Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity / 药物分析学报

Ribosomes are abundant,large RNA-protein complexes that are the sites of all protein synthesis in cells.Defects in ribosomal proteins(RPs),including proteoforms arising from genetic variations,alternative splicing of RNA transcripts,post-translational modifications and alterations of protein expression level,have been linked to a diverse range of diseases,including cancer and aging.Comprehensive character-ization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets.In the present work,using E.coli 70S RPs as an example,we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry(MS)system,and then applied it to the HeLa 80S ribosome.The results were complemented by a bottom-up approach.In total,50 out of 55 RPs were identified using the top-down approach.Among these,more than 30 RPs were found to have their N-terminal methionine removed.Additional modifications such as methylation,acetylation,and hydroxylation were also observed,and the modification sites were identified by bottom-up MS.In a HeLa 80S ribosomal sample,we identified 98 ribosomal proteoforms,among which multiple truncated 80S ribosomal proteoforms were observed,the type of information which is often overlooked by bottom-up experiments.Although their relevance to diseases is not yet known,the integration of top-down and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.

Analysis on the structural changes of intestinal and pulmonary flora in mice with sepsis and acute lung injury / 中华急诊医学杂志

Objective:To investigate the microecological structure changes and correlation in blood, lung tissue and fecal intestine of mice with sepsis and acute lung injury.Methods:A total of 12 healthy male C57BL/6J mice were divided into the cecal ligation and perforation (CLP) group and sham operation (sham) group by random number table method, with six mice in each group. In the CLP group, acute lung injury model of sepsis mice was prepared by CLP method. In the sham group, only laparotomy but no perforation of cecal ligation was performed. Eye blood, lung tissue, and feces were collected from mice in each group 24 h after surgery. Lung tissue morphological changes were observed by HE staining, and 16s ribosome RNA sequencing was used to analyze the structural changes of microecology of the bacterial flora at each site in sepsis mice and find out the correlation.Results:(1) HE staining showed that mice in the CLP group had exudation into the alveolar cavity of the lung, disordered lung tissue structure, accompanied by a large number of inflammatory cell infiltration, and the lung histopathological score was significantly higher than that in the sham group ( P < 0.01). (2)α diversity analysis showed that there was no statistical significance in blood and fecal samples between the sham group and CLP group, while Ace index, Chao index and Simpson index in lung tissue samples were statistically significant ( P < 0.05). (3) β diversity analysis showed that the differences in blood and fecal samples were greater between the sham group and CLP group than that within the group, and analysis of Bray Curtis, weighted, and unweighted indexes were statistically significant ( P < 0.05). (4) At the phylum level, compared with the sham group, the abundance of Proteobacteria gradually increased, and the abundance of Firmicutes and actinobacteria was decreased in the CLP group. At the genus level, the sham group was dominated by Acinetobacter and Duchenne, while the CLP group was dominated by Escherichia coli and unclassified Enterobacter. Blood flora was more similar to lung tissue flora composition as compared with fecal flora. Conclusions:The distribution of bacterial flora in blood, lung tissue and intestine of sepsis mice with acute lung injury is partially overlapped.

Research progress on ribosomal proteins and their functions in diseases / 药学实践杂志

Ribosomal proteins (RP) are important components of ribosomes and play key roles in ribosome biogenesis and protein translation. In addition, ribosomal proteins also possess many extra-ribosomal functions, such as regulation of gene expression, cell proliferation, differentiation, apoptosis, DNA repair, and many other cellular processes. The dysfunction of RP is closely related to the occurrence and development of various diseases including blood, metabolism, cardiovascular diseases and tumors, and RP might become potential therapeutic targets for a variety of diseases. The research progress on RP, including the basic functions of RP, extra-ribosomal properties, and the connections with human diseases were reviewed and their potential as biomarkers and therapeutic targets in diseases were discussed in this paper.

Prevalence and molecular characterization of Cryptosporidium in captive-bred Mustela putorius furo in Jiangsu Province / 中国血吸虫病防治杂志

Objective To investigate the prevalence and molecular features of Cryptosporidium in captive-bred Mustela putorius furo in Jiangsu Province.. Methods A total of 290 fresh stool samples were collected from a ferret farm in Jiangsu Province on May 2017, and the small subunit rRNA (SSU rRNA) gene of Cryptosporidium was amplified in stool samples using nested PCR assay. The actin, cowp and gp60 genes were amplified in positive samples and sequenced to characterize Cryptosporidium species/genotypes. Results A total of 18 stool samples were tested positive for Cryptosporidium SSU rRNA gene, with a detection rate of 6.2%. Sequence and phylogenetic analyses of SSU rRNA, actin and cowp genes characterized Cryptosporidium isolated from captive-bred ferrets as Cryptosporidium sp. ferret genotype. In addition, gp60 gene was amplified in 10 out of 18 stool samples tested positive for Cryptosporidium. Conclusions Cryptosporidium is widely prevalent in captive-bred ferrets in Jiangsu Province, and Cryptosporidium sp. ferret genotype is the only Cryptosporidium genotype in ferrets.

