Zhejiang Institute of Microbiology

Hangzhou, China

Zhejiang Institute of Microbiology

Hangzhou, China

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Xu G.,Institute of Nuclear Agricultural science | Lu H.,Institute of Nuclear Agricultural science | Wang L.,Institute of Nuclear Agricultural science | Chen H.,Institute of Nuclear Agricultural science | And 5 more authors.
DNA Repair | Year: 2010

The bacterium Deinococcus radiodurans can survive extremely high exposure to ionizing radiation. The repair mechanisms involved in this extraordinary ability are still being investigated. ddrB is one gene that is highly up-regulated after irradiation, and it has been proposed to be involved in RecA-independent repair in D. radiodurans. Here we cloned, expressed and characterized ddrB in order to define its roles in the radioresistance of D. radiodurans. DdrB preferentially binds to single-stranded DNA. Moreover, it interacts directly with single-stranded binding protein of D. radiodurans DrSSB, and stimulates single-stranded DNA annealing even in the presence of DrSSB. The post-irradiation DNA repair kinetics of a ddrB/recA double mutant were compared to ddrB and recA single mutants by pulsed-field gel electrophoresis (PFGE). DNA fragment rejoining in the ddrB/recA double mutant is severely compromised, suggesting that DdrB-mediated single-stranded annealing plays a critical role in the RecA-independent DNA repair of D. radiodurans. © 2010 Elsevier B.V. All rights reserved.

Lu H.,Zhejiang University | Chen H.,Zhejiang Institute of Microbiology | Xu G.,Zhejiang University | Shah A.M.-U.-H.,Zhejiang University | Hua Y.,Zhejiang University
DNA Repair | Year: 2012

The extremely radioresistant bacterium. Deinococcus radiodurans possesses a rapid and efficient but poorly known DNA damage response mechanism that mobilizes one-third of its genome to survive lethal radiation damage. Deinococcal PprI serves as a general switch to regulate the expression of dozens of proteins from different pathways after radiation, including the DNA repair proteins RecA, PprA and SSB. However, the underlying mechanism is poorly understood. In this study, we analyzed the dynamic alteration in global transcriptional profiles in wildtype and. pprI mutant strains by combining microarrays and time-course sampling. We found that PprI up-regulated transcription of at least 210 genes after radiation, including 21 DNA repair and replication-related genes. We purified PprI and a helix-turn-helix (HTH) domain mutant and found that PprI specifically bound to the promoters of. recA and. pprA in vitro but did not bind nonspecific double-strand DNA. Chromatin immunoprecipitation (ChIP) assays confirmed that PprI specifically interacted with the promoter DNA of. recA and. pprA after radiation. Finally, we showed that a DNA-binding activity-deficient pprI mutant only partially restored resistance of the. pprI mutant strain to γ radiation, UV radiation, and mitomycin C. Taken together, these results indicate that DNA-binding activity is essential for PprI to program the DNA repair process and cellular survival of. D. radiodurans in response to radiation damage. © 2011 Elsevier B.V..

Song C.,Shaoxing Peoples Hospital | Chen H.,Zhejiang Institute of Microbiology | Wang T.,Zhejiang Institute of Microbiology | Zhang W.,Shaoxing Peoples Hospital | And 2 more authors.
Prostate | Year: 2015

BACKGROUND. Prostate cancer (PCa) is the second leading cause of tumor mortality among males in western societies. In China, the diagnostic and fatality rate of PCa is increasing yearly. METHODS. To characterize underlying molecular mechanisms, the microRNA (miRNA) profile of high-grade PCa, low-grade PCa, and benign prostate hyperplasia (BPH) were compared using high-throughput Illumina sequencing and quantitative real-time PCR (qRT-PCR) methods. Moreover, a variety of biological information softwares and databases were applied to predict the target genes of miRNA, molecular functions, and signal pathways. RESULTS. Eighteen miRNAs were differentially expressed (fold change ≥2, P < 0.05), of which thirteen were upregulated and five were downregulated by sequencing. This was confirmed by qRT-PCR in more clinical tissue samples. In the tumors, miRNAs (miR-125b-5p, miR-126-5p, miR-151a-5p, miR-221-3p, and miR-222-3p) were significantly upregulated with downregulation of miR-486-5p. In addition, 13 novel miRNAs were identified from three prostate tissue libraries, with 12 of them assayed in 21 human normal tissues by qRT-PCR. Multiple databases indicated target genes for these differentially expressed miRNAs. Function annotation of target genes indicated that most of them tend to target genes involved in signal transduction and cell communication, especially cancer-related PI3K-Akt and p53 signaling pathway. CONCLUSIONS. The small RNA transcriptomes obtained in this study uncovers six differentially expressed miRNAs and 12 novel miRNAs, and provides a better understanding of the expression and function of miRNAs in the development of PCa and reveals several miRNAs in PCa that may have biomarker and therapeutic potentials. © 2015 Wiley Periodicals, Inc.

