The novel fish miRNA, Soc-miR-118, functions as a negative regulator in NF-κB-mediated inflammation by targeting IL-6 in teleost fish.

Inflammation is initiated as a protective response of the organism to remove invading bacterial and initiate the healing process. Prolonged inflammation and excessive production of inflammatory cytokines lead to inflammatory disorders or autoimmune diseases. Thus, different layers of negative regulators are needed to achieve balances between protective immunity and inflammatory pathology. Accumulating evidences show that miRNAs act as significant and multifunctional regulators involved in regulating networks of host-pathogen interactions. However, the functions and mechanisms of miRNAs in directly targeting and regulating inflammatory cytokines remains largely unknown in lower vertebrates. In this study, we report a novel miRNA, Soc-miR-118, identified from Sciaenops ocellatus, which plays a negative role in antibacterial immunity by regulating Interleukin-6 (IL-6). Specifically, we found that Soc-miR-118 directly targets IL-6 and suppresses the production of inflammatory cytokines through the NF-κB signaling pathway, thereby avoiding excessive inflammatory response. Particularly, the mechanism by which Soc-miR-118 regulates IL-6 expression also exist in other fish, suggesting that the miRNA in fish has evolutionarily conserved regulatory systems. The collective results that Soc-miR-118 acts as a negative regulator involved in host antibacterial immunity through directly regulating inflammatory cytokines, will greatly enrich the intricate networks of host-pathogen interaction in lower vertebrates.

Comparative transcriptome analysis reveals potential regulatory mechanisms of genes and immune pathways following Vibrio harveyi infection in red drum (Sciaenops ocellatus).

Red drum (Sciaenops ocellatus), as an important economical marine fish, has been affected by various bacterial diseases in recent years. Vibrio harveyi cause fatal vibriosis in S. ocellatus, leading to massive mortality and causing significant setbacks in aquaculture. However, the regulatory mechanisms of S. ocellatus response to V. harveyi infection are poorly understood. In this regard, we performed transcriptomic analysis with head kidney tissues of S. ocellatus after V. harveyi infection from 12 h to 48 h to reveal genes, gene expression profiles, and pathways involved in immune and inflammation responses. Specifically, a total of 9,599, 5,728, and 7144 differentially expressed genes (DEGs) were identified after V. harveyi infection at 12 h, 24 h, and 48 h, respectively, and 1,848 shared DEGs have been identified from the above three comparison groups. Subsequent pathway analysis revealed that the shared DEGs following V. harveyi were involved in complement and coagulation cascades (C1R, C1QC, C3, C4, C5, C7, C8A, C8B, C8G, C9, CFB, CFH, and CFI), MAPK signaling pathway, chemokine signaling pathway (CCL19, CXCL8, CXCL12, CXCL14, CCR4, CCR7, and CXCR2), PPAR signaling pathway (PPAR-α, PPAR-γ and PPAR-ß), and TNF signaling pathway. Finally, the expression patterns of DEGs in head kidney tissues and S. ocellatus macrophages were validated by qRT-PCR, suggesting the reliability of RNA sequencing for gene expression analysis. This dynamic transcriptome analyses provided insights into gene expression regulation and immune related pathways involved in S. ocellatus after V. harveyi infection, and provides useful information for further study on the immune defense mechanisms in S. ocellatus as well as other teleost species.

Long noncoding RNA LTCONS4500 promotes antibacterial immune responses via targeting miR-3570-5p in teleost fish Miichthys miiuy.

There is accumulating evidence demonstrated that long noncoding RNAs (lncRNA) act as gene regulators in various biological processes, including innate immunity, in which lncRNAs could play their regulatory roles by interacting with miRNAs. Compared with mammals, there is little attention paid to the mechanism of the lncRNA-miRNA regulatory network in teleost fish. Herein, we found a long noncoding RNAs LTCONS4500 that could function as a positive regulator of the immune response in miiuy croaker (Miichthys miiuy). Specifically, we found that the expression of LTCONS4500 could be upregulated by gram-negative bacteria, such as Vibrio anguillarum and Vibrio harveyi. Upregulated LTCONS4500 could promote the expression of inflammatory cytokines. Further study showed that LTCONS4500 could act as a competing endogenous RNA (ceRNA) to interact with miR-3570-5p to facilitate MyD88 expression and thus enhance antibacterial immune responses. Our data suggests the function and mechanism of lncRNAs in antibacterial immune responses of teleost fish, which will enrich the gene regulatory network of vertebrates.

Environmental and economic benefits of substituting chemical potassium fertilizer with crop straw residues in China.

