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The unique genomic landscape and prognostic mutational signature of Chinese clear cell renal cell carcinoma
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作者 Wenhao Xu Aihetaimujiang Anwaier +6 位作者 Wangrui Liu Xi Tian Jiaqi Su Guohai Shi yuanyuan qu Hailiang Zhang Dingwei Ye 《Journal of the National Cancer Center》 2022年第3期162-170,共9页
Background:The genomic background affects the occurrence and metastasis of cancers,including clear cell renal cell carcinoma(ccRCC).However,reports focusing on the prognostic mutational signature of Chinese ccRCC are ... Background:The genomic background affects the occurrence and metastasis of cancers,including clear cell renal cell carcinoma(ccRCC).However,reports focusing on the prognostic mutational signature of Chinese ccRCC are lacking.Methods:Overall,929 patients,including a training cohort with Chinese patients(n=201),a testing cohort with Caucasian patients(n=274),and a validation cohort(n=454)were analyzed for the genomic landscape of ccRCC.Then,machine-learning algorithms were used to identify and evaluate the genomic mutational signature(GMS)in ccRCC.Analyses for prognosis,immune microenvironment,association with independent clinicopathological features,and predictive responses for immune checkpoint therapies(ICTs)were performed.Results:The DNA variation data of 929 patients with ccRCC suggested markedly differential genomic mutational frequency of the most frequent genes,such as VHL,PBRM1,BAP1,SETD2,and KDM5C between the Chinese and Caucasian populations.PBRM1 showed significant co-occurrence with VHL and SETD2.We then successfully iden-tified a seven-gene mutational signature(GMS^(Mut))that included mutations in FBN1,SHPRH,CELSR1,COL6A6,DST,ABCA13,and BAP1.The GMS^(Mut)significantly predicted progressive progression(P<0.0001,HR=2.81)and poor prognosis(P<0.0001,HR=3.89)in the Chinese training cohort.Moreover,ccRCC patients with the GMS^(Mut)had poor survival rates in the testing cohort(P=0.020)and poor outcomes were predicted for those treated with ICTs in the validation cohort(P=0.036).Interestingly,a favorable clinical response to ICTs,ele-vated expression of immune checkpoints,and increased abundance of tumor-infiltrated lymphocytes,specifically CD8^(+)T cells,Tregs,and macrophages,were observed in the GMS^(Mut)cluster.Conclusions:This study described the pro-tumorigenic GMS^(Mut)cluster that improved the prognostic accuracy in Chinese patients with ccRCC.Our discovery of the novel independent prognostic signature highlights the relationship between tumor phenotype and genomic mutational characteristics of ccRCC. 展开更多
关键词 Clear cell renal cell carcinoma Genomic mutation Immune checkpoint therapies Prognosis Tumor microenvironment
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Tuning the Water Desalination Performance of Graphenic Layered Nanomaterials by Element Doping and Inter-Layer Spacing
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作者 Fuxin Wang Chao Zhang +4 位作者 Yanmei Yang yuanyuan qu Yong-Qiang Li Baoyuan Man Weifeng Li 《Chinese Physics Letters》 SCIE CAS CSCD 2020年第11期48-54,共7页
Through atomic molecular dynamics simulations,we investigate the performance of two graphenic materials,boron(BC3)and nitrogen doped graphene(C3 N),for seawater desalination and salt rejection,and take pristine graphe... Through atomic molecular dynamics simulations,we investigate the performance of two graphenic materials,boron(BC3)and nitrogen doped graphene(C3 N),for seawater desalination and salt rejection,and take pristine graphene as a control.Effects of inter-layer separation have been explored.When water is filtered along the transverse directions of three-layered nanomaterials,the optimal inter-layer separation is 0.7–0.9 nm,which results in high water permeability and salt obstruction capability.The water permeability is considerably higher than porous graphene filter,and is about two orders of magnitude higher than commercial reverse osmosis(RO)membrane.By changing the inter-layer spacing,the water permeability of three graphenic layered nanomaterials follows an order of C3 N≥GRA>BC3 under the same working conditions.Amongst three nanomaterials,BC3 is more sensitive to inter-layer separation which offers a possibility to control the water desalination speed by mechanically changing the membrane thickness.This is caused by the intrinsic charge transfer inside BC3 that results in periodic distributed water clusters around the layer surface.Our present results reveal the high potentiality of multi-layered graphenic materials for controlled water desalination.It is hopeful that the present work can guide design and fabrication of highly efficient and tunable desalination architectures. 展开更多
关键词 SEPARATION LAYER filtered
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Tumor microenvironment-based signatures distinguish intratumoral heterogeneity, prognosis, and immunogenomic features of clear cell renal cell carcinoma
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作者 Aihetaimujiang Anwaier Wenhao Xu +6 位作者 Wangrui Liu Shiyin Wei Xi Tian yuanyuan qu Jianfeng Yang Hailiang Zhang Dingwei Ye 《Journal of the National Cancer Center》 2023年第3期236-249,共14页