Song C.,Shaoxing University | Huan C.,Zhejiang Institute of Microbiology | Xu C.,Shaoxing University | Ru G.,Shaoxing University
IUBMB Life | Year: 2014

Prostate cancer (PCa) is the second most commonly occurring malignant tumor in Europe and America. Normal and neoplastic growth of prostate gland are dependent on androgen receptor (AR) expression and function. PCa is driven by androgen and its receptor, and they continue to be the key drivers of castration-resistant prostate cancer (CRPC). CRPC is the terminal stage of PCa and seriously jeopardizes the patient's quality of life and lifespan. miRNAs are small noncoding RNAs, 18-25 nt in length that destabilize mRNA or repress protein synthesis by interacting with the 3′-untranslated regions (3'-UTR) of target mRNAs. miRNAs can regulate AR or be regulated by AR and then affect various signaling pathways related to cellular functions and tumor processes. In this review, we focus on the relationship between miRNAs and AR in PCa and elucidate their roles in the induction of malignant changes in PCa. © 2014 The Authors IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

Shen S.,Peking Union Medical College | Sun Q.,Peking Union Medical College | Liang Z.,Peking Union Medical College | Cui X.,Cedars Sinai Medical Center | And 4 more authors.
PLoS ONE | Year: 2014

Objective: Triple-negative breast cancer (TNBC) is an aggressive but heterogeneous subtype of breast cancer. This study aimed to identify and validate a prognostic signature for TNBC patients to improve prognostic capability and to guide individualized treatment. Methods: We retrospectively analyzed the prognostic performance of clinicopathological characteristics and miRNAs in a training set of 58 patients with invasive ductal TNBC diagnosed between 2002 and 2012. A prediction model was developed based on independent clinicopathological and miRNA covariates. The prognostic value of the model was further validated in a separate set of 41 TNBC patients diagnosed between 2007 and 2008. Results: Only lymph node status was marginally significantly associated with poor prognosis of TNBC (P = 0.054), whereas other clinicopathological factors, including age, tumor size, histological grade, lymphovascular invasion, P53 status, Ki-67 index, and type of surgery, were not. The expression levels of miR-27b-3p, miR-107, and miR-103a-3p were significantly elevated in the metastatic group compared with the disease-free group (P value: 0.008, 0.005, and 0.050, respectively). The Cox proportional hazards regression analysis revealed that lymph node status and miR-27b-3p were independent predictors of poor prognosis (P value: 0.012 and 0.027, respectively). A logistic regression model was developed based on these two independent covariates, and the prognostic value of the model was subsequently confirmed in a separate validation set. The two different risk groups, which were stratified according to the model, showed significant differences in the rates of distant metastasis and breast cancer-related death not only in the training set (P value: 0.001 and 0.040, respectively) but also in the validation set (P value: 0.013 and 0.012, respectively). Conclusion: This model based on miRNA and node status covariates may be used to stratify TNBC patients into different prognostic subgroups for potentially individualized therapy. © 2014 Shen et al.

PubMed | Zhejiang Institute of Microbiology and Zhejiang University
Type: | Journal: Scientific reports | Year: 2016

A new process consisting of a landfill bioreactor, partial-nitritation (PN) and the anammox process has been developed for landfill leachate treatment. In this study, the landfill bioreactor exhibited excellent performance in methane-rich biogas recovery, with a specific biogas yield of 0.47L gas g(-1) COD and methane percentages of 53-76%. PN was achieved in the aerobic reactor by high free ammonia (10183mg NH3 L(-1)) inhibition for nitrite-oxidizing bacteria, and the desired PN effluent composition (effluent nitrite: ammonium ratio of 1.10.3) was controlled by adjusting the alkalinity concentration per unit of ammonium oxidized to approximately 14.3mg CaCO3 mg(-1) N in the influent. The startup of anammox process was successfully achieved with a membrane bioreactor in 160d, and a maximum nitrogen removal rate of 216mg N L(-1) d(-1) was attained for real landfill leachate treatment. The quantitative polymerase chain reaction results confirmed that the cell-specific anammox activity was approximately 68-95fmol N cell(-1) d(-1), which finally led to the stable operation of the system.

