Antimicrobial susceptibility and genetic characteristics of multi-drug resistant Acinetobacter baumannii isolates in Northwest China.

Introduction: In recent decades, widespread multi-drug resistant (MDR) bacteria have become a serious problem in healthcare facilities. Methods: To systematically summarize and investigate the prevalence and genomic features of clinical MDR Acinetobacter baumannii (A. baumannii) clinical isolates recovered from the first hospital of Lanzhou University, we collected 50 MDR A. baumannii isolates isolated in the first quarter of 2022 and using whole-genome sequencing investigate the genotypic characteristics. Results: All of these isolates were generally resistant to the common ß-lactamase antibiotics. Resistance to cefoperazone-sulbactam varies greatly between different clones. The proportion of CC208 isolates resistant and mediated to cefoperazone-sulbactam is as high as 84.6%. There were no isolates resistant to tigecycline and colistin. The presence of blaOXA - 23 (94.0%) and blaOXA - 66 (98.0%) were the most frequent determinants for carbapenem resistance. Two main endemic clones were identified, one (ST469oxf) was predominantly circulating in ICUs and carried the same resistance genes, virulence genes and transposons, and the other clone (CC208) carried more resistance genes and had more widely disseminated. Discussion: Our study showed that clinical MDR A. baumannii isolates circulating in our hospital exhibited highly similar genetic features. We should take timely and effective measures to control the further epidemic of these isolates.

Epigenetic Regulation of Subgenomic Gene Expression in Allotetraploid Brassica napus.

The allotetraploid Brasscia napus has now been extensively utilized to reveal the genetic processes involved in hybridization and polyploidization. Here, transcriptome, WGBS, and Chip-Seq sequencing data were obtained to explore the regulatory consequences of DNA methylation and histone modifications on gene expression in B. napus. When compared with diploid parents, the expression levels of 14,266 (about 32%) and 17,054 (about 30%) genes were altered in the An and Cn subgenomes, respectively, and a total of 4982 DEGs were identified in B. napus. Genes with high or no expression in diploid parents often shifted to medium or low expression in B. napus. The number of genes with elevated methylation levels in gene promoters and gene body regions has increased in An and Cn subgenomes. The peak number of H3K4me3 modification increased, while the peak number of H3K27ac and H3K27me3 decreased in An and Cn subgenomes, and more genes that maintained parental histone modifications were identified in Cn subgenome. The differential multiples of DEGs in B. napus were positively correlated with DNA methylation levels in promoters and the gene body, and the differential multiples of these DEGs were also affected by the degree of variation in DNA methylation levels. Further analysis revealed that about 99% of DEGs were of DNA methylation, and about 68% of DEGs were modified by at least two types of DNA methylation and H3K4me3, H3K27ac, and H3K27me3 histone modifications. These results demonstrate that DNA methylation is crucial for gene expression regulation, and different epigenetic modifications have an essential function in regulating the differential expression of genes in B. napus.

Oligosaccharide and short-chain fatty acid: A double-edged sword in obese mice by regulating food intake and fat synthesis.

Dietary fiber has been used to prevent obesity by regulating the intestinal flora and promoting the production of short-chain fatty acids (SCFAs). However, it is insufficient to conclude the decisive role of microbiota and SCFAs by adding oligosaccharides to foods without caloric balance. In this study, the effects of oligosaccharides and their regulated microflora on the development of obesity in mice were studied by designing a high-fat diet with equal calories but different contents of oligosaccharides. Isocaloric diets demonstrated that appropriate rather than excess oligosaccharides prevent obesity by regulating appetite. Such an appetite was inhibited by oligosaccharides but promoted by SCFAs. Furthermore, promoted appetite was tightly related to decreased insulin and increased acyl-CoA binding protein, which was correlated with SCFA-induced fat degradation. Interestingly, drinking butyrate alleviated obesity even with higher calorie intake. Molecular docking demonstrated that conversion of butyrate to butyryl-CoA converted from butyrate, as a structural analog of acetyl-CoA, inhibits the activity of acetyl-CoA carboxylase. Together, these findings demonstrate that fermentable fiber supplements may have limits in obesity treatment, and we provide possible obesity therapeutic targets that inhibit bacterial fermentation or increase the ratio of butyrate/acetate.

The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus.

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors.

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

Evaluation of recombinant SjLAP and SjFBPA in detecting antibodies to Schistosoma japonicum.

