Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters.

To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.

Integration of deep learning and habitat radiomics for predicting the response to immunotherapy in NSCLC patients.

BACKGROUND: The non-invasive biomarkers for predicting immunotherapy response are urgently needed to prevent both premature cessation of treatment and ineffective extension. This study aimed to construct a non-invasive model for predicting immunotherapy response, based on the integration of deep learning and habitat radiomics in patients with advanced non-small cell lung cancer (NSCLC). METHODS: Independent patient cohorts from three medical centers were enrolled for training (n = 164) and test (n = 82). Habitat imaging radiomics features were derived from sub-regions clustered from individual's tumor by K-means method. The deep learning features were extracted based on 3D ResNet algorithm. Pearson correlation coefficient, T test and least absolute shrinkage and selection operator regression were used to select features. Support vector machine was applied to implement deep learning and habitat radiomics, respectively. Then, a combination model was developed integrating both sources of data. RESULTS: The combination model obtained a strong well-performance, achieving area under receiver operating characteristics curve of 0.865 (95% CI 0.772-0.931). The model significantly discerned high and low-risk patients, and exhibited a significant benefit in the clinical use. CONCLUSION: The integration of deep-leaning and habitat radiomics contributed to predicting response to immunotherapy in patients with NSCLC. The developed integration model may be used as potential tool for individual immunotherapy management.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks.

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.

Infantile Cranial Fasciitis: A Clinicopathologic Evaluation.

OBJECTIVE: To investigate the clinicopathologic features, immunophenotype, molecular genetic changes, and differential diagnosis of cranial fasciitis (CF). METHODS: The clinical manifestations, imaging, surgical technique, pathologic characteristics, special staining, and immunophenotype, as well as break-apart fluorescence in situ hybridization assay for USP6 of 19 CF cases were analyzed, retrospectively. RESULTS: The patients were 11 boys and 8 girls, aged 5 to 144 months, with a median age of 29 months. There were 5 cases (26.31%) in the temporal bone, 4 cases (21.05%) in the parietal bone, 3 cases (15.78%) in the occipital bone, 3 cases (15.78%) in the frontotemporal bone, 2 cases (10.52%) in the frontal bone, 1 case (5.26%) in the mastoid of middle ear, and 1 case (5.26%) in the external auditory canal. The main clinical manifestations were painless, with the presentation of masses that grew rapidly and frequently eroded the skull. There was no recurrence and no metastasis after the operation. Histologically, the lesion consists of spindle fibroblasts/myofibroblasts arranged in bundles, braided or atypical spokes. Mitotic figures could be seen, but not atypical forms. Immunohistochemical studies showed diffuse strong positive SMA and Vimentin in all CFs. These cells were negative for Calponin, Desmin, ß-catenin, S-100, and CD34. The ki-67 proliferation index was 5% to 10%. Ocin blue-PH2.5 staining showed blue-stained mucinous features in the stroma. The positive rate of USP6 gene rearrangement detected by fluorescence in situ hybridization assay was about 10.52%, and the positive rate was not related to age. All patients were observed for 2 to 124 months and showed no signs of recurrence or metastasis. CONCLUSIONS: In summary, CF was a benign pseudosarcomatous fasciitis that occurs in the skull of infants. Preoperative diagnosis and differential diagnosis were difficult. Computed tomography typing might be beneficial for imaging diagnosis, and pathologic examination might be the most reliable way to diagnose CF.

Clinicopathological Analysis of Sturge-Weber Syndrome with Focal Cortical Dysplasia FCD IIIc.

Objective: To investigate the clinicopathological features of children with Sturge-Weber syndrome and to analyze the correlation between the distribution area of leptomeningeal angiomatosis, the degree of cerebral cortical calcification, and the degree of cerebral atrophy associated with epileptic seizures. Methods: 10 children were diagnosed with SWS with FCD IIIc by histopathology and immunohistochemistry. Spearman correlation analysis was used to calculate the association of SWS with FCD IIIc and seizures in children. Results: The leptomeningeal angiomatosis area was markedly positively correlated with the degree of brain atrophy in 10 children with SWS (r = 0.783, p = 0.007). The distribution of leptomeningeal hemangiomatosis, the degree of cortical calcification, and brain atrophy were not significantly correlated with epilepsy. Conclusion: SWS may be accompanied by FCD IIIc. The more extensive the cerebral lobes of leptomeningeal angiomatosis in SWS, the more pronounced the brain atrophy.

Glucosylation of (Z)-3-hexenol informs intraspecies interactions in plants: A case study in Camellia sinensis.

