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Article ; Online: Single-Cell RNA-Sequencing Reveals Heterogeneity and Transcriptional Dynamics in Porcine Circulating CD8

Han, Pingping / Guo, Yaping / Zhang, Wei / Wang, Daoyuan / Wu, Yalan / Li, Xinyun / Zhu, Mengjin

2024 Volume 13, Issue 8

Abstract: Pigs are the most important source of meat and valuable biomedical models. However, the porcine immune system, especially the heterogeneity of CD8 T cell subtypes, has not been fully characterized. Here, using single-cell RNA sequencing, we identified 14 ...

Abstract	Pigs are the most important source of meat and valuable biomedical models. However, the porcine immune system, especially the heterogeneity of CD8 T cell subtypes, has not been fully characterized. Here, using single-cell RNA sequencing, we identified 14 major cell types from peripheral blood circulating cells of pigs and observed remarkable heterogeneity among CD8 T cell types. Upon re-clustering of CD8
MeSH term(s)	Animals ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Swine ; Single-Cell Analysis ; Sequence Analysis, RNA/methods ; Transcriptome/genetics ; Cell Differentiation/genetics ; Transcription, Genetic
Language	English
Publishing date	2024-04-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells13080692
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Article ; Online: Comparative transcriptome analysis of T lymphocyte subpopulations and identification of critical regulators defining porcine thymocyte identity.

Han, Pingping / Zhang, Wei / Wang, Daoyuan / Wu, Yalan / Li, Xinyun / Zhao, Shuhong / Zhu, Mengjin

Frontiers in immunology

2024 Volume 15, Page(s) 1339787

Abstract: Introduction: The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in ... ...

Abstract	Introduction: The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. Method: Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. Results: The comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. Discussion: Our findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.
MeSH term(s)	Swine ; Animals ; Thymocytes ; Leukocytes, Mononuclear ; T-Lymphocyte Subsets/metabolism ; Transcriptome ; Gene Expression Profiling ; Mammals
Language	English
Publishing date	2024-02-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1339787
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Article ; Online: N-Type Polyoxadiazole Conductive Polymer Binders Derived High-Performance Silicon Anodes Enabled by Crosslinking Metal Cations.

Sun, Zhaomei / Zhu, Jiadeng / Yang, Chen / Xie, Qibao / Jiang, Yan / Wang, Kaixiang / Jiang, Mengjin

ACS applied materials & interfaces

2023 Volume 15, Issue 10, Page(s) 12946–12956

Abstract: The dilemma of employing high-capacity battery materials and maintaining the electrodes' electrical and mechanical integrity requires a unique binder system design. Polyoxadiazole (POD) is an n-type conductive polymer with excellent electronic and ionic ... ...

Abstract	The dilemma of employing high-capacity battery materials and maintaining the electrodes' electrical and mechanical integrity requires a unique binder system design. Polyoxadiazole (POD) is an n-type conductive polymer with excellent electronic and ionic conductive properties, which has acted as a silicon binder to achieve high specific capacity and rate performance. However, due to its linear structure, it cannot effectively alleviate the enormous volume change of silicon during the process of lithiation/delithiation, resulting in poor cycle stability. This paper systematically studied metal ion (i.e., Li
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.2c19587
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Article ; Online: H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig.

Kuang, Renzhuo / Xu, Zhixiang / Zhou, Honghong / Zhang, Zhao / Peng, Hao / Wang, Daoyuan / Xu, Xuewen / Zhao, Shuhong / Zhao, Yunxia / Zhu, Mengjin

Animal genetics

2024 Volume 55, Issue 2, Page(s) 217–229

Abstract: The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and ... ...

Abstract	The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.
MeSH term(s)	Swine/genetics ; Animals ; Muscle, Skeletal/physiology ; Adipose Tissue/physiology ; Base Sequence ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/genetics ; Meat/analysis
Chemical Substances	Transcription Factors
Language	English
Publishing date	2024-01-31
Publishing country	England
Document type	Journal Article
ZDB-ID	632766-7
ISSN	1365-2052 ; 0268-9146 ; 0268-9154
ISSN (online)	1365-2052
ISSN	0268-9146 ; 0268-9154
DOI	10.1111/age.13400
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Article ; Online: Macrocyclic Polyoxometalates: Selective Polyanion Binding and Ultrahigh Proton Conduction.

Zhu, Minghui / Iwano, Tsukasa / Tan, Mengjin / Akutsu, Daiki / Uchida, Sayaka / Chen, Guanying / Fang, Xikui

Angewandte Chemie (International ed. in English)

2022 Volume 61, Issue 15, Page(s) e202200666

Abstract: The rational development of an anion templation strategy for the construction of macrocycles has been historically limited to small anions, but large polyoxoanions can offer unmatched structural diversity and ample binding sites. Here we report the ... ...

