A Hierarchical Graph Neural Network Framework for Predicting Protein-Protein Interaction Modulators with Functional Group Information and Hypergraph Structure.

Accurate prediction of small molecule modulators targeting protein-protein interactions (PPIMs) remains a significant challenge in drug discovery. Existing machine learning-based models rely on manual feature engineering, which is tedious and task-specific. Recently, deep learning models based on graph neural networks have made remarkable progress in molecular representation learning. However, many graph-based approaches ignore molecular hierarchical structure modeling guided by domain knowledge. In chemistry, the functional groups of a molecule determine its interaction with specific targets. Therefore, we propose a hierarchical graph neural network framework (called HiGPPIM) for predicting PPIMs by integrating atom-level and functional group-level features of molecules. HiGPPIM constructs atom-level and functional group-level graphs based on chemical knowledge and learns graph representations using graph attention networks. Furthermore, a hypergraph attention network is designed in HiGPPIM to aggregate and transform two-level graph information. We evaluate the performance of HiGPPIM on eight PPI families and two prediction tasks, namely PPIM identification and potency prediction. Experimental results demonstrate that HiGPPIM achieves state-of-the-art performance on both tasks and that using functional group information to guide PPIM prediction is effective. The source code and datasets are freely available at https://github.com/1zzt/HiGPPIM.

Apple E3 ligase MdPUB23 mediates ubiquitin-dependent degradation of MdABI5 to delay ABA-triggered leaf senescence.

ABSCISIC ACID-INSENSITIVE5 (ABI5) is a core regulatory factor that mediates the ABA signaling response and leaf senescence. However, the molecular mechanism underlying the synergistic regulation of leaf senescence by ABI5 with interacting partners and the homeostasis of ABI5 in the ABA signaling response remain to be further investigated. In this study, we found that the accelerated effect of MdABI5 on leaf senescence is partly dependent on MdbHLH93, an activator of leaf senescence in apple. MdABI5 directly interacted with MdbHLH93 and improved the transcriptional activation of the senescence-associated gene MdSAG18 by MdbHLH93. MdPUB23, a U-box E3 ubiquitin ligase, physically interacted with MdABI5 and delayed ABA-triggered leaf senescence. Genetic and biochemical analyses suggest that MdPUB23 inhibited MdABI5-promoted leaf premature senescence by targeting MdABI5 for ubiquitin-dependent degradation. In conclusion, our results verify that MdABI5 accelerates leaf senescence through the MdABI5-MdbHLH93-MdSAG18 regulatory module, and MdPUB23 is responsible for the dynamic regulation of ABA-triggered leaf senescence by modulating the homeostasis of MdABI5.

Effect mechanism of capsaicin and dihydrocapsaicin in chili on the oxidative stability of myoglobin in duck meat.

BACKGROUND: Myoglobin (Mb) in duck meat is commonly over-oxidized when heated at high temperatures, which may worsen the color of the meat. Enhancing the oxidative stability of Mb is essential for improving the color of duck meat. Capsaicin and dihydrocapsaicin (CA-DI) in chili exhibit antioxidant properties. This study investigated the effects of CA-DI on the structure and oxidative damage of Mb by fluorescence spectroscopy, differential scanning calorimetry analysis and particle size in duck meat during heat treatment. RESULTS: When the ratio of CA-DI to Mb was 10:1 g kg-1 and heat-treated for 36 min, oxymyoglobin significantly increased, and metmyoglobin significantly decreased compared with the control group (P < 0.05). In parallel, the carbonyl content of Mb in the CA-DI group decreased by 43.40 ± 0.10%, the sulfhydryl content increased by 188 ± 0.21%, and the free radical scavenging activity of Mb was significantly enhanced (P < 0.05). Moreover, the addition of CA-DI resulted in a significant decrease in the particle size of the Mb surface (P < 0.05). When the ratio of CA-DI to Mb was 10:1 g kg-1, CA-DI enhanced the thermal stability and significantly increased the thermal denaturation temperature of Mb. The molecular docking results indicated that hydrophobic interactions and hydrogen bonds were involved in the binding of CA-DI to Mb. CONCLUSION: CA-DI could combine with Mb and improve the oxidation stability of Mb in duck meat. This suggested that CA-DI could be a potential natural antioxidant that improves the color of meat products. © 2024 Society of Chemical Industry.

