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| 2. |
- 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. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 4. |
- Sun, Fengbo, et al.
(author)
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1,5-Diiodocycloctane: a cyclane solvent additive that can extend the exciton diffusion length in thick film organic solar cells
- 2024
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In: Energy and Environmental Sciences. - 1754-5692 .- 1754-5706. ; 17:5, s. 1916-1930
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Journal article (peer-reviewed)abstract
- The short exciton diffusion length associated with most state-of-the-art organic semiconductors used in organic solar cells (OSCs) imposes severe limits on the exciton transport in the larger donor/acceptor domains and the exciton dissociation at the interface, which hinder further improvements in the power conversion efficiencies (PCE) of the thick-film devices. In this study, a new cyclane, 1,5-diiodocycloctane (DICO), was employed as a solvent additive to effectively extend the exciton LD within the bulk-heterojunction blend, which can function with the multiple photovoltaic materials system. Due to the great enhancement of molecular stacking and exclusively large domain sizes of photovoltaic materials with the assistance of the DICO additive, the trap density in devices is significantly reduced, thereby nearly doubling the LD in the thick film OSCs. Notably, the DICO-processed PM6/L8-BO-based OSC showed high thickness tolerance for the bulk-heterojunction (BHJ) layer, delivering a high PCE of 19.1% in the case of a 110 nm thick film and still maintaining an excellent PCE of 17.2% in the case of a 300 nm thick film. Crucially, a noticeably increased stability of the multiple materials system was observed in the DICO-processed OSCs. These findings enrich the additive family with new cyclane systems to extend the exciton LD in thick film OSCs with high performance.
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| 5. |
- 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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| 6. |
- Wang, Longxin, et al.
(author)
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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)
- 2023
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Journal article (peer-reviewed)abstract
- The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.
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| 7. |
- Yang, Dong, et al.
(author)
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Air- and Light-Stable P-4 and As-4 within an Anion-Coordination-Based Tetrahedral Cage
- 2017
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In: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 139:16, s. 5946-5951
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Journal article (peer-reviewed)abstract
- In contrast to the stable dinitrogen molecule, white phosphorus (P-4) and yellow arsenic (As-4) are very reactive allotropic modifications of these two heavier pnictogen elements, which has greatly hampered the study of their properties and applications. Thus, the safe storage and transport of them is imperative. Supramolecular caged structures are one of the most efficient approaches for the encapsulation and stabilization of reactive species; however, their use in the P-4 and As-4 chemistry is very rare. In the current work, we demonstrate a new design strategy for constructing finite cages and including guests based on anion coordination chemistry. The phosphate-coordination-based tetrahedral cages can readily accommodate the tetrahedral guests P-4 and As-4, which is facilitated by the shape and size complementarity as well as favorable sigma-pi and lone-pair-pi interactions. Moreover, the latter case represents the first example of As-4 inclusion in a well-defined tetrahedral cage.
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| 8. |
- Yang, Dong, et al.
(author)
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Encapsulation of Halocarbons in a Tetrahedral Anion Cage
- 2015
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In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 54:30, s. 8658-8661
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Journal article (peer-reviewed)abstract
- Caged supramolecular systems are promising hosts for guest inclusion, separation, and stabilization. Well-studied examples are mainly metal-coordination-based or covalent architectures. An anion-coordination-based cage that is capable of encapsulating halocarbon guests is reported for the first time. This A(4)L(4)-type (A=anion) tetrahedral cage, [(PO4)(4)L-4](12-), assembled from a C-3-symmetric tris(bisurea) ligand (L) and phosphate ion (PO43-), readily accommodates a series of quasi-tetrahedral halocarbons, such as the Freon components CFCl3, CF2Cl2, CHFCl2, and C(CH3)F-3, and chlorocarbons CH2Cl2, CHCl3, CCl4, C(CH3)Cl-3, C(CH3)(2)Cl-2, and C(CH3)(3)Cl. The guest encapsulation in the solid state is confirmed by crystal structures, while the host-guest interactions in solution were demonstrated by NMR techniques.
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| 9. |
- Zhao, Jie, et al.
(author)
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Phosphate-induced fluorescence of a tetraphenylethene-substituted tripodal tris(urea) receptor
- 2016
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In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 45:17, s. 7360-7365
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Journal article (peer-reviewed)abstract
- A tetraphenylethene (TPE)-decorated tripodal tris(urea) ligand L was synthesized, which shows large emission enhancement when binding to an orthophosphate anion (PO43-), but exhibits only weak or no fluorescence with other anions. The anion-binding and fluorescence properties were studied by X-ray crystal structure, NMR and fluorescence spectroscopy, and by DFT computations and the results demonstrate that the different fluorescence performance may be determined by the anion-binding modes (i.e., full-or half-encapsulation).
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| 10. |
- Zhao, Yan, et al.
(author)
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Objective sleep characteristics and continuous glucose monitoring profiles of type 2 diabetes patients in real-life settings
- 2023
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In: Diabetes, obesity and metabolism. - : John Wiley & Sons. - 1462-8902 .- 1463-1326. ; 25:3, s. 823-831
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Journal article (peer-reviewed)abstract
- BACKGROUND: Given the significant role of sleep in glycemic control, the association between sleep and glycemic variability determined by continuous glucose monitoring (CGM) is worth investigating among patients with type 2 diabetes (T2D).METHODS: CGM was carried out among 28 T2D patients (aged 62.3±4.8 years, 57% women). Sleep characteristics were assessed by actigraphy within the CGM period. CGM-derived outcomes included glucose level, percentages of time in range (TIR) and time above range (TAR) during the monitoring period. Associations between intraindividual night-to-night variations of sleep characteristics and overall CGM outcomes were analyzed by linear regression. Associations between sleep characteristics in each night and time-matched CGM outcomes were analyzed by linear mixed models.RESULTS: A total 249 person-days of CGM coupled with 221 nights of sleep characteristics were documented. Greater standard deviation (SD) of objective sleep duration (minutes) between measurement nights was associated with higher glucose level (mmol/L, Coefficient [95% CI]: 0.018 [0.004, 0.033], P=0.017), smaller proportion of TIR (% in observation period, -0.20 [-0.36, -0.03], P=0.023), and greater proportion of TAR (0.22 [0.06, 0.39], P=0.011). Later sleep midpoint (minutes from 00:00) was associated with greater SD of glucose during the same sleep period (0.002 [0.0001, 0.003], P=0.037), longer nocturnal sleep duration was associated with smaller coefficient of variance of glucose level in the upcoming day (%, -0.015 [-0.03, -0.001], P=0.041).CONCLUSION: Objectively-determined sleep duration and sleep midpoint, as well as their daily variability, are associated with CGM-derived glucose profiles in T2D patients.
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