We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment ...indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets,
N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Sustainable growth of the lithium-ion battery (LIB) industry requires a safe supply of raw materials and proper end-of-life management for products. The lack of research on domestic critical raw ...materials and on management systems has limited the formulation of relevant policies for LIB-related industries. Here, a critical raw material (CRM) evaluation model was developed to identify the criticality associated with the supply risk (SR) and economic importance (EI) of different materials for the Chinese LIB industry. Dynamic materials flow analyses of the relevant critical materials were carried out by integrating a trade-linked model. Criticality analysis identifies the importance of different materials and optimizes the subsequent materials flow analysis. The results showed that the in-use stocks share large portions of material flow for Li, Ni, Co and graphite and further suggests that the market will not be saturated before 2025. For the end-of-life stage, less than 40 wt% of the materials in LIBs can be recycled under the current scheme of materials flow in China; this finding puts significant pressure on proper waste management. Consequently, it is very important to identify effective methods for utilizing the growing amount of waste materials and to provide a resource supplement for the Chinese LIB industry. This research provides guidelines for improving management strategies relevant to the critical materials in the LIB industry, for increasing resource efficiency, and for managing critical resources.
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•MFA for multiple elements in LIB industry is still scattered.•A CRMs evaluation system was proposed to optimize the further MFA.•Sankey diagrams of Li, Co, Ni and C reveal their status in Chinese LIB industry.•The stock and obsolete amount from 2012 to 2025 were estimated and forecasted.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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•Increasing the melt-spinning speed to 50 m/s refines the grain size.•Changing the crystallization process is the mechanism of grain refinement.•The size of equiaxed grains in the ...annealed ribbons is reduced to 50–200 nm.•The intense exchange coupling effect contributes to the higher remanence.•The microstructure evolution models are proposed.
Given the uneven grain size distribution in the ribbons melt-spun at 25 m/s, the strategy of improving the microstructure and magnetic properties of the ribbons by increasing the melt-spinning speed is discussed. The experimental results show that the grain size of Nd13.65Fe73.55B5.6Co6.6Ga0.6 ribbons annealed at 700 °C is reduced to 50–200 nm by melt-spinning at 50 m/s. The change in the crystallization process is the primary mechanism for grain refinement. At high quenching speed, the amorphous matrix is formed first in the as-spun ribbons, and then uniform crystallization can be achieved through annealing. Compared to the annealed ribbons melt-spun at 25 m/s, the Mr and M2T increased by ∼8 % due to the intense exchange coupling effect and the refined grains.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Sedimentary fecal sterols and other sterol biomarkers, combined with bulk total organic carbon (TOC) and its stable carbon isotope were applied to characterize the sewage contamination across a ca. ...280 km transect from the Xiaoqing River to the Laizhou Bay, a typical river-estuary system subjected to extensive anthropogenic stress due to rapid regional urbanization and industrialization in eastern China. Two sampling events were performed in both spring and summer seasons in the Laizhou Bay adjacent to the Xiaoqing River in order to assess the potential seasonal variation. Fecal sterols such as coprostanol and epicoprostanol, which are typical indicators of anthropogenic sewage input, displayed high concentrations of up to 63.2 μg g−1 dry weight (dw) and 13.1 μg g−1 dw, respectively. Results suggested that most of the stations along the Xiaoqing River were severely contaminated by fecal inputs with a decreasing trend from the river to the estuary that was mainly explained by the increasing distance from the diffuse sewage sources and the gradual dilution by sea water. Although there was no significant difference in fecal sterol concentrations between spring and summer in the Laizhou Bay, suggestive of no significant difference in sewage abundance, significantly higher average epicoprostanol/coprostanol and lower coprostanol/epicoprostanol ratios were observed in spring than summer, indicative of different sewage sources (e.g., human vs. non-human). Seasonal discharge and land-runoff, air temperature related to microbial activity differences and different extend of animal manure irrigation during agricultural planting could be additional reasons and need further investigation. Nevertheless, fecal sterol concentrations, distributions and diagnostic ratios should all be taken into consideration to better understand sewage inputs and source dynamics in river-estuary ecosystems.
The upper left panel showing the formation of 5α- and 5β-stanols is mainly modified from Bull et al., 2002. Display omitted
•Mutiple sedimentary sterols used for the sewage contamination assessment.•Higher sewage input observed in the Xiaoqing River than the Laizhou Bay.•Significant spatial instead of seasonal variation in fecal sterol concentrations observed.•Seasonal variation of two fecal sterol-based ratios observed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, ...structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.
