Predicting protein conformational motions using energetic frustration analysis and AlphaFold2.

Proteins perform their biological functions through motion. Although high throughput prediction of the three-dimensional static structures of proteins has proved feasible using deep-learning-based methods, predicting the conformational motions remains a challenge. Purely data-driven machine learning methods encounter difficulty for addressing such motions because available laboratory data on conformational motions are still limited. In this work, we develop a method for generating protein allosteric motions by integrating physical energy landscape information into deep-learning-based methods. We show that local energetic frustration, which represents a quantification of the local features of the energy landscape governing protein allosteric dynamics, can be utilized to empower AlphaFold2 (AF2) to predict protein conformational motions. Starting from ground state static structures, this integrative method generates alternative structures as well as pathways of protein conformational motions, using a progressive enhancement of the energetic frustration features in the input multiple sequence alignment sequences. For a model protein adenylate kinase, we show that the generated conformational motions are consistent with available experimental and molecular dynamics simulation data. Applying the method to another two proteins KaiB and ribose-binding protein, which involve large-amplitude conformational changes, can also successfully generate the alternative conformations. We also show how to extract overall features of the AF2 energy landscape topography, which has been considered by many to be black box. Incorporating physical knowledge into deep-learning-based structure prediction algorithms provides a useful strategy to address the challenges of dynamic structure prediction of allosteric proteins.

Oxygen doping of cobalt-single-atom coordination enhances peroxymonosulfate activation and high-valent cobalt-oxo species formation.

The high-valent cobalt-oxo species (Co(IV)=O) is being increasingly investigated for water purification because of its high redox potential, long half-life, and antiinterference properties. However, generation of Co(IV)=O is inefficient and unsustainable. Here, a cobalt-single-atom catalyst with N/O dual coordination was synthesized by O-doping engineering. The O-doped catalyst (Co-OCN) greatly activated peroxymonosulfate (PMS) and achieved a pollutant degradation kinetic constant of 73.12 min-1 g-2, which was 4.9 times higher than that of Co-CN (catalyst without O-doping) and higher than those of most reported single-atom catalytic PMS systems. Co-OCN/PMS realized Co(IV)=O dominant oxidation of pollutants by increasing the steady-state concentration of Co(IV)=O (1.03 × 10-10 M) by 5.9 times compared with Co-CN/PMS. A competitive kinetics calculation showed that the oxidation contribution of Co(IV)=O to micropollutant degradation was 97.5% during the Co-OCN/PMS process. Density functional theory calculations showed that O-doping influenced the charge density (increased the Bader charge transfer from 0.68 to 0.85 e), optimized the electron distribution of the Co center (increased the d-band center from -1.14 to -1.06 eV), enhanced the PMS adsorption energy from -2.46 to -3.03 eV, and lowered the energy barrier for generation of the key reaction intermediate (*O*H2O) during Co(IV)=O formation from 1.12 to 0.98 eV. The Co-OCN catalyst was fabricated on carbon felt for a flow-through device, which achieved continuous and efficient removal of micropollutants (degradation efficiency of >85% after 36 h operation). This study provides a new protocol for PMS activation and pollutant elimination through single-atom catalyst heteroatom-doping and high-valent metal-oxo formation during water purification.

Dual Regulation of Cytochrome P450 Gene Expression by Two Distinct Small RNAs, a Novel tasiRNA and miRNA, in Marchantia polymorpha.

The miR390-derived TAS3 trans-acting short-interfering RNAs (tasiRNAs) module represents a conserved RNA silencing pathway in the plant kingdom; however, its characterization in the bryophyte Marchantia polymorpha is limited. This study elucidated that MpDCL4 processes MpTAS3 double-stranded RNA (dsRNA) to generate tasiRNAs, primarily from the 5'- and 3'-ends of dsRNA. Notably, we discovered a novel tasiRNA, tasi78A, which can negatively regulate a cytochrome P450 gene, MpCYP78A101. Additionally, tasi78A was abundant in MpAGO1, and transient expression assays underscored the role of tasi78A in repressing MpCYP78A101. A microRNA, miR11700, also regulates MpCYP78A101 expression. This coordinate regulation suggests a role in modulating auxin signaling at apical notches of gemma, influencing the growth and sexual organ development of M. polymorpha and emphasizing the significance of RNA silencing in MpCYP78A101 regulation. However, phylogenetic analysis identified another paralog of the CYP78 family, Mp1g14150, which may have a redundant role with MpCYP78A101, explaining the absence of noticeable morphological changes in loss-of-function plants. Taken together, our findings provide new insights into the combined regulatory roles of miR390/MpTAS3/miR11700 in controlling MpCYP78A101 and expand our knowledge about the biogenesis and regulation of tasiRNAs in M. polymorpha.

