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单细胞转录组学 1

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宣肺败毒方 1

巨噬细胞活化 1

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炎症 1

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脱氧核糖核酸 1

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Transcriptomics and proteomics in stem cell research

null

《医学前沿（英文）》 2014年第8卷第4期页码 433-444 doi: 10.1007/s11684-014-0336-0

摘要：

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

关键词： 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

《农业科学与工程前沿（英文）》 2016年第3卷第4期页码 295-307 doi: 10.15302/J-FASE-2016126

摘要： 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.

关键词： 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

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 72-88 doi: 10.1007/s11705-016-1580-4

摘要： 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.

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

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Sepsis biomarkers: an omics perspective

null

《医学前沿（英文）》 2014年第8卷第1期页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis biomarker genomics transcriptomics proteomics metabolomics

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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

《农业科学与工程前沿（英文）》 2014年第1卷第2期页码 104-113 doi: 10.15302/J-FASE-2014003

摘要： Oocytes are unique cells with the inherent capability to reprogram nuclei. The reprogramming of the somatic nucleus from its original cellular state to a totipotent state is essential for term development after somatic cell nuclear transfer. The nuclear-associated factors contained within oocytes are critical for normal fertilization by sperm or for somatic cell nuclear reprogramming. The chromatin of somatic nuclei can be reprogrammed by factors in the egg cytoplasm whose natural function is to reprogram sperm chromatin. The oocyte first obtains its reprogramming capability in the early fetal follicle, and then its capacity is enriched in the late growth phase and reaches its highest capability for reprogramming as fully-grown germinal vesicle oocytes. The cytoplasmic milieu most likely contains all of the specific transcription and/or reprogramming factors necessary for cellular reprogramming. Certain transcription factors in the cytoplast may be critical as has been demonstrated for induced pluripotent stem cells. The maternal pronucleus exerts a predominant, transcription-dependent effect on embryo cytofragmentation, with a lesser effect imposed by the ooplasm and the paternal pronucleus. With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal transcription factors inducing cellular reprogramming will be identified.

关键词： nuclear reprogramming somatic cell transcription factors transcriptomics

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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

《工程（英文）》 doi: 10.1016/j.eng.2023.06.001

摘要：

The widespread use of artemisinin (ART) and its derivatives has significantly reduced the global burden of malaria; however, malaria still poses a serious threat to global health. Although significant progress has been achieved in elucidating the antimalarial mechanisms of ART, the most crucial target proteins and pathways of ART remain unknown. Knowledge on the exact antimalarial mechanisms of ART is urgently needed, as signs of emerging ART resistance have been observed in some regions of the world. Here, we used a combined strategy involving mass spectrometry-coupled cellular thermal shift assay (MS-CETSA) and transcriptomics profiling to identify a group of putative antimalarial targets of ART. We then conducted a series of validation experiments on five prospective protein targets, demonstrating that ART may function against malaria parasites by interfering with redox homeostasis, lipid metabolism, and protein synthesis processes. Taken together, this study provides fresh perspectives on the antimalarial mechanisms of ART and identifies several crucial proteins involved in parasite survival that can be targeted to combat malaria.

关键词： Artemisinin Antimalaria Target identification MS-CETSA 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

《农业科学与工程前沿（英文）》页码 215-230 doi: 10.15302/J-FASE-2021382

摘要： 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.

关键词： harvest season metabolites tea shoots transcriptomics untargeted metabolomics

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信息科学应引领未来的生物医学研究 Perspective

Kenta Nakai

《工程（英文）》 2019年第5卷第6期页码 1155-1158 doi: 10.1016/j.eng.2019.07.023

摘要：

笔者从长期回顾的角度阐述了对人工智能（AI）/数据科学与生物医学之间关系的看法。随着新技术的不断出现，现代生物医学的发展持续加速。由于所有生命系统基本上都受其自身DNA中信息的支配，因此信息科学对生物医学的研究具有特别重要的意义。与物理学不同，在生物学中没有发现（或很少有）主导定律。因此，在生物学中，“数据到知识”方法很重要。人工智能在历史上一直应用于生物医学，最近的新闻表明，基于人工智能的方法在国际蛋白质结构预测竞争中获得了最佳性能，这可能被视为该领域的另一个里程碑。类似的方法可能有助于解决基因组序列解释中的问题，如确定患者基因组中的癌症驱动突变。最近，新一代测序（NGS）的爆炸性发展已产生大量数据，并且这种趋势将加速。NGS不仅用于“读取”DNA序列，而且还用于在单细胞水平上获得各种类型的信息。这些数据可以视为气候模拟中的网格数据点。数据科学和人工智能对于这些数据的综合解释/模拟都将变得至关重要，并将在未来的精密医学中起主导作用。

关键词：数据科学人工智能下一代测序脱氧核糖核酸癌症基因组单细胞转录组学

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基于转录组学及多尺度生物测定多模态鉴定宣肺败毒方抑制巨噬细胞免疫反应的活性成分 Article

赵璐, 刘豪, 王迎超, 王书芳, 荀得金, 王毅, 程翼宇, 张伯礼

《工程（英文）》 2023年第20卷第1期页码 63-76 doi: 10.1016/j.eng.2021.09.007

摘要：

宣肺败毒方（XFBD）是一种临床用于治疗新型冠状病毒肺炎（COVID-19）病患的中药方剂，在临床实践中表现出了显著的疗效，但对其潜在的药理学机制尚不清楚。本研究结合网络药理学、转录组学和多模型系统生物测定等综合研究方法，研究了XFBD生物活性物质及其药理作用机制。通过高分辨质谱与分子网络相结合，对XFBD中的主要活性物质进行了分析，共鉴定或初步鉴定了104种化合物，包括黄酮类、萜类、羧酸类和其他类型的成分。基于所鉴定的XFBD化学组分，开展了网络药理学分析并将炎症相关通路确定为主要靶点。在脂多糖诱导的急性炎症小鼠模型中，XFBD明显减轻了肺部炎症，降低了血清促炎细胞因子水平。转录组学分析表明，经XFBD治疗后，与巨噬细胞功能相关的基因表达水平发生改变。在巨噬细胞细胞系和斑马鱼创伤模型中，XFBD对巨噬细胞的激活和迁移均有很强的抑制作用。最终，通过多模型系统筛选，发现XFBD中虎杖、芦根、化橘红显著下调巨噬细胞活化，虎杖苷、异甘草苷、毛蕊花糖苷为活性化合物；青蒿和麻黄显著抑制内源性巨噬细胞迁移，麻黄碱、白术内酯和山奈酚为活性化合物。综上所述，本研究通过多模态方法研究了XFBD调节炎症的活性成分以及相关药理学机制，从而为XFBD的临床疗效提供了生物学例证。

关键词：炎症巨噬细胞活化巨噬细胞迁移多模态鉴定宣肺败毒方

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标题作者时间类型操作

Transcriptomics and proteomics in stem cell research

null

期刊论文

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

期刊论文

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

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

期刊论文

Sepsis biomarkers: an omics perspective

null

期刊论文

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

Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI

期刊论文

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

期刊论文

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

期刊论文

信息科学应引领未来的生物医学研究

Kenta Nakai

期刊论文

基于转录组学及多尺度生物测定多模态鉴定宣肺败毒方抑制巨噬细胞免疫反应的活性成分

赵璐, 刘豪, 王迎超, 王书芳, 荀得金, 王毅, 程翼宇, 张伯礼

期刊论文

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