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Data mining of microarray for differentially expressed genes in liver metastasis from gastric cancer

Ling XU MM, Feng WANG MM, Xuan-Fu XU MD, Wen-Hui MO BM, Rong WAN MD, Chuan-Yong GUO MD, Xing-Peng WANG MD,

《医学前沿（英文）》 2010年 第4卷 第2期   页码 247-253 doi: 10.1007/s11684-010-0027-4

摘要： Tumor metastasis is the leading cause of death for gastric cancer. Metastasis is the main reason for the failure of clinical treatment for gastric cancer. In order to find metastasis-related genes and abnormal signal transduction pathway of high-invasive gastric cancer, samples of gastric cancer with liver metastasis were collected for microarray detection; up-regulated or down-regulated genes in all three cases were simultaneously screened out. Subsequently, from the preliminary screened genes, molecular pathways possibly impacting liver metastasis from gastric cancer were investigated by the Gene Cluster with Literature Profiles (GenCLip) analysis software. Many biological effects including apoptosis have been validated. Functional analysis of differentially expressed genes revealed that a variety of biological pathways, such as blood circulation and gas exchange, vasodilation and vasoconstriction regulation, and immune defense, could be significantly activated. Besides, gene sequences, specific keywords or gene regulatory networks were further searched by GenCLiP. We conclude that data mining allows to quickly identify a series of special signal transduction pathways involving abnormally expressed genes.

关键词： gastric carcinoma     metastasis     signal transduction     gene chips    

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Identification of differentially expressed miRNAs associated with chronic kidney disease–mineral bone

null

《医学前沿（英文）》 2017年 第11卷 第3期   页码 378-385 doi: 10.1007/s11684-017-0541-8

摘要：

The purpose of this study is to characterize a meta-signature of differentially expressed mRNA in chronic kidney disease (CKD) to predict putative microRNA (miRNA) in CKD–mineral bone disorder (CKD–MBD) and confirm the changes in these genes and miRNA expression under uremic conditions by using a cell culture system. PubMed searches using MeSH terms and keywords related to CKD, uremia, and mRNA arrays were conducted. Through a computational analysis, a meta-signature that characterizes the significant intersection of differentially expressed mRNA and expected miRNAs associated with CKD–MBD was determined. Additionally, changes in gene and miRNA expressions under uremic conditions were confirmed with human Saos-2 osteoblast-like cells. A statistically significant mRNA meta-signature of upregulated and downregulated mRNA levels was identified. Furthermore, miRNA expression profiles were inferred, and computational analyses were performed with the imputed microRNA regulation based on weighted ranked expression and putative microRNA targets (IMRE) method to identify miRNAs associated with CKD occurrence. TLR4 and miR-146b levels were significantly associated with CKD–MBD. TLR4 levels were significantly downregulated, whereas pri-miR-146b and miR-146b were upregulated in the presence of uremic toxins in human Saos-2 osteoblast-like cells. Differentially expressed miRNAs associated with CKD-MBD were identified through a computational analysis, and changes in gene and miRNA expressions were confirmed with an in vitro cell culture system.

关键词： chronic kidney disease     microRNA     mineral bone disorder     uremia    

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Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

《农业科学与工程前沿（英文）》 2014年 第1卷 第3期   页码 214-222 doi: 10.15302/J-FASE-2014024

摘要： With the increase in consumer demand, wheat grain quality improvement has become a focus in China and worldwide. Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. In this study, two cDNA libraries from the developing grain and leaf-stem components of bread wheat cultivar, Nongda211, were sequenced using Roche/454 technology. There were 1061274 and 1516564 clean reads generated from grain and leaf-stem, respectively. A total of 61393 high-quality unigenes were obtained with an average length of 1456 bp after assembly. The analysis of the 61393 unigenes involved in the biological processes of the grain showed that there were 7355 differentially expressed genes upregulated in the grain library. Gene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that many transcription products and transcription factors associated with carbohydrate and protein metabolism were abundantly expressed in the grain. These results contribute to excavate genes associated with wheat quality and further study how they interact.

关键词： transcriptome analysis     wheat grain     differentially expressed genes     enrichment analysis    

