Advancing predictive markers in lung adenocarcinoma: A machine learning-based immunotherapy prognostic prediction signature.

The prognosis of lung adenocarcinoma (LUAD) is generally poor. Immunotherapy has emerged as a promising therapeutic modality, demonstrating remarkable potential for substantially prolonging the overall survival of individuals afflicted with LUAD. However, there is currently a lack of reliable signatures for identifying patients who would benefit from immunotherapy. We conducted a comparative analysis of two immunotherapy cohorts (OAK and POPLAR) and utilized single-factor COX regression to identify genes that significantly impact the prognosis of LUAD. Based on the TCGA-LUAD dataset, we employed a combination of 101 machine learning algorithms to construct a model and selected the optimal model. The model was validated on five GEO datasets and compared with 144 previously published signatures to assess its performance. Subsequently, we explored the underlying biological mechanisms through tumor mutation burden analysis, enrichment analysis, and immune infiltration analysis. An immunotherapy prognostic prediction signature (IPPS) was constructed based on 13 genes, showing robust performance in the TCGA-LUAD dataset. IPPS exhibited consistent predictive accuracy in the validation cohorts. Compared to 144 previously published signatures, IPPS consistently ranked among the top in terms of C-index values. Further exploration revealed differences between high and low-IPPS groups in terms of tumor mutation burden, pathway enrichment, and immune infiltration. IPPS demonstrates strong predictive capabilities for the prognosis of LUAD patients, offering the potential to identify suitable candidates for immunotherapy and contribute to precision treatment strategies for LUAD.

BRCC3 Regulation of ALK2 in Vascular Smooth Muscle Cells: Implication in Pulmonary Hypertension.

BACKGROUND: An imbalance of antiproliferative BMP (bone morphogenetic protein) signaling and proliferative TGF-ß (transforming growth factor-ß) signaling is implicated in the development of pulmonary arterial hypertension (PAH). The posttranslational modification (eg, phosphorylation and ubiquitination) of TGF-ß family receptors, including BMPR2 (bone morphogenetic protein type 2 receptor)/ALK2 (activin receptor-like kinase-2) and TGF-ßR2/R1, and receptor-regulated (R) Smads significantly affects their activity and thus regulates the target cell fate. BRCC3 modifies the activity and stability of its substrate proteins through K63-dependent deubiquitination. By modulating the posttranslational modifications of the BMP/TGF-ß-PPARγ pathway, BRCC3 may play a role in pulmonary vascular remodeling, hence the pathogenesis of PAH. METHODS: Bioinformatic analyses were used to explore the mechanism of BRCC3 deubiquitinates ALK2. Cultured pulmonary artery smooth muscle cells (PASMCs), mouse models, and specimens from patients with idiopathic PAH were used to investigate the rebalance between BMP and TGF-ß signaling in regulating ALK2 phosphorylation and ubiquitination in the context of pulmonary hypertension. RESULTS: BRCC3 was significantly downregulated in PASMCs from patients with PAH and animals with experimental pulmonary hypertension. BRCC3, by de-ubiquitinating ALK2 at Lys-472 and Lys-475, activated receptor-regulated Smad1/5/9 (Smad1/5/9), which resulted in transcriptional activation of BMP-regulated PPARγ, p53, and Id1. Overexpression of BRCC3 also attenuated TGF-ß signaling by downregulating TGF-ß expression and inhibiting phosphorylation of Smad3. Experiments in vitro indicated that overexpression of BRCC3 or the de-ubiquitin-mimetic ALK2-K472/475R attenuated PASMC proliferation and migration and enhanced PASMC apoptosis. In SM22α-BRCC3-Tg mice, pulmonary hypertension was ameliorated because of activation of the ALK2-Smad1/5-PPARγ axis in PASMCs. In contrast, Brcc3-/- mice showed increased susceptibility of experimental pulmonary hypertension because of inhibition of the ALK2-Smad1/5 signaling. CONCLUSIONS: These results suggest a pivotal role of BRCC3 in sustaining pulmonary vascular homeostasis by maintaining the integrity of the BMP signaling (ie, the ALK2-Smad1/5-PPARγ axis) while suppressing TGF-ß signaling in PASMCs. Such rebalance of BMP/TGF-ß pathways is translationally important for PAH alleviation.

LncRNA RASAL2-AS1 promotes METTL14-mediated m6A methylation in the proliferation and progression of head and neck squamous cell carcinoma.

