Identification of Key Inflammation-related Genes as Potential Diagnostic Biomarkers of Sepsis.

Context: Sepsis is one of the leading causes of mortality for patients with severe infections who had been admitted to intensive care units (ICUs). Early diagnosis, accurate treatment, and management of sepsis remain extremely difficult in clinical settings, due to a lack of early biomarkers and diverse clinical manifestations. Objective: The study intended to identify the key genes and pathways associated with inflammation in sepsis-using microarray technology combined with bioinformatics and key inflammation-related genes (IRGs)-to perform an enrichment analysis and evaluate the value of those genes for the diagnosis and evaluation of prognosis for patients with sepsis. Design: The research team performed a genetic analysis. Setting: The study took place at the Center for Emergency and Critical Medicine at Jinshan Hospital of Fudan University in Jinshan District, Shanghai, China. Groups: The research team created two groups, the sepsis group, individuals with sepsis, and the control group, individuals without sepsis, using data for those groups from five microarray datasets obtained from the Gene Expression Omnibus (GEO) database. Outcome Measures: The research team: (1) downloaded the GSE57065, GSE28750, GSE9692, GSE13904, and GSE54514 datasets from the Gene Expression Omnibus (GEO) database for analysis; (2) analyzed the GSE57065, GSE28750, and GSE9692 datasets to detect the differentially expressed genes (DEGs) in the sepsis and control groups; (3) used Venn diagrams to obtain the intersection of DEGs and inflammation-related genes (IRGs); (4) mapped the protein-protein interaction (PPI) network using the Search Tool for Retrieval of Interacting Genes (STRING) database; (5) detected the hub genes using Cytoscape and cytoHubba; (6) performed an enrichment analysis of hub IRGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG); (7) validated the expression of hub IRGs in sepsis using the GSE13904 dataset; and (8) performed a survival analysis in sepsis using the GSE54514 dataset to explore the prognostic value of the hub IRGs. Results: The research team: (1) identified 104 upregulated DEGs and 4 downregulated DEGs; (2) after defining the intersection of DEGs and IRGs, detected nine differentially expressed IRGs (DEIRGs); and (3) identified five IRGs- haptoglobin (HP), high affinity immunoglobulin gamma Fc receptor I (FCGR1A), cluster of differentiation 163 (CD163), complement C3a receptor 1 human (C3AR1), C-type lectin domain containing 5A (CLEC5A)-that overlapped DEIRGs. The GO and KEGG pathway analyses showed that the hub IRGs became enriched during acute-phase response, acute inflammatory response, specific granule, specific granule membrane, endocytic vesicle membrane, tertiary granule, immunoglobulin G (IgG) binding, complement receptor activity, Ig binding, scavenger receptor activity, and scaffold protein binding. The DEGs also played a significant role in Staphylococcus aureus (S. aureus) infection. The ROC curves showed that HP (AUC: 0.956, 95% CI: 0.924-0.988); FCGR1A (AUC: 0.895,95% CI: 0.827-0.963); CD163 (AUC: 0.838, 95% CI: 0.774-0.901); C3AR1 (AUC: 0.953, 95% CI: 0.913-0.993); and CLEC5A (AUC: 0.951, 95% CI: 0 920-0 981) had meaningful diagnostic value for sepsis. Survival analysis showed that the sepsis and control groups had significant differences in HP (P = .043) and CLEC5A (P < .001). Conclusions: HP, FCGR1A, CD163, C3AR1, and CLEC5A have value for clinical application. Clinicians can use them as diagnostic biomarkers, and they provide research direction for treatment targets for sepsis.

High phosphorus fertilization changes the speciation and distribution of manganese in wheat grains grown in a calcareous soil.

The physiological disorders in humans resulting from the excess dietary intake of manganese (Mn) via whole-grain food has attracted considerable attention. However, the speciation and bioavailability of Mn in wheat grains and their response to different phosphorus (P) fertilization rates are still unclear. In the current study, using a long-term field trial with P application rates of 0, 21.8, 43.6, 65.5 and 87.3 kg/ha, we examined changes in the concentration, distribution, and speciation of Mn of wheat grains using synchrotron-based X-ray fluorescence microscopy and X-ray absorption spectroscopy. The total Mn concentration in grains was found to be increased by phosphorus fertilization, especially in embryo in the form of Mn(II), but this phosphorus fertilization also decreased Mn concentrations in the nucellar projection. In this study, the speciation of Mn in different wheat grain tissues was examined, and results indicate that in calcareous soils, high rates of P fertilizers can increase Mn concentrations in wheat grain, including Mn which is likely to be of high bioavailability, and thus may increase the risk for human to expose to high Mn intake via whole-grain food.

Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants.

Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a "barcoding" bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.