Real-World Effectiveness of Omalizumab in Chronic Urticaria: A Clinical Observational Study.

INTRODUCTION: The purpose of this study was to assess the clinical effectiveness and safety profile of omalizumab as a therapeutic intervention for chronic urticaria (CU). METHODS: From March 1, 2023, to September 30, 2023, data on a cohort comprising 96 patients with CU, who underwent treatment with omalizumab at our medical institution's allergy clinic, were systematically compiled. Subsequent to the administration of omalizumab, the therapeutic efficacy was assessed utilizing the 7-day urticaria activity score and the urticaria control test. RESULTS: Based on the statistical analysis, the mean duration of therapeutic intervention was 2.4 ± 1.3 months, with a corresponding mean cumulative dosage of 765 ± 450 mg. Of the subset of 42 patients with CU who were subjected to a follow-up period exceeding 3 months, it was observed that the treatment led to complete symptom remission, and no instances of recurrence were documented. Notably, there were statistically significant differences in the treatment duration and the cumulative dosage between patients who experienced co-morbid conditions and those who did not (p < 0.01, 95% CI: 0.280-1.326; p < 0.01, 95% CI: 0.597-2.997). Furthermore, there were significant differences in the treatment duration and cumulative dosage between patients in the combined allergic rhinitis group and those in the non-combined allergic rhinitis group (p < 0.01, 95% CI: 0.204-1.305; p = 0.01, 95% CI: 0.326-2.860). CONCLUSION: Omalizumab demonstrates efficacy in the management of CU among Chinese patients by exerting effective symptom control and facilitating the regression of skin lesions. The assessment of its therapeutic efficacy typically requires a 12-week treatment period. Moreover, the co-occurrence of CU with other allergic disorders serves as a pertinent consideration for the adjustment of omalizumab dosing regimens.

Lysine Methyltransferase 5A Promotes the Progression of Growth Hormone Pituitary Neuroendocrine Tumors through the Wnt/ß-Catenin Signaling Pathway.

INTRODUCTION: Growth hormone (GH) secreting pituitary adenoma is considered one of the most harmful types of Pituitary Neuroendocrine Tumors (PitNETs). Our previous research has found that high expression of Lysine methyltransferase 5A (KMT5A) is closely related to the proliferation of PitNETs. The aim of this study was to investigate the role and molecular mechanism of KMT5A in the progression of GH PitNETs. METHODS: Immunohistochemistry, qRT-PCR, and Western blot (WB) were used to assess the expression levels of KMT5A in human normal pituitary and GH PitNETs, as well as in rat normal pituitary and GH3 cells. Additionally, we utilized RNA interference technology and treatment with a selective KMT5A inhibitor to decrease the expression of KMT5A in GH3 cells. CCK-8, EdU, flow cytometry (FCM), clone formation, and WB assay were further employed to evaluate the impact of KMT5A on the proliferation of GH3 cells in vitro. A xenograft model was established to evaluate the role of KMT5A in GH PitNETs progression in vivo. RESULTS: KMT5A was highly expressed in GH PitNETs and GH3 cells. Moreover, the reduction of KMT5A expression led to inhibited growth of GH PitNETs and increased apoptosis of tumor cells, as indicated by the findings from CCK-8, EdU, clone formation, and FCM assays. Additionally, WB analysis identified the Wnt/ß-catenin signaling pathway as a potential mechanism through which KMT5A promotes GH PitNETs progression. CONCLUSION: Our research suggests that KMT5A may facilitate the progression of GH PitNETs via the Wnt/ß-catenin signaling pathway. Therefore, KMT5A may serve as a potential therapeutic target and molecular biomarker for GH PitNETs.

Arginine alleviates LPS-induced leukocytes inflammation and apoptosis via adjusted NODs signaling.

