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  1. Article ; Online: Characterization and Function of Circular RNAs in Plants

    Peijing Zhang / Sida Li / Ming Chen

    Frontiers in Molecular Biosciences, Vol

    2020  Volume 7

    Abstract: CircRNAs are covalently closed-loop single-stranded RNA molecules ubiquitously expressing in eukaryotes. As an important member of the endogenous ncRNA family, circRNAs are associated with diverse biological processes and can regulate transcription, ... ...

    Abstract CircRNAs are covalently closed-loop single-stranded RNA molecules ubiquitously expressing in eukaryotes. As an important member of the endogenous ncRNA family, circRNAs are associated with diverse biological processes and can regulate transcription, modulate alternative splicing, and interact with miRNAs or proteins. Compared to abundant advances in animals, studies of circRNAs in plants are rapidly emerging. The databases and analysis tools for plant circRNAs are constantly being developed. Large numbers of circRNAs have been identified and characterized in plants and proved to play regulatory roles in plant growth, development, and stress responses. Here, we review the biogenesis, characteristics, bioinformatics resources, and biological functions of plant circRNAs, and summarize the distinct circularization features and differentially expression patterns comparison with animal-related results.
    Keywords circRNA ; plant ; circularization ; characterization ; regulation ; stress response ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants

    Haoyu Chao / Yueming Hu / Liang Zhao / Saige Xin / Qingyang Ni / Peijing Zhang / Ming Chen

    International Journal of Molecular Sciences, Vol 23, Iss 3695, p

    2022  Volume 3695

    Abstract: Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have been classified into two broad categories based on their biogenesis and ... ...

    Abstract Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have been classified into two broad categories based on their biogenesis and mechanisms of action, housekeeping ncRNAs and regulatory ncRNAs. With advances in RNA sequencing technology and computational methods, bioinformatics resources continue to emerge and update rapidly, including workflow for in silico ncRNA analysis, up-to-date platforms, databases, and tools dedicated to ncRNA identification and functional annotation. In this review, we aim to describe the biogenesis, biological functions, and interactions with DNA, RNA, protein, and microorganism of five major regulatory ncRNAs (miRNA, siRNA, tsRNA, circRNA, lncRNA) in plants. Then, we systematically summarize tools for analysis and prediction of plant ncRNAs, as well as databases. Furthermore, we discuss the silico analysis process of these ncRNAs and present a protocol for step-by-step computational analysis of ncRNAs. In general, this review will help researchers better understand the world of ncRNAs at multiple levels.
    Keywords ncRNA ; plant ; ncRNA resource ; ncRNA function ; ncRNA interaction ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 580
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Coarse-to-Fine Image Registration for Multi-Temporal High Resolution Remote Sensing Based on a Low-Rank Constraint

    Peijing Zhang / Xiaoyan Luo / Yan Ma / Chengyi Wang / Wei Wang / Xu Qian

    Remote Sensing, Vol 14, Iss 573, p

    2022  Volume 573

    Abstract: For multi-temporal high resolution remote sensing images, the image registration is important but difficult due to the high resolution and low-stability land-cover. Especially, the changing of land-cover, solar altitude angle, radiation intensity, and ... ...

    Abstract For multi-temporal high resolution remote sensing images, the image registration is important but difficult due to the high resolution and low-stability land-cover. Especially, the changing of land-cover, solar altitude angle, radiation intensity, and terrain fluctuation distortion in the overlapping areas can represent different image characteristics. These time-varying properties cause traditional registration methods with known reference information to fault. Therefore, in this paper we propose a comprehensive coarse-to-fine registration (CCFR) algorithm. First, we design a low-rank constraint-based batch reference extraction (LRC-BRE) method. Under the low-rank constraint, the stable features with highly spatial co-occurrence can be reconstructed via matrix decomposition, and are set as reference images to batch registration. Second, we improve the general feature registration with block feature matching and local linear transformation (BFM-LLT) operators including match outlier filtering (MOF) on regional mutual information and dual-weighted block fitting (DWBF). Finally, based on combining LRC-BRE and BFM-LLT, CCFR is integrated. Experimental results show that the proposed method has a good batch alignment effect, especially in the registration of large difference image pairs. The proposed CCFR achieves a significant performance improvement over many state-of-the-art registration algorithms.
    Keywords registration ; multi-temporal remote sensing images ; high resolution ; low-rank matrix factorization ; optical satellite ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: SIPA1 Enhances Aerobic Glycolysis Through HIF-2α Pathway to Promote Breast Cancer Metastasis