BACKGROUND: Long non-coding RNAs (lncRNAs) are key regulators of the 6-methyladenosine (m6A) epigenetic modification, playing a role in the initiation and progression of tumors. However, the regulatory mechanisms in head and neck squamous cell carcinoma (HNSCC) remain elusive. In this study, we investigated the molecular regulatory mechanisms of the lncRNA RASAL2-AS1 in the occurrence and development of HNSCC tumors. METHODS: A bioinformatics analysis was conducted to analyze the expression level of RASAL2-AS1 in HNSCC and normal tissues. RASAL2-AS1 mRNA and protein levels were detected using RT-PCR and Western blotting. Wound healing, transwell assays, flow cytometry, M6A dot blot, and RNA immunoprecipitation experiments were conducted to explore the regulatory role of the RASAL2-AS1 and downstream targets METTL14/LIS1 signaling pathway in HNSCC. Immunohistochemical examination was conducted to evaluate the expression of METTL14 and LIS1 in HNSCC and normal tissues. A tumor xenograft model of BALB/c nude mice was established to assess the impact of RASAL2-AS1 on cell proliferation and growth. RESULTS: RASAL2-AS1 high expression in HNSCC and cells deteriorated with survival rates of HNSCC. RASAL2-AS1 overexpression in HNSCC accelerated cell migration, colony formation, cell proliferation, cell cycle in S stage, while RASAL2-AS1 knockdown in HNSC cells inhibited cell cycle in G1 stage. After silencing METTL14, the above effects induced by overexpression of the RASAL2-AS1 were reversed. RASAL2-AS1 overexpression prompted LIS1 expression, whereas RASAL2-AS1 silencing reduced LIS1 levels in HNSCC cells, which was confirmed by immunohistological staining. Results demonstrated elevated expression of METTL14 or LIS1 in tongue cancer tissues. Overexpression of RASAL2-AS1 promoted tumor weight and tumor volume, which was counteracted by pcDNA3.1 RASAL2-AS1 plus silencing METTL14 and METTL14 and LIS1 were significantly decreased. CONCLUSION: Our study highlights the functional importance of the LncRNA RASAL2-AS1 in HNSCC and might assist in the development of a prognostic stratification and therapeutic approach. Which regulates HNSCC with the dependence of m6a manner.

An Exceptionally Active and Highly Selective Perchlorate Transporter Containing a Trimesic Amide Scaffold.

We report here a series of alkyl group-modified trimesic amide molecules (TAs) with excellent anion transport activities. Among them, TA6, with the highest ion transport activity and excellent selectivity, efficiently transports anions across the membrane in the order of ClO4- > I- > NO3- > Br- > Cl-, with an EC50 value as low as 17.6 nM (0.022 mol% relative to lipid molecules) for ClO4-, which outperforms other anions by 5- to 22-folds and manifests as the best perchlorate transporter ever reported.

Impact of comprehensive air pollution control policies on six criteria air pollutants and acute myocardial infarction morbidity, Weifang, China: A quasi-experimental study.

Comprehensive air pollution control policies may reduce pollutant emissions. However, the impact on disease morbidity of the change for the concentration of air pollutants following the policies has been insufficiently studied. We aim to assess the impact of comprehensive air pollution control policies on the levels of six criteria air pollutants and acute myocardial infarction (AMI) morbidity in Weifang, China. This study performed an interrupted time series analysis. The linear model with spline terms and generalized additive quasi-Poisson model were used to estimate the immediate change from 2016 to 2019 in the daily concentration of six air pollutants (PM2.5, PM10, SO2, NO2, O3, and, CO) and AMI incident cases (Age ≥35) associated with the implementation of air pollution control policies in Weifang, respectively. After the implementation of air pollution control policies, air quality in Weifang had been improved. Specifically, the daily concentrations of PM2.5, PM10, SO2, and, CO immediately decreased by 27.9 % (95 % CI: 6.6 % to 44.3 %), 32.9 % (95 % CI: 17.5 % to 45.5 %), 14.6 % (95 % CI: 0.4 % to 26.8 %), and 33.9 % (95 % CI: 22.0 % to 44.0 %), respectively. In addition, the policies implementation was also associate with the immediate decline in the AMI morbidity (-6.5 %, 95 % CI: -10.4 % to -2.3 %). And subgroup analyses indicate that the health effects of the policy intervention were only observed in female (-9.4 %, 95 % CI: -14.4 % to -4.2 %) and those aged ≥65 years (-10.5 %, 95 % CI: -14.6 % to -6.2 %). During the final 20 months of the study period, the policy intervention was estimated to prevent 1603 (95 % CI: 574 to 2587) cases of incident AMI in Weifang. Our results provide strong rationale that the policy intervention significantly reduced ambient pollutant concentrations and AMI morbidity, which highlighted the importance for a comprehensive and rigorous air pollution control policy in regions with severe air pollution.

