Exosome-delivered miR-410-3p reverses epithelial-mesenchymal transition, migration and invasion of trophoblasts in spontaneous abortion.

Current studies have indicated that insufficient trophoblast epithelial-mesenchymal transition (EMT), migration and invasion are crucial for spontaneous abortion (SA) occurrence and development. Exosomal miRNAs play significant roles in embryonic development and cellular communication. Hereon, we explored the roles of serum exosomes derived from SA patients on trophoblast EMT, migration and invasion. Exosomes were isolated from normal control (NC) patients with abortion for unplanned pregnancy and SA patients, then characterized by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA) and western blotting. Exosomal miRNA profiles were identified by miRNA sequencing. The effects of serum exosomes on trophoblast migration and invasion were detected by scratch wound healing and transwell assays, and other potential mechanisms were revealed by quantitative real-time PCR (RT-PCR), western blotting and dual-luciferase reporter assay. Finally, animal experiments were used to explore the effects of exosomal miR-410-3p on embryo absorption in mice. The serum exosomes from SA patients inhibited trophoblast EMT and reduced their migration and invasion ability in vitro. The miRNA sequencing showed that miR-410-3p was upregulated in SA serum exosomes. The functional experiments showed that SA serum exosomes restrained trophoblast EMT, migration and invasion by releasing miR-410-3p. Mechanistically, SA serum exosomal miR-410-3p inhibited trophoblast cell EMT, migration and invasion by targeting TNF receptor-associated factor 6 (TRAF6) at the post-transcriptional level. Besides, SA serum exosomal miR-410-3p inhibited the p38 MAPK signalling pathway by targeting TRAF6 in trophoblasts. Moreover, milk exosomes loaded with miR-410-3p mimic reached the maternal-fetal interface and aggravated embryo absorption in female mice. Clinically, miR-410-3p and TRAF6 expression were abnormal and negatively correlated in the placental villi of SA patients. Our findings indicated that exosome-derived miR-410-3p plays an important role between SA serum and trophoblasts in intercellular communication, suggesting a novel mechanism by which serum exosomal miRNA regulates trophoblasts in SA patients.

Total Synthesis of (±)-Simonsol C.

Total synthesis of simonsol C has been achieved, focusing on the postdearomatization transformations. Our methodology integrates an efficient combination of dearomatization and Zn/AcOH reduction to introduce an allyl group, followed by oxo-Michael addition, to construct the 6/5/6 benzofuran skeleton. It offers a novel method for synthesizing allyl-containing quaternary carbon atoms in a straightforward manner.

Advanced molecular mechanisms of modified DRV compounds in targeting HIV-1 protease mutations and interrupting monomer dimerization.

HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for studying drug resistance to inhibitors. The inhibitor, darunavir (DRV), exhibits a high genetic barrier to viral resistance, but with mutations of residues in the PR, there is also some resistance to DRV. Inhibitors can impede PR in two ways: one involves binding to the active site of the dimerization protease, and the other involves binding to the PR monomer, thereby preventing dimerization. In this study, we aimed to investigate the inhibitory effect of DRV with a modified inhibitor on PR, comparing the differences between wild-type and mutated PR, using molecular dynamics simulations. The inhibitory effect of the inhibitors on PR monomers was subsequently investigated. And molecular mechanics Poisson-Boltzmann surface area evaluated the binding free energy. The energy contribution of individual residues in the complex was accurately calculated by the alanine scanning binding interaction entropy method. The results showed that these inhibitors had strong inhibitory effects against PR mutations, with GRL-142 exhibiting potent inhibition of both the PR monomer and dimer. Improved inhibitors could strengthen hydrogen bonds and interactions with PR, thereby boosting inhibition efficacy. The binding of the inhibitor and mutation of the PR affected the distance between D25 and I50, preventing their dimerization and the development of drug resistance. This study could accelerate research targeting HIV-1 PR inhibitors and help to further facilitate drug design targeting both mechanisms.

Evaluating mAbs binding abilities to Omicron subvariant RBDs: implications for selecting effective mAb therapies.

The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein-protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses.

Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease.

