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immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq

Frontiers of Medicine doi: 10.1007/s11684-023-1017-7

Abstract: By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive

Keywords： single-cell RNA-seq     glioma     radial glia     primitive oligodendrocyte precursor cell     immune escape    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Frontiers of Medicine 2021, Volume 15, Issue 1,   Pages 144-154 doi: 10.1007/s11684-020-0792-7

Abstract: RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocytes

Keywords： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Frontiers of Medicine   Pages 185-192 doi: 10.1007/s11684-020-0754-0

Abstract: To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seqThrough scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney

Keywords： 2019-nCoV     ACE2     single-cell RNA-seq    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 72-88 doi: 10.1007/s11705-016-1580-4

Abstract: used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA

Keywords： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.

Keywords： BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA    

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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Frontiers of Medicine 2016, Volume 10, Issue 3,   Pages 297-310 doi: 10.1007/s11684-016-0452-0

Abstract: However, analysis focusing on the integration of the three RNA types has yet to be done.

Keywords： erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Frontiers of Agricultural Science and Engineering   Pages 196-214 doi: 10.15302/J-FASE-2020379

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.

Keywords： BSR-seq     PmUGT72B3     Prunus mume     UDP-glycosyltransferase     weeping shoots     WGCNA    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Frontiers of Medicine 2022, Volume 16, Issue 2,   Pages 251-262 doi: 10.1007/s11684-021-0915-9

Abstract: Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomicHere, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seqRobustness of these tools has been tested on various real and simulated scRNA-seq datasets.

Keywords： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Ribozyme and the mechanisms that underlie RNA catalysis

Timothy J. Wilson,Yijin Liu,David M. J. Lilley

Frontiers of Chemical Science and Engineering 2016, Volume 10, Issue 2,   Pages 178-185 doi: 10.1007/s11705-016-1558-2

Abstract: Ribozymes are widespread, and catalyze some extremely important reactions in the cell. Mechanistically most fall into one of two classes, using either metal ions or general acid-base catalysis. The nucleolytic ribozymes fall into the latter class, mostly using nucleobases. A sub-set of these use a combination of guanine base plus adenine acid to catalyze the cleavage reaction. New ribozymes are still being discovered at regular intervals and we can speculate on the potential existence of ribozymes that catalyze chemistry beyond phosphoryl transfer reactions, perhaps using small-molecule coenzymes.

Keywords： RNA catalysis     RNA structure     catalytic mechanism    

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Characterization of chromatin accessibility in psoriasis

Frontiers of Medicine 2022, Volume 16, Issue 3,   Pages 483-495 doi: 10.1007/s11684-021-0872-3

Abstract: The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.

Keywords： psoriasis     ATAC-seq     epigenetics     transcription factor    

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Anti RNA Viruses Related Biomaterials

Yao Kangde,Yin Yuji,Zhang Baolian,Zhao Liguo

Strategic Study of CAE 2003, Volume 5, Issue 7,   Pages 17-23

Abstract:

The structure, reproduction, replication and transcription of RNA viruses were introduced.Antivirus strategies including design of anti - SARS drugs, RNA interference, DNA vaccine delivery systemThese examples imply the interactions of RNA viruses with proteins, DNA, and polysaccharides.

Keywords： Anti-RNA viruses     protein     DNA     polysaccharide     biomaterials    

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RNA-Based Biocontrols—A New Paradigm in Crop Protection Review

Matthew Bramlett, Geert Plaetinck, Peter Maienfisch

Engineering 2020, Volume 6, Issue 5,   Pages 522-527 doi: 10.1016/j.eng.2019.09.008

Abstract: Over the last years, the RNA interference (RNAi) process has been identified as a very promising newRNA-based active ingredients (AIs) possess a unique mode of action and can be implemented via both geneticRNA-based AIs promise to deliver the selectivity and sustainability desired in future crop protectionresearch progress toward RNA-based biocontrols against the Colorado potato beetle (CPB), corn rootwormMany challenges still exist on the road to the implementation of a broad range of RNA-based products