MT1G Regulates c-MYC/P53 Signal to Inhibit Proliferation, Invasion and Migration and Promote Apoptosis in Colon Cancer Cells.

INTRODUCTION: Colon cancer is a common and malignant cancer featuring high morbidity and poor prognosis. AIMS: This study was performed to explore the regulatory role of MT1G in colon cancer as well as its unconcealed molecular mechanism. METHODS: The expressions of MT1G, c-MYC, and p53 were assessed with the application of RT-qPCR and western blot. The impacts of MT1G overexpression on the proliferative ability of HCT116 and LoVo cells were measured by CCK-8 and BrdU incorporation assays. Additionally, transwell wound healing, and flow cytometry assays were employed to evaluate the invasive and migrative capacities as well as the apoptosis level of HCT116 and LoVo cells. Moreover, the activity of the P53 promoter region was assessed with the help of a luciferase reporter assay. RESULTS: It was found that the expressions of MT1G at both mRNA and protein levels were greatly decreased in human colon cancer cell lines, particularly in HCT116 and LoVo cell lines. After transfection, it was discovered that the MT1G overexpression suppressed the proliferation, migration and invasion but promoted the apoptosis of HCT116 and LoVo cells, which were then partially reversed after overexpressing c-MYC. Additionally, MT1G overexpression reduced c-MYC expression but enhanced the p53 expression, revealing that the MT1G overexpression could regulate c-MYC/P53 signal. Elsewhere, it was also shown that c-MYC overexpression suppressed the regulatory effects of MT1G on P53. CONCLUSION: To conclude, MT1G was verified to regulate c-MYC/P53 signal to repress the proliferation, migration and invasion but promote the apoptosis of colon cancer cells, which might offer a novel targeted-therapy for the improvement of colon cancer.

Synthesis and Evaluation of Functionalized Polyurethanes for pH-Responsive Delivery of Compounds in Chronic Wounds.

Chronic wounds, depending on the bacteria that caused the infection, can be associated with an extreme acidic or basic pH. Therefore, the application of pH-responsive hydrogels has been instigated for the delivery of therapeutics to chronic wounds. Herein, with the aim of developing a flexible pH-responsive hydrogel, we functionalized hydrophilic polyurethanes with either cationic (polyethylene imine) or anionic (succinic anhydride) moieties. A comprehensive physicochemical characterization of corresponding polymers was carried out. Particularly, when tested in aqueous buffers, the surface charge of hydrogel films was closely correlated with the pH of the buffers. The loading of the cationic and anionic hydrogel films with various compound models (bromophenol blue; negatively charged or Pyronin Y; positively charged) showed that the electrostatic forces between the polymeric backbone and the compound model will determine the ultimate release rate at any given pH. The potential application of these films for chronic wound drug delivery was assessed by loading them with an antibiotic (ciprofloxacin). In vitro bacterial culturing was performed using Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Results showed that at the same drug dosage, different release profiles achievable from cationic and anionic polyurethanes can yield different degrees of an antibacterial effect. Overall, our results suggest the potential application of cationic and anionic hydrophilic polyurethanes as flexible pH-responsive materials for the delivery of therapeutics to chronic wounds.

Sulfur-Containing Foldamer-Based Artificial Lithium Channels.

Unlike many other biologically relevant ions (Na+ , K+ , Ca2+ , Cl- , etc) and protons, whose cellular concentrations are closely regulated by highly selective channel proteins, Li+ ion is unusual in that its concentration is well tolerated over many orders of magnitude and that no lithium-specific channel proteins have so far been identified. While one naturally evolved primary pathway for Li+ ions to traverse across the cell membrane is through sodium channels by competing with Na+ ions, highly sought-after artificial lithium-transporting channels remain a major challenge to develop. Here we show that sulfur-containing organic nanotubes derived from intramolecularly H-bonded helically folded aromatic foldamers of 3.6 Šin hollow cavity diameter could facilitate highly selective and efficient transmembrane transport of Li+ ions, with high transport selectivity factors of 15.3 and 19.9 over Na+ and K+ ions, respectively.

