Phosphorylation of LSD1 at serine 54 regulates genes involved in follicle selection by enhancing demethylation activity in chicken ovarian granulosa cells.

Follicle selection in chicken refers to the process of selecting a follicle to enter hierarchy from a cohort of small yellow follicles (SY) with a diameter of 6 to 8 mm. The follicle being selected will develop rapidly and ovulate. Follicle selection is a key stage affecting chicken egg-laying performance. Our previous study showed that the phosphorylation level of lysine (K)-specific demethylase 1A (LSD1) at serine 54 (LSD1Ser54p) was significantly increased in F6 follicles compared to prehierarchal SY follicles, but its function was unclear. Here, the mechanism of this modification, the effect of LSD1Ser54p dephosphorylation on gene expression profile of chicken hierarchal granulosa cells and the function of fibroblast growth factor 9 (FGF9) that is regulated by LSD1Ser54p were further investigated. The modification of LSD1Ser54p was predicted to be mediated by cyclin-dependent kinase 5 (CDK5) and glycogen synthase kinase 3 (GSK3). Treatment of chicken hierarchal granulosa cells with CDK5 inhibitor significantly decreased LSD1Ser54p level (P < 0.05) and LSD1Ser54p interacted with CDK5, suggesting that, in the granulosa cells of chicken hierarchal follicles, LSD1Ser54p modification was carried out by CDK5. When the LSD1Ser54p level decreased in the granulosa cells of chicken hierarchal follicles, both the mRNA expression of FGF9 and α-actinin 2 (ACTN2) and the H3K4me2 level in their promoter regions significantly increased (P < 0.05), indicating that this phosphorylation modification enhanced the demethylation activity of LSD1. Moreover, in chicken hierarchal granulosa cells, overexpression of chicken FGF9 stimulated their proliferation and increased the mRNA expression of hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 (Hsd3b) and steroidogenic acute regulatory protein (StAR). This study collectively revealed that phosphorylation of LSD1 at serine 54 by CDK5 enhanced its demethylation activity in chicken ovarian granulosa cells and regulated genes including FGF9 that is engaged in chicken follicle selection.

TMT-labeled quantitative malonylome analysis on the longissimus dorsi muscle of Laiwu pigs reveals the role of ACOT7 in fat deposition.

The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by an extremely high level of intramuscular fat (IMF) content (9% âˆ¼ 12%), but the regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. In this study, the TMT-labeled quantitative malonylome of the longissimus dorsi muscle in Laiwu pigs at the fastest IMF deposition stage (240 d vs 120 d) was compared to analyze the molecular mechanism of IMF variation in pigs. In Laiwu pigs aged 240 days/120 days, we identified 291 malonylated lysine sites across 188 proteins in the longissimus dorsi muscle. Among these, 38 sites across 31 proteins exhibited differential malonylation. Annotation analysis and enrichment analysis were performed for differentially malonylated proteins (DMPs). These DMPs were mainly clustered into 12 GO functional categories accounting for 5 biological processes, 4 cellular components and 3 molecular functions, and 2 signaling pathways by KEGG enrichment analysis. The function of differentially malonylated protein ACOT7 in the process of fat deposition was further investigated during the differentiation of 3 T3-L1 cells. The results showed that the protein level of ACOT7 in 3 T3-L1 cells decreased but the malonylated level of ACOT7 increased significantly. The malonyl-CoA that is synthesized by ACSF3 affected the malonylation level of ACOT7 in 3 T3-L1 cells. SIGNIFICANCE: The intramuscular fat (IMF) content, by affecting sensory quality traits of meat, such as tenderness, flavor and juiciness, plays an important role in meat quality. Using TMT-based quantitative malonylated proteome analysis, we identified malonylated proteins in LD muscle samples in two stages (120 d and 240 d) of development and further identified differentially malonylated proteins, such as SLC25A4, ANXA5, TPM3 and ACOT7, that are associated with intramuscular fat deposition and fat metabolism in pigs. These differentially malonylated proteins could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs. In addition, we found that the malonyl-CoA in 3 T3-L1 cells is mainly synthesized by ACSF3, affecting the malonylated level of ACOT7. The study provides some data concerning the role of protein malonylation in regulating the variation in porcine IMF content.

Two-timescale projection neural networks in collaborative neurodynamic approaches to global optimization and distributed optimization.

