IL-33 Enhances the Lipopolysaccharide-Induced Secretion of Inflammatory Cytokines and Ameliorates Lipopolysaccharide Desensitization in Macrophages

Background: Lipopolysaccharide (LPS) desensitization, which is characterized by hyporesponsiveness and a form of immunosuppression, is important in the negative regulation of responses to LPS and inflammatory disease such as sepsis. However, effect of IL-33 in the desensitization to LPS remains unclear. Methods: We used RNA-sequencing technology to analyze changes in mRNA in bone-marrow-derived macrophages (BMDMs) stimulated with LPS. Changes in expression and secretion of inflammatory cytokines were detected by qPCR and ELISA, respectively. Mechanisms were further studied through p65 phosphorylation detection. Results: IL-33 expression was significantly increased in LPS-treated macrophages, indicating its involvement in LPS-induced inflammation. Exogenous IL-33 increased the inflammatory response and ameliorated LPS desensitization by increasing the secretion of proinflammatory cytokines. It also activated p65 phosphorylation in resistant cells. Conclusion: IL-33 can enhance the inflammatory response induced by LPS and ameliorate LPS desensitization possibly by activating the NF-κB pathway in mouse macrophages.

Effect Mechanism of Land Consolidation on Soil Bacterial Community: A Case Study in Eastern China

Farmland consolidation is an effective tool to improve farmland infrastructures, soil quality, and sustain a healthy farmland ecosystem and rural population, generating contributions to food security and regional sustainable development. Previous studies showed that farmland consolidation regulates soil physical and chemical properties. Soil microorganisms also play an important role in soil health and crop performance; however, few studies reported how farmland consolidation influence soil microecology. Here, we used DNA sequencing technology to compare bacterial community structure in farmlands with and without consolidation. DNA sequencing technology is the most advanced technology used to obtain biological information in the world, and it has been widely used in the research of soil micro-ecological environment. In September 2018, we collected soil samples in Jiashan County, Zhejiang Province, China, and used DNA sequence technology to compare the bacterial community structure in farmlands with and without consolidation. Our results found that (1) farmland consolidation had significant impacts on soil microbial characteristics, which were mainly manifested as changes in microbial biomass, microbial diversity and community structure. Farmland consolidation can increase the relative abundance of the three dominant bacteria phyla and the three fungal dominant phyla, but it also negatively affects the relative abundance of the six dominant bacteria phyla and the three fungal dominant phyla. (2) Farmland consolidation had an indirect impact on soil bacterial community structure by adjusting the soil physical and chemical properties. (3) The impact of heavy metals on bacterial community structure varied significantly under different levels of heavy metal pollution in farmland consolidation areas. There were 6, 3, 3, and 5 bacterial genera that had significant correlations with heavy metal content in cultivated land with low pollution, light pollution, medium pollution, and heavy pollution, respectively. The number of heavy metal-tolerant bacteria in the soil generally increased first and then decreased under heavy metal polluted conditions. Our study untangled the relationship between varied farmland consolidation strategies and bacteria through soil physcicochemical properties and metal pollution conditions. Our results can guide farmland consolidation strategies and sustain soil health and ecological balance in agriculture.

Collaboration between clinical and academic laboratories for sequencing SARS-CoV-2 genomes

Genomic sequencing of SARS-CoV-2 continues to provide valuable insight into the ever-changing variant makeup of the COVID-19 pandemic. More than three million SARS-COV-2 genomes have been deposited in GISAID, but contributions from the United States, particularly through 2020, lagged behind the global effort. The primary goal of clinical microbiology laboratories is seldom rooted in epidemiologic or public health testing and many labs do not contain in-house sequencing technology. However, we recognized the need for clinical microbiologists to lend expertise, share specimen resources, and partner with academic laboratories and sequencing cores to assist in SARS-COV-2 epidemiologic sequencing efforts. Here we describe two clinical and academic laboratory collaborations for SARS-COV-2 genomic sequencing. We highlight roles of the clinical microbiologists and the academic labs, outline best practices, describe two divergent strategies in accomplishing a similar goal, and discuss the challenges with implementing and maintaining such programs.

Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components

“Chinese paocai” is typically made by fermenting red radish or cabbage with aged brine (6–8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography–mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.

Review on the Development and Applications of Medicinal Plant Genomes

With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.

Current and Future Methodology for Quantitation and Site-specific Mapping the Location of DNA Adducts

Formation of DNA adducts is a key event for a genotoxic mode of action and its formation is often use as surrogate for mutation and cancer. Interest in DNA adducts are twofold, first, to demonstrate exposure, and second, to link DNA adduct location to subsequent mutations or altered gene regulation. High chemically specific mass spectrometry methods have been established for DNA adduct quantitation and elegant bio-analytic methods utilizing enzymes, various chemistries, and molecular biology methods to visualize the location of DNA adducts. Traditionally, these highly specific methods cannot be combined, and the results are incomparable. Initially developed for single-molecule DNA sequencing, nanopore-type technologies are expected to enable simultaneous quantitation and location of DNA adducts across the genome. We will briefly summarize the current methodologies for state-of-the-art quantitation of DNA adduct levels and mapping of DNA adducts and describe novel single-molecule DNA sequencing technology that is expected to achieve both measures simultaneously. Emerging technologies are expected to soon provide a comprehensive picture of the exposome and identify gene regions susceptible to DNA adduct formation.