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10. Identification of Metabolites in Muscles of Lueyang Black-Bone Chickens: A Comparative Analysis of Caged and Cage-Free Rearing Modes Using Untargeted Metabolomic Techniques.

Author

Wang, Ling, Gao, Jie, Li, Guojin, Cheng, Jia, Yuan, Guoqiang, Zhang, Tao, Zeng, Wenxian, and Lu, Hongzhao

Subjects
CHICKEN as food, MEAT flavor & odor, VOLATILE organic compounds, LEG muscles, PROLINE metabolism
Abstract

Simple Summary: The Lueyang black-bone chicken is a vital poultry resource originating from China. This study aimed to investigate the effects of different rearing systems on the meat quality of Lueyang black-bone chickens via untargeted metabolomics. Compared with caged rearing, cage-free rearing significantly reduced chicken carcass yield and increased the shear force of leg muscles. In addition, the cage-free rearing mode promoted the accumulation of nutrients, such as phospholipids, unsaturated fatty acids, glutamate, and adenosin 3′-monophosphate. Moreover, the cage-free rearing system also enhanced the accumulation of volatile organic compounds, such as aldehydes, alcohols, and ketones, which greatly contribute to the meat flavor. In summary, this study provides a theoretical basis for cage-free rearing as a better rearing mode for Lueyang black-bone chickens. The Lueyang black-bone chicken is a specific native chicken strain in China. This study aimed to investigate the effects of different rearing systems on the meat quality of Lueyang black-bone chickens. Six hundred Lueyang black-bone hens were randomly divided into two groups at 7 weeks of age and raised in cage and cage-free systems for 20 weeks. The carcass yield, meat quality, and total metabolites were measured in both the leg and breast muscles. By comparison, the carcass yield of hens in the cage-free (CF) group (1.26 ± 0.09 kg) was significantly lower than that in the caged rearing (CR) group (1.52 ± 0.15 kg). However, the shear force of leg muscles in the CF group (27.98 ± 2.43 N) was significantly greater than that in the CR group (24.15 ± 1.93 N). In addition, six samples from each group were randomly selected and their metabolites were detected by the non-targeted metabolomics technique. Among these metabolites, 408 and 354 significantly differentially abundant metabolites were identified in breast and leg muscles, which were mainly involved in glycerophospholipid metabolism, unsaturated fatty acid biosynthesis, arginine and proline metabolism, and nucleotide metabolism. We found that the levels of 19 phospholipids, mainly phosphatidylcholines and lysophosphatidylcholines, were significantly greater in the CF group than in the CR group. Additionally, the contents of eight unsaturated fatty acids, linoleic acid, and linolenic acid were dramatically greater in the CF group than in the caged group. The accumulation of 4-hydroxy-proline, glutamate, and adenosine 3′-monophosphate (AMP) was enhanced in the CF group. Moreover, many more volatile organic compounds were identified in the muscles of the cage-free group, enhancing the flavor of the chicken meat. In conclusion, the cage-free rearing mode facilitates the accumulation of nutrients and flavor substances in the chicken meat and is a better rearing system for Lueyang black-bone chickens. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Phosphorylated Adapter RNA Export Protein Is Methylated at Lys 381 by an Methyltransferase-like 21C (METTL21C).

Author

Ke, Meiling, Yu, Xiaoke, Sun, Yuanyuan, Han, Shuai, Wang, Ling, Zhang, Tao, Zeng, Wenxian, and Lu, Hongzhao

Subjects
INHIBITION of cellular proliferation, LIQUID chromatography-mass spectrometry, CELL cycle, CELLULAR control mechanisms, CELL proliferation, CHICKEN embryos, IMMUNOPRECIPITATION, HISTONES
Abstract