In this paper, we propose a two-timescale projection neural network (PNN) for solving optimization problems with nonconvex functions. We prove the convergence of the PNN with sufficiently different timescales to a local optimal solution. We develop a collaborative neurodynamic approach with multiple such PNNs to search for global optimal solutions. In addition, we develop a collaborative neurodynamic approach with multiple PNNs connected via a directed graph for distributed global optimization. We elaborate on four numerical examples to illustrate the characteristics of the approaches.

ActionCLIP: Adapting Language-Image Pretrained Models for Video Action Recognition.

The canonical approach to video action recognition dictates a neural network model to do a classic and standard 1-of-N majority vote task. They are trained to predict a fixed set of predefined categories, limiting their transferability on new datasets with unseen concepts. In this article, we provide a new perspective on action recognition by attaching importance to the semantic information of label texts rather than simply mapping them into numbers. Specifically, we model this task as a video-text matching problem within a multimodal learning framework, which strengthens the video representation with more semantic language supervision and enables our model to do zero-shot action recognition without any further labeled data or parameters' requirements. Moreover, to handle the deficiency of label texts and make use of tremendous web data, we propose a new paradigm based on this multimodal learning framework for action recognition, which we dub "pre-train, adapt and fine-tune." This paradigm first learns powerful representations from pre-training on a large amount of web image-text or video-text data. Then, it makes the action recognition task to act more like pre-training problems via adaptation engineering. Finally, it is fine-tuned end-to-end on target datasets to obtain strong performance. We give an instantiation of the new paradigm, ActionCLIP, which not only has superior and flexible zero-shot/few-shot transfer ability but also reaches a top performance on general action recognition task, achieving 83.8% top-1 accuracy on Kinetics-400 with a ViT-B/16 as the backbone. Code is available at https://github.com/sallymmx/ActionCLIP.git.

Expression and regulation of Noggin4 gene in chicken ovarian follicles and its role in the proliferation and differentiation of granulosa cells.

As a member of Noggin family, Noggin4 is reported to play an important role in the formation of head structure during the embryo development of Xenopus laevis and chicken. We previously detected an increase of Noggin4 transcript in the granulosa cells of chicken hierarchal follicles (Post-GCs) compared to pre-hierarchal follicles (Pre-GCs) by ONT transcriptome sequencing. To further clarify the role of Noggin4 in chicken follicle selection, in this study, we investigated its expression, regulation and function in follicles and granulosa cells. The mRNA expression of chicken Noggin4 exhibited dynamic changes during follicle development. It was significantly higher in the small yellow follicles than in the small white, F6, F5 and F4 follicles, and also increased in Post-GCs than in Pre-GCs. The Noggin4 mRNA could be stimulated by follicle stimulating hormone (FSH) and bone morphogenetic protein 4 (BMP4) in both Pre-GCs and Post-GCs. However, the estrogen and progesterone could exert opposing transcriptional regulations on Noggin 4 mRNA in both Pre- and Post-GCs. In chicken Post-GCs, knockdown of Noggin4 by siRNA reduced the mRNA expression of steroidogenic acute regulatory protein (STAR), cytochrome P450 family 11 subfamily A member 1 (CYP11A1), but increased that of Wnt family member 4 (Wnt4), while overexpression of Noggin4 significantly decreased the mRNA expression of Wnt4 but had no marked effects on that of STAR and CYP11A1. Moreover, Noggin4 significantly decreased the mRNA expression of BMP4 in both Pre-GCs and Post-GCs. Overexpression of Noggin4 inhibited the proliferation of both Pre-GCs and Post-GCs. These data collectively suggest an important role of Noggin4 in chicken follicle selection, especially on the proliferation of granulosa cells.

How does the development of digital inclusive finance in China affect green technology innovation? A theoretical mechanism study and empirical analysis.

This study employed fixed effects (FE) models, difference-in-differences (DID) methods, and mediating effect (ME) models to explore the total effect, structural effect, heterogeneous characteristics, and impact mechanism of digital inclusive finance (DIF) on green technology innovation (GTI) from 2011 to 2020. We derived the following results. First, DIF can significantly improve the level of GTI, and the positive role of internet digital inclusive finance is greater than that of traditional banks, but the three dimensions of the DIF index have different impacts on such innovation. Second, the impact of DIF on GTI has a "siphon effect," which is significantly promoted in regions with stronger economic power and inhibited in those with weaker economic power. Finally, there is an influence mechanism of "digital inclusive finance → financing constraints → green technology innovation." Our findings provide evidence to establish a lasting effect mechanism for DIF to promote GTI, and they have important reference value for other countries to develop DIF.

