Article
Reproductive Biology
Raquel Gonzalez, Eva Pericuesta, Alfonso Gutierrez-Adan, Ylva C. B. Sjunnesson
Summary: In a study on porcine embryo development, exposure to the altered endocrine environment from ACTH-treated sows did not have harmful consequences for embryo development. Differences in blastocyst quality by morphology assessment were observed, but this did not correlate with significant differences in gene expression profiles among groups, suggesting that the effect of the altered environment may have been too short-lived to impact embryo development significantly.
Article
Genetics & Heredity
Haiwei Zuo, Xia Li, Xixi Zheng, Qiuwen Sun, Qianqian Yang, Yong Xin
Summary: This study elucidated the regulatory network and functional mechanism of circRNA-related ceRNAs in LUAD through analyzing gene expression data. A novel circRNA regulatory network related to LUAD was constructed, revealing the biological processes and signal pathways regulated by DEcircRNAs. Survival analysis was used to select DEmRNAs related to prognosis, and a ceRNA hub regulatory network containing circRNAs, miRNAs, and mRNAs was established.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Qingqing Qiu, Jieyi Li, Qiaofeng Chen, Xiaokai Zhao, Ru Zhou, Wenpeng Zhang, Ziying Gong, Daoyun Zhang, Mingliang Wang
Summary: This study investigated the technical feasibility of using quantitative RT-PCR (qRT-PCR) to replace immunohistochemistry (IHC) for PD-L1 detection in gastrointestinal tumors. The results showed that PD-L1 expression is related to tumor stage and primary therapy outcomes, but not significantly correlated with overall survival time in patients. Additionally, high PD-L1 expression in blood was found to be associated with a better response to immunotherapy. This study provides a novel strategy for rapidly distinguishing patients with gastrointestinal cancer based on their response to immunotherapy.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hager Tarek H. Ismail, Manar AbdelMageed, Gudrun Lindmark, Marie-Louise Hammarstrom, Sten Hammarstrom, Basel Sitohy
Summary: This study investigated the prognostic value of GPR55 in colon cancer. Combining GPR55 with CEA, CXCL16, or CXCL17 improved the discrimination between high and low expression groups. The GPR55/CEA ratio showed the best result, with a significant increase in mean survival time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Allergy
Ying Zhou, Qingqing Li, Ruilin Pan, Qiong Wang, Xuming Zhu, Cunyin Yuan, Fangfang Cai, Ya-dong Gao, Yubao Cui
Summary: The study filled a gap by investigating the regulation of allergen gene expression by miRNA in Tyrophagus putresecentiae. It identified a regulatory network between miRNAs and allergen-encoding mRNAs throughout the mite's life cycle.
Review
Mathematical & Computational Biology
Mu Hu, JieLai Yang, Yang Xu, Jiao Liu
Summary: This study found that the citrate cycle pathway was inactivated in acute lung injury (ALI), specifically involving the downregulation of MDH1 and MDH2 genes. Through animal and cell experiments, it was discovered that MDH1 and MDH2 promoted the biological function of AT2 cells and increased cellular vitality by enhancing glucose intake.
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
(2022)
Article
Genetics & Heredity
Jin Zhou, Shaolin He, Boyuan Wang, Wenling Yang, Yuqi Zheng, Shijiu Jiang, Dazhu Li, Jibin Lin
Summary: This study aims to explore the mechanism of circRNA-related ceRNA network in AMI and identify the corresponding immune infiltration characteristics. The results contribute to understanding the mechanism of AMI and providing potential therapeutic targets in the future.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Natalia Mitiushkina, Alexandr A. Romanko, Elena Preobrazhenskaya, Vladislav Tiurin, Tatiana Ermachenkova, Alexandr S. Martianov, Rimma S. Mulkidjan, Tatiana N. Sokolova, Maksim M. Kholmatov, Ilya Bizin, Alexandr O. Ivantsov, Olga S. Yatsuk, Olga A. Zaitseva, Aglaya G. Iyevleva, Ekatherina Sh Kuligina, Evgeny N. Imyanitov
Summary: The study analyzed ALK/ROS1 fusions and 5'-/3'-end unbalanced expression in NSCLC samples. It demonstrated that variant-specific PCR tests can detect common ALK and ROS1 rearrangements, with additional rare ALK fusions identified by PCR or NGS. While unbalanced gene expression can comprehensively analyze ALK, it is more complicated for the detection of ROS1 fusions, suggesting that variant-specific PCR assays are preferable for ROS1 testing.