Rational molecular design converting fascaplysin derivatives to potent broad-spectrum inhibitors against bacterial pathogens via targeting FtsZ.

The filamentous temperature-sensitive mutant Z protein (FtsZ), a key player in bacterial cell division machinery, emerges as an attractive target to tackle the plight posed by the ever growing antibiotic resistance over the world. Therefore in this regard, agents with scaffold diversities and broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens are highly needed. In this study, a new class of marine-derived fascaplysin derivatives has been designed and synthesized by Suzuki-Miyaura cross-coupling. Some compounds exhibited potent bactericidal activities against a panel of Gram-positive (MIC = 0.024-6.25 µg/mL) and Gram-negative (MIC = 1.56-12.5 µg/mL) bacteria including methicillin-resistant S. aureus (MRSA). They exerted their effects by dual action mechanism via disrupting the integrity of the bacterial cell membrane and targeting FtsZ protein. These compounds stimulated polymerization of FtsZ monomers and bundling of the polymers, and stabilized the resulting polymer network, thus leading to the dysfunction of FtsZ in cell division. In addition, these agents showed negligible hemolytic activity and low cytotoxicity to mammalian cells. The studies on docking and molecular dynamics simulations suggest that these inhibitors bind to the hydrophilic inter-domain cleft of FtsZ protein and the insights obtained in this study would facilitate the development of potential drugs with broad-spectrum bioactivities.

PPII-AEAT: Prediction of protein-protein interaction inhibitors based on autoencoders with adversarial training.

Protein-protein interactions (PPIs) have shown increasing potential as novel drug targets. The design and development of small molecule inhibitors targeting specific PPIs are crucial for the prevention and treatment of related diseases. Accordingly, effective computational methods are highly desired to meet the emerging need for the large-scale accurate prediction of PPI inhibitors. However, existing machine learning models rely heavily on the manual screening of features and lack generalizability. Here, we propose a new PPI inhibitor prediction method based on autoencoders with adversarial training (named PPII-AEAT) that can adaptively learn molecule representation to cope with different PPI targets. First, Extended-connectivity fingerprints and Mordred descriptors are employed to extract the primary features of small molecular compounds. Then, an autoencoder architecture is trained in three phases to learn high-level representations and predict inhibitory scores. We evaluate PPII-AEAT on nine PPI targets and two different tasks, including the PPI inhibitor identification task and inhibitory potency prediction task. The experimental results show that our proposed PPII-AEAT outperforms state-of-the-art methods.

Bioinformatics analysis of the prognostic role of alternative splicing data in lung adenocarcinoma.

Background: As a post-transcriptional regulatory mechanism, alternative splicing (AS) is engaged in a variety of pathophysiological processes, and it has been widely reported in connection with the occurrence, progression, metastasis, and drug resistance of cancer. However, the research on AS in lung adenocarcinoma (LUAD) is very limited. In addition, the prognostic effect of AS event (ASE) on LUAD and its related mechanism are not clear. This study aimed to explore the role and potential prognostic value of ASE in LUAD. Methods: Relevant data and ASE datasets of the sample were acquired from The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases. We constructed a new prognostic criterion based on ASEs. Then, Cox regression and least absolute shrinkage and selection operator (LASSO) regression analysis were used to construct the model. Based on this model, the risk score of each ASE was calculated, and the reliability of this model was evaluated by Kaplan-Meier survival and receiver operating characteristic (ROC) curve analyses. Finally, these results were verified on different network platforms. Results: We identified seven types of ASEs related to survival. The prognostic risk model for ASEs was established. The Kaplan-Meier curve showed that compared to the low-risk group, the overall survival (OS) rate of LUAD patients in the high-risk group was lower. ROC curve analysis showed that the prognostic risk model of LUAD patients was well predicted, and the area under the curve (AUC) also confirmed this. Conclusions: This study screened the ASE related to the prognosis of LUAD patients, and provided a theoretical basis for further study of the correlation between ASE and the prognosis of LUAD patients. It has provided new ideas for developing new biomarkers and therapeutic targets for LUAD patients.

