Genome assembly of Ottelia alismoides, a multiple-carbon utilisation aquatic plant.

OBJECTIVES: Ottelia Pers. is in the Hydrocharitaceae family. Species in the genus are aquatic, and China is their centre of origin in Asia. Ottelia alismoides (L.) Pers., which is distributed worldwide, is a distinguishing element in China, while other species of this genus are endemic to China. However, O. alismoides is also considered endangered due to habitat loss and pollution in some Asian countries. Ottelia alismoides is the only submerged macrophyte that contains three carbon dioxide-concentrating mechanisms, i.e. bicarbonate (HCO3-) use, crassulacean acid metabolism and the C4 pathway. In this study, we present its first genome assembly to help illustrate the various carbon metabolism mechanisms and to enable genetic conservation in the future. DATA DESCRIPTION: Using DNA and RNA extracted from one O. alismoides leaf, this work produced ∼ 73.4 Gb HiFi reads, ∼ 126.4 Gb whole genome sequencing short reads and ∼ 21.9 Gb RNA-seq reads. The de novo genome assembly was 6,455,939,835 bp in length, with 11,923 scaffolds/contigs and an N50 of 790,733 bp. Genome assembly completeness assessment with Benchmarking Universal Single-Copy Orthologs revealed a score of 94.4%. The repetitive sequence in the assembly was 4,875,817,144 bp (75.5%). A total of 116,176 genes were predicted. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

Identification of STAT3 as a biomarker for cellular senescence in liver fibrosis: A bioinformatics and experimental validation study.

BACKGROUND: Cellular senescence is associated with a dysregulated inflammatory response, which is an important driver of the development of liver fibrosis (LF). This study aimed to investigate the effect of cellular senescence on LF and identify potential key biomarkers through bioinformatics analysis combined with validation experiments in vivo and in vitro. METHODS: The Gene Expression Omnibus (GEO) database and GeneCards database were used to download the LF dataset and the aging-related gene set, respectively. Functional enrichment analysis of differential genes was then performed using GO and KEGG. Hub genes were further screened using Cytoscape's cytoHubba. Diagnostic values for hub genes were evaluated with a receiver operating characteristic (ROC) curve. Next, CIBERSORTx was used to estimate immune cell types and ratios. Finally, in vivo and in vitro experiments validated the results of the bioinformatics analysis. Moreover, molecular docking was used to simulate drug-gene interactions. RESULTS: A total of 44 aging-related differentially expressed genes (AgDEGs) were identified, and enrichment analysis showed that these genes were mainly enriched in inflammatory and immune responses. PPI network analysis identified 6 hub AgDEGs (STAT3, TNF, MMP9, CD44, TGFB1, and TIMP1), and ROC analysis showed that they all have good diagnostic value. Immune infiltration suggested that hub AgDEGs were significantly associated with M1 macrophages or other immune cells. Notably, STAT3 was positively correlated with α-SMA, COL1A1, IL-6 and IL-1ß, and was mainly expressed in hepatocytes (HCs). Validation experiments showed that STAT3 expression was upregulated and cellular senescence was increased in LF mice. A co-culture system of HCs and hepatic stellate cells (HSCs) further revealed that inhibiting STAT3 reduced HCs senescence and suppressed HSCs activation. In addition, molecular docking revealed that STAT3 was a potential drug therapy target. CONCLUSIONS: STAT3 may be involved in HCs senescence and promote HSCs activation, which in turn leads to the development of LF. Our findings suggest that STAT3 could be a potential biomarker for LF.

Influenza A virus inhibits influenza virus replication by inducing IL-37.

BACKGROUNDS: The influenza virus is one of the major pathogens that seriously affect human health. It can cause a strong immune response and trigger a series of complications. Interleukin 37 (IL-37) is a newly discovered cytokine that plays an important regulatory role in infection and immunity. To date, there have been few studies on the correlation between influenza virus infection and IL-37. METHODS: Serum levels of IL-37 in 115 patients with influenza A virus (IAV) infection and 102 healthy subjects were measured by an enzyme-linked immunosorbent assay (ELISA). Real-time quantitative PCR (RT-qPCR) was used to detect differences in IL-37 expression in peripheral blood mononuclear cells (PBMCs) between IAV patients and healthy subjects. IL-37 expression was measured in A549 cells and PBMCs infected with IAV H3N2 using ELISA and RT-qPCR. After the H3N2-infected A549 cells were treated with human IL-37, the concentration of viral RNA was determined using RT-qPCR, and the titer of influenza virus was determined by a hemagglutination test. RESULTS: The IL-37 levels in the sera and PBMCs of patients infected with IAV were higher than those of healthy subjects. The expression of IL-37 mRNA and protein in IAV-infected A549 cells and PBMCs was upregulated, and IL-37 protein was able to inhibit the replication of IAV RNA. CONCLUSION: IAV-induced IL-37 expression inhibits IAV replication.

Rapid genotyping of APOA5 -1131T>C polymorphism using high resolution melting analysis with unlabeled probes.

The APOA5 -1131 T/C polymorphism (rs662799) exhibits a very strong association with elevated TG levels in different racial groups. High resolution melting (HRM) analysis with the use of unlabeled probes has shown to be a convenient and reliable tool to genotyping, but not yet been used for detecting rs662799 polymorphism. We applied the unlabeled probe HRM analysis and direct DNA sequencing to assay the -1131T>C SNP in 130 cases DNA samples blindly. This HRM analysis can be completed in <3 min for each sample. The two melting peaks were displayed at 66.1±0.4°C for CC homozygote and 68.7±0.2°C for TT homozygote; TC heterozygote showed the both melting peaks. The genotyping results by HRM method were completely concordant with direct DNA sequencing. The distribution of CC, TC, and TT genotypes for the -1131T>C SNP was 9.2, 49.2, and 41.5%, respectively. This assay was sensitive enough to detect C allele down to 20% and 10% for T allele. The limit of detection for C and T allele was 6.2 and 2.5 ng/µL DNA, respectively. The developed unlabeled probe HRM method provides an alternative mean to detect ApoA5 -1131T>C SNP rapidly and accurately.

Chemzymes: a new class of structurally rigid tricyclic amphibian organocatalyst inspired by natural product.

A new class of structurally rigid tricyclic amphibian chiral catalyst was rationally designed based on the hexahydropyrrolo[2,3-b]indole skeleton as a new type of chemzyme. This new type of chemzyme possesses a structurally rigid tricyclic skeleton and a chiral pocket which provides a well-organized chiral environment for asymmetric induction, as well as a hydrophobic pocket to enable organocatalytic reactions to proceed smoothly both in organic solvents and in water.