Bacterial accumulation in intestinal folds induced by physical and biological factors.

BACKGROUND: The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment. RESULTS: We discovered that E. coli spread was considerably suppressed within the intestinal folds, leading to a strong physical accumulation in the folds. Moreover, a higher concentration of E. coli on the dorsal side than on the ventral side was observed. Our in vitro microfluidic experiments and theoretical analysis revealed that the overall distribution of E. coli in the intestines was established by a combination of physical factor and bacterial taxis. CONCLUSIONS: Our findings provide valuable insight into how the intestinal microenvironment affects bacterial motility and accumulation, enhancing our understanding of the behavioral and ecological dynamics of the intestinal microbiota.

Prognostic value of a novel glycolysis-related gene expression signature for gastrointestinal cancer in the Asian population.

BACKGROUND: Globally, gastrointestinal (GI) cancer is one of the most prevalent malignant tumors. However, studies have not established glycolysis-related gene signatures that can be used to construct accurate prognostic models for GI cancers in the Asian population. Herein, we aimed at establishing a novel glycolysis-related gene expression signature to predict the prognosis of GI cancers. METHODS: First, we evaluated the mRNA expression profiles and the corresponding clinical data of 296 Asian GI cancer patients in The Cancer Genome Atlas (TCGA) database (TCGA-LIHC, TCGA-STAD, TCGA-ESCA, TCGA-PAAD, TCGA-COAD, TCGA-CHOL and TCGA-READ). Differentially expressed mRNAs between GI tumors and normal tissues were investigated. Gene Set Enrichment Analysis (GSEA) was performed to identify glycolysis-related genes. Then, univariate, LASSO regression and multivariate Cox regression analyses were performed to establish a key prognostic glycolysis-related gene expression signature. The Kaplan-Meier and receiver operating characteristic (ROC) curves were used to evaluate the efficiency and accuracy of survival prediction. Finally, a risk score to predict the prognosis of GI cancers was calculated and validated using the TCGA data sets. Furthermore, this risk score was verified in two Gene Expression Omnibus (GEO) data sets (GSE116174 and GSE84433) and in 28 pairs of tissue samples. RESULTS: Prognosis-related genes (NUP85, HAX1, GNPDA1, HDLBP and GPD1) among the differentially expressed glycolysis-related genes were screened and identified. The five-gene expression signature was used to assign patients into high- and low-risk groups (p < 0.05) and it showed a satisfactory prognostic value for overall survival (OS, p = 6.383 × 10-6). The ROC curve analysis revealed that this model has a high sensitivity and specificity (0.757 at 5 years). Besides, stratification analysis showed that the prognostic value of the five-gene signature was independent of other clinical characteristics, and it could markedly discriminate between GI tumor tissues and normal tissues. Finally, the expression levels of the five prognosis-related genes in the clinical tissue samples were consistent with the results from the TCGA data sets. CONCLUSIONS: Based on the five glycolysis-related genes (NUP85, HAX1, GNPDA1, HDLBP and GPD1), and in combination with clinical characteristics, this model can independently predict the OS of GI cancers in Asian patients.

What causes the spatial heterogeneity of bacterial flora in the intestine of zebrafish larvae?

Microbial flora in the intestine has been thoroughly investigated, as it plays an important role in the health of the host. Jemielita et al. (2014) showed experimentally that Aeromonas bacteria in the intestine of zebrafish larvae have a heterogeneous spatial distribution. Although bacterial aggregation is important biologically and clinically, there is no mathematical model describing the phenomenon and its mechanism remains largely unknown. In this study, we developed a computational model to describe the heterogeneous distribution of bacteria in the intestine of zebrafish larvae. The results showed that biological taxis could cause the bacterial aggregation. Intestinal peristalsis had the effect of reducing bacterial aggregation through mixing function. Using a scaling argument, we showed that the taxis velocity of bacteria must be larger than the sum of the diffusive velocity and background bulk flow velocity to induce bacterial aggregation. Our model and findings will be useful to further the scientific understanding of intestinal microbial flora.

Mixing and pumping functions of the intestine of zebrafish larvae.