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iTRAQ-based quantitative proteomic analysis on differentially expressed proteins of rat mandibular condylar

null

《医学前沿（英文）》 2017年 第11卷 第1期   页码 97-109 doi: 10.1007/s11684-016-0496-1

摘要：

As muscle activity during growth is considerably important for mandible quality and morphology, reducing dietary loading directly influences the development and metabolic activity of mandibular condylar cartilage (MCC). However, an overall investigation of changes in the protein composition of MCC has not been fully described in literature. To study the protein expression and putative signaling in vivo, we evaluated the structural changes of MCC and differentially expressed proteins induced by reducing functional loading in rat MCC at developmental stages. Isobaric tag for relative and absolute quantitation-based 2D nano-high performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization time-of-flight/ time-of-flight (MALDI-TOF/TOF) technologies were used. Global protein profiling, KEGG and PANTHER pathways, and functional categories were analyzed. Consequently, histological and tartrate-resistant acid phosphatase staining indicated the altered histological structure of condylar cartilage and increased bone remodeling activity in hard-diet group. A total of 805 differentially expressed proteins were then identified. GO analysis revealed a significant number of proteins involved in the metabolic process, cellular process, biological regulation, localization, developmental process, and response to stimulus. KEGG pathway analysis also suggested that these proteins participated in various signaling pathways, including calcium signaling pathway, gap junction, ErbB signaling pathway, and mitogen-activated protein kinase signaling pathway. Collagen types I and II were further validated by immunohistochemical staining and Western blot analysis. Taken together, the present study provides an insight into the molecular mechanism of regulating condylar growth and remodeling induced by reducing dietary loading at the protein level.

关键词： condylar cartilage     mechanical loading     proteomic analysis     iTRAQ     bioinformatics analysis    

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Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 308-320 doi: 10.15302/J-FASE-2016113

摘要： A full-length cDNA library from leaf and root tissues of cassava ( ) Arg7 and one accession of its wild ancestor W14 ( ssp. ) has been constructed. The library is comprised of four sub-libraries, containing 32640 recombinant clones, 6028 cDNA clones from their 5′ ends, and 128 clones from the 3′ ends were sequenced. In total, 5013 high-quality expressed sequence tags (ESTs) and 1259 unigenes were obtained. Of these, 746 unigenes were identified by their sequence homologies to ESTs from model plants, and 323 unigenes were mapped onto 114 different KEGG pathways. From these, 24 differentially expressed genes involved in starch metabolism and photosynthesis were identified and five of them were selected to compare their expression level between Arg7 and W14. Notably, Arg7 has a higher net photosynthesis rate in leaves, higher ribulose-1,5-bisphosphate carboxy-lase oxygenase activities in leaves, and higher AGPase activity in roots. This resource is the first EST collection from wild cassava and should be of value for gene discovery, genome annotation and studies of evolution.

关键词： Manihot esculenta     expressed sequence tag     unigene     pathway     expression pattern    

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4-1BBL expressed by eukaryotic cells activates immune cells and suppresses the progression of murine

Hui QIU, Hui ZHANG, Zuohua FENG

《医学前沿（英文）》 2009年 第3卷 第1期   页码 20-25 doi: 10.1007/s11684-009-0006-9

摘要： The interaction by co-stimulatory molecules 4-1BB and 4-1BB ligand (4-1BBL) plays an important role in the activation, proliferation and differentiation of T lymphocytes. The function of 4-1BB/4-1BBL expressed by the immune cells has been the focus for many tumor immunotherapy efforts. In this study, 4-1BBL was expressed in non-immune cells and non-tumor cells, and the role of 4-1BBL in lymphocyte activation and tumor suppression was investigated. The plasmid p4-1BBL containing the full length of mouse 4-1BBL cDNA sequence was constructed, and the plasmid was transfected into baby hamster kidney (BHK) cells and murine muscle cells by means of lipofectin-mediated or naked plasmid DNA injection into the muscle directly. The study demonstrated that the molecule 4-1BBL expressed by BHK cells could enhance the proliferation and cytotoxicity of lymphocytes, and it could increase the expression level of IL-2 and IFN-γ. The treatment with plasmid p4-1BBL revealed that the number of CD8 T cells in the peri-tumoral tissue increased markedly, and the growth rate of the tumor was significantly lower than that of control group. These findings suggest that expression of 4-1BBL by normal cells in the tumor microenvironment can enhance the proliferation and other functions of T lymphocytes. This therapeutic method may provide a promising approach for tumor immunotherapy.

关键词： 4-1BB ligand     tumor immunotherapy     tumor microenvironment    

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Soluble triggering receptor expressed on myeloid cell-1 (sTREM-1): a potential biomarker for the diagnosis

Changlin Cao, Jingxian Gu, Jingyao Zhang

《医学前沿（英文）》 2017年 第11卷 第2期   页码 169-177 doi: 10.1007/s11684-017-0505-z

摘要： Sensitive and useful biomarkers for the diagnosis and prognosis of infectious diseases have been widely developed. An example of these biomarkers is triggering receptor expressed on myeloid cell-1 (TREM-1), which is a cell surface receptor expressed on monocytes/macrophages and neutrophils. TREM-1 amplifies inflammation by activating the TREM-1/DAP12 pathway. This pathway is triggered by the interaction of TREM-1 with ligands or stimulation by bacterial lipopolysaccharide. Consequently, pro-inflammatory cytokines and chemokines are secreted. Soluble TREM-1 (sTREM-1) is a special form of TREM-1 that can be directly tested in human body fluids and well-known biomarker for infectious diseases. sTREM-1 level can be potentially used for the early diagnosis and prognosis prediction of some infectious diseases, including infectious pleural effusion, lung infections, sepsis, bacterial meningitis, viral infections (e.g., Crimean Congo hemorrhagic fever and dengue fever), fungal infections (e.g., infection), and burn-related infections. sTREM-1 is a more sensitive and specific biomarker than traditional indices, such as C-reactive protein and procalcitonin levels, for these infectious diseases. Therefore, sTREM-1 is a feasible biomarker for the targeted therapy and rapid and early diagnosis of infectious diseases.