Arginine plays a key role in regulating the immune function of fish. To evaluate the effect of arginine on the immune response of largemouth bass (Micropterus salmoides), the effects of arginine on cell viability, NADPH oxidase activity, respiratory burst activity, and NO production of leukocytes were analyzed both in vitro and in vivo. In this study, we found that arginine could promote the respiratory burst activity of leucocytes both in vivo and in vitro. By incubating leukocytes with the combination of LPS and arginine, we found that arginine supplementation inhibited the expression of inflammatory genes (tumor necrosis factor-alpha, tnfα; interleukin(il) 8 and il10) and apoptotic genes (caspase 3, caspase 8, and caspase 9) induced by LPS, as well as promoted the arginine metabolism. Arginine supplementation significantly induced (cd4-like) cd4 gene expression after LPS challenge. Further studies showed that LPS could significantly increase nucleotide-binding oligomerization domain containing 1 (nod1) gene expression, but decreased the nod2 gene. The arginine supplementation increased nuclear factor kappa-B (NF-κB) protein level. In conclusion, arginine can alleviate LPS-induced inflammatory response and apoptosis as well as induce cd4 gene expression against LPS challenge via adjusting the expression of NODs signaling.

Integrated analysis of transcriptome and metabolome reveals the regulatory mechanism of largemouth bass (Micropterus salmoides) in response to Nocardia seriolae infection.

Nocardia seriolae is a severe bacterial pathogen that has seriously affected the development of aquaculture industry. Largemouth bass (Micropterus salmoides) is a commercially significant freshwater fish that suffers a variety of environmental threats, including bacterial pathogens. However, the immune responses and metabolic alterations of largemouth bass to N. seriolae infection remain largely unclear. We discovered that N. seriolae caused pathological alterations in largemouth bass and shifted the transcript of immune-related and apoptotic genes in head kidney after infection. To answer the aforementioned question, a combined transcriptome and metabolome analysis was employed to explore the alterations in genes, metabolites, and metabolic pathways in largemouth bass following bacterial infection. A total of 3579 genes and 1929 metabolites are significant differentially changed in the head kidney post infection. In response to N. seriolae infection, host modifies the PI3K-Akt signaling pathway, TCA cycle, glycolysis, and amino acid metabolism. The integrated analysis of transcriptome and metabolome suggested that with the arginine metabolism pathway as the core, multiple biomarkers (arg gene, arginine) are involved in the antibacterial and immune functions of largemouth bass. Thus, we hypothesized that arginine plays a crucial role in the immune responses of largemouth bass against N. seriolae infection, and increasing arginine levels suitably is beneficial for the host against bacterial infection. Our results shed light on the regulatory mechanism of largemouth bass resistance to N. seriolae infection and contributed to the development of more effective N. seriolae resistance strategies.

Efficient Electrocatalytic Hydrodechlorination and Detoxification of Chlorophenols by Palladium-Palladium Oxide Heterostructure.

Electrocatalytic hydrodechlorination is a promising approach for simultaneous pollutant purification and valorization. However, the lack of electrocatalysts with high catalytic activity and selectivity limits its application. Here, we propose a palladium-palladium oxide (Pd-PdO) heterostructure for efficient electrocatalytic hydrodechlorination of recalcitrant chlorophenols and selective formation of phenol with superior Pd-mass activity (1.35 min-1 mgPd-1), which is 4.4 times of commercial Pd/C and about 10-100 times of reported Pd-based catalysts. The Pd-PdO heterostructure is stable in real water matrices and achieves selective phenol recovery (>99%) from the chlorophenol mixture and efficient detoxification along chlorophenol removal. Experimental results and computational modeling reveal that the adsorption/desorption behaviors of zerovalent Pd and PdO sites in the Pd-PdO heterostructure are optimized and a synergy is realized to promote atomic hydrogen (H*) generation, transfer, and utilization: H* is efficiently generated at zerovalent Pd sites, transferred to PdO sites, and eventually consumed in the dechlorination reaction at PdO sites. This work provides a promising strategy to realize the synergy of Pd with different valence states in the metal-metal oxide heterostructure for simultaneous decontamination, detoxification, and resource recovery from halogenated organic pollutants.

Phototransformation of Brominated Disinfection Byproducts and Toxicity Elimination in Sunlit-Ozonated Reclaimed Water.

