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Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

《医学前沿（英文）》 2014年 第8卷 第1期   页码 42-57 doi: 10.1007/s11684-014-0303-9

摘要：

The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics     whole-exome sequencing     Mendelian disease     disease gene    

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Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

《医学前沿（英文）》 2022年 第16卷 第2期   页码 240-250 doi: 10.1007/s11684-021-0909-7

摘要： The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3′-terminal nucleotides via 2′-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2′-O-methylation at the RNA 3′-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3′-terminal 2′-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3′-terminal 2′-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3′-terminal 2′-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3′-terminal 2′-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

关键词： small RNAs     2′-O-methylation     sequencing     RT-qPCR    

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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要：

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA     whole-transcriptome sequencing     HCC     liver cancer    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿（英文）》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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Comparative study on microbial community in intermittently aerated sequencing batch reactors (SBR) and

Xiaolin Sheng, Rui Liu, Xiaoyan Song, Lujun Chen, Kawagishi Tomoki

《环境科学与工程前沿（英文）》 2017年 第11卷 第3期 doi: 10.1007/s11783-017-0929-3

摘要： A traditional sequencing batch reactor (SBR) and two intermittently aerated sequencing batch reactors (IASBRs) were parallelly operated for treating digested piggery wastewater. Their microbial communities were analyzed, and the nitrogen removal performance was compared during the long–term run. IASBRs demonstrated higher removal rates of total nitrogen (TN) and ammonium nitrogen (NH -N) than the SBR, and also demonstrated higher resistance against TN shock load. It was found that the more switch times between aerobic/anoxic in an IASBR, the higher the removal rates of TN and NH –N. All the reactors were predominated by , and , which were considered to be species of denitrifiers, ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), respectively. However, the abundance and diversity was of great difference. Compared with SBR, IASBRs achieved higher abundance of denitrification–related bacteria. IASBR 1 with four aerobic/anoxic switch times was detected with 25.63% of , higher than that in IASBR 2 with two aerobic/anoxic switch times (11.57% of ), and much higher than that in the SBR (only 6.19% of ). IASBR 2 had the highest percentage of AOB, while IASBR 1 had the lowest percentage. The denitrifiers abundance was significantly positive correlated with the TN removal rate. However, the NH –N removal rate showed no significant correlation with the AOB abundance, but might relate to the AOB activity which was influenced by the average free ammonium (FA) concentration. was the only NOB genus detectable in all reactors, and were less than 0.03%.

关键词： Digested piggery wastewater     Intermittent aeration     Microbial community     Partial nitrification–denitrification process     Sequencing batch reactor (SBR)    

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Simultaneous denitrifying phosphorus accumulation in a sequencing batch reactor

YUAN Linjiang, HAN Wei, WANG Lei, YANG Yongzhe, WANG Zhiying

《环境科学与工程前沿（英文）》 2007年 第1卷 第1期   页码 23-27 doi: 10.1007/s11783-007-0004-6

摘要： In order to achieve simultaneous nitrogen and phosphorus removal in the biological treatment process, denitrifying phosphorus accumulation (DNPA) and its affecting factors were studied in a sequencing batch reactor (SBR) with synthetic wastewater. The results showed that when acetate was used as the sole carbon resource in the influent, the sludge acclimatized under anaerobic/aerobic operation had good phosphorus removal ability. Denitrifying phosphorus accumulation was observed soon when fed with nitrate instead of aeration following the anaerobic stage, which is a vital premise to DNPA. If DNPA sludge is fed with nitrate prior to the anaerobic stage, the DNPA would weaken or even disappear. At the high concentration of nitrate fed in the anoxic stage, the longer anoxic time needed, the better the DNPA was. Induced DNPA did not disappear even though an aerobic stage followed the anoxic stage, but the shorter the aerobic stage lasted, the higher the proportions of phosphorus removal via DNPA to total removal.

关键词： SBR     synthetic wastewater     Induced DNPA     resource     removal ability    

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Improvement of nitrification efficiency by bioaugmentation in sequencing batch reactors at low temperature

Di CUI,Ang LI,Tian QIU,Rui CAI,Changlong PANG,Jihua WANG,Jixian YANG,Fang MA,Nanqi REN

