Article
Agriculture, Dairy & Animal Science
Jia Luo, Linyuan Shen, Mailin Gan, Anan Jiang, Lei Chen, Jideng Ma, Long Jin, Yihui Liu, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Xuewei Li, Shunhua Zhang, Li Zhu
Summary: This study investigated muscle growth in QingYu pigs at different developmental stages and compared the differences in the lncRNA transcriptome of muscle. The results showed significant changes in muscle composition and gene expression related to muscle growth and lipid metabolism between the growth inflection point and plateau phase.
Article
Agriculture, Dairy & Animal Science
Chao Xu, Jing Shi, Rufeng Huang, Zhengchang Wu, Shenglong Wu, Wenbin Bao
Summary: This study investigates the role of lncRNA-mRNA in immune regulation by studying the transcriptome of Meishan pig spleen. A competing endogenous RNA network involving lncRNA-miRNA-mRNA was identified, which may play a critical role in immune regulation of Meishan pigs.
Article
Genetics & Heredity
Xiaojin Li, Yanan Yang, Lei Li, Man Ren, Mei Zhou, Shenghe Li
Summary: This study investigated the expression changes in the longissimus dorsi of Wannanhua pigs at different growth stages using transcriptome sequencing technology. Differentially expressed genes (DEGs) associated with lipid metabolism and muscle development were identified, most of which were significantly up-regulated in LD120 and LD240 compared to LD60.
Article
Agriculture, Dairy & Animal Science
Mahmoud Abdelsattar, Yimin Zhuang, Kai Cui, Yanliang Bi, Naifeng Zhang
Summary: Modeling growth curves of digestive tract in goat kids is essential for optimizing feeding management systems to improve production efficiency.Various mathematical models were compared to determine the age-related changes in body weight and digestive tract development, with different models showing varying degrees of fit based on different variables.
Article
Agriculture, Multidisciplinary
Hongyu Wang, Pengke Xia, Zhiyang Lu, Yong Su, Weiyun Zhu
Summary: Time-restricted feeding (TRF) can effectively regulate metabolism and health, and its effects on hypothalamic function were investigated in this study. The results showed that TRF altered the activities of digestive enzymes and gastrointestinal hormones. In addition, TRF affected the metabolism of aromatic amino acids and modulated the gene expression in the hypothalamus. These findings suggest that TRF improves nutrient digestion and absorption, and may influence hypothalamic functions, including drug addictions.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Environmental Sciences
Khim Hoong Chu
Summary: The Belter model is a theoretical tool used to correlate experimental breakthrough curves of water pollutants with similarities to the Bohart-Adams model. The original Belter model is highly symmetric, resulting in poor fits for asymmetric breakthrough curves, whereas the improved version can better accommodate a variety of curve types.
WATER AIR AND SOIL POLLUTION
(2021)
Article
Food Science & Technology
Wei Wei, Chengwan Zha, Aiwen Jiang, Zhe Chao, Liming Hou, Honglin Liu, Ruihua Huang, Wangjun Wu
Summary: Skeletal muscle fiber types can affect pork quality parameters. This study identified key proteins regulating muscle fiber types in pigs using proteomics and transcriptome data, and explored potential regulatory mechanisms through functional enrichment and protein-protein interaction analysis.
Article
Mathematics, Applied
Ting Wei, Yuezan Tao, Honglei Ren, Fei Lin
Summary: This study constructs a one-dimensional heat conduction model with a complex boundary temperature variation over time based on measured data, and derives a theoretical solution using Fourier transform. The model can be solved quickly, and the variation laws of the appearance moment of the inflection point are obtained.
Article
Plant Sciences
Chaw Su Su Htwe, Subramani Rajkumar, Pooja Pathania, Anuradha Agrawal
Summary: This study investigated the cryopreservation mechanism of banana through transcriptomic analysis and identified differentially expressed genes at different stages, providing a basis for developing an effective cryopreservation protocol.
Article
Biology
Yan Gong, Yuebo Zhang, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jianhua He, Haiming Ma
Summary: The study investigated the expression profiles and functional networks of mRNAs and lncRNAs in the liver of Ningxiang piglets at different developmental stages. DEmRNAs were upregulated at 30 days, while most DElncRNAs were downregulated at 210 days. The complex interaction between mRNAs and lncRNAs was identified, suggesting lncRNAs may play a critical regulatory role in mRNA expression. Genes in specific modules showed similar expression patterns, indicating functional and regulatory relationships between mRNAs and lncRNAs.