Papain-like protease (PLpro), a non-structural protein encoded by SARS-CoV-2, is an important therapeutic target. Regions 1 and 5 of an existing drug, GRL0617, can be optimized to produce cooperativity with PLpro binding, resulting in stronger binding affinity. This work investigated the origin of the cooperativity using molecular dynamics simulations combined with the interaction entropy (IE) method. The regions' improvement exhibits cooperativity by calculating the binding free energies between the complex of PLpro-inhibitor. The thermodynamic integration method further verified the cooperativity generated in the drug improvement. To further determine the specific source of cooperativity, enthalpy and entropy in the complexes were calculated using molecular mechanics/generalized Born surface area and IE. The results show that the entropic change is an important contributor to the cooperativity. Our study also identified residues P248, Q269, and T301 that play a significant role in cooperativity. The optimization of the inhibitor stabilizes these residues and minimizes the entropic loss, and the cooperativity observed in the binding free energy can be attributed to the change in the entropic contribution of these residues. Based on our research, the application of cooperativity can facilitate drug optimization, and provide theoretical ideas for drug development that leverage cooperativity by reducing the contribution of entropy through multi-locus binding.

Image Improved Intravoxel Incoherent Motion MRI With Optimized Trigger Delays Based on Strain Curve Analysis to Evaluate Myocardial Microvascular Dysfunction of Exertional Heat Illness.

BACKGROUND: Intravoxel incoherent motion (IVIM) MRI has not been widely used and its role in evaluating exertional heat illness (EHI)-related myocardial involvement remains unknown. PURPOSE: To investigate the feasibility of strain curve-derived trigger delay (TD) IVIM-MRI and its role in assessing myocardial diffusion and microvascular perfusion of EHI patients. STUDY TYPE: Prospective. SUBJECTS: A total of 42 male EHI patients (median age: 21 years) and 22 age- and sex-matched healthy controls (HC). FIELD STRENGTH/SEQUENCE: A 3-T, diffusion-weighted spin-echo echo-planar-imaging sequence. ASSESSMENT: IVIM-MRI was acquired by conventional TD method (group A) or strain curve-based TD method (group B) in random order. IVIM image quality was evaluated on a 3-point Likert scale (1, nondiagnostic; 2, moderate; 3, good). Technical success was defined as image quality score = 3. IVIM-MRI-derived parameters (pseudo diffusion in the capillaries [D*], perfusion fraction [f], and slow apparent diffusion coefficient [D]) were compared between EHI and HC. STATISTICAL TESTS: Student's t-tests, chi-square tests, one-way analysis of variance, receiver operating characteristic (ROC) curve analysis, Pearson's correlation coefficient (r). The statistical significance level was set at P < 0.05. RESULTS: IVIM-MRI image quality score (median [interquartile range]: 3 [2, 3] vs. 2 [1-3]) and technical success rate (61.9%[13/21] vs. 28.6%[6/21]) were significantly improved in group B. EHI patients showed significantly decreased D* (118.1 ± 23.3 × 10-3  mm2 /sec vs. 142.7 ± 42.6 × 10-3  mm2 /sec) and f values (0.42 ± 0.12 vs. 0.51 ± 0.11) and significantly higher D values (3.0 ± 0.9 × 10-3  mm2 /sec vs. 2.5 ± 0.6 × 10-3  mm2 /sec) compared to HC. Relative to D and D*, f showed the most robust efficacy for detecting EHI-related myocardial injury with the highest area under the ROC curve (0.906: 95% confidence interval, 0.799, 0.967) and sensitivity of 88.5% and specificity of 85.6%. CONCLUSION: The strain curve-based TD method significantly improved image quality and technical success rate of IVIM-MRI, and f value may be an effective biomarker to assess myocardial microcirculation abnormalities of EHI patients. EVIDENCE LEVEL: 2. TECHNICAL EFFICACY: Stage 3.

Organic Matter Transfer Caused by Concentration Difference Creates TC4 Surfaces with Switchable Wettability.