Abstract	The rational development of an anion templation strategy for the construction of macrocycles has been historically limited to small anions, but large polyoxoanions can offer unmatched structural diversity and ample binding sites. Here we report the formation of a {Mo
Language	English
Publishing date	2022-02-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202200666
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Article ; Online: {Mo

Zhu, Minghui / Han, Shicheng / Liu, Junrui / Tan, Mengjin / Wang, Wei / Suzuki, Kosuke / Yin, Panchao / Xia, Debin / Fang, Xikui

Angewandte Chemie (International ed. in English)

2022 Volume 61, Issue 50, Page(s) e202213910

Abstract: Here we report the formation of giant { ... ...

Abstract	Here we report the formation of giant {Mo
Language	English
Publishing date	2022-11-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202213910
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Article ; Online: The Significance of Florigen Activation Complex in Controlling Flowering in Rice

Chu, Xiaobo / Dong, Zhang / Zhu, Mengjin / Hu, Weimin / Hu, Jin / Chen, Min / Guan, Yajing

Critical Reviews in Plant Sciences. 2023 Sept. 3, v. 42, no. 5 p.300-323

2023

Abstract: Yield potential, plant height and flowering time are three classes of traits that determine the productivity of rice. Rice heading greatly depends on the accurate measurement of environment changes, particularly in day length and temperature. We discuss ... ...

Abstract	Yield potential, plant height and flowering time are three classes of traits that determine the productivity of rice. Rice heading greatly depends on the accurate measurement of environment changes, particularly in day length and temperature. We discuss all genes reported to be related to the heading time in this review. The accumulation of florigen, such as Hd3a or RFT1, is the key factor for rice heading. Florigen is found in the rice leaf and then transports into the shoot apical meristem (SAM), where floral initiation occurs. We discuss the formation of florigen activation complex (FAC) with 14-3-3 and FD1 proteins to induce the expression of flowering genes. In addition, two key pathways related to heading date, GI-Hd1-Hd3a and Ghd7-Ehd1-Hd3a/RFT1 are introduced in this review. We summarize proteins with histone modification functions, due to the modification of histone is also significant for heading date. The flowering time also extremely dependent on the environments, including nutrient availability, abiotic and biotic stresses, we argue the phenotypes of rice heading date under different extreme environments, as well. Lastly, we gather genes that are reported having a change in heading time, but their detail molecular regulation is still elusive. Thus, this review introduces heading time systematically, providing knowledge and ideas for researchers to study further the phenotype of heading time.
Keywords	apical meristems ; florigen ; heading ; histone code ; histones ; leaves ; nutrient availability ; phenotype ; photoperiod ; plant height ; rice ; temperature ; Abiotic and biotic stress ; epigenetics ; florigen activation complex ; heading time
Language	English
Dates of publication	2023-0903
Size	p. 300-323.
Publishing place	Taylor & Francis
Document type	Article ; Online
ISSN	1549-7836
DOI	10.1080/07352689.2023.2233241
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: N‑Type Polyoxadiazole Conductive Polymer Binders Derived High-Performance Silicon Anodes Enabled by Crosslinking Metal Cations

Sun, Zhaomei / Zhu, Jiadeng / Yang, Chen / Xie, Qibao / Jiang, Yan / Wang, Kaixiang / Jiang, Mengjin

ACS Applied Materials & Interfaces. 2023 Mar. 02, v. 15, no. 10 p.12946-12956

2023

Abstract	The dilemma of employing high-capacity battery materials and maintaining the electrodes' electrical and mechanical integrity requires a unique binder system design. Polyoxadiazole (POD) is an n-type conductive polymer with excellent electronic and ionic conductive properties, which has acted as a silicon binder to achieve high specific capacity and rate performance. However, due to its linear structure, it cannot effectively alleviate the enormous volume change of silicon during the process of lithiation/delithiation, resulting in poor cycle stability. This paper systematically studied metal ion (i.e., Li⁺, Na⁺, Mg²⁺, Ca²⁺, and Sr²⁺)-crosslinked PODs as silicon anode binders. The results show that the ionic radius and valence state remarkably influence the polymer's mechanical properties and the electrolyte's infiltration. Electrochemical methods have thoroughly explored the effects of different ion crosslinks on the ionic and electronic conductivity of POD in the intrinsic and n-doped states. Attributed to the excellent mechanical strength and good elasticity, Ca-POD can better maintain the overall integrity of the electrode structure and conductive network, significantly improving the cycling stability of the silicon anode. The cell with such binders still retains a capacity of 1770.1 mA h g-¹ after 100 cycles at 0.2 C, which is ∼285% that of the cell with the PAALi binder (620.6 mA h g-¹). This novel strategy using metal-ion crosslinking polymer binders and the unique experimental design provides a new pathway of high-performance binders for next-generation rechargeable batteries.
Keywords	anodes ; batteries ; calcium ; crosslinking ; electrochemistry ; electrolytes ; experimental design ; polymers ; silicon ; strength (mechanics) ; systems engineering ; Si anode ; conductive polymer binder ; n-type mixed ionic-electronic conductor ; ion-crosslinking ; ionic radius
Language	English
Dates of publication	2023-0302
Size	p. 12946-12956.
Publishing place	American Chemical Society
Document type	Article ; Online
ISSN	1944-8252
DOI	10.1021/acsami.2c19587
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pleiotropic architectures of porcine immune and growth trait pairs revealed by a self‐product‐based transcriptome method