Long-read sequencing reveals the effect of follicle-stimulating hormone on the mRNA profile of chicken granulosa cells from prehierarchical follicles.

Follicle selection is an important step in the laying process of chicken, which is closely related to the laying performance and fecundity of hens. Follicle selection mainly depends on the regulation of follicle-stimulating hormone (FSH) secreted by pituitary gland and the expression of follicle stimulation hormone receptor. To uncover the role of FSH in chicken follicle selection, in this study, we analyzed the changes in the mRNA transcriptome profiles of FSH-treated chicken granulosa cells from prehierarchical follicles by long-read sequencing Oxford Nanopore Technologies (ONT) approach. Among the 10,764 genes detected, 31 differentially expressed (DE) transcripts of 28 DE genes were significantly upregulated by FSH treatment. These DE transcripts (DETs) were mainly related to the steroid biosynthetic process by GO analysis and enriched in pathways of ovarian steroidogenesis and aldosterone synthesis and secretion by KEGG analysis. Among these genes, the mRNA and protein expression of TNF receptor associated factor 7 (TRAF7) was upregulated after FSH treatment. Further study revealed that TRAF7 stimulated the mRNA expression of steroidogenic enzymes steroidogenic acute regulatory protein (StAR) and cytochrome P450 family 11 subfamily A member 1 (CYP11A1) genes and the proliferation of granulosa cells. This is the first study to investigate differences in chicken prehierarchical follicular granulosa cells before and after FSH treatment by using ONT transcriptome sequencing, which provides a reference for a more comprehensive understanding of the molecular mechanism of follicle selection in chicken.

Phosphoproteomic analysis on ovarian follicles reveals the involvement of LSD1 phosphorylation in Chicken follicle selection.

BACKGROUND: Follicle selection in chickens refers to the process of selecting one follicle from a group of small yellow follicles (SY, 6-8 mm in diameter) for development into 12-15 mm hierarchal follicles (usually F6 follicles), which is controlled by sex hormones including follicle-stimulating factor (FSH), estrogen and progesterone. Follicle selection is a critical process impacting egg production in chicken, therefore, is the focus of many studies. Phosphorylation is important for the proper function of proteins, thus, needs to be analyzed by proteomic level. RESULT: In this study, we compared the phosphoproteomes of SY and F6 follicles in laying hens and identified 2,386 phosphoproteins and 5,940 phosphosites, of which 4,235 sites of 1,963 phosphoproteins were quantified. From SY to F6 follicles, 190 phosphorylation sites of 149 proteins changed significantly, among which the phosphorylation level of lysine demethylase 1 A (LSD1) at the conserved 54th serine (LSD1Ser54p) was significantly upregulated in F6 follicles compared to SY follicles (p < 0.05); however, the expression of chicken LSD1 were not significantly different on both mRNA and protein levels. LSD1Ser54p is mainly located in the nucleus of both SY and F6 follicles, and was higher in F6 follicles than that of SY follicles revealed by both immunofluorescence and Western blotting. LSD1Ser54p level increased after treatment with 5 ng/mL and 10 ng/mL of FSH in the theca cells and the granulosa cells of pre-hierarchal follicles, and with 50 ng/mL in granulosa cells of hierarchal follicles. In the theca cells of hierarchal follicles, estrogen stimulated the level of LSD1Ser54p in a dosage-dependent manner, and in granulosa cells of pre-hierarchal follicles, 10 ng/mL of estrogen increased LSD1Ser54p expression. Treatment with 50 ng/mL of progesterone increased LSD1Ser54p expression in theca cells of pre-hierarchal follicles, and with 10 to 100 ng/ml enhanced LSD1Ser54p expression in the granulosa cells of hierarchal follicles. CONCLUSION: The expression dynamics of LSD1Ser54p in follicles from SY to F6 and its regulation by sex hormones suggest that it is involved in chicken follicle selection.

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.