Methyltransferase-like 21C (METTL21C) is a member of the non-histone methyltransferase superfamily, which mainly mediates the methylation of lysine (Lys) residues. The main types of modification are Lys dimethylation and trimethylation. However, at present, most of the studies on METTL21C are focused on humans and mice, and there are few reports on poultry. Therefore, chicken embryo fibroblasts (DF-1) were selected as the object of study. To explore the function of chicken METTL21C (chMETTL21C) in the proliferation of DF-1 cells, flow cytometry and qPCR were used to detect the function of chicken METTL21C in the proliferation of DF-1 cells. The results showed that overexpression of METTL21C blocked the cell cycle in the G1max S phase, thus inhibiting cell proliferation. In addition, based on proteomic analysis, stable overexpression of METTL21C may inhibit the proliferation of DF-1 cells by mediating lysine trimethylation of proliferation-related proteins phosphorylated adapter RNA export protein (PHAX), nucleoside diphosphate kinases (NDPKs), eukaryotic transcription extension factor (eukaryotic translation elongation factor 1A,e EF1A), and inversin (Invs). Through immunoprecipitation (co-IP) and liquid chromatography-mass spectrometry (LC-MS/MS) analysis, METTL21C-mediated PHAX Lys-381 methylation was confirmed to be involved in the regulation of DF-1 cell proliferation. The results of this study provide a reference for analyzing the methylation function of METTL21C and the mechanism of regulating the growth and development of chicken cells. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Statistical Robust Estimation of Spatial Symmetric Transformations Based on Mahalanobis Distance

Author

Hu, Yu, Fang, Xing, Zeng, Wenxian, Kutterer, Hansjorg, and Li, Dawei

Abstract

This article explores the problem of symmetric transformation in the presence of outliers for photogrammetric and remote-sensing applications. We propose a pointwise robust objective for symmetric coordinate transformation by assuming the corresponding structure of the downweighting matrix and choosing the squared Mahalanobis distance (MD) as the statistic to evaluate the downweighting factors. Compared with the previous work, our method regards all the coordinates of one point as a whole. It is practical, in principle, since the displacement and correspondence relation are pointwise; it is statistically rigorous, since the stochasticity of both frames is considered; it is flexible, since the incorporated constraints enable all kinds of transformation. By utilizing the parameter partition technique, a more intelligent iteration manner is proposed for the implementation aspect, which specially suits globally distributed geoscience data. The developed method is vetted in the synthetic and real examples, including geodetic datum conversion and point cloud registration. The algorithms have potential in many areas, including cross-source registration, image analysis, pattern recognition, surface modeling, and remote-sensing image registration.

Published
2024
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18. YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia†

Author

Guo, Ming, Li, Xueliang, Li, Tianjiao, Liu, Ruifang, Pang, Weijun, Luo, Jun, Zeng, Wenxian, and Zheng, Yi

Abstract

Genomic integrity is critical for sexual reproduction, ensuring correct transmission of parental genetic information to the descendant. To preserve genomic integrity, germ cells have evolved multiple DNA repair mechanisms, together termed as DNA damage response. The RNA N6-methyladenosine is the most abundant mRNA modification in eukaryotic cells, which plays important roles in DNA damage response, and YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) is a well-acknowledged N6-methyladenosine reader protein regulating the mRNA decay and stress response. Despite this, the correlation between YTHDF2 and DNA damage response in germ cells, if any, remains enigmatic. Here, by employing a Ythdf2-conditional knockout mouse model as well as a Ythdf2-null GC-1 mouse spermatogonial cell line, we explored the role and the underlying mechanism for YTHDF2 in spermatogonial DNA damage response. We identified that, despite no evident testicular morphological abnormalities under the normal circumstance, conditional mutation of Ythdf2in adult male mice sensitized germ cells, including spermatogonia, to etoposide-induced DNA damage. Consistently, Ythdf2-KO GC-1 cells displayed increased sensitivity and apoptosis in response to DNA damage, accompanied by the decreased SET domain bifurcated 1 (SETDB1, a histone methyltransferase) and H3K9me3 levels. The Setdb1knockdown in GC-1 cells generated a similar phenotype, but its overexpression in Ythdf2-null GC-1 cells alleviated the sensitivity and apoptosis in response to DNA damage. Taken together, these results demonstrate that the N6-methyladenosine reader YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia, which provides novel insights into the mechanisms underlying spermatogonial genome integrity maintenance and therefore contributes to safe reproduction.Loss or reduction of the m6A reader YTHDF2 sensitizes spermatogonia to DNA damage, which is mediated, at least in part, by the H3K9 methyltransferase SETDB1.Graphical Abstract