We report the dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a COVID-19 patient: from successive negative results to successive single positive ...nucleocapsid gene, to two positive target genes (orf1ab and nucleocapsid) by RT-PCR testing of SARS-Cov-2, and describe the diagnosis, clinical course, and management of the case. In this case, negative results of RT-PCR testing was not excluded to diagnose a suspected COVID-19 patient, clinical signs and symptoms, other laboratory findings, and chest CT images should be taken into account for the absence of enough positive evidence. This case highlights the importance of successive sampling and testing SARS-Cov-2 by RT-PCR as well as the increased value of single positive target gene from pending to positive in two specimens to diagnose laboratory-confirmed COVID-19.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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•The crystallization and magnetic properties of SmCo4B-based ribbons are sensitive to melt-spinning speeds.•The critical cooling rate for forming an amorphous matrix in SmCo4B-based ...ribbons is 35–40 m/s.•A low melt-spinning speed tends to obtain uniform microstructure, while a high speed improves the magnetization.•The high content of amorphous phase in the 40 m/s ribbons forms three sizes of platelet-shaped grains during annealing.•The Mr and Ms increased by 38.5 % and 28.5 % by melt-spinning at 40 m/s.
The SmCo4B-based ribbons were melt-spun at 35 m/s and 40 m/s, respectively, and annealed at 800 °C for 30 min. The dependence of the annealed ribbons’ microstructure and magnetic properties on melt-spinning speed sensitivity was studied. The results show that the as-spun ribbons comprise an amorphous matrix and Sm-Co-B nanograins. For SmCo4B-based ribbons, the critical cooling rate to obtain an amorphous matrix is 35–40 m/s. Compared to the annealed ribbons melt-spun at 40 m/s, the formation of the uniform platelet-shaped grains in the annealed ribbons prepared at 35 m/s helps to improve coercivity but decreases the remanence and saturation magnetization. These results provide a reference for a comprehensive understanding of the relationship between the microstructure and magnetic properties of SmCo4B-based magnets.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) are prevalent throughout the world resulting in a major public health burden. In this research, we isolated and identified 28 MDR UPEC ...from one university hospital in China, investigated MDR and pathogenic mechanisms by PCR, including 55 antibiotic resistance determinants (ARDs) genes, 13 genetic markers of mobile genetic elements (MGEs) and 6 virulence factors (VFs) genes. In these isolates, we identified 23 ARDs genes and 6 genetic markers of MGEs that played a key role in MDR phenotypes. In addition, we found 2 VFs genes, hofQ and ompT, which could be associated with pathogenicity and invasiveness of these strains in urinary tract infections (UTIs).
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Protostemonine （PSN） is the main anti-inflammatory alkaloid extracted from the roots of Stemona sessilifolia （known as ＂Baibu＂ in traditional Chinese medicine）. Here, we reported the inhibitory ...effects of PSN on lipopolysaccharide （LPS）-induced macrophage activation in vitro and LPS-induced acute lung injury in mice. Macrophage cell line RAW264.7 cells and mouse bone marrow-derived macrophages （BMDMs） were treated with PSN （1, 3, 10, 30 and 100 pmol/L） for 0.5 h and then challenged with LPS （0.1 pg/mL） for 24 h. Pretreatment with PSN significantly inhibited LPS-induced phosphorylation of MAPKs and AKT, iNOS expression and NO production in the macrophages. C57BL/6 mice were intratracheally injected with LPS （5 mg/kg） to induce acute lung injury （ALl）. The mice were subsequently treated with PSN （10 mg/kg, ip） at 4 and 24 h after LPS challenge. PSN administration significantly attenuated LPS-induced inflammatory cell infiltration, reduced pro-inflammatory cytokine （TNF-α, IL-113 and IL-6） production and eliminated LPS-mediated lung edema. Furthermore, PSN administration significantly inhibited LPS-induced pulmonary MPO activity. Meanwhile, LPS-induced phosphorylation of p38 MAPK, iNOS expression and NO production in the lungs were also suppressed. The results demonstrate that PSN effectively attenuates LPS-induced inflammatory responses in vitro and in vivo; the beneficial effects are associated with the decreased phosphorylation of MAPK and AKT and the reduced expression of pro-inflammatory mediators, such as iNOS, NO and cytokines. These data suggest that PSN may be a potential therapeutic agent in the treatment of ALl.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
DNA polymerase η (Polη) facilitates translesion DNA synthesis (TLS) across ultraviolet (UV) irradiation- and cisplatin-induced DNA lesions implicated in skin carcinogenesis and chemoresistant ...phenotype formation, respectively. However, whether post-translational modifications of Polη are involved in these processes remains largely unknown. Here, we reported that human Polη undergoes O-GlcNAcylation at threonine 457 by O-GlcNAc transferase upon DNA damage. Abrogation of this modification results in a reduced level of CRL4
-dependent Polη polyubiquitination at lysine 462, a delayed p97-dependent removal of Polη from replication forks, and significantly enhanced UV-induced mutagenesis even though Polη focus formation and its efficacy to bypass across cyclobutane pyrimidine dimers after UV irradiation are not affected. Furthermore, the O-GlcNAc-deficient T457A mutation impairs TLS to bypass across cisplatin-induced lesions, causing increased cellular sensitivity to cisplatin. Our findings demonstrate a novel role of Polη O-GlcNAcylation in TLS regulation and genome stability maintenance and establish a new rationale to improve chemotherapeutic treatment.
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