Article
Biology
Yan Gong, Jun He, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jianhua He, Haiming Ma
Summary: This study reveals the transcription profiles and functional networks in lncRNA and mRNA in subcutaneous adipose tissue of Ningxiang piglets at different developmental stages. Most DEmRNAs were up-regulated in piglets, while they were down-regulated in late fattening stages, with DElncRNAs being up-regulated in late fattening stages. Modules 2 and 5 exhibit similar transcription modes, mainly involved in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism.
Article
Biochemistry & Molecular Biology
Mingyu Chu, Tiaoye Wang, Wenfang Li, Yashi Liu, Zhiyuan Bian, Juan Mao, Baihong Chen
Summary: This study conducted a genome-wide identification of Q-type C2H2 zinc finger protein (ZFP) genes in grapevine genomes and explored their characteristics and functions. The results showed that the physical and chemical properties of these ZFPs exhibited differences, but they were all hydrophobic and stable proteins. The phylogenetic analysis revealed the evolutionary relationships among these genes and their distribution on different chromosomes. The study also demonstrated the involvement of these genes in response to hormones and low-temperature stress using gene expression and localization experiments. Overall, this research provides valuable insights into the response mechanisms of grapes to exogenous hormones and low temperatures and lays a foundation for future molecular breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Abhirami Venugopal, Jessie Gillick-Walker, Agnes Michalczyk, Mustafa Khasraw, M. Leigh Ackland
Summary: This study investigated the expression levels of multiple markers in tumour and non-tumour tissue of a patient with a pancreatic neuroendocrine tumour using qRT-PCR and IHC. Significant differences in mRNA levels between tumour and non-tumour tissue were observed, with a correlation between qRT-PCR data and IHC for fifteen markers. The combination of qRT-PCR and IHC may have clinical utility in improving tumour stratification and distinguishing tumour grades.
BMC GASTROENTEROLOGY
(2021)
Article
Multidisciplinary Sciences
Caroline Ngetsa, Victor Osoti, Dorcas Okanda, Faith Marura, Krupali Shah, Henry Karanja, Daisy Mugo, John Gitonga, Martin Mutunga, Clement Lewa, Benedict Orindi, Philip Bejon, Lynette Isabella Ochola-Oyier
Summary: Normal saline, PBS, and REVITAL Viral Transport Media can be used for COVID-19 sample collection and testing, expanding the range of SARS-CoV-2 viral collection media.
Article
Endocrinology & Metabolism
Shoumeng Yan, Mengzi Sun, Lichao Gao, Nan Yao, Tianyu Feng, Yixue Yang, Xiaotong Li, Wenyu Hu, Weiwei Cui, Bo Li
Summary: This study identified key lncRNAs related to blood glucose through weighted gene co-expression network analysis, providing important references for potential biomarkers of type 2 diabetes mellitus.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sanja Ramljak, Matthias Schmitz, Cendrine Repond, Inga Zerr, Luc Pellerin
Summary: This study investigated the impact of cellular prion protein deficiency on neuroenergetics by analyzing the expression of genes involved in lactate/pyruvate metabolism. The results show that the absence of PrP(C) leads to altered MCT1 and MCT4 expression levels in different brain regions, indicating a potential role of PrP(C) in the regulation of monocarboxylate transport.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Cheng Wang, Cuiping Zhang, Quan Fu, Nan Zhang, Meng Ding, Zhen Zhou, Xi Chen, Fengmin Zhang, Chunni Zhang, Chen-Yu Zhang, Jun-Jun Wang
Summary: This study identified three piRNAs with significantly increased levels in the serum of patients with brucellosis. The combination of these three piRNAs could serve as a novel blood-based auxiliary tool for detecting brucellosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
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)