Chemical potassium (K) fertilizer plays a crucial role in improving crop productivity, yet its production and application also result in environmental issues including greenhouse gas emission and atmospheric pollution emissions. In addition, the abandon or open burning of crop straw not only causes the wasting of resource, but also creates environmental problems. On-present studies recognize the importance of the substitution of straw resource utilization for chemical K fertilizer, yet whether such action can effectively mitigate the emissions of greenhouse gas and pollutants remains unclear. In this study, we examine the effects of substituting straw for chemical K fertilizer on the emissions of greenhouse gas and pollutants and the associated direct and damage cost implications in China at the provincial level. Results showed that the useable straw contributed 2750 Gg of K from 2000 to 2009 and 3567 Gg from 2010 to 2017, equaling 121% and 57.3% of chemical K fertilizer, respectively. Chemical K fertilizer substitution with straw can also reduce annual emissions of greenhouse gases, ammonia, nitrogen oxide, and fine particulate matter by 664 Gg, 18.5 Gg, 10.7 Gg, and 1.48 Gg, respectively. The average abatement cost reached 4790 million USD during 2000-2009 and 3898 million USD during 2010-2017, respectively. And the mitigation potential of the emissions of greenhouse gas and pollutants and average abatement cost showed a large spatial heterogeneity at the provincial level. Overall, replacing chemical K fertilizer with straw is an efficient strategy to reduce environmental risk and utilize agricultural waste.

A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria.

Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N2O) and perform the first step of nitrification, but their contribution to N2O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the "indicator microbe" as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N2O emissions and increased 71.4% of soil NH 4 + concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N2O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N2O emissions with NI addition was significantly correlated with AOB changes (R 2 = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in NH 4 + concentration and AOB amoA gene abundance after NI application (R 2 = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.

Pseudolaric acid B ameliorates synovial inflammation and vessel formation by stabilizing PPARγ to inhibit NF-κB signalling pathway.

Synovial macrophage polarization and inflammation are essential for osteoarthritis (OA) development, yet the molecular mechanisms and regulation responsible for the pathogenesis are still poorly understood. Here, we report that pseudolaric acid B (PAB) attenuated articular cartilage degeneration and synovitis during OA. PAB, a diterpene acid, specifically inhibited NF-κB signalling and reduced the production of pro-inflammatory cytokines, which further decreased M1 polarization and vessel formation. We further provide in vivo and in vitro evidences that PAB suppressed NF-κB signalling by stabilizing PPARγ. Using PPARγ antagonist could abolish anti-inflammatory effect of PAB and rescue the activation of NF-κB signalling during OA. Our findings identify a previously unrecognized role of PAB in the regulation of OA and provide mechanisms by which PAB regulates NF-κB signalling through PPARγ, which further suggest targeting synovial inflammation or inhibiting vessel formation at early stage could be an effective preventive strategy for OA.

Lifeceramics-treated water reduces serum uric acid levels and improves hemorheological activity in hyperuricemic rats.

Lifeceramics (LC) is made of zeolite and oyster shell and is hypothesized to act as an anti-oxidative agent. In the present study, the effects of LC-treated water (LC water) on the concentration of serum uric acid (SUA) and the hemorheological parameters in male rats with hyperuricemia (HUA) was assessed. To prepare LC water, distilled water was mixed with LC particles. HUA was induced in rats by daily potassium oxonate (PO) injection (250 mg/kg). The PO-injected rats were separated into three different groups and were administered distilled water (PO rats), allopurinol [a xanthine oxidase (XOD) inhibitor] solution [PO + allopurinol (AP) rats] or LC water (PO+LC rats) by gavage. Control rats were intraperitoneally injected with sodium carboxymethyl cellulose solution and administered untreated distilled water by gavage. After injection and gavage for 5 weeks, the SUA concentration, hemorheology index and antioxidant index were measured. The SUA concentration and blood deformation index of the PO rats were significantly higher and lower, respectively, compared with the control rats. However, in the PO+LC rats, the SUA concentration and blood deformation index decreased and increased, respectively, to a level similar to that of the control as well as that in the PO+AP rats. Furthermore, the PO-induced increase in XOD activity was suppressed by combined treatment with LC water, resulting in a decrease in malondialdehyde concentration. These results suggest that LC water can reduce the SUA concentration, increase serum antioxidant activity and improve hemorheological activity in hyperuricemic rats.

A novel regeneration method for deactivated commercial NH3-SCR catalysts with promoted low-temperature activities.

