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Psoralen could inhibit the proliferation of human breast cancer cells, however, the molecular mechanism was unclear. We evaluated the anti-proliferative effects of psoralen by MTT, plate colony formation assay and cell cycle analysis in MCF-7 and MDA-MB-231 cells. The effects of psoralen on activation of Wnt/β-catenin and the related target genes were examined by quantitative real-time PCR, western blotting and cell immunofluorescence. The tumor growth was conducted in BALB/c nude mice and the pathological changes of heart, liver and kidney were also observed. Our results demonstrate that psoralen significantly inhibited cell proliferation by inducing G0/G1 phase arrest in MCF-7 cells and G2/M phase arrest in MDA-MB-231 cells. The expression of Fra-1 was reduced and Axin2 was promoted both in MCF-7 and MDA-MB-231 cells after psoralen treatment. The cytoplasmic accumulation and nuclear translocation of β-catenin were significantly reduced by psoralen. Psoralen increased the levels of phospho-(Y142) β-catenin, while decreased the expression of total β-catenin and its downstream target Fra-1 in vitro and vivo. Moreover, psoralen didn’t cause any significant toxicity at the effective concentration. Overall, our results might provide theoretical basis for clinical application of psoralen in breast cancer.

Daily transcription cycling in the baboon Much of our knowledge about the important effects of circadian rhythms in physiology comes from studies of mice, which are nocturnal. Mure et al. report transcriptional profiles from many tissues and brain regions in baboons over a 24-hour period (see the Perspective by Millius and Ueda). The results emphasize how extensive rhythmic expression is, with more than 80% of protein-coding genes involved. They also highlight unanticipated differences between the mouse and baboon in the cycling of transcripts in various tissues. The findings provide a comprehensive analysis of circadian variation in gene expression for a diurnal animal closely related to humans. Science , this issue p. eaao0318 ; see also p. 1210

Sepsis-induced acute lung injury (ALI) is an inflammatory pulmonary condition characterized by a complex pathophysiological mechanism. The development and progression of sepsis-induced ALI are accompanied by significant oxidative damage. This study aimed to identify key oxidative stress-related genes associated with sepsis-induced ALI. Samples, including sepsis, sepsis-induced ALI, and control groups, were obtained from the Gene Expression Omnibus database. Key oxidative stress-related genes in sepsis-induced ALI were identified using Weighted Gene Co-expression Network Analysis (WGCNA), Protein-Protein Interaction (PPI) network analysis, logistic regression, and LASSO regression analysis. Functional information regarding these genes was explored through Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA). A logistic regression model was constructed based on the identified hub oxidative stress-related genes. The diagnostic value of this model for sepsis-induced ALI was assessed using the receiver operating characteristic (ROC) curve. The relative abundance of 22 human immune cell types was calculated using CIBERSORT software. The expression levels of hub genes in the blood samples of sepsis-induced ALI patients were analyzed through RT-PCR and ELISA. A total of 1,055 genes associated with sepsis-induced ALI were identified via WGCNA, of which 145 genes were linked to oxidative stress. GSVA revealed that these 145 genes were significantly enriched in 79 biological pathways, while GSEA indicated a strong association with immune-related signaling pathways. Additionally, the top 20 genes were selected through PPI network analysis. The logistic regression model was constructed using VDAC1 , HSPA8 , SOD1 , HSPA9 , TXN , and SNCA . In the training set and the validation set, the AUC values of logistic regression model were 0.9091 and 0.8279, respectively, suggesting good discriminability when distinguishing normal from sepsis-induced ALI. Notably, these six genes were correlated with immune cell infiltration in sepsis-induced ALI, with HSPA8 , SOD1 , and HSPA9 showing downregulation in sepsis-induced ALI. In conclusion, VDAC1 , HSPA8 , SOD1 , HSPA9 , TXN , and SNCA have been identified as oxidative stress-related genes associated with sepsis-induced ALI. The logistic regression model developed using these six genes could identify patients with sepsis-induced ALI. Our findings might provide novel research strategies for the molecular therapeutic target of sepsis-induced ALI.

