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Single-cell gene regulatory network analysis for mixed cell populations

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Quantitative Biology 2024年第4期12卷 375-388页

作者： Junjie Tang changhu wang Feiyi Xiao Ruibin Xi School of Mathematical Sciences and Center of Statistical Science Peking UniversityBeijingChina Academy for Advanced Interdisciplinary Studies Peking UniversityBeijingChina

Gene regulatory network(GRN)refers to the complex network formed by regulatory interactions between genes in living *** this paper,we consider inferring GRNs in single cells based on single-cell RNA sequencing(scRNA-seq)*** scRNA-seq,single cells are often profiled from mixed populations,and their cell identities are unknown.A common practice for single-cell GRN analysis is to first cluster the cells and infer GRNs for every cluster ***,this two-step procedure ignores uncertainty in the clustering step and thus could lead to inaccurate estimation of the ***,we consider the mixture Poisson lognormal model(MPLN)for network inference of count data from mixed *** precision matrices of the MPLN are the GRNs of different cell *** avoid the intractable optimization of the MPLN’s log-likelihood,we develop an algorithm called variational mixture Poisson log-normal(VMPLN)to jointly estimate the GRNs of different cell types based on the variational inference *** compare VMPLN with state-of-the-art single-cell regulatory network inference *** simulation shows that VMPLN achieves better performance,especially in scenarios where different cell types have a high mixing *** on real scRNA-seq data also demonstrates that VMPLN can provide more accurate network estimation in most ***,we apply VMPLN to a large scRNA-seq dataset from patients infected with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and find that VMPLN identifies critical differences in regulatory networks in immune cells between patients with moderate and severe *** source codes are available on the GitHub website(***/XiDsLab/SCVMPLN).

关键词： gene regulatory network graphical model precision matrix variational inference single-cell RNA sequencing

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Reduction of Cd in Rice through Expression of OXS3-like Gene Fragments

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Molecular Plant 2016年第2期9卷 301-304页

作者： wang, changhu Guo, Weili Ye, Shan Wei, Pengcheng Ow, David W. Chinese Acad Sci South China Bot Garden Plant Gene Engn Ctr 723 Xingke Rd Guangzhou 510650 Guangdong Peoples R China Anhui Acad Agr Sci Inst Rice Res Hefei 230031 Peoples R China

Dear Editor,Cadmium （Cd） is a toxic heavy metal and carcinogen, and its en- try into the food chain has serious effects on food security and public health （Uraguchi et al., 2011）. As rice is a staple food crop for half of the world＇s population, Cd in rice grain has become a major source of dietary Cd for this part of the world.

关键词： become effective decided

CHANGES IN LIPIDS OF MUSSEL DURING STORAGE

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中国水产科学 1995年第4期 56-63页

作者： Xue changhu, wang Yisheng, Li Zhaojie, Lou Weifeng(Ocaan University of Qingdao 266003)

ＣＨＡＮＧＥＳＩＮＬＩＰＩＤＳＯＦＭＵＳＳＥＬＤＵＲＩＮＧＳＴＯＲＡＧＥＸｕｅＣｈａｎｇｈｕ，ＷａｎｇＹｉｓｈｅｎｇ，ＬｉＺｈａｏｊｉｅ，ＬｏｕＷｅｉｆｅｎｇ（ＯｃａａｎＵｎｉｖｅｒｓｉｔｙｏｆＱｉｎｇｄａｏ２６６０... 详细信息

ＣＨＡＮＧＥＳＩＮＬＩＰＩＤＳＯＦＭＵＳＳＥＬＤＵＲＩＮＧＳＴＯＲＡＧＥＸｕｅＣｈａｎｇｈｕ，ＷａｎｇＹｉｓｈｅｎｇ，ＬｉＺｈａｏｊｉｅ，ＬｏｕＷｅｉｆｅｎｇ（ＯｃａａｎＵｎｉｖｅｒｓｉｔｙｏｆＱｉｎｇｄａｏ２６６００３）ＣＨＡＮＧＥＳＩＮＬＩＰＩＤ...

关键词： Mussel Lipid Oxidation

Sea cucumber intestinal hydrolysates alleviate insulin resistance through regulating IRS1/PI3K/AKT signaling pathway mediated by glutamine metabolism in high-fat and high-sucrose diet-induced mice

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Food Science and Human Wellness 2025年

作者： Meng wang Man Yao Hao Yue Yingying Tian Zifang Zhao changhu Xue Tiantian Zhang Yuming wang SKL of Marine Food Processing & Safety Control， College of Food Science and Engineering， Ocean University of China Institute of Food & Nutrition Science and Technology， Shandong Academy of Agricultural Sciences Hainan Huayan Collagen Technology Co. Sanya Institute of Oceanography， Ocean University of China

It has been reported that sea cucumber intestine hydrolysates (SCIH) could promote glutamine metabolism in mice， while there is a close connection between glutamine metabolism and insulin sensitivity. However， the effect of SCIH on insulin resistance is still unclear. The results showed that SCIH hydrolyzed by flavor protease had significant activity using the insulin-induced HepG2 cell model. Animal experiments exhibited that SCIH supplementation significantly improved the high-fat and high-sucrose diet-induced impaired glucose tolerance， reduced fasting serum glucose and glycosylated serum protein. Besides， SCIH ameliorated islet vacuolization and decreased the pancreas TNF-α and IL-6 by 32.1% and 36.2%， respectively. Immunofluorescence staining results showed that SCIH promoted insulin secretion. Interestingly， SCIH significantly increased the liver glutamine levels and upregulated the expression of glutaminase1 (GLS1) and glutamate dehydrogenase 1 (GLUD1). Furthermore， SCIH increased liver acetyl-CoA levels to enhance histone acetylation and activate the gene transcription and translation on glucose metabolism-related IRS/PI3K/AKT signaling pathway， thereby attenuating insulin resistance. The present findings proposed the potential value for developing functional foods in SCIH utilization.

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