Background:The tumor microenvironment(TME)performs a crucial function in the tumorigenesis and response to immunotherapies of clear cell renal cell carcinoma(ccRCC).However,a lack of recognized pre-clinical TME-based ... Background:The tumor microenvironment(TME)performs a crucial function in the tumorigenesis and response to immunotherapies of clear cell renal cell carcinoma(ccRCC).However,a lack of recognized pre-clinical TME-based risk models poses a great challenge to investigating the risk factors correlated with prognosis and treatment responses for patients with ccRCC.Methods:Stromal and immune contexture were assessed to calculate the TMErisk score of a large sample of patients with ccRCC from public and real-world cohorts using machine-learning algorithms.Next,analyses for prognostic efficacy,correlations with clinicopathological features,functional enrichment,immune cell distribu-tions,DNA variations,immune response,and heterogeneity were performed and validated.Results:Clinical hub genes,including INAFM2,SRPX,DPYSL3,VSIG4,APLNR,FHL5,A2M,SLFN11,ADAMTS4,IFITM1,NOD2,CCR4,HLA-DQB2,and PLAUR,were identified and incorporated to develop the TMErisk signature.Patients in the TME high risk group(category)exhibited a considerably grim prognosis,and the TMErisk model was shown to independently function as a risk indicator for the overall survival(OS)of ccRCC patients.Expression levels of immune checkpoint genes were substantially increased in TME high risk group,while those of the human leukocyte antigen(HLA)family genes were prominently decreased.In addition,tumors in the TME high group showed significantly high infiltration levels of tumor-infiltrated lymphocytes,including M2 macrophages,CD8+T cells,B cells,and CD4+T cells.In heterogeneity analysis,more frequent somatic mutations,including pro-tumorigenic BAP1 and PBRM1,were observed in the TME high group.Importantly,19.3%of patients receiving immunotherapies in the TME high group achieved complete or partial response compared with those with immune tolerance in the TME low group,suggesting that TMErisk prominently differentiates prognosis and responses to immunotherapy for patients with ccRCC.Conclusions:We first established the TMErisk score of ccRCC using machine-learning algorithms based on a large-scale population.The TMErisk score can be utilized as an innovative independent prognosis predictive marker with high sensitivity and accuracy.Our discovery also predicted the efficacy of immunotherapy in ccRCC patients,indicating the intimate link between tumor immune microenvironment and intratumoral heterogeneity. 展开更多
关键词 Clear cell renal cell carcinoma Tumor microenvironment Risk group Immunogenomic feature
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Health consequences of early-onset compared with late-onset type 2 diabetes mellitus 被引量:1
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作者 Can Hou Huazhen Yang +6 位作者 yuanyuan qu Wenwen Chen Yu Zeng Yao Hu K.M.Venkat Narayan Huan Song Dong Li 《Precision Clinical Medicine》 2022年第2期100-107,共8页
Background:Although cumulating evidence has suggested that early-onset type 2 diabetes mellitus(T2DM)conferred on patients a broader tendency for complications beyond vascular ones,a comprehensive analysis of patterns... Background:Although cumulating evidence has suggested that early-onset type 2 diabetes mellitus(T2DM)conferred on patients a broader tendency for complications beyond vascular ones,a comprehensive analysis of patterns of complications across all relevant systems is currently lacking.Method:We prospectively studied 1777 early-onset(age at diagnosis≤45 years)and 35889 late-onset(>45 years)T2DM patients with matched unexposed individuals from the UK Biobank.Diabetes-specific and-related complications were examined using phenomewide association analysis,with patterns identified by comorbidity network analysis.We also evaluated the effect of lifestyle modifications and glycemic control on complication development.Results:The median follow-up times for early-onset and late-onset T2DM patients were 17.83 and 9.39 years,respectively.Compared to late-onset T2DM patients,patients with early-onset T2DM faced a significantly higher relative risk of developing subsequent complications that primarily affected sense organs[hazard ratio(HR)3.46 vs.1.72],the endocrine/metabolic system(HR 3.08 vs.2.01),and the neurological system(HR 2.70 vs.1.81).Despite large similarities in comorbidity patterns,a more complex and well-connected network was observed for early-onset T2DM.Furthermore,while patients with early-onset T2DM got fewer benefits(12.67%reduction in pooled HR for all studied complications)through fair glycemic control(median HbA1c≤53 mmol/mol)compared to late-onset T2DM patients(18.01%reduction),they seemed to benefit more from favorable lifestyles,including weight control,healthy diet,and adequate physical activity.Conclusions:Our analyses reveal that early-onset T2DM is an aggressive disease resulting in more complex complication networks than late-onset T2DM.Aggressive glucose-lowering intervention,complemented by lifestyle modifications,are feasible strategies for controlling early-onset T2DM-related complications. 展开更多