In this paper, low-cost electrochemical processing and heat treatment were adopted to fabricate titanium alloy surfaces with switchable wettability. Meanwhile, surface structure, roughness, and oxide content were regulated by electrochemical processing voltage. The effects of surface structure, roughness, oxide content, temperature, and time of heat treatment on switchable wettability were investigated. In addition to suitable structural conditions, surface chemistry is also crucial to preparing metal surfaces with switchable wettability. The surface chemistry of electrochemical processed surfaces was changed by organic matter transfer during heat treatment. In a certain voltage range, suitable surface structure, high roughness, and surface oxide content by high voltage contribute to the organic matter transfer. In a certain range of heating temperature and time, the concentration difference of organic matter is the premise of organic matter transfer. Concurrently, the higher the temperature, the faster the speed of organic matter transfer. Different from other relevant studies, the hypothesis that the concentration difference promotes organic matter transfer is proposed and verified by interesting experiments. The difference concentration of organic matter between the environment and the samples, as well as between the two samples, was created to promote organic matter transfer. Therefore, the electrochemical processed surfaces with switchable wettability were obtained by organic matter transfer in two ways.

Multiparametric cardiac magnetic resonance reveals persistent myocardial inflammation in patients with exertional heat illness.

OBJECTIVES: To explore the clinical potential of multiparametric cardiac magnetic resonance (CMR) in evaluating myocardial inflammation in patients with exertional heat illness (EHI). METHODS: This prospective study enrolled 28 males with EHI (18 patients with exertional heat exhaustion (EHE) and 10 with exertional heat stroke (EHS)) and 18 age-matched male healthy controls (HC). All subjects underwent multiparametric CMR, and 9 patients had follow-up CMR measurements 3 months after recovery from EHI. CMR-derived left ventricular geometry, function, strain, native T1, extracellular volume (ECV), T2, T2*, and late gadolinium enhancement (LGE) were obtained and compared among different groups. RESULTS: Compared with HC, EHI patients showed increased global ECV, T2, and T2* values (22.6% ± 4.1 vs. 19.7% ± 1.7; 46.8 ms ± 3.4 vs. 45.1 ms ± 1.2; 25.5 ms ± 2.2 vs. 23.8 ms ± 1.7; all p < 0.05). Subgroup analysis showed that ECV was higher in the EHS patients than those in EHE and HC groups (24.7% ± 4.9 vs. 21.4% ± 3.2, 24.7% ± 4.9 vs. 19.7% ± 1.7; both p < 0.05). Repeated CMR measurements at 3 months after baseline CMR showed persistently higher ECV than HC (p = 0.042). CONCLUSIONS: With multiparametric CMR, EHI patients demonstrated increased global ECV, T2, and persistent myocardial inflammation at 3-month follow-up after EHI episode. Therefore, multiparametric CMR might be an effective method in evaluating myocardial inflammation in patients with EHI. CLINICAL RELEVANCE STATEMENT: This study showed persistent myocardial inflammation after an exertional heat illness (EHI) episode demonstrated by multiparametric CMR, which is a potential promising method to evaluate the severity of myocardial inflammation and guide return to work, play, or duty in EHI patients. KEY POINTS: • EHI patients showed an increased global extracellular volume (ECV), late gadolinium enhancement, and T2 value, indicating myocardial edema and fibrosis. • ECV was higher in the exertional heat stroke patients than exertional heat exhaustion and healthy control groups (24.7% ± 4.9 vs. 21.4% ± 3.2, 24.7% ± 4.9 vs. 19.7% ± 1.7; both p < 0.05). • EHI patients showed persistent myocardial inflammation with higher ECV than healthy controls 3 months after index CMR (22.3% ± 2.4 vs. 19.7% ± 1.7, p = 0.042).

Explore the pharmacological basis of ShengJiYiSui decoction in the treatment of amyotrophic lateral sclerosis based on network pharmacology and molecular docking technology.