Article
Biotechnology & Applied Microbiology
Jaya Bharati, N. H. Mohan, Satish Kumar, Jayashree Gogoi, Sai Kumar, Bosco Jose, Meeti Punetha, Sanjib Borah, Amit Kumar, Mihir Sarkar
Summary: RNA-Seq was used to identify differentially expressed genes (DEGs) in porcine corpus luteum (CL) during different physiological stages, revealing significant enrichment of gene functions in early, mid, and late stages. Apoptosis was most active in the regressed stage. Pathway analysis indicated lipid metabolism, translation, immune, and endocrine system pathways were associated with CL function. Gene network analysis identified novel hub genes AR, FOS, CDKN1A potentially regulating CL physiology.
Article
Agronomy
Yihu Hu, Xinying Luo, Zicheng Gao, Ao Du, Hao Guo, Alexey Ruchay, Francesco Marinello, Andrea Pezzuolo
Summary: This paper proposes a novel curve skeleton extraction method for livestock point clouds. By constructing 2D top view and side views, the skeletons are extracted using discrete skeleton evolution algorithm, and then divided into torso and leg branches. Extensive experiments show that this method can extract high-quality curve skeletons from various livestock species.
Article
Materials Science, Composites
Jian-Yong Zhu, Wei-Rong Huang
Summary: The fatigue behavior of asphalt mixture impacts the service performance and life of asphalt pavement. Research on asphalt binder damage helps reveal the fatigue failure mechanism. Using complex modulus as an evaluation index, the damage behavior of asphalt binder was studied and analyzed.
JOURNAL OF THERMOPLASTIC COMPOSITE MATERIALS
(2022)
Article
Multidisciplinary Sciences
Jihye Hwang, Eun Hwa Choi, Bia Park, Gyeongmin Kim, Chorong Shin, Joon Ha Lee, Jae Sam Hwang, Ui Wook Hwang
Summary: In this study, the gene expression abundance related to wing development and metamorphosis in the white-spotted flower chafer Protaetia brevitarsis seulensis was explored based on large-scale RNA-seq data. The transcriptome assembly consisted of 23,551 high-quality transcripts with a coverage of approximately 96.7%. A total of 265 wing development genes, 19 metamorphosis genes, and 1,314 candidates were identified. Network centrality analyses revealed that wing development- and metamorphosis-related genes had a high degree of betweenness centrality. These genes were expressed most highly in eggs, moderately in pupa and adults, and lowest in larva. This study provides valuable clues for understanding the genetic modulation mechanism of wing development and metamorphosis in P. b. seulensis.
Article
Chemistry, Physical
Yongqiang Luo, Xu Cui, Elsie Cheruba, Yong Kang Chua, Charmaine Ng, Rui Zhen Tan, Ker-Kan Tan, Lih Feng Cheow
Summary: In the past decade, breakthroughs in sequencing technology have paved the way for studying the impact of microbial communities on human health and disease. There is a growing interest in accurately analyzing the microbiota in various medical specialties for diagnostic and therapeutic purposes. However, the current next-generation sequencing approach for microbiome profiling is costly and labor-intensive, making it challenging to use for routine diagnostics. This study presents SAMBA, a novel platform for digital melting polymerase chain reaction with multiplexing capability, which can accurately distinguish and quantify bacteria species in mixtures. SAMBA is applied to analyze gut microbiome composition and identify microbial dysbiosis related to colorectal cancer. This rapid, cost-effective, and high-throughput approach has the potential to revolutionize microbiome diagnostics in clinical laboratories and routine medical practice.