Plants emit a variety of volatiles in response to herbivore attack, and (Z)-3-hexenol and its glycosides have been shown to function as defence compounds. Although the ability to incorporate and convert (Z)-3-hexenol to glycosides is widely conserved in plants, the enzymes responsible for the glycosylation of (Z)-3-hexenol remained unknown until today. In this study, uridine-diphosphate-dependent glycosyltransferase (UGT) candidate genes were selected by correlation analysis and their response to airborne (Z)-3-hexenol, which has been shown to be taken up by the tea plant. The allelic proteins UGT85A53-1 and UGT85A53-2 showed the highest activity towards (Z)-3-hexenol and are distinct from UGT85A53-3, which displayed a similar catalytic efficiency for (Z)-3-hexenol and nerol. A single amino acid exchange E59D enhanced the activity towards (Z)-3-hexenol, whereas a L445M mutation reduced the catalytic activity towards all substrates tested. Transient overexpression of CsUGT85A53-1 in tobacco significantly increased the level of (Z)-3-hexenyl glucoside. The functional characterization of CsUGT85A53 as a (Z)-3-hexenol UGT not only provides the foundation for the biotechnological production of (Z)-3-hexenyl glucoside but also delivers insights for the development of novel insect pest control strategies in tea plant and might be generally applicable to other plants.

miRNA-seq provides novel insight into the response to hyper- and hypo- salinity acclimation in Crassostrea hongkongensis.

The Hong Kong oyster, Crassostrea hongkongensis, is a significant bivalve species with economic importance. It primarily inhabits the estuarine intertidal zones in southern China, making it susceptible to salinity fluctuations. Consequently, investigating the molecular mechanisms governing salinity regulation in C. hongkongensis is essential. In this study, we conducted miRNA-seq on C. hongkongensis to compare miRNA expression differences under varying salinities (5‰, 25‰, and 35‰). The miRNA sequencing revealed 51 known miRNAs and 95 novel miRNAs across nine small RNA libraries (S5, S25, and S35). Among these miRNAs, we identified 6 down-regulated differentially expressed (DE) miRNAs in response to hypo-salinity stress (5‰), while 1 up-regulated DE miRNA and 5 down-regulated DE miRNAs were associated with hyper-salinity stress (35‰). Additionally, we predicted 931 and 768 potential target genes for hypo- and hyper-salinity stress, respectively. Functional gene annotation indicated that the target genes under hypo-salinity stress were linked to vesicle-mediated transport and metal ion binding. Conversely, those under hyper-salinity stress were primarily involved in signal transduction and metabolic processes. These findings have provided insights into the regulatory role of miRNAs, their potential target genes and associated pathways in oyster hypo- and hyper-salinity stress, which establish a foundation for future studies on the roles of miRNAs in salinity acclimation mechanisms in C. hongkongensis.

Transcriptional responses of Crassostrea hongkongensis under high and low salinity stress.

Salinity, a key limiting factor, affects the distribution and survival of marine species. The Hong Kong oyster (Crassostrea hongkongensis), a euryhaline species found along the coast of the South China Sea, has become a major aquaculture bivalve species. To determine the molecular mechanism by which oysters respond to coastal waters with varying salinity levels, we used RNA-seq to sequence the gill samples of oysters exposed to normal (25 ‰, S25), low (5 ‰, S5) and high (35 ‰, S35) salinity conditions for one month. The results revealed different expression transcriptome levels among oysters living under low and high salinity conditions. Using high-throughput sequencing, we identified 811 up-regulated genes and 769 down-regulated genes. As determined by KEGG pathway mapping, the differentially expressed genes (DEGs) were significantly enriched in the prion diseases, histidine metabolism, arginine and proline metabolism, and beta-alanine metabolism pathways in both the S5 vs. S25 and S35 vs. S25 group comparison. Several DEGs including heat shock 70 kDa protein 12B-like, poly (ADP-ribose) polymerase (PARP), and tripartite motif-containing protein 2 (TRIM2), and low-density lipoprotein receptor-like, as well as KEGG pathways, including arginine and proline metabolism, apoptosis, PPAR signaling pathway, the thyroid hormone signaling pathway, were concerning response to salinity stress. Additionally, eight DEGs involved in salinity adaptation were selected for RT-qPCR validation, and the results confirmed the credibility of the transcriptome sequencing data. Overall, we designed a one-month, medium-term experiment to examine the responses of C. hongkongensis exposed to different levels of salinity stress and performed transcriptome analysis using high-throughput sequencing. Our results enhance current understanding of the molecular mechanisms of salinity stress responses in C. hongkongensis and provided insights into the osmotic biology of oysters.

A fluorescence aptamer sensor utilizing WS2 nanosheets for sensitive detection of patulin: enhanced specificity and wide applicability.