Neurodegenerative illnesses have long been handled clinically by traditional Chinese medicine. This study is the first time to explore the pharmacological basis of application in amyotrophic lateral sclerosis (ALS) through network pharmacology and molecular docking techniques. In the present investigation, the TCMSP database and HIT2 database were examined for 9 TCM constituents of Sheng Ji Yu Sui Decoction (SJYSD), and the desired sites for the components were searched in the Drugbank database. and the Sjysd-target network was constructed. Associated targets for Amyotrophic lateral sclerosis (ALS) were then retrieved and collected in the OMIM, TTD, Genecards and DisGeNET databases. Protein-protein interaction and enrichment analysis were performed for the common targets of drugs and diseases, and molecular anchoring for the chosen core targets and related molecules was carried out. The results showed that SJYSD had 100 active compounds corresponding to 598 targets. ALS has a total of 5,325 genes. SJYSD and ALS share 163 genes, and these targets involve PI3K-AKT signaling, p53 signaling and IL-17 signaling, etc. The core components of luteolin and quercetin were discovered and may be used to treat ALS by regulating PI3K-AKT signaling pathway by HSP90AB1 protein.

Comprehensive analysis unveils altered binding kinetics of 5-/6-methylCytosine/adenine modifications in R2R3-DNA system.

Recent studies have shown that DNA methylation is an important epigenetic marker. Two prominent forms are methylation of the C5 position of cytosine and methylation of the C6 position of adenine. Given the vital significance of DNA methylation, investigating the mechanisms that influence protein binding remains a compelling pursuit. This study used molecular dynamics simulations to investigate the binding patterns of R2R3 protein and four differentially methylated DNAs. The alanine scanning combined with interaction entropy method was used to identify key residues that respond to different methylation patterns. The order of protein binding ability to DNA is as follows: unmethylated DNA > A11 methylation (5'-A6mAC-3') (6m2A system) > A10 methylation (5'-6mAAC-3') (6m1A system) > both A10 and A11 methylation (5'-6mA6mAC-3') (6mAA system) > C12 methylation (5'-AA5mC-3') (5mC system). All methylation systems lead to the sixth α helix (H6) (residues D105 to L116) moving away from the binding interface, and in the 5mC and 6m1A systems, the third α helix (H3) (residues G54 to L65) exhibits a similar trend. When the positively charged amino acids in H3 and H6 move away from the binding interface, their electrostatic and van der Waals interactions with the negatively charged DNA are weakened. Structural changes induced by methylation contributed to the destabilization of the hydrogen bond network near the original binding site, except for the 6m2A system. Moreover, there is a positive correlation between the number of methylated sites and the probability of distorting the DNA structure. Our study explores how different methylation patterns affect binding and structural adaptability, and have implications for drug discovery and understanding diseases related to abnormal methylation.

Clinical features and prognosis of autosomal dominant polycystic kidney disease with cerebrovascular complications.

OBJECTIVES: This retrospective study was used to evaluate the clinical and imaging characteristics and the prognosis of autosomal dominant polycystic kidney disease (ADPKD) with cerebrovascular complications. MATERIALS AND METHODS: We retrospectively analyzed 30 patients with ADPKD complicated with intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH), unruptured intracranial aneurysms (UIAs), or Moyamoya disease (MMD) who were admitted to Jinling Hospital from January 2001 to January 2022. We analyzed the clinical manifestations and imaging characteristics of ADPKD patients with cerebrovascular complications and followed up on their long-term outcomes. RESULTS: 30 patients, 17 men and 13 women, with an average age of 47.5 (40.0, 54.0) years were included in this study, including 12 cases of ICH, 12 cases of SAH, 5 cases of UIA, and 1 case of MMD. The 8 patients who died during follow-up had a lower Glasgow Coma Scale (GCS) on admission (p = 0.024) and a significantly higher serum creatinine (p = 0.004) and blood urea nitrogen (p = 0.006) than the 22 patients with long-term survival. CONCLUSION: Intracranial aneurysms, SAH, and ICH are the most common cerebrovascular diseases in ADPKD. Patients with low GCS score or worse renal function have a poor prognosis, which can lead to disability and even death.

Femtosecond Dynamics of a Polariton Bosonic Cascade at Room Temperature.