    Chenguang Yao / Jun Weng / Lingyun Feng / Wanjun Zhang / Yan Xu / Peijing Zhang / Yoshimasa Tanaka / Li Su

    Frontiers in Cell and Developmental Biology, Vol

    2022  Volume 9

    Abstract: Increased dependence on aerobic glycolysis is characteristic of most cancer cells, whereas the mechanism underlying the promotion of aerobic glycolysis in metastatic breast cancer cells under ambient oxygen has not been well understood. Here, we ... ...

    Abstract Increased dependence on aerobic glycolysis is characteristic of most cancer cells, whereas the mechanism underlying the promotion of aerobic glycolysis in metastatic breast cancer cells under ambient oxygen has not been well understood. Here, we demonstrated that aberrant expression of signal-induced proliferation-associated 1 (SIPA1) enhanced aerobic glycolysis and altered the main source of ATP production from oxidative phosphorylation to glycolysis in breast cancer cells. We revealed that SIPA1 promoted the transcription of EPAS1, which is known as the gene encoding hypoxia-inducible factor-2α (HIF-2α) and up-regulated the expression of multiple glycolysis-related genes to increase aerobic glycolysis. We also found that blocking aerobic glycolysis by either knocking down SIPA1 expression or oxamate treatment led to the suppression of tumor metastasis of breast cancer cells both in vitro and in vivo. Taken together, aberrant expression of SIPA1 resulted in the alteration of glucose metabolism from oxidative phosphorylation to aerobic glycolysis even at ambient oxygen levels, which might aggravate the malignancy of breast cancer cells. The present findings indicate a potential target for the development of therapeutics against breast cancers with dysregulated SIPA1 expression.
    Keywords aerobic glycolysis ; breast cancer ; EPAS1 ; HIF-2α ; signal-induced proliferation-associated 1 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: CircPlant

    Peijing Zhang / Yongjing Liu / Hongjun Chen / Xianwen Meng / Jitong Xue / Kunsong Chen / Ming Chen

    Genomics, Proteomics & Bioinformatics, Vol 18, Iss 3, Pp 352-

    An Integrated Tool for circRNA Detection and Functional Prediction in Plants

    2020  Volume 358

    Abstract: The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, ...

    Abstract The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
    Keywords Circular RNA ; Plant ; MicroRNA ; RNA-seq ; Identification ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: An analytical framework for decoding cell type-specific genetic variation of gene regulation

    Yanyu Xiao / Jingjing Wang / Jiaqi Li / Peijing Zhang / Jingyu Li / Yincong Zhou / Qing Zhou / Ming Chen / Xin Sheng / Zhihong Liu / Xiaoping Han / Guoji Guo

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: Abstract A deeper understanding of genetic regulation and functional mechanisms underlying genetic associations with complex traits and diseases is impeded by cellular heterogeneity and linkage disequilibrium. To address these limits, we introduce Huatuo, ...

    Abstract Abstract A deeper understanding of genetic regulation and functional mechanisms underlying genetic associations with complex traits and diseases is impeded by cellular heterogeneity and linkage disequilibrium. To address these limits, we introduce Huatuo, a framework to decode genetic variation of gene regulation at cell type and single-nucleotide resolutions by integrating deep-learning-based variant predictions with population-based association analyses. We apply Huatuo to generate a comprehensive cell type-specific genetic variation landscape across human tissues and further evaluate their potential roles in complex diseases and traits. Finally, we show that Huatuo’s inferences permit prioritizations of driver cell types associated with complex traits and diseases and allow for systematic insights into the mechanisms of phenotype-causal genetic variation.
    Keywords Science ; Q
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: ChIP-Hub provides an integrative platform for exploring plant regulome

    Liang-Yu Fu / Tao Zhu / Xinkai Zhou / Ranran Yu / Zhaohui He / Peijing Zhang / Zhigui Wu / Ming Chen / Kerstin Kaufmann / Dijun Chen

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

    2022  Volume 15

    Abstract: A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue- ...