Keywords： RNA-based biocontrols     RNA interference (RNAi)     Colorado potato beetle (CPB)     Corn rootworm (CRW)     Soy    

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Knockdown of a Specific Circular Non-coding RNA Significantly Suppresses Osteosarcoma Progression Article

Shidong Wang, Hongliang Zhang, Bo Li, Chenglong Chen, Tingting Ren, Yi Huang, Kai Liu, Jingjing Li, Wei Guo

Engineering 2023, Volume 21, Issue 2,   Pages 187-193 doi: 10.1016/j.eng.2021.12.007

Abstract:

Osteosarcoma (OS) is a malignant mesenchymal tissue tumor known to occur in children and adolescents, and pulmonary metastasis often leads to death in these patients. The mechanism underlying OS progression remains unclear. Therefore, identifying new therapeutic targets and treatment modalities for OS is urgently needed. Abnormally expressed non-coding circular RNAs (circRNAs) are crucial for the occurrence and development of OS. The purpose of this study was to explore the expression and role of a novel circRNA circ_000203 in OS and elucidate the underlying mechanism. circ_000203 was demonstrated highly expressed in OS cell lines and tissues, and circ_000203 knockdown significantly inhibited OS progression in vitro and in vivo. Furthermore, we found that circ_000203 is a sponge of miR-26b-5p, an upstream regulator of bone morphogenetic protein receptor 2 (BMPR2). Thus, the overexpression of BMPR2 could reduce the inhibitory effect on OS progression. This indicates that knockdown of circ_000203 suppresses OS progression through microRNA (miRNA)-mediated BMPR2 downregulation. Our findings provide important insights for understanding the occurrence and development of OS. 

Keywords： Non-coding RNA     Osteosarcoma     CircRNA     Molecular mechanism     Knockdown    

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Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

Frontiers of Medicine 2008, Volume 2, Issue 2,   Pages 166-170 doi: 10.1007/s11684-008-0030-1

Abstract: Murine Rip2 small interfering RNA (siRNA) plasmids were constructed and transfected into macrophage and
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Overexpressed long noncoding RNA CRNDE with distinct alternatively spliced isoforms in multiple cancers

Xuefei Ma, Wei Zhang, Rong Zhang, Jingming Li, Shufen Li, Yunlin Ma, Wen Jin, Kankan Wang

Frontiers of Medicine 2019, Volume 13, Issue 3,   Pages 330-343 doi: 10.1007/s11684-017-0557-0

Abstract: CRNDE is a long noncoding RNA with alternative splicing and is implicated in the pathogenesis of several

Keywords： long noncoding RNA     CRNDE     alternative splicing    

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Title Author Date Type Operation

immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq

Journal Article

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Journal Article

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Journal Article

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Journal Article

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Journal Article

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Journal Article

Ribozyme and the mechanisms that underlie RNA catalysis

Timothy J. Wilson,Yijin Liu,David M. J. Lilley

Journal Article

Characterization of chromatin accessibility in psoriasis

Journal Article

Anti RNA Viruses Related Biomaterials

Yao Kangde,Yin Yuji,Zhang Baolian,Zhao Liguo

Journal Article

RNA-Based Biocontrols—A New Paradigm in Crop Protection

Matthew Bramlett, Geert Plaetinck, Peter Maienfisch

Journal Article

Knockdown of a Specific Circular Non-coding RNA Significantly Suppresses Osteosarcoma Progression

Shidong Wang, Hongliang Zhang, Bo Li, Chenglong Chen, Tingting Ren, Yi Huang, Kai Liu, Jingjing Li, Wei Guo

Journal Article

Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

Journal Article

Overexpressed long noncoding RNA CRNDE with distinct alternatively spliced isoforms in multiple cancers

Xuefei Ma, Wei Zhang, Rong Zhang, Jingming Li, Shufen Li, Yunlin Ma, Wen Jin, Kankan Wang

Journal Article