Whispering gallery modes in a microwire are characterized by a nearly equidistant energy spectrum. In the strong exciton-photon coupling regime, this system represents a bosonic cascade: a ladder of discrete energy levels that sustains stimulated transitions between neighboring steps. Here, by using a femtosecond angle-resolved spectroscopic imaging technique, the ultrafast dynamics of polaritons in a bosonic cascade based on a one-dimensional ZnO whispering gallery microcavity are explicitly visualized. Clear ladder-form build-up processes from higher to lower energy branches of the polariton condensates are observed, which are well reproduced by modeling using rate equations. Remarkably, a pronounced superbunching feature, which could serve as solid evidence for bosonic cascades, is demonstrated by the measured second-order time correlation factor. In addition, the nonlinear polariton parametric scattering dynamics on a time scale of hundreds of femtoseconds are revealed. Our understandings pave the way toward ultrafast coherent control of polaritons at room temperature.

Prevalence, clinical characteristics, and 3-dimensional radiographic analysis of supernumerary teeth in Guangzhou, China: a retrospective study.

OBJECTIVE: The aim was to investigate the prevalence and clinical and 3-dimensional (3D) radiographic characteristics of supernumerary teeth (ST) in a paediatric dental population. The factors associated with ST eruption potential were analysed, and the optimal extraction time for nonerupted ST was discussed. METHODS: A retrospective study was performed in a 13,336-participant baseline population aged 3-12 years for whom panoramic radiographs had been obtained in the hospital from 2019 to 2021. The medical records and radiographic data were reviewed to identify patients with ST. Both the demographic variables and ST characteristics were recorded and analysed . RESULTS: In total, 890 patients with 1,180 ST were screened from the 13,336 baseline population. The ratio of males (679) to females (211) was approximately 3.2:1. Generally, ST occurred singularly and were frequently found in the maxilla (98.1%). A total of 40.8% of ST were erupted, and the 6-year-old age group presented the highest eruption rate (57.8%). The eruption rate of ST was highly negatively correlated with age. A total of 598 patients additionally underwent cone- beam computed tomography (CBCT). According to the CBCT images, the majority of ST were conical, normally oriented, palatally situated, nonerupted and symptomatic. The most common ST-associated complication was failed eruption of adjacent teeth. In addition, symptomatic ST were more common in the 7- to 8- and 9- to 10-year-old age groups. The eruption rate of ST was 25.3% among the patients who had undergone CBCT. A normal orientation and the labial position were significant protective factors for ST eruption, with odds ratios (ORs) of 0.004 (0.000-0.046) and 0.086 (0.007-1.002), respectively. Age and the palatal position were significant risk factors, with ORs of 1.193 (1.065-1.337) and 2.352 (1.377-4.02), respectively. CONCLUSIONS: This study provides a detailed analysis of ST characteristics in 3-12 year old children. Age as well as the position and orientation of ST were reliable predictors of the ST eruption. An age of 6 years old may be the optimal time for extraction of nonerupted ST to maximize the utilization of eruption potential and reduce the incidence of ST-associated complications.

Optically Controlled Femtosecond Polariton Switch at Room Temperature.

Exciton polaritons have shown great potential for applications such as low-threshold lasing, quantum simulation, and dissipation-free circuits. In this paper, we realize a room temperature ultrafast polaritonic switch where the Bose-Einstein condensate population can be depleted at the hundred femtosecond timescale with high extinction ratios. This is achieved by applying an ultrashort optical control pulse, inducing parametric scattering within the photon part of the polariton condensate via a four-wave mixing process. Using a femtosecond angle-resolved spectroscopic imaging technique, the erasure and revival of the polariton condensates can be visualized. The condensate depletion and revival are well modeled by an open-dissipative Gross-Pitaevskii equation including parametric scattering process. This pushes the speed frontier of all-optical controlled polaritonic switches at room temperature towards the THz regime.

Time-dependent cardiac structural and functional changes after kidney transplantation: a multi-parametric cardiac magnetic resonance study.

