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陈松林,徐文腾,陈张帆
《中国工程科学》 2019年 第21卷 第6期 页码 39-47 doi: 10.15302/J-SSCAE-2019.06.007
本文主要从基因组和转录组层面分析了极地动物基因资源的研究现状，梳理了本领域研究中存在的问题，并提出了未来发展战略。极地动物基因组测序起步较晚，迄今只完成了 13种极地动物的全基因组测序。在转录组研究方面，人们对极地的 31个物种进行了转录组测序，并在以下四个方向重点开展了研究：环境适应性研究；污染物应激反应的分子机制研究；不同发育阶段或不同组织中的转录组分析；功能基因挖掘。
关键词： 极地动物 基因组，转录组，基因资源
大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征 Article
杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松
《工程（英文）》 2021年 第7卷 第11期 页码 1592-1602 doi: 10.1016/j.eng.2021.10.001
通过原位观察揭示人体肠道微生物组的重建和动态变化 Article
刘小林, 戴敏, Yue Ma, 赵娜, Ziyu Wang, Ying Yu, Yakun Xu, Huijie Zhang, Liyuan Xiang, He Tian, 税光厚, 张发明, 王军
《工程（英文）》 2022年 第15卷 第8期 页码 89-101 doi: 10.1016/j.eng.2021.03.015
人体肠道微生物组主要通过使用粪便样本进行研究，这种做法已经得到了关于胃肠道微生物群落的组成和功能的重要知识。在我们的研究中，我们利用结肠途径经内镜肠内导管（一种最初为粪便微生物群移植开发的技术）每天两次对回盲部微生物组进行采样；然后对这些样品进行宏基因组和宏转录组学分析。在5 名志愿者中分析的回盲部和粪便微生物组被发现在宏基因组分析中相似，但它们的活性基因（宏转录组）被发现高度不同。两种微生物组在泻药暴露后都受到干扰；随着时间的推移，它们表现出与治疗前状态的差异减少，从而证明了作为肠道微生物组的先天特性——恢复力，尽管它们在我们的观察时间窗口内没有完全恢复。粪便和尿液样本中的代谢组学分析反映出了肠道微生物组的扰动和恢复，表明肠道微生物组对参与宿主健康的诸多关键代谢物的重要贡献。
时间序列多组学整合分析揭示原代肝细胞体外培养去分化过程伴随非降解性泛素化修饰的增加 Article
姜正一, 孙泽宇, 欧阳晓希, 赵亚磊, 周梦豪, 王保红, 李启睿, 范林骁, 张赛男, 李兰娟
《工程（英文）》 2020年 第6卷 第11期 页码 1302-1314 doi: 10.1016/j.eng.2020.02.011
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
流动电极微生物电合成提高产物生成速率及降低能量消耗 Article
褚娜, 王东麟, 王厚锋, 梁勤军, 常佳丽, 高瑜, 蒋永, 曾建雄
《工程（英文）》 2023年 第25卷 第6期 页码 157-167 doi: 10.1016/j.eng.2021.09.015
微生物电合成（microbial electrosynthesis, MES）利用可再生电力驱动微生物固定CO2合成化学品，在推进碳循环经济中具有一定潜力，受到广泛关注。但是，很少有研究通过高效反应器设计来促进产乙酸并降低能耗。本研究中，新型流动电极MES反应器的总产乙酸速率[(16 ± 1) g·m−2·d−1]比无粉末活性炭（powder activated carbon, PAC）对照[(8 ± 3) g·m−2·d−1]高两倍。流动电极MES反应器的库伦效率为43.5% ± 3.1%，能量消耗为(0.020 ± 0.005) kWh·g−1，产乙酸的能量效率为18.7% ± 1.3%。基于PAC的流动电极能够降低水跨膜通量、传质阻力，但是对装置电压、流变行为、乙酸吸附的影响较小。流动电极MES反应器中，能量代谢相关基因高表达，Acetobacterium的丰度增加。MES反应器中同时存在用于碳固定的还原性乙酰辅酶A途径（Wood–Ljungdahl pathway, WLP）与还原性三羧酸循环途径（reductive citric acid cycle, rTCA）。堆叠型流动电极MES中的乙酸浓度达7.0 g·L−1。本研究提供一种构建可扩展MES反应器的新方法，促进CO2利用以及产物生成。
代谢组扩展生物学的“旁中心法则”——对理解基因组学-糖组学-代谢组学-表观基因组学互作的意义
Albert Stuart Reece
《工程（英文）》 2023年 第26卷 第7期 页码 16-16 doi: 10.1016/j.eng.2022.07.011
The central dogma of biology holds that the transcription of DNA into RNA and the translation of RNA into proteins forms the primary axis of biological activity [1]. Following major advances in the description of the complex glycan and lipid chains that are added onto these basic building blocks, the glycome and lipidome have recently been added to this doctrine as an exciting new extension named the ‘‘paracentral dogma” [2]. However, it has been pointed out that biological systems can include many layers, which are described in modern omics technology platforms relating to both cell-intrinsic and cell-extrinsic layers of control, including metabolomic, microbiomic, immunological, epigenomic, epitranscriptomic, proteomic and phosphoproteomic layers [3].