Article
Agriculture, Multidisciplinary
Lin-zhen Zhang, Li He, Ning Wang, Jia-hua An, Gen Zhang, Jin Chai, Yu-jie Wu, Chang-jiu Dai, Xiao-han Li, Ting Lian, Ming-zhou Li, Long Jin
Summary: This study identified a natural antisense transcript, APMAP-AS, which is associated with lipid synthesis and positively regulates adipogenic differentiation. APMAP-AS forms an RNA-RNA duplex with APMAP, increasing its stability and promoting lipid metabolism while inhibiting the expression of inflammatory factors.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Genetics & Heredity
Zhiming Wang, Jin Chai, Yuhao Wang, Yiren Gu, Keren Long, Mingzhou Li, Long Jin
Summary: Animal fat deposition has a significant impact on meat flavor and texture. In this study, we investigated the regulatory role of lncPLAAT3-AS in promoting preadipocyte proliferation and adipocyte differentiation. Our findings suggest that lncPLAAT3-AS upregulates PLAAT3 expression through a sponge-like mechanism involving miR-503-5p binding.
Article
Agriculture, Dairy & Animal Science
Hulong Lei, Qian Du, Naisheng Lu, Xueyuan Jiang, Mingzhou Li, Dong Xia, Keren Long
Summary: This study compared the effects of copper sulfate and copper glycinate on fecal microbiota and metabolites in pigs, and found that copper glycinate had more positive effects on gut health.
Article
Biochemistry & Molecular Biology
Xiaokai Li, Zhining Zhong, Ruowei Zhang, Jiaman Zhang, Yu Zhang, Sha Zeng, Qinjiao Du, Haoming Wang, Songling Zhang, Lu Lu, Mingzhou Li, Keren Long
Summary: In this study, a muscular dystrophy mouse model was created by Ptrf knockout, and single-nucleus RNA sequencing was used to investigate the transcriptional changes in skeletal muscle. The study revealed significant alterations in the transcriptome of different types of muscle fibers and mononuclear cells in response to muscular dystrophy, providing valuable insights into the molecular mechanisms of muscular dystrophy.
Article
Multidisciplinary Sciences
Long Jin, Danyang Wang, Jiaman Zhang, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang, Mingzhou Li
Summary: Using a pig model, the study investigates how chromatin architecture in adipose tissue is regulated in relation to obesity. Analysis of the data reveals similarities and differences in chromatin architecture between humans and pigs, providing valuable insights into the regulation of obesity-related genes.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yujie Wang, Xun Wang, Yi Luo, Jiaman Zhang, Yu Lin, Jie Wu, Bo Zeng, Lei Liu, Peiqi Yan, Jiyuan Liang, Hongrui Guo, Long Jin, Qianzi Tang, Keren Long, Mingzhou Li
Summary: This study generated a de novo pigeon genome assembly and conducted a high resolution spatio-temporal transcriptomic analysis of the crop epithelium in pigeons. The study identified "lactation"-related genes involved in lipid and protein metabolism and revealed extensive reorganization of promoter-enhancer interactions linked to the expression of these genes. The spatial localization of gene expression in specific epithelial layers was correlated with phenotypic changes in the crop.
Article
Biology
Qin Zou, Rong Yuan, Yu Zhang, Yifei Wang, Ting Zheng, Rui Shi, Mei Zhang, Yujing Li, Kaixin Fei, Ran Feng, Binyun Pan, Xinyue Zhang, Zhengyin Gong, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Summary: Studying cellular specialization in different anatomical regions of pig skin can enhance our understanding of skin information and provide insights for human skin research.