OBJECTIVES: To map time-dependent cardiac structural and functional change patterns after renal transplantation (KT) using cardiac magnetic resonance (CMR). METHODS: Fifty-three patients with pre-KT and post-KT CMR exams were retrospectively analyzed. Patients were divided into three groups according to the time of post-KT CMR: group 1 (3 months post-KT, n = 16), group 2 (6 months post-KT, n = 21), and group 3 (over 9 months post-KT, n = 16). Twenty-one age- and sex-matched healthy controls (HC) were recruited for the study. CMR-derived left ventricular (LV) volumes, LV mass index (LVMi), LV ejection fraction (LVEF), global radial strain (GRS), global circumferential strain (GCS), global longitudinal strain (GLS), and native T1 value were compared. The association between the changes of CMR parameters was assessed. RESULTS: LVMi post-KT decreased in groups 2 (p < 0.001) and 3 (p = 0.004) but both groups had higher LVMi values compared to HC (both p < 0.001). GLS post-KT was decreased in group 1 (p = 0.021), but slightly increased in group 2 (p = 0.728) and group 3 (p = 0.100) without significant difference. GLS post-KT in group 3 was not different from HC (p = 0.104). LVEF, GRS, and GCS post-KT in groups 2 and 3 significantly increased and showed no significant difference from HC. The post-KT native T1 value in all three groups significantly decreased; however, no group showed any significant difference from HC. The change of LVEF was associated with the change of GCS, GRS, and GLS. CONCLUSIONS: Although GRS, GCS, GLS, and native T1 values reversed to normal level, LVMi remained impaired in median 14 months after KT. KEY POINTS: • Kidney transplantation has favorable effects on cardiac structure and function. • In a median 14 months of follow-up after KT, left ventricle strain and native T1 value reversed to normal level while LV mass index (LVMi) did not. Left ventricular hypertrophy may help to explain why KT recipients are still at increased cardiovascular risk. • The reason for the decrease of native T1 value after KT may be more than myocardial fibrosis and needs to be further studied.

Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight.

The continuous spread of the newly emerged SARS-CoV-2 Omicron variant (B.1.1.529) has become an important reason for the surge in COVID-19 infections. Its numerous mutated residues containing key sites on the receptor-binding domain (RBD) undoubtedly pose new challenges for epidemic control. Although the preventive measures are becoming more sophisticated, the effects of mutations on the binding of the virus to the receptor protein remain to be elucidated. Here, we used molecular dynamics (MD) simulations to investigate the differences in the binding mode between the Omicron variant and the angiotensin-converting enzyme 2 (ACE2) compared to the wild-type strain (WT). Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts. The stronger electrostatic interaction was the main reason for its enhanced binding affinity as compared to WT. This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites. The appearance of these highly polar hydrophilic amino acids may cause local perturbations and affect the electrostatic complementarity of RBD with the ACE2, and further mediate conformational changes. Thus, a more extensive interaction network was found in the mutation system and the complex interaction cluster was formed near E37@ACE2, which was essential for the stable binding of the two. In addition, we speculated that these mutations may affect the electrostatic complementarity with the four potential antibodies to reduce the sensitivity of the virus to antibodies. This study reveals the key details of the Omicron variant binding to ACE2 and provides important theoretical views for the enhanced infectivity of this variant. We hope that these observations can provide timely molecular insights for responding to the Omicron variant pandemic.

Insights from computational analysis: how does the SARS-CoV-2 Delta (B.1.617.2) variant hijack ACE2 more effectively?

The SARS-CoV-2 Delta (B.1.617.2) variant was identified in India in October 2020, and it has quickly become the mainstream strain with strong toxicity and spread, posing great challenges to epidemic control. However, the molecular mechanism of its powerful infectivity remains unclear. It is meaningful to investigate the process of Delta variant's receptor-binding domain (RBD) binding to angiotensin-converting enzyme 2 (ACE2). Here, we performed three repeated molecular dynamics simulations for each system to avoid accidents, and the alanine scanning combined with the interaction entropy (ASIE) method was utilized to evaluate the binding free energy. Through the detailed energy and conformational analysis, the binding mechanism of the Delta variant was illustrated. The results showed that the existence of L452R and T478K mutations can trigger the effective hijacking of ACE2 by the Delta variant through the following three ways: (i) these two mutations can significantly enhance the electrostatic energy of the system by the introduction of two positively charged amino acids (Arg and Lys), thereby increasing the binding affinity of RBD and ACE2, (ii) the Loops 1, 3, and 4 in the receptor-binding motif (RBM) of RBD form a tighter conformation under the dominance of the T478K mutation, allowing ACE2 to be captured more effectively than the wild-type system, and (iii) these conformational changes lead to a more stable hydrogen bond in the Delta variant, which further ensures the stability of the binding. In addition, to explore the effect of mutations on the antibody, the key residues contributing to the changes in the binding ability of RBD in the Delta variant with the existing 42 neutralizing monoclonal antibodies (mAbs) have been preliminarily evaluated. The present study reveals the molecular mechanism for the increased infectivity of SARS-CoV-2 caused by mutations, and the key sites that cause antigenic changes were screened. It provides important theoretical insights for the development of novel targeted RBD drugs and antibodies.

