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A new metagenome binning method based on gene uniqueness
Yulin Kang,Cheng Wan,Sifen Lu,Zhehan Fu,Antony K. Chen,Zuhong Lu 한국유전학회 2020 Genes & Genomics Vol.42 No.8
Background The human gut microbiome contains millions of genes and many undetected bacteria species. Recovering bacterial genomes from large complex metagenomes remains highly challenging, and current binning methods show insufficient recall rates. Objective This study was performed to put forward a new metagenome binning method with promising recall rate and accuracy. Methods We found that more than 85% of the genes could be aligned to only one bacteria species by using strict BLAST parameters (identity > 90% and aligning length > 100 bp). This phenomenon was called “the gene uniqueness”, which indicated that the most bacterial genes could be exclusive to the species’ taxonomy. In our new metagenome binning method, we could cluster contigs based on gene similarity via a graph model. Any contig shared with same gene under Strict Blast parameters would be clustered into one bin. Results we obtained 1,131 bins and reconstructed the genomes of 12 unknown species for MetaHIT data Our method exhibited a more promising recall rate, faster running speed and lower time complexity than the current methods. Conclusions The present new metagenome binning method based on gene uniqueness had high recall rate and low error, which could be applied to assemble the bacterial genomes efficiently in complex metagenome.
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Haifei Yang,Guosheng Chen,Yulin Zhu,Yanyan Liu,Jun Cheng,Li-Fen Hu,Ying Ye,Jia-Bin Li 대한진단검사의학회 2013 Annals of Laboratory Medicine Vol.33 No.2
Background: Shigella is a frequent cause of bacterial dysentery in the developing world. Treatment with antibiotics is recommended for shigellosis, but the options are limited due to globally emerging resistance. This study was conducted to determine the frequency and pattern of antimicrobial susceptibility of Shigella in China. Methods: We studied the antimicrobial resistance profiles of 308 Shigella spp. strains (260S. flexneri, 40 S. sonnei, 5 S. boydii, and 3 S. dysenteriae) isolated from fecal samples of patients (age, from 3 months to 92 yr) presenting with diarrhea in different districts of Anhui,China. The antimicrobial resistance of strains was determined by the agar dilution method according to the CSLI guidelines. Results: The most common serogroup in the Shigella isolates was S. flexneri (n=260, 84.4%),followed by S. sonnei (n=40, 13.0%). The highest resistance rate was found for nalidixic acid (96.4%), followed by ampicillin (93.2%), tetracycline (90.9%), and trimethoprim/sulfamethoxazole (80.8%). Among the isolates tested, 280 (91.0%) were multidrug resistant (resistant to ≥2 agents). The most common resistance pattern was the combination of ampicillin,tetracycline, and trimethoprim/sulfamethoxazole (70.8%). Resistance to ampicillin and tetracycline were more common among S. flexneri than among S. sonnei isolates. Conclusions: S. flexneri is predominant in Anhui, China, and its higher antimicrobial resistance rate compared with that of S. sonnei is a cause for concern. Continuous monitoring of resistance patterns is necessary to control the spread of resistance in Shigella. The recommendations for antimicrobial treatment must be updated regularly based on surveillance results.
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Identification and expression analysis of ERECTA family genes in grape (Vitis vinifera L.)
Min Liu,Wanping Li,Zhuo Min,Xianghan Cheng,Yulin Fang 한국유전학회 2019 Genes & Genomics Vol.41 No.6
Background ERECTA family (ERf) genes are found in many dicots and monocots, and play important roles in plant developmental processes and stress responses. However, there is little known on ERf genes in grape (Vitis vinifera L.). Objectives The primary objective of this study was to identify the ERf genes in grape, and to analyze their expression profiles in different organs, during development, and in response to hormone treatments and abiotic/biotic stresses. Methods ERf protein sequences of dicots were aligned in the grape genome (V. vinifera cv. Pinot Noir, PN40024, 12X) with Blast server. The locus tags obtained were inputted in NCBI to retrieve corresponding nucleotide and protein accession numbers. The subcellular localization experiment was performed by the transient expression of VvERECTA-GFP and VvERL2-GFP in mesophyll protoplasts of Arabidopsis. The expression levels of ERf genes in grape leaves were detected by qRT-PCR after hormone treatments and abiotic/biotic stresses. Results We first identified the ERf genes in the grape genome, including VvERECTA and VvERL2. Their cDNA full-length sequences were obtained with the accession numbers MG601756 and MG601757. The result of subcellular localization indicated that the fusion proteins of VvERECTA and VvERL2 were localized in the plasma membrane. There were four conserved domains identified in VvERECTA and VvERL2, including a LRRNT-2, a LRR, a transmembrane and a protein kinase domain. The grape ERf genes expressed highly in young aboveground organs. As grape leaves or berries becoming mature, VvERECTA expressed in a declining trend. The transcript abundance of VvERL2 decreased during leaves development, but showed no significant differences during berries development. The hormone treatments of ABA, SA, MeJA and BR could induce the expression of VvERECTA and VvERL2. The treatments of heat, drought, downy and powdery mildew significantly increased the expression levels of the grape ERf genes. Conclusion The grape ERECTA gene family might play crucial roles in response to abiotic and biotic stresses. We provide the first description of the grape ERf genes and the most comprehensive analysis of their expressions in different biological processes.
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Effects of Ginsenosides Rg1 on Osteoblasts Cultured with Ti Particles
( Yu Lin ),( Yin Sheng Wu ),( Jia Cheng He ),( Yun Mei Huang ),( Yan Ping Lin ) 한국응용약물학회 2012 Biomolecules & Therapeutics(구 응용약물학회지) Vol.20 No.1
The aim of this study was to explore the role and effect of ginsenosides Rg1 on osteoblasts cultured with Ti particles. Osteoblasts from neonatal rats were cultured with particles and different doses of Rg1, the main active ingredient in ginsenosides Rg1. We found that the COX-2, PGE2, TNF-α, IL-1, and IL -6 concentrations in the medium of cells cultured with Ti particles significantly increased as compared with that of the control cells (p<0.05 or p<0.01). In addition, cells cultured with Ti particles alone exhibited the highest concentrations of these molecules. The PGE2, TNF-α, IL-1, and IL-6 levels in the medium of cells cultured with Rg1 were in between those of the control cells and the cells cultured with Ti particles alone. The IL-1ra level in the group cultured with Ti and medium-dose Rg1 was the highest followed by the cells cultured with Ti and high-dose Rg1 and those cultured with Ti and low-dose Rg1 (p<0.05). In conclusion, ginsenosides can reduce the levels of inflammatory cytokines produced by osteoblasts on induction with Ti particles and can prevent prosthesis loosening.
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