Vitamin B6 Turnover Predicts Long-term Mortality Risk in Patients with Type 2 Diabetes.

Background: Inflammation can increase vitamin B6 uptake and catabolism. Higher vitamin B6 turnover [4-pyridoxic acid (4-PA)/pyridoxal 5'-phosphate (PLP) ratio], was associated with mortality risk in the general population. Objectives: We aimed to investigate the association between 4-PA/PLP and long-term mortality in patients with type 2 diabetes mellitus (T2DM), an inflammatory disease. Methods: In this prospective cohort study from the National Health and Nutrition Examination Survey (NHANES) cycles 2005-2010, the concentrations of 4-PA and PLP in plasma were measured using high-performance liquid chromatography, with mortality data updated to 31 December 2019. We included 2074 patients with T2DM aged between 20 and 85 y at baseline. Results: There were 739 deaths among 2279 patients with T2DM with a median follow-up of 11.83 y. In the age- and sex-adjusted COX model (model 1), 4-PA/PLP was positively associated with mortality in patients with T2DM [hazard ratio (HR) and 95% confidence interval (CI) highest compared with lowest quartiles: 35.55 (18.29, 69.09); P < 0.001], and in model 3, which was adjusted for demographics as well as inflammation, nutrition, and renal function, high 4-PA/PLP concentrations remained an independent risk factor for mortality in patients with T2DM [HR (95% CI) highest compared with lowest quartiles: 5.03 (2.46, 10.30); P < 0.001]. In restricted cubic spline (RCS), the link between 4-PA/PLP and all-cause mortality displays a positive correlation. Patients with died within the previous 2 y were excluded, the sensitivity analysis had no effect on the association between 4-PA/PLP and mortality in patients with T2DM. Finally, comparable results were found in subgroup analyses of specific-cause mortality. Conclusion: Higher vitamin B6 turnover is associated with long-term mortality risk in patients with T2DM. 4-PA/PLP may serve as a convenient prognostic marker in T2DM management.

Predictors of amputation in patients with diabetic foot ulcers: a multi-centre retrospective cohort study.

PURPOSE: Investigating risk factors for amputation in patients with diabetic foot ulcer (DFU) and developing a nomogram prediction model. METHODS: We gathered case data of DFU patients from five medical institutions in Anhui Province, China. Following eligibility criteria, a retrospective case-control study was performed on data from 526 patients. RESULTS: Among the 526 patients (mean age: 63.32 ± 12.14), 179 were female, and 347 were male; 264 underwent amputation. Univariate analysis identified several predictors for amputation, including Blood type-B, Ambulation, history of amputation (Hx. Of amputation), Bacterial culture-positive, Wagner grade, peripheral arterial disease (PAD), and laboratory parameters (HbA1c, Hb, CRP, ALB, FIB, PLT, Protein). In the multivariate regression, six variables emerged as independent predictors: Blood type-B (OR = 2.332, 95%CI [1.488-3.657], p < 0.001), Hx. Of amputation (2.298 [1.348-3.917], p = 0.002), Bacterial culture-positive (2.490 [1.618-3.830], p <0.001), Wagner 3 (1.787 [1.049-3.046], p = 0.033), Wagner 4-5 (4.272 [2.444-7.468], p <0.001), PAD (1.554 [1.030-2.345], p = 0.036). We developed a nomogram prediction model utilizing the aforementioned independent risk factors. The model demonstrated a favorable predictive ability for amputation risk, as evidenced by its area under the receiver operating characteristics (ROC) curve of 0.756 and the well-fitted corrected nomogram calibration curve. CONCLUSION: Our findings underscore Blood type-B, Hx. Of amputation, Bacterial culture-positive, Wagner 3-5, and PAD as independent risk factors for amputation in DFU patients. The resultant nomogram exhibits substantial accuracy in predicting amputation occurrence. Timely identification of these risk factors can reduce DFU-related amputation rates.

Transcriptome Analysis of White- and Red-Fleshed Apple Fruits Uncovered Novel Genes Related to the Regulation of Anthocyanin Biosynthesis.

