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BPA 1

DNA assembly 1

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Epstein-Barr virus 1

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Gcov 1

Glycosylation 1

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Mutation profiling of 16 candidate genes in

Yang Zhang, Fang Wang, Xue Chen, Wenjing Liu, Jiancheng Fang, Mingyu Wang, Wen Teng, Panxiang Cao, Hongxing Liu

Frontiers of Medicine 2019, Volume 13, Issue 2,   Pages 229-237 doi: 10.1007/s11684-018-0616-1

Abstract: Mutation profiling of 16 candidate genes were performed in bone marrow samples by using Sanger sequencingThe results showed certain rules in the mutation profiling and concurrence of AML patients, which was

Keywords： leukemia     myeloid     acute     gene     mutation    

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Profiling influences of gene overexpression on heterologous resveratrol production in

Duo Liu,Bingzhi Li,Hong Liu,Xuejiao Guo,Yingjin Yuan

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 117-125 doi: 10.1007/s11705-016-1601-3

Abstract: Metabolic engineering of heterologous resveratrol production in faces challenges as the precursor L-tyrosine is stringently regulated by a complex biosynthetic system. We overexpressed the main gene targets in the upstream pathways to investigate their influences on the downstream resveratrol production. Single-gene overexpression and DNA assembly-directed multigene overexpression affect the production of resveratrol as well as its precursor -coumaric acid. Finally, the collaboration of selected gene targets leads to an optimal resveratrol production of 66.14±3.74 mg·L , 2.27 times higher than the initial production in YPD medium (4% glucose). The newly discovered gene targets expressing phosphoribosylanthranilate isomerase, expressing 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, and expressing 4-coumaryl-CoA ligase show notable positive impacts on resveratrol production in .

Keywords： resveratrol     aromatic amino acid     DNA assembly     metabolic engineering     gene overexpression    

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Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Frontiers of Medicine 2016, Volume 10, Issue 1,   Pages 61-75 doi: 10.1007/s11684-016-0436-0

Abstract:

The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.

Keywords： Epstein-Barr virus     paired-end transcriptome sequencing     latency genes     lytic genes     nasopharyngeal carcinoma    

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Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

Frontiers of Information Technology & Electronic Engineering 2015, Volume 16, Issue 2,   Pages 135-151 doi: 10.1631/FITEE.1400239

Abstract: Accurate and fast performance estimation is necessary to drive design space exploration and thus support important design decisions. Current techniques are either time consuming or not accurate enough. In this paper, we solve these problems by presenting a hybrid method for multimedia multiprocessor system-on-chip (MPSoC) performance estimation. A general coverage analysis tool GNU gcov is employed to profile the execution statistics during the native simulation. To tackle the complexity and keep the analysis and simulation manageable, the orthogonalization of communication and computation parts is adopted. The estimation result of the computation part is annotated to a transaction accurate model for further analysis, by which a gradual refinement of MPSoC performance estimation is supported. The implementation and its experimental results prove the feasibility and efficiency of the proposed method.

Keywords： MPSoC     Gradual refinement     Native simulation     Performance estimation     Profiling     Annotation     Gcov    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Frontiers of Medicine 2021, Volume 15, Issue 1,   Pages 144-154 doi: 10.1007/s11684-020-0792-7

Abstract: Oocyte cryopreservation is widely used for clinical and social reasons. Previous studies have demonstrated that conventional slow-freezing cryopreservation procedures, but not storage time, can alter the gene expression profiles of frozen oocytes. Whether vitrification procedures and the related frozen storage durations have any effects on the transcriptomes of human metaphase II oocytes remain unknown. Four women (30–32 years old) who had undergone IVF treatment were recruited for this study. RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocytes were cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution. A total of 1987 genes were differentially expressed in the 13 vitrified-thawed oocytes. However, no differentially expressed genes were found between any two groups among the 1-, 2-, 3-, and 12-month storage groups. Further analysis revealed that the aberrant genes in the vitrified oocytes were closely related to oogenesis and development. Our findings indicated that the effects of vitrification on the transcriptomes of mature human oocytes are induced by the procedure itself, suggesting that long-term cryostorage of human oocytes is safe.