Molecular investigation of the dual inhibition mechanism for targeted P53 regulator MDM2/MDMX inhibitors.

Inhibitors that competitively bind MDM2/MDMX can block the inhibition of P53 by MDM2/MDMX and restart its tumor-suppressive effect. Molecular studies targeting MDM2/MDMX inhibitors have always been a hot topic in anticancer drug design. Although numerous inhibitors have been designed previously against MDM2/MDMX, their dual inhibition efficacy has not been demonstrated, and few studies assessed the general causes affecting the dual inhibition of MDM2/MDMX by these inhibitors. Here, molecular dynamics simulations and alanine scanning combined with the interaction entropy method were employed to precisely investigate whether 16 inhibitors could dually inhibit MDM2/MDMX and the similarities and differences in the interaction modes. Thereby addressing the key residue sites affecting dual inhibition. Residues L54/M53, I61/60, M62/61, Y67/66, and V93/92 of MDM2/MDMX, which are in corresponding positions in both protein structures, provide significant conditions for these inhibitors to bind to MDM2/MDMX tightly. In addition, most of these inhibitors prefer to bind MDM2 than MDMX, and residues H96 and I99 in MDM2 are attractive targets for inhibitors, resulting in inhibitors binding to MDM2/MDMX with different affinity. These key residues should be considered in the development of dual inhibitors. For these 16 inhibitors, most have dual inhibitory potential for MDM2/MDMX based on the binding affinity of the complexes. Still, it is questionable whether they can exert excellent dual inhibition considering the assessment of the hot-spots. At least their binding affinity for MDMX is not superior to that for MDM2 due to the difference in energy of the van der Waals interactions at the key sites. Furthermore, based on the analysis of three representative inhibitors (TUZ/HRH and HRQ with different binding preferences for MDM2/MDMX), 3-chloropyridine in TUZ leads to the differential binding affinity between the inhibitor and MDM2/MDMX. It readily forms hydrophobic interactions with the surrounding residues H96 and I99. But this phenomenon does not occur in the TUZ-MDMX system, implying the critical role of residues H96/P95 and I99/L98. And the completely different binding mechanism of HRQ binding to MDM2/MDMX explains its inability to inhibit MDM2 well. Thus, we are cautious about its dual inhibitory ability. Besides, HRH is more prone to strong van der Waals interactions with MDM2 than MDMX whereas its 2-chlorofluorobenzene is detrimental to this. We hope that these findings will provide reliable molecular insights for the screening and optimization of targeting MDM2/MDMX dual inhibitors.

First Report of Brown Rot Caused by Phytophthora nicotianae on Navel Orange Fruit in China.

