Inhibition of Notch3/Hey1 ameliorates peribiliary hypoxia by preventing hypertrophic hepatic arteriopathy in biliary atresia progression.

Emerging evidence indicates the presence of vascular abnormalities and ischemia in biliary atresia (BA), although specific mechanisms remain undefined. This study examined both human and experimental BA. Structural and hemodynamic features of hepatic arteries were investigated by Doppler ultrasound, indocyanine green angiography, microscopic histology, and invasive arterial pressure measurement. Opal multiplex immunohistochemistry, western blot, and RT-PCR were applied to assess Notch3 expression and the phenotype of hepatic arterial smooth muscle cells (HASMCs). We established animal models of Notch3 inhibition, overexpression, and knockout to evaluate the differences in overall survival, hepatic artery morphology, peribiliary hypoxia, and HASMC phenotype. Hypertrophic hepatic arteriopathy was evidenced by an increased wall-to-lumen ratio and clinically manifested as hepatic arterial hypertension, decreased hepatic artery perfusion, and formation of hepatic subcapsular vascular plexuses (HSVPs). We observed a correlation between overactivation of Notch3 and phenotypic disruption of HASMCs with the exacerbation of peribiliary hypoxia. Notch3 signaling mediated the phenotype alteration of HASMCs, resulting in arterial wall thickening and impaired oxygen supply in the portal microenvironment. Inhibition of Notch3/Hey1 ameliorates portal hypoxia by restoring the balance of contractile/synthetic HASMCs, thereby preventing hypertrophic arteriopathy in BA.

Beyond the ß-amino alcohols framework: identification of novel ß-hydroxy pyridinium salt-decorated pterostilbene derivatives as bacterial virulence factor inhibitors.

BACKGROUND: Bacterial virulence factors are involved in various biological processes and mediate persistent bacterial infections. Focusing on virulence factors of phytopathogenic bacteria is an attractive strategy and crucial direction in pesticide discovery to prevent invasive and persistent bacterial infection. Hence, discovery and development of novel agrochemicals with high activity, low-risk, and potent anti-virulence is urgently needed to control plant bacterial diseases. RESULTS: A series of novel ß-hydroxy pyridinium cation decorated pterostilbene derivatives were prepared and their antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo) were systematacially assessed. Among these pterostilbene derivatives, compound 4S exhibited the best antibacterial activity against Xoo in vitro, with an half maximal effective concentration (EC50) value of 0.28 µg mL-1. A series of biochemical assays including scanning electron microscopy, crystal violet staining, and analysis of biofilm formation, swimming motility, and related virulence factor gene expression levels demonstrated that compound 4S could function as a new anti-virulence factor inhibitor by interfering with the bacterial infection process. Furthermore, the pot experiments provided convinced evidence that compound 4S had the high control efficacy (curative activity: 71.4%, protective activity: 72.6%), and could be used to effectively manage rice bacterial leaf blight in vivo. CONCLUSION: Compounds 4S is an attractive virulence factor inhibitor with potential for application in treating plant bacterial diseases by suppressing production of several virulence factors. © 2024 Society of Chemical Industry.

Risk factors for anxiety and its impacts on acute exacerbation in older patients with chronic obstructive pulmonary disease.

Background: Anxiety is common in patients with chronic obstructive pulmonary disease (COPD), especially in older patients with the definition of age over 60 years old. Few studies have focused on anxiety in older COPD patients. This study aimed to analyze the risk factors of anxiety in older COPD patients and the impacts of anxiety on future acute exacerbation. Methods: The general information, questionnaire data, previous acute exacerbation and pulmonary function were collected. Hamilton Anxiety Rating Scale (HAMA) was used to evaluate the anxiety of older COPD patients. The patients were followed up for one year, the number and the degrees of acute exacerbations of COPD were recorded. Results: A total of 424 older COPD patients were included in the analysis. 19.81% (N = 84) had anxiety symptoms, and 80.19% (N = 340) had no anxiety symptoms. There were increased pack-years, more comorbidities, and more previous acute exacerbations in older COPD patients with anxiety compared to those without anxiety (P < 0.05). Meanwhile, a higher modified Medical Research Council (mMRC), a higher COPD assessment test (CAT) score and a shorter six-minute walking distance (6MWD) were found in older COPD patients with anxiety (P < 0.05). The BODE index, mMRC, CAT score, comorbidities and acute exacerbations were associated with anxiety. Eventually, anxiety will increase the risk of future acute exacerbation in older COPD patients (OR = 4.250, 95% CI: 2.369-7.626). Conclusion: Older COPD patients with anxiety had worsening symptoms, more comorbidities and frequent acute exacerbation. Meanwhile, anxiety may increase the risk of acute exacerbation in the future. Therefore, interventions should be provided to reduce the risk of anxiety in older COPD patients at an early stage.

Morphological, Anatomical, and Physiological Characteristics of Heteroblastic Acacia melanoxylon Grown under Weak Light.

Acacia melanoxylon is a fast-growing macrophanerophyte with strong adaptability whose leaf enables heteromorphic development. Light is one of the essential environmental factors that induces the development of the heteroblastic leaf of A. melanoxylon, but its mechanism is unclear. In this study, the seedlings of A. melanoxylon clones were treated with weak light (shading net with 40% of regular light transmittance) and normal light (control) conditions for 90 d and a follow-up observation. The results show that the seedlings' growth and biomass accumulation were inhibited under weak light. After 60 days of treatment, phyllodes were raised under the control condition while the remaining compound was raised under weak light. The balance of root, stem, and leaf biomass changed to 15:11:74 under weak light, while it was 40:15:45 under control conditions. After comparing the anatomical structures of the compound leaves and phyllode, they were shown to have their own strategies for staying hydrated, while phyllodes were more able to control water loss and adapt to intense light. The compound leaves exhibited elevated levels of K, Cu, Ca, and Mg, increased antioxidant enzyme activity and proline content, and higher concentrations of chlorophyll a, carotenoids, ABA, CTK, and GA. However, they displayed a relatively limited photosynthetic capacity. Phyllodes exhibited higher levels of Fe, cellulose, lignin, IAA content, and high photosynthetic capacity with a higher maximum net photosynthetic rate, light compensation point, dark respiration rate, and water use efficiency. The comparative analysis of compound leaves and phyllodes provides a basis for understanding the diverse survival strategies that heteroblastic plants employ to adapt to environmental changes.

Comparative physiological, biochemical, metabolomic, and transcriptomic analyses reveal the formation mechanism of heartwood for Acacia melanoxylon.

Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and regulatory mechanism of heartwood during wood development remain largely unclear. In this study, both microscopic observation and content determination proved that total amount of starches decreased and phenolics and flavonoids increased gradually from sapwood (SW) to HW. We also obtained the metabolite profiles of 10 metabolites related to phenolics and flavonoids during HW formation by metabolomics. Additionally, we collected a comprehensive overview of genes associated with the biosynthesis of sugars, terpenoids, phenolics, and flavonoids using RNA-seq. A total of ninety-one genes related to HW formation were identified. The transcripts related to plant hormones, programmed cell death (PCD), and dehydration were increased in transition zone (TZ) than in SW. The results of RT-PCR showed that the relative expression level of genes and transcription factors was also high in the TZ, regardless of the horizontal or vertical direction of the trunk. Therefore, the HW formation took place in the TZ for A. melanoxylon from molecular level, and potentially connected to plant hormones, PCD, and cell dehydration. Besides, the increased expression of sugar and terpenoid biosynthesis-related genes in TZ further confirmed the close connection between terpenoid biosynthesis and carbohydrate metabolites of A. melanoxylon. Furthermore, the integrated analysis of metabolism data and RNA-seq data showed the key transcription factors (TFs) regulating flavonoids and phenolics accumulation in HW, including negative correlation TFs (WRKY, MYB) and positive correlation TFs (AP2, bZIP, CBF, PB1, and TCP). And, the genes and metabolites from phenylpropanoid and flavonoid metabolism and biosynthesis were up-regulated and largely accumulated in TZ and HW, respectively. The findings of this research provide a basis for comprehending the buildup of metabolites and the molecular regulatory processes of HW formation in A. melanoxylon.