Keywords： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

Yue Yu, Jie He

Frontiers of Medicine 2013, Volume 7, Issue 2,   Pages 157-171 doi: 10.1007/s11684-013-0272-4

Abstract:

Non-small-cell lung cancer (NSCLC) is the most common cause of premature death among the malignant diseases worldwide. The current staging criteria do not fully capture the complexity of this disease. Molecular biology techniques, particularly gene expression microarrays, proteomics, and next-generation sequencing, have recently been developed to facilitate effectively its molecular classification. The underlying etiology, pathogenesis, therapeutics, and prognosis of NSCLC based on an improved molecular classification scheme may promote individualized treatment and improve clinical outcomes. This review focuses on the molecular classification of NSCLC based on gene expression microarray technology reported during the past decade, as well as their applications for improving the diagnosis, staging and treatment of NSCLC, including the discovery of prognostic markers or potential therapeutic targets. We highlight some of the recent studies that may refine the identification of NSCLC subtypes using novel techniques such as epigenetics, proteomics, or deep sequencing.

Keywords： non-small-cell lung cancer     molecular typing     individualized medicine     molecular-targeted therapy     gene expression profiling    

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Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

Frontiers of Environmental Science & Engineering 2023, Volume 17, Issue 1, doi: 10.1007/s11783-023-1604-5

Abstract:

● Metabolomic temporal profiling of cells exposed to xenobiotics.

Keywords： Metabolomics     BPA     MCF-7     Temporal profiling     Metabolic adaption     Dysregulation correlation    

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ANTIVIRAL EFFECTS OF BACTERIOCIN AGAINST ANIMAL-TO-HUMAN TRANSMITTABLE MUTATED SARS-COV-2: A SYSTEMATIC REVIEW

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 4,   Pages 603-622 doi: 10.15302/J-FASE -2021397

Abstract:

The COVID-19 infections caused by SARS-CoV-2 have resulted in millions of people being infected and thousands of deaths globally since November 2019. To date, no unique therapeutic agent has been developed to slow the progression of this pandemic. Despite possessing antiviral traits the potential of bacteriocins to combat SARS-CoV-2 infection has not been fully investigated. This review summarizes the mechanisms by which bacteriocins can be manipulated and implemented as effective virus entry blockers with infection suppression potential properties to highly transmissible viruses through comprehensive immune modulations that are potentially effective against COVID-19. These antimicrobial peptides have been suggested as effective antiviral therapeutics and therapeutic supplements to prevent rapid virus transmission. This review also provides a new insight into the cellular and molecular alterations which have made SARS-CoV-2 self-modified with diversified infection patterns. In addition, the possible applications of antimicrobial peptides through both natural and induced mechanisms in infection prevention perspectives on changeable virulence cases are comprehensively analyzed. Specific attention is given to the antiviral mechanisms of the molecules along with their integrative use with synthetic biology and nanosensor technology for rapid detection. Novel bacteriocin based therapeutics with cutting-edge technologies might be potential substitutes for existing time-consuming and expensive approaches to fight this newly emerged global threat.

 

Keywords： antimicrobial proteins / antiviral profiling of bacteriocins / antiviral therapeutics / immunomodulation    

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Profiling the Antimalarial Mechanism of Artemisinin by Identifying Crucial Target Proteins Article

Peng Gao, Jianyou Wang, Jiayun Chen, Liwei Gu, Chen Wang, Liting Xu, Yin Kwan Wong, Huimin Zhang, Chengchao Xu, Lingyun Dai, Jigang Wang

Engineering 2023, Volume 31, Issue 12,   Pages 86-97 doi: 10.1016/j.eng.2023.06.001

Abstract: strategy involving mass spectrometry-coupled cellular thermal shift assay (MS-CETSA) and transcriptomics profiling

Keywords： Artemisinin     Antimalaria     Target identification     MS-CETSA     Transcriptomics    

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High-Throughput Profiling of Serological Immunoglobulin G N-Glycome as a Noninvasive Biomarker Article

