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1.
Sci Rep ; 10(1): 8329, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32433581

RESUMO

The gloomy outcome of liver cancer is mainly due to the high rates of metastasis and recurrence, even after curative resection for early stage liver cancer. Our study was conducted to find the animal model suitable for the study of liver cancer metastasis. In our study, two liver cancer cells were obtained from N-nitrosodiethylamine (DEN) and N-nitrosomorpholine (NMOR) induced rats, and they were cultivated, screened and cloning cultivated. Bionomics of cells was analyzed. The results show that 2 cells had different metastatic potentiality. They were named Wrh-f2 and Wrh-s2, and they have the characteristics of Hepatocellular carcinoma cells. The bionomics of 2 cells showed: (1) The chromosome karyotype analysis showed that the mode of Wrh-f2 was 80-83 and Wrh-s2 was 55-57; (2) AFP positive cytoplasmic staining was observed in Wrh-f2 and Wrh-s2. Cytokeratin (CK) 7 and CK8 positive staining was present in Wrh-f2. CK8 positive staining was present in Wrh-s2; (3) The numbers of Wrh-f2 and Wrh-s2 that passed through the Transwells were 98 ± 12 and 55 ± 15;(4) Wrh-f2 had the significant higher colony formation (78%) than Wrh-s2(8%) (P < 0.01). (5) The animal models generated solid tumours when 2 cells were inoculated to nude mouse and rat. And Wrh-f2 developed stable pulmonary metastasis. The established cell lines with different metastatic potential showed obvious advantages over liver cancer in mimicking the biological properties of malignant liver cancer tumors. It provided a suitable model for the mechanism of liver cancer metastasis in vivo and in vitro.

2.
Adv Ther ; 2020 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-32418143

RESUMO

INTRODUCTION: Dual antiplatelet therapy, aspirin and a P2Y12 inhibitor, is recommended to prevent thrombotic complications of acute coronary syndrome. Clopidogrel plus acetylsalicylic acid combination is the most commonly used dual antiplatelet therapy recommended by international guidelines and in Chinese clinical practice. Poor adherence to dual antiplatelet therapy or premature interruption of dual antiplatelet therapy is an important contributor to cardiovascular mortality and lethal cardiovascular events. Clopidogrel + acetylsalicylic acid fixed-dose combination enhances adherence to dual antiplatelet therapy. Herein, we aimed to evaluate bioequivalence of acetylsalicylic acid and clopidogrel in fixed-dose combination compared with simultaneous administration of their individual formulations in healthy Chinese subjects under fasting conditions. METHODS: This was a randomized, single-center, open-label, three-sequence, three-period, two-treatment, crossover study with a washout period of 10 days conducted in healthy Chinese volunteers. Subjects were randomized to receive Co-Plavix® (test formulation- fixed-dose combination of 100 mg acetylsalicylic acid and 75 mg clopidogrel) once and reference formulations (coadministration of individual formulations of 100 mg acetylsalicylic acid and 75 mg clopidogrel) twice during the study period. Pharmacokinetic parameters were analyzed for acetylsalicylic acid, its metabolite salicylic acid, clopidogrel, and its metabolite SR26334. As acetylsalicylic acid shows high intrasubject variability, the reference-scaled average bioequivalence (RSABE) approach was implemented for acetylsalicylic acid analysis, while bioequivalence of clopidogrel was assessed using the average bioequivalence method. Point ratios and confidence intervals (CIs) for AUC, AUClast, and Cmax for acetylsalicylic acid and clopidogrel were calculated. RESULTS: In total, 171 healthy subjects were enrolled in this study. Subjects were randomized and 170 subjects were treated with test or reference formulation; 164 subjects completed the study. Regarding acetylsalicylic acid exposure, as reference within-subject standard deviation (SDW) was at least 0.294 for acetylsalicylic acid Cmax, AUClast, and AUC, the RSABE analysis method was used to assess bioequivalence for all three parameters. The point estimates were within the 0.80-1.25 range (1.19, 1.09, and 1.04, respectively), and upper one-sided 95% CIs of scaled average bioequivalence metric were at most 0 (- 0.30, - 0.14, and - 0.10, respectively). Thus, bioequivalence was demonstrated with acetylsalicylic acid. Bioequivalence was also achieved with clopidogrel as the 90% CIs for geometric mean ratios of clopidogrel Cmax, AUClast, and AUC were within the bioequivalence range (0.80-1.25). CONCLUSION: Application of the reference-scaled average bioequivalence approach to evaluate bioequivalence of acetylsalicylic acid in Chinese male and female healthy volunteers under fasting conditions demonstrated bioequivalence of test and reference formulations. TRIAL REGISTRATION: CTR20181695.