Dynamic myocardial perfusion computed tomography with mental stress test to detect changes in myocardial microcirculation in patients with anxiety and no obstructive coronary artery disease.

OBJECTIVE: Mental stress can induce myocardial ischemia in patients with anxiety and other psychological disorders. Computed tomography myocardial perfusion imaging (CT-MPI) has the potential to quantitatively diagnose myocardial ischemia. The aim of this study was to measure changes in myocardial microcirculation perfusion (MMP) in patients with anxiety who have angina symptoms/ischemia but no obstructive coronary artery disease (INOCA) using dynamic CT-MPI in combination with a mental stress test. METHODS: Patients with INOCA were divided into five subgroups (none, minimal, mild, moderate, and severe) according to the generalized anxiety disorder scale. Patients underwent dynamic CT-MPI with mental stress testing using a series of the standardized color word/arithmetic stressors. Myocardial blood flow (MBF) during resting and stress phases of CT-MPI was recorded. RESULTS: Fifty-eight patients with 986 segments were included for final analysis. Compared to patients with none, minimal, mild, and moderate anxiety, those with severe anxiety had the largest rate of MBF decrease and the largest MBF decrease value. At the same time, those with no anxiety had the largest rate of MBF increase, the largest MBF increase value (all p < 0.05). As anxiety intensified, the rate of MBF increased and the MBF value increased (r = -0.24, r = -0.27, p < 0.05). Concomitantly, the rate of MBF decreased and the MBF value decreased (r = 0.63, r = 0.43, p < 0.05). CONCLUSIONS: Dynamic CT-MPI with a mental stress test can be used to evaluate MMP in patients with anxiety and INOCA. Mental stress resulted in significant differences in changes in the rate and value of MBF among patients with different anxiety degrees. KEY POINTS: • Dynamic CT-MPI with mental stress test worked well to quantitatively evaluate myocardial microcirculation perfusion in patients with anxiety and INOCA. • The rates of MBF decrease and MBF decrease value were positively correlated with anxiety degree of anxiety patients with INOCA. • MBF change derived from CT-MPI with mental stress test had a good performance to predicting anxiety degree of patients with anxiety and INOCA.

CCCP Facilitates Aminoglycoside to Kill Late Stationary-Phase Escherichia coli by Elevating Hydroxyl Radical.

Improving the efficacy of existing antibiotics is significant for combatting antibiotic resistance that poses a major threat to human health. Carbonyl cyanide m-chlorophenylhydrazine (CCCP), a well-known protonophore for dissipating proton motive force (PMF), has been widely used to block the PMF-dependent uptake of aminoglycoside antibiotics and thus suppress aminoglycoside lethality. Here, we report that CCCP and its functional analog FCCP, but not other types of protonophores, unprecedently potentiate aminoglycosides (e.g., tobramycin and gentamicin) by 3-4 orders of magnitude killing of Escherichia coli, Staphylococcus aureus, Shigella flexneri, and Vibrio alginolyticus cells in stationary phase but not these cells in exponential phase nor other 12 bacterial species we examined. Overall, the effect of CCCP on aminoglycoside lethality undergoes a gradual transition from suppression against E. coli exponential-phase cells to potentiation against late stationary-phase cells, with the cell growth status and culture medium being crucial. Consistently, disturbance of the PMF by changing transmembrane proton gradient (ΔpH) or electric potential (ΔΨ) also potentiates tobramycin. Nevertheless, CCCP neither increases the intracellular concentration of tobramycin nor decreases the MIC of the antibiotic, thus excluding that CCCP acts as an efflux pump inhibitor to potentiate aminoglycosides. Rather, we show that the combined treatment dramatically enhances the cellular level of hydroxyl radical under both aerobic and anaerobic culturing conditions, under which the antioxidant N-acetyl cysteine fully suppresses both hydroxyl radical accumulation and cell death. Together, these findings open a new avenue to develop certain protonophores as aminoglycoside adjuvants against pathogens in stationary phase and also illustrate an essential role of hydroxyl radical in aminoglycoside lethality regardless of aerobic respiration.

A K+-selective channel with a record-high K+/Na+ selectivity of 20.1.

