Genome-wide identification, expression pattern and genetic variation analysis of SWEET gene family in barley reveal the artificial selection of HvSWEET1a during domestication and improvement.

SWEET (Sugars Will Eventually be Exported Transporter) proteins, an essential class of sugar transporters, are involved in vital biological processes of plant growth and development. To date, systematical analysis of SWEET family in barley (Hordeum vulgare) has not been reported. In this study, we genome-wide identified 23 HvSWEET genes in barley, which were further clustered into four clades by phylogenetic tree. The members belonging to the same clade showed relatively similar gene structures and conserved protein motifs. Synteny analysis confirmed the tandem and segmental duplications among HvSWEET genes during evolution. Expression profile analysis demonstrated that the patterns of HvSWEET genes varied and the gene neofunctionalization occurred after duplications. Yeast complementary assay and subcellular localization in tobacco leaves suggested that HvSWEET1a and HvSWEET4, highly expressed in seed aleurone and scutellum during germination, respectively, functioned as plasma membrane hexose sugar transporters. Furthermore, genetic variation detection indicated that HvSWEET1a was under artificial selection pressure during barley domestication and improvement. The obtained results facilitate our comprehensive understanding and further functional investigations of barley HvSWEET gene family, and also provide a potential candidate gene for de novo domestication breeding of barley.

Machine learning for prediction of bleeding in acute myocardial infarction patients after percutaneous coronary intervention.

Background: Prediction of bleeding is critical for acute myocardial infarction (AMI) patients after percutaneous coronary intervention (PCI). Machine learning methods can automatically select the combination of the important features and learn their underlying relationship with the outcome. Objectives: We aimed to evaluate the predictive value of machine learning methods to predict in-hospital bleeding for AMI patients. Design: We used data from the multicenter China Acute Myocardial Infarction (CAMI) registry. The cohort was randomly partitioned into derivation set (50%) and validation set (50%). We applied a state-of-art machine learning algorithm, eXtreme Gradient Boosting (XGBoost), to automatically select features from 98 candidate variables and developed a risk prediction model to predict in-hospital bleeding (Bleeding Academic Research Consortium [BARC] 3 or 5 definition). Results: A total of 16,736 AMI patients who underwent PCI were finally enrolled. 45 features were automatically selected and were used to construct the prediction model. The developed XGBoost model showed ideal prediction results. The area under the receiver-operating characteristic curve (AUROC) on the derivation data set was 0.941 (95% CI = 0.909-0.973, p < 0.001); the AUROC on the validation set was 0.837 (95% CI = 0.772-0.903, p < 0.001), which was better than the CRUSADE score (AUROC: 0.741; 95% CI = 0.654-0.828, p < 0.001) and ACUITY-HORIZONS score (AUROC: 0.731; 95% CI = 0.641-0.820, p < 0.001). We also developed an online calculator with 12 most important variables (http://101.89.95.81:8260/), and AUROC still reached 0.809 on the validation set. Conclusion: For the first time, we developed the CAMI bleeding model using machine learning methods for AMI patients after PCI. Trial registration: NCT01874691. Registered 11 Jun 2013.

Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method.

Accurate estimation of solvation free energy (SFE) lays the foundation for accurate prediction of binding free energy. The Poisson-Boltzmann (PB) or generalized Born (GB) combined with surface area (SA) continuum solvation method (PBSA and GBSA) have been widely used in SFE calculations because they can achieve good balance between accuracy and efficiency. However, the accuracy of these methods can be affected by several factors such as the charge models, polar and nonpolar SFE calculation methods and the atom radii used in the calculation. In this work, the performance of the ABCG2 (AM1-BCC-GAFF2) charge model as well as other two charge models, that is, RESP (Restrained Electrostatic Potential) and AM1-BCC (Austin Model 1-bond charge corrections), on the SFE prediction of 544 small molecules in water by PBSA/GBSA was evaluated. In order to improve the performance of the PBSA prediction based on the ABCG2 charge, we further explored the influence of atom radii on the prediction accuracy and yielded a set of atom radius parameters for more accurate SFE prediction using PBSA based on the ABCG2/GAFF2 by reproducing the thermodynamic integration (TI) calculation results. The PB radius parameters of carbon, oxygen, sulfur, phosphorus, chloride, bromide and iodine, were adjusted. New atom types, on, oi, hn1, hn2, hn3, were introduced to further improve the fitting performance. Then, we tuned the parameters in the nonpolar SFE model using the experimental SFE data and the PB calculation results. By adopting the new radius parameters and new nonpolar SFE model, the root mean square error (RMSE) of the SFE calculation for the 544 molecules decreased from 2.38 to 1.05 kcal/mol. Finally, the new radius parameters were applied in the prediction of protein-ligand binding free energies using the MM-PBSA method. For the eight systems tested, we could observe higher correlation between the experiment data and calculation results and smaller prediction errors for the absolute binding free energies, demonstrating that our new radius parameters can improve the free energy calculation using the MM-PBSA method.

Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2.

In tauopathies such as Alzheimer's disease (AD), aberrant phosphorylation causes the dissociation of tau proteins from microtubules. The dissociated tau then aggregates into sequent forms from soluble oligomers to paired helical filaments and insoluble neurofibrillary tangles (NFTs). NFTs is a hallmark of AD, while oligomers are found to be the most toxic form of the tau aggregates. Therefore, understanding tau oligomerization with regard to abnormal phosphorylation is important for the therapeutic development of AD. In this study, we investigated the impact of phosphorylated Ser289, one of the 40 aberrant phosphorylation sites of full-length tau proteins, on monomeric and dimeric structures of tau repeat R2 peptides. We carried out intensive replica exchange molecular dynamics simulation with a total simulation time of up to 0.1 ms. Our result showed that the phosphorylation significantly affected the structures of both the monomer and the dimer. For the monomer, the phosphorylation enhanced ordered-disordered structural transition and intramolecular interaction, leading to more compactness of the phosphorylated R2 compared to the wild-type one. As to the dimer, the phosphorylation increased intermolecular interaction and ß-sheet formation, which can accelerate the oligomerization of R2 peptides. This result suggests that the phosphorylation at Ser289 is likely to promote tau aggregation. We also observed a phosphorylated Ser289-Na+-phosphorylated Ser289 bridge in the phosphorylated R2 dimer, suggesting an important role of cation ions in tau aggregation. Our findings suggest that phosphorylation at Ser289 should be taken into account in the inhibitor screening of tau oligomerization.

Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method.

The logarithm of n-octanol-water partition coefficient (logP) is frequently used as an indicator of lipophilicity in drug discovery, which has substantial impacts on the absorption, distribution, metabolism, excretion, and toxicity of a drug candidate. Considering that the experimental measurement of the property is costly and time-consuming, it is of great importance to develop reliable prediction models for logP. In this study, we developed a transfer free energy-based logP prediction model-FElogP. FElogP is based on the simple principle that logP is determined by the free energy change of transferring a molecule from water to n-octanol. The underlying physical method to calculate transfer free energy is the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), thus this method is named as free energy-based logP (FElogP). The superiority of FElogP model was validated by a large set of 707 structurally diverse molecules in the ZINC database for which the measurement was of high quality. Encouragingly, FElogP outperformed several commonly-used QSPR or machine learning-based logP models, as well as some continuum solvation model-based methods. The root-mean-square error (RMSE) and Pearson correlation coefficient (R) between the predicted and measured values are 0.91 log units and 0.71, respectively, while the runner-up, the logP model implemented in OpenBabel had an RMSE of 1.13 log units and R of 0.67. Given the fact that FElogP was not parameterized against experimental logP directly, its excellent performance is likely to be expanded to arbitrary organic molecules covered by the general AMBER force fields.

First report of Fusarium meridionale causing Fusarium head blight of wheat in Henan Province, China.