3.
Sci Total Environ ; 731: 139242, 2020 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-32438084

RESUMO

Accurate quantification of the airborne antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is critically important to assess their health risks. However, the currently widely used high-volume filter sampler (HVFS) often causes the desiccation of the sample, interfering with subsequent bacterial culture. To overcome this limitation, a high-volume tandem liquid impinging sampler (HVTLIS) was developed and optimized to investigate the airborne bacterial microbiomes and antibiotic resistomes under different weathers in Tianjin, China. Results revealed that HVTLIS can capture significantly more diverse culturable bacteria, ARB, and ARGs than HVFS. Compared with fine and hazy weathers, dusty weather had significantly more diverse and abundant airborne bacteria, ARGs, and human opportunistic pathogens with the resistance to last-resort antibiotics of carbapenems and polymyxin B, implicating a potential human health threat of dusty bioaerosols. Intriguingly, we represented the first report of Saccharibacteria predominance in the bioaerosol, demonstrating that the potential advantage of HVTLIS in collecting airborne microbes.

4.
Sci Total Environ ; 726: 138288, 2020 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-32305750

RESUMO

With the increasing production and application, engineered nanomaterials (ENMs) are being discharged into the environment, where they can interact with co-existing contaminants, causing complicated joint toxicity to organisms that needs to be studied. The case study of ENMs-contaminant joint toxicity and the understanding of relative mechanisms are very insufficient, particularly the mechanisms of molecular interactions and governing processes. Herein, a typical ENMs, carbon nanotubes (CNTs, 0-60 mg/L), and a common antibiotic, ciprofloxacin (CIP, 0-900 mg/L), were selected as the analytes. Their joint toxicity to a model microbe Escherichia coli was specifically investigated via biochemical, transcriptomics, and metabolomics approaches. The result revealed an antagonistic effect on growth inhibition between CNTs and CIP. Mitigations in cell membrane disruption and oxidative stress were involved in the antagonistic action. CIP (48.8-244 mg/L) decreased the bioaccumulation of CNTs (7.2 mg/L) via reducing cell-surface hydrophobicity and hindering the bio-nano interaction, which could attenuate the toxicity of CNTs to bacteria. CNTs (7.2 and 14.4 mg/L) alleviated the disturbance of CIP (122 and 244 mg/L) to gene expressions especially related to nitrogen compound metabolism, oxidoreductase activity, and iron-sulfur protein maturation, probably through relieving the CIP-induced inhibition of DNA gyrase activity. Further, CNTs (7.2 and 14.4 mg/L) offset the impact of CIP (122 and 244 mg/L) on bacterial metabolome via the regulation of biosynthesis of unsaturated fatty acids and metabolisms of some amino acids and glutathione. The findings shed new light on the molecular mechanisms by which ENMs present joint effect on contaminant toxicity, and provide important information for risk assessments of CNTs and fluoroquinolones in the environment.

5.
Int J Mol Sci ; 21(8)2020 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-32326049

RESUMO

Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous progress in the understanding of cellular mechanisms, disease progression, and the relationship between genotype and phenotype. Though many popular bioinformatics methods in proteomics are derived from other omics studies, novel analysis strategies are required to deal with the unique characteristics of proteomics data. In this review, we discuss the current developments in the bioinformatics methods used in proteomics and how they facilitate the mechanistic understanding of biological processes. We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods that have been developed to perform comprehensive analysis in proteomics studies. We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks.

