| 1. |
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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. |
- Chen, Y. B., et al.
(author)
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Inhibitory effects of endomorphin-2 on excitatory synaptic transmission and the neuronal excitability of sacral parasympathetic preganglionic neurons in young rats
- 2015
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In: Frontiers in Cellular Neuroscience. - : Frontiers Media SA. - 1662-5102. ; 9
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Journal article (peer-reviewed)abstract
- The function of the urinary bladder is partly controlled by parasympathetic preganglionic neurons (PPNs) of the sacral parasympathetic nucleus (SPN). Our recent work demonstrated that endomorphin-2 (EM-2)-immunoreactive (IR) terminals form synapses with mu-opioid receptor (MOR)-expressing PPNs in the rat SPN. Here, we examined the effects of EM-2 on excitatory synaptic transmission and the neuronal excitability of the PPNs in young rats (24-30 days old) using a whole-cell patch-clamp approach. PPNs were identified by retrograde labeling with the fluorescent tracer tetramethylrhodamine-dextran (TMR). EM-2 (3 mu M) markedly decreased both the amplitude and the frequency of the spontaneous and miniature excitatory postsynaptic currents (sEPSCs and mEPSCs) of PPNs. EM-2 not only decreased the resting membrane potentials (RMPs) in 61.1% of the examined PPNs with half maximal response at the concentration of 0.282 mu M, but also increased the rheobase current and reduced the repetitive action potential firing of PPNs. Analysis of the current voltage relationship revealed that the EM-2-induced current was reversed at -95 +/- 2.5 mV and was suppressed by perfusion of the potassium channel blockers 4-aminopyridine (4 AP) or BaCl2 or by the addition of guanosine 5'-[beta-thioldiphosphate trilithium salt (GDP-beta-S) to the pipette solution, suggesting the involvement of the G-protein-coupled inwardly rectifying potassium (GIRK) channel. The above EM-2-invoked inhibitory effects were abolished by the MOR selective antagonist D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2 (CTOP), indicating that the effects of EM-2 on PPNs were mediated by MOR via pre- and/or post-synaptic mechanisms. EM-2 activated pre- and post-synaptic MORs, inhibiting excitatory neurotransmitter release from the presynaptic terminals and decreasing the excitability of PPNs due to hyperpolarization of their membrane potentials, respectively. These inhibitory effects of EM-2 on PPNs at the spinal cord level may explain the mechanism of action of morphine treatment and morphine-induced bladder dysfunction in the clinic.
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| 4. |
- Ma, Jiang, et al.
(author)
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Investigating hollandite-perovskite composite ceramics as a potential waste form for immobilization of radioactive cesium and strontium
- 2021
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In: Journal of Materials Science. - : Springer Nature. - 0022-2461 .- 1573-4803. ; 56:16, s. 9644-9654
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Journal article (peer-reviewed)abstract
- Ceramic matrix containing zirconolite, hollandite, and perovskite phases is proposed as a potential host for HLW immobilization. Hollandite phase principally immobilizes Cs, while perovskite phase mainly immobilizes Sr. In this study, hollandite–perovskite composite ceramics are considered as a specialized waste form for immobilizing the separated Cs and Sr from HLW streams and synthesized by a solid-state reaction method at 1300 °C for 5 h. The phase compositions of the synthesized composites were characterized by XRD and BSE. The XRD results indicated that the as-prepared ceramics are composed of tetragonal hollandite Ba0.8Cs0.4Al2Ti6O16, cubic perovskite SrTiO3, alongside a lesser amount of TiO2. The BSE—EDX results confirm that Cs partitions into the hollandite matrix, while Sr incorporates into perovskite host with homogenous distribution. In addition, aqueous durability testing was carried out using the MCC-1 static leach test method. The normalized release rates of Cs and Sr in HP-3 sample (i.e., 75 wt% Ba0.8Cs0.4Al2Ti6O16 + 25 wt% SrTiO3) were < 10−2 g·m−2·d−1 after 42 days, exhibiting excellent chemical durability. These results indicate that the hollandite–perovskite ceramic matrix could be considered as a customized host matrix for immobilization of the separated Cs and Sr from HLW streams.
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| 5. |
- Wang, Lijing, et al.
(author)
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Antioxidant High-Conductivity Copper Pastes Based on Core-Shell Copper Nanoparticles for Flexible Printed Electronics
- 2023
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In: Advanced Functional Materials. - : John Wiley & Sons. - 1616-301X .- 1616-3028. ; 33:26
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Journal article (peer-reviewed)abstract
- As a nontoxic and cost-effective material, copper pastes have attracted great attention in both academia and industry. However, achieving the long-term stability of copper pastes remains challenging due to their susceptibility to oxidation. Therefore, stable copper nanoparticles with a Cu(0)-Cu(I) core-shell structure containing a surface passivation layer of formate ions-involved Cu(I) coordination polymers are developed. Based on the self-reducing nature of the passivation layer, the nanoparticle-based copper pastes can be sintered in <1 min, showing high electrical conductivity (220 000 S cm(-1)), mechanical flexibility, and long-term stability after sintering. The excellent properties of the developed copper pastes are even comparable with the ones of silver pastes. These stable copper pastes have broad applications in printed electronics (e.g., glucose sensors, RFID tags, and electromagnetic shielding films), showing great potential in the fabrication of flexible printed electronics.
