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Book: Autophagy: biology and diseases

Xie, Zhiping

technology and methodology

(Advances in experimental medicine and biology ; volume 1208)

2021

Author's details	Zhiping Xie editor
Series title	Advances in experimental medicine and biology ; volume 1208
Collection
Language	English
Size	xiv, 453 Seiten, Illustrationen, Diagramme
Publisher	Springer
Publishing place	Singapore
Publishing country	Singapore
Document type	Book
HBZ-ID	HT020999310
ISBN	978-981-16-2829-0 ; 9789811628306 ; 981-16-2829-7 ; 9811628300
Database	Catalogue ZB MED Medicine, Health

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Article: Gender difference in association between low muscle mass and risk of non-alcoholic fatty liver disease among Chinese adults with visceral obesity.

Lu, Yayun / Xia, Qing / Wu, Liangyu / Xie, Zhiping

Frontiers in nutrition

2023 Volume 10, Page(s) 1026054

Abstract: Background and aims: Although the association between low muscle mass and the risk of non-alcoholic fatty liver disease is well-known, it has not been explored in viscerally obese populations by gender. Besides, whether low muscle mass still increases ... ...

Abstract	Background and aims: Although the association between low muscle mass and the risk of non-alcoholic fatty liver disease is well-known, it has not been explored in viscerally obese populations by gender. Besides, whether low muscle mass still increases the NAFLD risk in subjects with visceral obesity, independent of obesity, is still unknown. The aim of this study was to explore the gender-specific association between low muscle mass and the risk of non-alcoholic fatty liver disease (NAFLD) in subjects with visceral obesity. Methods: Overall, 1,114 participants aged 19-89 years were recruited in this retrospective study. Liver disease was diagnosed by hepatic ultrasound. Skeletal muscle mass was estimated by bioimpedance analysis and defined by the appendicular skeletal muscle index (ASMI). Gender-specific differences in the ASMI value were compared between NAFLD and control groups. Restricted cubic spline and multivariate logistic regression were performed to analyze the association (stratified by gender and age) between the ASMI and the risk of NAFLD, respectively. Results: Middle-aged females (40-60 years) and males (of any age) with NAFLD had a significantly lower ASMI compared with controls ( Conclusion: Among those with visceral obesity, low muscle mass increased the risk of NAFLD in males of any age, and middle-aged females, this may be explained by the postmenopausal decline in estrogen.
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2776676-7
ISSN	2296-861X
ISSN	2296-861X
DOI	10.3389/fnut.2023.1026054
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Article ; Online: Ginsenoside Rg1 attenuation of neurogenesis disorder and neuronal apoptosis in the rat hippocampus after spinal cord injury may involve brain-derived neurotrophic factor/extracellular signal-regulated kinase signaling.

Xi, Bin / Fu, Jieping / Wan, Dengfeng / Xie, Zhiping

Neuroreport

2023 Volume 34, Issue 5, Page(s) 290–298

Abstract: Objective: We previously demonstrated that spinal cord injury (SCI) induced hippocampus injury and depression in rodents. Ginsenoside Rg1 effectively prevents neurodegenerative disorders. Here, we investigated the effects of ginsenoside Rg1 on the ... ...

Abstract	Objective: We previously demonstrated that spinal cord injury (SCI) induced hippocampus injury and depression in rodents. Ginsenoside Rg1 effectively prevents neurodegenerative disorders. Here, we investigated the effects of ginsenoside Rg1 on the hippocampus after SCI. Methods: We used a rat compression SCI model. Western blotting and morphologic assays were used to investigate the protective effects of ginsenoside Rg1 in the hippocampus. Results: Brain-derived neurotrophic factor/extracellular signal-regulated kinases (BDNF/ERK) signaling was altered in the hippocampus at 5 weeks after SCI. SCI attenuated neurogenesis and enhanced the expression of cleaved caspase-3 in the hippocampus; however, ginsenoside Rg1 attenuated cleaved caspase-3 expression and improved neurogenesis and BDNF/ERK signaling in the rat hippocampus. The results suggest that SCI affects BDNF/ERK signaling, and ginsenoside Rg1 can attenuate hippocampal damage after SCI. Conclusion: We speculate that the protective effects of ginsenoside Rg1 in hippocampal pathophysiology after SCI may involve BDNF/ERK signaling. Ginsenoside Rg1 shows promise as a therapeutic pharmaceutical product when seeking to counter SCI-induced hippocampal damage.
MeSH term(s)	Rats ; Animals ; Extracellular Signal-Regulated MAP Kinases ; Brain-Derived Neurotrophic Factor ; Caspase 3 ; Spinal Cord Injuries/drug therapy ; Hippocampus ; Apoptosis ; Neurogenesis
Chemical Substances	Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24) ; Brain-Derived Neurotrophic Factor ; ginsenoside Rg1 (PJ788634QY) ; Caspase 3 (EC 3.4.22.-)
Language	English
Publishing date	2023-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1049746-8
ISSN	1473-558X ; 0959-4965
ISSN (online)	1473-558X
ISSN	0959-4965
DOI	10.1097/WNR.0000000000001891
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Article: CRISPR/Cas9-Mediated Generation of Mutant Lines in