Fusarium graminearum and F. asiaticum have been found as a major cause of Fusarium head blight (FHB) of wheat (Triticum aestivum L.), especially in Henan Province of China (Zhang et al. 2014; Xu et al. 2021). In May 2021, a survey to determine the composition of Fusarium species infecting wheat heads was conducted in commercial fields in Henan. A total of 395 diseased spikes with premature whitening symptom were collected from 31 commercial fields in Henan. Symptomatic spikelets were excised, surface-sterilized for 10 s in 70% ethanol followed by 1 min in 3% sodium hypochlorite, rinsed three times with autoclaved distilled water, and then plated onto potato dextrose agar (PDA) medium. Isolated colonies that resembled Fusarium species were transferred to fresh PDA plates and purified using a single spore method. Species were identified based on sequence analysis of the translation elongation factor-1α (TEF) and trichothecene 3-Oacetyltransferase (Tri 101) gene (Proctor et al. 2009). The results indicated that F. graminearum (43.3%), F. asiaticum (47.8%), F. pseudograminearum (6.6%) were the main causal agents of FHB in Henan. However, nine isolates (2.3%) were found to be identical to F. meridionale by sequence comparison in GenBank, and eight isolates of which came from three fields with 1% to 2% diseased spikes near Reservoir Luhun (34.1255° N, 112.1111° E, altitude: 388 m above sea level), Songxian County of Henan. The isolates of F. meridionale were transferred onto carnation leaf agar (CLA) and incubated at 20℃ under black light blue illumination. Macroconidia were abundant, relatively slender, curved to almost straight, commonly six- to seven-septate, and 27.0 to 61.0 (average 44.0) µm × 3.2 to 6.8 (average 5.3) µm. Microconidia were not observed. The TEF sequences (Accession nos. OM460748 to OM460756) and the Tri 101 sequences (OM460759 to OM460767) of the nine isolates showed 99 to 100% similarity with the TEF and Tri 101 sequences of F. meridionale NRRL 28436 and NRRL 28723 (AF212435 and AF212436 (TEF); AF212582 and AF212683 (Tri 101)). To complete Koch's postulates, the pathogenicity of the fungus was tested by using the single floret inoculation method by injecting 20-µl conidial suspension (5 × 105 conidia per milliliter) into healthy inflorescences of wheat cultivar Bainong 207 at anthesis in the field. Another 30 healthy inflorescences were injected with sterile distilled water. The heads were covered with polyethylene bags that were removed after 2 days. Twenty days after inoculation, while control inflorescences were asymptomatic, the F. meridionale-inoculated inflorescences showed 12% bleached spikelets per spike. By using the methodology described above, the fungus was re-isolated from infected spikelets of inoculated wheat heads but not from the controls. Although F. meridionale has frequently been reported in association with Fusarium ear rot (FER) of maize in Chongqing City and Gansu Province (Zhang et al. 2014; Zhou et al. 2018), and rice FER in Sichuan Province (Dong et al. 2020), to our knowledge, this is the first report of F. meridionale from diseased wheat heads in Henan, China. Further investigation is needed to gain a better understanding of this species by collecting isolates from different cropping system in Henan, which maize-wheat and rice-wheat rotation fields have coexisted in the region.

Carboxyl-terminal modulator protein (CTMP) deficiency mitigates denervation-induced skeletal muscle atrophy.

Denervated skeletal muscles show decreased Akt activity and phosphorylation, resulting in atrophy. Akt inhibits downstream transcription of atrophy-associated ubiquitin ligases like muscle ring-finger protein 1 (MuRF-1). In addition, reduced Akt signaling contributes to aberrant protein synthesis in muscles. In ALS mice, we recently found that carboxyl-terminator modulator protein (CTMP) expression is increased and correlated with reduced Akt signaling in atrophic skeletal muscle. CTMP has also been implicated in promoting muscle degeneration and catabolism in an in vitro muscle atrophy model. The present study examined whether sciatic nerve injury (SNI) stimulated CTMP expression in denervated skeletal muscle during muscle atrophy. We hypothesized that CTMP deficiency would reduce neurogenic atrophy and reverse Akt signaling downregulation. Compared to the unaffected contralateral muscle, wild-type (WT) gastrocnemius muscle had a significant increase in CTMP (p < 0.05). Furthermore, denervated CTMP knockout (CTMP-KO) gastrocnemius weighed more than WT muscle (p < 0.05). Denervated CTMP-KO gastrocnemius also showed higher Akt and downstream glycogen synthase kinase 3ß (GSK3ß) phosphorylation compared to WT muscle (p < 0.05) as well as ribosomal proteins S6 and 4E-BP1 phosphorylation (p < 0.001 and p < 0.05, respectively). Moreover, CTMP-KO mice showed significantly lower levels of E3 ubiquitin ligase MuRF-1 and myostatin than WT muscle (p < 0.05). Our findings suggest that CTMP is essential to muscle atrophy after denervation and it may act by reducing Akt signaling, protein synthesis, and increasing myocellular catabolism.

Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study.

Phosphorylation, the most popular post-translational modification of tau protein, plays an important role in regulating tau physiological functions. However, aberrant phosphorylation attenuates the binding affinity of tau to a microtubule (MT), resulting in MT destabilization followed by accumulation of neurofibrillary tangles in the brain. There are in total 85 potential phosphorylation sites in a full-length tau protein, and about half of them are abnormal as they occur in tau of Alzheimer's disease (AD) brain only. In this work, we investigated the impact of abnormal Ser289, Ser293, and Ser289/Ser293 phosphorylation on tau R2-MT binding and the conformation of tau R2 using molecular dynamics simulation. We found that the phosphorylation significantly affected R2-MT interaction and reduced the binding affinity of tau R2 peptides to MTs. Free energy decomposition analysis suggested that the post-translational modified residues themselves made a significant contribution to destabilize tau repeat R2-MT binding. Therefore, the phosphorylation may attenuate the binding affinity of tau to MTs. Additionally, the phosphorylation also enhanced helix-coil transition of monomeric R2 peptides, which may result in the acceleration of tau aggregation. Since these phosphorylated sites have not been examined in previous experimental studies, our finding through all-atom molecular dynamics simulations and free energy analysis can inspire experimental scientists to investigate the impact of the phosphorylation on MT binding and aggregation of full-length tau and the pathological roles of the phosphorylation at those sites in AD development through in vitro/in vivo assays.

The influence of shorter red blood cell lifespan on the rate of HbA1c target achieved in type 2 diabetes patients with a HbA1c detection value lower than 7.

BACKGROUND: Variations in the red blood cell (RBC) lifespan can affect glycosylated hemoglobin (HbA1c) test values, but there is still a lack of evidence regarding how and to what degree the RBC lifespan influences HbA1c in the type 2 diabetes mellitus (T2DM) population owing to the restriction of traditional RBC lifespan-detection means. This study aimed to investigate the influence of RBC lifespan variation on HbA1c values in T2DM patients with a HbA1c detection value lower than 7%. METHODS: Patients with HbA1c <7% were divided into two groups: RBC lifespan <90 days and RBC lifespan ≥90 days. We collected blood glucose levels at seven time points for three consecutive months, assessed the HbA1c and glycosylated albumin levels, and calculated the hemoglobin glycation index (HGI) for each patient. RESULTS: There were no statistical differences in the HbA1c value between two groups, but the estimated glycosylated hemoglobin (eHbA1c) was significantly higher in patients with an RBC lifespan <90 days. The proportion of the eHbA1c ≥7% in the group with an RBC lifespan <90 days was significantly higher than the other group (33.87% vs. 12.50%, p < .01). Pearson analysis showed a significant negative correlation between RBC lifespan and the HGI in patients with T2DM (r = -0.348, p < .01). CONCLUSION: A reduced RBC lifespan in T2DM patients caused a noticeable underestimate of the blood glucose levels as presented by HbA1c detection value.

Investigation of the Structure of Full-Length Tau Proteins with Coarse-Grained and All-Atom Molecular Dynamics Simulations.

Tau proteins not only have many important biological functions but also are associated with several neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease (AD). However, it is still a challenge to identify the atomic structure of full-length tau proteins due to their lengthy and disordered characteristics and the factor that there are no crystal structures of full-length tau proteins available. We performed multi- and large-scale molecular dynamics simulations of the full-length tau monomer (the 2N4R isoform and 441 residues) in aqueous solution under biological conditions with coarse-grained and all-atom force fields. The obtained atomic structures produced radii of gyration and chemical shifts that are in excellent agreement with those of experiment. The generated monomer structure ensemble would be very useful for further studying the oligomerization mechanism and discovering tau oligomerization inhibitors, which are important events in AD drug development.

ssDNA-C3N4 conjugates-based nanozyme sensor array for discriminating mycotoxins.