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| 6. |
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| 7. |
- Erdem, Cemal, et al.
(author)
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Proteomic screening and lasso regression reveal differential signaling in insulin and insulin-like growth factor I (IGF1) pathways
- 2016
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In: Molecular & Cellular Proteomics. - : Elsevier. - 1535-9476 .- 1535-9484. ; 15:9, s. 3045-3057
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Journal article (peer-reviewed)abstract
- Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro.
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| 8. |
- Gao, Xin-Fen, et al.
(author)
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Three new species of Corydalis (Fumariaceae) from northwestern Sichuan China
- 2008
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In: Novon. - : Missouri Botanical Garden Press. - 1055-3177 .- 1945-6174. ; 18:3, s. 330-335
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Journal article (peer-reviewed)abstract
- The jiuding Ridge (Sichuan, China) has been explored during the past several years by a team from chengdu Institute of Biology. Chinese Academy of Sciences, and three undescribed species of Corydalis DC. (Fumariaceae) have been revealed and are apparently endemic to this mountain. The new species were observed in forest (C. capitata X.F. Cao, Liden & Y.W. Wang), and alpine rocky limestone areas (C. schistostigma X.F. Cao, Liden, Y.W. Wang & Y.L. Peng). The two first species have their closest relatives in the Wolong-Balangshan District in the Wolong-Balangshan District (Wenchuan. Sichuan). Corydalis aeaeae differs from C. panada Liden & Y.W. Wang in its small size, few-flowered racemes, and broadly obtuse outer petals with low, short erests. Corydalis capitata differs from the C. flexuosa Franchet complex in the capitate racemes, small flowers with deeply serrate petals, and the peculiar, thin, strictly ecect lateral branches. corydalis schistostinma is unique in the C. curviflora Maximowicz ex Hemsley group, in the deeply cleft stigma and very forward-projecting crests to the inner petals, and possibly has iits affinities more to the north and northwest in the Hengduan Mountains.
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| 9. |
- 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
-
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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| 10. |
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| 11. |
- Ma, Jiang-Jiang, et al.
(author)
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High-Temperature Mechanical and Dynamical Properties of gamma-(U,Zr) Alloys
- 2023
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In: Materials. - : MDPI. - 1996-1944. ; 16:7
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Journal article (peer-reviewed)abstract
- High-temperature body-centered cubic (BCC) gamma-U is effectively stablized by gamma-(U,Zr) alloys that also make it feasible to use it as a nuclear fuel. However, relatively little research has focused on gamma-(U,Zr) alloys due to their instability at room temperature. The effect of Zr composition on its mechanical properties is not clear yet. Herein, we perform molecular dynamics simulations to investigate the mechanical and dynamical stabilities of gamma-(U,Zr) alloys under high temperatures, and we calculate the corresponding lattice constants, various elastic moduli, Vickers hardness, Debye temperature, and dynamical structure factor. The results showed that gamma-U, beta-Zr, and gamma-(U,Zr) are all mechanically and dynamically stable at 1200 K, which is in good agreement with the previously reported high-temperature phase diagram of U-Zr alloys. We found that the alloying treatment on ?-U with Zr can effectively improve its mechanical strength and melting points, such as Vickers hardness and Debye temperature, making it more suitable for nuclear reactors. Furthermore, the Zr concentrations in gamma-(U,Zr) alloys have an excellent effect on these properties. In addition, the dynamical structure factor reveals that gamma-U shows different structural features after alloying with Zr. The present simulation data and insights could be significant for understanding the structures and properties of UZr alloy under high temperatures.
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| 12. |
- Wang, Kai-Tuo, et al.
(author)
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Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA
- 2012
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 40:11, s. 48-5138
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Journal article (peer-reviewed)abstract
- The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.
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| 13. |
- Wang, Mei jun, et al.
