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Article ; Online: Correction: Post-abortion needs-based education via the WeChat platform to lessen fear and encourage effective contraception: a post-abortion care service intervention-controlled trial.

Shi, Danfeng / Liu, Chenyin / Huang, Lingna / Chen, Xiao-Qian

2024 Volume 24, Issue 1, Page(s) 194

Language	English
Publishing date	2024-03-25
Publishing country	England
Document type	Published Erratum
ZDB-ID	2050444-5
ISSN	1472-6874 ; 1472-6874
ISSN (online)	1472-6874
ISSN	1472-6874
DOI	10.1186/s12905-024-03033-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Studies of the Mechanism of Nucleosome Dynamics

Danfeng Shi / Yuxin Huang / Chen Bai

Polymers, Vol 15, Iss 1763, p

A Review on Multifactorial Regulation from Computational and Experimental Cases

2023 Volume 1763

Abstract: The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been ... ...

Abstract	The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
Keywords	nucleosome dynamics ; mechanism studies ; multifactorial regulation ; Organic chemistry ; QD241-441
Subject code	612
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Post-abortion needs-based education via the WeChat platform to lessen fear and encourage effective contraception: a post-abortion care service intervention-controlled trial.

Shi, Danfeng / Liu, Chenyin / Huang, Lingna / Chen, Xiao-Qian

BMC women's health

2024 Volume 24, Issue 1, Page(s) 159

Abstract: Objective: Our study aims to investigate post-abortion needs-based education via the WeChat platform for women who had intended abortion in the first trimester, whether they are using effective contraception or becoming pregnant again.: Design: This ... ...

Abstract	Objective: Our study aims to investigate post-abortion needs-based education via the WeChat platform for women who had intended abortion in the first trimester, whether they are using effective contraception or becoming pregnant again. Design: This single hospital intervention-controlled trial used a nearly 1:1 allocation ratio. Women who had intended abortions were randomly assigned to a Wechat group (needs-based education) and a control group (Traditional education). The women's ability to use effective contraception was the main result. Whether they unknowingly became pregnant again was the second result. Another result was patient anxiousness. Before and after education, women filled out questionnaires to assess their contraception methods and anxiety. Methods: Based on the theoretical framework of contraceptions of IBL (inquiry-based learning), post-abortion women were included in WeChat groups. We use WeChat Group Announcement, regularly sending health education information, one-on-one answers to questions, and consultation methods to explore the possibilities and advantages of WeChat health education for women after abortion. A knowledge paradigm for post-abortion health education was established: From November 2021 until December 2021, 180 women who had an unintended pregnancy and undergone an induced or medical abortion were recruited, their progress was tracked for four months, and the PAC service team monitored the women's speech, discussed and classified the speech entries and summarized the common post-abortion needs in 8 aspects. At least 2 research group members routinely extracted records and categorized the outcomes. Results: Before education, there were no appreciable variations between the two groups regarding sociodemographic characteristics, obstetrical conditions, abortion rates, or methods of contraception (P > 0.05). Following education, the WeChat group had a greater rate of effective contraception (63.0%) than the control group (28.6%), and their SAS score dropped statistically more than that of the control group (P < 0.05). Following the education, there were no unwanted pregnancies in the WeChat group, whereas there were 2 in the traditional PAC group. Only 5 participants in the WeChat group and 32 in the conventional PAC group reported mild anxiety after the education.
MeSH term(s)	Pregnancy ; Female ; Humans ; Educational Status ; Abortion, Induced ; Contraception ; Fear ; Health Education
Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2050444-5
ISSN	1472-6874 ; 1472-6874
ISSN (online)	1472-6874
ISSN	1472-6874
DOI	10.1186/s12905-024-03004-3
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Article ; Online: Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.

Shi, Danfeng / Huang, Yuxin / Bai, Chen

Polymers

2023 Volume 15, Issue 7

Abstract: The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein-DNA complex, its structural and dynamic features have been ... ...

Abstract	The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein-DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome's dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
Language	English
Publishing date	2023-04-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym15071763
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Article ; Online: Exploring the activation mechanism of metabotropic glutamate receptor 2.