MOTIVATION: Protein-protein interaction (PPI) networks and transcriptional regulatory networks are critical in regulating cells and their signaling. A thorough understanding of PPIs can provide more insights into cellular physiology at normal and disease states. Although numerous methods have been proposed to predict PPIs, it is still challenging for interaction prediction between unknown proteins. In this study, a novel neural network named AFTGAN was constructed to predict multi-type PPIs. Regarding feature input, ESM-1b embedding containing much biological information for proteins was added as a protein sequence feature besides amino acid co-occurrence similarity and one-hot coding. An ensemble network was also constructed based on a transformer encoder containing an AFT module (performing the weight operation on vital protein sequence feature information) and graph attention network (extracting the relational features of protein pairs) for the part of the network framework. RESULTS: The experimental results showed that the Micro-F1 of the AFTGAN based on three partitioning schemes (BFS, DFS and the random mode) on the SHS27K and SHS148K datasets was 0.685, 0.711 and 0.867, as well as 0.745, 0.819 and 0.920, respectively, all higher than that of other popular methods. In addition, the experimental comparisons confirmed the performance superiority of the proposed model for predicting PPIs of unknown proteins on the STRING dataset. AVAILABILITY AND IMPLEMENTATION: The source code is publicly available at https://github.com/1075793472/AFTGAN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Identification of nucleotide polymorphisms in the key promoter region of chicken annexins A2 gene associatied with egg laying traits.

Annexin A2 (ANXA2) is a member of the A subfamily of a multifunctional calcium dependent membrane phospholipid binding protein family. The mRNA expression of ANXA2 is consistent with ovary function and egg laying in chickens. In this study, six nucleotide polymorphisms in the key promoter region of chicken ANXA2 gene (-2861 bp to -1394 bp), i.e.,: g.-2337 indel (GT), g.-2255 C > T, g. -2248 A > G, g.-2188 A > G, g.-2169 G > A, g.-2160 A > C, were identified. Their distributions in populations of Xinyang Brown, Recessive White Rock, Wenchang and Wenshang Barred chickens were analyzed. In the Recessive White Rock chicken population, CAA, CAG and TGG were three major haplotypes. Association analysis indicated that the individuals with diplotype TGG/TGG laid more eggs at 32 weeks, and the individual with diplotype CAG/TGG laid at the earlier age. Luciferase activity assay showed that mutation from C to T at -2255 increased trascriptional activity of chicken ANXA2, which is consistent with its effect on egg laying traits.

Probabilistic Regularized Extreme Learning for Robust Modeling of Traffic Flow Forecasting.

The adaptive neurofuzzy inference system (ANFIS) is a structured multioutput learning machine that has been successfully adopted in learning problems without noise or outliers. However, it does not work well for learning problems with noise or outliers. High-accuracy real-time forecasting of traffic flow is extremely difficult due to the effect of noise or outliers from complex traffic conditions. In this study, a novel probabilistic learning system, probabilistic regularized extreme learning machine combined with ANFIS (probabilistic R-ELANFIS), is proposed to capture the correlations among traffic flow data and, thereby, improve the accuracy of traffic flow forecasting. The new learning system adopts a fantastic objective function that minimizes both the mean and the variance of the model bias. The results from an experiment based on real-world traffic flow data showed that, compared with some kernel-based approaches, neural network approaches, and conventional ANFIS learning systems, the proposed probabilistic R-ELANFIS achieves competitive performance in terms of forecasting ability and generalizability.

Identification of oogonial stem cells in chicken ovary.

OBJECTIVES: Oogonial stem cells (OSCs) are germ cells that can sustain neo-oogenesis to replenish the pool of primary follicles in adult ovaries. In lower vertebrates, fresh oocytes are produced by numerous OSCs through mitosis and meiosis during each reproduction cycle, but the OSCs in adult mammals are rare. The birds have retained many conserved features and developed unique features of ovarian physiology during evolution, and the presence of OSCs within avian species remain unknown. MATERIALS AND METHODS: In this study, we investigated the existence and function of OSCs in adult chickens. The chicken OSCs were isolated and expanded in culture. We then used cell transplantation system to evaluate their potential for migration and differentiation in vivo. RESULTS: DDX4/SSEA1-positive OSCs were identified in both the cortex and medulla of the adult chicken ovary. These putative OSCs undergo meiosis in the reproductively active ovary. Furthermore, the isolated OSCs were expanded in vitro for months and found to express germline markers similar to those of primordial germ cells. When transplanted into the bloodstream of recipient embryos, these OSCs efficiently migrated into developing gonads, initiated meiosis, and then derived oocytes in postnatal ovaries. CONCLUSIONS: This study has confirmed the presence of functional OSCs in birds for the first time. The identification of chicken OSCs has great potential for improving egg laying and preserving endangered species.