(author)
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SIRT1-dependent deacetylation of Txnip H3K9ac is critical for exenatide-improved diabetic kidney disease
- 2023
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In: Biomedicine and Pharmacotherapy. - 0753-3322. ; 167
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Journal article (peer-reviewed)abstract
- Glucagon-like peptide 1 receptor agonist exenatide (exendin-4) has potential protective capabilities against diabetic kidney disease (DKD). However, the underlying mechanism has not been fully elucidated. The expression of thioredoxin-interacting protein (Txnip) is upregulated during DKD progression by histone acetylation. Sirtuin 1 (SIRT1) is a deacetylase and is decreased in DKD, which indicates that it may regulate Txnip in this disease. Here, we used whole-body heterozygous Sirt1 knockout (Sirt1+/-) and kidney-specific Sirt1 knockout (KSK) mice to investigate whether SIRT1 regulates Txnip via histone deacetylation in DKD and exenatide-alleviated DKD. Exenatide substantially improved renal pathological damage, decreased the albumin-to-creatinine ratio (ACR), upregulated SIRT1 expression, and downregulated Txnip expression in kidneys of high-fat diet-treated C57BL/6J mice. However, these effects diminished in Sirt1+/- and KSK mice under exenatide treatment. The downregulation of Txnip expression by exendin-4 in high-glucose-treated SV40 MES13 cells was hampered during Sirt1 knockdown. These results demonstrate that kidney SIRT1 is indispensable in exenatide-improved DKD and downregulation of Txnip expression. Exendin-4 mechanistically downregulated Txnip histone 3 lysine 9 acetylation (H3K9ac) in a SIRT1-dependent manner and decreased spliced X-box binding protein 1 (XBP1s) recruitment to the Txnip promoter. These findings provide epigenetic evidence elucidating the specific mechanism for exenatide-mediated DKD alleviation and highlight the importance of Txnip as a promising therapeutic target for DKD.
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| 14. |
- Wang, Yong, et al.
(author)
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Developing Platform Supply Chain Contract Coordination and a Numerical Analysis Considering Fresh-Keeping Services
- 2023
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In: Sustainability. - : MDPI AG. - 2071-1050. ; 15:18
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Journal article (peer-reviewed)abstract
- With changes in demand and the emergence of new distribution channels, consumer-centric buyer’s markets for many products have been formed. The platform supply chain has been continuously optimized and upgraded. Supply chain leaders have moved downstream to the end of the supply chain. The operational value has been further enhanced. The corresponding systematic construction of the platform supply chain has become an important driving force for future development. The model in this paper is different from the traditional supply chain contract model, which mainly focuses on suppliers or demand. In order to meet the requirements of fresh-keeping services and the goal of revenue sharing, we integrate the production and circulation characteristics of fresh produce into the design of a contract model. In this paper, a revenue-sharing contract model of the fresh produce supply chain is constructed based on the core position of retailers, the uncertainty of the market size, and the consideration of a fresh-keeping service. The model is mainly composed of the core retailer and the supplier. Through further numerical analysis, we verify the effectiveness of the revenue-sharing contract model in supply chain coordination. We also analyze the change trends in the optimal retail price, optimal freshness level, and optimal order quantity caused by changes in both the fresh-keeping service capacity and the revenue-sharing coefficient. The results show that after changing these two parameters, the supply chain can achieve coordination under the specified parameter values. The changed parameters will also lead to certain change trends in the optimal retail price, optimal freshness level, and optimal order quantity, and will have a corresponding impact on the stability of supply chain operation. This research provides a relevant theoretical and empirical basis for a fresh produce supply chain contract model with retailers at the core position. We also provide guidance and reference for optimizing the supply chain management mode and improving the overall operational efficiency of the fresh produce supply chain.
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| 15. |
- Wang, Zhenqian, et al.
(author)
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Northward migration of the East Asian summer monsoon northern boundary during the twenty-first century
- 2022
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12
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Journal article (peer-reviewed)abstract
- The northern fringe area of the East Asian summer monsoon (EASM) between arid and semiarid regions is a fragile eco-environment zone and ecological transition zone, and it is highly sensitive to climate change. Predicting the future migration of the northern boundary of the EASM is important for understanding future East Asian climate change and formulating of decisions on ecological protection and economic development in arid and semiarid regions. The reanalysis dataset and simulations of 23 models from the Coupled Models Intercomparison Project Phase 6 (CMIP6) were used to investigate the response of the boundary of the ESAM to the global warming. The multi-model ensemble showed a northwestward migration of the EASM northern boundary during the near-term (2020–2060) and late-term (2061–2099) of the twenty-first century under various Shared Socioeconomic Pathways (SSPs). The northern boundary migrated northwestward by 23–28 and 74–76 km in the near-term and late-term respectively, under SSP1-2.6, 2-4.5 and 3-7.0 and by ~ 44 km and ~ 107 km respectively during the near-term and late-term under SSP5-8.5. During the twenty-first century, under various SSPs, the surface of the East Asian subcontinent warmed more than the ocean, thereby increasing the contrast of near-surface temperature and sea level pressure in summer between the East Asian subcontinent and the surrounding oceans. In turn, the intensified land–sea thermal contrast reinforced the EASM meridional circulation and thus transported more moisture from the Indian Ocean into northern China. Additionally, a poleward migration and weakening of the East Asian subtropical westerly jet would also favor an increase in precipitation, eventually caused a northwestward migration of the EASM northern boundary. The results suggest that the arid and semiarid ecotone will become wetter, which could dramatically improve the eco-environment in the future.
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| 16. |
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