Nitrate and sulfate account for a significant fraction of PM₂.₅ mass and are generally secondary in nature. Contributions to these two inorganic aerosol components from major sources need to be ...identified for policy makers to develop cost effective regional emission control strategies. In this work, a source-oriented version of the Community Multiscale Air Quality (CMAQ) model that directly tracks the contributions from multiple emission sources to secondary PM₂.₅ is developed to determine the regional contributions of power, industry, transportation and residential sectors as well as biogenic sources to nitrate and sulfate concentrations in China in January and August 2009. The source-oriented CMAQ model is capable of reproducing most of the available PM₁₀ and PM₂.₅ mass, and PM₂.₅ nitrate and sulfate observations. Model prediction suggests that monthly average PM₂.₅ inorganic components (nitrate + sulfate + ammonium ion) can be as high as 60 μg m⁻³ in January and 45 μg m⁻³ in August, accounting for 20–40% and 50–60% of total PM₂.₅ mass. The model simulations also indicate significant spatial and temporal variation of the nitrate and sulfate concentrations as well as source contributions in the country. In January, nitrate is high over Central and East China with a maximum of 30 μg m⁻³ in the Sichuan Basin. In August, nitrate is lower and the maximum concentration of 16 μg m⁻³ occurs in North China. In January, highest sulfate occurs in the Sichuan Basin with a maximum concentration of 18 μg m⁻³ while in August high sulfate concentration occurs in North and East China with a similar maximum concentration. Power sector is the dominating source of nitrate and sulfate in both January and August. Transportation sector is an important source of nitrate (20–30%) in both months. Industry sector contributes to both nitrate and sulfate concentrations by approximately 20–30%. Residential sector contributes to approximately 10–20% of nitrate and sulfate in January but its contribution is low in August.
Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA （ccfDNA） remain limited. Here we ...describe a methylated CpG tan- dems amplification and sequencing （MCTA-Seq） method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples （n = 151） of hepatocellular carcinoma （HCC） patients and control subjects, identifying dozens of high-performance markers in blood for detecting smaU HCC （≤ 3 cm）. Among these markers, 4 （RGS10, ST8SIA6, RUNX2 and VIM） are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients （n = 36） and control subjects including cirrho- sis patients （n = 17） and normal individuals （n = 38）. Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting.
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot ...simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas.
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron ...simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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•Carbohydrates are important components of a healthy diet, their excessive consumption has increasingly been linked to negative health outcomes such as obesity, type II diabetes, ...cardiovascular disease, and cancer.•Based on this, LCD consumption has gained increased popularity as a sole or combined strategy for above medical conditions; however, the current evidence is inconsistent and not clear conclusion.•In this review, from the microbiome viewpoint, we compared with the low carbohydrate diet and another important functional food (Resist starch diet) effect on prostate cancer, breast cancer, and colorectal cancer risk which will may open new research avenues culminating in new treatment and prevention options.
Extensive research has established the benefits of incorporating low carbohydrate diets (LCDs) for managing obesity, diabetes, and metabolic syndrome (Mets). Recent findings indicate that LCDs could additionally impact cancer development and progression by creating an unfavorable metabolic micro-environment that promotes reprogrammed metabolism in cancer cells. This has led to LCDs being considered as a possible complementary treatment for cancer. Our review specifically examines the association between cancer risk, consumption of dietary carbohydrate, glycemic index (GI), and glycemic load (GL), with a focus on prostate, breast, and colorectal cancer. We also explore relevant mechanism underlying the potential anti-tumor effects of LCD diets, especially in gut microbiota modulation. However, findings in this area remain controversial, and further research is needed to evaluate their application in clinical practice. On the other hand, resistant starch (RS) has gained attention as a healthy and high-quality component of carbohydrate diets. It not only serves as a dietary fiber but also acts as a valuable source of prebiotics due to its ability to influence gut microbial composition, leading to improved metabolic control. This has positioned RS as a potential means for preventing and treating cancer. In this review, we also summarized the RS-gut microbiota-cancer risk axis to enhance our understanding of the health effects of RS consumption. From a clinical perspective, RS supplementation shows promise as a strategy for preventing diseases and managing cancer. It is evident that simply assessing the quantity of dietary carbohydrate intake may not be enough to determine cancer risk; the quality of carbohydrates should also be considered to draw definitive conclusions which will help clinician and nutritionist make a reasonable choice in management cancer.
It is recognized that autism spectrum disorder (ASD) is a highly complex neurodevelopmental disorder with communication deficits as well as multiple social barriers. The core symptoms of ASD are not ...treatable with current therapeutics. Therefore, finding new treatment strategies for ASD is urgently needed. Mesenchymal stem cells (MSC) have been shown to be a promising therapeutic approach in previous studies. However, the underlying mechanisms of MSC treatment for ASD through gut microbiota remain unclear and require further investigation.
BTBR mice were used as ASD model and then randomly assigned to the human bone marrow-derived mesenchymal stem cell (hBMMSC) intravenous treatment group or vehicle treatment group. C57BL/6J (C57) mice served as control. Multiple social behavioral tests were performed during the 6-week period and fecal samples were collected at different time points for 16 s rRNA sequencing analysis.
The administration of hBMMSC improved social deficits of BTBR mice in the open field test (OFT), light-dark box test (LBT), novel object recognition (NOR), and free social test (FST), while also significantly reducing stereotypic behaviors. Additionally, hBMMSC administration notably reversed the alterations of microbiota abundance in BTBR mice, particularly the Firmicutes/Bacteroidetes ratio. Several specific differential taxa were further selected and showed a correlation with the prognosis and behavioral scores of ASD.