For compounds each containing a phenylalanine moiety with its two ends amidated to have a 15-crown-5 unit and an alkyl chain, a simple tuning of the alkyl chain length delivered a K+-selective channel with a record-high K+/Na+ selectivity of 20.1.

Heat shock potentiates aminoglycosides against gram-negative bacteria by enhancing antibiotic uptake, protein aggregation, and ROS.

The potentiation of antibiotics is a promising strategy for combatting antibiotic-resistant/tolerant bacteria. Herein, we report that a 5-min sublethal heat shock enhances the bactericidal actions of aminoglycoside antibiotics by six orders of magnitude against both exponential- and stationary-phase Escherichia coli. This combined treatment also effectively kills various E. coli persisters, E. coli clinical isolates, and numerous gram-negative but not gram-positive bacteria and enables aminoglycosides at 5% of minimum inhibitory concentrations to eradicate multidrug-resistant pathogens Acinetobacter baumannii and Klebsiella pneumoniae. Mechanistically, the potentiation is achieved comprehensively by heat shock-enhanced proton motive force that thus promotes the bacterial uptake of aminoglycosides, as well as by increasing irreversible protein aggregation and reactive oxygen species that further augment the downstream lethality of aminoglycosides. Consistently, protonophores, chemical chaperones, antioxidants, and anaerobic culturing abolish heat shock-enhanced aminoglycoside lethality. We also demonstrate as a proof of concept that infrared irradiation- or photothermal nanosphere-induced thermal treatments potentiate aminoglycoside killing of Pseudomonas aeruginosa in a mouse acute skin wound model. Our study advances the understanding of the mechanism of actions of aminoglycosides and demonstrates a high potential for thermal ablation in curing bacterial infections when combined with aminoglycosides.

Biopolymeric Coatings for Local Release of Therapeutics from Biomedical Implants.

The deployment of structures that enable localized release of bioactive molecules can result in more efficacious treatment of disease and better integration of implantable bionic devices. The strategic design of a biopolymeric coating can be used to engineer the optimal release profile depending on the task at hand. As illustrative examples, here advances in delivery of drugs from bone, brain, ocular, and cardiovascular implants are reviewed. These areas are focused to highlight that both hard and soft tissue implants can benefit from controlled localized delivery. The composition of biopolymers used to achieve appropriate delivery to the selected tissue types, and their corresponding outcomes are brought to the fore. To conclude, key factors in designing drug-loaded biopolymeric coatings for biomedical implants are highlighted.

Investigation on the impact of quality characteristics and storage stability of foxtail millet induced by air cold plasma.

The aim of this work was to investigate the effects of dielectric barrier discharge-air cold plasma (DBD-ACP, 15-35 kV, 2-12 min) on the quality of foxtail millets. The L and b* values were evaluated by a digital colorimeter representing that the color of millets was significantly changed at 25 kV for 4-12 min or at 35 kV for 2-12 min. The results were consistent with the change of total yellow pigment in millets, indicating that DBD-ACP damaged the carotenoids if the treatment condition was too high. The activity of lipoxygenase and lipase, involving the oxidation and hydrolysis of lipids of millet, decreased significantly induced by DBD-ACP. For example, the lipoxygenase and lipase activity of Mizhi millet was decreased from 44.0 to 18.7 U g-1min-1, 56.0-15.1 U/(mg pro) (p<0.05) after being exposed to 25 kV for 2-12 min, respectively. Changes of color, lipoxygenase and lipase activity, and malondialdehyde content of millets were determined during accelerated storage (40 ± 2°C and 75% Relative Humidity) for 15 days after being treated by DBD-ACP under 15 and 25 kV for 4 min. Results showed that millets treated by DBD-ACP at 15 kV kept a better color with lower malondialdehyde content, and lower lipoxygenase and lipase activity compared to control. This work implied that DBD-ACP is an underlying approach for the storage of foxtail millets.

Scinderin Is a Novel Oncogene for Its Correlates with Poor Prognosis, Immune Infiltrates and Matrix Metalloproteinase-2/9 (MMP2/9) in Glioma.