Published
2024
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28. Polyamines protect boar sperm from oxidative stress in vitro

Author

Li, Rongnan, primary, Wu, Xiaodong, additional, Zhu, Zhendong, additional, Lv, Yinghua, additional, Zheng, Yi, additional, Lu, Hongzhao, additional, Zhou, Kaifeng, additional, Wu, De, additional, Zeng, Wenxian, additional, Dong, Wuzi, additional, and Zhang, Tao, additional

Published
2022
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33. Multiframe Transformation With Variance Component Estimation

Author

Hu, Yu, Fang, Xing, Zeng, Wenxian, and Kutterer, Hansjorg

Abstract

The modern global navigation satellite system (GNSS) technique is one of the most effective geoscience and remote sensing tool to observe crustal motions and quantify plate tectonics dynamics. Given multiple installed continuously operating GNSS observing stations, the multiframe transformation is implemented to connect the time-varying GNSS coordinates by the traditional stepwise method. Compared with the stepwise treatment of each pair of frames, the proposed structured total least-squares method considers the combined estimation for all frames, guaranteeing unique and consistent results for the multiframe symmetric transformation. Furthermore, we introduce the variance component (VC) as the nutshell and flexible indicator for land movement. The VCs can quantify the movement coordinatewise, regionalwise, or framewise if the VCs are estimable as we analyze. The simulated experiment shows that the multiframe symmetric transformation is statistically superior to the traditional stepwise treatment. For the application, the deformation caused by the Tohoku earthquake that happened in 2011 in northeast Japan is analyzed.

Published
2023
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34. On an Improved Iterative Reweighted Least Squares Algorithm in Robust Estimation

Author

FANG Xing, HUANG Lixiong, ZENG Wenxian, and WU Yun

Subjects
lcsh:Mathematical geography. Cartography, robust estimation, lcsh:GA1-1776, iterative reweighted least-squares, matrix inversion
Abstract

In geodesy,classical least squares (LS) estimation methods rely heavily on assumptions which are often not met in practice.In particular,it is often assumed that the data errors are zero mean distributed,at least appproximately.Unfortunately,when there are outliers in the data,the classical LS estimators frequently have meaningless performance.In this case,robust estimation such as M-type estimation is usually applied,which is numerically implemented by a so called iterative reweighted least squares algorithm.In the current reweighting process,however,the equivalent normal matrix is required to be inverted in every iteration,which needs an expensive computation demand,especially when the number of the unknown parameters is large.Therefore,in this contribution,the numerical process of the iterative reweighted least squares algorithm is essentially improved,which is mainly represented by avoiding the inversion of the equivalent normal matrix.The numerical example shows that the improved version is performed much superior to the previous one.

Published
2018

35. Additional file 5 of Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis

Author

Zhang, Lingkai, Li, Fuyuan, Lei, Peipei, Guo, Ming, Liu, Ruifang, Wang, Ling, Yu, Taiyong, Lv, Yinghua, Zhang, Tao, Zeng, Wenxian, Lu, Hongzhao, and Zheng, Yi

Abstract

Additional file 5 Fig. S3 (Relates to Fig. 3) (A) Density plot show the distribution of gene expression in spermatogonia, spermatocytes and spermatids. (B) The correlation between bulk and scRNA-seq data illustrated by Pearson correlation analysis. (C) Data visualization according to the cluster analysis. Each line shows a single gene expression from all samples.