Ozonation is universally used during water treatment but can form hazardous brominated disinfection byproducts (Br-DBPs). While sunlight exposure is advised to reduce the risk of Br-DBPs, their phototransformation pathways remain insufficiently understood. Here, sunlight irradiation was found to reduce adsorbable organic bromine by 63%. Applying high-resolution mass spectrometry, the study investigated transformations of dissolved organic matter in sunlit-ozonated reclaimed water, revealing the number and abundance of assigned formulas decreased after irradiation. The Br-DBPs with O/C < 0.6 and MW > 400 Da were decreased or removed after irradiation, with the majority being CHOBr compounds. The peak intensity reduction ratio of CHOBr compounds correlated positively with double bound equivalent minus oxygen ratios but negatively with O/C, suggesting that photo-susceptible CHOBr compounds were highly unsaturated. Mass difference analysis revealed that the photodegradation pathways were mainly oxidation aligned with debromination. Three typical CHOBr molecular structures were resolved, and their photoproducts were proposed. Toxicity estimates indicated decreased toxicity in these photoproducts compared to their parent compounds, in line with experimentally determined values. Our proposed phototransformation pathways for Br-DBPs enhance our comprehension of their degradation and irradiation-induced toxicity reduction in reclaimed water, further illuminating their transformation under sunlight in widespread environmental scenarios.

Multiple Roles of Anions on the Degradation Efficiency and Mineralization Pathway of Recalcitrant Acetaldehyde by Vacuum Ultraviolet (185 nm) Oxidation.

Vacuum-UV (185 nm, VUV) is widely applied to polish reverse osmosis permeate (ROP), such as the production of electronics-grade ultrapure water. In this study, the VUV oxidation of acetaldehyde, a common carbonyl in ROP, was found to be influenced by anions even at low concentrations. Interestingly, the influencing extent and mechanism varied depending on the anions. Bicarbonate minimally affected the VUV-photon absorption and •OH consumption, but at 5000 µg-C·L-1, it decreased the degradation of acetaldehyde by 58.7% possibly by scavenging organic radicals or other radical chain reactions. Nitrate strongly competed for VUV-photon absorption and •OH scavenging through the formation of nitrite, and at 500 µg-N·L-1, it decreased the removal rate of acetaldehyde degradation by 71.2% and the mineralization rate of dissolved organic carbon by 53.4%. Chloride competed for VUV-photon absorption and also generated reactive chlorine species, which did not affect acetaldehyde degradation but influenced the formation of organic byproducts. The radical chain reactions or activation of anions under VUV irradiation could compensate for the decrease in oxidation performance and need further investigation. In real ROPs, the VUV oxidation of acetaldehyde remained efficient, but mineralization was hindered due to nitrate and chloride anions. This study deepens the understanding of the photochemistry and feasibility of VUV in water with low concentrations of anions.

Assessing the Chemical-Free Oxidation of Trace Organic Chemicals by VUV/UV as an Alternative to Conventional UV/H2O2.

Low-pressure mercury lamps with high-purity quartz can emit both vacuum-UV (VUV, 185 nm) and UV (254 nm) and are commercially available and promising for eliminating recalcitrant organic pollutants. The feasibility of VUV/UV as a chemical-free oxidation process was verified and quantitatively assessed by the concept of H2O2 equivalence (EQH2O2), at which UV/H2O2 showed the same performance as VUV/UV for the degradation of trace organic contaminants (TOrCs). Although VUV showed superior H2O activation and oxidation performance, its performance highly varied as a function of light path length (Lp) in water, while that of UV/H2O2 proportionally decreased with decreasing H2O2 dose regardless of Lp. On increasing Lp from 1.0 to 3.0 cm, the EQH2O2 of VUV/UV decreased from 0.81 to 0.22 mM H2O2. Chloride and nitrate hardly influenced UV/H2O2, but they dramatically inhibited VUV/UV. The competitive absorbance of VUV by chloride and nitrate was verified as the main reason. The inhibitory effect was partially compensated by •OH formation from the propagation reactions of chloride or nitrate VUV photolysis, which was verified by kinetic modeling in Kintecus. In water with an Lp of 2.0 cm, the EQH2O2 of VUV/UV decreased from 0.43 to 0.17 mM (60.8% decrease) on increasing the chloride concentration from 0 to 15 mM and to 0.20 mM (53.5% decrease) at 4 mM nitrate. The results of this study provide a comprehensive understanding of VUV/UV oxidation in comparison to UV/H2O2, which underscores the suitability and efficiency of chemical-free oxidation with VUV/UV.

