Analysis of Microbial Communities Responsible for Enhanced Biological Phosphorus Rremoval in an Anaerobic/Aerobic SBR Rreactor using Stable Isotope Probing Approaches

Shipeng Lu,Minjeong Park(박민정),Che Ok Jeon(전체옥) 한국생물공학회 2005 한국생물공학회 학술대회 Vol.2005 No.10

Simplicispira limi sp. nov., isolated from activated sludge

Lu, Shipeng,Ryu, Seung Hyun,Chung, Bok Sil,Chung, Young Ryun,Park, Woojun,Jeon, Che Ok Microbiology Society 2007 International journal of systematic and evolutiona Vol.57 No.1

Analysis of Microbial Communities Using Culture-dependent and Culture-independent Approaches in an Anaerobic/Aerobic SBR Reactor

Shipeng Lu,박민정,노현수,이대성,박우준,전체옥 한국미생물학회 2006 The journal of microbiology Vol.44 No.2

Comparative analysis of microbial communities in a sequencing batch reactor whichperformed enhanced biological phosphorus removal (EBPR) was carried out using acultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocoland a modified PCR protocol with low PCR cycle was applied to the two clone librariesof the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and theresulting 424 clones were analyzed using restriction fragment length polymorphisms(RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that themodified PCR protocol decreased the incidence of distinct fragment patterns from about63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under themodified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles)can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained usingthe modified PCR method revealed that the clones were affiliated with at least 11 phyla orclasses of the domain Bacteria. However, the analyses of 327 colonies, which were groupedinto just 41 distinct types by RFLP analysis, showed that they could be classified into fivemajor bacterial lineages: α, β, γ- Proteobacteria, Actinobacteria, and the phylumBacteroidetes, which indicated that the microbial community yielded from the cultivationbasedmethod was still much simpler than that yielded from the PCR-based molecularmethod. In this study, the discrepancy observed between the communities obtained fromPCR-based and cultivation-based methods seems to result from low culturabilities ofbacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed toreduce this discrepancy.

Analysis of Microbial Communities Using Culture-dependent and Culture-independent Approaches in an Anaerobic/Aerobic SBR Reactor

Lu Shipeng,Park Min-Jeong,Ro Hyeon-Su,Lee Dae-Sung,Park Woo-Jun,Jeon Che-Ok The Microbiological Society of Korea 2006 The journal of microbiology Vol.44 No.2

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

Flavobacterium croceum sp. nov., isolated from activated sludge.

Park, Minjeong,Lu, Shipeng,Ryu, Seung Hyun,Chung, Bok Sil,Park, Woojun,Kim, Chang-Jin,Jeon, Che Ok Society for General Microbiology 2006 International journal of systematic and evolutiona Vol.56 No.10

<P>A Gram-negative, non-motile, rod-shaped bacterium, designated strain EMB47(T), was isolated from activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor. Growth was observed between 10 and 40 degrees C (optimum, 25-35 degrees C) and between pH 5.0 and 8.5 (optimum, pH 7.5-8.0). The predominant fatty acids of strain EMB47(T) were iso-C(16 : 0) 3-OH, iso-C(15 : 1) G, C(15 : 0), iso-C(15 : 0), iso-C(14 : 0) and iso-C(16 : 0) and it contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine as polar lipids. The G+C content of the genomic DNA was 40.8 mol% and the major quinone was MK-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB47(T) formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with respect to Flavobacterium species were below 94.7 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB47(T) represents a novel species within the genus Flavobacterium, for which the name Flavobacterium croceum sp. nov. is proposed. The type strain is EMB47(T) (=KCTC 12611(T)=DSM 17960(T)).</P>

Identification and functional gene analysis of a novel subgroup of uncultured gammaproteobacterial glycogen-accumulating organisms in an anaerobic-aerobic activated sludge

Qian Wang,Shipeng Lu,Che Ok Jeon 한국생물공학회 2007 한국생물공학회 학술대회 Vol.2007 No.10

Incomplete Cholesky Decomposition based Kernel Cross Modal Factor Analysis for Audiovisual Continuous Dimensional Emotion Recognition

( Xia Li ),( Guanming Lu ),( Jingjie Yan ),( Haibo Li ),( Zhengyan Zhang ),( Ning Sun ),( Shipeng Xie ) 한국인터넷정보학회 2019 KSII Transactions on Internet and Information Syst Vol.13 No.2

Recently, continuous dimensional emotion recognition from audiovisual clues has attracted increasing attention in both theory and in practice. The large amount of data involved in the recognition processing decreases the efficiency of most bimodal information fusion algorithms. A novel algorithm, namely the incomplete Cholesky decomposition based kernel cross factor analysis (ICDKCFA), is presented and employed for continuous dimensional audiovisual emotion recognition, in this paper. After the ICDKCFA feature transformation, two basic fusion strategies, namely feature-level fusion and decision-level fusion, are explored to combine the transformed visual and audio features for emotion recognition. Finally, extensive experiments are conducted to evaluate the ICDKCFA approach on the AVEC 2016 Multimodal Affect Recognition Sub-Challenge dataset. The experimental results show that the ICDKCFA method has a higher speed than the original kernel cross factor analysis with the comparable performance. Moreover, the ICDKCFA method achieves a better performance than other common information fusion methods, such as the Canonical correlation analysis, kernel canonical correlation analysis and cross-modal factor analysis based fusion methods.

Diabetes Promotes Myocardial Fibrosis via AMPK/EZH2/PPAR-γ Signaling Pathway

Shan-Shan Li,Lu Pan,Zhen-Ye Zhang,Meng-Dan Zhou,Xu-Fei Chen,Ling-Ling Qian,Min Dai,Juan Lu,Zhi-Ming Yu,Shipeng Dang,Ru-Xing Wang 대한당뇨병학회 2024 Diabetes and Metabolism Journal Vol.48 No.4

Background: Diabetes-induced cardiac fibrosis is one of the main mechanisms of diabetic cardiomyopathy. As a common histone methyltransferase, enhancer of zeste homolog 2 (EZH2) has been implicated in fibrosis progression in multiple organs. However, the mechanism of EZH2 in diabetic myocardial fibrosis has not been clarified.Methods: In the current study, rat and mouse diabetic model were established, the left ventricular function of rat and mouse were evaluated by echocardiography and the fibrosis of rat ventricle was evaluated by Masson staining. Primary rat ventricular fibroblasts were cultured and stimulated with high glucose (HG) <i>in vitro</i>. The expression of histone H3 lysine 27 (H3K27) trimethylation, EZH2, and myocardial fibrosis proteins were assayed.Results: In STZ-induced diabetic ventricular tissues and HG-induced primary ventricular fibroblasts in vitro, H3K27 trimethylation was increased and the phosphorylation of EZH2 was reduced. Inhibition of EZH2 with GSK126 suppressed the activation, differentiation, and migration of cardiac fibroblasts as well as the overexpression of the fibrotic proteins induced by HG. Mechanical study demonstrated that HG reduced phosphorylation of EZH2 on Thr311 by inactivating AMP-activated protein kinase (AMPK), which transcriptionally inhibited peroxisome proliferator-activated receptor γ (PPAR-γ) expression to promote the fibroblasts activation and differentiation.Conclusion: Our data revealed an AMPK/EZH2/PPAR-γ signal pathway is involved in HG-induced cardiac fibrosis.