关键词 early-onset type 2 diabetes mellitus phenome-wide association analysis comorbidity network analysis late-onset type 2 diabetes mellitus
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Zwitterionic ring-opening polymerization of macrocyclic ethyleneoxy-substituted carbonate:Access to cyclic PEG-like polycarbonate
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作者 Jin Huang Jinwen Li +7 位作者 Rui Yan yuanyuan qu Fengzhen Guo Lei Shen Can-liang Ma Jie Sun Zhenjiang Li Kai Guo 《Chinese Chemical Letters》 SCIE CAS CSCD 2024年第3期282-286,共5页
The innovation in polymer design to rival conventional polyethylene glycol(PEG)is an important approach to achieving a more sustainable society.Here,cyclic PEG-like polycarbonates having high molecular weight(4.4–49.... The innovation in polymer design to rival conventional polyethylene glycol(PEG)is an important approach to achieving a more sustainable society.Here,cyclic PEG-like polycarbonates having high molecular weight(4.4–49.5 kg/mol)were enabled through zwitterionic ring-opening polymerization(ZROP)of macrocyclic carbonates(MCs)mediated by N-heterocyclic carbene(NHC).The thermodynamic behavior of polymerization depends on the ring size of monomers.During this process,the ZROP of 11-membered MC was driven by the change of enthalpy(ΔH_(p))which differed from the ZROP of 14-membered MC driven by the entropic change(ΔS_(p)).Cyclic polycarbonates depicted improved thermostability(T_(d5%)≥204℃)and higher glass transition temperatures(T_(g)>–40℃)in comparison to their linear analogues(T_(d5%)≤185℃,T_(g)~–50℃).In addition,the mechanism of ZROP of MC was addressed through computational study.A distinct mechanism of polymerization distinguishable from the well-known NHC-mediated ZROP of cyclic esters was revealed,where the zwitterion from nucleophilic addition to MC,i.e.tetrahedral intermediate,cannot be ring-opened probably due to the delocalization of negative charge on the carbonate group,but serves as an active center for the polymerization.In comparison to PEG,the attained polymer demonstrated comparable hydrophilic and biocompatible properties,as revealed by the results of contact angle and in vitro cytotoxicity studies,suggesting that cyclic polycarbonate hold the promise as the alternative of PEG. 展开更多
关键词 Zwitterionic ring-opening polymerization Cyclic polycarbonate Macrocycles Tetrahedral intermediate NHC carbene
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吲哚——种间及跨界信号分子新成员 被引量:7
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作者 曲媛媛 戴春晓 +1 位作者 张旭旺 马桥 《生物工程学报》 CAS CSCD 北大核心 2019年第11期2177-2188,共12页
吲哚作为一种典型的氮杂环芳烃化合物,在自然界中广泛存在。近年来,越来越多的研究表明吲哚具有一定的生物活性,是一种新型种间及跨界的信号分子。研究发现,吲哚不仅可以调节微生物的毒性、耐药性、生物膜形成以及群感效应等生理生化行... 吲哚作为一种典型的氮杂环芳烃化合物,在自然界中广泛存在。近年来,越来越多的研究表明吲哚具有一定的生物活性,是一种新型种间及跨界的信号分子。研究发现,吲哚不仅可以调节微生物的毒性、耐药性、生物膜形成以及群感效应等生理生化行为,调控植物生长发育和防御系统的形成过程,还能够影响动物的肠道炎症、细胞氧化压力及荷尔蒙分泌等生理健康。因此吲哚在微生物代谢、动物健康和植物生长等多个方面扮演了重要角色,具有重要的生物学及生态学双重意义。文中综述了吲哚从生物代谢到信号传递的研究历史,及其在微生物种内或种间以及微生物-动植物之间跨界的信号传导与调控作用的研究进展,旨在为揭示复杂环境中吲哚生物代谢及信号调控的生物学意义与生态学机制提供重要的理论指导。 展开更多
关键词 吲哚 氮杂环芳烃化合物 种间信号 跨界信号
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Community structure and elevational diversity patterns of soil Acidobacteria 被引量:22
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作者 Yuguang Zhang Jing Cong +5 位作者 Hui Lu Guangliang Li yuanyuan qu Xiujiang Su Jizhong Zhou Diqiang Li 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2014年第8期1717-1724,共8页
Acidobacteria is one of the most dominant and abundant phyla in soil,and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational d... Acidobacteria is one of the most dominant and abundant phyla in soil,and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest,deciduous broadleaved forest,coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition,elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16 S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites,and Subdivision 6 has the highest number of detectable operational taxonomic units(OTUs). A significant single peak distribution pattern(P 〈 0.05) between the OTU number and the elevation was observed. The Jaccard and Bray–Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased(P 〈 0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship(P 〈 0.01) with different soil enzymes. Therefore,soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH,soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. 展开更多
关键词 Elevational pattern Potential metabolic activity Acidobacterial subdivision Soil pH Driving factor Environmental change
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Nasal delivery of broadly neutralizing antibodies protects mice from lethal challenge with SARS-CoV-2 delta and omicron variants 被引量:6
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作者 Jia Lu Qiangling Yin +18 位作者 Rongjuan Pei Qiu Zhang yuanyuan qu Yongbing Pan Lina Sun Ding Gao Cuiqin Liang Jingwen Yang Wei Wu Jiandong Li Zongqiang Cui Zejun Wang Xinguo Li Dexin Li Shiwen Wang Kai Duan Wuxiang Guan Mifang Liang Xiaoming Yang 《Virologica Sinica》 SCIE CAS CSCD 2022年第2期238-247,共10页