Published
2021
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36. Additional file 6 of Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis

Author

Zhang, Lingkai, Li, Fuyuan, Lei, Peipei, Guo, Ming, Liu, Ruifang, Wang, Ling, Yu, Taiyong, Lv, Yinghua, Zhang, Tao, Zeng, Wenxian, Lu, Hongzhao, and Zheng, Yi

Subjects
endocrine system, urogenital system, reproductive and urinary physiology
Abstract

Additional file 6 Fig. S4 (Relates to Fig. 4) (A) Single-cell transcriptomes from porcine undifferentiated spermatogonia, differentiating spermatogonia, Leptotene and Zygotene spermatocytes were used for cell trajectories ordered in pseudotime (right) and cells colored according to cell cluster (left). (B) Heatmaps show the top 50 variable genes across pseudotime from porcine undifferentiated spermatogonia, differentiating spermatogonia, Leptotene and Zygotene spermatocytes (scaled expression according to legend). (C) Visualization of marker gene expression across the differentiation states of spermatogonia in the violin plot. Unbiased cell clusters are distinguished by color according to the key. (D) Expression patterns of new defined marker genes for undifferentiated and differentiating spermatogonia visualized in t-SNE plots for all cell types.

Published
2021
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37. Additional file 3 of Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis

Author

Zhang, Lingkai, Li, Fuyuan, Lei, Peipei, Guo, Ming, Liu, Ruifang, Wang, Ling, Yu, Taiyong, Lv, Yinghua, Zhang, Tao, Zeng, Wenxian, Lu, Hongzhao, and Zheng, Yi

Abstract

Additional file 3 Fig. S1 Data quality and cell type annotation by other genes (Relates to Fig. 1). (A) Distribution of cell attributes in the pig dataset. (B) The correlation between the number of genes and UMI counts. (C) Heatmap showed expression of 45 marker genes in 6 cell types. (D) Visualization of marker gene expression across unselected clusters in the violin plot. Unbiased cell clusters are distinguished by color according to the key.

Published
2021
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38. Additional file 4 of Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis

Author

Zhang, Lingkai, Li, Fuyuan, Lei, Peipei, Guo, Ming, Liu, Ruifang, Wang, Ling, Yu, Taiyong, Lv, Yinghua, Zhang, Tao, Zeng, Wenxian, Lu, Hongzhao, and Zheng, Yi

Abstract

Additional file 4 Fig. S2 Expression of CD63 in porcine testis. (A) Coimmunofluorescence examination of the expression of CD63 with PNA. Scale bars = 50 ��m. (B) Immunohistochemical staining of CD63 in porcine testis. Scale bars = 50 ��m.

Published
2021
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44. Early cleavage of preimplantation embryos is regulated by tRNAGln-TTG–derived small RNAs present in mature spermatozoa

Author

Chen, Xiaoxu, primary, Zheng, Yi, additional, Lei, Anmin, additional, Zhang, Hanxue, additional, Niu, Huimin, additional, Li, Xueliang, additional, Zhang, Pengfei, additional, Liao, Mingzhi, additional, Lv, Yinghua, additional, Zhu, Zhendong, additional, Pan, Chuanying, additional, Dong, Wuzi, additional, Chen, Hong, additional, Wu, De, additional, Liu, Wansheng, additional, Hamer, Geert, additional, Zeng, Shenming, additional, and Zeng, Wenxian, additional

Published
2020
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50. Distinct H3K9me3 and DNA methylation modifications during mouse spermatogenesis

Author

Liu, Yingdong, primary, Zhang, Yanping, additional, Yin, Jiqing, additional, Gao, Yawei, additional, Li, Yanhe, additional, Bai, Dandan, additional, He, Wenteng, additional, Li, Xueliang, additional, Zhang, Pengfei, additional, Li, Rongnan, additional, Zhang, Lingkai, additional, Jia, Yanping, additional, Zhang, Yalin, additional, Lin, Jiaming, additional, Zheng, Yi, additional, Wang, Hong, additional, Gao, Shaorong, additional, Zeng, Wenxian, additional, and Liu, Wenqiang, additional

Published
2019
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