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Novel Time-dependent Multi-omics Integration in Sepsis-associated Liver Dysfunction

Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1101-1116页

作者： Ann-Yae Na Hyojin Lee Eun Ki Min Sanjita Paudel So Young Choi HyunChae Sim Kwang-Hyeon Liu Ki-Tae Kim Jong-Sup Bae Sangkyu Lee Research Institute of Pharmaceutical Sciences Kyungpook National UniversityDaegu 41566Republic of Korea Department of Environmental Engineering Seoul National University of Science and TechnologySeoul 01811Republic of Korea BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit College of PharmacyKyungpook National UniversityDaegu 41566Republic of Korea School of Pharmacy Sungkyunkwan UniversitySuwon 16419Republic of Korea

The recently developed technologies that allow the analysis of each single omics have provided an unbiased insight into ongoing disease ***,it remains challenging to specify the study design for the subsequent integration strategies that can associate sepsis pathophysiology and clinical ***,we conducted a time-dependent multi-omics integration(TDMI)in a sepsis-associated liver dysfunction(SALD)*** successfully deduced the relation of the Toll-like receptor 4(TLR4)pathway with *** TLR4 is a critical factor in sepsis progression,it is not specified in single-omics analyses but only in the TDMI *** finding indicates that the TDMI-based approach is more advantageous than single-omics analyses in terms of exploring the underlying pathophysiological mechanism of ***,TDMI-based approach can be an ideal paradigm for insightful biological interpretations of multi-omics datasets that will potentially reveal novel insights into basic biology,health,and diseases,thus allowing the identification of promising candidates for therapeutic strategies.

关键词： Multi-omics omics technology Sepsis-associated liver dysfunction Single omics Time-dependent integration

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Advances in Genomic,Transcriptomic,and Metabolomic Analyses of Fruit Quality in Fruit Crops

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Horticultural Plant Journal 2020年第6期6卷 361-371页

作者： Chunmei Zhang Yu-Jin Hao State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River College of ForestryShandong Agricultural UniversityTai’anShandong 271018China National Key Laboratory of Crop Biology Ministry of Agriculture Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai’anShandong 271018China

Fruit quality is the main factor determining market competitiveness;it represents the combination of fruit flavor,color,size,and the contents of aromatic and bioactive *** on the genetic basis of fruit quality can provide new information about fruit biology,promote genomic-assisted breeding,and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental ***-throughput sequencing is a powerful research method for studying fruit quality traits,and reference genome sequences for many important fruit crops have provided vast amounts of genomic *** study fruit quality,it is important to select appropriate omics strategies and to analyze omics data ***,we summarize genomic mechanisms of fruit quality formation:gene duplication,transposable element insertion,structural variations and genome methylation in functional *** review the genomic,transcriptomic,and metabolomic strategies that have been used to study the genetic basis of fruit quality *** also describe some of the genes associated with fruit traits;these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits,such as fruit color,size,hardness,aroma components,sugar and acid ***,to maximize the application of omics information,we propose some further directions for research using omics strategies.

关键词： Fruit quality Selective sweep GWAS QTL mapping omics technology

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Metabolic engineering based on systems biology for chemicals production

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Frontiers in Biology 2009年第3期4卷 260-265页

作者： Jianzhong LIU Zhiming WENG Yue WANG Hui CHAO Zongwan MAO Biotechnology Research Center Zhongshan(Sun Yat-Sen)UniversityGuangzhou 510275China MOE Key Laboratory of Bioinorganic and Synthetic Chemistry Zhongshan(Sun Yat-Sen)UniversityGuangzhou 510275China

Microorganisms have been the main sources for the production of *** of chemicals requires the development of low-cost and higher-yield *** this goal,microbial strains with higher levels of production should be first *** engineering has been used extensively over the past two to three decades to increase production of these *** in omics technology and computational simulation are allowing us to perform metabolic engineering at the systems *** combining the results of omics analyses and computational simulation,systems biology allows us to understand cellular physiology and characteristics,which can subsequently be used for designing ***,we review the current status of metabolic engineering based on systems biology for chemical production and discuss future prospects.

