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Article: Biological Control of Rapeseed Clubroot (

Li, Guoqing / Cheng, Junyun / Luo, Tao / Zhang, Jing / Wu, Mingde / Yang, Long / Chen, Weidong

2024

Abstract: Didymella macrostoma P2 was isolated from rapeseed (Brassica napus), and it is an endophyte of rapeseed and an antagonist of three rapeseed pathogens, Botrytis cinerea, Leptosphaeria biglobosa and Sclerotinia sclerotiorum. However, whether or not P2 has ... ...

Abstract	Didymella macrostoma P2 was isolated from rapeseed (Brassica napus), and it is an endophyte of rapeseed and an antagonist of three rapeseed pathogens, Botrytis cinerea, Leptosphaeria biglobosa and Sclerotinia sclerotiorum. However, whether or not P2 has a suppressive effect on infection of rapeseed by the clubroot pathogen Plasmodiophora brassicae remains unknown. This study was conducted to detect production of antimicrobials by P2 and to determine efficacy of the antimicrobials and P2 pycnidiospores in suppression of rapeseed clubroot. Results showed that cultural filtrates (CF) of P2 in potato dextrose broth and the substances in pycnidiospore mucilages exuded from P2 pycnidia were inhibitory to P. brassicae. In the indoor experiment, seeds of the susceptible rapeseed cultivar Zhongshuang No.9 treated with P2 CF and the P2 spore suspension (P2 SS, 1 × 107 spores/ml) reduced clubroot severity by 31% to 70% on the 30-day-old seedlings compared to the control (seeds treated with water). P2 was re-isolated from the roots of the seedlings in the treatment of P2 SS, the average isolation frequency in the healthy roots (26%) was much higher than that (5%) in the diseased roots. In the field experiment, seeds of another susceptible rapeseed cultivar Huayouza 50 (HYZ50) treated with P2 CF, P2 CE (chloroform extract of P2 CF, 30 µg/ml) and P2 SS reduced clubroot severity by 29% to 48% on 60-day-old seedlings and by 28% to 59% on adult plants (220 days old) compared to the control treatment. The three P2 treatments on HYZ50 produced significantly (P < 0.05) higher seed yield than the control treatment on this rapeseed cultivar, and they even generated seed yield similar to that produced by the resistant rapeseed cultivar Shengguang 165R in one of the two seasons. These results suggest that D. macrostoma P2 is an effective biocontrol agent against rapeseed clubroot.
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-09-23-1921-RE
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: High-throughput transcriptional profiling of perturbations by

Cheng, Junyun / Chen, Jie / Liao, Jie / Wang, Tianhao / Shao, Xin / Long, Jinbo / Yang, Penghui / Li, Anyao / Wang, Zheng / Lu, Xiaoyan / Fan, Xiaohui

Journal of pharmaceutical analysis

2023 Volume 13, Issue 4, Page(s) 376–387

Abstract: ... Panax ... ...

Abstract	Panax ginseng
Language	English
Publishing date	2023-02-23
Publishing country	China
Document type	Journal Article
ZDB-ID	2630174-X
ISSN	2214-0883 ; 2095-1779
ISSN (online)	2214-0883
ISSN	2095-1779
DOI	10.1016/j.jpha.2023.02.009
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution.

Guo, Wenbo / Hu, Yining / Qian, Jingyang / Zhu, Lidan / Cheng, Junyun / Liao, Jie / Fan, Xiaohui

Journal of genetics and genomics = Yi chuan xue bao

2023 Volume 50, Issue 9, Page(s) 641–651

Abstract: Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus ... ...

Abstract	Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus on spatial heterogeneity, there is a growing need for unbiased, spatially resolved omics technologies. Laser capture microdissection (LCM) is a cutting-edge method for acquiring spatial information that can quickly collect regions of interest (ROIs) from heterogeneous tissues, with resolutions ranging from single cells to cell populations. Thus, LCM has been widely used for studying the cellular and molecular mechanisms of diseases. This review focuses on the differences among four types of commonly used LCM technologies and their applications in omics and disease research. Key attributes of application cases are also highlighted, such as throughput and spatial resolution. In addition, we comprehensively discuss the existing challenges and the great potential of LCM in biomedical research, disease diagnosis, and targeted therapy from the perspective of high-throughput, multi-omics, and single-cell resolution.
MeSH term(s)	Laser Capture Microdissection/methods ; Multiomics ; Biomedical Research
Language	English
Publishing date	2023-08-05
Publishing country	China
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2374568-X
ISSN	1873-5533 ; 1673-8527
ISSN (online)	1873-5533
ISSN	1673-8527
DOI	10.1016/j.jgg.2023.07.011
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution

Guo, Wenbo / Hu, Yining / Qian, Jingyang / Zhu, Lidan / Cheng, Junyun / Liao, Jie / Fan, Xiaohui