《环境科学与工程前沿（英文）》 2014年 第8卷 第6期   页码 937-944 doi: 10.1007/s11783-014-0668-7

摘要： Bioaugmentation is an effective method of treating municipal wastewater with high ammonia concentration in sequencing batch reactors (SBRs) at low temperature (10°C). The cold-adapted ammonia- and nitrite- oxidizing bacteria were enriched and inoculated, respectively, in the bioaugmentation systems. In synthetic wastewater treatment systems, the average -N removal efficiency in the bioaugmented system (85%) was much higher than that in the unbioaugmented system. The effluent -N concentration of the bioaugmented system was stably below 8 mg·L after 20 d operation. In municipal wastewater systems with bioaugmentation, the effluent -N concentration was below 8 mg·L after 15 d operation. The average -N removal efficiency in unbioaugmentation system (about 82%) was lower compared with that in the bioaugmentation system. By inoculating the cold-adapted nitrite-oxidizing bacteria (NOB) into the SBRs after 10 d operation, the nitrite concentration decreased rapidly, reducing the -N accumulation effectively at low temperature. The functional microorganisms were identified by PCR-DGGE, including uncultured sp., uncultured sp., sp. and uncultured sp. The results suggested that the cold-adapted microbial agent of ammonia-oxidizing bacteria (AOB) and NOB could accelerate the start-up and promote achieving the stable operation of the low-temperature SBRs for nitrification.

关键词： nitrification     sequencing batch reactors (SBRs)     bioaugmentation     low temperature    

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Effects of La, Ce on nitrogen removal in sequencing batch reactor

Qing XIA , Rui LIANG , Yuning HONG , Lili DING , Hongqiang REN , Yuxiang MAO , Mingyu ZHAO ,

《环境科学与工程前沿（英文）》 2009年 第3卷 第3期   页码 369-374 doi: 10.1007/s11783-009-0036-1

摘要： Batch experiments were conducted to study the short-term biological effects of rare earth ions (La, Ce) and their mixture on the nitrogen removal in a sequencing batch reactor (SBR). The data showed that higher NH―N removal rate, total inorganic nitrogen removal efficiency, and denitrification efficiency were achieved at lower concentrations of rare earth elements (REEs) (<1mg/L). In the first hour of the aeration stage of SBR, the presence of REEs increased the total inorganic nitrogen removal efficiency and NH―N removal efficiency by 15.7% and 10%―15%, respectively. When the concentrations of REEs were higher than 1mg/L, the total inorganic nitrogen removal efficiency decreased, and nitrate was found to accumulate in the effluent. When the concentrations of REEs was up to 50.0mg/L, the total inorganic nitrogen removal efficiency was less than 30% of the control efficiency with a high level of nitrate. Lower concentrations of REEs were found to accelerate the nitrogen conversion and removal in SBR.

关键词： rare earth     La3+     Ce3+     inorganic nitrogen     nitrogen removal     sequencing batch reactor    

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METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

《农业科学与工程前沿（英文）》 2023年 第10卷 第3期   页码 403-423 doi: 10.15302/J-FASE-2022471

摘要：

● Methane production from fresh straw was 7.50% higher than dry straw.

关键词： fresh corn straw     high solid anaerobic digestion     metagenomics     microbial communities     thermophilic    

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Nitrifying and denitrifying bacteria in aerobic granules formed in sequencing batch airlift reactors

WANG Fang, YANG Fenglin, QI Aijiu

《环境科学与工程前沿（英文）》 2007年 第1卷 第2期   页码 184-189 doi: 10.1007/s11783-007-0032-2

摘要： The purpose of this study was to investigate nitrifying bacteria and denitrifying bacteria isolated from aerobic granules. Aerobic granules were formed in an internal-circulate sequencing batch airlift reactor (SBAR) and biodegradation of NH3--N was analyzed in the reactor. Bacteria were isolated and determined from aerobic granules using selected media. The growth properties and morphology of bacteria colonies were observed by controlling aerobic or anaerobic conditions in the culture medium. It was found that bacteria in aerobic granules were diverse and some of them were facultative aerobes. The diversity of bacteria in aerobic granules was a premise of simultaneous nitrification and denitrification.
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microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing

Yiwen LIN,Dan LI,Siyu ZENG,Miao HE

《环境科学与工程前沿（英文）》 2016年 第10卷 第3期   页码 539-547 doi: 10.1007/s11783-016-0830-5

摘要： This study employed 454-pyrosequencing to investigate microbial and pathogenic communities in two wastewater reclamation and distribution systems. A total of 11972 effective 16S rRNA sequences were acquired from these two reclamation systems, and then designated to relevant taxonomic ranks by using RDP classifier. The Chao index and Shannon diversity index showed that the diversities of microbial communities decreased along wastewater reclamation processes. was the most dominant phylum in reclaimed water after disinfection, which accounted for 83% and 88% in two systems, respectively. Human opportunistic pathogens, including , , and , were selected and enriched by disinfection processes. The total chlorine and nutrients (TOC, NH -N and NO -N) significantly affected the microbial and pathogenic communities during reclaimed water storage and distribution processes. Our results indicated that the disinfectant-resistant pathogens should be controlled in reclaimed water, since the increases in relative abundances of pathogenic bacteria after disinfection implicate the potential public health associated with reclaimed water.