A Novel Single-Nucleotide Polymorphism in WNT4 Promoter Affects Its Transcription and Response to FSH in Chicken Follicles.

The signaling pathway of the wingless-type mouse mammary tumor virus integration site (Wnt) plays an important role in ovarian and follicular development. In our previous study, WNT4 was shown to be involved in the selection and development of chicken follicles by upregulating the expression of follicle-stimulating hormone receptors (FSHR), stimulating the proliferation of follicular granulosa cells, and increasing the secretion of steroidal hormones. FSH also stimulates the expression of WNT4. To further explore the molecular mechanism by which FSH upregulates WNT4 and characterize the cis-elements regulating WNT4 transcription, in this study, we determined the critical regulatory regions affecting chicken WNT4 transcription. We then identified a single-nucleotide polymorphism (SNP) in this region, and finally analyzed the associations of the SNP with chicken production traits. The results showed that the 5' regulatory region from −3354 to −2689 of WNT4 had the strongest activity and greatest response to FSH stimulation, and we identified one SNP site in this segment, −3015 (G > C), as affecting the binding of NFAT5 (nuclear factor of activated T cells 5) and respones to FSH stimulation. When G was replaced with C at this site, it eliminated the NFAT5 binding. The mRNA level of WNT4 in small yellow follicles of chickens with genotype GG was significantly higher than that of the other two genotypes. Moreover, this locus was found to be significantly associated with comb length in hens. Individuals with the genotype CC had longer combs. Collectively, these data suggested that SNP−3015 (G > C) is involved in the regulation of WNT4 gene expression by responding FSH and affecting the binding of NFAT5 and that it is associated with chicken comb length. The current results provide a reference for further revealing the response mechanism between WNT and FSH.

Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs.

In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.

Identification of a promoter polymorphism affecting GPAT3 gene expression that is likely related to intramuscular fat content in pigs.

The intramuscular fat content (IMF) is an economically important trait in pigs and the Laiwu pig is famous for its excessively extremely high level of IMF. Our previous transcriptome study revealed that the dynamic expression of glycerol-phosphate acyltransferase 3 (GPAT3) is consistent with changes in the IMF of Laiwu pigs. In this study, we further analyzed the expression and polymorphism of GPAT3 in its promoter region. The results indicated that the expression of GPAT3 increased dramatically from 120 to 240 days and is consistent with changes in IMF deposition, and at both mRNA and protein levels, GPAT3 expression was markedly higher in the LD muscle of Laiwu pigs than that of Duroc × Landrace × Yorkshire pigs. Deletion from -1695 to -1187 of porcine GPAT3 greatly increased its transcription. Of the two SNPs identified, the transition from C to T at -1526 site increased the transcription of porcine GPAT3 and allele T mainly distributed in Laiwu pig population. These results collectively suggest that the SNP at -1526 site of GPAT3 may contribute to IMF deposition by affecting its expression in pigs.

Identification of genes involved in chicken follicle selection by ONT sequencing on granulosa cells.

In chickens, follicle selection is an important process affecting laying traits, which is characterized by the differentiation of granulosa cells and the synthesis of progesterone by granulosa cells from hierarchical follicles. By using Oxford Nanopore Technologies (ONT) approach, we compared the transcriptomes of granulosa cells between pre-hierarchical (Pre-GCs) and hierarchical follicles (Post-GCs) to identify genes underlying chicken follicle selection. A total of 2,436 differentially expressed genes (DEGs), 3,852 differentially expressed transcripts (DETs) and 925 differentially expressed lncRNA transcripts were identified between chicken Pre-GCs and Post-GCs. For all of the significant DETs, the alternative 3'splice sites (A3) accounted for a maximum of 23.74% of all alternative splicing events. Three DETs of the 7-dehydrocholesterol reductase gene (DHCR7) named as T1, T3, and T4, differing in 5'untranslated regions (UTRs), increased in Post-GCs with different folds (T1: 1.83, T3: 2.42, T4: 5.06). The expression of the three DHCR7 transcripts was upregulated by estrogen in a dose-dependent manner, while was downregulated by bone morphogenetic protein 15 (BMP15) and transforming growth factor-beta 1 (TGF-ß1). Follicle-stimulating hormone (FSH) and bone morphogenetic protein 4 (BMP4) promoted the expression of the three DHCR7 transcripts in Pre-GCs at lower concentrations, while repressed their expression at higher concentrations. The data from this study may provide a reference for better understanding of the genetic mechanisms underlying follicle selection in chicken and other poultry species.