Navel orange (Citrus sinensis Osbeck cv. Newhall) is widely planted in southern China. From September to November 2021, severe outbreaks of Phytophthora brown rot were observed on navel orange fruit in three local orchards in Ganzhou City (28.80N, 115.53E), Jiangxi Province, China, with a disease incidence of 25 to 35%. Symptomatic fruit was mostly observed 1-m from the ground. Initial symptoms on infected fruit were circular, pale-brown to brown, water-soaked, slightly sunken lesions, covered with sparse white mycelia-like growth. As the disease progressed, the lesions turned dark brown and enlarged on the fruit surface. Three to four infected fruits were randomly collected from each orchard, placed in transparent plastic bags and immediately brought back to the laboratory for isolations. Infected fruits were surface-disinfested with 70% ethanol for 60 sec, and rinsed three times with sterile water. Symptomatic tissues from the margin between necrotic and healthy tissues were cut into 5 mm × 5 mm pieces, placed onto potato dextrose agar and incubated at 28°C for 5 days. Nine isolates were obtained. Colonies of three isolates (JFRL 03-16, 03-18, 03-19) in 10-day-old 20% V8 juice agar consisted of abundant, white, cottony aerial mycelia. Hyphal swellings and coenocytic mycelium were observed. Sporangia were ovoid, ellipsoid to spherical, papillate, and ranged in size from 17.2 to 60.1 µm × 15.8 to 48.6 µm (x ̅=46.2 ± 5.5 × 32.4 ± 4.8 µm, n=50). Chlamydospores were spherical, suborbicular, and ranged from 17.8 to 45.9 µm diam (x ̅=30.5 ± 3.5 µm, n=50). Oospores were not observed in pure cultures. These morphological characteristics were consistent with those of P. nicotianae (LaMondia et al. 2014). Genomic DNA was extracted from a representative isolate, JFRL 03-18, using the NuClean Plant Genomic DNA kit (CWBIO, China). The internal transcribed spacer (ITS) region, ras-related protein ypt1 (YPT), ß-tubulin (TUB) gene were amplified by Polymerase Chain Reaction using primers ITS1/ITS4 (White et al. 1990), Yph1F/Yph2R (Schena et al. 2008), and TUBUF2/TUBUR1 (Kroon et al. 2004), respectively. All sequences were deposited in GenBank (Accession Nos. ON231777 for ITS, ON246910 for YPT, ON246908 for TUB). BLASTN homology search for these nucleotide sequences showed 100% identical to the ITS (MH341621), YPT (MK058408), TUB (MH760160) sequences of P. nicotianae. Sequences of twelve Phytophthora species and Pythium ostracodes were downloaded from GenBank. The phylogenetic tree of combined ITS, YPT, TUB sequences showed that the isolate JFRL 03-18 clustered with P. nicotianae. To complete Koch's postulates, zoospore suspensions were prepared from the cultures grown on 10-day-old V8 juice agar of isolates (JFRL 03-16, 03-18, 03-19). Pathogenicity tests were performed on healthy and surface-disinfested navel orange fruit. Nine fruits were gently wounded with a needle, inoculated with 10 µl zoospore suspension (104 zoospores/ml) of three isolates separately, and three fruit treated with sterilized water as controls. All fruit were incubated at 25℃ with 80% relative humidity and the test was repeated three times. After 7 days of incubation, the fruit inoculated with P. nicotianae showed similar brown rot symptoms and the control fruit remained symptomless. The pathogen was re-isolated from all inoculated fruits and confirmed as P. nicotianae by morphological and molecular analysis. Phytophthora nicotianae was previously reported on Hamlin sweet orange (Citrus sinensis (L.) Osbeck) fruit causing Phytophthora brown rot in Florida (Graham and Timmer 1995; Hao et al. 2018). To our knowledge, this is the first report of P. nicotianae causing Phytophthora brown rot of navel orange fruit in China. Based on the severity of this disease, local growers should develop and implement integrated disease management strategies for control.

Experimental Investigation on the Influence of Depth on Rockburst Characteristics in Circular Tunnels.

To investigate the influence of depth on the rockburst of surrounding rock in a circular tunnel, true-triaxial tests at different depths were carried out on cubic granite specimens with a circular through-going hole. A micro camera was used to monitor the rockburst process of the circular hole sidewall in real time. The test results show that the failure process at different depths can be divided into four periods: the calm period, the particle ejection period, the rock fragment exfoliation period, and the rock bursting period. With an increase in depth, the three-dimensional unequal stress state gradually increased; the failure range and the size of rock fragments increased, the initial failure vertical stress linearly increased, and the strength and stability of the surrounding rock were enhanced. Therefore, the support range of surrounding rock should be increased as the depth increased to improve the overall stability of surrounding rock and reduce the failure range.