In contrast to cancers with high immunotherapy responsiveness, such as lung cancer and melanoma, thyroid carcinoma (THCA) immunotherapy remains investigational. To establish a theoretical foundation for THCA immunotherapy, we investigated the association between genetic mutations and tumor microenvironment (TME) by analyzing RNA-sequencing data and somatic mutation profiles from 571 THCA samples in The Cancer Genome Atlas (TCGA) database. The ESTIMATE algorithm was first applied to calculate ImmuneScores and StromalScores. Samples were subsequently stratified into immune-high and immune-low groups, as well as stromal-high and stromal-low groups, based on median score thresholds. We then identified differentially expressed genes (DEGs) and differentially mutated genes (DMGs). Significant disparities in mutation frequencies of BRAF , NRAS , and HRAS were observed both between immune stratification groups (high vs low) and stromal stratification groups (high vs low). Correlation analysis between DMGs and clinicopathological features revealed that BRAF / NRAS expression levels were associated with THCA clinical stage. CIBERSORT computational algorithm was also used to quantify the relative abundance of tumor-infiltrating immune cells (TICs), demonstrating that 11 types of activated TICs were strongly associated with BRAF expression. Finally, we examined target DMGs expression in relation to immune checkpoint proteins (ICPs) to identify potential therapeutic targets. THCA specimens with suppressed BRAF expression demonstrated upregulated ICPs expression, indicating potential susceptibility to checkpoint blockade immunotherapy.

There is growing recognition that the gut microbial community regulates a wide variety of important functions in its animal hosts, including host health. However, the complex interactions between gut microbes and environment are still unclear. Honey bees are ecologically and economically important pollinators that host a core gut microbial community that is thought to be constant across populations. Here, we examined whether the composition of the gut microbial community of honey bees is affected by the environmental landscape the bees are exposed to. We placed honey bee colonies reared under identical conditions in two main landscape types for 6 weeks: either oilseed rape farmland or agricultural farmland distant to fields of flowering oilseed rape. The gut bacterial communities of adult bees from the colonies were then characterized and compared based on amplicon sequencing of the 16S rRNA gene. While previous studies have delineated a characteristic core set of bacteria inhabiting the honey bee gut, our results suggest that the broad environment that bees are exposed to has some influence on the relative abundance of some members of that microbial community. This includes known dominant taxa thought to have functions in nutrition and health. Our results provide evidence for an influence of landscape exposure on honey bee microbial community and highlight the potential effect of exposure to different environmental parameters, such as forage type and neonicotinoid pesticides, on key honey bee gut bacteria. This work emphasizes the complexity of the relationship between the host, its gut bacteria, and the environment and identifies target microbial taxa for functional analyses. We examine whether the composition of the gut microbial community of honey bees is affected by the environmental landscape the bees are exposed to. We find that the broad environment that forager bees are exposed to influences the relative abundance of members of the dominant microbial community, including taxa thought to have functions in nutrition and health.

Accurate interpretation of qPCR data continues to present significant challenges, particularly at low target concentrations where technical variability, stochastic amplification, and efficiency fluctuations confound quantification. The widespread assumption that qPCR outputs are intrinsically reliable, coupled with inconsistent adherence to best-practice guidelines, has exacerbated issues of reproducibility and contributed to misleading conclusions. This may distort pathogen load quantification in diagnostic settings, whilst in gene expression studies, it can lead to overinterpretation of small fold changes. This study presents a systematic, cross-platform evaluation of qPCR performance across a wide dynamic range using defined reaction mixes and technical replicates. We show that calculated copy numbers can closely match expected values over more than three orders of magnitude, but that variability increases markedly at low input concentrations, often exceeding the magnitude of biologically meaningful differences. We conclude that establishing and reporting confidence intervals from the data itself is essential for transparency and for distinguishing reliable quantification from technical noise.

Summary Intestinal flora provides an important contribution to the development of pulmonary tuberculosis (PTB). We performed a cross‐sectional study in 52 healthy controls (HCs) and 83 patients with untreated active PTB to assess the differences in their microbiomic and metabolic profiles in faeces via V3‐V4 16S rRNA gene sequencing and gas chromatography–mass spectrometry. Patients with PTB had considerable reductions in phylogenetic alpha diversity and the production of short‐chain fatty acids, dysbiosis of the intestinal flora and alterations in the faecal metabolomics composition compared with HCs. Significant alterations in faecal metabolites were associated with changes in the relative abundance of specific genera. Our study describes the imbalance of the gut microbiota and altered faecal metabolomics profiles in patients with PTB; the results indicate that the gut microbiota and faecal metabolomic profiles can be used as potential preventive and therapeutic targets for PTB. The imbalance of the gut microbiota and altered faecal metabolomics profiles in patients with PTB;Mtb infection decreased the production of SCFAs in faeces.