It is well known that stem and progenitor cells have a metabolism that is based on glycolysis and glutaminolysis [4]. Although this provides less energy to the cell than oxidative phosphorylation, it suffices for these cells’ needs, since such cells are generally relatively quiescent and normally suppress energy-intensive processes such as genome duplication and transcription. Moreover, it has been shown that the high intracellular lactate levels involved in such states not only inhibits the key gatekeeper enzymes of oxidative phosphorylation (i.e., pyruvate dehydrogenase and carnitine palmitoyl acyltransferase) but also actually covalently modifies them by lactylation in order to maintain this inhibited metabolic–epigenomic state [5]. In addition, intermediate metabolism and nutrients are the source of the very extensive library of post-translational modifications to DNA, RNA, and proteins, as well as supplying cellular energy for many of the required reactions. Hence, the metabolic state locks in and reinforces the epigenomic state, and the metabolome and epigenome thereby play mutually reinforcing roles. This self-reinforcing coordination explains why it is so difficult to generate induced pluripotent cells and is a contributory explanation for why the described protocols typically have such low cellular yields.
These concepts become even more important when it is considered that cancer cells are de-differentiated, similarly rely on glycolysis and glutaminolysis, and are similarly metabolically–epigenomically–genomically synchronized. The disruption of this metabolic system is a key focus of mechanistic cancer research.
These important considerations imply that the descriptive and predictive power of the newly described ‘‘paracentral dogma” of biology may be usefully and meaningfully extended by including the metabolome, along with the genome, transcriptome, proteome, glycome, and lipidome, to describe cell-intrinsic regulation—not only in terms of another omics analytical layer but also as a fully predictive and interactive partner in the symphonic-like multilayer coordination that evidently comprises cellular regulatory layering.