Zhu, Xiaohong / Luo, Mengqi / An, Ke / Shi, Danfeng / Hou, Tingjun / Warshel, Arieh / Bai, Chen

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 21, Page(s) e2401079121

Abstract: Homomeric dimerization of metabotropic glutamate receptors (mGlus) is essential for the modulation of their functions and represents a promising avenue for the development of novel therapeutic approaches to address central nervous system diseases. Yet, ... ...

Abstract	Homomeric dimerization of metabotropic glutamate receptors (mGlus) is essential for the modulation of their functions and represents a promising avenue for the development of novel therapeutic approaches to address central nervous system diseases. Yet, the scarcity of detailed molecular and energetic data on mGlu2 impedes our in-depth comprehension of their activation process. Here, we employ computational simulation methods to elucidate the activation process and key events associated with the mGlu2, including a detailed analysis of its conformational transitions, the binding of agonists, G
MeSH term(s)	Receptors, Metabotropic Glutamate/metabolism ; Receptors, Metabotropic Glutamate/chemistry ; Humans ; Protein Multimerization ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Binding
Chemical Substances	Receptors, Metabotropic Glutamate ; metabotropic glutamate receptor 2
Language	English
Publishing date	2024-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2401079121
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Article: A Novel PDMS-Based Flexible Thermoelectric Generator Fabricated by Ag

Guo, Rui / Shi, Weipeng / Yang, Chenyu / Chen, Yi / Wang, Yonghua / Cui, Danfeng / Liu, Dan / Xue, Chenyang

Nanomaterials (Basel, Switzerland)

2024 Volume 14, Issue 6

Abstract: Flexible thermoelectric generators (FTEGs), which can overcome the energy supply limitations of wearable devices, have received considerable attention. However, the use of toxic Te-based materials and fracture-prone electrodes constrains the application ... ...

Abstract	Flexible thermoelectric generators (FTEGs), which can overcome the energy supply limitations of wearable devices, have received considerable attention. However, the use of toxic Te-based materials and fracture-prone electrodes constrains the application of FTEGs. In this study, a novel Ag
Language	English
Publishing date	2024-03-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano14060542
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Article ; Online: A predicted structure of NADPH Oxidase 1 identifies key components of ROS generation and strategies for inhibition.

Yezhou Liu / Shiyu Liang / Danfeng Shi / Yue Zhang / Chen Bai / Richard D Ye

PLoS ONE, Vol 18, Iss 5, p e

2023 Volume 0285206

Abstract: NADPH oxidase 1 (NOX1) is primarily expressed in epithelial cells and responsible for local generation of reactive oxygen species (ROS). By specifically manipulating the local redox microenvironment, NOX1 actively engages in epithelial immunity, ... ...

Abstract	NADPH oxidase 1 (NOX1) is primarily expressed in epithelial cells and responsible for local generation of reactive oxygen species (ROS). By specifically manipulating the local redox microenvironment, NOX1 actively engages in epithelial immunity, especially in colorectal and pulmonary epithelia. To unravel the structural basis of NOX1 engaged epithelial immune processes, a predicted structure model was established using RaptorX deep learning models. The predicted structure model illustrates a 6-transmembrane domain structure, a FAD binding domain, and an NADPH binding/NOXO1 interacting region. The substrate/cofactor binding scheme with respect to this proposed model highly correlates with published reports and is verified in our site-directed mutagenesis assays. An electron transport chain, from NADPH to FAD and the two heme groups, was well supported by the predicted model. Through molecular docking analysis of various small molecule NOX1 inhibitors and subsequent experimental validation, we identified pronounced active sites for potent NOX1 inhibition. Specifically, LEU60, VAL71, MET181, LEU185, HIS208, PHE211, TYR214, and TYR280 in the transmembrane domain form an active pocket for insertion of the small molecule inhibitors to inhibit electron transfer between the heme groups, thus affecting extracellular ROS generation. Altogether, our study provides structural information to help elucidate the role of NOX1 in epithelial generation of ROS and sheds light on the development of therapeutics for NOX1 related illnesses.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effect of Surfactant Formula on the Film Forming Capacity, Wettability, and Preservation Properties of Electrically Sprayed Sodium Alginate Coats.