6.
Mol Plant Pathol ; 21(6): 834-853, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32301267

RESUMO

Simultaneous transcriptome analyses of both host plants and pathogens, and functional validation of the identified differentially expressed genes (DEGs) allow us to better understand the mechanisms underlying their interactions. Here, we analyse the mixed transcriptome derived from Botrytis cinerea (the causal agent of grey mould) infected tomato leaves at 24 hr after inoculation, a critical time point at which the pathogen has penetrated and developed in the leaf epidermis, whereas necrotic symptoms have not yet appeared. Our analyses identified a complex network of genes involved in the tomato-B. cinerea interaction. The expression of fungal transcripts encoding candidate effectors, enzymes for secondary metabolite biosynthesis, hormone and reactive oxygen species (ROS) production, and autophagy-related proteins was up-regulated, suggesting that these genes may be involved in the initial infection processes. Specifically, tomato genes involved in phytoalexin production, stress responses, ATP-binding cassette transporters, pathogenesis-related proteins, and WRKY DNA-binding transcription factors were up-regulated. We functionally investigated several B. cinerea DEGs via gene replacement and pathogenicity assays, and demonstrated that BcCGF1 was a novel virulence-associated factor that mediates fungal development and virulence via regulation of conidial germination, conidiation, infection structure formation, host penetration, and stress adaptation. The fungal infection-related development was controlled by BcCGF-mediated ROS production and exogenous cAMP restored the mutant infection-related development. Our findings provide new insights into the elucidation of the simultaneous tactics of pathogen attack and host defence. Our systematic elucidation of BcCGF1 in mediating fungal pathogenesis may open up new targets for fungal disease control.

7.
Environ Pollut ; 263(Pt A): 114376, 2020 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-32203849

RESUMO

With increasing release of nanoparticles (NPs) into the environment, soil organisms likely suffer from high dose and long duration of NPs contamination, while the effect of NPs across multiple generations in soil is rarely studied. Herein, we investigated how multigenerational exposure to different crystal forms (anatase, rutile, and their mixture) of TiO2 NPs (nTiO2) affected the survival, behavior, physiological and biochemical traits, and lifespan of nematodes (C. elegans) in a paddy soil. The soil property changed very slightly after being spiked with nTiO2, and the toxicities of three nTiO2 forms were largely comparable. The nTiO2 exposure adversely influenced the survival and locomotion of nematodes, and increased intracellular reactive oxygen species (ROS) generation. Interestingly, the toxic effect gradually attenuated and the lifespan of survived nematodes increased from the P0 to F3 generation, which was ascribed to the survivor selection and stimulatory effect. The lethal effect and the increased oxidative stress may continuously screen out offspring possessing stronger anti-stress capabilities. Moreover, key genes (daf-2, age-1, and skn-1) in the insulin/IGF-like signaling (IIS) pathway actively responded to the nTiO2 exposure, which further optimized the selective expression of downstream genes, increased the antioxidant enzyme activities and antioxidant contents, and thereby increased the stress resistance and longevity of survived nematodes across successive generations. Our findings highlight the crucial role of bio-responses in the progressively decreased toxicity of nTiO2, and add new knowledge on the long-term impact of soil nTiO2 contamination.

8.
Environ Sci Technol ; 54(7): 3900-3908, 2020 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-32208626

RESUMO

Landfill and incineration are the primary disposal practices for municipal solid waste (MSW) and have been considered as the critical reservoir of antibiotic resistance genes (ARGs). However, the possible transmission of ARGs from the municipal solid waste treatment system (MSWT system) to ambient air is still unclear. In this study, we collected inside and ambient air samples (PM10 and PM2.5) and potential source samples (leachate and solid waste) in the MSWT system. The results showed that the MSWT system contributed to the increased ambient airborne bacteria and associated ARGs. Forty-one antibiotic-resistant bacteria (ARB) harboring blaTEM-1 were isolated, and the full-length nucleotide sequences of the blaTEM-1 gene (harbored by identical bacillus) from air (downwind samples) were 100% identical with those in the leachate and solid waste, indicating that the MSWT system was the important source of disperse bacteria and associated ARGs in the ambient air. The daily intake (DI) burden level of ARGs via PM inhalation was comparable with that via ingestion of drinking water but lower than the DI level via ingestion of raw vegetables. The antibiotic-resistant opportunistic pathogen Bacillus cereus was isolated from air, with a relatively high DI level of Bacillus via inhalation (104-106 copies/day) in the MSWT system. This study highlights the key pathway of airborne ARGs to human exposure.