Single-atom Ag-loaded carbon nitride photocatalysts for efficient degradation of acetaminophen: The role of Ag-atom and O2.

Carbon nitride has been extensively used as a visible-light photocatalyst, but it has the disadvantages of a low specific surface area, rapid electron-hole recombination, and relatively low light absorbance. In this study, single-atom Ag was successfully anchored on ultrathin carbon nitride (UTCN) via thermal polymerization, the catalyst obtained is called AgUTCN. The Ag hardly changed the carbon nitride's layered and porous physical structure. AgUTCN exhibited efficient visible-light photocatalytic performances in the degradation of various recalcitrant pollutants, eliminations of 85% were achieved by visible-light irradiation for 1 hr. Doping with Ag improved the photocatalytic performance of UTCN by narrowing the forbidden band gap from 2.49 to 2.36 eV and suppressing electron-hole pair recombination. In addition, Ag doping facilitated O2 adsorption on UTCN by decreasing the adsorption energy from -0.2 to -2.22 eV and favored the formation of O2·-. Electron spin resonance and radical-quenching experiments showed that O2·- was the major reactive species in the degradation of Acetaminophen (paracetamol, APAP).

Vitamin D regulates microflora and ameliorates LPS-induced placental inflammation in rats.

Preeclampsia is a pregnancy-specific disease, which has become an essential cause of perinatal and neonatal death. Gut microflora becomes the regulator of host immunity through the metabolic pathway. Epidemiological studies provide convincing evidence that vitamin D supplementation can prevent the onset of preeclampsia. However, research on the microbial mechanisms and effective treatment strategies for placental inflammation induced by lipopolysaccharide is lacking. In this study, pregnant rats were induced by LPS to establish a rat model of preeclampsia. Sixteen-sequence analysis was used to determine the composition of microflora in feces. In addition, the protective effect of vitamin D supplementation on LPS-preeclampsia rats was evaluated. The results showed that the blood pressure and creatinine of pregnant rats in the LPS group were significantly higher than those in the control group. In addition, LPS disturbed the intestinal microbial community and reduced microbial diversity. Vitamin D supplementation improves the symptoms of preeclampsia, increases the abundance of intestinal beneficial flora, normalizes the level of inflammatory factors LPS-induced by inhibiting the TLR4/MYD88/NF-κB pathway, and effectively resists the disturbance of uterine spiral artery remodeling induced by LPS. This study established that vitamin D-mediated microbial mechanisms and their inhibition are potential therapeutic targets for the treatment of preeclampsia.

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.

The recent development of artificial intelligence provides us with new and powerful tools for studying the mysterious relationship between organism evolution and protein evolution. In this work, based on the AlphaFold Protein Structure Database (AlphaFold DB), we perform comparative analyses of the proteins of different organisms. The statistics of AlphaFold-predicted structures show that, for organisms with higher complexity, their constituent proteins will have larger radii of gyration, higher coil fractions, and slower vibrations, statistically. By conducting normal mode analysis and scaling analyses, we demonstrate that higher organismal complexity correlates with lower fractal dimensions in both the structure and dynamics of the constituent proteins, suggesting that higher functional specialization is associated with higher organismal complexity. We also uncover the topology and sequence bases of these correlations. As the organismal complexity increases, the residue contact networks of the constituent proteins will be more assortative, and these proteins will have a higher degree of hydrophilic-hydrophobic segregation in the sequences. Furthermore, by comparing the statistical structural proximity across the proteomes with the phylogenetic tree of homologous proteins, we show that, statistical structural proximity across the proteomes may indirectly reflect the phylogenetic proximity, indicating a statistical trend of protein evolution in parallel with organism evolution. This study provides new insights into how the diversity in the functionality of proteins increases and how the dimensionality of the manifold of protein dynamics reduces during evolution, contributing to the understanding of the origin and evolution of lives.

Changes in endemic patterns of respiratory syncytial virus infection in pediatric patients under the pressure of nonpharmaceutical interventions for COVID-19 in Beijing, China.