关键词： soluble triggering receptor expressed on myeloid cells-1     infectious diseases     diagnosis and prognosis     biomarker    

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Alternative splicing of inner-ear-expressed genes

null

《医学前沿（英文）》 2016年 第10卷 第3期   页码 250-257 doi: 10.1007/s11684-016-0454-y

摘要：

Alternative splicing plays a fundamental role in the development and physiological function of the inner ear. Inner-ear-specific gene splicing is necessary to establish the identity and maintain the function of the inner ear. For example, exon 68 of Cadherin 23 (Cdh23) gene is subject to inner-ear-specific alternative splicing, and as a result, Cdh23(+68) is only expressed in inner ear hair cells. Alternative splicing along the tonotopic axis of the cochlea contributes to frequency tuning, particularly in lower vertebrates, such as chickens and turtles. Differential splicing of Kcnma1, which encodes for the α subunit of the Ca2+-activated K+ channel (BK channel), has been suggested to affect the channel gating properties and is important for frequency tuning. Consequently, deficits in alternative splicing have been shown to cause hearing loss, as we can observe in Bronx Waltzer (bv) mice and Sfswap mutant mice. Despite the advances in this field, the regulation of alternative splicing in the inner ear remains elusive. Further investigation is also needed to clarify the mechanism of hearing loss caused by alternative splicing deficits.

关键词： alternative splicing     inner ear     hearing loss     hair cells    

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Metagenomic analysis on resistance genes in water and microplastics from a mariculture system

《环境科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 4-4 doi: 10.1007/s11783-021-1438-y

摘要：

Microplastics existing widely in different matrices have been regarded as a reservoir for emerging contaminants. Mariculture systems have been observed to host microplastics and antibiotic resistance genes (ARGs). However, more information on proliferation of ARGs and metal resistance genes (MRGs) in mariculture system at the presence of microplastics is needed.

关键词： Antibiotic resistance genes     Metal resistance genes     Metagenomic analysis     Microplastics     Mariculture    

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Distribution and removal of antibiotic resistance genes during anaerobic sludge digestion with alkaline

Mengli Wang, Ruying Li, Qing Zhao

《环境科学与工程前沿（英文）》 2019年 第13卷 第3期 doi: 10.1007/s11783-019-1127-2

摘要：

Sludge digestion is critical to control the spread of ARGs from wastewater to soil.

Fate of ARGs in three pretreatment-AD processes was investigated.

UP was more efficient for ARGs removal than AP and THP in pretreatment-AD process.

The total ARGs concentration showed significant correlation with 16S rRNA gene.

The bacteria carrying ARGs could be mainly affiliated with Proteobacteria.

关键词： Tetracycline resistance genes     Sulfonamide resistance genes     16S rRNA gene     Sludge pretreatment     Anaerobic sludge digestion    

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Environmental effects and risk control of antibiotic resistance genes in the organic solid waste aerobic

《环境科学与工程前沿（英文）》 2021年 第15卷 第6期 doi: 10.1007/s11783-021-1415-5

摘要：

• ARGs were detected in livestock manure, sludge, food waste and fermentation dregs.

关键词： Antibiotic resistance genes     Organic solid waste     Aerobic composting     Livestock manure     Sludge    

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ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes

《环境科学与工程前沿（英文）》 2022年 第16卷 第8期 doi: 10.1007/s11783-022-1521-z

摘要：

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

关键词： UV/chlorine process     Pathogen     Antibiotic resistance genes     High-throughput qPCR     Reclaimed water    

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Development of the expressed immunoglobulin μ chain repertoire during maturation of mice B cells