9.
Sci Rep ; 10(1): 4282, 2020 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-32152330

RESUMO

Cryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on all but the most pristine density maps (<2.5 Å resolution). Here we introduce a deep learning model that uses a set of cascaded convolutional neural networks (CNNs) to predict Cα atoms along a protein's backbone structure. The cascaded-CNN (C-CNN) is a novel deep learning architecture comprised of multiple CNNs, each predicting a specific aspect of a protein's structure. This model predicts secondary structure elements (SSEs), backbone structure, and Cα atoms, combining the results of each to produce a complete prediction map. The cascaded-CNN is a semantic segmentation image classifier and was trained using thousands of simulated density maps. This method is largely automatic and only requires a recommended threshold value for each protein density map. A specialized tabu-search path walking algorithm was used to produce an initial backbone trace with Cα placements. A helix-refinement algorithm made further improvements to the α-helix SSEs of the backbone trace. Finally, a novel quality assessment-based combinatorial algorithm was used to effectively map protein sequences onto Cα traces to obtain full-atom protein structures. This method was tested on 50 experimental maps between 2.6 Å and 4.4 Å resolution. It outperformed several state-of-the-art prediction methods including Rosetta de-novo, MAINMAST, and a Phenix based method by producing the most complete predicted protein structures, as measured by percentage of found Cα atoms. This method accurately predicted 88.9% (mean) of the Cα atoms within 3 Å of a protein's backbone structure surpassing the 66.8% mark achieved by the leading alternate method (Phenix based fully automatic method) on the same set of density maps. The C-CNN also achieved an average root-mean-square deviation (RMSD) of 1.24 Å on a set of 50 experimental density maps which was tested by the Phenix based fully automatic method. The source code and demo of this research has been published at https://github.com/DrDongSi/Ca-Backbone-Prediction.

10.
Biomed Res Int ; 2020: 8970340, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32190687

RESUMO

Breast cancer is the most common cancer observed in adult females, worldwide. Due to the heterogeneity and varied molecular subtypes of breast cancer, the molecular mechanisms underlying carcinogenesis in different subtypes of breast cancer are distinct. Recently, long noncoding RNAs (lncRNAs) have been shown to be oncogenic or play important roles in cancer suppression and are used as biomarkers for diagnosis and therapy. In this study, we identified 134 lncRNAs and 6,414 coding genes were differentially expressed in triple-negative (TN), human epidermal growth factor receptor 2- (HER2-) positive, luminal A-positive, and luminal B-positive breast cancer. Of these, 37 lncRNAs were found to be dysregulated in all four subtypes of breast cancers. Subtypes of breast cancer special modules and lncRNA-mRNA interaction networks were constructed through weighted gene coexpression network analysis (WGCNA). Survival analysis of another public datasets was used to verify the identified lncRNAs exhibiting potential indicative roles in TN prognosis. Results from heat map analysis of the identified lncRNAs revealed that five blocks were significantly displayed. High expressions of lncRNAs, including LINC00911, CSMD2-AS1, LINC01192, SNHG19, DSCAM-AS1, PCAT4, ACVR28-AS1, and CNTFR-AS1, and low expressions of THAP9-AS1, MALAT1, TUG1, CAHM, FAM2011, NNT-AS1, COX10-AS1, and RPARP-AS1 were associated with low survival possibility in TN breast cancers. This study provides novel lncRNAs as potential biomarkers for the therapeutic and prognostic classification of different breast cancer subtypes.

11.
J Genet Genomics ; 47(2): 93-103, 2020 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-32178980

RESUMO

Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of the maize long arm of chromosome 1 (1L) was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression. While previously available methods require a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms. The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms. Thus, a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible, in both hypoploids and hyperploids, compared with euploid controls. Previous studies observed the inverse trans effect, in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region. This response was also the major type of changes found globally in this study. Many genes varied in dosage showed proportional expression changes, though some were seen to be partly or fully dosage compensated. It was also found that the effects of aneuploidy were progressive, with more severe aneuploids producing effects of greater magnitude.

