataset correlates distinct gene clusters with specific morphological changes, and provides the first framework for the molecular basis of early chicken embryogenesis. Analysis of gene expression in the developing chicken embryo highlighted the dynamic nature and complexity of the chicken transcriptome and demonstrated that dramatically increased IR events are associated with distinct gene sets.

Global Investigation of Cytochrome P450 Genes in the Chicken Genome.

Cytochrome P450 (CYP) superfamily enzymes are broadly involved in a variety of physiological and toxicological processes. However, genome-wide analysis of this superfamily has never been investigated in the chicken genome. In this study, genome-wide analyses identified 45 chicken CYPs (cCYPs) from the chicken genome, and their classification and evolutionary relationships were investigated by phylogenetic, conserved protein motif, and gene structure analyses. The comprehensive evolutionary data revealed several remarkable characteristics of cCYPs, including the highly divergent and rapid evolution of the cCYPs, and the loss of cCYP2AF in the chicken genome. Furthermore, the cCYP expression profile was investigated by RNA-sequencing. The differential expression of cCYPs in developing embryos revealed the involvement of cCYPs in embryonic development. The significantly regulated cCYPs suggested its potential role in hepatic metabolism. Additionally, 11 cCYPs, including cCYP2AC1, cCYP2C23a, and cCYP2C23b, were identified as estrogen-responsive genes, which indicates that these cCYPs are involved in the estrogen-signaling pathway. Meanwhile, an expression profile analysis highlights the divergent role of different cCYPs. These data expand our view of the phylogeny and evolution of cCYPs, provide evolutionary insight, and can help elucidate the roles of cCYPs in physiological and toxicological processes in chicken.