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Article ; Online: Organoid Culture of Different Intestinal Segments from Human and Mouse.

Wang, Yalong / Tan, Ronghui / Chen, Ye-Guang

Methods in molecular biology (Clifton, N.J.)

2024

Abstract: The intestine comprises distinct segments, each characterized by unique cell populations and functions. Intestinal organoids faithfully replicate the cellular composition and functions of the intestine. Over the past decade, the organoid model has ... ...

Abstract	The intestine comprises distinct segments, each characterized by unique cell populations and functions. Intestinal organoids faithfully replicate the cellular composition and functions of the intestine. Over the past decade, the organoid model has garnered considerable attention for its application in investigation of organ development, renewal and functional performance. While the organoid culture systems for mouse small intestine and human large intestine have widely adopted, a comparison summary for different segments of the human or mouse intestine is lacking. In this study, we present a systematically detailed culture methodology for intestinal organoids, encompassing both the small intestine and the large intestine from humans or mice. This method provides a robust in vitro tool for intestinal research, and expands the possible clinical application of organoids.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/7651_2024_542
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Unveiling new horizons in heart research: the promise of multi-chamber cardiac organoids.

Hou, Junjie / Chen, Ye-Guang / Xiong, Jing-Wei

Cell regeneration (London, England)

2024 Volume 13, Issue 1, Page(s) 10

Abstract: Human cardiac and other organoids have recently emerged as a groundbreaking tool for advancing our understanding the developmental biology of human organs. A recent paper from Sasha Mendjan's laboratory published in the journal Cell on December 7, 2023, ... ...

Abstract	Human cardiac and other organoids have recently emerged as a groundbreaking tool for advancing our understanding the developmental biology of human organs. A recent paper from Sasha Mendjan's laboratory published in the journal Cell on December 7, 2023, reported the generation of multi-chamber cardioids from human pluripotent stem cells, a transformative technology in the field of cardiology. In this short highlight paper, we summarize their findings. Their cardioids remarkably recapitulate the complexity of the human embryonic heart, including tissue architecture, cellular diversity, and functionality providing an excellent in vitro model for investigation of human heart development, disease modeling, precision medicine, and regenerative medicine. Thus, generating cardioids is an important step forward for understanding human heart development and developing potential therapies for heart diseases.
Language	English
Publishing date	2024-04-23
Publishing country	China
Document type	Journal Article
ZDB-ID	2682438-3
ISSN	2045-9769
ISSN	2045-9769
DOI	10.1186/s13619-024-00193-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Discovery of Tetrazolamide-benzimidazol-2-ones as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors.

Cai, Zhuo-Mei / Huang, Guang-Yi / Dong, Jin / Chen, Li-Jun / Ye, Bao-Qing / Lin, Hong-Yan / Wang, Da-Wei / Yang, Guang-Fu

Journal of agricultural and food chemistry

2024 Volume 72, Issue 8, Page(s) 3884–3893

Abstract: 4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is one of the most valuable herbicide targets due to its unique biological functions. In search of HPPD inhibitors with promising biological performance, we designed and synthesized a series of ... ...

Abstract	4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is one of the most valuable herbicide targets due to its unique biological functions. In search of HPPD inhibitors with promising biological performance, we designed and synthesized a series of novel tetrazolamide-benzimidazol-2-ones using a structure-based drug design strategy. Among the synthesized compounds, 1-(2-chlorobenzyl)-3-methyl-
MeSH term(s)	Molecular Structure ; Structure-Activity Relationship ; 4-Hydroxyphenylpyruvate Dioxygenase/chemistry ; Herbicides/pharmacology ; Herbicides/chemistry ; Arabidopsis/metabolism ; Enzyme Inhibitors/pharmacology ; Enzyme Inhibitors/chemistry ; Benzimidazoles
Chemical Substances	benzimidazol-2-one (43135-91-7) ; 4-Hydroxyphenylpyruvate Dioxygenase (EC 1.13.11.27) ; Herbicides ; Enzyme Inhibitors ; Benzimidazoles
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.3c06798
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Article ; Online: The Interplay Between TGF-β Signaling and Cell Metabolism

Huidong Liu / Ye-Guang Chen

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 10

Abstract: The transforming growth factor-β (TGF-β) signaling plays a critical role in the development and tissue homeostasis in metazoans, and deregulation of TGF-β signaling leads to many pathological conditions. Mounting evidence suggests that TGF-β signaling ... ...