OBJECTIVE: To investigate the early response of immunoglobulin G (IgG) antibody responses to Schistosoma japonicum infection in mice by using the recombinant proteins, S. japonicum leucine aminopeptidase (rSjLAP) and S. japonicum fructose-1, 6-bisphosphate aldolase (rSjFBPA), and evaluate the potential of rSjLAP and rSjFBPA in diagnosis as well as in assessment of therapeutic efficacy in human schistosomiasis. METHODS: rSjLAP or rSjFBPA was induced from Escherichia coli BL21 strain transfected with the expression vectors, pET-28a-rSjFBPA/BL21 or pET-28a-rSjLAP/BL21 using isopropyl-beta-D-thiogalactoside (IPTG), and purified by Ni-NTA His Bind resin. 88 BALB/c female mice, inbred and 6 to 8 weeks old, were randomly divided into 4 groups. Groups A, B and C each made up of 21 mice and group D comprised 25 mice. Groups A, B and C were infected with 5, 15 and 25 S. japonicum cercariae respectively. As control, mice in group D were left uninfected. 3 mice from each of groups A, B and C were sacrificed and sera collected on days 3, 7, 10, 14, 20, 30, and 60 post infection. All the 25 mice in group D were sacrificed on the first day of the experiment for serum collection. rSjLAP and rSjFBPA were screened and used in ELISA to test the antibody response of the serum samples. Also, sera of 38 acute patients, 96 chronic patients with schistosomiasis japonica, 90 healthy donors and patients with other parasite infections including Clonorchis sinensis (33 cases), Paragonimus westermani (40) and hookworms (37) were tested using the recombinant protein-based ELISA. In addition, 36 sera each from the acute and chronic patients 12 months after treatment with praziquantel and 64 of the chronic patients in more than 2 years post-treatment of praziquantel were tested. The dosage of praziquantel for both acute and chronic patients was 60 mg/kg, 2 times/dx2 d. RESULTS: IgG antibody response was first detected at day 10 post infection by rSjLAP, rSjFBPA or the combined antigen assay. The mean absorbance (A450) on this day were 0.535 +/- 0.053, 0.595 +/- 0.033, 0.696 +/- 0.104 for group B; 0.548 +/- 0.060, 0.608 +/- 0.063, 0.621 +/- 0.090 for group C; and 0.415 +/- 0.038, 0.455 +/- 0.056, 0.498 +/- 0.077 for group A for rSjLAP, rSjFBPA and the combined assay respectively (P < 0.05). Early antibody level to both antigens was significantly higher in mice infected with 15 or 25 cercariae than those with 5 cercariae (P < 0.05). However, ELISA results in patients with confirmed schistosomiasis revealed positive rates of 97.4% (37/38) and 87.5% (84/96) for acute and chronic schistosomiasis with rSjLAP , 94.7% (36/38) and 88.5% (85/96) for acute and chronic schistosomiasis with rSjFBPA and 94.7% (36/38)and 85.4%(82/96) with both rSjLAP and rSjFBPA respectively. Statistical analysis showed no significant difference in the positive rate (P > 0.05). Also, rSjLAP and combined antigens showed a specificity of 96.7% (87/90) while that of rSjFBPA was 97.8% (88/90). There was a general decrease in the antibody titer of the patients after treatment. In 12 months after treatment it was 0.236 +/- 0.212 with rSjLAP, 0.287 +/- 0.191 with rSjFBPA, and 0.235 +/- 0.120 with both antigens respectively for acute cases; For chronic patients, it was 0.266 +/- 0.124, 0.261 +/- 0.143 and 0.265 +/- 0.140 in 12 months post-treatment, and 0.204 +/- 0.074, 0.176 +/- 0.074, and 0.176 +/- 0.073 in 2 years, respectively. For healthy control, it was 0.188 +/- 0.056, 0.173 +/- 0.45, and 0.184 +/- 0.051, respectively. No significant difference on antibody titer was found between treated patients and control (P > 0.05). The cross reaction with C. sinensis was 15.2% (5/33) for rSjLAP, 12.1% (4/33) for rSjFBPA and 9.2% (3/33) for combined antigens. With P. westermani, it was 15.0% (6/40), 12.5% (5/40) and 15.0% (6/40), respectively, and 8.1% (3/37) with hookworm infection. CONCLUSION: The study showed a satisfactory sensitivity and specificity of rSjLAP and rSjFBPA by ELISA which is promising for the immunological diagnosis of schistosomiasis.