A nanozyme sensor array based on the ssDNA-distensible C3N4 nanosheet sensor elements for discriminating multiple mycotoxins commonly existing in contaminated cereals has been explored. The sensor array exploited (a) three DNA nonspecific sequences (A40, T40, C40) absorbed on the C3N4 nanosheets as sensor elements catalyzing the oxidation of TMB; (b) the presence of five mycotoxins affected the catalytic activity of three nanozymes with various degrees. The parameter (A0-A) was employed as the signal output to obtain the response patterns for different mycotoxins with the same concentration where A0 and A were the absorption peak values at 650 nm of oxTMB in the absence and presence of target mycotoxins, respectively. After the raw data was subjected to principal component analysis, 3D canonical score plots were obtained. The sensor array was capable of separating five mycotoxins from each other with 100% accuracy even if the concentration of the mycotoxins was as low as 1 nM. Moreover, the array performed well in discriminating the mycotoxin mixtures with different ratios. Importantly, the practicality of this sensor array was demonstrated by discriminating the five mycotoxins spiking in corn-free samples in 3D canonical score plots, validating that the sensor array can act as a flexible detection tool for food safety. A nanozyme sensor array was developed based on the ssDNA-distensible C3N4 NSs sensor elements for discriminating muitiple mycotoxins.

First report of Fusarium falciforme causing root rot of soybean (Glycine max L.) in Henan, China.

Soybean (Glycine max L.) is an important crop in China owing to its high oil and protein content, with approximately 9.88 million ha of production in 2020. In September 2021, soybean plants showing wilting, root necrosis, and brown discoloration were observed, with an average incidence of approximately 36% in seven fields in Yongcheng City and Shangqiu City, Henan, China. Fungi were isolated from small pieces of symptomatic root tissues after being surface-sterilized (70% ethanol for 50 s followed by 3% NaClO for 1.0 min), rinsed three times in sterile distilled water, and then placed on PDA and incubated at 25℃ for 5 days in the dark. Single-spore cultures of twenty isolates were obtained by dilution plating (Leslie and Summerell 2006), and then were cultured on carnation leaf agar at 25℃ for 14 days. Macroconidia were mostly 3-septate, hyaline, falcate, with slightly curved apexes, with well-developed foot cells and blunt apical cells, and measured 29.3 to 45.0 (average 34.7) µm × 4.6 to 8.0 (average 6.0) µm. Microconidia were one to two celled, hyaline, and measured 11.9 to 29.0 (average 20.1) µm × 3.9 to 7.6 (average 5.7) µm. These morphological characteristics were consistent with previous descriptions of the Fusarium solani species complex (FSSC) (Leslie and Summerell 2006; Summerell et al. 2003). Partial sequences of translation elongation factor-1α (TEF) and RNA polymerase II subunit (RPB2) gene were PCR amplified using region specific primers as described by O'Donnell et al. (2008). The nucleotide sequences obtained from twenty isolates were deposited in GenBank with accession numbers of ON375405-ON375423, ON697187 (TEF) and ON331917-ON331936 (RPB2). Phylogenetic analysis revealed the isolates were nested within F. falciforme based on the DNA sequences of the above two genes (Chitrampalam and Nelson 2016). Pathogenicity tests of two representative isolates (21BeanYC3-3 and 21BeanYC7-5) were performed on two-week-old healthy soybean seedlings (cv. Shengdou 101) by injecting and cutting root method with a conidial suspension (1×106 conidia per mL) of F. falciforme (2 mL to one seedling). Control seedlings were inoculated with 2 mL distilled water. After 40 days under 25℃, 16h light/8h dark, the root system of all inoculated soybean plants exhibited dark brown lesions over the entire taproot, while control plants remained healthy. The fungus was reisolated from inoculated plants and identified as F. falciforme based on morphological characteristics and molecular methods described above. To our knowledge, this is the first report of root rot in soybean (Glycine max L.) caused by F. falciforme in Henan, China. The results are important for soybean production and breeding programs.

Arf GTPase activates the WAVE regulatory complex through a distinct binding site.