Abstract	The transforming growth factor-β (TGF-β) signaling plays a critical role in the development and tissue homeostasis in metazoans, and deregulation of TGF-β signaling leads to many pathological conditions. Mounting evidence suggests that TGF-β signaling can actively alter metabolism in diverse cell types. Furthermore, metabolic pathways, beyond simply regarded as biochemical reactions, are closely intertwined with signal transduction. Here, we discuss the role of TGF-β in glucose, lipid, amino acid, redox and polyamine metabolism with an emphasis on how TGF-β can act as a metabolic modulator and how metabolic changes can influence TGF-β signaling. We also describe how interplay between TGF-β signaling and cell metabolism regulates cellular homeostasis as well as the progression of multiple diseases, including cancer.
Keywords	TGF-β signaling ; Smad ; glucose metabolism ; lipid metabolism ; amino acid metabolism ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: On the genus

Qin, Yao-Guang / Chen, Hai-Feng / Li, Cheng-de / Chen, Ye

ZooKeys

2022 Volume 1091, Page(s) 119–138

Abstract: Two new species belonging to ... ...

Abstract	Two new species belonging to the
Language	English
Publishing date	2022-04-01
Publishing country	Bulgaria
Document type	Journal Article
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.1091.80065
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Article: Welcome to Cell Regeneration.

Chen, Ye-Guang / Lou, Ying

Cell regeneration (London, England)

2020 Volume 9, Issue 1, Page(s) 1

Language	English
Publishing date	2020-06-02
Publishing country	China
Document type	Editorial
ZDB-ID	2682438-3
ISSN	2045-9769
ISSN	2045-9769
DOI	10.1186/s13619-020-00050-8
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Article ; Online: Image Recovery Matters: A Recovery-Extraction Framework for Robust Fetal Brain Extraction From MR Images.

Chen, Jian / Lu, Ranlin / Ye, Shilin / Guang, Mengting / Tassew, Tewodros Megabiaw / Jing, Bin / Zhang, Guofu / Chen, Geng / Shen, Dinggang

IEEE journal of biomedical and health informatics

2024 Volume 28, Issue 2, Page(s) 823–834

Abstract: The extraction of the fetal brain from magnetic resonance (MR) images is a challenging task. In particular, fetal MR images suffer from different kinds of artifacts introduced during the image acquisition. Among those artifacts, intensity inhomogeneity ... ...

Abstract	The extraction of the fetal brain from magnetic resonance (MR) images is a challenging task. In particular, fetal MR images suffer from different kinds of artifacts introduced during the image acquisition. Among those artifacts, intensity inhomogeneity is a common one affecting brain extraction. In this work, we propose a deep learning-based recovery-extraction framework for fetal brain extraction, which is particularly effective in handling fetal MR images with intensity inhomogeneity. Our framework involves two stages. First, the artifact-corrupted images are recovered with the proposed generative adversarial learning-based image recovery network with a novel region-of-darkness discriminator that enforces the network focusing on artifacts of the images. Second, we propose a brain extraction network for more effective fetal brain segmentation by strengthening the association between lower- and higher-level features as well as suppressing task-irrelevant features. Thanks to the proposed recovery-extraction strategy, our framework is able to accurately segment fetal brains from artifact-corrupted MR images. The experiments show that our framework achieves promising performance in both quantitative and qualitative evaluations, and outperforms state-of-the-art methods in both image recovery and fetal brain extraction.
MeSH term(s)	Humans ; Image Processing, Computer-Assisted/methods ; Magnetic Resonance Imaging/methods ; Brain/diagnostic imaging ; Head ; Fetus/diagnostic imaging
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2695320-1
ISSN	2168-2208 ; 2168-2194
ISSN (online)	2168-2208
ISSN	2168-2194
DOI	10.1109/JBHI.2023.3333953
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Zs.A 5483: Show issues

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Article: The Interplay Between TGF-β Signaling and Cell Metabolism.

