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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Chen, Jian, et al.
(author)
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AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling
- 2018
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In: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 3:3, s. 302-309
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Journal article (peer-reviewed)abstract
- Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barre syndrome(1,2). While progress has been made in understanding the causal link between ZIKV infection and microcephaly(3-9), the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role of AXL, a TAM family kinase receptor that was initially described as the entry receptor for ZIKV(10-22). Here, we show that while genetic ablation of AXL protected primary human astrocytes and astrocytoma cell lines from ZIKV infection, AXL knockout did not block the entry of ZIKV. We found, instead, that the presence of AXL attenuated the ZIKV-induced activation of type I interferon (IFN) signalling genes, including several type I IFNs and IFN-stimulating genes. Knocking out type I IFN receptor alpha chain (IFNAR1) restored the vulnerability of AXL knockout astrocytes to ZIKV infection. Further experiments suggested that AXL regulates the expression of SOCS1, a known type I IFN signalling suppressor, in a STAT1/STAT2-dependent manner. Collectively, our results demonstrate that AXL is unlikely to function as an entry receptor for ZIKV and may instead promote ZIKV infection in human astrocytes by antagonizing type I IFN signalling.
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| 4. |
- Chen, Jian, et al.
(author)
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Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects
- 2017
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In: Emerging Microbes & Infections. - : NATURE PUBLISHING GROUP. - 2222-1751. ; 6
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Journal article (peer-reviewed)abstract
- Zika virus (ZIKV) infection can cause fetal developmental abnormalities and Guillain-Barre syndrome in adults. Although progress has been made in understanding the link between ZIKV infection and microcephaly, the pathology of ZIKV, particularly the viral reservoirs in human, remains poorly understood. Several studies have shown that compared to serum samples, patients' urine samples often have a longer duration of ZIKV persistency and higher viral load. This finding suggests that an independent viral reservoir may exist in the human urinary system. Despite the clinical observations, the host cells of ZIKV in the human urinary system are poorly characterized. In this study, we demonstrate that ZIKV can infect renal proximal tubular epithelial cells (RPTEpiCs) in immunodeficient mice in vivo and in both immortalized and primary human renal proximal tubular epithelial cells (hRPTEpiCs) in vitro. Importantly, ZIKV infection in mouse kidneys caused caspase-3-mediated apoptosis of renal cells. Similarly, in vitro infection of immortalized and primary hRPTEpiCs resulted in notable cytopathic effects. Consistent with the clinical observations, we found that ZIKV infection can persist with prolonged duration in hRPTEpiCs. RNA-Seq analyses of infected hRPTEpiCs revealed a large number of transcriptional changes in response to ZIKV infection, including type I interferon signaling genes and anti-viral response genes. Our results suggest that hRPTEpiCs are a potential reservoir of ZIKV in the human urinary system, providing a possible explanation for the prolonged persistency of ZIKV in patients' urine.
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| 5. |
- Li, Biao, et al.
(author)
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Voltage-Price Coupling in Distribution Networks
- 2024
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In: IEEE Transactions on Smart Grid. - : Institute of Electrical and Electronics Engineers (IEEE). - 1949-3053 .- 1949-3061. ; 15:2, s. 1438-1449
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Journal article (peer-reviewed)abstract
- Demand-side users are practical and economical resources for participating in voltage regulation of distribution networks, whose regulation effect is closely related to the price. This paper proposes a novel voltage-price coupling (VPC) mechanism to construct a fair voltage-based nodal pricing method for distribution networks to encourage demand-side users to participate in voltage regulation to improve voltage quality. The voltage impact factor is established to fairly characterize the impact of each nodal power on the voltage deviation in the distribution network. Further, the VPC mechanism is constructed to highly couple the nodal price with the voltage in both spatial and time dimensions by establishing distribution rules of prices at different nodes and different horizons. The VPC mechanism forms a fair and adaptable voltage-based nodal pricing method for distribution networks, which also considers the impact on the existing pricing mechanism, and the balance between the voltage regulation effect and user experience. Then, a price-driven voltage regulation (PVR) model is proposed for the distribution network to reduce voltage deviations and user costs, which integrates the demand-side resource management, voltage regulation, and voltage-based nodal pricing. Case studies verify the effectiveness of the VPC mechanism and the PVR model.