A tungsten disulfide (WS2) nanosheet-based aptamer sensor was developed to detect patulin (PAT). The 5'-end of the PAT aptamer was modified with a cyanine 3 (Cy3) fluorophore, which self-assembled on WS2 nanosheets. The interaction between the Cy3 fluorophore at the 5'-end of the PAT aptamer and the WS2 nanosheets resulted in reduced fluorescence (FL) intensity due to fluorescence resonance energy transfer (FRET). The introduction of PAT into this sensing system led to hybridization with the PAT aptamer, forming a G-quadruplex/PAT complex with low affinity for the WS2 nanosheet surface. This hybridization increased the distance between the Cy3 fluorophore and the WS2 nanosheets, inhibiting FRET and producing a strong FL signal. Under optimal experimental conditions, the FL intensity of the sensing system demonstrated an excellent linear correlation with PAT concentrations ranging from 0.5 to 40.0 ng mL-1, and it achieved a detection limit (S/N = 3) of 0.23 ng mL-1. This sensing system offers enhanced specificity for PAT detection and has the potential for broad application in detecting other toxins by substituting the sequence of the recognition aptamer.

Leaf-like ionic covalent organic framework for the highly efficient and selective removal of non-steroidal anti-inflammatory drugs: Adsorption performance and mechanism insights.

In recent years, ionic covalent organic frameworks (iCOFs) have become popular for the removal of contaminants from water. Herein, we employed 2-hydroxybenzene-1,3,5-tricarbaldehyde (TFP) and 1,3-diaminoguanidine monohydrochloride (DgCl) to develop a novel leaf-like iCOF (TFP-DgCl) for the highly efficient and selective removal of non-steroidal anti-inflammatory drugs (NSAIDs). The uniformly distributed adsorption sites, suitable pore sizes, and functional groups (hydroxyl groups, guanidinium groups, and aromatic groups) of the TFP-DgCl endowed it with powerful and selective adsorption capacities for NSAIDs. Remarkably, the optimal leaf-like TFP-DgCl demonstrated an excellent maximum adsorption capacity (1100.08 mg/g) for diclofenac sodium (DCF), to the best of our knowledge, the largest adsorption capacity ever achieved for DCF. Further testing under varying environmental conditions such as pH, different types of anions, and multi-component systems confirmed the practical suitability of the TFP-DgCl. Moreover, the prepared TFP-DgCl exhibited exceptional reusability and stability through six adsorption-desorption cycles. Finally, the adsorption mechanisms of NSAIDs on leaf-like TFP-DgCl were confirmed as electrostatic interactions, hydrogen bonding, and π-π interactions. This work significantly supplements to our understanding of iCOFs and provides new insights into the removal of NSAIDs from wastewater.

Skeletal muscle depletion predicts death in severe community-acquired pneumonia patients entering ICU.

BACKGROUND: Sarcopenia, or skeletal muscle depletion, was common in the elderly and often led to a poor prognosis of diseases. The area of the psoas muscle in abdominal computed tomography (CT) is the most common used for diagnosing sarcopenia. However, patients with pneumonia routinely only undergo chest CT. OBJECTIVES: This study aimed to determine whether paraspinal muscle area (PMA) obtained by chest CT can predict death for community-acquired pneumonia (SCAP) patients entering intensive care unit (ICU). METHODS: This study enrolled 208 SCAP patients admitted to ICU after undergoing chest CT. PMA, paraspinal muscle radiodensity (PMD), and lean paraspinal muscle area (LPMA) were calculated on chest CT images. The main outcome was mortality during hospitalization. Logistic regression, receiver operating characteristic (ROC) curve, and Kaplan-Meier curves were used to evaluate forecasting effectiveness. RESULTS: The primary outcome occurred in 76 (36.53%) patients. In multivariate logistic regression, PMA, lactic dehydrogenase (LDH), invasive mechanical ventilation (IMV), red blood cell (RBC) and age≥ 65 years were independent risk factors predicting death during hospitalization (adjusted Odds Ratio [OR]: 0.886, 1.002, 3.178, 0.612 and 2.003, respectively). The area under curve (AUC) of PMA to predict death was 0.720 (P< 0.001). During hospitalization, the median survival time of high-PMA (51.00 days) and low-PMA groups (20.00 days) was statistically significant (P< 0.001). CONCLUSION: Lower PMA was associated with an increased risk of death for SCAP patients admitted to the ICU. In other words, PMA may help early identify adverse prognosis of SCAP patients admitted to ICU.

A sensitive MnO2 nanosheet sensing platform based on a fluorescence aptamer sensor for the detection of zearalenone.