A series of nonpharmaceutical interventions (NPIs) was launched in Beijing, China, on January 24, 2020, to control coronavirus disease 2019. To reveal the roles of NPIs on the respiratory syncytial virus (RSV), respiratory specimens collected from children with acute respiratory tract infection between July 2017 and Dec 2021 in Beijing were screened by capillary electrophoresis-based multiplex PCR (CEMP) assay. Specimens positive for RSV were subjected to a polymerase chain reaction (PCR) and genotyped by G gene sequencing and phylogenetic analysis using iqtree v1.6.12. The parallel and fixed (paraFix) mutations were analyzed with the R package sitePath. Clinical data were compared using SPSS 22.0 software. Before NPIs launched, each RSV endemic season started from October/November to February/March of the next year in Beijing. After that, the RSV positive rate abruptly dropped from 31.93% in January to 4.39% in February 2020; then, a dormant state with RSV positive rates ≤1% from March to September, a nearly dormant state in October (2.85%) and November (2.98%) and a delayed endemic season in 2020, and abnormal RSV positive rates remaining at approximately 10% in summer until September 2021 were detected. Finally, an endemic RSV season returned in October 2021. There was a game between Subtypes A and B, and RSV-A replaced RSV-B in July 2021 to become the dominant subtype. Six RSV-A and eight RSV-B paraFix mutations were identified on G. The percentage of severe pneumonia patients decreased to 40.51% after NPIs launched. NPIs launched in Beijing seriously interfered with the endemic season of RSV.

Triglyceride glucose index is a significant predictor of severe disturbance of consciousness and all-cause mortality in critical cerebrovascular disease patients.

OBJECTIVE: The association of the triglyceride-glucose (TyG) index with severe consciousness disturbance and in-hospital mortality in patients with cerebrovascular disease in the intensive care unit (ICU) is unclear. This study aimed to investigate the TyG index's predictive ability on the severity of impaired consciousness and in-hospital mortality in patients with cerebrovascular disease in the ICU. METHOD: Patients diagnosed with non-traumatic cerebral hemorrhage and cerebral infarction were extracted from the MIMIC-IV database and analyzed as two cohorts. The association between the TyG index and the severity of patients' impairment of consciousness and in-hospital mortality was analyzed using logistic regression models. Using restricted cubic spline curves, we analyzed potential nonlinear relationships between TyG indices and outcome indicators. receiver operating characteristic (ROC) curves were utilized to evaluate the predictive ability of the TyG index for outcome indicators. RESULT: The study's last two cohorts comprised 537 patients with traumatic cerebral hemorrhage and 872 patients with cerebral infarction. TyG index was a significant predictor of the severity of impaired consciousness and in-hospital mortality in patients with cerebrovascular disease, as determined by logistic regression. The risk of severe consciousness impairment and in-hospital mortality increased roughly linearly with increasing TyG index. CONCLUSION: The TyG index was found to be a significant predictor for severe impairment of consciousness and in-hospital death in patients with cerebrovascular disease in the ICU, and it provides some predictive value for the severity of consciousness disturbances and in-hospital mortality in cerebrovascular disease patients.

The changed endemic pattern of human adenovirus from species B to C among pediatric patients under the pressure of non-pharmaceutical interventions against COVID-19 in Beijing, China.

BACKGROUND: Under the pressure of non-pharmaceutical interventions (NPIs) targeting severe acute respiratory syndrome coronavirus 2, the prevalence of human adenovirus (HAdV) was monitored before and after NPIs launched on Jan 24, 2020 in pediatric patients in Beijing, China. METHODS: Respiratory samples collected from children hospitalized with acute respiratory infections from Jan 2015 to Dec 2021 were screened by direct immunofluorescence test or capillary electrophoresis-based multiplex PCR assay. The hexon, penton base, and fiber genes were amplified from HAdV positive specimens, then sequenced. For HAdV typing, phylogenetic trees were built by MEGA X. Then clinical data of HAdV positive cases were collected. All data were evaluated using SPSS Statistics 22.0 software. RESULTS: A total of 16,097 children were enrolled and 466 (2.89%, 466/16,097) were HAdV-positive. The positive rates of HAdV varied, ranging from 4.39% (151/3,438) in 2018 to1.25% (26/2,081) in 2021, dropped from 3.19% (428/13,408) to 1.41% (38/2,689) from before to after NPIs launched (P < 0.001). There were 350 cases typed into nine types of species B, C, or E and 34 recorded as undetermined. Among them, HAdV-B3 (51.56%, 198/384) was the most prevalent types from 2015 to 2017, and HAdV-B7 (29.17%, 112/384) co-circulated with HAdV-B3 from 2018 to 2019. After NPIs launched, HAdV-B3 and B7 decreased sharply with HAdV-B7 undetected in 2021, while HAdV-C1 became the dominant one and the undetermined were more. CONCLUSIONS: The endemic pattern of HAdV changed in Beijing because of the NPIs launched for COVID-19. Especially, the dominant types changed from HAdV-B to HAdV-C.

Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions.

Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.

Prevalence and genomic analysis of t203-like G9 (G9-VI) rotaviruses circulating in children with gastroenteritis in Beijing, China.

Our previous surveillance revealed that t203-like G9 (tentatively designated subtype G9-VI) rotaviruses re-emerged in 2010 in Beijing and rapidly prevailed over the G9-III subtype (the most common G9 subtype globally) and previously predominant G genotypes over the following two years. G9-VI belongs to the VP7 evolutionary lineage VI, which includes unusual and sporadic human rotaviruses from China (t203) and Japan. To obtain insight into the epidemiology, evolution, and transmission advantages of G9-VI rotavirus, we performed follow-up surveillance (2014-2017) and whole-genome analysis of 12 representative G9 strains. The results showed that the G9 genotype was predominant (77.4%), with a marked increase in prevalence (previously 43.5%). Within the G9 genotype, subtype G9-VI accounted for the majority (98.3%) of cases. The most prevalent P-genotype was P[8] (93.7%), within which subtype P[8]b was rare (0.7%). Phylogenetically, the G9-VI subtype strains in this study clustered closely with contemporary emerging human rotaviruses from many other countries in VP7 lineage VI, indicating that this subtype is capable of spreading globally. These currently emerging G9-VI rotaviruses formed a distinct monophyletic subcluster when compared to early G9-VI rotaviruses. Furthermore, four specific amino acid substitutions and synonymous codon substitutions were observed in the VP7 genes between the current G9-VI and globally common G9-III rotaviruses. The remaining nine genes of all of the analyzed representative G9 strains, whether G9-VI or G9-III, combined with the P[8]a, P[8]b, or P[6] genotype and exhibited the same Wa-like backbone constellation.

Overlooked Cytotoxicity and Genotoxicity to Mammalian Cells Caused by the Oxidant Peroxymonosulfate during Wastewater Treatment Compared with the Sulfate Radical-Based Ultraviolet/Peroxymonosulfate Process.

Byproduct formation (chlorate, bromate, organic halogen, etc.) during sulfate radical (SO4•-)-based processes like ultraviolet/peroxymonosulfate (UV/PMS) has aroused widespread concern. However, hypohalous acid (HOCl and HOBr) can form via two-electron transfer directly from PMS, thus leading to the formation of organic halogenated byproducts as well. This study found both PMS alone and UV/PMS can increase the toxicity to mammalian cells of wastewater, while the UV/H2O2 decreased the toxicity. Cytotoxicity of two wastewater samples increased from 5.6-8.3 to 15.7-29.9 mg-phenol/L, and genotoxicity increased from 2.8-3.1 to 5.8-12.8 µg 4-NQO/L after PMS treatment because of organic halogen formation. Organic halogen formation from bromide rather than chloride was found to dominate the toxicity increase. The SO4•--based process UV/PMS led to the formation of both organic halogen and inorganic bromate and chlorate. However, because of the very low concentration (<20 µg/L) and relatively low toxicity of bromate and chlorate, contributions of inorganic byproducts to toxicity increase were negligible. PMS would not form chlorate and bromate, but it generated a higher concentration of total organic halogen, thus leading to a more toxic treated wastewater than UV/PMS. UV/PMS formed less organic halogen and toxicity because of the destruction of byproducts by UV irradiation and the removal of byproduct precursors. Currently, many studies focused on the byproducts bromate and chlorate during SO4•--based oxidation processes. This work revealed that the oxidant PMS even needs more attention because it caused higher toxicity due to more organic halogen formation.