A novel route is developed for regeneration of deactivated commercial NH3-SCR catalysts, which includes an initial in situ construction of anatase TiO2 porous film, followed by loading of MnOx, CeOx, and Mn-Ce mixed oxides as active components. The regenerated catalysts present largely improved low-temperature denitrification performance due to the synergetic effect of MnOx and CeOx. The denitrification efficiency could reach a high value of 97% at 200 °C and 100% at 250 °C when the Ce-Mn mixed oxides are loaded at the optimized molar quantity ratio of 10:9 (Ce:Mn). Properties and reaction mechanisms of the regenerated catalysts are investigated with characterizations of X-ray photoelectron spectroscopy (XPS), NH3 temperature-programmed desorption (NH3-TPD), H2 temperature-programmed reduction (H2-TPR), and in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). Our results demonstrate that the adsorption and oxidation of NO plays a crucial role for these three catalysts even though a difference exists on the reaction pathways. Graphical abstract.

Genome-Wide Analysis of the Glucose-6-Phosphate Dehydrogenase Family in Soybean and Functional Identification of GmG6PDH2 Involvement in Salt Stress.

Glucose-6-phosphate dehydrogenase (G6PDH) is known as a critical enzyme responsible for nicotinamide adenine dinucleotide phosphate (NADPH) generation in the pentose phosphate pathway (PPP), and has an essential function in modulating redox homeostasis and stress responsiveness. In the present work, we characterized the nine members of the G6PDH gene family in soybean. Phylogenic analysis and transit peptide prediction showed that these soybean G6PDHs are divided into plastidic (P) and cytosolic (Cy) isoforms. The subcellular locations of five GmG6PDHs were further verified by confocal microscopy in Arabidopsis mesophyll protoplasts. The respective GmG6PDH genes had distinct expression patterns in various soybean tissues and at different times during seed development. Among them, the Cy-G6PDHs were strongly expressed in roots, developing seeds and nodules, while the transcripts of P-G6PDHs were mainly detected in green tissues. In addition, the activities and transcripts of GmG6PDHs were dramatically stimulated by different stress treatments, including salt, osmotic and alkali. Notably, the expression levels of a cytosolic isoform (GmG6PDH2) were extraordinarily high under salt stress and correlated well with the G6PDH enzyme activities, possibly implying a crucial factor for soybean responses to salinity. Enzymatic assay of recombinant GmG6PDH2 proteins expressed in Escherichia coli showed that the enzyme encoded by GmG6PDH2 had functional NADP+-dependent G6PDH activity. Further analysis indicated overexpression of GmG6PDH2 gene could significantly enhance the resistance of transgenic soybean to salt stress by coordinating with the redox states of ascorbic acid and glutathione pool to suppress reactive oxygen species generation. Together, these results indicate that GmG6PDH2 might be the major isoform for NADPH production in PPP, which is involved in the modulation of cellular AsA-GSH cycle to prevent the oxidative damage induced by high salinity.

Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing.

Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing.

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

Identification of Soybean Genes Related to Soybean Seed Protein Content Based on Quantitative Trait Loci Collinearity Analysis.

Increasing the protein content of soybean seeds through a higher ratio of glycinin is important for soybean breeding and food processing; therefore, the integration of different quantitative trait loci (QTLs) is of great significance. In this study, we investigated the collinearity of seed protein QTLs. We identified 192 collinear protein QTLs that formed six hotspot regions. The two most important regions had seed protein 36-10 and seed protein 36-20 as hub nodes. We used a chromosome segment substitution line (CSSL) population for QTL validation and identified six CSSL materials with collinear QTLs. Five materials with higher protein and glycinin contents in comparison to the recurrent parent were analyzed. A total of 13 candidate genes related to seed protein from the QTL hotspot intervals were detected, 8 of which had high expression in mature soybean seeds. These results offer a new analysis method for molecular-assisted selection (MAS) and improvement of soybean product quality.

Identification of Major QTLs Associated With First Pod Height and Candidate Gene Mining in Soybean.

First pod height (FPH) is a quantitative trait in soybean [Glycine max (L.) Merr.] that affects mechanized harvesting. A compatible combination of the FPH and the mechanized harvester is required to ensure that the soybean is efficiently harvested. In this study, 147 recombinant inbred lines, which were derived from a cross between 'Dongnong594' and 'Charleston' over 8 years, were used to identify the major quantitative trait loci (QTLs) associated with FPH. Using a composite interval mapping method with WinQTLCart (version 2.5), 11 major QTLs were identified. They were distributed on five soybean chromosomes, and 90 pairs of QTLs showed significant epistatic associates with FPH. Of these, 3 were main QTL × main QTL interactions, and 12 were main QTL × non-main QTL interactions. A KEGG gene annotation of the 11 major QTL intervals revealed 8 candidate genes related to plant growth, appearing in the pathways K14486 (auxin response factor 9), K14498 (serine/threonine-protein kinase), and K13946 (transmembrane amino acid transporter family protein), and 7 candidate genes had high expression levels in the soybean stems. These results will aid in building a foundation for the fine mapping of the QTLs related to FPH and marker-assisted selection for breeding in soybean.

Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development.

Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.