Journal of Genetics and Genomics. 2023 Aug. 05,

2023

Abstract	Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus on spatial heterogeneity, there is a growing need for unbiased, spatially-resolved omics technologies. Laser capture microdissection (LCM) is a cutting-edge method for acquiring spatial information that can quickly collect regions of interest (ROIs) from heterogeneous tissues, with resolutions ranging from single cells to cell populations. Thus, LCM has been widely used for studying the cellular and molecular mechanisms of diseases. This review focuses on the differences among four types of commonly used LCM technologies and their applications in omics and disease research. Key attributes of application cases are also highlighted, such as throughput and spatial resolution. In addition, we comprehensively discuss the existing challenges and the great potential of LCM in biomedical research, disease diagnosis, and targeted therapy from the perspective of high-throughput, multi-omics, and single-cell resolution.
Keywords	biomedical research ; disease diagnosis ; genomics ; laser capture microdissection ; multiomics ; spatial data ; spatial variation ; therapeutics ; Spatial omics ; Single-cell resolution ; Multiplexed barcoding ; Disease microenvironment
Language	English
Dates of publication	2023-0805
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	2374568-X
ISSN	1873-5533 ; 1673-8527
ISSN (online)	1873-5533
ISSN	1673-8527
DOI	10.1016/j.jgg.2023.07.011
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multiplexing Methods for Simultaneous Large-Scale Transcriptomic Profiling of Samples at Single-Cell Resolution.

Cheng, Junyun / Liao, Jie / Shao, Xin / Lu, Xiaoyan / Fan, Xiaohui

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2021 Volume 8, Issue 17, Page(s) e2101229

Abstract: Barcoding technology has greatly improved the throughput of cells and genes detected in single-cell RNA sequencing (scRNA-seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of ... ...

Abstract	Barcoding technology has greatly improved the throughput of cells and genes detected in single-cell RNA sequencing (scRNA-seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of samples, as it has greatly reduced the processing time, technical batch effects, and library preparation costs, and lowered the per-sample cost. In this review, the various DNA-based barcoding methods for sample multiplexing are focused on, specifically, on the four major barcoding strategies. A detailed comparison of the barcoding methods is also presented, focusing on aspects such as sample/cell throughput and gene detection, and guidelines for choosing the most appropriate barcoding technique according to the personalized requirements are developed. Finally, the critical applications of sample multiplexing and technical challenges in combinatorial labeling, barcoding in vivo, and multimodal tagging at the spatially resolved resolution, as well as, the future prospects of multiplexed scRNA-seq, for example, prioritizing and predicting the severity of coronavirus disease 2019 (COVID-19) in patients of different gender and age are highlighted.
Language	English
Publishing date	2021-07-08
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202101229
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multiplexing Methods for Simultaneous Large‐Scale Transcriptomic Profiling of Samples at Single‐Cell Resolution

Junyun Cheng / Jie Liao / Xin Shao / Xiaoyan Lu / Xiaohui Fan

Advanced Science, Vol 8, Iss 17, Pp n/a-n/a (2021)

2021

Abstract: Abstract Barcoding technology has greatly improved the throughput of cells and genes detected in single‐cell RNA sequencing (scRNA‐seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the ... ...

Abstract	Abstract Barcoding technology has greatly improved the throughput of cells and genes detected in single‐cell RNA sequencing (scRNA‐seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of samples, as it has greatly reduced the processing time, technical batch effects, and library preparation costs, and lowered the per‐sample cost. In this review, the various DNA‐based barcoding methods for sample multiplexing are focused on, specifically, on the four major barcoding strategies. A detailed comparison of the barcoding methods is also presented, focusing on aspects such as sample/cell throughput and gene detection, and guidelines for choosing the most appropriate barcoding technique according to the personalized requirements are developed. Finally, the critical applications of sample multiplexing and technical challenges in combinatorial labeling, barcoding in vivo, and multimodal tagging at the spatially resolved resolution, as well as, the future prospects of multiplexed scRNA‐seq, for example, prioritizing and predicting the severity of coronavirus disease 2019 (COVID‐19) in patients of different gender and age are highlighted.
Keywords	DNA‐based barcoding ; sample multiplexing ; single‐cell RNA sequencing ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Revealing spatial multimodal heterogeneity in tissues with SpaTrio.

Yang, Penghui / Jin, Lijun / Liao, Jie / Jin, Kaiyu / Shao, Xin / Li, Chengyu / Qian, Jingyang / Cheng, Junyun / Yu, Dingyi / Guo, Rongfang / Xu, Xiao / Lu, Xiaoyan / Fan, Xiaohui

Cell genomics

2023 Volume 3, Issue 12, Page(s) 100446

Abstract: Capturing and depicting the multimodal tissue information of tissues at the spatial scale remains a significant challenge owing to technical limitations in single-cell multi-omics and spatial transcriptomics sequencing. Here, we developed a computational ...