P-limitation regulates the accumulation of soil aggregates organic carbon during the restoration of Pinus tabuliformis forest.

Artificial forest restoration is widely recognized as a crucial approach to enhance the potential of soil carbon sequestration. Nevertheless, there is still limited understanding regarding the dynamics of aggregate organic carbon (OC) and the underlying mechanisms driving these dynamics after artificial forest restoration. To address this gap, we studied Pinus tabuliformis forests and adjacent farmland in three recovery periods (13, 24 and 33 years) in the Loess Plateau region. Samples of undisturbed soil from the surface layer were collected and divided into three aggregate sizes: >2 mm (large aggregate), 0.25-2 mm (medium aggregate), and <0.25 mm (small aggregate). The aim was to examine the distribution of OC and changes in enzyme activity within each aggregate size. The findings revealed a significant increase in OC content for all aggregate sizes following the restoration of Pinus tabuliformis forests. After 33 years of recovery, the OC of large aggregates, medium aggregates and micro-aggregates increased by (30.23 ± 9.85)%, (36.71 ± 21.60)% and (37.88 ± 16.07)% respectively compared with that of farmland. Moreover, the restoration of Pinus tabuliformis forests lead to increased activity of hydrolytic enzymes and decreased activity of oxidative enzymes. It is noteworthy that the regulation of carbon in all aggregates is influenced by soil P-limitation. In large aggregates, P-limitation promotes the enhancement of hydrolytic enzyme activity, thereby facilitate OC accumulation. Conversely, in medium and small aggregates, P-limitation inhibits the increase in oxidative enzyme activity, resulting in OC accumulation. The results emphasize the importance of P restriction in regulating OC accumulation during the restoration of Pinus tabulaeformis forest, in which large aggregates play a leading role.

Effects and long-term outcomes of endurance versus resistance training as an adjunct to standard medication in patients with stable COPD: a multicenter randomized trial.

BACKGROUND: Comparisons between endurance training (ET) and resistance training (RT) have produced equivocal findings in chronic obstructive pulmonary disease (COPD) patients. The purpose of our study is to investigate the effectiveness and long-term outcomes of adding ET and RT to conventional medical treatment in patients with COPD. A secondary objective is to investigate the clinical improvements resulting from exercise training in patients with different disease severities. METHODS: The study was a multicenter, prospective trial in people with stable COPD. The cohort was randomized to three groups: individualized medical treatment group (MT), MT + endurance training group (MT + ET) and MT + resistance training group (MT + RT). Exercise was performed 3 times weekly over a 12-week period. The endpoints of exercise capacity, health-related quality of life, COPD symptoms, lung function, and anxiety and depression questionnaires were re-evaluated at baseline, at the completion of the intervention and at 6 and 12-month follow-up. According to the COPD assessment tool offered by GOLD guidelines, patients were stratified into GOLD A and B groups and GOLD C and D groups for further subgroup analysis. RESULTS: The intention-to-treat (ITT) population included 366 patients, 328 of them completed the study protocol over 12 months (the PP-population). There were no significant differences in the primary outcome, quality of life, between patients who underwent medical treatment (MT) alone, MT + endurance training (MT + ET), or MT + resistance training (MT + RT) at the completion of the intervention, 6-, or 12-month follow-up. Additionally, no significant differences were observed between MT, MT + RT, or MT + ET groups concerning the primary outcome, exercise capacity (3MWD), after initial 3 months of intervention. However, a small statistically significant difference was noted in favor of MT + ET compared to MT + RT at 12 months (ITT: Δ3MWD in ET vs RT = 5.53 m, 95% confidence interval: 0.87 to 13.84 m, P = 0.03) (PP: Δ3MWD in ET vs RT = 7.67 m, 95% confidence interval: 0.93 to 16.27 m, P = 0.04). For patients in the GOLD C and D groups, improvement in quality of life following ET or RT was significantly superior to medical intervention alone. Furthermore, upon completion of the exercise regimen, RT exhibited a greater improvement in anxiety compared to ET in these patients (ITT: ΔHAD-A at 3-month: RT = -1.63 ± 0.31 vs ET = -0.61 ± 0.33, p < 0.01) (PP: ΔHAD-A at 3-month: RT = -1.80 ± 0.36 vs ET = -0.75 ± 0.37, p < 0.01). CONCLUSIONS: Our study presents evidence of the beneficial effects of ET and RT in combination with standard medical treatment, as well as the long-term effects over time after the intervention. While the statistically significant effect favoring ET over RT in terms of exercise capacity was observed, it should be interpreted cautiously. Patients in severe stages of COPD may derive greater benefits from either ET or RT and should be encouraged accordingly. These findings have implications for exercise prescription in patients with COPD. TRIAL REGISTRATION: ChiCTR-INR-16009892 (17, Nov, 2016).

Comparative analysis of CRASH and IMPACT in predicting the outcome of 340 patients with traumatic brain injury.

Background: Both the International Mission for Prognosis and Analysis of Clinical Trials (IMPACT) and the Corticosteroid randomization after significant head injury (CRASH) models are globally acknowledged prognostic algorithms for assessing traumatic brain injury (TBI) outcomes. The aim of this study is to externalize the validation process and juxtapose the prognostic accuracy of the CRASH and IMPACT models in moderate-to-severe TBI patients in the Chinese population. Methods: We conducted a retrospective study encompassing a cohort of 340 adult TBI patients (aged > 18 years), presenting with Glasgow Coma Scale (GCS) scores ranging from 3 to 12. The data were accrued over 2 years (2020-2022). The primary endpoints were 14-day mortality rates and 6-month Glasgow Outcome Scale (GOS) scores. Analytical metrics, including the area under the receiver operating characteristic curve for discrimination and the Brier score for predictive precision were employed to quantitatively evaluate the model performance. Results: Mortality rates at the 14-day and 6-month intervals, as well as the 6-month unfavorable GOS outcomes, were established to be 22.06, 40.29, and 65.59%, respectively. The IMPACT models had area under the curves (AUCs) of 0.873, 0.912, and 0.927 for the 6-month unfavorable GOS outcomes, with respective Brier scores of 0.14, 0.12, and 0.11. On the other hand, the AUCs associated with the six-month mortality were 0.883, 0.909, and 0.912, and the corresponding Brier scores were 0.15, 0.14, and 0.13, respectively. The CRASH models exhibited AUCs of 0.862 and 0.878 for the 6-month adverse outcomes, with uniform Brier scores of 0.18. The 14-day mortality rates had AUCs of 0.867 and 0.87, and corresponding Brier scores of 0.21 and 0.22, respectively. Conclusion: Both the CRASH and IMPACT algorithms offer reliable prognostic estimations for patients suffering from craniocerebral injuries. However, compared to the CRASH model, the IMPACT model has superior predictive accuracy, albeit at the cost of increased computational intricacy.

Overexpression of OsDUF6 increases salt stress tolerance in rice.

