MicroProteinDB: A database to provide knowledge on sequences, structures and function of ncRNA-derived microproteins.

Omics-based technologies have revolutionized our comprehension of microproteins encoded by ncRNAs, revealing their abundant presence and pivotal roles within complex functional landscapes. Here, we developed MicroProteinDB (http://bio-bigdata.hrbmu.edu.cn/MicroProteinDB), which offers and visualizes the extensive knowledge to aid retrieval and analysis of computationally predicted and experimentally validated microproteins originating from various ncRNA types. Employing prediction algorithms grounded in diverse deep learning approaches, MicroProteinDB comprehensively documents the fundamental physicochemical properties, secondary and tertiary structures, interactions with functional proteins, family domains, and inter-species conservation of microproteins. With five major analytical modules, it will serve as a valuable knowledge for investigating ncRNA-derived microproteins.

CancerProteome: a resource to functionally decipher the proteome landscape in cancer.

Advancements in mass spectrometry (MS)-based proteomics have greatly facilitated the large-scale quantification of proteins and microproteins, thereby revealing altered signalling pathways across many different cancer types. However, specialized and comprehensive resources are lacking for cancer proteomics. Here, we describe CancerProteome (http://bio-bigdata.hrbmu.edu.cn/CancerProteome), which functionally deciphers and visualizes the proteome landscape in cancer. We manually curated and re-analyzed publicly available MS-based quantification and post-translational modification (PTM) proteomes, including 7406 samples from 21 different cancer types, and also examined protein abundances and PTM levels in 31 120 proteins and 4111 microproteins. Six major analytical modules were developed with a view to describe protein contributions to carcinogenesis using proteome analysis, including conventional analyses of quantitative and the PTM proteome, functional enrichment, protein-protein associations by integrating known interactions with co-expression signatures, drug sensitivity and clinical relevance analyses. Moreover, protein abundances, which correlated with corresponding transcript or PTM levels, were evaluated. CancerProteome is convenient as it allows users to access specific proteins/microproteins of interest using quick searches or query options to generate multiple visualization results. In summary, CancerProteome is an important resource, which functionally deciphers the cancer proteome landscape and provides a novel insight for the identification of tumor protein markers in cancer.

A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling.

Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein-ligand complex studies.

Thermostable and nonflammable polyimide/zirconia compound separator for lithium-ion batteries with superior electrochemical and safe properties.

Separators are applied to segregate cathode and anode, and provide ion transport channels in lithium-ion batteries (LIBs). Nevertheless, present commercial polyolefin separators represent high thermal shrinkage and inferior electrolyte wettability, seriously limiting wider development of LIBs. In this work, we prepared zirconia (ZrO2) nanolayer encapsulated polyimide (PI) nanofiber compound separator through in-situ polar adsorption and hydrolysis strategy. The obtained PI/ZrO2 compound separator has superior thermal stability, electrolyte wettability and flame retardance in comparison with polypropylene (PP) separator. The shrinkage ratio of prepared PI/ZrO2 compound separator is 0 even at 300 °C, while the PP separator significantly shrank at 160 °C. Furthermore, the ionic conductivity of PI/ZrO2 separator reaches up to 1.32 mS cm-1, far higher than 0.34 mS cm-1 of PP separator. Besides, the coin batteries of LiNi0.8Co0.1Mn0.1O2 (NCM811)/electrolyte-separator/lithium (Li) assembled with PI/ZrO2 compound separator exhibit enhanced rate performance, high discharge capacity retention rate of 88.3% after 100 cycles at 1C and excellent battery safety performance even at 140 °C. Thus, combined with its advantages, such as preparation, thermostability, electrolyte wettability, electrochemical property and safety, the PI/ZrO2 compound separator exhibits promising prospect in the application of commercial LIBs.

FAP-α+ immunofibroblasts in oral lichen planus promote CD4+ T-cell infiltration via CCL5 secretion.

