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transcriptomics 4

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Transcriptomics and proteomics in stem cell research

Hai Wang,Qian Zhang,Xiangdong Fang

Frontiers of Medicine 2014, Volume 8, Issue 4,   Pages 433-444 doi: 10.1007/s11684-014-0336-0

Abstract: Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most

Keywords： embryonic stem cells     transcriptomics     proteomics    

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Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

Frontiers of Agricultural Science and Engineering 2016, Volume 3, Issue 4,   Pages 295-307 doi: 10.15302/J-FASE-2016126

Abstract: Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

Keywords： cassava     comparative transcriptomics     energy transport     photosynthesis     starch synthesis    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 72-88 doi: 10.1007/s11705-016-1580-4

Abstract: Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of overexpression in an industrial strain of WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that , and were upregulated in all conditions. Then the three genes were over-expressed in WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.

Keywords： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Frontiers of Medicine 2014, Volume 8, Issue 1,   Pages 58-67 doi: 10.1007/s11684-014-0318-2

Abstract: This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics

Keywords： sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

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Multi-omics in nanoplastic research: a spotlight on aquatic life

Frontiers of Environmental Science & Engineering 2024, Volume 18, Issue 11, doi: 10.1007/s11783-024-1893-3

Abstract:

● We integrate omics data to analyze the aquatic toxicodynamics of nanoplastics.

Keywords： Ecotoxicity     Transcriptomics     Metabolomics     Proteomics     Plastic pollution     Toxicity mechanisms    

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Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer: a review

Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 2,   Pages 104-113 doi: 10.15302/J-FASE-2014003

Abstract: With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal

Keywords： nuclear reprogramming     somatic cell     transcription factors     transcriptomics    

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Information Science Should Take a Lead in Future Biomedical Research Perspective

Kenta Nakai

Engineering 2019, Volume 5, Issue 6,   Pages 1155-1158 doi: 10.1016/j.eng.2019.07.023

Abstract:

In this commentary, I explain my perspective on the relationship between artificial intelligence (AI)/data science and biomedicine from a long-range retrospective view. The development of modern biomedicine has always been accelerated by the repeated emergence of new technologies. Since all life systems are basically governed by the information in their own DNA, information science has special importance for the study of biomedicine. Unlike in physics, no (or very few) leading laws have been found in biology. Thus, in biology, the "data-to-knowledge" approach is important. AI has historically been applied to biomedicine, and the recent news that an AI-based approach achieved the best performance in an international competition of protein structure prediction may be regarded as another landmark in the field. Similar approaches could contribute to solving problems in genome sequence interpretation, such as identifying cancer-driving mutations in the genome of patients. Recently, the explosive development of next-generation sequencing (NGS) has been producing massive data, and this trend will accelerate. NGS is not only used for "reading" DNA sequences, but also for obtaining various types of information at the single-cell level. These data can be regarded as grid data points in climate simulation. Both data science and AI will become essential for the integrative interpretation/simulation of these data, and will take a leading role in future precision medicine.

Keywords： Data science     Artificial intelligence     Next-generation sequencing     DNA     Cancer genome     Single-cell transcriptomics    

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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA (

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

Frontiers of Agricultural Science and Engineering   Pages 215-230 doi: 10.15302/J-FASE-2021382

Abstract: Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

Keywords： harvest season     metabolites     tea shoots     transcriptomics     untargeted metabolomics    

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Multimodal Identification by Transcriptomics and Multiscale Bioassays of Active Components in Xuanfeibaidu Article

Lu Zhao, Hao Liu, Yingchao Wang, Shufang Wang, Dejin Xun, Yi Wang, Yiyu Cheng, Boli Zhang

Engineering 2023, Volume 20, Issue 1,   Pages 63-76 doi: 10.1016/j.eng.2021.09.007

Abstract: Here, we combine a comprehensive research approach that includes network pharmacology, transcriptomics

Keywords： Xuanfeibaidu Formula     Multimodal identification     Inflammation     Macrophage activation     Macrophage migration    

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

Keywords： Artemisinin     Antimalaria     Target identification     MS-CETSA     Transcriptomics    

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Title Author Date Type Operation

Transcriptomics and proteomics in stem cell research

Hai Wang,Qian Zhang,Xiangdong Fang

Journal Article

Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

Journal Article

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Journal Article

Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Journal Article

Multi-omics in nanoplastic research: a spotlight on aquatic life

Journal Article

Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer: a review

Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI

Journal Article

Information Science Should Take a Lead in Future Biomedical Research

Kenta Nakai

Journal Article

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA (

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

Journal Article

Multimodal Identification by Transcriptomics and Multiscale Bioassays of Active Components in Xuanfeibaidu

Lu Zhao, Hao Liu, Yingchao Wang, Shufang Wang, Dejin Xun, Yi Wang, Yiyu Cheng, Boli Zhang

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