Overall, intravenous treatment with hBMMSC had a beneficial impact on ASD by ameliorating social deficits and modifying microbiota compositions. This outcome indicates that hBMMSC intravenous transplantation could be a promising therapeutic strategy for enhancing ASD symptoms improvements.
Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. ...However, existing methods generally rely on feature engineering, and ignore the natural similarity between the two types of protein translational modification. This study is the first all-in-one deep network to predict protein Ubiquitylation and SUMOylation sites from protein sequences as well as their crosstalk sites simultaneously. Our deep learning architecture integrates several meta classifiers that apply deep neural networks to protein sequence information and physico-chemical properties, which were trained on multi-label classification mode for simultaneously identifying protein Ubiquitylation and SUMOylation as well as their crosstalk sites.
The promising AUCs of our method on Ubiquitylation, SUMOylation and crosstalk sites achieved 0.838, 0.888, and 0.862 respectively on tenfold cross-validation. The corresponding APs reached 0.683, 0.804 and 0.552, which also validated our effectiveness.
The proposed architecture managed to classify ubiquitylated and SUMOylated lysine residues along with their crosstalk sites, and outperformed other well-known Ubiquitylation and SUMOylation site prediction tools.
This research performed four experiments to investigate the influence of infant schema cues on charitable donation intention and examine the moderating effect of gender. The results indicate that: ...(1) individuals stimulated by infant schema (vs. adult schema) cues had a higher willingness to donate when facing charity promotion; (2) the main effect was not due to the perceived cuteness of character in posters; (3) empathy played an entirely mediating role in the relationship between infant schema cues and donation intention; (4) gender moderated the influence of infant schema on donation intention: infant schema cues are effective for improving females’ donation intention, but ineffective for males. These findings contributed to the literature on infant schema and provide practical significance for introducing infant schema in charity promotion.
•178 nitrate modeling studies in China published during 2007–2021 were reviewed.•Model performance on nitrate and possible reasons for model-observation biases were summarized.•The contribution of ...N2O5 heterogeneous chemistry to nitrate varies from 21.0% to 51.6% among studies.•Decreased SO2 emission, enhanced AOC, and weakened deposition account for increasing PM2.5 nitrate fraction.•Multiple-pollutant control strategies involving NH3, NOx, and VOCs are needed to mitigate nitrate pollution.
Particulate nitrate (pNO3) is now becoming the principal component of PM2.5 during severe winter haze episodes in many cities of China. To gain a comprehensive understanding of the key factors controlling pNO3 formation and driving its trends, we reviewed the recent pNO3 modeling studies which mainly focused on the formation mechanism and recent trends of pNO3 as well as its responses to emission controls in China. The results indicate that although recent chemical transport models (CTMs) can reasonably capture the spatial–temporal variations of pNO3, model-observation biases still exist due to large uncertainties in the parameterization of dinitrogen pentoxide (N2O5) uptake and ammonia (NH3) emissions, insufficient heterogeneous reaction mechanism, and the predicted low sulfate concentrations in current CTMs. The heterogeneous hydrolysis of N2O5 dominates nocturnal pNO3 formation, however, the contribution to total pNO3 varies among studies, ranging from 21.0% to 51.6%. Moreover, the continuously increasing PM2.5 pNO3 fraction in recent years is mainly due to the decreased sulfur dioxide emissions, the enhanced atmospheric oxidation capacity (AOC), and the weakened nitrate deposition. Reducing NH3 emissions is found to be the most effective control strategy for mitigating pNO3 pollution in China. This review suggests that more field measurements are needed to constrain the parameterization of heterogeneous N2O5 and nitrogen dioxide (NO2) uptake. Future studies are also needed to quantify the relationships of pNO3 to AOC, O3, NOx, and volatile organic compounds (VOCs) in different regions of China under different meteorological conditions. Research on multiple-pollutant control strategies involving NH3, NOX, and VOCs is required to mitigate pNO3 pollution, especially during severe winter haze events.
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•Demonstrated the antibacterial effects of methicillin-resistant Staphylococcus aureus and high biocompatibility of Low-molecular-weight fucoidan.•Neutrophil membrane-coated ...nanoparticles can escape immune recognition and accumulate in the infection site.•Developed a novel antimicrobial agent and target drug delivery system to heal methicillin-resistant Staphylococcus aureus-infected wounds.•The accumulation and antibacterial effects of the nanoparticles are demonstrated by in vitro and in vivo experiments.•Infection-targeted nanoparticles loading with alternative antimicrobial agents is a useful strategy for the targeted treatment of infection therapy.
Treatment of methicillin-resistant Staphylococcus aureus (MRSA)-infected wounds remains an important clinical challenge. Current treatments using vancomycin usually result in high side effects with low treatment efficacy because of strong drug toxicity and weak targeting specificity. It is emergently needed to develop a novel antimicrobial agent and target drug delivery system. Herein, we developed anti-infection nanoparticles (LMM NPs) with autonomous targeting ability, loading low-molecular-weight fucoidan (LMWF) and coated by neutrophil membranes, and used for the therapy of MRSA-infected wounds. The LMWF molecules possess similar anti-MRSA effects as vancomycin but lower nephrotoxicity. Nanoparticles coated with the neutrophil membrane can escape immune recognition due to the retained cell membrane components and accumulate in the infection site. Furthermore, the MRSA-infected wound model confirms that the LMM NPs accumulate efficiently in MRSA-infected tissues and have good biocompatibility and excellent antibacterial ability in MRSA-infected wounds, which promote MRSA-accompanied wound healing. These novel infection-targeted LMWF-loaded NPs could be applied as a useful strategy for the targeted treatment of infection therapy. This will provide a meaningful reference to extend clinical treatment in MRSA infection of deep tissues.
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