Abstract	Capturing and depicting the multimodal tissue information of tissues at the spatial scale remains a significant challenge owing to technical limitations in single-cell multi-omics and spatial transcriptomics sequencing. Here, we developed a computational method called SpaTrio that can build spatial multi-omics data by integrating these two datasets through probabilistic alignment and enabling further analysis of gene regulation and cellular interactions. We benchmarked SpaTrio using simulation datasets and demonstrated its accuracy and robustness. Next, we evaluated SpaTrio on biological datasets and showed that it could detect topological patterns of cells and modalities. SpaTrio has also been applied to multiple sets of actual data to uncover spatially multimodal heterogeneity, understand the spatiotemporal regulation of gene expression, and resolve multimodal communication among cells. Our data demonstrated that SpaTrio could accurately map single cells and reconstruct the spatial distribution of various biomolecules, providing valuable multimodal insights into spatial biology.
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2023.100446
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Massively Parallel CRISPR‐Based Genetic Perturbation Screening at Single‐Cell Resolution

Junyun Cheng / Gaole Lin / Tianhao Wang / Yunzhu Wang / Wenbo Guo / Jie Liao / Penghui Yang / Jie Chen / Xin Shao / Xiaoyan Lu / Ling Zhu / Yi Wang / Xiaohui Fan

Advanced Science, Vol 10, Iss 4, Pp n/a-n/a (2023)

2023

Abstract: Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)‐based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single‐cell CRISPR screening (scCRISPR) techniques, which ... ...

Abstract	Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)‐based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single‐cell CRISPR screening (scCRISPR) techniques, which result from the combination of single‐cell toolkits and CRISPR screening, allow dissecting regulatory networks in complex biological systems at unprecedented resolution. These methods allow cells to be perturbed en masse using a pooled CRISPR library, followed by high‐content phenotyping. This is technically accomplished by annotating cells with sgRNA‐specific barcodes or directly detectable sgRNAs. According to the integration of distinct single‐cell technologies, these methods principally fall into four categories: scCRISPR with RNA‐seq, scCRISPR with ATAC‐seq, scCRISPR with proteome probing, and imaging‐based scCRISPR. scCRISPR has deciphered genotype–phenotype relationships, genetic regulations, tumor biological issues, and neuropathological mechanisms. This review provides insight into the technical breakthrough of scCRISPR by systematically summarizing the advancements of various scCRISPR methodologies and analyzing their merits and limitations. In addition, an application‐oriented approach guide is offered to meet researchers’ individualized demands.
Keywords	CRISPR/Cas ; genetic screening ; imaging‐based phenotyping ; multiplexed perturbations ; single‐cell sequencing ; Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk

Xin Shao / Chengyu Li / Haihong Yang / Xiaoyan Lu / Jie Liao / Jingyang Qian / Kai Wang / Junyun Cheng / Penghui Yang / Huajun Chen / Xiao Xu / Xiaohui Fan

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 15

Abstract: Cell-cell communication is a vital feature involving numerous biological processes. Here, the authors develop SpaTalk, a cell-cell communication inference method using knowledge graph for spatially resolved transcriptomic data, providing valuable ... ...

Abstract	Cell-cell communication is a vital feature involving numerous biological processes. Here, the authors develop SpaTalk, a cell-cell communication inference method using knowledge graph for spatially resolved transcriptomic data, providing valuable insights into spatial intercellular tissue dynamics.
Keywords	Science ; Q
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice.

Shao, Xin / Liao, Jie / Li, Chengyu / Lu, Xiaoyan / Cheng, Junyun / Fan, Xiaohui

Briefings in bioinformatics

2020 Volume 22, Issue 4

Abstract: Cell-cell communications in multicellular organisms generally involve secreted ligand-receptor (LR) interactions, which is vital for various biological phenomena. Recent advancements in single-cell RNA sequencing (scRNA-seq) have effectively resolved ... ...

Abstract	Cell-cell communications in multicellular organisms generally involve secreted ligand-receptor (LR) interactions, which is vital for various biological phenomena. Recent advancements in single-cell RNA sequencing (scRNA-seq) have effectively resolved cellular phenotypic heterogeneity and the cell-type composition of complex tissues, facilitating the systematic investigation of cell-cell communications at single-cell resolution. However, assessment of chemical-signal-dependent cell-cell communication through scRNA-seq relies heavily on prior knowledge of LR interaction pairs. We constructed CellTalkDB (http://tcm.zju.edu.cn/celltalkdb), a manually curated comprehensive database of LR interaction pairs in humans and mice comprising 3398 human LR pairs and 2033 mouse LR pairs, through text mining and manual verification of known protein-protein interactions using the STRING database, with literature-supported evidence for each pair. Compared with SingleCellSignalR, the largest LR-pair resource, CellTalkDB includes not only 2033 mouse LR pairs but also 377 additional human LR pairs. In conclusion, the data on human and mouse LR pairs contained in CellTalkDB could help to further the inference and understanding of the LR-interaction-based cell-cell communications, which might provide new insights into the mechanism underlying biological processes.
MeSH term(s)	Animals ; Cell Communication ; Databases, Factual ; Humans ; Ligands ; Mice ; RNA-Seq ; Receptors, Cell Surface/metabolism ; Single-Cell Analysis
Chemical Substances	Ligands ; Receptors, Cell Surface
Language	English
Publishing date	2020-11-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbaa269
Database	MEDical Literature Analysis and Retrieval System OnLINE

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