Dissecting the association between gut microbiota and liver cancer in European and East Asian populations using Mendelian randomization analysis

BackgroundAmple evidence suggests an important role of the gut microbiome in liver cancer, but the causal relationship between gut microbiome and liver cancer is unclear. This study employed Mendelian randomization (MR) analysis to examine the causal relationship between the gut microbiome and liver cancer in European and East Asian populations.MethodsWe sourced genetic variants linked to gut microbiota from the MiBioGen consortium meta-analysis, and procured liver cancer genome-wide association study (GWAS) summary data from the FinnGen consortium and Biobank Japan. We employed the inverse variance weighted method for primary statistical analysis, fortified by several sensitivity analyses such as MR-PRESSO, MR-Egger regression, weighted median, weighted mode, and maximum likelihood methods for rigorous results. We also evaluated heterogeneity and horizontal pleiotropy.ResultsThe study examined an extensive set of gut microbiota, including 131 genera, 35 families, 20 orders, 16 classes, and 9 phyla. In Europeans, ten gut microbiota types displayed a suggestive association with liver cancer (p < 0.05). Notably, Oscillospira and Mollicutes RF9 exhibited a statistically significant positive association with liver cancer risk, with odds ratios (OR) of 2.59 (95% CI 1.36–4.95) and 2.03 (95% CI 1.21–3.40), respectively, after adjusting for multiple testing. In East Asians, while six microbial types demonstrated suggestive associations with liver cancer, only Oscillibacter displayed a statistically significant positive association (OR = 1.56, 95% CI 1.11–2.19) with an FDR < 0.05. Sensitivity analyses reinforced these findings despite variations in p-values.ConclusionThis study provides evidence for a causal relationship between specific gut microbiota and liver cancer, enhancing the understanding of the role of the gut microbiome in liver cancer and may offer new avenues for preventive and therapeutic strategies

PuCRZ1, an C2H2 transcription factor from Polyporus umbellatus, positively regulates mycelium response to osmotic stress

Polyporus umbellatus is an edible and medicinal mushroom with the capacity to produce sclerotia. However, the mechanism of P. umbellatus sclerotia formation is unclear. CRZ1 is a C2H2 family transcription factor involved in the Ca2+-calcineurin signaling pathway, which has the function of regulating sclerotia formation, maintaining ion homeostasis, and responding to stress. In this study, we identified 28 C2H2 transcription factors in P. umbellatus genome, 13 of which are differentially expressed between mycelium and sclerotia, including PuCRZ1. Combining DNA affinity purification and sequencing (DAP-seq) and quantitative real-time PCR (qRT-PCR), three genes (PuG10, PuG11, PuG12) were identified as putative PuCRZ1 target genes containing a putative binding motif (GTGGCG) within their promoter. Yeast single hybridization (Y1H) and EMSA further confirmed that PuCRZ1 can bind to the promoter region of PuG10, PuG11, and PuG12. PuCRZ1 gene could reduce the sensitivity of NaCl in yeast cells. Furthermore, overexpression of the PuCRZ1 target gene, especially the FVLY domain containing gene PuG11, could improve the mycelia growth rate and mannitol tolerance in P. umbellatus. These results demonstrate that PuCRZ1 in the Ca2+-calcineurin signaling pathway plays an important role in mycelia growth, as well as osmotic stress tolerance

A Multi-Center Study to Evaluate the Performance of Phage Amplified Biologically Assay for Detecting TB in Sputum in the Pulmonary TB Patients

Objective: To evaluate the performance of phage amplified biologically assay (PhaB) for detecting tuberculosis (TB) in sputum in the pulmonary tuberculosis (PTB) patients. Methods: Shanghai Tuberculosis Key Laboratory of Shanghai Pulmonary Hospital participated in the project in collaboration with the laboratories of six hospitals and a total of 1660 eligible participants (1351 PTB patients and 309 non-TB patients) were included in the study. The sputum samples from the participants were detected by smear microscopy, PhaB, and Löwenstein-Jensen (L-J) culture method, respectively. Results: The overall sensitivity of PhaB were higher than that of L-J culture and smear microscopy (p,0.05). The sensitivity of PhaB for detecting smear-negative specimens was obviously higher than that of L-J culture (p,0.05). Compared with L-J culture, the overall sensitivity, specificity, PPV, NPV, ACC and Kappa value of PhaB were 98.4 (95 % Cl: 96.9–99.3), 71.6 (95% Cl: 68.4–74.6), 67.7, 98.7, 81.7 % and 0.643, respectively. The detection median time of PhaB only needed 48 hours, which was significantly less than that (31 days) of L-J culture method. Conclusion: PhaB method is a rapid and sensitive method for detecting TB in sputum in PTB patients; especially for th