Cross-talk between Rho- and Arf-family guanosine triphosphatases (GTPases) plays an important role in linking the actin cytoskeleton to membrane protrusions, organelle morphology, and vesicle trafficking. The central actin regulator, WAVE regulatory complex (WRC), integrates Rac1 (a Rho-family GTPase) and Arf signaling to promote Arp2/3-mediated actin polymerization in many processes, but how WRC senses Arf signaling is unknown. Here, we have reconstituted a direct interaction between Arf and WRC. This interaction is greatly enhanced by Rac1 binding to the D site of WRC. Arf1 binds to a previously unidentified, conserved surface on the Sra1 subunit of WRC, which, in turn, drives WRC activation using a mechanism distinct from that of Rac1. Mutating the Arf binding site abolishes Arf1-WRC interaction, disrupts Arf1-mediated WRC activation, and impairs lamellipodia formation and cell migration. This work uncovers a new mechanism underlying WRC activation and provides a mechanistic foundation for studying how WRC-mediated actin polymerization links Arf and Rac signaling in cells.

Oncogenic role of microRNA-19b-3p-mediated SOCS3 in glioma through activation of JAK-STAT pathway.

The altered expression of microRNA (miRNA) has been implicated in glioma. Here, the current study aimed to clarify the oncogenic effects of miR-19b-3p on cellular processes of glioma and to elucidate the underlying mechanism associated with SOCS3 and the JAK-STAT signaling pathway. Differentially expressed genes related to glioma were initially identified via microarray analysis. Twenty-five glioma patients were selected for clinical data collection, while additional 12 patients with traumatic brain injuries were selected as controls. Cell senescence was assessed by ß-galactosidase staining, proliferation by MTT assay and apoptosis by flow cytometry following gain- and/or loss-of-function of miR-19b-3p or SOCS3. Glioma xenograft mouse model was developed through subcutaneous injection to nude mice to provide evidence in vivo. The glioma patients exhibited overexpressed miR-19b-3p and poorly-expressed SOCS3. SOCS3 was identified as a target gene of miR-19b-3p through dual-luciferase reporter gene assay. miR-19b-3p repressed SOCS3 expression and activated the JAK-STAT signaling pathway. Furthermore, miR-19b-3p inhibition promoted apoptosis and senescence, and suppressed cell proliferation through inactivation of the JAK-STAT signaling pathway and up-regulation of SOCS3. The reported regulatory axis was validated in nude mice as evidenced by suppressed tumor growth. Taken together, this study demonstrates that miR-19b-3p facilitates glioma progression via activation of the JAK-STAT signaling pathway by targeting SOCS3, highlighting a novel therapeutic target for glioma treatment.

Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse.

It has been widely accepted that cancer cells are softer than their normal counterparts. This motivates us to propose, as a proof-of-concept, a method for the efficient delivery of therapeutic agents into cancer cells, while normal cells are less affected. The basic idea of this method is to use a water jet generated by the collapse of the bubble under shockwaves to perforate pores in the cell membrane. Given a combination of shockwave and bubble parameters, the cancer membrane is more susceptible to bending, stretching, and perforating than the normal membrane because the bending modulus of the cancer cell membrane is smaller than that of the normal cell membrane. Therefore, the therapeutic agent delivery into cancer cells is easier than in normal cells. Adopting two well-studied models of the normal and cancer membranes, we perform shockwave induced bubble collapse molecular dynamics simulations to investigate the difference in the response of two membranes over a range of shockwave impulse 15-30 mPa s and bubble diameter 4-10 nm. The simulation shows that the presence of bubbles is essential for generating a water jet, which is required for perforation; otherwise, pores are not formed. Given a set of shockwave impulse and bubble parameters, the pore area in the cancer membrane is always larger than that in the normal membrane. However, a too strong shockwave and/or too large bubble results in too fast disruption of membranes, and pore areas are similar between two membrane types. The pore closure time in the cancer membrane is slower than that in the normal membrane. The implications of our results for applications in real cells are discussed in some details. Our simulation may be useful for encouraging future experimental work on novel approaches for cancer treatment.

A prognostic risk model for glioma patients by systematic evaluation of genomic variations.