Liu, Huidong / Chen, Ye-Guang

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 846723

Abstract	The transforming growth factor-β (TGF-β) signaling plays a critical role in the development and tissue homeostasis in metazoans, and deregulation of TGF-β signaling leads to many pathological conditions. Mounting evidence suggests that TGF-β signaling can actively alter metabolism in diverse cell types. Furthermore, metabolic pathways, beyond simply regarded as biochemical reactions, are closely intertwined with signal transduction. Here, we discuss the role of TGF-β in glucose, lipid, amino acid, redox and polyamine metabolism with an emphasis on how TGF-β can act as a metabolic modulator and how metabolic changes can influence TGF-β signaling. We also describe how interplay between TGF-β signaling and cell metabolism regulates cellular homeostasis as well as the progression of multiple diseases, including cancer.
Language	English
Publishing date	2022-03-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.846723
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Article ; Online: Data mining-based identification of epigenetic signatures with discrimination potential of lung adenocarcinoma and squamous cell carcinoma.

Pang, Wen-Guang / Ye, Min / Chen, Jia-Rong / Zhang, Liang / Wang, Zheng

Molecular biology reports

2024 Volume 51, Issue 1, Page(s) 255

Abstract: Background: Mounting evidence suggests that lung adenocarcinoma (LAC) and lung squamous cell carcinoma (LSC) have different biological behaviors and therapeutic regimens in clinical practice. However, limited improvements in molecular differential ... ...

Abstract	Background: Mounting evidence suggests that lung adenocarcinoma (LAC) and lung squamous cell carcinoma (LSC) have different biological behaviors and therapeutic regimens in clinical practice. However, limited improvements in molecular differential diagnosis of the two entities have been achieved in recent decades. We aimed to find novel markers that could define non-small cell lung cancer (NSCLC) subtypes. Methods: We first explored publically available databases to search for DNA methylation signatures that enable a precise discrimination of LAC and LSC. Next-generation sequencing (NGS) was then used to analyze the methylation status and sites of candidate genes in LAC/LSC tissue samples, and a quantitative methylation-sensitive PCR (qMS-PCR) assay was conducted to test the performance of the selected maker in tissue samples and bronchoalveolar lavage fluid (BALF) specimens. Results: We screened 19 top-ranked methylation loci that are differentially methylated between LAC and LSC. Among these hits, 6 methylation sites are enriched within the PREX1 gene promoter, thus becoming our focus. NGS analysis confirmed markedly higher PREX1 methylation levels in LAC than in LSC and revealed the right sites for detection of PREX1 methylation. Furthermore, PREX1 methylation analysis in lung cancer tissue samples defined 9 of 11 pathologically proven LACs, as well as 12 of 14 LSCs. In addition, ~ 80% LAC BALF samples showed methylated PREX1 compared to substantially lower test positivity (0-9%) of it in LSC and other lung conditions (P < 0.01). Conclusion: Our pilot study identified a unique epigenetic signature that could effectively distinguish LAC from LSC in various lung samples. It may enhance our in-depth understanding of the biology of lung cancer and pave the way for better accurate diagnosis and treatment stratification in the future.
MeSH term(s)	Humans ; Carcinoma, Non-Small-Cell Lung/genetics ; Lung Neoplasms/pathology ; Pilot Projects ; Adenocarcinoma/pathology ; DNA Methylation/genetics ; Adenocarcinoma of Lung/genetics ; Carcinoma, Squamous Cell/genetics ; Epigenesis, Genetic/genetics ; Biomarkers, Tumor/genetics
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2024-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-024-09216-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1140: Show issues

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Article ; Online: S-Shaped Helical Singlet Diradicaloid and Its Transformation to Circumchrysene via a Two-Stage Cyclization.

Hu, Jinlian / Xiang, Qin / Tian, Xiaoqi / Ye, Lei / Wang, Yanpei / Ni, Yong / Chen, Xing / Liu, Yuxia / Chen, Guang / Sun, Zhe

Journal of the American Chemical Society

2024 Volume 146, Issue 15, Page(s) 10321–10330

Abstract: Polycyclic hydrocarbons with diradical and polyradical characters usually display unique reactivities in ring-cyclization reactions. However, such reactions are rarely used to construct π-extended polycyclic aromatic hydrocarbons. Here, we describe the ... ...

Abstract	Polycyclic hydrocarbons with diradical and polyradical characters usually display unique reactivities in ring-cyclization reactions. However, such reactions are rarely used to construct π-extended polycyclic aromatic hydrocarbons. Here, we describe the synthesis of an S-shaped doubly helical singlet diradicaloid compound and its facile transformation into an unprecedented circumchrysene via a two-stage ring cyclization, which includes: (1) an eletrocylization from diradicaloid precursor and (2) a Scholl reaction. The reaction mechanism was investigated through
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c11585
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