The red flesh coloration of apples is a result of a biochemical pathway involved in the biosynthesis of anthocyanins and anthocyanidins. Based on apple genome analysis, a high number of regulatory genes, mainly transcription factors such as MYB, which are components of regulatory complex MYB-bHLH-WD40, and several structural genes (PAL, 4CL, CHS, CHI, F3H, DFR, ANS, UFGT) involved in anthocyanin biosynthesis, have been identified. In this study, we investigated novel genes related to the red-flesh apple phenotype. These genes could be deemed molecular markers for the early selection of new apple cultivars. Based on a comparative transcriptome analysis of apples with different fruit-flesh coloration, we successfully identified and characterized ten potential genes from the plant hormone transduction pathway of auxin (GH3); cytokinins (B-ARR); gibberellins (DELLA); abscisic acid (SnRK2 and ABF); brassinosteroids (BRI1, BZR1 and TCH4); jasmonic acid (MYC2); and salicylic acid (NPR1). An analysis of expression profiles was performed in immature and ripe fruits of red-fleshed cultivars. We have uncovered genes mediating the regulation of abscisic acid, salicylic acid, cytokinin, and jasmonic acid signaling and described their role in anthocyanin biosynthesis, accumulation, and degradation. The presented results underline the relationship between genes from the hormone signal transduction pathway and UFGT genes, which are directly responsible for anthocyanin color transformation as well as anthocyanin accumulation during apple-fruit ripening.

Chinese expert consensus on imaging diagnosis of drug-resistant pulmonary tuberculosis.

Tuberculosis (TB) remains one of the major infectious diseases in the world with a high incidence rate. Drug-resistant tuberculosis (DR-TB) is a key and difficult challenge in the prevention and treatment of TB. Early, rapid, and accurate diagnosis of DR-TB is essential for selecting appropriate and personalized treatment and is an important means of reducing disease transmission and mortality. In recent years, imaging diagnosis of DR-TB has developed rapidly, but there is a lack of consistent understanding. To this end, the Infectious Disease Imaging Group, Infectious Disease Branch, Chinese Research Hospital Association; Infectious Diseases Group of Chinese Medical Association of Radiology; Digital Health Committee of China Association for the Promotion of Science and Technology Industrialization, and other organizations, formed a group of TB experts across China. The conglomerate then considered the Chinese and international diagnosis and treatment status of DR-TB, China's clinical practice, and evidence-based medicine on the methodological requirements of guidelines and standards. After repeated discussion, the expert consensus of imaging diagnosis of DR-PB was proposed. This consensus includes clinical diagnosis and classification of DR-TB, selection of etiology and imaging examination [mainly X-ray and computed tomography (CT)], imaging manifestations, diagnosis, and differential diagnosis. This expert consensus is expected to improve the understanding of the imaging changes of DR-TB, as a starting point for timely detection of suspected DR-TB patients, and can effectively improve the efficiency of clinical diagnosis and achieve the purpose of early diagnosis and treatment of DR-TB.

The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism.

The aromatic amino acids (AAAs) phenylalanine, tyrosine, and tryptophan are basic protein units and precursors of diverse specialized metabolites that are essential for plant growth. Despite their significance, the mechanisms that regulate AAA homeostasis remain elusive. Here, we identified a cytosolic aromatic aminotransferase, REVERSAL OF SAV3 PHENOTYPE 1 (VAS1), as a suppressor of arogenate dehydrogenase 2 (adh2) in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses determined that VAS1 uses AAAs as amino donors, leading to the formation of 3-carboxyphenylalanine and 3-carboxytyrosine. These pathways represent distinct routes for AAA metabolism that are unique to specific plant species. Furthermore, we show that VAS1 is responsible for cytosolic AAA biosynthesis, and its enzymatic activity can be inhibited by 3-carboxyphenylalanine. These findings provide valuable insights into the crucial role of VAS1 in producing 3-carboxy AAAs, notably via recycling of AAAs in the cytosol, which maintains AAA homeostasis and allows plants to effectively coordinate the complex metabolic and biosynthetic pathways of AAAs.

CO2-philicity to CO2-phobicity Transition on Smooth and Stochastic Rough Cu-like Substrate Surfaces.