12.
Methods Mol Biol ; 2093: 161-171, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32088896

RESUMO

Dosage effects in plants are caused by changes in the copy number of chromosomes, segments of chromosomes, or multiples of individual genes. Genes often exhibit a dosage effect in which the amount of product is closely correlated with the number of copies present. However, when larger segments of chromosomes are varied, there are trans-acting effects across the genome that are unleashed that modulate gene expression in cascading effects. These appear to be mediated by the stoichiometric relationship of gene regulatory machineries. There are both positive and negative modulations of target gene expression, but the latter is the plurality effect. When this inverse effect is combined with a dosage effect, compensation for a gene can occur in which its expression is similar to the normal diploid regardless of the change in chromosomal dosage. In contrast, changing the whole genome in a polyploidy series has fewer relative effects as the stoichiometric relationship is not disrupted. Together, these observations suggest that the stoichiometry of gene regulation is important as a reflection of the mode of assembly of the individual subunits involved in the effective regulatory macromolecular complexes. This principle has implications for gene expression mechanisms, quantitative trait genetics, and the evolution of genes depending on the mode of duplication, either segmentally or via whole-genome duplication.

13.
Ecotoxicol Environ Saf ; 192: 110305, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32070782

RESUMO

Environmental xenoestrogens are the most accessible endocrine disrupting chemicals that have been reported with harmful effects on human health. Although the influences of xenoestrogens on the endocrine system have been extensively studied, it remains unclear whether these xenoestrogens can affect the digestive system in mammals. This study aimed to investigate the inhibitory effects and the underlying mechanism of six non-steroidal synthetic estrogens (including hexestrol, diethylstilbestrol, dienestrol, bisphenol A, bisphenol AF and bisphenol Z) on pancreatic lipase (PL), a key digestive enzyme responsible for lipid digestion and absorption in mammals. The results clearly demonstrated that hexestrol, diethylstilbestrol and dienestrol exhibited strong inhibition on PL, with the IC50 values of less than 1.0 µM. Further investigations elucidated that these three synthetic estrogens functioned as mixed inhibitors of PL, with the Ki values of less than 1 µM. Moreover, molecular dynamics simulations showed that diethylstilbestrol and its analogues might block the binding of substrate on PL via occupying the portal to the active site of PL and thereby inhibit the hydrolytic activity of this key enzyme. Collectively, these results suggested that diethylstilbestrol and its analogues were potent PL inhibitors, which might play a profound role in lipid absorption and weight gain in mammals.


Assuntos
Disruptores Endócrinos/toxicidade , Poluentes Ambientais/toxicidade , Inibidores Enzimáticos/toxicidade , Lipase/antagonistas & inibidores , Pâncreas/enzimologia , Animais , Domínio Catalítico , Estrogênios não Esteroides/toxicidade , Humanos , Lipase/química , Lipase/metabolismo , Xenobióticos
14.
J Virol ; 94(10)2020 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-32102888

RESUMO

Porcine reproductive and respiratory syndrome (PRRS) is a serious viral disease affecting the global swine industry. Its causative agent, PRRS virus (PRRSV), is an enveloped virus, and therefore membrane fusion between its envelope and host cell target membrane is critical for viral infection. Though much research has focused on PRRSV infection, the detailed mechanisms involved in its membrane fusion remain to be elucidated. In the present study, we performed confocal microscopy in combination with a constitutively active (CA) or dominant negative (DN) mutant, specific inhibitors, and small interfering RNAs (siRNAs), as well as multiple other approaches, to explore PRRSV membrane fusion. We first observed that PRRSV membrane fusion occurred in Rab11-recycling endosomes during early infection using labeled virions and subcellular markers. We further demonstrated that low pH and cathepsin E in Rab11-recycling endosomes are critical for PRRSV membrane fusion. Moreover, PRRSV glycoprotein 5 (GP5) is identified as being cleaved by cathepsin E during this process. Taken together, our findings provide in-depth information regarding PRRSV pathogenesis, which support a novel basis for the development of antiviral drugs and vaccines.IMPORTANCE PRRS, caused by PRRSV, is an economically critical factor in pig farming worldwide. As PRRSV is a lipid membrane-wrapped virus, merging of the PRRSV envelope with the host cell membrane is indispensable for viral infection. However, there is a lack of knowledge on its membrane fusion. Here, we first explored when and where PRRSV membrane fusion occurs. Furthermore, we determined which host cell factors were involved in the process. Importantly, PRRSV GP5 is shown to be cleaved by cathepsin E during membrane fusion. Our work not only provides information on PRRSV membrane fusion for the first time but also deepens our understanding of the molecular mechanisms of PRRSV infection, which provides a foundation for future applications in the prevention and control of PRRS.

