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Making topological protein links using enzymatic reactions

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National Science Review 2024年第3期11卷 50-51页

作者： Roger Castells-Graells Todd O.Yeates department of Chemistry and Biochemistry University of California UCLA-DOE Institute for genomics and Proteomics

Proteins are exceedingly complex molecules though, at their heart, they are essentially linear polymers. Pull at their ends and one obtains an extended backbone. While that is true in most cases, some natural proteins...

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First Complete Genome Sequence of a Probiotic Enterococcus faecium Strain T-110 and Its Comparative Genome Analysis with Pathogenic and Non-pathogenic Enterococcus faecium Genomes

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Journal of Genetics and genomics 2015年第1期42卷 43-46页

作者： Purushothaman Natarajan Madasamy Parani genomics Laboratory Department of Genetic EngineeringSRM University

Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.

关键词： 110 First Complete Genome Sequence of a Probiotic Enterococcus faecium Strain T-110 and Its Comparative Genome Analysis with Pathogenic and Non-pathogenic Enterococcus faecium Genomes ORFs

CRISPR/Cas9 and Genome Editing in Drosophila

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Journal of Genetics and genomics 2014年第1期41卷 7-19页

作者： Andrew R.Bassett Ji-Long Liu MRC Functional genomics Unit University of Oxford Department of Physiology Anatomy and Genetics

Recent advances in our ability to design DNA binding factors with specificity for desired sequences have resulted in a revolution in genetic engineering, enabling directed changes to the genome to be made relatively easily. Traditional techniques for generating genetic mutations in most organisms have relied on selection from large pools of randomly induced mutations for those of particular interest, or time-consuming gene targeting by homologous recombination. Drosophila melanogaster has always been at the forefront of genetic analysis, and application of these new genome editing techniques to this organism will revolutionise our approach to performing analysis of gene function in the future. We discuss the recent techniques that apply the CRISPR/Cas9 system to Drosophila, highlight potential uses for this technology and speculate upon the future of genome engineering in this model organism.

关键词： Drosophila melanogaster CRISPR Cas9 Genome engineering Targeted mutagenesis

Development and application of functional gene arrays for microbial community analysis

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中国有色金属学会会刊：英文版 2008年第6期18卷 1319-1327页

作者： Z. L. HE J. D. VAN NOSTRAND L.Y. WU J. Z. ZHOU Institute for Environmental genomics Department of Botany and Microbiology University of Oklahoma Norman OK 73019 USA

功能的基因标记能关于功能的基因差异和微生物引起的社区的潜在的活动提供重要信息。尽管 microarray 技术成功地被使用了为纯文化学习基因表示，简单、人工的微生物引起的社区，改编如此的一种技术分析复杂微生物引起的社区仍然以设计... 详细信息

功能的基因标记能关于功能的基因差异和微生物引起的社区的潜在的活动提供重要信息。尽管 microarray 技术成功地被使用了为纯文化学习基因表示，简单、人工的微生物引起的社区，改编如此的一种技术分析复杂微生物引起的社区仍然以设计，样品准备，和数据分析提出很多挑战。这个工作集中于功能的基因数组(FGA ) 的开发和应用程序为微生物引起的社区研究指向关键功能的基因标记。一些与 FGA 有关明确地给问题调音，例如 oligonucleotide 探查设计， nucleic 酸抽取和纯化，数据分析，特性，敏感，和量的能力详细被讨论。最近的研究证明了 FGA 能从许多自然环境关于微生物引起的社区提供特定、敏感、潜在地量的信息并且控制生态系统。这种技术被期望革命化微生物引起的社区的分析，并且连接微生物引起的结构到生态系统工作。

关键词：微数列应用函数基因标记微生物种群

Structure-Based Prediction of Transcription Factor Binding Sites

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Tsinghua Science and Technology 2014年第6期19卷 568-577页

作者： Jun-tao Guo Shane Lofgren Alvin Farrel department of Bioinformatics and genomics University of North Carolina at Charlotte Charlotte NC 28223 USA

Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many *** of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.

关键词： transcription factor binding site structure-based predictions knowledge-based potential physics-based potential

Big Roles of Small Kinases:The Complex Functions of Receptor-Like Cytoplasmic Kinases in Plant Immunity and Development

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Journal of Integrative Plant Biology 2013年第12期55卷 1188-1197页

作者： Wenwei Lin Xiyu Ma Libo Shan Ping He department of Plant Pathology and Microbiology and Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege Station department of Biochemistry and Biophysics and Institute for Plant Genomics and BiotechnologyTexas A&M UniversityCollege Station

Plants have evolved a large number of receptor-like cytoplasmic kinases （RLCKs） that often functionally and physically associate with receptor-like kinases （RLKs） to modulate plant growth, development and immune responses. Without any apparent extracellular domain, RLCKs relay intracellular signaling often via RLK complex-mediated transphosphorylation events. Recent advances have suggested essential roles of diverse RLCKs in concert with RLKs in regulating various cellular and physiological responses. We summarize here the complex roles of RLCKs in mediating plant immune responses and growth regulation, and discuss specific and overlapping functions of RLCKs in transducing diverse signaling pathways.

关键词： Phosphorylation plant development plant immunity receptor-like cytoplasmic kinases.