李炜
《中国工程科学》 2002年 第4卷 第1期 页码 82-88
概述了组播路由协议。分析了协议独立的组播路由一稀疏模式（PIM-SM)的缺陷，提出多个会聚 点（RPs)的PIM-SM的改进机制。分析了 PIM-SM实现细 节和组播技术的前景。
人类蛋白质N-糖基化的十二年全基因组关联研究 Review
Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko
《工程（英文）》 2023年 第26卷 第7期 页码 17-31 doi: 10.1016/j.eng.2023.03.013
Most human-secreted and membrane-bound proteins have covalently attached oligosaccharide chains, or glycans. Glycosylation influences the physical and chemical properties of proteins, as well as their biological functions. Unsurprisingly, alterations in protein glycosylation have been implicated in a growing number of human diseases, and glycans are increasingly being considered as potential therapeutic targets, an essential part of therapeutics, and biomarkers. Although glycosylation pathways are biochemically well-studied, little is known about the networks of genes that guide the cell- and tissue-specific regulation of these biochemical reactions in humans in vivo. The lack of a detailed understanding of the mechanisms regulating glycome variation and linking the glycome to human health and disease is slowing progress in clinical applications of human glycobiology. Two of the tools that can provide much sought-after knowledge of human in vivo glycobiology are human genetics and genomics, which offer a powerful data-driven agnostic approach for dissecting the biology of complex traits. This review summarizes the current state of human populational glycogenomics. In Section 1, we provide a brief overview of the N-glycan's structural organization, and in Section 2, we give a description of the major blood plasma glycoproteins. Next, in Section 3, we summarize, systemize, and generalize the results from current N-glycosylation genome-wide association studies (GWASs) that provide novel knowledge of the genetic regulation of the populational variation of glycosylation. Until now, such studies have been limited to an analysis of the human blood plasma N-glycome and the N-glycosylation of immunoglobulin G and transferrin. While these three glycomes make up a rather limited set compared with the enormous multitude of glycomes of different tissues and glycoproteins, the study of these three does allow for powerful analysis and generalization. Finally, in Section 4, we turn to genes in the established loci, paying particular attention to genes with strong support in Section 5. At the end of the review, in Sections 6 and 7, we describe special cases of interest in light of new discoveries, focusing on possible mechanisms of action and biological targets of genetic variation that have been implicated in human protein N-glycosylation.
甲状腺乳头状癌菌群失调及与肿瘤信号通路异常的相关性研究 Article
喻爽, 丁彦强, 王雪洁, Siu Kin Ng, 曹思婷, 刘伟鑫, 郭朱明, 谢宇彬, 洪澍彬, 许丽霞, 李晓星, 李杰, 吕伟明, 彭穗, 李延兵, 沈祖尧, 于君, 肖海鹏
《工程（英文）》 2023年 第28卷 第9期 页码 179-192 doi: 10.1016/j.eng.2023.01.007
宿主微生物组内的基因组突变——适应性进化或净化选择 Review
张家超, Rob Knight
《工程（英文）》 2023年 第20卷 第1期 页码 96-102 doi: 10.1016/j.eng.2021.11.018
二代测序技术转变了人们评估宿主相关微生物区系和微生物组的分类组成功能的能力。未来10 年将会开展更多的人类微生物组研究，特别是那些探索微生物组内基因组突变的研究。本文聚焦于微生物组内菌株之间的共同进化，塑造了宿主肠道微生物种内和种间的菌株水平多样性。还探讨了微生物基因组突变与常见代谢疾病之间的关联，以及病原体和益生菌在入侵和定植过程中的适应性进化。最后，讨论了注释和分析微生物基因组突变方法和算法的研究进展。
论智能起源中的简约与自洽原则 Position Paper
马毅1,曹颖2,沈向洋3
《信息与电子工程前沿（英文）》 2022年 第23卷 第9期 页码 1298-1323 doi: 10.1631/FITEE.2200297
标题 作者 时间 类型 操作
大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征
杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松
期刊论文
通过原位观察揭示人体肠道微生物组的重建和动态变化
刘小林, 戴敏, Yue Ma, 赵娜, Ziyu Wang, Ying Yu, Yakun Xu, Huijie Zhang, Liyuan Xiang, He Tian, 税光厚, 张发明, 王军
期刊论文
甲状腺乳头状癌菌群失调及与肿瘤信号通路异常的相关性研究
喻爽, 丁彦强, 王雪洁, Siu Kin Ng, 曹思婷, 刘伟鑫, 郭朱明, 谢宇彬, 洪澍彬, 许丽霞, 李晓星, 李杰, 吕伟明, 彭穗, 李延兵, 沈祖尧, 于君, 肖海鹏
期刊论文
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