Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

This file reports the functional annotation of 99,092 DXWR transcripts from the NCBI NR database using the software blast2go. This file is in the tab delimited format and can be opened using the software Excel. (TXT 12649 kb

Humic acid production from the degradation of Yima coal by Cunninghamella elegans combined with Bacillus sp.

Biodegradation is one of the important ways for the clean and efficient utilization of coal. However, the effectiveness of degradation by the combination of fungi and bacteria has not been well understood. In the present study, the combined degradation of the Yima coal was tested. The coal samples were firstly oxidized with nitric acid, followed by cultured in the media of Cunninghamella elegans and Bacillus sp.. The absorbance of A450, pH and metallic element (Cr, As, Mn, Pb, Co, Ni, Cu, Zn, Mo) contents of the degradation solution were determined by UV-visible spectrophotometry, pH meter and inductively coupled plasma mass spectrometry, respectively. The humic acid was analyzed by element analyzer, Fourier transform infrared spectroscopy and gas chromatog-raphy-mass spectrometry. The results showed that the humic acid yields of C. elegans, Bacillus sp. and their mixture were 58.17%, 61.00% and 67.17%, respectively. The pH of the degradation solution of mixed strains was similar to that of the bacteria. The characteristic products of the bacteria degradation were detected in the humic acid samples derived from mixed strains, while the opposite was true for the fungi. It was suggested that the combination of the two strains enhanced the alkaline environment and improved the degradation rate of nitric acid-treated coal. The bacteria played a leading role in the degradation process. Metallic elements (Cr, As, Mn, Pb, Co, Ni, Cu, Zn, Mo) were transferred from coal to the degradation solution during the degradation process, and the contents of Cr, As, Pb, Ni, Cu and Mo were fitted with A450, the coefficient of determination (R2) were greater than 0.6. It indicated that the contents of these six metal elements in the degradation solution could represent the degradation rate. Chemically extracted humic acid and biologically extracted humic acid were rich in the active functional groups such as carboxyl, hydroxyl, carbonyl, long-chain fatty acids (C16, C18) and four pyrrole derivatives. The biologically extracted humic acid also contained fatty acids (C3, C4, C5, C13, C14, C15), of smaller molecular weight, as well as nitrogen-containing compounds such as two pyrrole derivatives and a furan. The contents of C and H elements in the biologically extracted humic acid were higher than that in the chemically extracted humic acid

Polytropic Influence of TRIB3 rs2295490 Genetic Polymorphism on Response to Antihypertensive Agents in Patients With Essential Hypertension

Tribbles homolog 3 (TRIB3) mediating signaling pathways are closely related to blood pressure regulation. Our previous findings suggested a greater benefit on vascular outcomes in patients carrying TRIB3 (251, A > G, rs2295490) G allele with good glucose and blood pressure control. And TRIB3 (rs2295490) AG/GG genotypes were found to reduce primary vascular events in type 2 diabetic patients who received intensive glucose treatment as compared to those receiving standard glucose treatment. However, the effect of TRIB3 genetic variation on antihypertensives was not clear in essential hypertension patients. A total of 368 patients treated with conventional dosage of antihypertensives (6 groups, grouped by atenolol/bisoprolol, celiprolol, doxazosin, azelnidipine/nitrendipine, imidapril, and candesartan/irbesartan) were enrolled in our study. Genetic variations were successfully identified by sanger sequencing. A linear mixed model analysis was performed to evaluate blood pressures among TRIB3 (251, A > G) genotypes and adjusted for baseline age, gender, body mass index, systolic blood pressure (SBP), diastolic blood pressure (DBP), total cholesterol and other biochemical factors appropriately. Our data suggested that TRIB3 (251, A > G) AA genotype carriers showed better antihypertensive effect than the AG/GG genotype carriers [P = 0.014 for DBP and P = 0.042 for mean arterial pressure (MAP)], with a maximal reduction of DBP by 4.2 mmHg and MAP by 3.56 mmHg after azelnidipine or nitrendipine treatment at the 4th week. Similar tendency of DBP-change and MAP-change was found for imidapril (ACEI) treatment, in which marginally significances were achieved (P = 0.073 and 0.075, respectively). Against that, we found that TRIB3 (251, A > G) AG/GG genotype carriers benefited from antihypertensive therapy of ARBs with a larger DBP-change during the period of observation (P = 0.036). Additionally, stratified analysis revealed an obvious difference of the maximal blood pressure change (13 mmHg for the MAP between male and female patients with AA genotype who took ARBs). Although no significant difference in antihypertensive effect between TRIB3 (251, A > G) genotypes in patients treated with α, β-ADRs was observed, we found significant difference in age-, sex-dependent manner related to α, β-ADRs. In conclusion, our data supported that TRIB3 (251, A > G) genetic polymorphism may serve as a useful biomarker in the treatment of hypertension

An individualized stemness‐related signature to predict prognosis and immunotherapy responses for gastric cancer using single‐cell and bulk tissue transcriptomes