BACKGROUND: Soil salinity is one of the primary environmental stresses faced in rice production. When plants are exposed to salt stress, a series of cellular balances will be disrupted. Dufulin is an immune-induced antiviral agent used in plants. The DUF gene family influences plant response to abiotic stress, and the functional role of OsDUF6(ABA98726.1) in rice response to salt stress is being investigated here. RESULTS: Based on the transcriptome analysis of Dufulin treatment in inducing salt tolerance in rice, we selected the OsDUF6 protein located on the cell membrane and studied its molecular function by overexpressing OsDUF6. Salt-induced decreases in root, stem, and leaf length and increased leaf yellowing rate and Na+ concentration in the wild-type plant were mitigated in the overexpressed lines. OsDUF6 overexpression increased the enzymatic antioxidant activities of superoxide dismutase, peroxidase, catalase, and phenylalanine ammonia-lyase. OsDUF6 also played a positive role in Na+ transport as reflected by the increased growth of a salt-sensitive yeast mutant complemented with OsDUF6 in the presence of salt stress. In addition, Reverse transcription quantitative PCR analysis confirmed that the overexpression of OsDUF6 significantly changed the expression level of other genes related to growth and stress tolerance. CONCLUSIONS: Combined with previously published data, our results supported the observation that OsDUF6 is an important functional factor in Dufulin-induced promotion of salt stress tolerance in rice.

The role of Sertoli cells-secreted factors in different stages of germ cells development in mice exposed to BDE-209.

Decabromodiphenyl ether (BDE-209), a frequently used brominated flame retardant, readily enters the environment and is difficult to degrade with bioaccumulation. BDE-209 could cause male reproductive toxicity, but the regulatory functions of Sertoli cells-secreted factors remain uncertain. In present study, male mice were treated with 75 mg/kg BDE-209 and then stopped exposure for 50 days. Exogenous Glial cell line-derived neurotrophic factor (GDNF), a Sertoli cell-secreted factor, was injected into testes of mice treated with BDE-209 for 50 days to explore the role of GDNF in BDE-209-induced reproductive toxicity. The mouse spermatogonia cell line GC-1 spg was used in vitro to further verify regulatory effects of Sertoli cells-secreted factors on meiotic initiation. The results showed that BDE-209 inhibited expressions of the self-renewal pathway GFRα-1/RAS/ERK1/2 in spermatogonial stem cells (SSCs), and reduced expressions of spermatogonia proliferation-related pathway NRG3/ERBB4 and meiosis initiation factor Stra8. Furthermore, BDE-209 decreased the levels of both GDNF and retinoic acid (RA) secreted by Sertoli cells in testes. Importantly, the alterations of above indicators induced by BDE-209 did not recover after 50-day recovery period. After exogenous GDNF injection, the decreased expression of GFRα-1/RAS/ERK in SSCs was reversed. However, the level of RA and expressions of NRG3/ERBB4/Stra8 were not restored. The in vitro experimental results showed that exogenous RA reversed the reductions in NRG3/ERBB4/Stra8 and ameliorated inhibition of GC-1 spg cells proliferation induced by BDE-209. These results suggested that Sertoli cells-secreted factors play roles in regulating various stages of germ cell development. Specifically, BDE-209 affected the self-renewal of SSCs by decreasing GDNF secretion resulting in the inhibition of GFRα-1/RAS/ERK pathway; BDE-209 hindered the proliferation of spermatogonia and initiation of meiosis by inhibiting the secretion of RA and preventing RA from binding to RARα, resulting in the suppression of NRG3/ERBB4/Stra8 pathway. As a consequence, spermatogenesis was compromised, leading to persistent male reproductive toxicity.

Synergistic evolution of water-energy-food system resilience and efficiency in urban agglomerations.

With increasing internal and external risks to the WEF system, a single emphasis on efficiency or a lopsided pursuit of resilience can lead to difficulties in adapting to complex changes and resource redundancy. Revealing the synergistic evolutionary characteristics between efficiency and resilience of the WEF system is an effective method to deal with systemic internal and external risks. However, the current study of the WEF system lacks a synergistic perspective on resilience and efficiency. Thus, taking Chengdu-Chongqing Economic Circle (CCEC) as the research object and its geospatial boundary as the system boundary, this paper adopted the entropy-topsis model to evaluate the WEF resilience, and applied the super-efficient SBM model to measure the WEF efficiency accurately, which fully considered the non-expected outputs in the process of resource utilization. Then, applying the development coordination degree model, the synergistic relationship between the two was measured. The results indicated that: the average value of WEF resilience in CCEC increased from 0.414 to 0.485 and showed spatial characteristics of west＞east＞central. The WEF efficiency interval was 0.79-0.93, and cities with average WEF efficiency reaching the effective production frontier accounted for only 37.5%. The clustered distribution of the synergy levels intensified. The number of cities with primary, medium, more advanced, and advanced levels was 6, 6, 1, and 3, respectively, with primary and medium synergy levels dominating. The findings suggest that cities should strengthen regional exchanges and formulate targeted measures based on their own situations. In addition, CCEC should possess a comprehensive understanding of the interdependencies and conflicts that arise between resilience and efficiency throughout the decision-making procedure.