Due to its transparency, the intestine of zebrafish larvae has been widely used in studies of gastrointestinal diseases and the microbial flora of the gut. However, transport phenomena in the intestine of zebrafish larvae have not been fully clarified. In this study, therefore, transport caused by peristaltic motion in the intestine of zebrafish larvae was investigated by numerical simulation. An anatomically realistic three-dimensional geometric model of the intestine at various times after feeding was constructed based on the experimental data of Field et al. (2009). The flow of digested chyme was analyzed using the governing equations of fluid mechanics, together with peristaltic motion and long-term contraction of the intestinal wall. The results showed that retrograde peristaltic motion was the main contributor to the mixing function. The dispersion caused by peristalsis over 30min was in the order of 10-12m2/s, which is greater than the Brownian diffusion of a sphere of 0.4µm diameter. In contrast, anterograde peristaltic motion contributed mainly to the pumping function. The pressure decrease due to peristalsis was in the order of millipascals, which may reduce the activation and maintenance heat of intestinal muscle. These findings enhance our understanding of the mixing and pumping functions of the intestine of zebrafish larvae.

Associations between the polymorphisms of GSTT1, GSTM1 and methylation of arsenic in the residents exposed to low-level arsenic in drinking water in China.

We carry out a study to analyze the relation between polymorphisms of GSTT1, GSTM1 and the capacity of arsenic methylation in a human population exposed to arsenic in drinking water. 230 randomly chose subjects were divided into four subgroups based on the arsenic levels, and then the associations between the polymorphisms of GSTT1, GSTM1 and methylation of arsenic were investigated. The levels of inorganic arsenic (iAs), monomethylated arsenic (MMA), dimethylated arsenic (DMA) and total arsenic (TAs) in urine were higher in males than that in females. Moreover, the levels of iAs and TAs in urine in the subjects with genotype of GSTM1(+) were significantly higher than those with GSTM1(-); the level of DMA in the subjects with GSTT1(+) and GSTM1(+) were higher than those with GSTT1(-) and GSTM1(-), although it is not statistically significant. Secondary methylation index (SMI) was significantly higher in the subjects with genotype of GSTT1(+) than those with GSTT1(-). The levels of TAs in urine, together with the genotypes of GSTT1/GSTM1 were associated with the levels of MMA and DMA. Our results suggested that the polymorphisms of GSTT1 and GSTM1 were associated with the methylation of arsenic, especially the levels of DMA and SMI.

Endotracheal tube, by the venturi effect, reduces the efficacy of increasing inlet pressure in improving pendelluft.

In mechanically ventilated severe acute respiratory distress syndrome patients, spontaneous inspiratory effort generates more negative pressure in the dorsal lung than in the ventral lung. The airflow caused by this pressure difference is called pendelluft, which is a possible mechanisms of patient self-inflicted lung injury. This study aimed to use computer simulation to understand how the endotracheal tube and insufficient ventilatory support contribute to pendelluft. We established two models. In the invasive model, an endotracheal tube was connected to the tracheobronchial tree with 34 outlets grouped into six locations: the right and left upper, lower, and middle lobes. In the non-invasive model, the upper airway, including the glottis, was connected to the tracheobronchial tree. To recreate the inspiratory effort of acute respiratory distress syndrome patients, the lower lobe pressure was set at -13 cmH2O, while the upper and middle lobe pressure was set at -6.4 cmH2O. The inlet pressure was set from 10 to 30 cmH2O to recreate ventilatory support. Using the finite volume method, the total flow rates through each model and toward each lobe were calculated. The invasive model had half the total flow rate of the non-invasive model (1.92 L/s versus 3.73 L/s under 10 cmH2O, respectively). More pendelluft (gas flow into the model from the outlets) was observed in the invasive model than in the non-invasive model. The inlet pressure increase from 10 to 30 cmH2O decreased pendelluft by 11% and 29% in the invasive and non-invasive models, respectively. In the invasive model, a faster jet flowed from the tip of the endotracheal tube toward the lower lobes, consequently entraining gas from the upper and middle lobes. Increasing ventilatory support intensifies the jet from the endotracheal tube, causing a venturi effect at the bifurcation in the tracheobronchial tree. Clinically acceptable ventilatory support cannot completely prevent pendelluft.

HOTAIR as a diagnostic and prognostic biomarker of gastrointestinal cancers: an updated meta-analysis and bioinformatics analysis based on TCGA data.