Han, Pingping / Wang, Chao / Zhang, Wei / Wu, Yalan / Wang, Daoyuan / Zhao, Shuhong / Zhu, Mengjin

Animal Genetics. 2023 Apr., v. 54, no. 2 p.123-131

2023

Abstract: Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy has been mainly identified by multi‐trait genome‐wide association studies, but this method has its disadvantages, and new ... ...

Abstract	Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy has been mainly identified by multi‐trait genome‐wide association studies, but this method has its disadvantages, and new developments for pleiotropy detection methods are needed. Here we define a novel metric, self‐product, to measure individual‐level co‐variation of two traits, and develop a novel self‐product‐based transcriptome method to detect pleiotropic genes (PGs). Our method was tested using four immune–growth trait pairs and four immune–immune trait pairs in pigs. Comparative transcriptome analyses identified hundreds of candidate PGs related to eight trait pairs from two tails of self‐product distribution. Gene Ontology enrichment analysis indicated that most of identified PGs were involved in immune‐ or growth‐related biological processes. We established PG interaction networks to exhibit core genes shared by eight trait pairs, of which CCL5 and IL‐10 genes were the hub genes. Genetic association analyses showed that SmaI‐polymorphisms of CCL5 and IL‐10 genes had significant associations with phenotypic co‐variations of multiple trait pairs, indicating that the variants in pleiotropic genes were also pleiotropic variants. Taken together, the validity of our proposed method was preliminarily verified, and our findings provide new insights into the genetic basis of pleiotropic architectures of immune and growth trait pairs in pigs.
Keywords	animal genetics ; gene ontology ; interleukin-10 ; phenotype ; pleiotropy ; swine ; transcriptome
Language	English
Dates of publication	2023-04
Size	p. 123-131.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	632766-7
ISSN	1365-2052 ; 0268-9146 ; 0268-9154
ISSN (online)	1365-2052
ISSN	0268-9146 ; 0268-9154
DOI	10.1111/age.13282
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Article ; Online: Reducing greenhouse gas intensity using a mixture of controlled-release urea and common urea combining suitable maize varieties in a summer maize system.

Ma, Mengjin / Wang, Yongchao / Li, Huan / Song, Miaomiao / Zhang, Yihan / Wang, Hongfei / Zhu, Yiming / Wang, Hao / Shao, Ruixin / Guo, Jiameng / Yang, Qinghua

The Science of the total environment

2024 Volume 918, Page(s) 170628

Abstract: The one-time application of common urea blended with controlled-release urea (CRU) is considered effective for improving nitrogen use efficiency and grain yield and reducing the greenhouse gas emissions of summer maize in intensive agricultural systems. ... ...

Abstract	The one-time application of common urea blended with controlled-release urea (CRU) is considered effective for improving nitrogen use efficiency and grain yield and reducing the greenhouse gas emissions of summer maize in intensive agricultural systems. However, the trade-off between the economic and environmental performances of different blended fertilizer treatments for different maize varieties remains unclear. Therefore, a consecutive two-year field experiment was conducted in the North China Plain to study the effects of different ratios of CRU and common urea on the yield, nitrous oxide (N
MeSH term(s)	Greenhouse Gases/analysis ; Soil ; Zea mays ; Delayed-Action Preparations ; Urea ; Fertilizers/analysis ; Ecosystem ; Methane/analysis ; Agriculture/methods ; Nitrogen ; Edible Grain/chemistry ; Nitrous Oxide/analysis ; China
Chemical Substances	Greenhouse Gases ; Soil ; Delayed-Action Preparations ; Urea (8W8T17847W) ; Fertilizers ; Methane (OP0UW79H66) ; Nitrogen (N762921K75) ; Nitrous Oxide (K50XQU1029)
Language	English
Publishing date	2024-02-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2024.170628
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