Zhang, Chun-Xiao / Li, Ru-Jie / Baude, Laura / Reinhardt, Didier / Xie, Zhi-Ping / Staehelin, Christian

Biology

2024 Volume 13, Issue 1

Abstract: CRISPR/Cas9 systems are commonly used for plant genome editing; however, the generation of homozygous mutant lines ... ...

Abstract	CRISPR/Cas9 systems are commonly used for plant genome editing; however, the generation of homozygous mutant lines in
Language	English
Publishing date	2024-01-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology13010053
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Article ; Online: The Efficacy of Different Material Scaffold-Guided Cell Transplantation in the Treatment of Spinal Cord Injury in Rats: A Systematic Review and Network Meta-analysis.

Wang, Zhihua / Li, Jun / Xu, Tianqi / Guo, Boyu / Xie, Zhiping / Li, Meihua

Cellular and molecular neurobiology

2024 Volume 44, Issue 1, Page(s) 43

Abstract: Cell transplantation is a promising treatment option for spinal cord injury (SCI). However, there is no consensus on the choice of carrier scaffolds to host the cells. This study aims to evaluate the efficacy of different material scaffold-mediated cell ... ...

Abstract	Cell transplantation is a promising treatment option for spinal cord injury (SCI). However, there is no consensus on the choice of carrier scaffolds to host the cells. This study aims to evaluate the efficacy of different material scaffold-mediated cell transplantation in treating SCI in rats. According to PRISMA's principle, Embase, PubMed, Web of Science, and Cochrane databases were searched, and relevant literature was referenced. Only original research on cell transplantation plus natural or synthetic scaffolds in SCI rats was included. Direct and indirect evidence for improving hind limb motor function was pooled through meta-analysis. A subgroup analysis of some factors that may affect the therapeutic effect was conducted to understand the results fully. In total, 25 studies met the inclusion criteria, in which 293 rats received sham surgery, 78 rats received synthetic material scaffolds, and 219 rats received natural materials scaffolds. The network meta-analysis demonstrated that although synthetic scaffolds were slightly inferior to natural scaffolds in terms of restoring motor function in cell transplantation of SCI rats, no statistical differences were observed between the two (MD: -0.35; 95% CI -2.6 to 1.9). Moreover, the subgroup analysis revealed that the type and number of cells may be important factors in therapeutic efficacy (P < 0.01). Natural scaffolds and synthetic scaffolds are equally effective in cell transplantation of SCI rats without significant differences. In the future, the findings need to be validated in multicenter, large-scale, randomized controlled trials in clinical practice. Trial registration: Registration ID CRD42024459674 (PROSPERO).
MeSH term(s)	Animals ; Spinal Cord Injuries/therapy ; Rats ; Tissue Scaffolds/chemistry ; Cell Transplantation/methods ; Network Meta-Analysis ; Treatment Outcome ; Recovery of Function
Language	English
Publishing date	2024-05-04
Publishing country	United States
Document type	Journal Article ; Systematic Review ; Meta-Analysis ; Review
ZDB-ID	283404-2
ISSN	1573-6830 ; 0272-4340
ISSN (online)	1573-6830
ISSN	0272-4340
DOI	10.1007/s10571-024-01465-6
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Article ; Online: Multi-platform omics sequencing dissects the atlas of plasma-derived exosomes in rats with or without depression-like behavior after traumatic spinal cord injury.

Wang, Zhihua / Xie, Zhiping / Zhang, Zhixiong / Zhou, Wu / Guo, Boyu / Li, Meihua

Progress in neuro-psychopharmacology & biological psychiatry

2024 Volume 132, Page(s) 110987

Abstract: Background: Exosomes can penetrate the blood-brain barrier for material exchange between the peripheral and central nervous systems. Differences in exosome contents could explain the susceptibility of different individuals to depression-like behavior ... ...