Multiple new variants of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)have constantly emerged,as the delta and omicron variants,which have developed resistance to currently gained neutralizing antibodie... Multiple new variants of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)have constantly emerged,as the delta and omicron variants,which have developed resistance to currently gained neutralizing antibodies.This highlights a critical need to discover new therapeutic agents to overcome the variants mutations.Despite the availability of vaccines against coronavirus disease 2019(COVID-19),the use of broadly neutralizing antibodies has been considered as an alternative way for the prevention or treatment of SARS-Co V-2 variants infection.Here,we show that the nasal delivery of two previously characterized broadly neutralizing antibodies(F61 and H121)protected K18-h ACE2 mice against lethal challenge with SARS-Co V-2 variants.The broadly protective efficacy of the F61 or F61/F121 cocktail antibodies was evaluated by lethal challenge with the wild strain(WIV04)and multiple variants,including beta(B.1.351),delta(B.1.617.2),and omicron(B.1.1.529)at 200or 1000 TCID_(50),and the minimum antibody administration doses(5-1.25 mg/kg body weight)were also evaluated with delta and omicron challenge.Fully prophylactic protections were found in all challenged groups with both F61 and F61/H121 combination at the administration dose of 20 mg/kg body weight,and corresponding mice lung viral RNA showed negative,with almost all alveolar septa and cavities remaining normal.Furthermore,low-dose antibody treatment induced significant prophylactic protection against lethal challenge with delta and omicron variants,whereas the F61/H121 combination showed excellent results against omicron infection.Our findings indicated the potential use of broadly neutralizing monoclonal antibodies as prophylactic and therapeutic agent for protection of current emerged SARS-Co V-2 variants infection. 展开更多
关键词 Coronavirus disease 2019(COVID-2019) Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) Prophylactic protection Omicron variant K18-h ACE2
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Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants 被引量:6
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作者 yuanyuan qu Xueyan Zhang +17 位作者 Meiyu Wang Lina Sun Yongzhong Jiang Cheng Li Wei Wu Zhen Chen Qiangling Yin Xiaolin Jiang Yang Liu Chuan Li Jiandong Li Tianlei Ying Dexin Li Faxian Zhan Youchun Wang Wuxiang Guan Shiwen Wang Mifang Liang 《Virologica Sinica》 SCIE CAS CSCD 2021年第5期934-947,共14页
Severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)has precipitated multiple variants resistant to therapeutic antibodies.In this study,12 high-affinity antibodies were generated from convalescent donors in e... Severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)has precipitated multiple variants resistant to therapeutic antibodies.In this study,12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries.Of them,two RBD-binding antibodies(F61 and H121)showed high-affinity neutralization against SARS-Co V-2,whereas three S2-target antibodies failed to neutralize SARS-Co V-2.Following structure analysis,F61 identified a linear epitope located in residues G446–S494,which overlapped with angiotensinconverting enzyme 2(ACE2)binding sites,while H121 recognized a conformational epitope located on the side face of RBD,outside from ACE2 binding domain.Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-Co V-2.Importantly,these two antibodies also showed efficient neutralizing activities to the variants including B.1.1.7 and B.1.351,and reacted with mutations of N501 Y,E484 K,and L452 R,indicated that it may also neutralize the recent India endemic strain B.1.617.The unchanged binding activity of F61 and H121 to RBD with multiple mutations revealed a broad neutralizing activity against variants,which mitigated the risk of viral escape.Our findings revealed the therapeutic basis of cocktail antibodies against constantly emerging SARS-Co V-2 variants and provided promising candidate antibodies to clinical treatment of COVID-19 patients infected with broad SARS-Co V-2 variants. 展开更多
关键词 Antibody cocktail Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) Broad neutralization SARS-CoV-2 variants Angiotensin-converting enzyme 2(ACE2)
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Seasonal variations of soil bacterial communities in Suaeda wetland of Shuangtaizi River estuary, Northeast China 被引量:4
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作者 Xuwang Zhang Zhe Ji +4 位作者 Yating Shao Chaochen Guo Hao Zhou Lifen Liu yuanyuan qu 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2020年第11期45-53,共9页