Pengcheng Liu, Xiaobing Wang, Aishe Dun, Yutong Li, Houqiang Li, Lu Wang, Yichun Zhang, Cancan Li, Jinxia Zhang, Xiaoyu Zhang, Lixing Ma, Haifeng Hou

Engineering 2023, Volume 26, Issue 7,   Pages 44-53 doi: 10.1016/j.eng.2023.02.008

Abstract:

Immunoglobulin G (IgG) N-glycosylation plays a crucial role in the development of inflammatory diseases. This study aimed to evaluate the diagnostic performance of IgG for gastrointestinal (GI) cancer subtypes. A total of 749 GI cancer patients were enrolled from the Cancer Hospital, Chinese Academy of Medical Sciences, including esophageal cancer (EC), gastric cancer (GC), colorectal cancer (CRC), and pancreatic cancer (PC) patients. Hydrophilic interaction liquid chromatography using ultra-performance liquid chromatography (HILIC-UPLC) was employed to analyze the composition of the plasma IgG N-glycome. The levels of circulating inflammatory cytokines were detected by means of a Bio-Plex Pro Human Th17 Cytokine Assay. Canonical correlation analysis (CCA) was used to explore the correlation between IgG N-glycosylation patterns and inflammatory cytokines. A Lasso algorithm, accompanied by a logistic regression model, was used to develop a glycan-based model for differentiating GI cancer patients from healthy individuals. The levels of sialylation and galactosylation were significantly decreased among EC, GC, CRC, and PC patients, whereas the abundance of glycans with bisecting Nacetylglucosamine (GlcNAc) was increased in GI cancer patients in comparison with the healthy controls. Moreover, only PC patients had a decreased level of fucosylation. The levels of interleukin 1β (IL-1β), IL- 31, and soluble CD40 ligand (sCD40L) were significantly higher in GI cancer patients than in the controls. In addition, the composition of IgG N-glycans was correlated with that of inflammatory cytokines (r = 0.556). The glycan-based models for diagnosing GI cancers exhibited an excellent performance, with areas under the receiver operating characteristic curves (AUCs) of 0.972 for EC, 0.871 for GC, 0.867 for CRC, and 0.907 for PC. Our findings demonstrate that IgG N-glycosylation plays an important role in modulating the pathogenesis of GI cancers. Serological IgG N-glycosylation is thus a potential candidate for noninvasively assisting in the clinical diagnosis of GI cancer subtypes.

Keywords： Gastrointestinal cancer     Glycosylation     Immunoglobulin G     Diagnostic biomarker    

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Title Author Date Type Operation

Mutation profiling of 16 candidate genes in

Yang Zhang, Fang Wang, Xue Chen, Wenjing Liu, Jiancheng Fang, Mingyu Wang, Wen Teng, Panxiang Cao, Hongxing Liu

Journal Article

Profiling influences of gene overexpression on heterologous resveratrol production in

Duo Liu,Bingzhi Li,Hong Liu,Xuejiao Guo,Yingjin Yuan

Journal Article

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Journal Article

Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

Journal Article

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Journal Article

Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

Yue Yu, Jie He

Journal Article

Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

Journal Article

ANTIVIRAL EFFECTS OF BACTERIOCIN AGAINST ANIMAL-TO-HUMAN TRANSMITTABLE MUTATED SARS-COV-2: A SYSTEMATIC REVIEW

Journal Article

Profiling the Antimalarial Mechanism of Artemisinin by Identifying Crucial Target Proteins

Peng Gao, Jianyou Wang, Jiayun Chen, Liwei Gu, Chen Wang, Liting Xu, Yin Kwan Wong, Huimin Zhang, Chengchao Xu, Lingyun Dai, Jigang Wang

Journal Article

High-Throughput Profiling of Serological Immunoglobulin G N-Glycome as a Noninvasive Biomarker

Pengcheng Liu, Xiaobing Wang, Aishe Dun, Yutong Li, Houqiang Li, Lu Wang, Yichun Zhang, Cancan Li, Jinxia Zhang, Xiaoyu Zhang, Lixing Ma, Haifeng Hou

Journal Article