Jingwen LIANG,Yingfeng LUO,Yi SUN,Meng LEI,Bing ZHANG,Songnian HU,Yaofeng ZHAO

《农业科学与工程前沿（英文）》 2014年 第1卷 第3期   页码 201-213 doi: 10.15302/J-FASE-2014017

摘要： In the bone marrow and spleen, the developing B cell populations undergo both negative and positive selections to shape their B cell receptor repertoire. To gain insight into the shift of the immunoglobulin heavy (IgH) chain repertoire during B cell development, we undertook large scale Ig μ chain repertoire analysis of pre-B, immature B and spleen B cell populations. We found that the majority of V gene segments, V families, J and D gene segments, were observed to have significantly different usage frequencies when three B cell populations were compared, but the usage profile of the V D, and J genes between different B cell populations showed high correlations. In both productive and nonproductive rearrangements, the length of CDRH3 shortened significantly on average when B cells entered the periphery. However, the CDRH3 length distribution of nonproductive rearrangements did not follow a Gaussian distribution, but decreased successively in the order 3 -2, 3 -1 and 3 , suggesting a direct correlation between mRNA stability and CDRH3 length patterns of nonproductive rearrangements. Further analysis of the individual components comprising CDRH3 of productive rearrangements indicated that the decrease in CDRH3 length was largely due to the reduction of N addition at the 5′ and 3′ junctions. Moreover, with development, the amino acid content of CDRH3 progressed toward fewer positively charged and nonpolar residues but more polar residues. All these data indicated that the expressed Ig μ chain repertoire, especially the repertoire of CDRH3, was fine-tuned when B cells passed through several checkpoints of selection during the process of maturation.

关键词： repertoire     complementarity determining region 3 of the IgH chain (CDRH3)     immunoglobulin     heavy chain     variable region    

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Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized

《环境科学与工程前沿（英文）》 2022年 第16卷 第3期 doi: 10.1007/s11783-021-1469-4

摘要：

• Distribution of ARGs in decentralized sewage facilities were investigated.

关键词： Decentralized sewage treatment facilities     Antibiotic resistance genes     Virus     Metagenomics     Network analysis    

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Research progress in pathogenic genes of hereditary non-syndromic mid-frequency deafness

null

《医学前沿（英文）》 2016年 第10卷 第2期   页码 137-142 doi: 10.1007/s11684-016-0449-8

摘要：

Hearing impairment is considered as the most prevalent impairment worldwide. Almost 600 million people in the world suffer from mild or moderate hearing impairment, an estimated 10% of the human population. Genetic factors play an important role in the pathogenesis of this disorder. Hereditary hearing loss is divided into syndromic hearing loss (associated with other anomalies) and non-syndromic hearing loss (not associated with other anomalies). Approximately 80% of genetic deafness is non-syndromic. On the basis of the frequency of hearing loss, hereditary non-syndromic hearing loss can be divided into high-, mid-, low-, and total-frequency hearing loss. An audiometric finding of mid-frequency sensorineural hearing loss, or a “bowl-shaped” audiogram, is uncommon. Up to now, merely 7 loci have been linked to mid-frequency hearing loss. Only four genetic mid-frequency deafness genes, namely, DFNA10 (EYA4), DFNA8/12 (TECTA), DFNA13 (COL11A2), DFNA44 (CCDC50), have been reported to date. This review summarizes the research progress of the four genes to draw attention to mid-frequency deafness genes.

关键词： hereditary non-syndromic hearing loss     mid-frequency hearing loss     deafness genes    

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标题 作者 时间 类型 操作

Data mining of microarray for differentially expressed genes in liver metastasis from gastric cancer

Ling XU MM, Feng WANG MM, Xuan-Fu XU MD, Wen-Hui MO BM, Rong WAN MD, Chuan-Yong GUO MD, Xing-Peng WANG MD,

期刊论文

Identification of differentially expressed miRNAs associated with chronic kidney disease–mineral bone

null

期刊论文

Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

期刊论文

iTRAQ-based quantitative proteomic analysis on differentially expressed proteins of rat mandibular condylar

null

期刊论文

Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

期刊论文

4-1BBL expressed by eukaryotic cells activates immune cells and suppresses the progression of murine

Hui QIU, Hui ZHANG, Zuohua FENG

期刊论文

Soluble triggering receptor expressed on myeloid cell-1 (sTREM-1): a potential biomarker for the diagnosis

Changlin Cao, Jingxian Gu, Jingyao Zhang

期刊论文

Alternative splicing of inner-ear-expressed genes

null

期刊论文

Metagenomic analysis on resistance genes in water and microplastics from a mariculture system

期刊论文

Distribution and removal of antibiotic resistance genes during anaerobic sludge digestion with alkaline

Mengli Wang, Ruying Li, Qing Zhao

期刊论文

Environmental effects and risk control of antibiotic resistance genes in the organic solid waste aerobic

期刊论文

ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes

期刊论文

Development of the expressed immunoglobulin μ chain repertoire during maturation of mice B cells

Jingwen LIANG,Yingfeng LUO,Yi SUN,Meng LEI,Bing ZHANG,Songnian HU,Yaofeng ZHAO

期刊论文

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized

期刊论文

Research progress in pathogenic genes of hereditary non-syndromic mid-frequency deafness

null

期刊论文