15.
Bioinformatics ; 36(4): 1091-1098, 2020 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-31504181

RESUMO

MOTIVATION: Deep learning has become the dominant technology for protein contact prediction. However, the factors that affect the performance of deep learning in contact prediction have not been systematically investigated. RESULTS: We analyzed the results of our three deep learning-based contact prediction methods (MULTICOM-CLUSTER, MULTICOM-CONSTRUCT and MULTICOM-NOVEL) in the CASP13 experiment and identified several key factors [i.e. deep learning technique, multiple sequence alignment (MSA), distance distribution prediction and domain-based contact integration] that influenced the contact prediction accuracy. We compared our convolutional neural network (CNN)-based contact prediction methods with three coevolution-based methods on 75 CASP13 targets consisting of 108 domains. We demonstrated that the CNN-based multi-distance approach was able to leverage global coevolutionary coupling patterns comprised of multiple correlated contacts for more accurate contact prediction than the local coevolution-based methods, leading to a substantial increase of precision by 19.2 percentage points. We also tested different alignment methods and domain-based contact prediction with the deep learning contact predictors. The comparison of the three methods showed deeper sequence alignments and the integration of domain-based contact prediction with the full-length contact prediction improved the performance of contact prediction. Moreover, we demonstrated that the domain-based contact prediction based on a novel ab initio approach of parsing domains from MSAs alone without using known protein structures was a simple, fast approach to improve contact prediction. Finally, we showed that predicting the distribution of inter-residue distances in multiple distance intervals could capture more structural information and improve binary contact prediction. AVAILABILITY AND IMPLEMENTATION: https://github.com/multicom-toolbox/DNCON2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

16.
Sci Total Environ ; 705: 135674, 2020 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-31785918

RESUMO

Human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). Although dysbacteriosis after the antibiotic course has been previously observed in the patient guts, a comprehensive comparison of gut resistomes, microbiota and antibiotic residues in healthy individuals and patients undergoing antibiotic administration is little. Using high-throughput qPCR, 16S rRNA gene amplicon sequencing and UPLC-MS/MS, we systematically examined the antibiotic resistome, gut microbiota, and antibiotic residues in fecal samples from both Chinese healthy individuals and patients receiving antibiotic therapy. Compared with healthy individuals, patients' guts harbored lower diverse gut resistome and microbiota, but higher concentrations of antibiotics and ARGs. Antibiotic concentration in human guts was positively correlated with ARG total abundance, but was negatively related to the diversity of both ARGs and bacterial communities, which demonstrated that antibiotic administration could shape the antibiotic resistomes and bacterial communities in the patient guts. Gene cfxA was evaluated as a potential biomarker to distinguish the patients receiving antibiotic therapy from the healthy individuals in China since its wide detection and significant enrichment in the guts of the patients. The detection of some veterinary antibiotics in human guts illustrated the potential transmission of antibiotic from the external environment to human via the food chain. The obtained results could help to better understand the influence of antibiotic therapy in shaping antibiotic reistomes and bacterial communities in Chinese individuals.