Gastrointestinal cancers are the most common type of cancer affecting humans. High expression of HOX transcript antisense intergenic RNA (HOTAIR), a long noncoding RNA (lncRNA), in various types of different tumors may be associated with poor prognosis. In the present study, we performed a meta-analysis of the relationship between HOTAIR expression and gastrointestinal cancers. Five databases were comprehensively searched for all literature until January 2023. Moreover, the target genes of HOTAIR were predicted by coexpression analysis based on The Cancer Genome Atlas (TCGA) gene expression matrix for six gastrointestinal cancer types. Finally, the mechanism through which HOTAIR affects tumors of the digestive system was systematically reviewed. Our results showed that the high HOTAIR expression group had worse outcomes with a pooled hazard ratio (HR) of 1.56 (95% confidence interval [CI] = 1.38-1.75, P<0.001). Furthermore, HOTAIR was identified as an unfavorable prognostic factor for overall survival (OS) in the esophageal carcinoma (ESCA) and gastric cancer (GC), as the HR were 1.94 and 1.58, respectively. The high correlation between the expression of homeobox C (HOXC) family genes and HOTAIR, with correlation coefficients of 0.863 (HOXC11), 0.664 (HOXC10), 0.645 (HOXC8), and 0.581 (HOXC12). The 'cell cycle' pathway and pathways relating to infections, namely 'herpes simplex virus 1 infection' and 'complement and coagulation cascades' were significantly enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Also, we perform a systematic review to summarize the related oncogenic mechanism of HOTAIR. In conclusion, the HOTAIR has been identified as a potential prognostic factor in patients with gastrointestinal cancers.

Janus microdimer swimming in an oscillating magnetic field.

Artificial microswimmers powered by magnetic fields have numerous applications, such as drug delivery, biosensing for minimally invasive medicine and environmental remediation. Recently, a Janus microdimer surface walker that can be propelled by an oscillating magnetic field near a surface was reported by Li et al. (Adv. Funct. Mater. 28, 1706066. (doi:10.1002/adfm.201706066)). To clarify the mechanism for the surface walker, we numerically studied in detail a Janus microdimer swimming near a wall actuated by an oscillating magnetic field. The results showed that a Janus microdimer in an oscillating magnetic field can produce magnetic torque in the y-direction, which eventually propels the Janus microdimer along the x-direction near a wall. Furthermore, we found that the Janus microdimer can also move along a special direction in an oscillating magnetic field with two orientations without a wall. The knowledge obtained in this study is fundamental for understanding the interactions between a Janus microdimer and surfaces in an oscillating magnetic field and is useful for controlling Janus microdimer motion with or without a wall.

Bacterial detachment from a wall with a bump line.

The interactions of bacteria with surfaces have important implications in numerous areas of research, such as bioenergy, biofilm, biofouling, and infection. Recently, several experimental studies have reported that the adhesion of bacteria can be reduced considerably by microscale wall features. To clarify the effect of wall configurations, we numerically investigated the behavior of swimming bacteria near a flat wall with a bump line. The results showed that the effects of bump configuration are significant; a detachment time larger than several seconds can be achieved in certain parameter sets. These results illustrate that the number density of bacteria near the wall may be reduced by appropriately controlling the parameter sets. When background shear flow was imposed, the near-wall bacterium mainly moved towards the vorticity axis. The detachment time of cells increased significantly by adjusting the bump line to have 45^{∘} relative to the flow direction. The knowledge obtained in this study is fundamental for understanding the interactions between bacteria and surfaces according to more complex geometries, and is useful for reducing the adhesion of cells to walls.

Emerging role of long non-coding RNA MALAT1 in predicting clinical outcomes of patients with digestive system malignancies: A meta-analysis.

Digestive system malignancies are the most common cancer types worldwide and exhibit an extremely low overall 5-year survival rate. Therefore, clinically applicable biomarkers for predicting clinical outcome are urgently required. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is abnormally expressed in several cancer types. However, to the best of our knowledge, the association between MALAT1 expression and the prognosis of digestive system malignancies remains unknown. Therefore, the current study performed a meta-analysis to comprehensively summarize the association between MALAT1 expression and digestive system malignancies. A total of 1,157 Asian patients from 12 eligible studies [eight studies that investigated overall survival (OS), two studies that investigated disease-free survival and two studies that investigated both indicators] were analyzed. The present results identified a significant association between MALAT1 abundance and poor OS in patients with digestive system malignancies, with a pooled hazard ratio (HR) of 1.62 [95% confidence interval (CI), 1.35-1.88; P<0.001]. The tumor type, region, sample size and analysis type did not alter the predictive value of MALAT1 as an independent factor for survival. Furthermore, MALAT1 overexpression was an unfavorable prognostic factor for the overall survival of patients with esophageal carcinoma, pancreatic cancer, hepatocellular carcinoma and gastric cancer, with HRs of 1.89 (95% CI, 1.29-2.49), 1.76 (95% CI, 0.89-2.63), 1.46 (95% CI, 0.76-2.17) and 1.41 (95% CI, 1.04-1.78), respectively. In particular, increased MALAT1 expression levels were significantly associated with decreased OS in patients with colorectal cancer (HR, 3.04; 95% CI, 1.77-4.31). In conclusion, lncRNA MALAT1 may be a potential prognostic factor for digestive system malignancies in Asian populations.