Estuarine wetland is the transitional interface linking terrestrial with marine ecosystems,and wetland microbes are crucial to the biogeochemical cycles of nutrients.The soil samples were collected in four seasons(spr... Estuarine wetland is the transitional interface linking terrestrial with marine ecosystems,and wetland microbes are crucial to the biogeochemical cycles of nutrients.The soil samples were collected in four seasons(spring,S1;summer,S2;autumn,S3;and winter,S4)from Suaeda wetland of Shuangtaizi River estuary,Northeast China,and the variations of bacterial community were evaluated by high-throughput sequencing.Soil properties presented a significant seasonal change,including p H,carbon(C)and total nitrogen(TN),and the microbial diversity,richness and structure also differed with seasons.Canonical correspondence analysis(CCA)and Mantel tests implied that soil p H,C and TN were the key factors structuring the microbial community.Gillisia(belonging to Bacteroidetes)and Woeseia(affiliating with Gammaproteobacteria)were the two primary components in the rhizosphere soils,displaying opposite variations with seasons.Based on PICRUSt(Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)prediction,the xenobiotics biodegradation related genes exhibited a seasonal decline,while the majority of biomarker genes involved in nitrogen cycle showed an ascending trend.These findings could advance the understanding of rhizosphere microbiota of Suaeda in estuarine wetland. 展开更多
关键词 Microbial community Suaeda RHIZOSPHERE Nitrogen metabolism Seasonal variation
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SNX11 Identified as an Essential Host Factor for SFTS Virus Infection by CRISPR Knockout Screening 被引量:3
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作者 Tiezhu Liu Jiajia Li +10 位作者 Yang Liu yuanyuan qu Aqian Li Chuan Li quanfu Zhang Wei Wu Jiandong Li Yan Liu Dexin Li Shiwen Wang Mifang Liang 《Virologica Sinica》 SCIE CAS CSCD 2019年第5期508-520,共13页
Severe fever with thrombocytopenia syndrome virus(SFTSV)is a highly pathogenic tick-borne bunyavirus that causes lethal infectious disease and severe fever with thrombocytopenia syndrome(SFTS)in humans.The molecular m... Severe fever with thrombocytopenia syndrome virus(SFTSV)is a highly pathogenic tick-borne bunyavirus that causes lethal infectious disease and severe fever with thrombocytopenia syndrome(SFTS)in humans.The molecular mechanisms and host cellular factors required for SFTSV infection remain uncharacterized.Using a genome-wide CRISPR-based screening strategy,we identified a host cellular protein,sorting nexin 11(SNX11)which is involved in the intracellular endosomal trafficking pathway,as an essential cell factor for SFTSV infection.An SNX11-KO HeLa cell line was established,and SFTSV replication was significantly reduced.The glycoproteins of SFTSV were detected and remained in later endosomal compartments but were not detectable in the endoplasmic reticulum(ER)or Golgi apparatus.pH values in the endosomal compartments of the SNX11-KO cells increased compared with the pH of normal HeLa cells,and lysosomal-associated membrane protein 1(LAMP1)expression was significantly elevated in the SNX11-KO cells.Overall,these results indicated that penetration of SFTSV from the endolysosomes into the cytoplasm of host cells was blocked in the cells lacking SNX11.Our study for the first time provides insight into the important role of the SNX11 as an essential host factor in the intracellular trafficking and penetrating process of SFTSV infection via potential regulation of viral protein sorting,membrane fusion,and other endocytic machinery. 展开更多
关键词 CRISPR screen Severe fever with thrombocytopenia syndrome virus(SFTSV) Host factor Sorting nexin 11(SNX11)
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Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies 被引量:2
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作者 Qiao Ma Nan Meng +7 位作者 Jiancheng Su Yujie Li Jiazheng Gu Yidi Wang Jingwei Wang yuanyuan qu Zelong Zhao Yeqing Sun 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2023年第5期688-699,共12页
3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain... 3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic.In this study,an efficient aerobic skatole-degrading consortium was obtained.Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses.Bioinformatic analyses indicated that the skatole downstream degradation wasmainly via the catechol pathway,and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase.Genome binning and gene analyses indicated that Pseudomonas,Pseudoclavibacter,and Raineyella should cooperate with Rhodococcus for the skatole degradation process.Moreover,a pure strain Rhodococcus sp.DMU1 was successfully obtained which could utilize skatole as the sole carbon source.Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium.Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway.Collectively,our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader,and the degradation mainly proceeded via the catechol pathway. 展开更多
关键词 SKATOLE Biodegradation Bacterial consortium Metagenomics and METATRANSCRIPTOMICS RHODOCOCCUS
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Performance and microbial community analysis of bioaugmented activated sludge for nitrogen-containing organic pollutants removal 被引量:2
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作者 Xuwang Zhang Zhaojian Song +4 位作者 Qidong Tang Minghuo Wu Hao Zhou Lifen Liu yuanyuan qu 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2021年第3期373-381,共9页
