工程技术最新文献

Antibiotic resistance is an important problem that threatens medical treatment. Differences in the resistance levels of microorganisms cause great difficulties in understanding the mechanisms of antibiotic resistance. Therefore, the molecular reasons underlying the differences in the level of antibiotic resistance need to be clarified. For this purpose, genomic and transcriptomic analyses were performed on three Escherichia coli strains with varying degrees of adaptive resistance to ampicillin. Whole-genome sequencing of strains with different levels of resistance detected five mutations in strains with 10-fold resistance and two additional mutations in strains with 95-fold resistance. Overall, three of the seven mutations occurred as a single base change, while the other four occurred as insertions or deletions. While it was thought that 10-fold resistance was achieved by the effect of mutations in the ftsI, marAR, and rpoC genes, it was found that 95-fold resistance was achieved by the synergistic effect of five mutations and the ampC mutation. In addition, when the general transcriptomic profiles were examined, it was found that similar transcriptomic responses were elicited in strains with different levels of resistance. This study will improve our view of resistance mechanisms in bacteria with different levels of resistance and provide the basis for our understanding of the molecular mechanism of antibiotic resistance in ampicillin-resistant E. coli strains. KEY POINTS: •The mutation of the ampC promoter may act synergistically with other mutations and lead to higher resistance. •Similar transcriptomic responses to ampicillin are induced in strains with different levels of resistance. •Low antibiotic concentrations are the steps that allow rapid achievement of high antibiotic resistance.

Ethylene glycol is an industrially important diol in many manufacturing processes and a building block of polymers, such as poly(ethylene terephthalate). In this study, we found that a mycolic acid-containing bacterium Rhodococcus jostii RHA1 can grow with ethylene glycol as a sole source of carbon and energy. Deletion of a putative glycolate dehydrogenase gene (RHA1_ro03227) abolished growth with ethylene glycol, indicating that ethylene glycol is assimilated via glycolate in R. jostii RHA1. Transcriptome sequencing and gene deletion analyses revealed that a gene homologous to mycofactocin (MFT)-associated dehydrogenase (RHA1_ro06057), hereafter referred to as EgaA, is essential for ethylene glycol assimilation. Furthermore, egaA deletion also negatively affected the utilization of ethanol, 1-propanol, propylene glycol, and 1-butanol, suggesting that EgaA is involved in the utilization of various alcohols in R. jostii RHA1. Deletion of MFT biosynthetic genes abolished growth with ethylene glycol, indicating that MFT is the physiological electron acceptor of EgaA. Further genetic studies revealed that a putative aldehyde dehydrogenase (RHA1_ro06081) is a major aldehyde dehydrogenase in ethylene glycol metabolism by R. jostii RHA1. KEY POINTS: • Rhodococcus jostii RHA1 can assimilate ethylene glycol via glycolate • A mycofactocin-associated dehydrogenase is involved in the oxidation of ethylene glycol • An aldehyde dehydrogenase gene is important for the ethylene glycol assimilation.

Due to the limited resources and environmental problems associated with fossil fuels, there is a growing interest in utilizing renewable resources for the production of biofuels through microbial fermentation. Isobutanol is a promising biofuel that could potentially replace gasoline. However, its production efficiency is currently limited by the use of naturally isolated microorganisms. These naturally isolated microorganisms often encounter problems such as a limited range of substrates, low tolerance to solvents or inhibitors, feedback inhibition, and an imbalanced redox state. This makes it difficult to improve their production efficiency through traditional process optimization methods. Fortunately, recent advancements in genetic engineering technologies have made it possible to enhance microbial hosts for the increased production of isobutanol from renewable resources. This review provides a summary of the strategies and synthetic biology approaches that have been employed in the past few years to improve naturally isolated or non-natural microbial hosts for the enhanced production of isobutanol by utilizing different renewable resources. Furthermore, it also discusses the challenges that are faced by engineered microbial hosts and presents future perspectives to enhancing isobutanol production. KEY POINTS: • Promising potential of isobutanol to replace gasoline • Engineering of native and non-native microbial host for isobutanol production • Challenges and opportunities for enhanced isobutanol production.

There is a huge quantity of microorganisms in the gut of fish, which exert pivotal roles in maintaining host intestinal and general health. The fish immunity can sense and shape the intestinal microbiota and maintain the intestinal homeostasis. In the meantime, the intestinal commensal microbes regulate the fish immunity, control the extravagant proliferation of pathogenic microorganisms, and ensure the intestinal health of the host. This review summarizes developments and progress on the known interactions between host immunity and intestinal microorganisms in fish, focusing on the recent advances in zebrafish (Danio rerio) showing the host immunity senses and shapes intestinal microbiota, and intestinal microorganisms tune host immunity. This review will offer theoretical references for the development, application, and commercialization of intestinal functional microorganisms in fish. KEY POINTS: • The interactions between the intestinal microorganisms and host immunity in zebrafish • Fish immunity senses and shapes the microbiota • Intestinal microbes tune host immunity in fish.