Oral lichen planus (OLP) is a T cell-mediated, chronic inflammatory disease. CD4+ T-cell infiltration plays a crucial role in the pathogenesis of OLP. Fibroblasts are activated under pathological conditions and perform various functions. This study was designed to explore the immune activation and biological functions of OLP fibroblasts on CD4+ T cells. We detected the expression of fibroblast activation protein-alpha (FAP-α) in the oral tissues of patients with OLP and healthy controls using immunohistochemistry. Furthermore, expression of FAP-α and C-C motif chemokine ligand 5 (CCL5) in fibroblasts isolated from oral tissues of patients with OLP and healthy controls was assayed by quantitative PCR, Western blotting and enzyme-linked immunosorbent assay. Moreover, we assessed the effects of fibroblasts on CD4+ T-cell proliferation, apoptosis and migration using flow cytometry and Transwell assays. We found that FAP-α expression in the oral tissues of patients with OLP was significantly higher than that in healthy controls. FAP-α and CCL5 expression levels were significantly upregulated in OLP fibroblasts. Moreover, OLP fibroblasts promoted CD4+ T-cell proliferation and migration and inhibited CD4+ T cell apoptosis. In summary, our findings indicate that OLP fibroblasts are immunologically activated and induce CD4+ T-cell infiltration in OLP.

Secondary aerosol formation from a Chinese gasoline vehicle: Impacts of fuel (E10, gasoline) and driving conditions (idling, cruising).

Chassis dynamometer experiments were conducted to investigate the effect of vehicle speed and usage of ethanol-blended gasoline (E10) on formation and evolution of gasoline vehicular secondary organic aerosol (SOA) using a Gothenburg Potential Aerosol Mass (Go: PAM) reactor. The SOA forms rapidly, and its concentration exceeds that of primary organic aerosol (POA) at an equivalent photochemical age (EPA) of ~1 day. The particle effective densities grow from 0.62 ± 0.02 g cm-3 to 1.43 ± 0.07 g cm-3 with increased hydroxyl radical (OH) exposure. The maximum SOA production under idling conditions (4259-7394 mg kg-fuel-1) is ~20 times greater than under cruising conditions. There was no statistical difference between SOA formation from pure gasoline and its formation from E10. The slopes in Van Krevelen diagram indicate that the formation pathways of bulk SOA includes the addition of both alcohol/peroxide functional groups and carboxylic acid formation from fragmentation. A closure estimation of SOA based on bottom-up and top-down methods shows that only 16%-38% of the measured SOA can be explained by the oxidation of measured volatile organic compounds (VOCs), suggesting the existence of missing precursors, e.g. unmeasured VOCs and probably semivolatile or intermediate volatile organic compounds (S/IVOCs). Our results suggest that applying parameters obtained from unified driving cycles to model SOA concentrations may lead to large discrepancies between modeled and ambient vehicular SOA. No reduction in vehicular `SOA production is realized by replacing normal gasoline with E10.

Humidity-Dependent Phase State of Gasoline Vehicle Emission-Related Aerosols.

The phase states of primarily emitted and secondarily formed aerosols from gasoline vehicle exhausts were investigated by quantifying the particle rebound fraction (f). The rebound behaviors of gasoline vehicle emission-related aerosols varied with engines, fuel types, and photochemical aging time, showing distinguished differences from biogenic secondary organic aerosols. The nonliquid-to-liquid phase transition of primary aerosols emitted from port fuel injection (PFI) and gasoline direct injection (GDI) vehicles started at a relative humidity (RH) = 50 and 60%, and liquefaction was accomplished at 60 and 70%, respectively. The RH at which f declined to 0.5 decreased from 70 to 65% for the PFI case with 92# fuel, corresponding to the photochemical aging time from 0.37 to 4.62 days. For the GDI case, such RH enhanced from 60 to 65%. Our results can be used to imply the phase state of traffic-related aerosols and further understand their roles in urban atmospheric chemistry. Taking Beijing, China, as an example, traffic-related aerosols were mainly nonliquid during winter with the majority ambient RH below 50%, whereas they were mostly liquid during the morning rush hour of summer, and traffic-related secondary aerosols fluctuated between nonliquid and liquid during the daytime and tended to be liquid at night with increased ambient RH.