Abstract	Background: Exosomes can penetrate the blood-brain barrier for material exchange between the peripheral and central nervous systems. Differences in exosome contents could explain the susceptibility of different individuals to depression-like behavior after traumatic spinal cord injury (TSCI). Methods: Hierarchical clustering was used to integrate multiple depression-related behavioral outcomes in sham and TSCI rats and ultimately identify non-depressed and depressed rats. The difference in plasma exosome contents between non-depressed and depressed rats after TSCI was assessed in 15 random subjects by performing plasma exosome transcriptomics, mass spectroscope-based proteomics, and non-targeted metabolomics analyses. Results: The results revealed that about 27.6% of the rats developed depression-like behavior after TSCI. Totally, 10 differential metabolites, 81 differentially expressed proteins (DEPs), 373 differentially expressed genes (DEGs), and 55 differentially expressed miRNAs (DEmiRNAs) were identified between non-depressed TSCI and sham rats. Meanwhile, 37 differential metabolites, 499 DEPs, 1361 DEGs, and 89 DEmiRNAs were identified between depressed and non-depressed TSCI rats. Enrichment analysis showed that the progression of depression-like behavior after TSCI may be related to amino acid metabolism disorder and dysfunction of multiple signaling pathways, including endocytosis, lipid and atherosclerosis, toll-like receptor, TNF, and PI3K-Akt pathway. Conclusion: Overall, our study systematically revealed for the first time the differences in plasma exosome contents between non-depressed and depressed rats after TSCI, which will help broaden our understanding of the complex molecular mechanisms involved in brain functional recombination after TSCI.
MeSH term(s)	Humans ; Rats ; Animals ; Depression/etiology ; Exosomes/metabolism ; Phosphatidylinositol 3-Kinases ; Spinal Cord Injuries/complications ; Spinal Cord Injuries/metabolism ; MicroRNAs
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; MicroRNAs
Language	English
Publishing date	2024-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	781181-0
ISSN	1878-4216 ; 0278-5846
ISSN (online)	1878-4216
ISSN	0278-5846
DOI	10.1016/j.pnpbp.2024.110987
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Article: Finite element simulation of mechanical properties of Rosa roxburghii under compression loading

Lang, Yancheng / Xie, Zhiping / Chen, Luqi

Journal of food process engineering. 2022 Jan., v. 45, no. 1

2022

Abstract: It is very necessary to understand the mechanical properties of Rosa roxburghii fruit for harvesting, packaging, processing, transportation, storage, and related equipment design and improvement. This research was to determine the mechanical properties ... ...

Abstract	It is very necessary to understand the mechanical properties of Rosa roxburghii fruit for harvesting, packaging, processing, transportation, storage, and related equipment design and improvement. This research was to determine the mechanical properties of R. roxburghii fruits through compressive experiments and finite element simulations and to verify the accuracy of the finite element model. In order to achieve finite element analysis, an accurate three‐dimensional (3D) geometric model was reconstructed by applying 3D laser technology and point cloud reconstruction algorithm. The elastic modulus and Poisson's ratio of R. roxburghii fruits were determined to be 4.0 MPa and 0.35 through experiments. The finite element simulation results provided valuable numerical data and visualized stress distribution. The simulation results showed that R. roxburghii fruits were damaged under the loads of 156.2 N (vertical) or 148.3 N (horizontal), with a maximum deformation of 5.0 mm (vertical) or 6.93 mm (horizontal), respectively. In the vertical and horizontal compression positions, the maximum relative errors between the experimental results and the finite element model are 24.71 and 13.99%, respectively. The results of the compressive strain energy of the fruit showed that the maximum relative error between the experimentally measured strain energy and the strain energy calculated by FEM simulation was 9.20 and 2.09% in the vertical and horizontal directions, respectively. PRACTICAL APPLICATIONS: As there is no relevant literature on the mechanical analysis of Rosa roxburghii fruit, the finite element method has been successfully applied to analyze the mechanical properties of R. roxburghii fruit under compressive load. At the same time, the simulation results have also been verified by experimental data, and the finite element technology has certain application prospects in food processing engineering. This study proposes a method based on 3D scanning technology and point cloud reconstruction algorithm to reconstruct an accurate geometric model of R. roxburghii fruit for finite element simulation, and conducts an in‐depth analysis on the stress, strain, and strain energy of the fruit. The purpose of this article is to propose a reliable method to predict the mechanical properties of the fruits under compressive load. The finite element simulation results can not only provide the basic data needed for fruit packaging and protection but also can be used for the design of automated fruit picking manipulators and the improvement of fruit processing equipment.
Keywords	Poisson distribution ; Rosa roxburghii ; algorithms ; automation ; compression strength ; data collection ; deformation ; energy ; equipment design ; finite element analysis ; fruits ; geometry ; models ; modulus of elasticity ; transportation
Language	English
Dates of publication	2022-01
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	752358-0
ISSN	0145-8876
ISSN	0145-8876
DOI	10.1111/jfpe.13939
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Visualizing Yeast Organelles with Fluorescent Protein Markers.