17.
New Phytol ; 225(2): 930-947, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31529514

RESUMO

Histone 3 Lysine 4 (H3K4) demethylation is ubiquitous in organisms, however the roles of H3K4 demethylase JARID1(Jar1)/KDM5 in fungal development and pathogenesis remain largely unexplored. Here, we demonstrate that Jar1/KDM5 in Botrytis cinerea, the grey mould fungus, plays a crucial role in these processes. The BcJAR1 gene was deleted and its roles in fungal development and pathogenesis were investigated using approaches including genetics, molecular/cell biology, pathogenicity and transcriptomic profiling. BcJar1 regulates H3K4me3 and both H3K4me2 and H3K4me3 methylation levels during vegetative and pathogenic development, respectively. Loss of BcJAR1 impairs conidiation, appressorium formation and stress adaptation; abolishes infection cushion (IC) formation and virulence, but promotes sclerotium production in the ΔBcjar1 mutants. BcJar1 controls reactive oxygen species (ROS) production and proper assembly of Sep4, a core septin protein and virulence determinant, to initiate infection structure (IFS) formation and host penetration. Exogenous cAMP partially restored the mutant appressorium, but not IC, formation. BcJar1 orchestrates global expression of genes for ROS production, stress response, carbohydrate transmembrane transport, secondary metabolites, etc., which may be required for conidiation, IFS formation, host penetration and virulence of the pathogen. Our work systematically elucidates BcJar1 functions and provides novel insights into Jar1/KDM5-mediated H3K4 demethylation in regulating fungal development and pathogenesis.

18.
J Hazard Mater ; 383: 121129, 2020 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-31546217

RESUMO

Antibiotics ingested in the human gut may create selective pressure to change the composition of the gut microbiota, which could adversely effect the immune system of the host. However, the occurrence and distribution of antibiotics in the human gut remains unclear. A total population of 180 individuals, across three Chinses regions with different economic development levels, including children, adults, and elders, were sampled in 2017. A total of 19 representative antibiotics, including both clinical and veterinary antibiotics, were investigated in human faeces. While clinical use and prescriptions were the main exposure pathways for children, environmental media were the exposure pathway to adults. In addition, significant differences (P < 0.05) in antibiotic residues in human faeces were observed amongst various economic development levels, where human faeces from underdeveloped areas were mostly associated with higher levels of antibiotics. This study first to investigate the occurrence and distribution of typical antibiotics in the faeces of a Chinese population and thereby provide a reference for the intensive study of the effects and mechanisms of antibiotics on human gut microbiota.

19.
Int J Biol Macromol ; 145: 620-633, 2020 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-31883893

RESUMO

Herbal medicines are frequently used for the prevention and treatment of obesity and obesity-related disorders. Our preliminary screening showed that St. John's Wort (SJW) displayed potent inhibition on pancreatic lipase (PL), a key hydrolase responsible for lipid digestion and absorption in mammals. Herein, the inhibition potentials and inhibitory mechanism of SJW extract and its major constituents on PL were fully investigated by a set of in vitro and in silico studies. The results clearly demonstrated that the naphthodianthrones, biflavones and most of flavonoids in SJW displayed strong to moderate inhibition on PL. Among all tested natural compounds, two naphthodianthrones (hypericin and pseudohypericin) and one biflavone (I3,II8-biapigenin) isolated from SJW exhibited potent PL inhibition activity, with the IC50 values of <1 µM. Inhibition kinetics analyses showed that hypericin, pseudohypericin and I3,II8-biapigenin inhibited PL via a mixed manner, while molecular dynamics simulations revealed that three newly identified PL inhibitors could bind on PL at both the catalytic cavity and the interface between colipase and the C-terminal domain of PL. Collectively, our findings suggested that part of major constituents in SJW displayed potent PL inhibition activities, which could be used as lead compounds for the development of novel PL inhibitors.

20.
Proteins ; 88(6): 775-787, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31860156

RESUMO

Many proteins are composed of several domains that pack together into a complex tertiary structure. Multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for individual domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the orientations between domains. Small-angle X-ray scattering (SAXS) reports the structural properties of entire proteins and has the potential for guiding homology modeling of multidomain proteins. In this article, we describe a novel multidomain protein assembly modeling method, SAXSDom that integrates experimental knowledge from SAXS with probabilistic Input-Output Hidden Markov model to assemble the structures of individual domains together. Four SAXS-based scoring functions were developed and tested, and the method was evaluated on multidomain proteins from two public datasets. Incorporation of SAXS information improved the accuracy of domain assembly for 40 out of 46 critical assessment of protein structure prediction multidomain protein targets and 45 out of 73 multidomain protein targets from the ab initio domain assembly dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at https://github.com/jianlin-cheng/SAXSDom.

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