Changes of gut microflora in newly diagnosed IgA nephropathy patients and its correlation with clinical risk factors / 北京大学学报(医学版)

OBJECTIVE@#To investigate the gut microbiota in newly diagnosed IgA nephropathy patients with chronic kidney disease (CKD) stages 1-2 and the association between the gut microbiota and the clinical risk factors of IgA nephropathy.@*METHODS@#Fresh fecal samples were collected from nineteen newly diagnosed IgA nephropathy patients with CKD stages 1-2 and fifteen age- and sex-matched healthy controls. Fecal bacterial DNA was extracted and microbiota composition were characterized using 16S ribosomal RNA (16S rRNA) high-throughput sequencing for the V3-V4 region. The Illumina Miseq platform was used to analyze the results of 16S rRNA high-throughput sequencing of fecal flora. At the same time, the clinical risk factors of IgA nephropathy patients were collected to investigate the association between the gut microbiota and the clinical risk factors.@*RESULTS@#(1) At the phylum level, the abundance of Bacteroidetes was significantly reduced (P=0.046), and the abundance of Actinobacteria was significantly increased (P=0.001). At the genus level, the abundance of Escherichia-Shigella, Bifidobacte-rium, Dorea and others were significantly increased (P < 0.05). The abundance of Lachnospira, Coprococcus_2 and Sutterella was significantly reduced (P < 0.05). (2) There was no significant difference in the abundance of gut microbiota between the newly diagnosed IgA nephropathy patients and the healthy control group (P>0.05), but there were differences in the structure of the gut microbiota between the two groups. The results of LEfSe analysis showed that there were 16 differential bacteria in the newly diagnosed IgA nephropathy patients and healthy controls. Among them, the abundance of the newly diagnosed IgA nephropathy patients was increased in Enterobacteriales, Actinobacteria, Escherichia-Shigella, etc. The healthy control group was increased in Bacteroidetes and Lachnospira. (3) The result of redundancy analysis (RDA) showed that Bifidobacterium was positively correlated with serum IgA levels, 24-hour urinary protein levels and the presence of hypertension. Lachnoclostridium was positively correlated with the presence of hypertension. Escherichia-Shigella was positively correlated with urine red blood cells account. Bifidobacterium was positively correlated with the proliferation of capillaries. Faecalibacterium was positively correlated with cell/fibrocytic crescents. Ruminococcus_2 was positively correlated with mesangial cell proliferation, glomerular segmental sclerosis and renal tubular atrophy/interstitial fibrosis.@*CONCLUSION@#The gut microbiota in the newly diagnosed IgA nephropathy patients with CKD stages 1-2 is different from that of the healthy controls. Most importantly, some gut bacteria are related to the clinical risk factors of IgA nephropathy. Further research is needed to understand the potential role of these bacteria in IgA nephropathy.

Anti-ribosomal P (anti-P) antibodies in patients with autoimmune hepatitis

ABSTRACT Objective Published studies have shown associations between anti-ribosomal P (anti-P) antibody and systemic lupus erythematosus with hepatic manifestations. This has been reported also in autoimmune hepatitis. However, the consistency of the latter association remains controversial. This study aimed to evaluate the frequency of anti-P antibodies in autoimmune hepatitis using two different immunoassays. Methods One-hundred and seventy-seven patients with autoimmune hepatitis were screened, and 142 were analyzed for anti-P antibody positivity. The samples were first analyzed using two different immunoassays: enzyme-linked immunosorbent assay (ELISA) and chemiluminescence and then compared with a group of 60 patients with systemic lupus erythematous. The positive samples were subjected to western blot analysis. Results Anti-P was found in 5/142 autoimmune hepatitis cases (3.5%) by chemiluminescence and in none by ELISA. Among the five chemiluminescence-positive autoimmune hepatitis samples, on anti-P western blot analysis one was negative, two were weakly positive, and two were positive. In contrast, anti-P was detected in 10/60 patients with systemic lupus erythematosus (16.7%) and presented higher chemiluminescence units than the autoimmune hepatitis samples. Conclusion A low frequency of anti-P antibodies was observed in autoimmune hepatitis, suggesting that this test is not useful for the diagnosis or management of this disease.

Prevalence and genotyping of Cryptosporidium spp. and Giardia lamblia in dogs and cats from a pet hospital in Shanghai Municipality / 中国血吸虫病防治杂志

Objective To investigate the prevalence and genotypes of Cryptosporidium spp. and Giardia lamblia in dogs and cats from a pet hospital in Shanghai Municipality. Methods A total of 145 fresh fecal samples were collected from pet dogs and cats in a pet hospital in Shanghai Municipality during the period from November 2021 to June 2022, including 99 dog fecal samples and 46 cat fecal samples. The small subunit ribosomal ribonucleic acid (SSU rRNA) gene of Cryptosporidium and the triose phosphate isomerase (TPI) gene of G. lamblia were amplified using nested PCR assay, and the positive amplification products were sequenced from both directions. The sequence assembly was performed using the software Clustal X 2.1, and sequence alignment was conducted using BLAST. A phylogenetic tree was created with the Neighbor-Joining method using MEGA 11.0 to identify parasite species or genotype. Results The overall prevalence of Cryptosporidium and G. lamblia was 20.00% (29/145) in 145 pet dog and cat fecal samples, with the prevalence of 0.69% (1/145) and 19.31% (28/145) in Cryptosporidium and G. lamblia, respectively. G. lamblia was only detected in dog fecal samples, with prevalence of 18.18% (18/99), while the detection rates of Cryptosporidium and G. lamblia were 2.17% (1/46) and 21.74% (10/46) in cat fecal samples. Nucleotide sequence analysis showed that one Cryptosporidium positive sample was characterized as C. felis, and 28 G. lamblia positive samples were all characterized as Giardia assemblage A, which showed 100% sequence homology with human isolates of Giardia. Phylogenetic analysis revealed that the sequences obtained in this study belonged to the same branch with the reported Giardia assemblage A. Conclusions Cryptosporidium and G. lamblia infection was prevalent in pet dogs and cats from the study pet hospital in Shanghai Municipality, and there is a zoonotic risk for the species and genotype. Intensified surveillance of Cryptosporidium and Giardia infection is recommended in pets and their owners, and improved management of pet keeping is required.

Effect of hexavalent chromium-induced ribosomal DNA copy number variation on DNA damage response in various cell lines / 预防医学

Objective@#To investigate the effect of ribosomal DNA (rDNA) copy number variation caused by hexavalent chromium exposure on DNA damage response in different cell lines, so as to provide insights into the involvement of hexavalent chromium-induced rDNA copy number variation in DNA damage responses. @*@#Methods Human lung epithelial BEAS-2B cells and human embryonic lung MRC-5 cells were treated with 2 μmol/L potassium dichromate for 24 hours, and then cells were transferred to fresh media for further incubation, while cells treated with the same volume of phosphate buffer solution served as controls. Cells treated with potassium dichromate for 24 hours, and 3 and 7 days post-detoxification, were harvested, and rDNA copy number was quantified in cells using a quantitative fluorescent real-time PCR assay. Cell cycle, apoptosis and DNA damage were detected using a Muse cell analyzer, and the DNA damage was evaluated with the proportion of ataxia telangiectasia-mutated (ATM) gene activation, proportion of double-strand DNA breaks and the percentage of the H2A.X variant histone phosphorylatio.@*@# Results The 45S and 5S rDNA copy numbers of were significantly higher in MRC-5 cells than in BEAS-2B cells [(1.54±0.26) vs. (1.02±0.18), P<0.05; (6.97±1.07) vs. (3.00±0.15), P<0.05]. The 45S rDNA copy number was lower in MRC-5 cells 3 days post-detoxification (0.80±0.04) than in controls (P<0.05), and was higher in BEAS-2B cells 3 days post-detoxification (1.43±0.07) than in controls (P<0.05) . G0/G1 phase arrest was found in MRC-5 cells 24 hours post-treatment, and the apoptotic rates were significantly higher in MRC-5 cells 3 and 7 days post-detoxification than in controls [(11.53±1.53)%, (18.33±0.70)% vs. (3.53±0.93)%, P<0.05]. The overall apoptotic rates 24 hours post-treatment and 3 days post-detoxification [(2.80±0.17)%, (3.33±0.57)% vs. (1.53±0.61)%, P<0.05], proportion of ATM gene activation 3 days post-detoxification [(3.37±0.67%) vs. (1.18±0.22)%, P<0.05], proportion of double-strand DNA breaks 3 days post-detoxification [(4.45±0.85)% vs. (0.97±0.21)%, P<0.05] and percentage of the H2A.X variant histone phosphorylation 3 days post-detoxification [(1.68±0.56)% vs. (0.29±0.06)%, P<0.05] in BEAS-2B cells were higher than in controls. @*Conclusions@#Hexavalent chromium-induced rDNA copy number variation affects DNA damage response in different cell lines. A stronger DNA damage response is found in BEAS-2B cells with a low rDNA copy number, and a relative stable response is observed in MRC-5 cells with a high rDNA copy number.

Analysis of the nail microbiome in patients with onychomycosis by high-throughput sequencing of 16S rDNA and internal transcribed spacer regions / 中华皮肤科杂志

Objective:To investigate differences in bacterial and fungal microbiome between infected nails and healthy nails among patients with onychomycosis.Methods:Nail scraping samples were collected from infected nails and healthy nails of 31 patients with onychomycosis, who visited Dalian Dermatosis Hospital from August 2020 to July 2021. The total DNA of nail microbiota was extracted, and the V3-V4 regions of the bacterial 16S rDNA gene and the fungal internal transcribed spacer (ITS) region were amplified and sequenced using Illumina technology. The USEARCH and mothur softwares were used for data cluster analysis to obtain the operational taxonomic units (OTUs) , Wilcoxon rank sum test was used to analyze α diversity, analysis of similarities (ANOSIM) was performed to analyze β diversity, linear discriminant analysis of effect size (LEfSe) was performed to evaluate the species difference.Results:Among the 31 patients with onychomycosis, 16 were males and 15 were females. According to the age, they were divided into young group (18 - 35 years old, 10 cases) , middle-aged group (36 - 60 years old, 11 cases) , and elderly group (over 60 years old, 10 cases) . As the α-diversity analysis revealed, the infected nail group showed significantly decreased Shannon index ( W = 290, P = 0.007) , but significantly increased Simpson index ( W = 663, P = 0.010) compared with the healthy nail group, suggesting that the diversity and evenness of bacterial communities were lower in the infected nail group than in the healthy nail group; however, there was no significant difference in the diversity of fungal communities between the infected nail group and healthy nail group. The β-diversity analysis based on the unweighted-UniFrac distance matrix showed no significant difference in the fungal or bacterial community composition between the infected nail group and healthy nail group (bacterial communities: R = 0.0052, P = 0.331; fungal communities: R = 0.0036, P = 0.337) ; the β-diversity analysis based on the weighted-UniFrac distance matrix showed significant differences in the abundance of bacterial and fungal communities between the two groups (both P = 0.001) . In terms of the species composition, the bacterial flora with significantly decreased abundance in the infected nail group compared with the healthy nail group included Bacteroidetes, Proteobacteria, Betaproteobacteria, Burkholderiales, Ralstonia, Sphingomonas and Streptococcus, while the abundance of Bacilli, Bacillales and Staphylococcus was significantly higher in the infected nail group than in the healthy nail group. Compared with the healthy nail group, the fungal flora with significantly increased abundance in the infected nail group included Eurotiomycetes, Onygenales, Leotiomycetes-ord-incertae-sedis, Arthrodermataceae, Periconia, Erysiphe, Tilletiopsis, Trichophyton, Erysiphe cruciferarum, Trichophyton rubrum, Malassezia sympodialis, while the abundance of Saccharomycetes, Saccharomycetales, Saccharomycetaceae, Dothioraceae, Candida and Alternaria was significantly lower in the infected nail group than in the healthy nail group. Conclusion:The diversity and abundance of bacterial communities significantly differed between infected nails and healthy nails among patients with onychomycosis, while only the abundance of fungal communities differed between the two groups, and perhaps there was correlations between some bacterial and fungal communities.

Molecular characteristics of clinically isolated Yersinia in Jiangsu Province from 2017 to 2021 / 中华地方病学杂志

Objective:To investigate the distribution and molecular characteristics of Yersinia isolated from diarrhea patients in Jiangsu Province. Methods:From 2017 to 2021, the stool samples of diarrhea patients were collected in Tongshan District of Xuzhou City and Dongtai City of Yancheng City, Jiangsu Province, where the national active monitoring sites of Yersinia enterocolitica, then Yersinia was isolated; meanwhile, suspected Yersinia strains were collected from sentinel hospitals in the province. The DNA of isolated strains was extracted for whole genome resequencing, and the data were uploaded to the EnteroBase database for Yersinia species identification; the original data were cleaned and processed for 16S ribosomal RNA (16S rRNA) gene polymorphism analysis. Five virulence genes (ail, ystA, ystB, yadA, virF) were scanned through the National Center for Biotechnology Information (NCBI) and Pathogen Virulence Factor Database (VFDB), and K-mer Tree was constructed and genomic characteristics were analyzed. Results:From 2017 to 2021, a total of 2 058 stool samples from diarrhea patients were collected, and 57 strains of Yersinia were isolated and identified; meanwhile, two Yersinia strains were collected from the sentinel hospital. Compared with EnteroBase database, 51 strains were identified as Yersinia enterocolitica, 4 strains as Yersinia proxima, 1 strain each as Yersinia aleksiciae, Yersinia massiliensis, Yersinia intermedia and Yersinia canariae. The 16S rRNA gene polymorphism analysis showed that all strains were clustered into 3 groups, which could distinguish Yersinia enterocolitica from other Yersinia. Among the 51 strains of Yersinia enterocolitica, 49 strains were virulence genotype Ⅲ(ail-, ystA-, ystB+, yadA-, virF-), two strains were virulence genotype Ⅱ(ail+, ystA+, ystB-, yadA-, virF-); and 8 other Yersinia strains were virulence genotype Ⅳ (ail-, ystA-, ystB-, yadA-, virF-). K-mer analysis could distinguish Yersinia enterocolitica from other Yersinia, JS-XZ-2020001 strain was far away from other Yersinia enterocolitica isolates, and serotype O8 strains were more concentrated. Conclusions:The clinical isolates of Yersinia enterocolitica from diarrhea patients are mainly Yersinia and other Yersinia co-exist in a small amount in Jiangsu Province, two new Yersinia species ( Yersinia proxima and Yersinia canariae) are discovered. The virulence genotype of Yersinia enterocolitica is mainly type Ⅲ. The 16S rRNA gene polymorphism analysis and K-mer analysis can effectively distinguish Yersinia enterocolitica from other Yersinia.

Effects of specific knockdown of ribosomal protein S5 in hepatic stellate cells on liver fibrosis / 药学实践杂志

Objective To observe the effect of specific knockdown of hepatic stellate cells (HSC) ribosomal protein S5 (RPS5) on liver fibrosis in rats. Methods The glial fibrillary acidic protein (GFAP) promoter-driven RPS5 shRNA adenovirus was established, and AdGFa2-shRPS5 and its control AdGFa2 shNC were used to transfect primary rat HSCs and hepatocytes, respectively. RPS5 was determined by Western-blot and Real Time PCR, α-SMA and type I collagen expression; the rat liver fibrosis model was established by dimethyl nitrosamine (DMN) and bile duct ligation (BDL), and intrahepatic HSC was specifically knocked down by tail vein injection of adenovirus of RPS5 levels. The pathological changes of liver tissue sections were analyzed by HE staining; the content of hydroxyproline, sections of Sirius red and Masson staining were used to evaluate collagen deposition; immunohistochemical staining was used to detect the expression of α-SMA and RPS5. Results AdGFa2-shRPS5 specifically knocked down the expression level of RPS5 in HSC and increased the expression of α-SMA and type I collagen in vitro. The in vivo results showed that in two animal models of chronic liver injury, specific knockdown of RPS5 expression in HSCs promoted HSC activation, increased the deposition of extracellular matrix, and promoted liver fibrosis. Conclusion RPS5 is essential for HSC activation and liver fibrosis, which could be a potential target for the treatment of liver fibrosis.

Effects of Ganbao capsules on intestinal mucosal barrier and gut microbiota in rats with non-alcoholic fatty liver disease / 中国药房

OBJECTIVE To study the effects of Ganbao capsules on intestinal mucosal barrier and gut microbiota in rats with non-alcoholic fatty liver disease （NAFLD）， and to explore its mechanism of prevention and treatment of NAFLD. METHODS Eight of 26 SD rats were randomly selected as blank group and fed with ordinary diet， and the remaining 18 rats were fed with high diet to establish NAFLD model （2 for modeling inspection）； after successful modeling， they were divided into model group and Ganbao group， with 8 rats in each group. Ganbao group were given Ganbao capsules solution （1 440 mg/kg） intragastrically， and the blank group and model group were given the constant volume of distilled water intragastrically， once a day， for consecutive 5 weeks. The contents of alanine aminotransferase （ALT）， aspartate aminotransferase （AST） and triglyceride （TG） in serum of rats were detected by automatic analyzer； the contents of lipopolysaccharide， tumor necrosis factor-α （TNF-α）， interleukin-6 （IL-6） and IL-1β in serum of rats were detected by enzyme-linked immunosorbent assay. The pathological morphology of liver and ileum tissues were observed by HE staining， the expressions of Occludin and zonula occludens-1 （ZO-1） were detected by immunohistochemistry method， and the intestinal flora were detected by 16S ribosomal RNA gene sequencing technology. RESULTS Compared with the model group， the serum contents of ALT， AST， TG， lipopolysaccharide， TNF-α， IL-6 and IL-1β in Ganbao group were decreased significantly （P＜0.01）， the pathological changes of liver and ileum tissues were improved 262 significantly， and the expressions of Occludin and ZO-1 were increased significantly （P＜0.01）. Intestinal microbiotaanalysis revealed that compared with the model group， Ganbao capsules could recover the abundance and diversity of the gut E-mail：hdf8833@126.com microbiota in rats. At the phylum level， Ganbao capsules could significantly increase the relative abundance of Bacteroidetes， and significantly reduce the relative abundance of Firmicutes and the ratio of Firmicutes to Bacteroidetes （P＜0.01）. At the genus level， Ganbao capsules could significantly increase the relative abundance of Lactobacillus， Blautia， Bacteroides and Akkermansia， and significantly reduce the relative abundance of Prevotella， Turicibacter， Weissella， SMB53 and Desulfovibrio （P＜0.05 or P＜0.01）. There were different species among the gut microbiota of rats in each group. CONCLUSIONS Ganbao capsules may improve NAFLD by protecting intestinal mucosal barrier function and regulating gut probiotics/harmful bacteria structure.

Progress in molecular diagnosis of Diamond-Blackfan anemia / 国际儿科学杂志

Diamond-Blackfan anemia(DBA)is a rare hereditary anemia.About 90% of them have symptoms in infancy, and about 50% are complicated with congenital malformations.Genetic abnormalities were found in 70% to 80% of DBA cases, mainly autosomal dominant inheritance, and a few were recessive or X-linked inheritance.The main gene mutations of DBA are ribosomal protein gene mutations and deletions.More than 20 mutation genes related to DBA have been found in the ribosomal protein(RP)gene encoding ribosome, of which RPS19 gene mutation is the most common.In addition, there are TSR2 genes related to ribosome function and non-RP genes related to DBA like phenotype, such as GATA1, EPO and ADA2 genes.These genes play a key role in the differentiation and proliferation of erythroid cells.Molecular diagnosis is an important criterion to diagnose and distinguish classical DBA from non-classical DBA.This review summarizes the latest research progress in the genetics, gene mutation and molecular diagnosis of DBA.

Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing / 中国血吸虫病防治杂志

Objective To investigate the bacterial community diversity in Dermatophagoides farinae. Methods Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software. Results A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus. Conclusions A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.

Effects of noise exposure on structure and functional prediction of intestinal microbiota in rats / 环境与职业医学

Background Noise has multiple negative effects on the organism, and gut microbes are influenced by the environment and are closely associated with the development of diseases. Currently, the effects of chronic noise exposure on intestinal microbiota are poorly understood. Objective To investigate the effects of noise exposure on the structure of rat gut microbiota and to make predictions of gut microbiota function. Methods Male Wistar rats (6 weeks old, 160-180 g) were randomly divided into control, NE_95dB, and NE_105dB groups, 10 rats in each group. Rats in the NE_95dB and the NE_105dB groups were exposed to noise at 95 dB sound pressure level (SPL) and 105 dB SPL, respectively, 4 h per day for consecutive 30 d, while the control group was exposed to background noise. Feces were collected after the last noise exposure for intestinal microbiota detection. Based on the 16S ribosomal RNA (rRNA) gene sequencing method, the diversity and structure of microbiota in rat intestinal contents were analyzed and compared. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to predict functions of the identified intestinal microbiota genes. Results Significant differences were found in the microbial structure of the rat gut after the designed noise exposure. In the α diversity results, there was a statistically significant difference in the Chao1 index between the NE_95dB group and the NE_105dB group (P=0.02), while there were no statistically significant differences in the Shannon and Simpson indexes between the noise exposure groups and the control group (P>0.05). The β diversity analysis results showed significant differences in species abundance between the control group and the noise exposure groups (P=0.001). Further species analysis results showed that the relative abundances of the Ruminococcaceae_NK4A214_group (P<0.05) and Peptococcaceae_unclassified (P<0.01) at the genus level were significantly higher in the NE_105dB group, and the relative abundance of Parasutterella (P<0.05) was significantly higher in the NE_95dB group compared to the control group. In addition, the Ruminococcaceae_NK4A214_group (P<0.05) was also significantly higher in the NE_105dB group compared to the NE_95dB group. The PICRUSt functional prediction analysis results showed that there were eight differential pathways between the control group and the NE_95dB group, in which D-arginine and D-ornithine metabolism, ascorbate and aldarate metabolism, carotenoid biosynthesis, glycerophospholipid metabolism, mineral absorption, NOD-like receptor signaling pathway and non-homologous end-joining were significantly down-regulated, and nucleotide metabolism was significantly up-regulated. There were 38 differential pathways between the control group and the NE_105dB group. Among them, D-arginine and D-ornithine metabolism, and mineral absorption were the differential metabolic pathways in both noise exposure groups, and both were down-regulated relative to the control group. Conclusion Chronic noise exposure could alter structure of rat gut microbiota and may affect metabolic functions of multiple microbiota genes.

Molecular epidemiological investigation on Theileria in yellow cattle from Xiangxi Autonomous Prefecture of Hunan Province / 中国血吸虫病防治杂志

Objective To investigate the prevalence and genetic variation of Theileria in yellow cattle in Xiangxi Autonomous Prefecture of Hunan Province. Methods A total of 184 blood specimens were collected from Fenghuang, Huanyuan and Baojing counties of Xiangxi Autonomous Prefecture during the period from August 2018 through August 2019, and were detect using PCR assay with the specific 18S ribosomal rRNA (18S rRNA) gene targeting Theileria. The gene sequences of positive specimens were aligned with the sequences recorded in GenBank, and a phylogenetic tree was created with Plasmodium ovale 18S rRNA as an outgroup. Results A total of 143 blood samples were positive for Theileria, with a mean detection rate of 77.7%. Theileria was prevalent in the blood samples from yellow cattle in all three counties, with detection rates of 85.0% in Fenghuang County, 88.3% in Huayuan County and 61.0% in Baojing County, respectively. There was no significant difference in the detection rate of Theileria between Xiangxi yellow cattle and normal yellow cattle (77.2% vs. 79.5%; χ2 = 0.08, P > 0.05), while the detection of Theileria was significantly lower in the housed yellow cattle than in free-range cattle (68.9% vs. 89.7%; χ2 = 22.36, P < 0.01). A total of 18 PCR positive samples were randomly selected for sequencing and analysis, and all samples showed more than 99.0% homology with T. luwenshuni isolates. Phylogenetic analysis showed that the 18 positive samples were clustered into the same branch with T. luwenshuni, but were far away from other isolates. Conclusions The prevalence of Theileria is high in yellow cattle from Xiangxi Autonomous Prefecture of Hunan Province, and T. luwenshuni may be the dominant parasite species.

Knockout of ribosomal genes bS22 and bL37 increases the sensitivity of mycobacteria to antibiotics / 生物工程学报

In recent years, two novel proteins in the ribosomes of mycobacteria have been discovered by cryo-electron microscopy. The protein bS22 is located near the decoding center of the 30S subunit, and the protein bL37 is located near the peptidyl transferase center of the 50S subunit. Since these two proteins bind to conserved regions of the ribosome targeted by antibiotics, it is speculated that they might affect the binding of related drugs to these targets. Therefore, we knocked out the genes encoding these two proteins in wild-type Mycolicibacterium smegmatis mc2155 through homologous recombination, and then determined the growth curves of these mutants and their sensitivity to related antibiotics. The results showed that compared with the wild-type strain, the growth rate of these two mutants did not change significantly. However, mutant ΔbS22 showed increased sensitivity to capreomycin, kanamycin, amikacin, streptomycin, gentamicin, paromomycin, and hygromycin B, while mutant ΔbL37 showed increased sensitivity to linezolid. These changes in antibiotics sensitivity were restored by gene complementation. This study hints at the possibility of using ribosomal proteins bS22 and bL37 as targets for drug design.

Development and application of ribosomal engineering in actinomycetes / 生物工程学报

Ribosomal engineering is a technique that can improve the biosynthesis of secondary metabolites in the antibiotics-resistant mutants by attacking the bacterial RNA polymerase or ribosome units using the corresponding antibiotics. Ribosomal engineering can be used to discover and increase the production of valuable bioactive secondary metabolites from almost all actinomycetes strains regardless of their genetic accessibility. As a consequence, ribosomal engineering has been widely applied to genome mining and production optimization of secondary metabolites in actinomycetes. To date, more than a dozen of new molecules were discovered and production of approximately 30 secondary metabolites were enhanced using actinomycetes mutant strains generated by ribosomal engineering. This review summarized the mechanism, development, and protocol of ribosomal engineering, highlighting the application of ribosomal engineering in actinomycetes, with the aim to facilitate future development of ribosomal engineering and discovery of actinomycetes secondary metabolites.

Effect of exposure to chrysotile on ribosomal DNA copy number variation and DNA damage response / 预防医学

Objective@#To investigate the effect of chrysotile exposure on ribosomal DNA (rDNA) copy number and DNA damage response, so as to provide insights into the mechanism of asbestos-induced carcinogenesis. @*Methods@#Human pleural mesothelial MeT-5A cells were treated with chrysotile suspensions at doses of 1.25, 2.5 and 5 μg/cm2 (low-, medium-, high-dose group), while PBS served as controls. MeT-5A cells were harvested 6, 24, 48 and 72 h post-treatment, and the rDNA copy numbers and the BIRC5, HRAS, GINS4 and RRM2 mRNA expression were determined using a quantitative real-time PCR (qPCR) assay. The apoptosis of MeT-5A cells and DNA damage were detected using Muse cell analyzer. The rDNA copy numbers, DNA damage responses and BIRC5, HRAS, GINS4 and RRM2 mRNA expression were compared in MeT-5A cells treated with different doses of chrysotile suspensions.@*Results@#There were significant differences in 45S rDNA copy numbers among low-, medium-, high-dose groups and the control groups 6, 48 and 72 h post-treatment with chrysotile suspensions, and significantly lower 45S rDNA copy numbers were measured in low-, medium- and high-dose groups than in the control group 6 h post-treatment, while significantly higher 45S rDNA copy numbers were found in the high-dose group than in low- and medium-dose groups 48 and 72 h post-treatment (all P<0.05). There were significant differences in 5S rDNA copy numbers among low-, medium-, high-dose groups and the control groups 24, 48 and 72 h post-treatment with chrysotile suspensions, and significantly lower 5S rDNA copy numbers were measured in medium- and high-dose groups than in the control group 24 and 48 h post-treatment, while significantly lower 5S rDNA copy numbers were found in medium- and high-dose groups than in the low-dose group 24, 72 h post-treatment (all P<0.05). There were significant differences in the overall apoptotic rate of MeT-5A cells among groups at different time points, and the overall apoptotic rate of MeT-5A cells were significantly higher in medium- and high-dose groups than in the control group (all P<0.05), with late-stage apoptosis predominantly detected. There were significant differences in the rates of ATM activation and DNA double-strand break in MeT-5A cells among groups 72 h post-treatment, and higher rates of ATM activation and DNA double-strand break were measured in medium- and high-dose groups than in the control group (all P<0.05). In addition, there were significant differences in the relative mRNA expression of BIRC5, HRAS, GINS4 and RRM2 genes among groups 24 and 48 h post-treatment, and significantly lower BIRC5, HRAS, GINS4 and RRM2 mRNA expression was quantified in medium- and high-dose groups than in the control group (all P<0.05).@*Conclusion@#Exposure to chrysotile may induce rDNA copy number variations and altered expression of nucleolar proteins in human pleural mesothelial cells, which may be involved in the regulation of DNA damage responses.

Gene mining and efficient biosynthesis of a fungal peptidyl alkaloid / 中草药·英文版

Objective: Peptidyl alkaloids, a series of important natural products can be assembled by fungal non-ribosomal peptide synthetases (NRPSs). However, many of the NRPSs associated gene clusters are silent under laboratory conditions, and the traditional chemical separation yields are low. In this study, we aim to discovery and efficiently prepare fungal peptidyl alkaloids assembled by fungal NRPSs. Methods: Bioinformatics analysis of gene cluster containing NRPSs from the genome of Penicillium thymicola, and heterologous expression of the putative gene cluster in Aspergillus nidulans were performed. Isolation, structural identification, and biological evaluation of the product from heterologous expression were carried out. Results: The putative tri-modular NRPS AncA was heterologous-expressed in A. nidulans to give anacine (1) with high yield, which showed moderate and selective cytotoxic activity against A549 cell line. Conclusion: Heterologous expression in A. nidulans is an efficient strategy for mining fungal peptidyl alkaloids.