Microbiome and pancreatic cancer: A comprehensive topic review of literature

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World Journal of Gastroenterology 2017年第10期23卷 1899-1908页

作者： Natalie Ertz-Archambault Paul Keim Daniel Von Hoff department of Internal Medicine Mayo School of Graduate Medical EducationMayo Clinic Arizona genomics Division Translational Genomics Institute and Regents Northern Arizona University Translational genomics Institute(TGen) Mayo Clinic Arizona

To review microbiome alterations associated with pancreatic cancer, its potential utility in diagnostics, risk assessment, and influence on disease *** comprehensive literature review was conducted by all-inclusive topic review from PubMed, MEDLINE, and Web of Science. The last search was performed in October *** microbiome alterations exist among several body sites including oral, gut, and pancreatic tissue, in patients with pancreatic cancer compared to healthy *** study successes in non-invasive screening strategies warrant further investigation for future translational application in early diagnostics and to learn modifiable risk factors relevant to disease prevention. Pre-clinical investigations exist in other tumor types that suggest microbiome manipulation provides opportunity to favorably transform cancer response to existing treatment protocols and improve survival.

关键词： Pancreatic Cancer Human microbiome Biomarkers cancer Cancer screening tests Treatment effectiveness

Influence of quasispecies on virological responses and disease severity in patients with chronic hepatitis C

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World Journal of Gastroenterology 2008年第5期14卷 701-708页

作者： Deepak Kumar Abdul Malik Mohammad Asim Anita Chakravarti Rakha H Das Premashis Kar department of Medicine department of Microbiology Maulana Azad Medical College New Delhi 110002 IndiaDeepak Comparative Genomics Unit Institute of Genomics and Integrative Biology Delhi University Campus Mall Road Delhi 110007 India department of Microbiology Maulana Azad Medical College New Delhi 110002 IndiaDeepak Comparative genomics Unit Institute of Genomics and Integrative Biology Delhi University Campus Mall Road Delhi 110007 India department of Microbiology Maulana Azad Medical College New Delhi 110002 India

AIM:To elucidate the influence of quasispecies on virological response and disease severity in patients with chronic hepatitis C. METHODS:Forty seven patients with hepatitis C [32 with chronic active hepatitis (CAH), 9 with cirrhosis, and 6 with hepatocellular carcinoma (HCC)] were screened for the presence of quasispecies by single stranded conformational polymorphism (SSCP) analysis in the hypervariable region (HVR) and non-structural 5B (NS5B) viral genes of hepatitis C virus. The 41 patients excluding those with HCC were on therapy and followed up for a year with the determination of virological response and disease severity. Virus isolated from twenty three randomly selected patients (11 non-responders and 12 showing a sustained virological response) was sequenced for the assessment of mutations. RESULTS:The occurrence of quasispecies was proportionately higher in patients with HCC and cirrhosis than in those with CAH, revealing a significant correlation between the molecular evolution of quasispecies and the severity of disease in patients with hepatitis C. The occurrence of complex quasispecies has a significant association (P < 0.05) with the non-responders, and leads to persistence of infection. Significant differences (P < 0.05) in viral load (log10 IU/mL) were observed among patients infected with complex quasispecies (CQS), those infected with simple quasispecies (SQS) and those with no quasispecies (NQS), after 12 wk (CQS-5.2 ± 2.3, SQS-3.2 ± 1.9, NQS-2.8 ± 2.4) and 24 wk (CQS-3.9 ± 2.2, SQS-3.0 ± 2.2, NQS-2.1 ± 2.3) in the HVR region. However, a statistically significant difference (P < 0.05) was observed between the viral loads of patients infected with CQS and those infected with NQS in NS5B viral gene after 24 wk (CQS-3.9 ± 2.2, SQS-3.0 ± 2.2, and NQS-2.1 ± 2.3) and 48 wk (CQS-3.1 ± 2.7, SQS-2.3 ± 2.4, NQS-2.0 ± 2.3) of therapy. Disease severity was significantly associated with viral load during therapy. The strains isolated from non-responders sho

关键词： Hepatitis C virus Single-strand conformational polymorphism Quasispecies Virological response Interferon therapy

CTP Synthase Is Required for Optic Lobe Homeostasis in Drosophila

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Journal of Genetics and genomics 2015年第5期42卷 261-274页

作者： Ömür Y.Tastan Ji-Long Liu Medical Research Council Functional genomics Unit Department of PhysiologyAnatomy and GeneticsUniversity of Oxford

CTP synthase （CTPsyn） is a metabolic enzyme responsible for the de novo synthesis of the nucleotide CTE Several recent studies have shown that CTPsyn forms filamentous subcellular structures known as cytoophidia in bacteria, yeast, fruit flies and humans. However, it remains elusive whether and how CTPsyn and cytoophidia play a role during development. Here, we show that cytoophidia are abundant in the neuroepithelial stem cells in Drosophila optic lobes. Optic lobes are underdeveloped in CTPsyn mutants as well as in CTPsyn RNAi. Moreover, overexpressing CTPsyn impairs the development of optic lobes, specifically by blocking the transition from neuro- epithelium to neuroblast. Taken together, our results indicate that CTPsyn is critical for optic lobe homeostasis in Drosophila.

关键词： CTP synthase Cytoophidium Drosophila Central nervous system Neuroepithelial stem cell