Abstract Background Currently, many stemness‐related signatures have been developed for gastric cancer (GC) to predict prognosis and immunotherapy outcomes. However, due to batch effects, these signatures cannot accurately analyze patients one by one, rendering them impractical in real clinical scenarios. Therefore, we aimed to develop an individualized and clinically applicable signature based on GC stemness. Methods Malignant epithelial cells from single‐cell RNA‐Seq data of GC were used to identify stemness‐related signature genes based on the CytoTRACE score. Using two bulk tissue datasets as training data, the enrichment scores of the signature genes were applied to classify samples into two subtypes. Then, using the identified subtypes as criteria, we developed an individualized stemness‐related signature based on the within‐sample relative expression orderings of genes. Results We identified 175 stemness‐related signature genes, which exhibited significantly higher AUCell scores in poorly differentiated GCs compared to differentiated GCs. In training datasets, GC samples were classified into two subtypes with significantly different survival times and genomic characteristics. Utilizing the two subtypes, an individualized signature was constructed containing 47 gene pairs. In four independent testing datasets, GC samples classified as high risk exhibited significantly shorter survival times, higher infiltration of M2 macrophages, and lower immune responses compared to low‐risk samples. Moreover, the potential therapeutic targets and corresponding drugs were identified for the high‐risk group, such as CD248 targeted by ontuxizumab. Conclusions We developed an individualized stemness‐related signature, which can accurately predict the prognosis and efficacy of immunotherapy for each GC sample

Evaluation of CO2-enhanced gas recovery and storage through coupled non-isothermal compositional two-phase flow and geomechanics modelling

CO2 injection into unconventional gas reservoir has been recognized as a promising approach to enhance unconventional gas recovery (CO2-EUGR) and sequester CO2 geologically. The CO2-EUGR is a complex multi-physics coupling process. To accurately assess the effectiveness of different injection strategies, this paper firstly presents a non-isothermal compositional two-phase flow model coupling with geomechanics, in which a multicomponent adsorption kinetics is incorporated to separate free phase and adsorbed phase. A hybrid numerical approach combining EbFVM and GFEM is used for numerical solutions. The performance of different injection strategies for CO2-EUGR is evaluated. The results indicate that CO2 injection is able to improve CH4 recovery significantly, over 90 % of injected CO2 can be adsorbed in reservoirs, The performance of CO2-EUGR is permeability dependent, the displacement effect occurs earlier when reservoir permeability is higher; Increase in temperature of injected gas and mixed CO2/N2 injection can further improve CH4 recovery, especially for low permeability gas reservoirs; Mixed gas injection also enables displacement effect to occur earlier; Cyclic injection can hardly lead to increase in CH4 production, especially when reservoir permeability is higher, while it can cause an increase in amount of adsorbed CO2 during injection period. Based on these findings, a geothermal-assisted CO2-EUGR method is proposed

Road traffic flow prediction based on dynamic spatiotemporal graph attention network

Abstract To improve the prediction accuracy of traffic flow under the influence of nearby time traffic flow disturbance, a dynamic spatiotemporal graph attention network traffic flow prediction model based on the attention mechanism was proposed. Considering the macroscopic periodic characteristics of traffic flow, the spatiotemporal features are extracted by constructing spatiotemporal blocks with an adjacent period, daily period, and weekly period respectively. The spatiotemporal block is mainly composed of a two-layer graph attention network and a gated recurrent unit to capture the hidden features of space and time. In space, based on considering adjacent road segments, the Pearson correlation coefficient is used to capture the hidden correlation characteristics between non-adjacent road segments according to a certain time step. In terms of time, due to the random disturbance of traffic flow at the micro level, the attention mechanism is introduced to use the adjacent time as the query matrix to weight the output characteristics of daily cycle and weekly cycle, and the three are connected in series to output the prediction results through the linear layer. Finally, the experimental results on the public data sets show that the proposed model is superior to the six baseline models

Analysis of landfill leachate promoting efficient application of weathered coal anaerobic fermentation

This research aimed to develop a new method for clean utilization and treatment of landfill leachate and solid waste weathered coal. Landfill leachate and weathered coal were adopted for combined anaerobic fermentation for methane production. The characteristics of microbial community, mechanism of biological methane production, and utilization characteristics of fermentation broth and solid residue for co-fermentation were analyzed through metagenomics, soluble organic matter detection and thermogravimetric (TG) analysis. The obtained results revealed that combined anaerobic fermentation increased methane production by 80.1%. Syntrophomonas, Salipiger, Methanosaeta and Methanothrix were highly correlated. Gene abundances of 2-oxoacid ferredoxin oxidoreductase and enolase were increased in methane conversion pathway mainly by acetic acid. Pyruvate-ferroredoxin oxidoreductase, 2-oxoglutarate synthase and succinate dehydrogenase acetate synthase intensified electron transfer pathways among microorganisms. Fulvic acid, tyrosine and tryptophan contents were high in fermentation broth. Volatile decomposition temperature, ignition point and residual char combustion temperature of residual coal were decreased and combustion was more stable. The obtained results showed that the co-fermentation of landfill leachate and weathered coal improved biological methane gas production, degraded weathered coal and improved combustion performance, which provided a new idea for weathered coal clean utilization

Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China

In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples—the most abundant phyla were Firmicutes (34.58%), Bacteroidetes (33.96%) and Verrucomicrobia (11.70%). At the genus level, a total of 66 genera were obtained—Rikenellaceae_RC9_gut_group (7.24%), Akkermansia (6.32%) and Ruminococcaceae_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (p < 0.05). Bacteroidete were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals