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Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

《环境科学与工程前沿（英文）》 2012年 第6卷 第1期   页码 82-97 doi: 10.1007/s11783-011-0306-6

摘要： Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant (WWTP). For the past 30 years, molecular biologic techniques explored for environmental microbial community (EMC) have spanned a broad range of approaches to facilitate the researches with the assistance of computer science: faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.

关键词： molecular biological technique     microbial community     denaturing gradient gel electrophoresis (DGGE)     terminal restriction fragment length polymorphism (T-RFLP)     environmental applications    

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Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

Hongyuan WANG, Xiaolu JIANG, Ya HE, Huashi GUAN

《环境科学与工程前沿（英文）》 2009年 第3卷 第2期   页码 194-199 doi: 10.1007/s11783-009-0018-3

摘要： Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, I and I, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from I and I both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With I as the sample, the pair wise -tests also revealed that variations were minor between each pair of marine environments, with ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites ( ranging from 0.282 to 0.349).

关键词： terminal restriction fragment length polymorphism (T-RFLP)     bacterial community structure     marine microbial diversity     HhaI     MspI    

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Diversity and vertical distributions of sediment bacteria in an urban river contaminated by nutrients and heavy metals

Xunan YANG, Shan HUANG, Qunhe WU, Renduo ZHANG, Guangli LIU

《环境科学与工程前沿（英文）》 2013年 第7卷 第6期   页码 851-859 doi: 10.1007/s11783-013-0569-1

摘要： The aim of this study was to investigate the benthic bacterial communities in different depths of an urban river sediment accumulated with high concentrations of nutrients and metals. Vertical distributions of bacterial operational taxonomic units (OTUs) and chemical parameters (nutrients: , , dissolved organic carbon, and acid volatile sulfur; metals: Fe, Zn, and Cu) were characterized in 30 cm sediment cores. The bacterial OTUs were measured using the terminal restriction fragment length polymorphism analysis. Biodiversity indexes and multivariate statistical analyses were used to characterize the spatial distributions of microbial diversity in response to the environmental parameters. Results showed that concentrations of the nutrients and metals in this river sediment were higher than those in similar studies. Furthermore, high microbial richness and diversity appeared in the sediment. The diversity did not vary obviously in the whole sediment profile. The change of the diversity indexes and the affiliations of the OTUs showed that the top layer had different bacterial community structure from deeper layers due to the hydrological disturbance and redox change in the surface sediment. The dominant bacterial OTUs ubiquitously existed in the deeper sediment layers (5–27 cm) corresponding to the distributions of the nutrients and metals. With much higher diversity than the dominant OTUs, the minor bacterial assemblages varied with depths, which might be affected by the sedimentation process and the environmental competition pressure.

关键词： heavy metals     nutrients     sediment profile     terminal restriction fragment length polymorphism    

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Response of bacterial communities to short-term pyrene exposure in red soil

Jingjing PENG, Hong LI, Jianqiang SU, Qiufang ZHANG, Junpeng RUI, Chao CAI

《环境科学与工程前沿（英文）》 2013年 第7卷 第4期   页码 559-567 doi: 10.1007/s11783-013-0501-8

摘要： Pyrene, a representative polycyclic aromatic hydrocarbon (PAH) compound produced mainly from incomplete combustion of fossil fuels, is hazardous to ecosystem health. However, long-term exposure studies did not detect any significant effects of pyrene on soil microorganism. In this study, short-term microcosm experiments were conducted to identify the immediate effect of pyrene on soil bacterial communities. A freshly-collected pristine red soil was spiked with pyrene at 0, 10, 100, 200, and 500 mg·kg and incubated for one day and seven days. The bacterial communities in the incubated soils were analyzed using 16S rRNA sequencing and terminal restriction fragment length polymorphism (T-RFLP) methods. The results revealed high bacterial diversity in both unspiked and pyrene-spiked soils. Only at the highest pyrene-spiking rate of 500 mg·kg , two minor bacteria groups of the identified 14 most abundant bacteria groups were completely suppressed. Short-term exposure to pyrene resulted in dominance of Proteobacteria in soil, followed by Acidobacteria, Firmutes, and Bacteroidetes. Our findings showed that bacterial community structure did respond to the presence of pyrene but recovered rapidly from the perturbation. The intensity of impact and the rate of recovery showed some pyrene dosage-dependent trends. Our results revealed that different levels of pyrene may affect the bacterial community structure by suppressing or selecting certain groups of bacteria. It was also found that the bacterial community was most susceptible to pyrene within one day of the chemical addition.

关键词： pyrene     bacterial communities     terminal restriction fragment length polymorphism     short-term exposure     rank-abundance plots    

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Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability

Xiaohui WANG, Xianghua WEN, Hengjing YAN, Kun DING, Man HU

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 92-98 doi: 10.1007/s11783-010-0254-6

摘要： To determine whether the functional stability of nitrification was correlated to a stable community structure of ammonia oxidizing bacteria (AOB) in a full-scale wastewater treatment plant, the AOB community dynamics in a wastewater treatment system was monitored over one year. The community dynamics were investigated using specific PCR followed by terminal restriction fragment length polymorphism (T-RFLP) analysis of the gene. The T-RFLP results indicated that during the period of nitrification stability, the AOB community structure in the full-scale wastewater treatment system was relatively stable, and the average change rate every 15 d of the system was 6.6%±5.8%. The phylogenetic analysis of the cloned gene showed clearly that the dominant AOB in the system was spp. The results of this study indicated that throughout the study period, the AOB community structure was relatively stable in the full-scale wastewater treatment system with functional stability of nitrification.

关键词： ammonia-oxidizing bacteria (AOB)     community dynamics     terminal restriction fragment length polymorphism (T-RFLP)     nitrification performance    

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Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

《医学前沿（英文）》 2007年 第1卷 第2期   页码 230-233 doi: 10.1007/s11684-007-0045-z

摘要： The relationship between the tenth exon C825T of G-protein β3 subunit (GNB) genetic polymorphism and hypertension in the Uygur population of China was investigated. A nested case-control study ( = 738) was carried out. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype GNB C825T polymorphism in 354 hypertensive (HT) and 384 normotensive (NT) Uygur subjects. The distributions of GNB C825T genotypes were CC (27.2%), TT (42.9%), and CT (29.9%) in the hypertensive subjects and CC (27.7%), TT (42.4%), CT (29.9%) in the normotensive subjects. There were no significant differences in the genotype distributions between the two groups ( = 0.0262 P = 0.99). The T allele was 51.4% in hypertensive subjects and 51.2% in normotensive subjects, which, between the two groups, was not a significant difference ( = 0.0016 P = 0.97). Further analysis shows that there is no association between C825T genotypes and age, body mass index (BMI), Glucose (GLU), Triglyceride (TG), Cholesterol (CHO), systolic blood pressure (SBP) and diastolic blood pressure (DBP). No evidence was found to suggest an association between GNB C825T polymorphism and hypertension in the Uygur population of China.

关键词： case-control     significant difference     reaction-restriction fragment     C825T polymorphism     evidence    

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Calorie restriction and its impact on gut microbial composition and global metabolism

Xiaojiao Zheng, Shouli Wang, Wei Jia

《医学前沿（英文）》 2018年 第12卷 第6期   页码 634-644 doi: 10.1007/s11684-018-0670-8

摘要：

Calorie restriction (CR) is a dietary regimen that reduces calorie intake without incurring malnutrition or a reduction in essential nutrients. It has long been recognized as a natural strategy for promoting health, extending longevity, and prevents the development of metabolic and age-related diseases. In the present review, we focus on the general effect of CR on gut microbiota composition and global metabolism. We also propose mechanisms for its beneficial effect. Results showed that probiotic and butyrate-producing microbes increased their relative abundance, whereas proinflammatory strains exhibited suppressed relative abundance following CR. Analyses of the gut microbial and host metabolisms revealed that most host microbial co-metabolites were changed due to CR. Examples of dramatic CR-induced changes in host metabolism included a decrease in the rate of lipid biosynthesis and an increase in the rates of fatty acid catabolism, β-oxidation, glycogenolysis, and gluconeogenesis. The observed phenotypes and the further verification of the direct link between gut microbiota and metabolome may benefit patients that are at risk for developing metabolic disease. Thus, improved gut microbiota composition and metabolome are potential biomarkers for determining the effectiveness of dietary interventions for age-related and metabolic diseases.

关键词： caloric restriction     gut microbiota     metabolome    

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CD176 single-chain variable antibody fragment inhibits the adhesion of cancer cells to endothelial cells

null

《医学前沿（英文）》 2016年 第10卷 第2期   页码 204-211 doi: 10.1007/s11684-016-0443-1

摘要：

CD176 (Thomsen-Friedenreich antigen) is a tumor-associated carbohydrate epitope (glycotope) functionally involved in blood spread and liver metastasis of cancer cells by mediating the adhesion of cancer cells to endothelial cells and hepatocytes, respectively. CD176 could be a promising target for antitumor immunotherapy. We applied B lymphocytes obtained from mice immunized with CD176 antigen and constructed a phage display library. A positive clone of CD176 single-chain variable antibody fragment (scFv) was successfully screened from this library. The CD176 scFv was expressed in Escherichia coli and purified. The purified scFv can bind to the natural CD176 expressed on the surface of cancer cells. Furthermore, the CD176 scFv inhibits the adhesion of CD176+ cancer cells to endothelial cells and hepatocytes. This CD176 scFv provides a basis for future development of recombinant CD176-specific antibodies that can be used in therapeutic application.

关键词： CD176     Thomsen-Friedenreich antigen     scFv     cancer     therapy     adhesion     metastasis    

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Key technological innovations in the construction of the main terminal of Beijing Daxing International

《工程管理前沿（英文）》 2022年 第9卷 第4期   页码 689-694 doi: 10.1007/s42524-022-0223-3

关键词： Beijing Daxing International Airport     main terminal     architectural technology innovation    

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Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

《医学前沿（英文）》 2022年 第16卷 第3期   页码 378-388 doi: 10.1007/s11684-021-0840-y

摘要： Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia     children     proteomics     Fc fragment of the IgG-binding protein     mechanistic target of rapamycin kinase inhibitor    

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Association of SIPA1 545 C>T polymorphism with survival in Chinese women with metastatic breast cancer

null

《医学前沿（英文）》 2013年 第7卷 第1期   页码 138-142 doi: 10.1007/s11684-013-0247-5

摘要：

It has been demonstrated that single nucleotide polymorphisms (SNPs) of SIPA1 (signal-induced proliferation associated gene 1) are associated with metastatic efficiency in both human and rodents. The purpose of this study was to determine whether SIPA1 545 C>T polymorphism was associated with overall survival in patients with metastatic breast cancer. In this study, SIPA1 545 C>T polymorphism was detected in 185 metastatic breast cancer patients using polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP). Survival curves for patients with SIPA1 545 C>T polymorphism was compared using the Kaplan-Meier method with log-rank tests. We found that SIPA1 545 C>T polymorphism was significantly associated with survival in 185 patients with metastatic breast cancer. Patients with SIPA1545 T/T genotype had a significantly worse overall survival (OS) than did patients with C/T or C/C genotype (50.0% vs. 62.9%, P = 0.042). Moreover, in multivariate analysis, as compared with the C/C or C/T genotype, the T/T genotype remained an independent unfavorable prognostic marker of OS in this cohort (hazard ratio [HR] = 2.16; 95% CI= 1.12–4.15; P = 0.022). Our findings indicate that metastatic breast cancer patients with SIPA1 545 T/T genotype have a poorer survival compared to patients with C/C or C/T genotype.

关键词： SIPA1     polymorphism     metastatic breast cancer     survival    

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The role of natriuretic peptide precursor A gene polymorphism in the development of coronary heart disease

Ripen NSENGA MD, Longxian CHENG PhD, Mei’an HE PhD, Tangchun WU PhD,

《医学前沿（英文）》 2009年 第3卷 第4期   页码 437-442 doi: 10.1007/s11684-009-0074-x

摘要： Natriuretic peptide precursor A (NPPA) is synthesized, stored, and released by atrial myocytes. Previous studies have shown that NPPA plays a significant role in the regulation of coronary circulation and in atherosclerosis. Rs5065 NPPA gene polymorphism leads to the translation of NPPA with two additional arginines and has been suggested to be associated with salt-sensitive hypertension. The purpose of the present study was to investigate the relationship between the rs5065 NPPA gene polymorphism and the risk of coronary heart disease (CHD) in Chinese Han population. We genotyped the single nucleotide polymorphism (SNP) rs5065 NPPA in the human NPPA gene in 1861 sex- and age-matched subjects, comprising of 904 CHD cases and 957 controls of Chinese Han population. Genotyping of SNP was performed with Taqman SNP allelic discrimination assays by means of an ABI 7900HT. Our study showed that the frequencies of rs5065 NPPA C allele in the case and the control groups were 0.012 and 0.005, respectively. There was significant difference in C allele frequency distribution between the two groups (OR=2.607, 95% CI: 1.197−5.678, =0.012). In the case group, there was significant difference between smokers and nonsmokers with subjects carrying C allele (=0.037), and no significant difference in gender, age, fasting total cholesterol (TC), triglycerides (TG), fasting plasma glucose (FPG), body mass index (BMI), and blood pressure (BP) between the cases and the controls (>0.05). Our results suggest that the C allele of rs5065 NPPA gene polymorphism may be associated with the risk of CHD.

关键词： natriuretic peptide precursor A     coronary heart disease     gene polymorphism     allelic discrimination     polymorphism     single nucleotide    

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Polymorphism of pharmaceutical molecules: perspectives on nucleation

Jie LU, Zhen LI, Xiaolin JIANG,

《化学科学与工程前沿（英文）》 2010年 第4卷 第1期   页码 37-44 doi: 10.1007/s11705-009-0294-2

摘要： Polymorphism is a widespread phenomenon observed in more than half of all drug substances. Various polymorphs frequently possess different physical, chemical, mechanical and thermal properties that can profoundly affect the bioavailability, stability and other performance characteristics of the drug. Accordingly, the elucidation of the relationship between the particular polymorph of a pharmaceutical molecule and its functional properties is crucial to select the most suitable polymorph of the pharmaceutical molecule for development into a drug product. This review briefly introduces recent advances in the discovery and control of the polymorphs of pharmaceutical molecules, in terms of the enhancement of the selective nucleation of a particular polymorph. In the light of this, some cases discussed in the following is to be considered controversial.

关键词： development     Polymorphism     elucidation     controversial     relationship    

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Effects of slip length and hydraulic diameter on hydraulic entrance length of microchannels with superhydrophobic

Wenchi GONG, Jun SHEN, Wei DAI, Zeng DENG, Xueqiang DONG, Maoqiong GONG

《能源前沿（英文）》 2020年 第14卷 第1期   页码 127-138 doi: 10.1007/s11708-020-0661-8

摘要： This paper investigated effects of slip length and hydraulic diameter on the hydraulic entrance length of laminar flow in superhydrophobic microchannels. Numerical investigations were performed for square microchannels with Re ranging between 0.1 and 1000. It is found that superhydrophobic microchannels have a longer hydraulic entrance length than that of conventional ones by nearly 26.62% at a low Re. The dimensionless hydraulic entrance length slightly increases with the increasing slip length at approximately Re<10, and does not vary with the hydraulic diameter. A new correlation to predict the entrance length in square microchannels with different slip lengths was developed, which has a satisfying predictive performance with a mean absolute relative deviation of 5.69%. The results not only ascertain the flow characteristics of superhydrophobic microchannels, but also suggest that super hydrophobic microchannels have more significant advantages for heat transfer enhancement at a low Re.