关键词： chemicals production metabolic engineering omics technology computational simulation systems biology

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Integration of multi-omics in investigations on the mechanisms of action of Chinese herbal medicine interventions in metabolic diseases

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Traditional Medicine Research 2022年第4期7卷 1-7页

作者： Yong-Jun Cao Han-Zhou Li Yu-Meng Sun Xiao-Qian Li Le Chen Xiao-Wen Jin Shu-Quan Lyu Wei-Bo Wen Jia-Bao Liao Department of Endocrinology Nantong Hospital Affiliated to Nanjing University of Chinese MedicineNantong 226001China Chengde Medical College Chengde 067000China Department of Endocrinology Integrated Chinese and Western Medicine Hospital of CangzhouCangzhou 061000China Department of Endocrinology Yunnan Provincial Hospital of Chinese MedicineKunming 650029China Department of Emergency Jiaxing Hospital of Traditional Chinese MedicineJiaxing 324000China

The rapid development of bioinformatics has provided novel approaches and methods for exploring the mechanisms of disease treatment via Chinese herbal *** Chinese herbal medicines formulas have complex compositions and are characterized by their multiple constituents and diverse array of biological ***,the mechanisms of action of most compound Chinese herbal medicines formulas cannot be adequately explained using a single *** technologies describe high-throughput-based analytical and detection techniques,which include transcriptomics,proteomics,and metabolomics and provide multilayer parameter information that can be integrated to characterize the overall relationships involved in the therapeutic effects of Chinese herbal medicines *** their combination with network biology and drug effect networks,omics technologies also enable investigations into the mechanisms of disease treatment in traditional Chinese *** integration of multiple omics technologies is in line with the concept of holism in traditional Chinese medicine and provides an approach for combining modern science and technology with traditional Chinese medicine *** recent years,omics technologies have been widely used to elucidate the mechanisms of action of Chinese herbal *** latest studies employing multi-omics integration for investigating the mechanisms of action of Chinese herbal medicines interventions in metabolic diseases have devoted greater attention to in-depth explorations of disease *** paper provides a review of the following multi-omics technologies,which are used in research on the treatment of common metabolic diseases(e.g.,type-2 diabetes mellitus,nonalcoholic fatty liver disease):network pharmacology combined with metabolomics,16S rRNA sequencing combined with transcriptomics,16S rRNA sequencing combined with metabolomics,and 16S rRNA sequencing combined with network pharmacology and metabolomic

关键词： omics technology Chinese herbal medicine metabolic disease mechanism of action

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Advances and applications in spatial transcriptomics

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分子科学学报 2024年第2期40卷 95-106页

作者： SUN Yueqiu YU Nianzuo ZHANG Junhu State Key Laboratory of Supermolecular Structure and Materials College of ChemistryJilin UniversityChangchun 130012China

Spatial transcriptomics is an organizational study done on tissue sections that preserves the spatial information of the *** transcriptomics aims to combine spatial information with gene expression data to quantify the mRNA expression of a large number of genes in the spatial context of tissues and *** a paradigm shift in biological research,spatial transcriptomics can provide both spatial location information and transcriptome-level cellular gene expression data,elucidating the interactions between cells and the *** the understanding of the entire functional life cycle of RNA to the characterization of molecular mechanisms to the mapping of gene expression in various tissue regions,by choosing the appropriate spatial transcriptome technology,researchers can achieve a deeper exploration of biological developmental processes,disease pathogenesis,*** recent years,the field of spatial transcriptomics has ushered in several challenges along with its rapid development,such as the dependence on sample types,the resolution of visualized genes,the difficulty of commercialization,and the ability to obtain detailed single-cell *** this paper,we summarize and review the four major categories of spatial transcriptome technologies and compare and analyze the technical advantages and major challenges of multiple research strategies to assist current experimental design and research ***,the importance of spatial transcriptomics in the integration of multi-omics analysis and disease modeling as well as the future development prospects are summarized and outlined.

关键词： spatial transcriptomics spatial position omics technology multi-omics

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