The discharge of industrial water requires the removal of its pollutants, where biological wastewater treatment plants (WWTPs) are the most used systems. Biological WWTPs make use of activated sludge (AS), where bacteria are responsible for the removal of pollutants. However, our knowledge of the microbial communities of industrial plants is limited. Understanding the microbial population is essential to provide solutions to industrial problems such as bulking. The aim of this study was to identify at a high taxonomic resolution the bacterial population of 29 industrial WWTPs using 16S rRNA amplicon sequencing. Our results revealed that the main functional groups were dominated by Thauera and Zoogloea within denitrifiers, Dechloromonas in phosphate-accumulating organisms, and Defluviicoccus in glycogen-accumulating organisms. The activated sludge characterization indicated that 59% of the industrial plants suffered from bulking sludge, with DSVI values of up to 448 mL g^-1. From the bulking cases, 72% corresponded to filamentous bulking with Thiothrix as the most abundant filament; meanwhile, the other 28% corresponded to viscous bulking sludge in which Zoogloea was the most abundant genus. Furthermore, the bacterial population did not share a core of taxa across all industrial plants. However, 20 genera were present in at least 50% of the plants comprising the general core, including Thauera, Ca. Competibacter, and several undescribed microorganisms. Moreover, statistical analysis revealed that wastewater salinity strongly affected the microbial richness of the industrial plants. The bacterial population across industrial plants differed considerably from each other, resulting in unique microbial communities that are attributed to the specificity of their wastewaters. KEY POINTS: • The general core taxa of industrial plants were mostly made up of undescribed bacterial genera. • Filamentous bacteria constituted on average 4.1% read abundance of the industrial WWTPs. • Viscous bulking remains a significant type of bulking within industrial WWTPs.

Dunaliella salina is a high-quality industrial effector for carotenoid production. The mechanism by which red light regulates carotenoid synthesis is still unclear. In this study, a transcription factor of DsGATA1 with a distinct structure was discovered in D. salina. The recognition motif of DsGATA1 was comparable to that of plant and fungal GATA, despite its evolutionary proximity to animal-derived GATA. The expression of DsGATA1 in D. salina was still noticeably decreased when exposed to red light. Analysis of physiological and biochemical transcriptomic data from overexpressed, interfering, and wild-type strains of DsGATA1 revealed that DsGATA1 acts as a global regulator of D. salina carotenoid synthesis. The upregulated genes in the CBP pathway by DsGATA1 were involved in its regulation of the synthesis of carotenoids. DsGATA1 also enhanced carotenoid accumulation under red light by affecting N metabolism. DsGATA1 was found to directly bind to the promoter of nitrate reductase to activate its expression, promoting D. salina nitrate uptake and accelerating biomass accumulation. DsGATA1 affected the expression of the genes encoding GOGAT, GDH, and ammonia transporter proteins. Moreover, our study revealed that the regulation of N metabolism by DsGATA1 led to the production of NO molecules that inhibited carotenoid synthesis. However, DsGATA1 significantly enhanced carotenoid synthesis by NO scavenger removal of NO. The D. salina carotenoid accumulation under red light was elevated by 46% in the presence of overexpression of DsGATA1 and NO scavenger. Nevertheless, our results indicated that DsGATA1 could be an important target for engineering carotenoid production. KEY POINTS: • DsGATA1 with a distinct structure and recognition motif was found in D. salina • DsGATA1 enhanced carotenoid production and biomass in D. salina under red light • DsGATA1 is involved in the regulation of N metabolism and carotenoid synthesis.

As a processed product of traditional Chinese medicine Curcumae Radix, Curcumae Radix Carbonisata (CRC) has been widely used in the treatment of liver diseases in ancient medical books. In this study, novel carbon dots (CDs) extending from 1.0 to 4.5 nm were separated from fluid extricates of CRC. Meanwhile, a liver fibrosis model induced by carbon tetrachloride (CCl₄) was utilized to determine the inhibitory effects of CRC-CDs against liver fibrosis. The results exhibited the CRC-CDs with a quantum yield of 1.34% have a significant inhibitory effect on CCl₄-induced liver fibrosis, as demonstrated by improving hepatocyte degeneration and necrosis, inflammatory cell infiltration and fibrotic tissue hyperplasia, downregulating the levels of alanine transaminase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), direct bilirubin (DBIL), total bile acid (TBA), triglyceride (TG), tumour necrosis factor-α (TNF-α), interleukin (IL)-6 and IL-1β in the serum, upregulating the contents of superoxide dismutase (SOD), reduced glutathione (GSH), and downregulating the concentration of malondialdehyde (MDA), which lays an important foundation for the development of CRC-CDs as a novel drug for the treatment of liver fibrosis, and provide a certain experimental basis for the clinical application of CRC-CDs in the future.