PURPOSE: The effect of scinderin (SCIN) on cancer progression has been studied, but its role in glioma remains unknown. This study describes the value of SCIN for the diagnosis, prognosis, and treatment of glioma. METHODS: The expression of SCIN was analyzed using the GEPIA, Oncomine, cBioPortal, and CGGA databases. GO/KEGG enrichment analysis of similar genes to SCIN were performed using the R software package, and the protein-protein interaction (PPI) network was analyzed by the STRING and GeneMANIA databases. The correlations of mRNA expression between SCIN and MMP2/9 were analyzed by TCGA glioma. Simultaneously, the TISIDB and TIMER databases were used to analyze the correlation between SCIN and immune infiltration. Finally, SCIN and MMP2/9 protein expression among different grades of glioma was performed and the results were obtained via immunohistochemistry and Western blot assays. We used the Kaplan-Meier method and Cox proportional hazards model to assess the impact of SCIN and MMP2/9 on glioma patients' survival. The correlations between SCIN and MMP2/9 were analyzed by immunohistochemistry and Western blot assays. RESULTS: SCIN was upregulated in glioma patients with a poor prognosis. The GO and KEGG enrichment analysis showed the functional relationship between SCIN and the immune cell activation and regulation. In addition, the expression of SCIN was related to MMP2/9 in glioma. The correlation analysis showed that SCIN expression was associated with tumor purity and immune infiltration. SCIN and MMP2/9 are negative prognostic factors resulting in worsening glioma patients' survival. CONCLUSION: Our studies demonstrated that SCIN expression was associated with MMP2/9, immune infiltration, and a poor prognosis in glioma. SCIN may serve as a potential prognostic marker and an immune therapy target for glioma.

5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus.

Antibiotic resistance of bacterial pathogens has become a severe threat to human health. To counteract antibiotic resistance, it is of significance to discover new antibiotics and also improve the efficacy of existing antibiotics. Here we show that 5-methylindole, a derivative of the interspecies signaling molecule indole, is able to directly kill various Gram-positive pathogens (e.g., Staphylococcus aureus and Enterococcus faecalis) and also Gram-negative ones (e.g., Escherichia coli and Pseudomonas aeruginosa), with 2-methylindole being less potent. Particularly, 5-methylindole can kill methicillin-resistant S. aureus, multidrug-resistant Klebsiella pneumoniae, Mycobacterium tuberculosis, and antibiotic-tolerant S. aureus persisters. Furthermore, 5-methylindole significantly potentiates aminoglycoside antibiotics, but not fluoroquinolones, killing of S. aureus. In addition, 5-iodoindole also potentiates aminoglycosides. Our findings open a new avenue to develop indole derivatives like 5-methylindole as antibacterial agents or adjuvants of aminoglycoside.

dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.

Mechanosensitive Channels Mediate Hypoionic Shock-Induced Aminoglycoside Potentiation against Bacterial Persisters by Enhancing Antibiotic Uptake.

Improving the efficacy of existing antibiotics is a promising strategy for combating antibiotic-resistant/tolerant bacterial pathogens that have become a severe threat to human health. We previously reported that aminoglycoside antibiotics could be dramatically potentiated against stationary-phase Escherichia coli cells under hypoionic shock conditions (i.e., treatment with ion-free solutions), but the underlying molecular mechanism remains unknown. Here, we show that mechanosensitive (MS) channels, a ubiquitous protein family sensing mechanical forces of cell membrane, mediate such hypoionic shock-induced aminoglycoside potentiation. Two-minute treatment under conditions of hypoionic shock (e.g., in pure water) greatly enhances the bactericidal effects of aminoglycosides against both spontaneous and triggered E. coli persisters, numerous strains of Gram-negative pathogens in vitro, and Pseudomonas aeruginosa in mice. Such potentiation is achieved by hypoionic shock-enhanced bacterial uptake of aminoglycosides and is linked to hypoionic shock-induced destabilization of the cytoplasmic membrane in E. coli. Genetic and biochemical analyses reveal that MscS-family channels directly and redundantly mediate aminoglycoside uptake upon hypoionic shock and thus potentiation, with MscL channel showing reduced effect. Molecular docking and site-directed mutagenesis analyses reveal a putative streptomycin-binding pocket in MscS, critical for streptomycin uptake and potentiation. These results suggest that hypoionic shock treatment destabilizes the cytoplasmic membrane and thus changes the membrane tension, which immediately activates MS channels that are able to effectively transport aminoglycosides into the cytoplasm for downstream killing. Our findings reveal the biological effects of hypoionic shock on bacteria and can help to develop novel adjuvants for aminoglycoside potentiation to combat bacterial pathogens via activating MS channels.

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.