CO2 on metal substrates is essential to CO2 liquefaction and transportation of CO2, yet the manipulation of the wettability of the CO2 and the elucidation of its underlying mechanism have not been fully achieved. Here, using molecular dynamics simulations, we report CO2 wetting characteristics on both smooth and stochastic rough Cu-like substrate surfaces. The results indicate that the apparent contact angle (CA) of the CO2 droplet on the smooth surface decreases from 180° to 0° as the CO2-solid characteristic interaction energy increases from 0.002 to 0.016 eV. In addition, the CAs become greater with increasing the density of surface asperities, regardless of the intrinsic surface wettability. This is attributed to the capillary drying-out of liquid CO2 molecules in gaps between surface asperities at the three-phase contact line of the droplet, which is usually overlooked in previous theoretical studies. Notably, the intrinsically CO2-philic surface transforms to the CO2-phobic due to an increase in the density of surface rugosity. Moreover, we verify the range of applicability of the CA prediction models concerning the nanoscale asperities. This work is beneficial for fully understanding the influence of nanoscale surface topography on CO2 wettability and shedding light on the design of functionalized and patterned surfaces to manipulate CO2 wettability.

Boric Acid-Functionalized Carbon Dots as a High-Performance Antibacterial Agent against Escherichia coli.

Bacterial infections and antibiotic abuse are a global threat to human health. In recent years, there has been a boom in research on antimicrobial agents with low toxicity and efficient nanomaterials. Boric acid-functionalized carbon dots (B-CDs) with negative surface charge were synthesized by the hydrothermal method. Covalent bonds were formed between the boric acid groups and the cis-diol groups of the polysaccharide in the bacterial cell wall, and numerous B-CDs were trapped on the bacterial surface. In the experiments of antibacterial activity, B-CDs presented strong bactericidal activity against Escherichia coli (E. coli) with a minimum bactericidal concentration of 12.5 µg/mL. The antibacterial mechanism suggested that B-CDs entered the cell interior by diffusion and posed significant damage to the double helix structure of E. coli DNA. Furthermore, B-CDs exhibited low toxicity. The results demonstrated that the novel antimicrobial B-CDs not only fought against E. coli infection and antibiotic misuse but also provided new ideas for safe and effective antimicrobial agents of carbon nanomaterials.

Natural Polymer-Based Hydrogels: From Polymer to Biomedical Applications.

Hydrogels prepared from natural polymer have attracted extensive attention in biomedical fields such as drug delivery, wound healing, and regenerative medicine due to their good biocompatibility, degradability, and flexibility. This review outlines the commonly used natural polymer in hydrogel preparation, including cellulose, chitosan, collagen/gelatin, alginate, hyaluronic acid, starch, guar gum, agarose, and dextran. The polymeric structure and process/synthesis of natural polymers are illustrated, and natural polymer-based hydrogels including the hydrogel formation and properties are elaborated. Subsequently, the biomedical applications of hydrogels based on natural polymer in drug delivery, tissue regeneration, wound healing, and other biomedical fields are summarized. Finally, the future perspectives of natural polymers and hydrogels based on them are discussed. For natural polymers, novel technologies such as enzymatic and biological methods have been developed to improve their structural properties, and the development of new natural-based polymers or natural polymer derivatives with high performance is still very important and challenging. For natural polymer-based hydrogels, novel hydrogel materials, like double-network hydrogel, multifunctional composite hydrogels, and hydrogel microrobots have been designed to meet the advanced requirements in biomedical applications, and new strategies such as dual-cross-linking, microfluidic chip, micropatterning, and 3D/4D bioprinting have been explored to fabricate advanced hydrogel materials with designed properties for biomedical applications. Overall, natural polymeric hydrogels have attracted increasing interest in biomedical applications, and the development of novel natural polymer-based materials and new strategies/methods for hydrogel fabrication are highly desirable and still challenging.

pH/Temperature Dual-Responsive Protein-Polymer Conjugates for Potential Therapeutic Hypothermia in Ischemic Stroke.