The overall survival rate of gliomas has not significantly improved despite new effective treatments, mainly due to tumor heterogeneity and drug delivery. Here, we perform an integrated clinic-genomic analysis of 1, 477 glioma patients from a Chinese cohort and a TCGA cohort and propose a potential prognostic model for gliomas. We identify that SBS11 and SBS23 mutational signatures are associated with glioma recurrence and indicate worse prognosis only in low-grade type of gliomas and IDH-Mut subtype. We also identify 42 genomic features associated with distinct clinical outcome and successfully used ten of these to develop a prognostic risk model of gliomas. The high-risk glioma patients with shortened survival were characterized by high level of frequent copy number alterations including PTEN, CDKN2A/B deletion, EGFR amplification, less IDH1 or CIC gene mutations, high infiltration levels of immunosuppressive cells and activation of G2M checkpoint and Oxidative phosphorylation oncogenic pathway.

ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction.

Lipophilicity (logD) and aqueous solubility (logSw) play a central role in drug development. The accurate prediction of these properties remains to be solved due to data scarcity. Current methodologies neglect the intrinsic relationships between physicochemical properties and usually ignore the ionization effects. Here, we propose an attention-driven mixture-of-experts (MoE) model named ALipSol, which explicitly reproduces the hierarchy of task relationships. We adopt the principle of divide-and-conquer by breaking down the complex end point (logD or logSw) into simpler ones (acidic pKa, basic pKa, and logP) and allocating a specific expert network for each subproblem. Subsequently, we implement transfer learning to extract knowledge from related tasks, thus alleviating the dilemma of limited data. Additionally, we substitute the gating network with an attention mechanism to better capture the dynamic task relationships on a per-example basis. We adopt local fine-tuning and consensus prediction to further boost model performance. Extensive evaluation experiments verify the success of the ALipSol model, which achieves RMSE improvement of 8.04%, 2.49%, 8.57%, 12.8%, and 8.60% on the Lipop, ESOL, AqSolDB, external logD, and external logS data sets, respectively, compared with Attentive FP and the state-of-the-art in silico tools. In particular, our model yields more significant advantages (Welch's t-test) for small training data, implying its high robustness and generalizability. The interpretability analysis proves that the atom contributions learned by ALipSol are more reasonable compared with the vanilla Attentive FP, and the substitution effects in benzene derivatives agreed well with empirical constants, revealing the potential of our model to extract useful patterns from data and provide guidance for lead optimization.

Glycyrrhizin mitigates acute lung injury by inhibiting the NLRP3 inflammasome in vitro and in vivo.

ETHNOPHARMACOLOGICAL RELEVANCE: Glycyrrhiza glabra L. is a widely used traditional Chinese medicine with antipyretic, detoxification, antibacterial and therapeutic effects against various diseases, including liver diseases. Glycyrrhizin (GL), the most significant active ingredient of Glycyrrhiza glabra L., exerts anti-inflammatory activity. However, the anti-inflammatory effect of GL remains to be determined. AIM OF THIS STUDY: Consequently, this research was carried out to discover the effects and mechanism of action of GL on ALI. MATERIALS AND METHODS: Cell experiments established an in vitro model of LPS-induced RAW 264.7 macrophages to verify the mechanism. The levels of NO, PEG2, and inflammatory cytokines were estimated by ELISA. The expression levels of proteins related to the NF-κB signalling pathway and NLRP3 inflammasome were determined by Western blotting. The nuclear translocation of NF-κB p65 and ASC was tested through immunofluorescence analysis. The inhibitory effect of NLRP3 inhibitor MCC950 on macrophage was evaluated. Male BALB/C mice were selected to establish the ALI model. The experiment was randomly divided into five groups: control, ALI, GLL, GLH, and DEX. Pathological alterations were explored by H&E staining. The weight ratios of lung W/D, MPO, and inflammatory cytokines were evaluated by ELISA. The expression levels of proteins related to the NF-κB signalling pathway or NLRP3 inflammasome were analysed by Western blotting. RESULTS: Here, we demonstrate that GL attenuates inflammation, nitric oxide, IL-18, IL-1ß, TNF-α, IL-6, and PGE2 levels and alveolar epithelial barrier permeability in macrophages and mice challenged with LPS. In addition, GL inhibits NLRP3 inflammasome initiation and activation and NF-κB signalling pathway activation. CONCLUSION: This research demonstrates that GL may alleviate ALI inflammation by interfering with the NF-κB/NLRP3 inflammasome signalling pathway.