关键词： laminar flow     hydraulic entrance length     super hydrophobic surface     slip length     hydraulic diameter    

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Genetic association between the polymorphism of cytosolic PLA2 gene family and schizophrenia

Qiong YU PhD, Xiang-Fei MENG PhD, Jie-Ping SHI, Ya-Qin YU PhD,

《医学前沿（英文）》 2010年 第4卷 第1期   页码 101-105 doi: 10.1007/s11684-010-0017-6

摘要： Abnormal phospholipid metabolism in the brain plays an important role in neuropsychiatric diseases. Phospholipase A2 (PLA2) is a crucial element for normal neuro-physiological function. This study aims to investigate the genetic association between the polymorphism of cytosolic phospholipase A2 (cPLA2) family genes and schizophrenia among Han Chinese in the northern part of China. The polymerase chain reaction-based ligase detection reaction (PCR-LDR) was applied to detect the genotype ten single nucleotide polymorphisms (SNPs) of cPLA2 family genes among 201 pedigrees consisting of fathers, mothers and affected offsprings with schizophrenia. The pedigrees were collected from 2000 to 2006. Haplotype relative risk (HRR) test, transmission disequilibrium test (TDT), haplotype transmission analysis and multiple locus analysis were conducted to analyze the genotyping data. The genotypic frequency of cPLA2 gene did not deviate from Hardy-Weinberg equilibrium either in case or control group. HRR and TDT showed that the ten SNPs were not associated with schizophrenia (>0.05). Analysis for haplotype transmission showed that no haplotype system was associated with schizophrenia (>0.05). The conditioning on allele (COA) and conditioning on gene (COG) tests showed disease associations with the haplotype of rs2162886-rs1668589, rs891014-rs1668589 and rs2307279-rs7542180 (χ=6.913, =0.032; χ=8.393, =0.015; χ=8.447, =0.038). Our data suggest that many loci in the cPLA2 family genes may be associated with schizophrenia.

关键词： schizophrenia     cytosolic phospholipase A2     ligase detection reaction     polymorphism    

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标题 作者 时间 类型 操作

Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

期刊论文

Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

Hongyuan WANG, Xiaolu JIANG, Ya HE, Huashi GUAN

期刊论文

Diversity and vertical distributions of sediment bacteria in an urban river contaminated by nutrients and heavy metals

Xunan YANG, Shan HUANG, Qunhe WU, Renduo ZHANG, Guangli LIU

期刊论文

Response of bacterial communities to short-term pyrene exposure in red soil

Jingjing PENG, Hong LI, Jianqiang SU, Qiufang ZHANG, Junpeng RUI, Chao CAI

期刊论文

Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability

Xiaohui WANG, Xianghua WEN, Hengjing YAN, Kun DING, Man HU

期刊论文

Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

期刊论文

Calorie restriction and its impact on gut microbial composition and global metabolism

Xiaojiao Zheng, Shouli Wang, Wei Jia

期刊论文

CD176 single-chain variable antibody fragment inhibits the adhesion of cancer cells to endothelial cells

null

期刊论文

Key technological innovations in the construction of the main terminal of Beijing Daxing International

期刊论文

Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

期刊论文

Association of SIPA1 545 C>T polymorphism with survival in Chinese women with metastatic breast cancer

null

期刊论文

The role of natriuretic peptide precursor A gene polymorphism in the development of coronary heart disease

Ripen NSENGA MD, Longxian CHENG PhD, Mei’an HE PhD, Tangchun WU PhD,

期刊论文

Polymorphism of pharmaceutical molecules: perspectives on nucleation

Jie LU, Zhen LI, Xiaolin JIANG,

期刊论文

Effects of slip length and hydraulic diameter on hydraulic entrance length of microchannels with superhydrophobic

Wenchi GONG, Jun SHEN, Wei DAI, Zeng DENG, Xueqiang DONG, Maoqiong GONG

期刊论文

Genetic association between the polymorphism of cytosolic PLA2 gene family and schizophrenia

Qiong YU PhD, Xiang-Fei MENG PhD, Jie-Ping SHI, Ya-Qin YU PhD,

期刊论文