Evaluation of a Novel Biphasic Culture Medium for Recovery of Mycobacteria: A Multi-Center Study

on L-J slants. Automated liquid culture systems are expensive. A low-cost culturing medium capable of rapidly indicating the presence of mycobacteria is needed. The aim of this study was to develop and evaluate a novel biphasic culture medium for the recovery of mycobacteria from clinical sputum specimens from suspected pulmonary tuberculosis patients.<0.001).

Impacts of Ground Fissures on Soil Properties in an Underground Mining Area on the Loess Plateau, China

Mining-induced ground fissures are the main type of geological disasters found on the Loess Plateau, China, and cause great impacts on the soil properties around ground fissures. However, little research has been conducted on the quantitative relationship between ground fissures and changes in soil properties. To address this, 40 ground fissures in the Yungang mining area, Datong City, Shanxi Province, China, were investigated, and changes in soil properties (soil organic matter, soil moisture, field capacity, bulk density, soil porosity, and grain compositions) were revealed by the difference in soil properties between the edge and contrast points around ground fissures. Redundancy analyses were used to illustrate the relationships between the value (Si_DV) and percentage (Si_DP) of the difference in soil properties between the edge and contrast points, as well as the ground fissures. The characteristics of ground fissures that had a significant correlation according to Pearson correlation analysis with Si_DP were selected and analyzed via multivariate linear fitting model, random forest model, and Back Propagation (BP) neural network model, respectively. Results show that soil organic matter, soil moisture content, bulk density, field capacity, and the content of clay at the edge points were significantly less than those at the contrast points; conversely, soil porosity at the edge points was significantly greater. The average percentage of the difference between the edge points and contrast points of ground fissures in these six properties was 15.27%, while soil moisture content showed the greatest change (20.65%). The Si_DP was significantly correlated with the width, slope, and vegetation coverage of ground fissures; however, the vegetation coverage was the determining factor. BP neural network model had the greatest performance in revealing the relationships between ground fissures and changes in soil properties. The model for soil organic matter had the highest accuracy (R2 = 0.89), and all others were above 0.5. This research provides insights into the quantitative relationship between ground fissures and their impacts on soil physical properties, which can be used in conjunction with remote sensing images to rapidly assess soil erosion risks caused by mining on a large scale, given that soil physical properties are closely related to topsoil stability

Formation and distribution of large low-permeability lithologic oil regions in Huaqing, Ordos Basin

Through in-depth analysis of sedimentary source, lake basin shape and tectonic events as well as careful study of high quality source rocks, reservoir-forming force and history in the Huaqing area, Ordos Basin, the accumulation mode of large low-permeability lithologic oil regions in the middle of the lake basin was established. The Ordos Basin is a typical inland depressed basin during the depositional period of the Upper Triassic Yanchang Formation. Rich-nutrient lake-basin sediments are developed in the Chang-7 Member during the maximum flooding period. High-quality source rocks of the Chang-7 Member have the characteristics of high abundance of organic matter, strong ability of hydrocarbon generation and expulsion, and wide distribution in Huaqing in the central basin. Delta is developed extensively in the depositional period of Chang-6 Member. Influenced by rich provenance and the bottom shape of slope break belts, thick layers of reservoir sands originated from the delta front and gravity flow are developed in the Chang-6 Member in Huaqing, and the favorable sedimentary facies and diagenetic facies control the extensive low-permeability reservoirs. The Chang-6 low-permeability reservoirs and the Chang-7 high-quality source rocks have a good association and form an accumulation mode characterized by “hydrocarbon-generating pressurization, proximal migration and accumulation, large-area charging, and continuous oil layers”. Key words: Ordos Basin, Huaqing area, source rock, gravity flow, low-permeability reservoir, large lithologic oil regio