PubMed | Zhejiang Institute of Microbiology and The Second Affiliated Hospital
Type: Journal Article | Journal: Oncotarget | Year: 2016

Many studies have demonstrated that some genes (e.g. APC, BRAF, KRAS, PTEN, TP53) are frequently mutated in cancer, however, underlying mechanism that contributes to their high mutation frequency remains unclear. Here we used Apriori algorithm to find the frequent mutational gene sets (FMGSs) from 4,904 tumors across 11 cancer types as part of the TCGA Pan-Cancer effort and then mined the hidden association rules (ARs) within these FMGSs. Intriguingly, we found that well-known cancer driver genes such as BRAF, KRAS, PTEN, and TP53 were often co-occurred with other driver genes and FMGSs size peaked at an itemset size of 3~4 genes. Besides, the number and constitution of FMGS and ARs differed greatly among different cancers and stages. In addition, FMGS and ARs were rare in endocrine-related cancers such as breast carcinoma, ovarian cystadenocarcinoma, and thyroid carcinoma, but abundant in cancers contact directly with external environments such as skin melanoma and stomach adenocarcinoma. Furthermore, we observed more rules in stage IV than in other stages, indicating that distant metastasis needed more sophisticated gene regulatory network.

PubMed | Zhejiang Institute of Microbiology and Zhejiang University
Type: Journal Article | Journal: PloS one | Year: 2016

The cyclic AMP receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. Here, we identify four homologs of the CRP family in Deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and DNA-damaging reagents. Transcriptional levels of CRP were increased under hydrogen peroxide (H2O2) treatment during the stationary growth phase, indicating that CRPs function in response to oxidative stress. By constructing all CRP single knockout mutants, we found that the dr0997 mutant showed the lowest tolerance toward H2O2, ultraviolet radiation, ionizing radiation, and mitomycin C, while the phenotypes of the dr2362, dr0834, and dr1646 mutants showed slight or no significant differences from those of the wild-type strain. Taking advantage of the conservation of the CRP-binding site in many bacteria, we found that transcription of 18 genes, including genes encoding chromosome-partitioning protein (dr0998), Lon proteases (dr0349 and dr1974), NADH-quinone oxidoreductase (dr1506), thiosulfate sulfurtransferase (dr2531), the DNA repair protein UvsE (dr1819), PprA (dra0346), and RecN (dr1447), are directly regulated by DR0997. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses showed that certain genes involved in anti-oxidative responses, DNA repair, and various cellular pathways are transcriptionally attenuated in the dr0997 mutant. Interestingly, DR0997 also regulate the transcriptional levels of all CRP genes in this bacterium. These data suggest that DR0997 contributes to the extreme stress resistance of D. radiodurans via its regulatory role in multiple cellular pathways, such as anti-oxidation and DNA repair pathways.

PubMed | Beijing Key Laboratory of Captive Wildlife Technologies, Northwestern University, Purdue University, Zhejiang Institute of Microbiology and 4 more.
Type: | Journal: Journal of microbiological methods | Year: 2016

Gut microbiota can provide great insight into host health, and studies of the gut microbiota in wildlife are becoming more common. However, the effects of field conditions on gut microbial samples are unknown. This study addresses the following questions: 1) How do environmental factors such as sunlight and insect infestations affect fecal microbial DNA? 2) How does fecal microbial DNA change over time after defecation? 3) How does storage method affect microbial DNA? Fresh fecal samples were collected, pooled, and homogenized from a family group of 6 spider monkeys, Ateles geoffroyi. Samples were then aliquoted and subjected to varying light conditions (shade, sun), insect infestations (limited or not limited by netting over the sample), and sample preservation methods (FTA - Fast Technology for Analysis of nucleic acid - cards, or freezing in liquid nitrogen then storing at -20C). Changes in the microbial communities under these conditions were assessed over 24h. Time and preservation method both effected fecal microbial community diversity and composition. The effect size of these variables was then assessed in relation to fecal microbial samples from 2 other primate species (Rhinopithecus bieti and R. brelichi) housed at different captive institutions. While the microbial community of each primate species was significantly different, the effects of time and preservation method still remained significant indicating that these effects are important considerations for fieldwork.

PubMed | Zhejiang Sci-Tech University, Zhejiang Economic & Trade Polytechnic and Zhejiang Institute of Microbiology
Type: | Journal: Microbiological research | Year: 2016

Kineococcus radiotolerans is a Gram-positive, radio-resistant bacterium isolated from a radioactive environment. The small noncoding RNAs (sRNAs) in bacteria are reported to play roles in the immediate response to stress and/or the recovery from stress. The analysis of K. radiotolerans transcriptome sequencing results can identify these sRNAs in a genome-wide detection, using RNA sequencing (RNA-seq) by the deep sequencing technique. In this study, the raw data of radiation-exposed samples (RS) and control samples (CS) were acquired separately from the sequencing platform. There were 217 common sRNA candidates in the two samples screened in the genome-wide scale by bioinformatics analysis. There were 43 differentially expressed sRNA candidates, including 28 up-regulated and 15 down-regulated ones. The down-regulated sRNAs were selected for the sRNA target prediction, of which 12 sRNAs that may modulate the genes related to the transcription regulation and DNA repair were considered as the candidates involved in the radio-resistance regulation system.

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