Association of gallbladder diseases with risk of gastrointestinal polyps.

BACKGROUND: It has not yet been determined whether gastroscopy and colonoscopy screening help patients with gallbladder diseases. We aim to retrospectively investigate the relationship between gallbladder diseases and gastrointestinal polyps in order to provide a theoretical basis for the early screening of gastrointestinal polyps in patients with gallbladder disease. METHODS: This is a retrospective cross-sectional study involving 1662 patients who underwent gastroscopy, colonoscopy, and abdominal ultrasound as part of their health check-up from January 2015 to July 2020. We also compared the patients with and without gallbladder diseases to determine the prevalence of gastrointestinal polyps. RESULTS: Patients with gallbladder polyps had greater odds of having colorectal polyps (adjusted odds ratio (OR)=1.77, 95% confidence interval [Cl]: 1.23 to 2.54, p=0.002) and gastric plus colorectal polyps (adjusted OR=2.94, 95%Cl: 1.62 to 5.32, p<0.001) than those without. Patients with multiple gallbladder polyps had greater odds of having colorectal polyps (adjusted OR=2.33, 95% CI: 1.33 to 4.07, p=0.003) and gastric plus colorectal polyps (adjusted OR=3.95, 95% CI: 1.72 to 9.11, p=0.001), and patients with gallbladder polyps had greater odds of having left-colon polyps (adjusted OR=1.90, 95% CI: 1.25 to 2.88, p=0.003) and colorectal adenoma (adjusted OR=1.78, 95% CI: 1.19 to 2.66, p=0.005). We also noted that women with gallbladder polyps had a higher prevalence of colorectal polyps (OR=2.13, 95% CI: 1.20 to 3.77, p=0.010) and gastric plus colorectal polyps (OR=3.69, 95% CI: 1.58 to 8.62, p=0.003). However, no positive correlation was observed between gallbladder stones and gastrointestinal polyps. CONCLUSIONS: Gallbladder polyps are significant indicators of colorectal and gastric plus colorectal polyps. Hence, gastroscopy and colonoscopy screening should be performed for patients with gallbladder polyps, particularly female patients and those with multiple gallbladder polyps.

Comparative study of the Rheum tanguticum's chemical contents based on spatial distribution characteristics.

Rheum tanguticum (R. tanguticum) has been widely used for the treatment of inflammatory diseases in clinical. However, limited research exist on the quality evaluation of various R. tanguticum locations, which has certain drawbacks. In this study, Fourier-transform infrared spectroscopy (FTIR) and high-performance liquid chromatography (HPLC) were used to comparative study on the chemical contents of R. tanguticum, to clarify the relationship between the chemical contents and the spatial distribution of R. tanguticum. First of all, the FTIR spectra of 18 batches of R. tanguticum were examined. Following the cluster analysis, the FTIR spectra of various production locations differed. To some extent, establishing the double index analysis sequence of common and variation peaks may differentiate distinct production locations of medicinal materials. The HPLC fingerprint of R. tanguticum was constructed to further explore the link between components and their origin. PCA of common peaks of 18 batches of R. tanguticum indicated that R. tanguticum grown in Gannan and Qinghai had a tendency to separate t[2], however this trend was not noticeable. Then, OPLS-DA model was established, and the key differential components of R. tanguticum produced in Gannan and Qinghai were discovered to be R16, R37, R46, and R47 (Aloe emodin) (VIP ≥ 1 and P < 0.05). At last, Pearson's test was used to examine the relationship between longitude, latitude, altitude, and composition. Longitude was significantly positively correlated with R28 and R30 (P < 0.05), and a very significantly positively correlated with R35, R36, R37, R46, and R47 (P < 0.01). Latitude was significantly negatively correlated with R34, R35, and R40 (P < 0.05), and extremely significantly negatively correlated with R28, R30, R36, R37, R46, and R47 (P < 0.01). Altitude was significantly positive correlation with R36 and R37 (P < 0.01). The results of our study can provide insights into R. tanguticum quality control and aid in establishing a natural medication traceability system.