A Route to Two-Dimensional Room-Temperature Organometallic Multiferroics: The Marriage of d-p Spin Coupling and Structural Inversion Symmetry Breaking.

Two-dimensional (2D) room-temperature multiferroic materials are highly desirable but still very limited. Herein, we propose a potential strategy to obtain such materials in 2D metal-organic frameworks (MOFs) by utilizing the d-p direct spin coupling in conjunction with center-symmetry-breaking six-membered heterocyclic rings. Based on this strategy, a screening of 128 2D MOFs results in the identification of three multiferroics, that is, Cr(1,2-oxazine)2, Cr(1,2,4-triazine)2, and Cr(1,2,3,4-trazine)2, simultaneously exhibiting room-temperature ferrimagnetism and ferroelectricity/antiferroelectricity. The room-temperature ferrimagnetic order (306-495 K) in these MOFs originates from the strong d-p direct magnetic exchange interaction between Cr cations and ligand anions. Specifically, Cr(1,2-oxazine)2 exhibits ferroelectric behavior with an out-of-plane polarization of 4.24 pC/m, whereas the other two manifest antiferroelectric characteristics. Notably, all three materials present suitable polarization switching barriers (0.18-0.31 eV). Furthermore, these MOFs are all bipolar magnetic semiconductors with moderate band gaps, in which the spin direction of carriers can be manipulated by electrical gating.

IInception-CBAM-IBiGRU based fault diagnosis method for asynchronous motors.

Aiming at the problems of insufficient extraction of asynchronous motor fault features by traditional deep learning algorithms and poor diagnosis of asynchronous motor faults in robust noise environments, this paper proposes an end-to-end fault diagnosis method for asynchronous motors based on IInception-CBAM-IBiGRU. The method first uses a signal-to-grayscale image conversion method to convert one-dimensional vibration signals into two-dimensional images and initially extracts shallow features through two-dimensional convolution; then the Improved Inception (IInception) module is used as a residual block to learning features at different scales with a residual structure, and extracts its important feature information through the Convolutional Block Attention Module (CBAM) to extract important feature information and adjust the weight parameters; then the feature information is input to the Improved Bi-directional Gate Recurrent Unit (IBiGRU) to extract its timing features further; finally, the fault identification is achieved by the SoftMax function. The primary hyperparameters in the model are optimized by the Weighted Mean Of Vectors Algorithm (INFO). The experimental results show that the method is effective in fault diagnosis of asynchronous motors, with an accuracy rate close to 100%, and can still maintain a high accuracy rate under the condition of low noise ratio, with good robustness and generalization ability.

Tryptanthrin Derivative B1 Binds Viral Genome-Linked Protein (VPg) of Potato Virus Y.

Potato virus Y (PVY) is a plant virus that is known to be responsible for substantial economic losses in agriculture. Within the PVY genome, viral genome-linked protein (VPg) plays a pivotal role in the viral translation process. In this study, VPg was used as a potential target for analyzing the antiviral activity of tryptanthrin derivatives. In vitro, the dissociation constants of B1 with PVY VPg were 0.69 µmol/L (measured by microscale thermophoresis) and 4.01 µmol/L (measured via isothermal titration calorimetry). B1 also strongly bound to VPg proteins from three other Potyviruses. Moreover, in vivo experiments demonstrated that B1 effectively suppressed the expression of the PVY gene. Molecular docking experiments revealed that B1 formed a hydrogen bond with N121 and that no specific binding occurred between B1 and the PVY VPgN121A mutant. Therefore, N121 is a key amino acid residue in PVY VPg involved in B1 binding. These results highlight the potential of PVY VPg as a potential target for the development of antiviral agents.

