Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials

IntroductionPseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.MethodsThis study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.ResultsGeneral genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.DisucssionThis study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity

The FOXK1-CCDC43 Axis Promotes the Invasion and Metastasis of Colorectal Cancer Cells

Background/Aims: The CCDC43 gene is conserved in human, rhesus monkey, mouse and zebrafish. Bioinformatics studies have demonstrated the abnormal expression of CCDC43 gene in colorectal cancer (CRC). However, the role and molecular mechanism of CCDC43 in CRC remain unknown. Methods: The functional role of CCDC43 and FOXK1 in epithelial-mesenchymal transition (EMT) was determined using immunohistochemistry, flow cytometry, western blot, EdU incorporation, luciferase, chromatin Immunoprecipitation (ChIP) and cell invasion assays. Results: The CCDC43 gene was overexpressed in human CRC. High expression of CCDC43 protein was associated with tumor progression and poor prognosis in patients with CRC. Moreover, the induction of EMT by CCDC43 occurred through TGF-β signaling. Furthermore, a positive correlation between the expression patterns of CCDC43 and FOXK1 was observed in CRC cells. Promoter assays demonstrated that FOXK1 directly bound and activated the human CCDC43 gene promoter. In addition, CCDC43 was necessary for FOXK1- mediated EMT and metastasis in vitro and vivo. Taken together, this work identified that CCDC43 promoted EMT and was a direct transcriptional target of FOXK1 in CRC cells. Conclusion: FOXK1-CCDC43 axis might be helpful to develop the drugs for the treatment of CRC

Extracellular vesicles of bacteria as potential targets for immune interventions

Bacterial infection is one of the most common and serious diseases. Extracellular vesicles (EVs) expressed by bacterial cells during infection and their biological functions have been a growing field in recent years. The study of the immune interaction mechanism between EVs and bacteria has become more significant. EVs are released into the extracellular microenvironment during bacterial infection. EVs carry various lipids, proteins, nucleic acids, and other substances of host bacteria and participate in various physiological and pathological processes. EV-based vaccines against bacterial infection are also being evaluated. This review focuses on the biological characteristics of EVs, the interaction between EVs and the host immune system, and the potential of EVs as new vaccines. A deeper understanding of the interaction between EVs and the immune system informs on the biological function and heterogeneity of EVs. This knowledge also can facilitate the development and application of EVs and their potential as vaccines

Recombinant adenovirus-mediated intestinal trefoil factor gene therapy for burn-induced intestinal mucosal injury.

Intestinal trefoil factor (ITF) is a small polypeptide with potential medical values whose main pharmacological effects are to alleviate gastrointestinal mucosal injury caused by various injury factors and promote the repair of damaged mucosa. However, its low yield limits its application. The purpose of our study was to construct a recombinant adenoviral vector containing the hITF gene and observe the therapeutic effect of burn-induced intestinal mucosal injury using in vitro and in vivo analysis. First, a recombinant shuttle plasmid was constructed by ligating a pAdTrack-CMV vector with a full-length hITF gene containing a signal peptide and the mature peptide, followed by the recombinant Ad-hITF adenovirus vector after linearization and homologous recombination with the backbone plasmid in the competent BJ5183 strain. Second, the hITF expression level was detected using reverse transcription polymerase chain reaction and western blotting after Ad-hITF infection of colon cancer HT-29 cells. The recombinant adenovirus significantly promoted cell migration in an in vitro wounding model. Finally, we confirmed that the recombinant adenovirus could significantly expedite the healing of intestinal mucosal injury after establishing a mouse model in which severe burns were stimulated and the recombinant adenovirus was delivered by intragastric injection. In summary, we constructed a recombinant adenoviral vector containing the hITF gene and confirmed its role in promoting repair of the intestinal mucosa. Our study provides a novel way to treat burn-induced intestinal mucosal injury

Hidden costs of non-green performance? The impact of air pollution awareness on loan rates for Chinese firms

Given the idea that financial institutions can have a significant impact on environmental performance, green credit, which essentially involves capital allocation under environmental awareness, is worth to be explored and implemented by banking sectors worldwide. This paper explores the impact of environmental awareness on firms' loan rates, with a focus on borrowers who have a record of environmental penalties. Using a comprehensive loan dataset from one of China's “Big Five” banks between 2010 and 2013, we employ the volatility of particulate matter 2.5 (PM2.5) as a proxy to measure environmental awareness. Our findings suggest that the volatility of air pollution has a positive effect on the floating ratio of the loan interest rate for firms with a history of environmental penalties. Furthermore, we find that this mechanism is particularly pronounced for private-owned enterprises (POEs), new loan customers, firms with low crediting ratings, and small-sized enterprises. We also confirm the role of environmental awareness in firms' loan costs by demonstrating that the volatility of air pollution is sensitive to variations in insolation duration, environmental attention, and PM2.5 monitoring stations. We suggest that the volatility of air pollution is a more meaningful indicator than the degree of air pollution, and that people's voluntary environmental awareness can transfer the environmental risk of firms to their internal operating costs. The significance of this study lies in its potential to aid policymakers and investors in advancing sustainable finance practices, as well as stimulating individual engagement with environmental awareness and prompting financial institutions to give greater importance to these issues

A New Classification Method for Ship Trajectories Based on AIS Data

Automatic identification systems (AIS) can record a large amount of navigation information about ships, including abnormal or illegal ship movement information, which plays an important role in ship supervision. To distinguish the trajectories of ships and analyze the behavior of ships, this paper adopts the method of supervised learning to classify the trajectories of ships. First, the AIS data for the ships were marked and divided into five types of ship tracks. The Tsfresh module was then used to extract various ship trajectory features, and a new ensemble classifier based on traditional classification using a machine learning algorithm was proposed for modeling and learning. Moreover, ten-fold cross validation was used to compare the ship trajectory classification results. The classification performance of the ensemble classifier was better than that of the other single classifiers. The average F1 score was 0.817. The results show that the newly proposed method and the new ensemble classifier have good classification effects on ship trajectories