Nitrogen-containing organic pollutants(quinoline,pyridine and indole)are widely distributed in coking wastewater,and bioaugmentation with specific microorganisms may enhance the removal of these recalcitrant pollutant... Nitrogen-containing organic pollutants(quinoline,pyridine and indole)are widely distributed in coking wastewater,and bioaugmentation with specific microorganisms may enhance the removal of these recalcitrant pollutants.The bioaugmented system(group B)was constructed through inoculation of two aromatics-degrading bacteria,Comamonas sp.Z1(quinoline degrader)and Acinetobacter sp.JW(indole degrader),into the activated sludge for treatment of quinoline,indole and pyridine,and the non-bioaugmented activated sludge was used as the control(group C).Both groups maintained high efficiencies(>94%)for removal of nitrogen-containing organic pollutants and chemical oxygen demand(COD)during the long-term operation,and group B was highly effective at the starting period and the operation stage fed with raw wastewater.High-throughput sequencing analysis indicated that nitrogen-containing organic pollutants could shape the microbial community structure,and communities of bioaugmented group B were clearly separated from those of non-bioaugmented group C as observed in non-metric multidimensional scaling(NMDS)plot.Although the inoculants did not remain their dominance in group B,bioaugmentation could induce the formation of effective microbial community,and the indigenous microbes might play the key role in removal of nitrogen-containing organic pollutants,including Dokdonella,Comamonas and Pseudoxanthomonas.Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(PICRUSt)analysis suggested that bioaugmentation could facilitate the enrichment of functional genes related to xenobiotics biodegradation and metabolism,probably leading to the improved performance in group B.This study indicated that bioaugmentation could promote the removal of nitrogen-containing organic pollutants,which should be an effective strategy for wastewater treatment. 展开更多
关键词 BIOAUGMENTATION Indigenous microbes Microbial community Nitrogen-containing organic pollutants Wastewater treatment
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Sex-specific association between coffee consumption and incident chronic kidney disease: a population-based analysis of 359,906 participants from the UK Biobank 被引量:2
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作者 Lei Tang Lina Yang +8 位作者 Wenwen Chen Chunyang Li Yu Zeng Huazhen Yang Yao Hu yuanyuan qu Huan Song Xiaoxi Zeng Ping Fu 《Chinese Medical Journal》 SCIE CAS CSCD 2022年第12期1414-1424,共11页
Background:The risk for chronic kidney disease(CKD)is influenced by genetic predisposition,sex,and lifestyle.Previous research indicates that coffee is a potentially protective factor in CKD.The current study aims to ... Background:The risk for chronic kidney disease(CKD)is influenced by genetic predisposition,sex,and lifestyle.Previous research indicates that coffee is a potentially protective factor in CKD.The current study aims to investigate whether sex disparity exists in the coffee–CKD association,and whether genetic risk of CKD or genetic polymorphisms of caffeine metabolism affect this association.Methods:A total of 359,906 participants from the UK Biobank who were enrolled between 2006 and 2010 were included in this prospective cohort study,which aimed to estimate the hazard ratios for coffee intake and incident CKD using a Cox proportional hazard model.Allele scores of CKD and caffeine metabolism were additionally adjusted for in a subsample with qualified genetic data(n=255,343).Analyses stratified by genetic predisposition,comorbidities,and sex hormones were performed.Tests based on Bayesian model averaging were conducted to ascertain the robustness of the results.Results:Coffee was inversely associated with CKD in a dose-dependent manner.The effects of coffee did not differ across different strata of genetic risk for CKD,but were more evident among slower genetically predicted caffeine metabolizers.Significant sex disparity was observed(P value for interaction=0.013),in that coffee drinking was only associated with the risk reduction of CKD in females.Subgroup analysis revealed that testosterone and sex hormone-binding globulin(SHBG),but not estradiol,modified the coffee–CKD association.Conclusions:In addition to the overall inverse coffee–CKD association that was observed in the general population,we could also establish that a sex disparity existed,in that females were more likely to experience the benefit of the association.Testosterone and SHBG may partly account for the sex disparity. 展开更多
关键词 COFFEE Chronic kidney diseases Genotype SEX
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Biodegradation of indole by a newly isolated Cupriavidus sp. SHE 被引量:6
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作者 yuanyuan qu E.Shen +7 位作者 Qiao Ma Zhaojing Zhang Ziyan Liu Wenli Shen Jingwei Wang Duanxing Li Huijie Li Jiti Zhou 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2015年第8期126-132,共7页
Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resou... Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resources are fairly limited. A bacterial strain designated as SHE was isolated and found to be an efficient indole degrader. It was identified as Cupriavidus sp. according to 16 SrRNA gene analysis. Strain SHE could utilize indole as the sole carbon source and almost completely degrade 100 mg/L of indole within 24 hr. It still harbored relatively high indole degradation capacity within p H 4–9 and temperature 25°C–35°C. Experiments also showed that some heavy metals such as Mn2+, Pb2+and Co2+did not pose severe inhibition on indole degradation. Based on high performance liquid chromatography–mass spectrum analysis, isatin was identified as a minor intermediate during the process of indole biodegradation. A major yellow product with m/z 265.0605(C15H8N2O3) was generated and accumulated, suggesting a novel indole conversion pathway existed. Genome analysis of strain SHE indicated that there existed a rich set of oxidoreductases, which might be the key reason for the efficient degradation of indole. The robust degradation ability of strain SHE makes it a promising candidate for the treatment of indole containing wastewater. 展开更多
关键词 Indole Biodegradation Cupriavidus sp. Metabolic pathway
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the National Natural Science Foundation of China(41877029,41961130383);Royal SocietyNewton Advanced Fellowship(NAF\R1\191017);Wuhan Science and Technology Bureau(2019020701011469). 被引量:1
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作者 Shuzhen Li Xiongfeng Du +10 位作者 Kai Feng Yueni Wu Qing He Zhujun Wang Yangying Liu Danrui Wang Xi Peng Zhaojing Zhang Arthur Escalas yuanyuan qu Ye Deng 《Soil Ecology Letters》 CAS 2022年第3期224-236,共13页
Due to the tremendous diversity of microbial organisms in topsoil,the estimation of saturated richness in a belowground ecosystem is still challenging.Here,we intensively surveyed the 16S rRNA gene in four 1 m2 sampli... Due to the tremendous diversity of microbial organisms in topsoil,the estimation of saturated richness in a belowground ecosystem is still challenging.Here,we intensively surveyed the 16S rRNA gene in four 1 m2 sampling quadrats in a typical grassland,with 141 biological or technical replicates generating over 11 million sequences per quadrat.Through these massive data sets and using both non-asymptotic extrapolation and non-parametric asymptotic approaches,results revealed that roughly 15919±193,27193±1076 and 56985±2347 prokaryotic species inhabited in 1 m2 topsoil,classifying by DADA2,UPARSE(97%cutoff)and Deblur,respectively,and suggested a huge difference among these clustering tools.Nearly 500000 sequences were required to catch 50%species in 1 m2,while any estimator based on 500000 sequences would still lose about a third of total richness.Insufficient sequencing depth will greatly underestimate both observed and estimated richness.At least~911000,~3461000,and~1878000 sequences were needed for DADA2,UPARSE,and Deblur,respectively,to catch 80%species in 1 m2 topsoil,and the numbers of sequences would be nearly twice to three times on this basis to cover 90%richness.In contrast,α-diversity indexes characterized by higher order of Hill numbers,including Shannon entropy and inverse Simpson index,reached saturation with fewer than 100000 sequences,suggesting sequencing depth could be varied greatly when focusing on exploring differentα-diversity characteristics of a microbial community.Our findings were fundamental for microbial studies that provided benchmarks for the extending surveys in large scales of terrestrial ecosystems. 展开更多
关键词 Grassland TOPSOIL PROKARYOTE Richness α-diversity Hill number
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Biosynthesis of gold nanoparticles by Trichoderma sp.WL-Go for azo dyes decolorization 被引量:3
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作者 yuanyuan qu Wenli Shen +5 位作者 Xiaofang Pei Fang Ma Shengnan You Shuzhen Li Jingwei Wang Jiti Zhou 《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2017年第6期79-86,共8页
Developing an eco-friendly approach for metallic nanoparticles synthesis is important in current nanotechnology research. In this study, green synthesis of gold nanoparticles (AuNPs) was carried out by a newly isola... Developing an eco-friendly approach for metallic nanoparticles synthesis is important in current nanotechnology research. In this study, green synthesis of gold nanoparticles (AuNPs) was carried out by a newly isolated strain Trichoderrna sp. WL-Go. UV-vis spectra of AuNPs showed a surface plasmon resonance peak at 550 nm, and transmission electron microscopy images revealed that the AuNPs were of varied shape with well dispersibility. The optimal conditions for AuNPs synthesis were HAuC14 1.0 mmol/L, biomass 0.5 g and pH 7-11. Moreover, the bio-AuNPs could efficiently catalyze the decolorization of various azo dyes. This research provided a new microbial resource candidate for green synthesis of AuNPs and demonstrated the potential application ofbio-AuNPs for azo dye decolorization. 展开更多