Covalent organic framework with donor-acceptor structure for rapid and sensitive photothermal sensing detection.

Given the serious harm caused by dietary intake of diethylstilbestrol (DES), it is urgent to explore rapid and sensitive DES sensing methods. In this work, a photothermal DES immunochromatography sensor based on covalent organic framework (COF) was constructed. The performance of COF in the field of photothermal sensing was systematically investigated for the first time. A donor-acceptor type of COF with a photothermal conversion rate of 51.17 % was synthesized. The logarithm of the DES concentrations-temperature change value standard curve was plotted. The intensity of the photothermal sensing signal was inversely proportional to the sample concentration. The detection limit of the proposed photothermal method (0.24 µg·L-1) was 10 times higher than that of visual detection (3 µg·L-1). This work not only constructed a novel detection method for DES sensing, but also provided a feasible demonstration for the application of COF in photothermal sensing and expanded the application of their photothermal properties.

Interplay between the ß-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.

Metallo-ß-lactamases (MßLs) stand as significant resistant mechanism against ß-lactam antibiotics in Gram-negative bacteria. The worldwide dissemination of New Delhi metallo-ß-lactamases (NDMs) intensifies antimicrobial resistance, posing severe threats to human health due to the absence of inhibitors available in clinical therapy. L3, a flexible ß-hairpin loop flanking the active site in MßLs, has been proven to wield influence over the reaction process by assuming a crucial role in substrate recognition and intermediate stabilization. In principle, it potentially retards product release from the enzyme, consequently reducing the overall turnover rate although the details regarding this aspect remain inadequately elucidated. In this study, we crystallized NDM-1 in complex with three penicillin substrates, conducted molecular dynamics simulations, and measured the steady-state kinetic parameters. These analyses consistently unveiled substantial disparities in their interactions with loop L3. We further synthesized a penicillin V derivative with increased hydrophobicity in the R1 side chain and co-crystallized it with NDM-1. Remarkably, this compound exhibited much stronger dynamic interplay with L3 during molecular dynamics simulation, showed much lower Km and kcat values, and demonstrated moderate inhibitory capacity to NDM-1 catalyzed meropenem hydrolysis. The data presented here may provide a strategic approach for designing mechanism-based MßL inhibitors focusing on structural elements external to the enzyme's active center.

The molecular mechanism of "Dahuang-Shengjiang-Banxia decoction" in the treatment of diabetic kidney disease was verified based on network pharmacology and molecular docking.

Background: Explore the molecular mechanism of Dahuang-Shengjiang-Banxia Decoction (DSBD) in the treatment of diabetic kidney disease (DKD), using network pharmacology and molecular docking technology. Method: The effective ingredients and targets of the DSBD were taken from the TCMSP database, while the disease targets were obtained via GeneCards, OMIM, DrugBank, TTD, and DisGeNET. Cytoscape 3.9.1 was used to create a drug-ingredient-target network diagram. STRING databases are also used to analyze the Protein-Protein Interaction (PPI) network of intersecting targets. The core targets was obtained by the intersection of the differential genes screened from the intersection target and GEO, and the core targets was enriched by Gene ontology (GO), Kyoto gene and genome (KEGG), and Gene Set Enrichment Analysis (GSEA). CIBERSORTx was used for immunoinfiltration analysis, and then the core targets was analyzed by Nephroseq V5 and KIT for clinical correlation analysis and single-cell sequencing. Lastly, AutoDock Vina was used for molecular docking of both the core targets and the top active elements. Results: A total of 177 DSBD and 2906 DKD targets were screened. Six core targets were identified by screening, which were IL1B, MMP9, EGF, VEGFA, HIF1A, and PTGS2. The top 6 active ingredients are 6-gingerol, baicalin, oleic acid, ß-sitosterol, linolenic acid, and aloe emodin. The core targets has good docking activity with the active ingredient. Conclusion: DSBD may exert its therapeutic effect on DKD through multicomponent, multipath, and multi-target analyses. It is possible that VEGFA is a key target in therapy, and that the VEGF/PI3K/AKT signaling pathway plays a key role in therapy.