Hesitant fuzzy multi-attribute decision making based on binary connection number of set pair analysis.

To objectively evaluate the influence of hesitant fuzziness on the ranking of alternatives in multi-attribute decision making with hesitant fuzzy or probabilistic hesitant fuzzy information, the binary connection number of set pair analysis is applied to hesitant fuzzy multi-attribute decision making. The hesitant or probabilistic hesitant fuzzy set is transformed to the binary connection number. A hesitant fuzzy multi-attribute decision making model based on binary connection number is then established. Binary connection number theory is utilized to obtain the hesitant fuzzy center and decision-making suggestions about the alternative ranking under different hesitant fuzzy conditions. Experimental examples show that the hesitant fuzzy multi-attribute decision making model based on binary connection number has a certain versatility. It can determine the optimal scheme under the influence of hesitant fuzziness on the alternative ranking and contains the results of the same hesitant fuzzy decision-making problem using other methods, which helps in targeted decision making according to different hesitant fuzzy conditions.

Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing.

BACKGROUND: As one of "γδ-high" species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using high-throughput sequencing. METHODS: In this study, we first obtained the detailed genomic organization of the TCRγ locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCRγ repertoire in the thymus of four chickens by using 5' Rapid Amplification of cDNA Ends (5' RACE) along with high-throughput sequencing (HTS). RESULTS: The chicken TCRγ locus contains a single Cγ gene, three functional Jγ segments and 44 Vγ segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken TCRγ locus against itself showed that almost all the entire zone containing Vγ segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 Vγ gene segments, has tandemly duplicated for four times. For the analysis of chicken TCRγ repertoire, more than 100,000 unique Vγ-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline Vγ and Jγ segments identified above, we found that the four chickens had similar repertoire profile of TCRγ. In brief, four Vγ segments (including Vγ3.7, Vγ2.13, Vγ1.6 and Vγ1.3) and six Vγ-Jγ pairs (including Vγ3.7-Jγ3, Vγ2.13-Jγ1, Vγ2.13-Jγ3, Vγ1.6-Jγ3, Vγ3.7-Jγ1 and Vγ1.6-Jγ1) were preferentially utilized by all four individuals, and vast majority of the unique CDR3γ sequences encoded 4 to 22 amino acids with mean 12.90 amino acids, which exhibits a wider length distribution and/or a longer mean length than CDR3γ of human, mice and other animal species. CONCLUSIONS: In this study, we present the first in-depth characterization of the TCRγ repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.

A 14 bp indel polymorphism in the promoter region is associated with different responses to porcine circovirus type 2 infection by regulating MRC1 transcription.

Mannose receptor, C type 1 (MRC1) is a key factor in regulating the body's immune response to resist pathogen invasions. In this study, mRNA expressions of MRC1 gene in nine porcine organs/tissues were compared between Laiwu (LW) and Yorkshire × Landrace crossbred (YL) pigs prior to and post PCV2 infection. We found that, for pigs uninfected with PCV2, MRC1 mRNA expressions in the lung, spleen, large intestine, small intestine and mesenteric lymph node tissues of LW were significantly higher than those of YL pigs (P < 0.05). After PCV2 infection, MRC1 mRNA levels in the liver, kidney and mesenteric lymph node were significantly increased in LW pigs (P < 0.05); while, significantly decreased in the heart and lung tissues of YL pigs (P < 0.05). The transcriptional activity of porcine MRC1 promoter was further analyzed to investigate the molecular mechanism underlying these expressional differences in response to PCV2 infection. Luciferase assay indicated that a 14 bp indel polymorphism "GTTTTTTTTTTTTT" at the site -864 of MRC1 promoter contributed to the transcriptional activity. The frequency of 14 bp insertion in LW and Dapulian pigs, generally resistant to PCV2 infection, was higher than that in Duroc, Landrace and Yorkshire pigs, which were sensitive to PCV2 infection. The promoter with 14 bp insertion displayed higher MRC1 transcription level both prior to and post PCV2 infection compared with that carrying no insertion in PK15 cells (P < 0.01). The results suggest that this 14 bp indel polymorphism is associated with different responses to PCV2 infection by regulating MRC1 transcription.