Thrombolytic therapy for ischemic stroke still has several limitations, such as a narrow therapeutic time window and adverse effects. Therapeutic hypothermia is a neuroprotective strategy for stroke. In this study, we developed pH/temperature dual-responsive protein-polymer conjugates (PEG-uPA-PEG-PPG-PEG) by modifying a urokinase-type plasminogen activator (uPA) with polyethylene glycol (PEG) and poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEG-PPG-PEG, a thermosensitive polymer) via pH-sensitive imine bonds and disulfide bonds, respectively. At 37 °C and pH 7.4 (normothermia and physiological pH), PEG-uPA-PEG-PPG-PEG exhibits antiprotease hydrolysis and masked bioactivity of uPA due to the protective effect of the polymer segments wrapped around the protein surface. However, at 33 °C and pH 6.0 (hypothermia and pH at the thrombotic site), uPA loses the protective effect and recovers its bioactivity due to PEG dissociation and PEG-PPG-PEG stretching. The masked bioactivity of uPA at normothermia and physiological pH could reduce the risk of acute hemorrhage complication, and the recovery of protein activity at acidic pH and 33 °C is of great significance for thrombolytic therapy at mild hypothermia. Thus, PEG-uPA-PEG-PPG-PEG provides promising potential for therapeutic hypothermia in ischemic stroke.

Application of hair transplantation combined with platelet-rich plasma injection for the treatment of androgenic alopecia.

Androgenic alopecia is a type of hair loss condition that is influenced by both genetic and environmental factors. This study aimed to investigate the effectiveness of combining hair transplantation with platelet-rich plasma injection for treating androgenic alopecia. From June 2019 to September 2021, a total of 147 patients with androgenic alopecia were selected and treated by our department. Out of these, 72 patients were assigned to the treatment group and received hair transplantation along with platelet-rich plasma treatment. The remaining 75 cases constituted the control group, receiving only hair transplantation. Clinical data was obtained by reviewing the patients' medical records and case reports. The area of hair loss in the treatment group was significantly smaller than that in the control group. The score of the hair pulling test in the treatment group was significantly lower than that in the control group. The hair regeneration score in the treatment group was significantly higher than that in the control group. After treatment, the total area of skin lesions in the treatment group was significantly reduced compared to the control group. There was a statistically significant difference between the two groups. Our study indicates that combining hair transplantation with platelet-rich plasma is superior to hair transplantation alone for the treatment of androgenic alopecia. This combination therapy shows promising potential for clinical applications.

Pinostrobin, a dietary bioflavonoid exerts antioxidant, anti-inflammatory, and anti-apoptotic protective effects against methotrexate-induced ovarian toxicity in rats.

This study investigated the protective activities of pinostrobin (PIN) against methotrexate (MTX)-induced ovarian toxicity. Female rats were administered with PIN (50 mg/kg) for 4 weeks, while MTX was administered from weeks 2-4 of PIN treatment. Serum hormonal profiles, ovarian oxidative stress, inflammatory and apoptotic biomarkers as well as ovarian histomorphometry were evaluated. MTX administration elicited profound deficit in serum progesterone and estrogen (E2) levels, while luteinizing hormone (LH) and follicle stimulating hormone (FSH) were significantly increased. Additionally, MTX administration was associated with significant increases in ovarian malondialdehyde, nitric oxide, NF-кB, TNF-α, IL-6, IL-1ß, iNOS and caspase-3 activity, as well as notable reduction in the activities of glutathione peroxidase, catalase and superoxide dismutase as well as the level of glutathione. Whereas, treatment with PIN significantly decreased serum levels of FSH and LH, as well as ovarian levels of NO, MDA, caspase 3, NF-κB, IL-1ß, IL-6, TNF-α and iNOS. PIN also significantly upregulated GSH, GPx, CAT and SOD in the ovarian tissues as well as increased serum E2 and progesterone levels compared to the MTX group. Furthermore, PIN significantly restored altered ovarian histoarchitecture in the treated group. These findings suggests that PIN exerts protective effects against MTX-triggered ovarian damages.

Scintillation mitigation via the cross phase of the Gaussian Schell-model beam in a turbulent atmosphere.

Scintillation is an important problem for laser beams in free space optical (FSO) communications. We derived the analytical expressions for the scintillation index of a Gaussian Schell-model beam with cross phase propagation in a turbulent atmosphere. The numerical results show that the quadratic phase can be used to mitigate turbulence-induced scintillation, and the effects of the turbulent strength and beam parameters at the source plane on the scintillation index are analyzed. The variation trend of the experimentally measured scintillation index is consistent with the numerical results. Our results are expected to be useful for FSO communications.