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Case report of neurofibromatosis type 1 combined with primary ciliary dyskinesia

《医学前沿（英文）》 2021年 第15卷 第6期   页码 933-937 doi: 10.1007/s11684-021-0860-7

摘要： Neurofibromatosis (NF) is a genetic disease in which the lungs are rarely involved. However, in NF cases with lung involvement, chest computed tomography may show bilateral basal reticulations, apical bullae, and cysts without bronchiectasis. Herein, we report a patient diagnosed with NF on the basis of the results of genetic testing who presented with early-onset wet cough and bronchiectasis. Considering the differential diagnosis of bronchiectasis combined with his early-onset wet cough, sinusitis, and sperm quality decline, we considered the possibility of primary ciliary dyskinesia (PCD). Further electron microscopy analysis of cilia and identification of homozygous mutations in the RSPH4A gene confirmed the diagnosis of PCD. Therefore, for patients with NF, when an image change exists in the lungs that does not correspond to NF, the possibility of other diagnoses, including PCD, must be considered.

关键词： primary ciliary dyskinesia     neurofibromatosis     bronchiectasis     transmission electron microscopy     genetic sequencing    

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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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Machine learning modeling identifies hypertrophic cardiomyopathy subtypes with genetic signature

《医学前沿（英文）》 2023年 第17卷 第4期   页码 768-780 doi: 10.1007/s11684-023-0982-1

摘要： Previous studies have revealed that patients with hypertrophic cardiomyopathy (HCM) exhibit differences in symptom severity and prognosis, indicating potential HCM subtypes among these patients. Here, 793 patients with HCM were recruited at an average follow-up of 32.78 ± 27.58 months to identify potential HCM subtypes by performing consensus clustering on the basis of their echocardiography features. Furthermore, we proposed a systematic method for illustrating the relationship between the phenotype and genotype of each HCM subtype by using machine learning modeling and interactome network detection techniques based on whole-exome sequencing data. Another independent cohort that consisted of 414 patients with HCM was recruited to replicate the findings. Consequently, two subtypes characterized by different clinical outcomes were identified in HCM. Patients with subtype 2 presented asymmetric septal hypertrophy associated with a stable course, while those with subtype 1 displayed left ventricular systolic dysfunction and aggressive progression. Machine learning modeling based on personal whole-exome data identified 46 genes with mutation burden that could accurately predict subtype propensities. Furthermore, the patients in another cohort predicted as subtype 1 by the 46-gene model presented increased left ventricular end-diastolic diameter and reduced left ventricular ejection fraction. By employing echocardiography and genetic screening for the 46 genes, HCM can be classified into two subtypes with distinct clinical outcomes.

关键词： machine learning methods     hypertrophic cardiomyopathy     genetic risk    

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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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Interplay between diet and genetic susceptibility in obesity and related traits

Tiange Wang, Min Xu, Yufang Bi, Guang Ning

《医学前沿（英文）》 2018年 第12卷 第6期   页码 601-607 doi: 10.1007/s11684-018-0648-6

摘要：

The incidence of obesity has been rapidly increasing, and this condition has become a major public health threat. A substantial shift in environmental factors and lifestyle, such as unhealthy diet, is among the major driving forces of the global obesity pandemic. Longitudinal studies and randomized intervention trials have shown that genetic susceptibility to obesity may interact with dietary factors in relation to the body mass index and risk of obesity. This review summarized data from recent longitudinal studies and intervention studies on variations and diets and discussed the challenges and future prospects related to this area and public health implications.

关键词： diet     genetic susceptibility     obesity     interaction    

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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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Optimal design of steel skeletal structures using the enhanced genetic algorithm methodology

Tugrul TALASLIOGLU

《结构与土木工程前沿（英文）》 2019年 第13卷 第4期   页码 863-889 doi: 10.1007/s11709-019-0523-9

摘要： This study concerns with the design optimization of steel skeletal structures thereby utilizing both a real-life specification provisions and ready steel profiles named hot-rolled I sections. For this purpose, the enhanced genetic algorithm methodology named EGAwMP is utilized as an optimization tool. The evolutionary search mechanism of EGAwMP is constituted on the basis of generational genetic algorithm (GGA). The exploration capacity of EGAwMP is improved in a way of dividing an entire population into sub-populations and using of a radial basis neural network for dynamically adjustment of EGAwMP’s genetic operator parameters. In order to improve the exploitation capability of EGAwMP, the proposed neural network implementation is also utilized for prediction of more accurate design variables associating with a new design strategy, design codes of which are based on the provisions of LRFD_AISC V3 specification. EGAwMP is applied to determine the real-life ready steel profiles for the optimal design of skeletal structures with 105, 200, 444, and 942 members. EGAwMP accomplishes to increase the quality degrees of optimum designations Furthermore, the importance of using the real-life steel profiles and design codes is also demonstrated. Consequently, EGAwMP is suggested as a design optimization tool for the real-life steel skeletal structures.

关键词： design optimization     genetic algorithm     multiple populations     neural network    

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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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Research progress on genetic improvement of

Chuanping YANG

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 391-401 doi: 10.15302/J-FASE-2017183

摘要： Suk. is one of the most widely distributed species of , the fourth most valuable timber species in north-eastern China and also a common tree species for landscaping. Over the past 30 years, effective progress has been made in genetic improvement and molecular breeding of . There has been extensive research on breeding techniques, including the collection and conservation of germplasm resources, provenance trials, intensive breeding techniques, crossbreeding and asexual propagation techniques, ploidy breeding and mutation breeding technology, genome sequencing, gene cloning, transgenic and molecular mechanisms of wood formation. A germplasm resource collection has been established by collecting different provenances, and full-sib and half-sib families. In addition, the geographic variation patterns of provenances have been revealed, and the provenance division and superior provenance selections made. flowering and seeding have been improved through intensive breeding techniques. Interspecific hybridization, intraspecific hybridization and parallel crosses were made using fine parents, and intensive seed orchards have been established. Systems of asexual propagation, including cuttings, grafting and tissue culture have been established. A tetraploid was successfully constructed and a triploid seed orchard established. The growth, wood property and resistance genes of have been cloned. An efficient transgenic system mediated by was established, and genes encoding insect resistance, drought resistance and salt tolerance, lignin synthesis, flowering, hormone transport and balance obtained. molecular markers were developed and the high density genetic map constructed. All this research has provided a model and data for the foundation of forest genetic improvement and applied research.

关键词： Betula platyphylla     genetic improvement     molecular breeding     seed orchard    

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标题 作者 时间 类型 操作

Case report of neurofibromatosis type 1 combined with primary ciliary dyskinesia

期刊论文

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

Machine learning modeling identifies hypertrophic cardiomyopathy subtypes with genetic signature

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

Interplay between diet and genetic susceptibility in obesity and related traits

Tiange Wang, Min Xu, Yufang Bi, Guang Ning

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

Optimal design of steel skeletal structures using the enhanced genetic algorithm methodology

Tugrul TALASLIOGLU

期刊论文

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

期刊论文

Research progress on genetic improvement of

Chuanping YANG

期刊论文