Studying the effects of the microbiome on the development of different types of cancer has recently received increasing research attention. In this context, the microbial content of organs of the gastrointestinal tract has been proposed to play a potential role in the development of pancreatic cancer (PC). Proposed mechanisms for the pathogenesis of PC include persistent inflammation caused by microbiota leading to an impairment of antitumor immune surveillance and altered cellular processes in the tumor microenvironment. The limited available diagnostic markers that can currently be used for screening suggest the importance of microbial composition as a non-invasive biomarker that can be used in clinical settings. Samples including saliva, stool, and blood can be analyzed by 16 s rRNA sequencing to determine the relative abundance of specific bacteria. Studies have shown the potentially beneficial effects of prebiotics, probiotics, antibiotics, fecal microbial transplantation, and bacteriophage therapy in altering microbial diversity, and subsequently improving treatment outcomes. In this review, we summarize the potential impact of the microbiome in the pathogenesis of PC, and the role these microorganisms might play as biomarkers in the diagnosis and determining the prognosis of patients. We also discuss novel treatment methods being used to minimize or prevent the progression of dysbiosis by modulating the microbial composition. Emerging evidence is supportive of applying these findings to improve current therapeutic strategies employed in the treatment of PC.

Background and aims Malus prunifolia (Chinese name: Fu Ping Qiu Zi), a wild relative of cultivated apple ( Malus x domestica Borkh), is extremely resistant to drought compared with domesticated cultivars, such as ‘Golden Delicious’. However, the molecular mechanisms underlying drought resistance of M. prunifolia have not been characterized. This study investigates a new regulatory mechanism to improve apple drought resistance. Methods M. prunifolia and ‘Golden Delicious’ were each grafted on M. hupehensis for gene expression analysis. The methylation level of the DREB2A promoter was determined by bisulfite sequencing and ChIP-qPCR. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify target genes of MpDREB2A in apple. Results The exposure to drought stress stimulated the expression level of DREB2A gene more than 100-fold in M. prunifolia, but only 16-fold in ‘Golden Delicious’. This difference in gene expression could not be explained in terms of difference in leaf relative water content. Correspondingly, the methylation level of M. prunifolia DREB2A ( MpDREB2A ) promoter region was significantly reduced. Additionally, MpDREB2A conferred enhanced drought resistance when ectopically expressed in Arabidopsis . Over 2800 potential downstream target genes of MpDREB2A were identified by ChIP-seq and these downstream genes have diverse potential functions related to stress resistance. Conclusions Methylation regulation in promoter of MpDREB2A may contribute to the drought resistance of M. prunifolia .

Trienoic fatty acids are essential constituents of biomembranes and precursors of jasmonates involved in plant defense responses. Two ω-3 desaturases, At FAD7 and At FAD8, synthetize trienoic fatty acids in the plastid. Promoter:GUS and mutagenesis analysis was used to identify cis -elements controlling AtFAD7 and AtFAD8 basal expression and their response to hormones or wounding. AtFAD7 promoter GUS activity was much higher than that of AtFAD8 in leaves, with specific AtFAD7 expression in the flower stamen and pistil and root meristem and vasculature. This specific tissue and organ expression of AtFAD7 was controlled by different cis -elements. Thus, promoter deletion and mutagenesis analysis indicated that WRKY proteins might be essential for basal expression of AtFAD7 in leaves. Two MYB target sequences present in the AtFAD7 promoter might be responsible for its expression in the flower stamen and stigma of the pistil and in the root meristem, and for the AtFAD7 wound-specific response. Two MYB target sequences detected in the distal region of the AtFAD8 gene promoter seemed to negatively control AtFAD8 expression, particularly in true leaves and flowers, suggesting that MYB transcription factors act as repressors of AtFAD8 gene basal expression, modulating the different relative abundance of both plastid ω-3 desaturases at the transcriptional level. Our data showed that the two ABA repression sequences detected in the AtFAD7 promoter were functional, suggesting an ABA-dependent mechanism involved in the different regulation of both ω-3 plastid desaturases. These results reveal the implication of different signaling pathways for the concerted regulation of trienoic fatty acid content in Arabidopsis.