Osteoarthritis (OA) is a degenerative disease closely associated with Anoikis. The objective of this work was to discover novel transcriptome-based anoikis-related biomarkers and pathways for OA progression.The microarray datasets GSE114007 and GSE89408 were downloaded using the Gene Expression Omnibus (GEO) database. A collection of genes linked to anoikis has been collected from the GeneCards database. The intersection genes of the differential anoikis-related genes (DEARGs) were identified using a Venn diagram. Infiltration analyses were used to identify and study the differentially expressed genes (DEGs). Anoikis clustering was used to identify the DEGs. By using gene clustering, two OA subgroups were formed using the DEGs. GSE152805 was used to analyse OA cartilage on a single cell level. 10 DEARGs were identified by lasso analysis, and two Anoikis subtypes were constructed. MEgreen module was found in disease WGCNA analysis, and MEturquoise module was most significant in gene clusters WGCNA. The XGB, SVM, RF, and GLM models identified five hub genes (CDH2, SHCBP1, SCG2, C10orf10, P FKFB3), and the diagnostic model built using these five genes performed well in the training and validation cohorts. analysing single-cell RNA sequencing data from GSE152805, including 25,852 cells of 6 OA cartilage.

Decellularization is a process to harvest the decellularized extra cellular matrix (dECM) that helps develop 3D scaffolds which mimic the native tissue composition. The decellularized tissues retain the structural and functional properties of the extracellular matrix (ECM) by an efficient decellularization process that retains tissue-specific biochemical and biophysical cues for tissue regeneration. In this study, we report an injection-based decellularization method, without perfusion setup. This study also compares the efficiency of the proposed protocol in the two animal models viz rat and mice. This method harvests rat and mice liver dECM using ethylenediamine tetra acetic acid (EDTA) and sodium dodecyl sulphate (SDS) within 08 h and 02 h respectively and preserved significant amount of ECM proteins. We reported that the harvested mice decellularized extracellular matrix (mdECM) and rat decellularized extracellular matrix (rdECM) had significant reduction in their DNA content (∼97%) and retained structural architecture resembling their native tissue counterparts. The total protein content retained in mdECM was ∼39% while that retained in rdECM was ∼65%. It was also found that the sGAG (sulphated glycosaminoglycan) content showed a no List of Figures.

Wheat and barley rank among the main crops cultivated on a global scale, providing the essential nutritional foundation for both humans and animals. Nevertheless, these crops are vulnerable to several fungal diseases, such as Septoria tritici blotch and net blotch, which significantly reduce yields by adversely affecting leaves and grain quality. To mitigate the effect of these diseases, chemical fungicides have proven to be genuinely effective; however, they impose a serious environmental burden. Currently, biocontrol agents have attracted attention as a sustainable alternative to fungicides, offering an eco-friendly option. The study aimed to assess the efficacy of Bacillus velezensis BE2 in reducing disease symptoms caused by Zymoseptoria tritici and Pyrenophora teres. This bacterium exhibited significant antagonistic effects in vitro by suppressing fungal development when pathogens and the beneficial strain were in direct confrontation. These findings were subsequently confirmed through microscopic analysis, which illustrated the strain's capacity to inhibit spore germination and mycelial growth in both pathogens. Additionally, the study analysed the cell-free supernatant of the bacterium using UPLC-MS (ultra-performance liquid chromatography-mass spectrometry). The results revealed that strain BE2 produces, among other metabolites, different families of cyclic lipopeptides that may be involved in biocontrol. Furthermore, the beneficial effects of strain BE2 in planta were assessed by quantifying the fungal DNA content directly at the leaf level after bacterization, using two different application methods (foliar and drenching). The results indicated that applying the beneficial bacterium at the root level significantly reduced pathogens pressure. Finally, gene expression analysis of different markers showed that BE2 application induced a priming effect within the first hours after infection. KEY POINTS: • BE2 managed Z. tritici and P. teres by direct antagonism and induced systemic resistance. • Strain BE2 produced seven metabolite families, including three cyclic lipopeptides. • Application of strain BE2 at the root level triggered plant defense mechanisms.