The mechanism of action and experimental verification of Gan-song Yin on renal clear cell carcinoma based on network pharmacology and bioinformatics.

BACKGROUND: Gan-song Yin (GSY) is originated from the scripture "Gan-song Pills", a medical work of the Ningxia ethnic minorities, and its treatment of kidney diseases has good results. Its method of treating Renal clear cell carcinoma (KIRC) is still unknown, nevertheless. METHODS: Firstly, utilizing a network pharmacology strategy to screen GSY for active components and targets and looking up KIRC-related targets in GeneCards and GEO databases. Secondly, protein interaction networks were constructed and analyzed for GO and KEGG enrichment. Molecular docking was then performed and clinical and other correlations of the network pharmacology results were analyzed using bioinformatic analysis methods. Finally, we performed in vitro cellular experiments with 786-O cells and ACHN cells to validate the results of network pharmacology and bioinformatic analysis. RESULTS: With the help of network pharmacological analysis, six hub targets were eliminated. Bioinformatics study revealed that the hub targets has clinically significant clinical guiding importance. The results showed that GSY inhibited the proliferation of 786-O cells and ACHN cells, induced cell apoptosis, blocked cell cycle, and reduced cell colony formation ability. qRT-PCR results showed that GSY promoted the expression of ALB and CASP3 genes, and inhibited the expression of EGFR, JUN, MYC and VEGFA genes. Western blot results showed that GSY could promote the expression of ALB and CASP3 protein, and inhibit the expression of EGFR, JUN, MYC and VEGFA protein. CONCLUSIONS: Network pharmacology and bioinformatics analysis showed that GSY could act on multiple targets through a variety of components to achieve the effect of treating KIRC. In this study, we confirmed that GSY inhibits KIRC by regulating the expression of core targets through in vitro cellular experiments, thus providing a reference for subsequent related studies.

Prognostic value and immunological role of PD-L1 gene in pan-cancer.

OBJECTIVE: PD-L1, a target of immune checkpoint blockade, has been proven to take the role of an oncogene in most human tumors. However, the role of PD-L1 in human pan-cancers has not yet been fully investigated. MATERIALS AND METHODS: Pan-cancer analysis was conducted to analyze expression, genetic alterations, prognosis analysis, and immunological characteristics of PD-L1. Estimating the correlation between PD-L1 expression and survival involved using pooled odds ratios and hazard ratios with 95% CI. The Kaplan-Meier (K-M) technique, COX analysis, and receiver operating characteristic (ROC) curves were applied to the survival analysis. Additionally, we investigated the relationships between PD-L1 and microsatellite instability (MSI), tumor mutational burden (TMB), DNA methyltransferases (DNMTs), the associated genes of mismatch repair (MMR), and immune checkpoint biomarkers using Spearman's correlation analysis. Also, immunohistochemical analysis and qRT-PCR were employed in evaluating PD-L1's protein and mRNA expression in pan-caner. RESULTS: PD-L1 showed abnormal mRNA and protein expression in a variety of cancers and predicted prognosis in cancer patients. Furthermore, across a variety of cancer types, the aberrant PD-L1 expression was connected to the MSI, MMR, TMB, drug sensitivity, and tumor immune microenvironment (TIME). Moreover, PD-L1 was significantly correlated with infiltrating levels of immune cells (T cell CD8 + , neutrophil, and so on). CONCLUSION: Our study provides a better theoretical basis and guidance for the clinical treatment of PD-L1.