关键词 Gold nanoparticlesBiosynthesisTrichodermaAzo dyesDecolorization
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Multistep conversion of cresols by phenol hydroxylase and 2,3-dihydroxy-biphenyl 1,2-dioxygenase
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作者 Shengnan SHI Fang MA +3 位作者 Tieheng SUN Ang LI Jiti ZHOU yuanyuan qu 《Frontiers of Environmental Science & Engineering》 SCIE EI CAS CSCD 2014年第4期539-546,共8页
A mulfistep conversion system composed of phenol hydroxylase (PHrND) and 2,3-dihydroxy-biphenyl 1,2-dioxygenase (BphCLA_4) was used to synthesize methylcatechols and semialdehydes from o- and m-cresol for the firs... A mulfistep conversion system composed of phenol hydroxylase (PHrND) and 2,3-dihydroxy-biphenyl 1,2-dioxygenase (BphCLA_4) was used to synthesize methylcatechols and semialdehydes from o- and m-cresol for the first time. Docking studies displayed by PyMOL predicted that cresols and methylcatechols could be theoretically transformed by this multistep conversion system~ High performance liquid chromatography mass spectrometry (HPLC-MS) analysis also indicated that the products formed from multistep conversion were the corresponding 3-methylcatechol, 4-methylcatechol, 2- hydroxy-3-methyl-6-oxohexa-2,4-dienoic acid (2- hydroxy-3-methyl-ODA) and 2-hydroxy-5-methyl-6-oxo- hexa-2,4-dienoic acid (2-hydroxy-5-methyl-ODA). The optimal cell concentrations of the recombinant E. coli strain BL21 (DE3) expressing phenol hydroxylase (PHrND) and 2,3-dihydroxy-biphenyl 1,2-dioxygenase (BphCLA_4) and pH for the multistep conversion of o- and m-cresol were 4.0 (g-L-1 cell dry weight) and pH 8.0, respectively. For the first step conversion, the formation rate of 3- methylcatechol (0.29μmol·L-1·min-1·mg-1cell dry weight) from o-cresol was similarly with that ofmethylca- techols (0.28 μmol·L-1·min-1·mg-1 cell dry weight) from m-cresol by strain PHrND. For the second step conversion, strain BphCLA_4 showed higher formation rate (0.83 μmol·L-1·min-1·mg-1 cell dry weight) for 2-hydroxy-3-methyl- ODA and 2-hydroxy-5-methyl-ODA from m-cresol, which was 1.1-fold higher than that for 2-hydroxy-3-methyl- ODA (0.77 μmol·L-1·min-1·mg-1. mglcell dry weight) from ocresol. The present study suggested the potential application of the multistep conversion system for the production of chemical synthons and high-value products. 展开更多
关键词 multistep conversion CRESOLS phenol hydro-xylase 2 3-dihydroxybiphenyl 1 2-dioxygenase methyl-catechols
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Systematical strategies for wastewater treatment and the generated wastes and greenhouse gases in China
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作者 Jingbo GUO Fang MA +2 位作者 yuanyuan qu Ang LI Liang WANG 《Frontiers of Environmental Science & Engineering》 SCIE EI CAS CSCD 2012年第2期271-279,共9页
China now faces double challenges of water resources shortage and severe water pollution. To resolve Chinese water pollution problems and reduce its impacts on human health, economic growth and social develop- ment, t... China now faces double challenges of water resources shortage and severe water pollution. To resolve Chinese water pollution problems and reduce its impacts on human health, economic growth and social develop- ment, the situation of wastewater treatment was investi- gated. Excess sludge and greenhouse gases (GHGs) emitted during wastewater treatment were also surveyed. It is concluded that Chinese water pollution problems should be systematically resolved with inclusion of wastewater and the solid waste and GHGs generated during wastewater treatment. Strategies proposed for the wastewater treatment in China herein were also adequate for other countries, especially for the developing countries with similar economic conditions to China. 展开更多
关键词 wastewater treatment solid waste greenhousegases systematical strategies
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Model and simulation of four-wheeled robot based on Mecanum wheel
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作者 Jianwei Zhao Yuanshuang Liu +2 位作者 yuanyuan qu Feng Bian Yu Ban 《International Journal of Modeling, Simulation, and Scientific Computing》 EI 2017年第2期124-138,共15页
Based on Mecanum wheels and“Y”-shaped planetary wheels,we combine these two kinds of wheels’respective motion principle with their advantages to design a new type of four-wheeled robot:install the Mecanum wheels at... Based on Mecanum wheels and“Y”-shaped planetary wheels,we combine these two kinds of wheels’respective motion principle with their advantages to design a new type of four-wheeled robot:install the Mecanum wheels at the end of“Y”-shaped planetary wheel group.The wheel designed based on Mecanum wheels and“Y”-shaped planetary wheel can adapt to the complex terrain such as stairs,steps,and at the same time it can achieve the rotation of the whole body in a limited space.This paper studies the adaptability of the four-wheeled robot to the stairs,analyzing and calculating the parameters of the four-wheeled robot and the stairs. 展开更多
关键词 Four-wheeled robot Mecanum wheel “Y”-shaped planetary wheel obstacle avoidance.
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