Deng, Wanqing / Zheng, Huiyuan / Zhu, Zichun / Deng, Yun / Shi, Yuchen / Wang, Danfeng / Zhong, Yu

Foods (Basel, Switzerland)

2023 Volume 12, Issue 11

Abstract: Surfactants are always added to coating formulations to ensure good adhesion of edible coatings to a product's surface and to maintain freshness. In this study, the effects of the mix surfactants Tween 20 and Span 80 with different hydrophile-lipophile ... ...

Abstract	Surfactants are always added to coating formulations to ensure good adhesion of edible coatings to a product's surface and to maintain freshness. In this study, the effects of the mix surfactants Tween 20 and Span 80 with different hydrophile-lipophile balance (HLB) values on the film-forming ability, wettability, and preservation capacity of blueberry sodium alginate coating were investigated. The results indicated that Tween 20 obviously ensured favorable wettability and improved the uniformity and mechanical properties of the resulting film. While the addition of Span 80 reduced the mean particle size of the coating, enhanced the water resistance of the film, and helped to reduce blueberry weight loss. A sodium alginate coating with low viscosity and medium HLB could better inhibit the galactose, sucrose, and linoleic acid metabolism of blueberries, reduce the consumption of phenols, promote the accumulation of flavonoids, and thus display superior coating performance. In summary, sodium alginate coating with medium HLB had comprehensive advantages in film-forming ability and wettability and was conducive to the fresh-keeping role.
Language	English
Publishing date	2023-05-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12112197
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Article ; Online: Phosphoglycerate mutase 5 exacerbates liver ischemia-reperfusion injury by activating mitochondrial fission.

Tang, Hongwei / Yu, Qiwen / Chen, Xu / Zhang, Jiakai / Guo, Danfeng / Guo, Wenzhi / Zhang, Shuijun / Shi, Xiaoyi

Scientific reports

2024 Volume 14, Issue 1, Page(s) 8535

Abstract: Although the death of hepatocytes is a crucial trigger of liver ischemia-reperfusion (I/R) injury, the regulation of liver I/R-induced hepatocyte death is still poorly understood. Phosphoglycerate mutase 5 (PGAM5), a mitochondrial Serine/Threonine ... ...

Abstract	Although the death of hepatocytes is a crucial trigger of liver ischemia-reperfusion (I/R) injury, the regulation of liver I/R-induced hepatocyte death is still poorly understood. Phosphoglycerate mutase 5 (PGAM5), a mitochondrial Serine/Threonine protein phosphatase, regulates mitochondrial dynamics and is involved in the process of both apoptosis and necrotic. However, it is still unclear what role PGAM5 plays in the death of hepatocytes induced by I/R. Using a PGAM5-silence mice model, we investigated the role of PGAM5 in liver I/R injury and its relevant molecular mechanisms. Our data showed that PGAM5 was highly expressed in mice with liver I/R injury. Silence of PGAM5 could decrease I/R-induced hepatocyte death in mice. In subcellular levels, the silence of PGAM5 could restore mitochondrial membrane potential, increase mitochondrial DNA copy number and transcription levels, inhibit ROS generation, and prevent I/R-induced opening of abnormal mPTP. As for the molecular mechanisms, we indicated that the silence of PGAM5 could inhibit Drp1(S616) phosphorylation, leading to a partial reduction of mitochondrial fission. In addition, Mdivi-1 could inhibit mitochondrial fission, decrease hepatocyte death, and attenuate liver I/R injury in mice. In conclusion, our data reveal the molecular mechanism of PGAM5 in driving hepatocyte death through activating mitochondrial fission in liver I/R injury.
MeSH term(s)	Animals ; Mice ; Hepatocytes ; Liver ; Mitochondrial Dynamics ; Phosphoglycerate Mutase/genetics ; Reperfusion Injury/genetics
Chemical Substances	Phosphoglycerate Mutase (EC 5.4.2.11) ; PGAM5 protein, mouse (EC 3.1.3.16)
Language	English
Publishing date	2024-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-58748-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines

Danfeng Shi / Ke An / Honghui Zhang / Peiyi Xu / Chen Bai

Entropy, Vol 24, Iss 620, p

2022 Volume 620

Abstract: Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also ... ...

Abstract	Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines.
Keywords	protein machines ; coarse-grained model ; conformational pathway ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
Subject code	612
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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