Liu, Chang-Yue / Zhu, Jing / Xie, Zhiping

Journal of visualized experiments : JoVE

2022 , Issue 182

Abstract: The budding yeast, Saccharomyces cerevisiae, is a classic model system in studying organelle function and dynamics. In our previous works, we have constructed fluorescent protein-based markers for major organelles and endomembrane structures, including ... ...

Abstract	The budding yeast, Saccharomyces cerevisiae, is a classic model system in studying organelle function and dynamics. In our previous works, we have constructed fluorescent protein-based markers for major organelles and endomembrane structures, including the nucleus, endoplasmic reticulum (ER), Golgi apparatus, endosomes, vacuoles, mitochondria, peroxisomes, lipid droplets, and autophagosomes. The protocol presented here describes the procedures for using these markers in yeast, including DNA preparation for yeast transformation, selection and evaluation of transformants, fluorescent microscopic observation, and the expected outcomes. The text is geared toward researchers who are entering the field of yeast organelle study from other backgrounds. Essential steps are covered, as well as technical notes about microscope hardware considerations and several common pitfalls. It provides a starting point for people to observe yeast subcellular entities by live-cell fluorescent microscopy. These tools and methods can be used to identify protein subcellular localization and track organelles of interest in time-lapse imaging.
MeSH term(s)	Biomarkers/metabolism ; Coloring Agents/metabolism ; Endoplasmic Reticulum/metabolism ; Golgi Apparatus/metabolism ; Humans ; Mitochondria/metabolism ; Organelles/metabolism ; Peroxisomes/metabolism ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Biomarkers ; Coloring Agents
Language	English
Publishing date	2022-04-20
Publishing country	United States
Document type	Journal Article ; Video-Audio Media ; Research Support, Non-U.S. Gov't
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/63846
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Article ; Online: Assays for Autophagy III: Observing Dynamic Protein Trafficking.

Zhu, Jing / Xie, Zhiping

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

2020 Volume 2196, Page(s) 211–222

Abstract: Macroautophagy, by its very nature, is a protein trafficking process. Cargos are transported and processed. Atg proteins come and go. In this chapter, we present three assays to monitor these dynamic events: a non-radioactive pulse-chase labeling assay ... ...

Abstract	Macroautophagy, by its very nature, is a protein trafficking process. Cargos are transported and processed. Atg proteins come and go. In this chapter, we present three assays to monitor these dynamic events: a non-radioactive pulse-chase labeling assay to monitor the transport of prApe1 and two fluorescent microscopy-based assays to assess the trafficking of Atg8 and Atg9.
MeSH term(s)	Autophagosomes/metabolism ; Autophagy ; Autophagy-Related Proteins/metabolism ; Microscopy, Fluorescence ; Protein Transport ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Vesicular Transport Proteins/metabolism
Chemical Substances	Autophagy-Related Proteins ; Saccharomyces cerevisiae Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2020-08-13
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0868-5_16
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Article: Geometric Modeling of Rosa roxburghii Fruit Based on Three-Dimensional Point Cloud Reconstruction

Xie, Zhiping / Lang, Yancheng / Chen, Luqi

Journal of food quality. 2021 Sept. 29, v. 2021

2021

Abstract: Fruit three-dimensional (3D) model is crucial to estimating its geometrical and mechanical properties and improving the level of fruit mechanical processing. Considering the complex geometrical features and the required model accuracy, this paper ... ...

Abstract	Fruit three-dimensional (3D) model is crucial to estimating its geometrical and mechanical properties and improving the level of fruit mechanical processing. Considering the complex geometrical features and the required model accuracy, this paper proposed a 3D point cloud reconstruction method for the Rosa roxburghii fruit based on a three-dimensional laser scanner, including 3D point cloud generation, point cloud registration, fruit thorns segmentation, and 3D reconstruction. The 3D laser scanner was used to obtain the original 3D point cloud data of the Rosa roxburghii fruit, and then the fruit thorns data were removed by the segmentation algorithm combining the statistical outlier removal and radius outlier removal. By analyzing the effects of five-point cloud simplification methods, the optimal simplification method was determined. The Poisson reconstruction algorithm, the screened Poisson reconstruction algorithm, the greedy projection triangulation algorithm, and the Delaunay triangulation algorithm were utilized to reconstruct the fruit model. The number of model vertices, the number of facets, and the relative volume error were used to determine the best reconstruction algorithm. The results indicated that this model can better reconstruct the actual surface of Rosa roxburghii fruit. The method provides a reference for the related application.
Keywords	Rosa roxburghii ; algorithms ; data collection ; food quality ; fruits ; geometry ; models ; scanners
Language	English
Dates of publication	2021-0929
Publishing place	Hindawi
Document type	Article
ZDB-ID	2175284-9
ISSN	1745-4557
ISSN	1745-4557
DOI	10.1155/2021/9990499
Database	NAL-Catalogue (AGRICOLA)

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