    Abstract A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
    Keywords Science ; Q
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Triple and Double Photons Absorption Process and Down-Conversion Laser Emitting Investigation of Er-Ion Doped Microsphere

    Yantang Huang / Peijing Zhang / Yu Huang / Changlei Guo

    Journal of Modern Physics, Vol 04, Iss 12, Pp 1622-

    2013  Volume 1626

    Abstract: We report a readily and cheap method to build taper optical fiber-Er 3+ doped microsphere platform to investigate upconversion fluorescence emission and down-conversion laser oscillation with low threshold pump power. We demonstrate to dope Er 3+ into ... ...

    Abstract We report a readily and cheap method to build taper optical fiber-Er 3+ doped microsphere platform to investigate upconversion fluorescence emission and down-conversion laser oscillation with low threshold pump power. We demonstrate to dope Er 3+ into silica microsphere surface by dipping a single-taper optical fiber into a certain concentration of erbium nitrate solution (Er(NO 3 )) , then dry it and use the electrical-arc of the optical fiber splicer to melt the tip of taper fiber to form the Er 3+ -doped silica microsphere due to surface tension induced. We also present a HF acid etching setup to fabricate low loss biconical optical taper fibers. We demonstrate the Er 3+ doped silica mic r osphere triple photons and dual photons absorption process of up-conversion fluorescence emission and down-conversion laser oscillation spectra by using the optical tapered fiber to couple 976 nm/1534 nm pump light source.
    Keywords Triple Photons Absorption Process ; Er 3+ Doped Microsphere ; Taper Optical Fiber ; Micro-Laser ; Physics ; QC1-999 ; Science ; Q ; DOAJ:Physics (General) ; DOAJ:Physics and Astronomy
    Language English
    Publishing date 2013-12-01T00:00:00Z
    Publisher Scientific Research Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Cell landscape of larval and adult Xenopus laevis at single-cell resolution

    Yuan Liao / Lifeng Ma / Qile Guo / Weigao E. / Xing Fang / Lei Yang / Fanwei Ruan / Jingjing Wang / Peijing Zhang / Zhongyi Sun / Haide Chen / Zhongliang Lin / Xueyi Wang / Xinru Wang / Huiyu Sun / Xiunan Fang / Yincong Zhou / Ming Chen / Wanhua Shen /
    Guoji Guo / Xiaoping Han

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

    2022  Volume 15

    Abstract: Single-cell RNA sequencing technology offers a unique opportunity to dissect cell heterogeneity of animals. Here, the authors construct a Xenopus cell landscape including larval and adult organs to dissect cell heterogeneity of the amphibian. ...

    Abstract Single-cell RNA sequencing technology offers a unique opportunity to dissect cell heterogeneity of animals. Here, the authors construct a Xenopus cell landscape including larval and adult organs to dissect cell heterogeneity of the amphibian.
    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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  10. Article ; Online: Publisher Correction

    Yuan Liao / Lifeng Ma / Qile Guo / Weigao E / Xing Fang / Lei Yang / Fanwei Ruan / Jingjing Wang / Peijing Zhang / Zhongyi Sun / Haide Chen / Zhongliang Lin / Xueyi Wang / Xinru Wang / Huiyu Sun / Xiunan Fang / Yincong Zhou / Ming Chen / Wanhua Shen /
    Guoji Guo / Xiaoping Han

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

    Cell landscape of larval and adult Xenopus laevis at single-cell resolution

    2022  Volume 1

    Keywords Science ; Q
    Language English
    Publishing date 2022-09-01T00:00:00Z
    Publisher Nature Portfolio
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    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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