Article
Geriatrics & Gerontology
Linyuan Shen, Tianci Liao, Qiuyang Chen, Yuhang Lei, Linghui Wang, Hao Gu, Yanhao Qiu, Ting Zheng, Yiting Yang, Chenggang Wei, Lei Chen, Ye Zhao, Lili Niu, Shunhua Zhang, Yan Zhu, Mingzhou Li, Jinyong Wang, Xuewei Li, Mailin Gan, Li Zhu
Summary: This study explores the role of tRNA-derived small RNAs (tsRNAs), specifically 5'tiRNA-Gly, in skeletal muscle regeneration. It is found that 5'tiRNA-Gly is significantly up-regulated after muscle injury and promotes inflammation through the TGF-beta signaling pathway. These findings provide a new potential target for skeletal muscle regeneration treatment.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Physiology
Jinwei Zhang, Yang Shen, Guitao Yang, Jing Sun, Chuang Tang, Hao Liang, Jideng Ma, Xiaoqian Wu, Haoran Cao, Meng Wu, Yuchun Ding, Mingzhou Li, Zuohua Liu, Liangpeng Ge
Summary: This study analyzed the impact of commensal microbiota on the host's mucosal immunity. It found that the absence of commensal microbiota led to smaller Peyer's patches in the gastrointestinal tract, particularly regarding B and T cells. Gene expression analysis revealed that commensal microbiota plays an important role in the development of mucosal immunity in the intestine. Overall, this study revealed the regulatory mechanisms of commensal microbiota in the host's Peyer's patches and emphasized the importance of early microbial colonization for mucosal immunity development.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Weiqiang Liu, Pingfen Zhu, Meng Li, Zihao Li, Yang Yu, Gaoming Liu, Juan Du, Xiao Wang, Jing Yang, Ran Tian, Inge Seim, Alaattin Kaya, Mingzhou Li, Ming Li, Vadim N. Gladyshev, Xuming Zhou
Summary: The variation in lifespan among mammals is significant, and the study aims to uncover the evolutionary forces and molecular features related to longevity. Comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species revealed that only a few genes have common expression patterns with longevity. However, pathways related to translation fidelity and methionine restriction showed correlation with lifespan. The study suggests that lifespan regulation through gene expression is driven by polygenic and indirect natural selection.
Article
Biochemistry & Molecular Biology
Jingyi Bai, Yu Lin, Jiaman Zhang, Ziyu Chen, Yujie Wang, Mingzhou Li, Jing Li
Summary: The study used ATAC-seq and rRNA-depleted RNA-seq to analyze the chromatin accessibility and transcriptional features in multiple tissues of newborn pigs and during porcine liver development. The researchers obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage, and found that tissue-specific accessible promoters were associated with active transcription and tissue-specific functions. Additionally, they observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. This study expands our understanding of epigenetic regulation in mammalian tissues and organ development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jing Yang, Xingxing Zhu, Rui Wang, Mingzhou Li, Qianzi Tang
Summary: In this study, we comprehensively evaluated the performance of 24 popular state-of-the-art methods for complete end-to-end Hi-C data analysis using manually curated or experimentally validated benchmark datasets. Our results indicate that HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances in different aspects, providing a reference for researchers to choose suitable Hi-C analysis tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Huan Liu, Dengke Pan, Pu Li, Dandan Wang, Bo Xia, Ruixin Zhang, Junfeng Lu, Xiangyang Xing, Jiaxiang Du, Xiao Zhang, Long Jin, Lin Jiang, Linong Yao, Mingzhou Li, Jiangwei Wu
Summary: A novel sepsis pig model is created by modifying the surgical strategy of cecal ligation and puncture (CLP), which for the first time recapitulates the whole course of sepsis in humans. Increased levels of ZBED6 in skeletal muscle are shown in this model and sepsis patients, and protection against sepsis-induced muscle wasting is demonstrated in ZBED6-deficient pigs. The direct target of ZBED6 is revealed to be DOCK3, and septic ZBED6-deficient pigs show increased DOCK3 expression in skeletal muscle and myocytes, activating the RAC1/PI3K/AKT pathway and protecting against sepsis-induced muscle wasting.
Article
Multidisciplinary Sciences
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Yan Li, Rui Liu, Mingzhou Li
Summary: The storage of lipids as energy in adipose tissue is conserved, but there are substantial differences in the physiological activities of adipose tissues among species. This study characterized the transcriptional and lipidomic profiles of subcutaneous and visceral adipose tissues across 15 vertebrate species, spanning more than 300 million years of evolution. The data revealed greater variation in AT transcriptome and lipidome among species than within the same species, providing a resource for future studies on functional differences among adipose tissues in vertebrate species.
Article
Biochemistry & Molecular Biology
Jing Li, Teng Yuan, Anjing Zhang, Peidong Yang, Li He, Keren Long, Chuang Tang, Li Chen, Mingzhou Li, Lu Lu
Summary: Macrophages are essential for immunity and play important roles in tissue homeostasis and metabolism. There is currently no standardized method for isolating and differentiating porcine macrophages. This study identified distinct M1 and M2 macrophage subsets in pigs and compared their gene expression profiles. The results showed that porcine macrophages have similar gene signatures to human and mouse macrophages. The study also demonstrated the potential prognostic value of macrophage signatures in differentiating pathogen infections.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)