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| 6. |
- Peng, Ningxin, et al.
(author)
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Platelet mitochondrial DNA methylation : A novel biomarker for myocardial infarction – A preliminary study
- 2023
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In: International Journal of Cardiology. - 0167-5273.
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Journal article (peer-reviewed)abstract
- Background: Platelet activation and thrombus formation play critical roles in the pathogenesis of myocardial infarction (MI). In addition to their role in energy production, platelet mitochondria also regulate cellular functions related to apoptosis, oxidative stress, and inflammation. Epigenetic modifications of platelet mitochondrial DNA (mtDNA) may influence platelet function and are believed to be an important factor in MI. Therefore, the aim of this study was to investigate the differences in platelet mtDNA methylation levels between MI patients and controls. Methods: The present study utilized propensity score matching to generate 45 multivariate matched apparently healthy controls for 45 patients with newly-onset acute MI. Platelet mtDNA methylation levels were assessed through bisulfite-PCR pyrosequencing and compared between the two groups, with further adjustments made in the sensitivity analysis. Results: Among the measured mitochondrial genes (MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-ATP6 and tRNA_Leu), patients with MI exhibited statistically significant differences in mtDNA methylation levels as compared to matched controls. Specifically, higher levels of mtDNA methylation were observed in MT-COX1, MT-COX3, and tRNA_Leu, while a lower level was observed in MT-ATP6 (all p < 0.0001). These results remained robust in the sensitivity analysis. Conclusion: Our study demonstrated significant variations in platelet mtDNA methylation levels between patients with MI and controls. Platelet mtDNA methylation may serve as a novel biomarker for MI. This observation also provided some insights into the etiology of MI.
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| 7. |
- Peng, Xu-Biao, et al.
(author)
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Application of topological soliton in modeling protein folding : Recent progress and perspective
- 2020
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In: Chinese Physics B. - : IOP Publishing. - 1674-1056. ; 29:10
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Research review (peer-reviewed)abstract
- Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone C(alpha)chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.
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| 8. |
- Zhao, Shijing, et al.
(author)
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Elucidating the reaction pathway of crystalline multi-metal borides for highly efficient oxygen-evolving electrocatalysts
- 2022
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In: Journal of Materials Chemistry A. - : ROYAL SOC CHEMISTRY. - 2050-7488 .- 2050-7496. ; 10:3, s. 1569-1578
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Journal article (peer-reviewed)abstract
- Understanding the fundamental principle of catalytic performance and the mechanism of multimetal-based electrocatalysts is essential for the rational design of advanced renewable energy systems. Here, highly crystalline MMMoB4 (M = Fe, Co) compounds with controllable compositions of multiple active metal atoms and polyacene-type boron networks were synthesized delicately by a one-step high-pressure technique to explore electrocatalytic selectivity and activity. CoFeMoB4 and Co2MoB4 are revealed to be highly active and durable oxygen evolution reaction (OER) electrocatalysts under alkaline conditions. The mutually promotive activation of metals with amorphous clusters and ultra-small grains on the surface are responsible for the enhanced activity of CoFeMoB4. More specifically, Co and Fe coupling in CoFeMoB4 facilitates surface reconstruction into active Co hydroxide and Fe oxyhydroxide, in contrast to Co oxyhydroxide in Co2MoB4 and Fe oxides in Fe2MoB4. Dissolving Mo may provide potential space for adsorbing hydroxyl, and the optimized electronic structure with boron is mainly responsible for the long-term durability. In contrast, Mo atoms are responsible for hydrogen evolution reaction (HER) properties, and the optimized d-band center and density of states at the Fermi level make Co2MoB4 a superior HER catalyst. Our findings provide insight into distinguishing the catalytic pathway of multi-metal borides with improved OER activity and different roles of Mo and Co/Fe in the HER and OER.
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