关键词： wastewater reclamation systems     microbial community     pathogenic community     454-pyrosequencing    

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Mechanism studies on nitrogen removal when treating ammonium-rich leachate by sequencing batch biofilm

XU Zhengyong, YANG Zhaohui, ZENG Guangming, XIAO Yong, DENG Jiuhua

《环境科学与工程前沿（英文）》 2007年 第1卷 第1期   页码 43-48 doi: 10.1007/s11783-007-0008-2

摘要： The nitrogen removal mechanism was studied and analyzed when treating the ammonium-rich landfill leachate by a set of sequencing batch biofilm reactors (SBBRs), which was designed independently. At the liquid temperature of (32?0.4)?C, and after a 58-days domestication period and a 33-days stabilization period, the efficiency of ammonium removal in the SBBR went up to 95%. Highly frequent intermittent aeration suppressed the activity of nitratebacteria, and also eliminated the influence on the activity of anaerobic ammonium oxidation (ANAMMOX) bacteria and nitritebacteria. This influence was caused by the accumulation of nitrous acid and the undulation of pH. During the aeration stage, the concentration of dissolved oxygen was controlled at 1.2 1.4 mg/L. The nitritebacteria became dominant and nitrite accumulated gradually. During the anoxic stage, along with the concentration debasement of the dissolved oxygen, ANAMMOX bacteria became dominant; then, the nitrite that was accumulated in the aeration stage was wiped off with ammonium simultaneously.

关键词： undulation     33-days stabilization     concentration debasement     temperature     accumulation    

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N2O emission from a sequencing batch reactor for biological N and P removal from wastewater

Lei SHEN,Yuntao GUAN,Guangxue WU,Xinmin ZHAN

《环境科学与工程前沿（英文）》 2014年 第8卷 第5期   页码 776-783 doi: 10.1007/s11783-013-0586-0

摘要： Nitrous oxide (N O) is a greenhouse gas that can be released during biological nitrogen removal from wastewater. N O emission from a sequencing batch reactor (SBR) for biological nitrogen and phosphorus removal from wastewater was investigated, and the aims were to examine which process, nitrification or denitrification, would contribute more to N O emission and to study the effects of heterotrophic activities on N O emission during nitrification. The results showed that N O emission was mainly attributed to nitrification rather than to denitrification. N O emission during denitrification mainly occurred with stored organic carbon as the electron donor. During nitrification, N O emission was increased with increasing initial ammonium or nitrite concentrations. The ratio of N O emission to the removed ammonium nitrogen (N O-N/NH -N) was 2.5% in the SBR system with high heterotrophic activities, while this ratio was in the range from 0.14% to 1.06% in batch nitrification experiments with limited heterotrophic activities.

关键词： biological nutrient removal     denitrification     greenhouse gas     nitrification     nitrous oxide    

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基因组测序成本将再次降低

Robert Pollie

《工程（英文）》 2023年 第23卷 第4期   页码 3-6 doi: 10.1016/j.eng.2023.02.002

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标题 作者 时间 类型 操作

Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

期刊论文

Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

期刊论文

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

Comparative study on microbial community in intermittently aerated sequencing batch reactors (SBR) and

Xiaolin Sheng, Rui Liu, Xiaoyan Song, Lujun Chen, Kawagishi Tomoki

期刊论文

Simultaneous denitrifying phosphorus accumulation in a sequencing batch reactor

YUAN Linjiang, HAN Wei, WANG Lei, YANG Yongzhe, WANG Zhiying

期刊论文

Improvement of nitrification efficiency by bioaugmentation in sequencing batch reactors at low temperature

Di CUI,Ang LI,Tian QIU,Rui CAI,Changlong PANG,Jihua WANG,Jixian YANG,Fang MA,Nanqi REN

期刊论文

Effects of La, Ce on nitrogen removal in sequencing batch reactor

Qing XIA , Rui LIANG , Yuning HONG , Lili DING , Hongqiang REN , Yuxiang MAO , Mingyu ZHAO ,

期刊论文

METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

期刊论文

Nitrifying and denitrifying bacteria in aerobic granules formed in sequencing batch airlift reactors

WANG Fang, YANG Fenglin, QI Aijiu

期刊论文

microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing

Yiwen LIN,Dan LI,Siyu ZENG,Miao HE

期刊论文

Mechanism studies on nitrogen removal when treating ammonium-rich leachate by sequencing batch biofilm

XU Zhengyong, YANG Zhaohui, ZENG Guangming, XIAO Yong, DENG Jiuhua

期刊论文

N2O emission from a sequencing batch reactor for biological N and P removal from wastewater

Lei SHEN,Yuntao GUAN,Guangxue WU,Xinmin ZHAN

期刊论文

基因组测序成本将再次降低

Robert Pollie

期刊论文