An aptamer sensor based on manganese dioxide (MnO2) nanosheets was developed for the detection of zearalenone (ZEN). The ZEN aptamer was modified at the 5'-end by a 6-carboxyfluorescein (6-FAM) fluorophore with self-assembly on MnO2 nanosheets. Interaction of the 6-FAM fluorophore at the 5'-end of the ZEN aptamer with the MnO2 nanosheet lowered fluorescence (FL) intensity due to fluorescence resonance energy transfer (FRET). The introduction of ZEN into the sensing system resulted in hybridization with the ZEN aptamer, forming a stable G-quadruplex/ZEN, which exhibited a low affinity for the MnO2 nanosheet surface. The distance between the 6-FAM fluorophore and MnO2 nanosheet hampered FRET, with a consequent strong FL signal. Under the optimal experimental conditions, the FL intensity of the sensing system showed a good linear correlation with ZEN concentration in the range of 1.5-10.0 ng mL-1, and a detection limit (S/N = 3) of 0.68 ng mL-1. The sensing system delivered enhanced specificity for the detection of ZEN, and can find wide application in the detection of other toxins by replacing the sequence of the recognition aptamer.

UGT74AF3 enzymes specifically catalyze the glucosylation of 4-hydroxy-2,5-dimethylfuran-3(2H)-one, an important volatile compound in Camellia sinensis.

4-Hydroxy-2,5-dimethylfuran-3(2H)-one (HDMF) is an important odorant in some fruits, and is proposed to play a crucial role in the caramel-like notes of some teas. However, its biosynthesis and metabolism in tea plants are still unknown. Here, HDMF glucoside was unambiguously identified as a native metabolite in tea plants. A novel glucosyltransferase UGT74AF3a and its allelic protein UGT74AF3b specifically catalyzed the glucosylation of HDMF and the commercially important structural homologues 2 (or 5)-ethyl-4-hydroxy-5 (or 2)-methylfuran-3(2H)-one (EHMF) and 4-hydroxy-5-methylfuran-3(2H)-one (HMF) to their corresponding ß-D-glucosides. Site-directed mutagenesis of UGT74AF3b to introduce a single A456V mutation resulted in improved HDMF and EHMF glucosylation activity and affected the sugar donor preference compared with that of the wild-type control enzyme. The accumulation of HDMF glucoside was consistent with the transcript levels of UGT74AF3 in different tea cultivars. In addition, transient UGT74AF3a overexpression in tobacco significantly increased the HDMF glucoside contents, and downregulation of UGT74AF3 transcripts in tea leaves significantly reduced the concentration of HDMF glucoside compared with the levels in the controls. The identification of HDMF glucoside in the tea plant and the discovery of a novel-specific UDP-glucose:HDMF glucosyltransferase in tea plants provide the foundation for improvement of tea flavor and the biotechnological production of HDMF glucoside.

The crosstalk between RNA m6A epitranscriptome and TGFß signaling pathway contributes to the arrest of cell cycle.

TGFß signaling pathway is critical for the cell division, differentiation and apoptosis, the aberrant regulation of which will result in severe diseases including cancer. N6-methyl-adenosine (m6A) is one of the most abundant modifications on mRNA, it is unclear yet how m6A epitranscriptome response to stimulation of TGFß. Here, we found that cellular m6A level of RNA was elevated after TGFß treatment, which might be regulated by upregulation of WTAP and METTL3. MeRIP-Seq of mRNAs of MCF7 with or without treated by TGFß showed that mRNA with upregulated m6A modification level after TGFß treatment were enriched in TGFß signaling pathway. Phosphorylated level of SMAD2 or SMAD3 induced by TGFß was impaired when WTAP was silenced. Moreover, the m6A modification and mRNA level of JunB, which is known as a cell cycle inhibitor, both were increased after induction of TGFß and decreased after knockdown of WTAP. Intriguingly, growth inhibition caused by TGFß was rescued in WTAP-knockdown cells. Collectively, these results reveal the key role that m6A pathway playing in the cell cycle arrest induced by TGFß signaling, providing new mechanisms explanation for growth inhibition mediated by TGFß.

Untargeted metabolomics coupled with chemometrics analysis reveals potential non-volatile markers during oolong tea shaking.

Shaking is a critical process in the formation of oolong tea quality, although the metabolites and their changes in this sensitive process have not yet been determined. In this study, untargeted analysis based on ultrahigh-performance liquid chromatography/quadrupole-Orbitrap mass spectrometry was conducted to comprehensively profile metabolite changes in different cultivars. Theanine glucoside was identified for the first time in oolong tea. Hierarchical cluster analysis indicated that shaking caused major changes in metabolite levels in oolong tea. Seventy-one, 83 and 73 potential features showed significant differences between pre- and post-shaking samples for var. sinensiscv. "Zimudan", "Shuixian", and "Huangmeigui," respectively. Chemometrics analysis of the three cultivars led to the identification of 18 shared metabolites, including epigallocatechin gallate, phenylalanine, tryptophan, proline, and hydroxy-jasmonic acid, as potential markers. This study identified the metabolites that allow monitoring of tea quality formation during both processing and preservation, and it provides a novel strategy for data reduction in studies to discover key metabolites.