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结直肠癌、基质和正常结肠黏膜显微解剖区域<em>Nem>-糖组的显著多样性 Article
Di Wang, Katarina Madunić , Tao Zhang, Guinevere S.M. Lageveen-Kammeijer, Manfred Wuhrer
《工程（英文）》 2023年 第26卷 第7期 页码 32-43 doi: 10.1016/j.eng.2022.08.016
Aberrant glycosylation is considered to be a hallmark of colorectal cancer (CRC), as demonstrated by various studies. While the N-glycosylation of cell lines and serum has been widely examined, the analysis of cancer-associated N-glycans from tissues has been hampered by the heterogeneity of tumors and the complexity of N-glycan structures. To overcome these obstacles, we present a study using laser capture microdissection that makes it possible to largely deconvolute distinct N-glycomic signatures originating from different regions of heterogeneous tissues including cancerous, stromal, and healthy mucosa cells. N-glycan alditols were analyzed by means of porous graphitized carbon liquid chromatography-electrospray ionization tandem mass spectrometry, enabling the differentiation and structural characterization of isomeric species. In total, 116 N-glycans were identified that showed profound differences in expression among cancer, stroma, and normal mucosa. In comparison with healthy mucosa, the cancer cells showed an increase in α2-6 sialylation and monoantennary N-glycans, as well as a decrease in bisected N-glycans. Moreover, specific sialylated and (sialyl-)LewisA/X antigen-carrying N-glycans were exclusively expressed in cancers. In comparison with cancer, the stroma showed lower levels of oligomannosidic and monoantennary N-glycans, LewisA/X epitopes, and sulfation, as well as increased expression of (core-)fucosylation and α2-3 sialylation. Our study reveals the distinct N-glycomic profiles of different cell types in CRC tumor and control tissues, proving the necessity of their separate analysis for the discovery of cancer-associated glycans.
关键词： 结直肠癌 肿瘤 多孔石墨化碳液相色谱-质谱 <em>Nem>-糖组 抗体反应
基于正交质谱的<em>Nem>-糖组谱揭示哈夫病潜在病原学 Article
刘思, 刘圆圆, 林佳静, 刘笔锋, 何振宇, 吴晓旻, 刘欣
《工程（英文）》 2023年 第26卷 第7期 页码 63-73 doi: 10.1016/j.eng.2022.09.012
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.
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.
黄志洵
《中国工程科学》 2005年 第7卷 第3期 页码 6-12
关键词： 狭义相对论 Maxwell方程组 Proca方程组 电磁波波速 光子的静止质量
组合材料芯片的个体化微区合成与表征 Article
项晓东,王刚,张晓琨,向勇,汪洪
《工程（英文）》 2015年 第1卷 第2期 页码 225-233 doi: 10.15302/J-ENG-2015041
用传统实验方法绘制材料相图，需要分别研究各个成分在一系列温度下的成相情况，这通常要汇集多个研究小组多年努力的成果。以高通量制备与表征为特征的组合材料芯片技术能够在一个覆盖完整成分分布的材料样品库上，测定某一温度下二元或三元材料体系的相图，显著提升了研究效率。但要完成整个温度区间的材料相图，仍需对多个材料样品库在一系列不同的温度下进行热处理。本文提出了一种“单芯片方法”， 即通过渐进的能量脉冲将组合材料芯片中某一微区独立地自低向高加热至不同温度，同时原位实时地监测这一微区在温度变化过程中的物相演化，从而获得该微区成分在完整温度区间内的物相信息。对组合材料芯片上各个微区分别独立地逐一重复该过程，就可以在一个组合材料芯片上通过一次实验构建出完整的二元或三元相图。我们采用“单芯片方法”测定了Ge-Sb-Te 三元合金体系非晶相与结晶相的相界，验证了这种方法的可行性。
血清<em>Nem>-聚糖生物标志物诊断ALT水平正常慢性乙型肝炎患者显著肝纤维化和肝硬化的临床意义 Article
王林, 刘艺琪, 顾启馨, 张驰, 徐蕾, 王蕾, 陈翠英, 刘学恩, 赵鸿, 庄辉
《工程（英文）》 2023年 第26卷 第7期 页码 151-158 doi: 10.1016/j.eng.2023.03.008
Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma
《医学前沿（英文）》 2023年 第17卷 第2期 页码 240-262 doi: 10.1007/s11684-022-0936-z
关键词： glioma progression molecular classification EM/PM subtyping intratumor heterogeneity
Xuebiao Nie, Wenjun Liu, Mo Chen, Minmin Liu, Lu Ao
《环境科学与工程前沿（英文）》 2016年 第10卷 第6期 doi: 10.1007/s11783-016-0884-4
关键词： Flow cytometry Escherichia coli Staphylococcusaureus UV CTC SYTO 9
VITHM1 mediated green synthesis of silver nanoparticles: Mechanism and biological applications
Mani Abirami, Krishnan Kannabiran
《化学科学与工程前沿（英文）》 2016年 第10卷 第4期 页码 542-551 doi: 10.1007/s11705-016-1599-6
关键词： Streptomyces ghanaensis VITHM1 nanoparticles 3D structure antibacterial activity
Guiying RAO, Kristen S. BRASTAD, Qianyi ZHANG, Rebecca ROBINSON, Zhen HE, Ying LI
《环境科学与工程前沿（英文）》 2016年 第10卷 第4期 doi: 10.1007/s11783-016-0854-x
关键词： Photo-activated disinfection Titanium dioxide Nanowire membrane Silver Copper
可去除染料——<em>Nem>-聚糖多方法深入分析中的缺失环节 Article
Samanta Cajic, René Hennig, Valerian Grote, Udo Reichl, Erdmann Rapp
《工程（英文）》 2023年 第26卷 第7期 页码 132-150 doi: https://doi.org/10.1016/j.eng.2023.02.016
As the roles of glycans in health and disease continue to be unraveled, it is becoming apparent that glycans' immense complexity cannot be ignored. To fully delineate glycan structures, we developed an integrative approach combining a set of cost-effective, widespread, and easy-to-handle analytical methods. The key feature of our workflow is the exploitation of a removable fluorescent label—exemplified by 9-fluorenylmethyl chloroformate (Fmoc)—to bridge the gap between diverse glycoanalytical methods, especially multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Through the detailed structural analysis of selected, dauntingly complex N-glycans from chicken ovalbumin, horse serum, and bovine transferrin, we illustrate the capabilities of the presented strategy. Moreover, this approach "visualizes" N-glycans that have been difficult to identify thus far—such as the sulfated glycans on human immunoglobulin A—including minute changes in glycan structures, potentially providing useful new targets for biomarker discovery.
Isolation and application of predatory
Ran Yu, Shiwen Zhang, Zhoukai Chen, Chuanyang Li
《环境科学与工程前沿（英文）》 2017年 第11卷 第1期 doi: 10.1007/s11783-017-0900-3
关键词： Bdellovibrio-and-like organisms (BALOs) Biolysis Activated sludge Dewaterability Predation
血清免疫球蛋白G <em>Nem>-糖基的高通量分析——一种消化道癌症的非侵入性生物标志物 Article
刘鹏程, 王小兵, 顿爱社, 李昱潼, 李厚强, 王璐, 张怡春, 李灿灿, 张金霞, 张晓雨, 马立兴, 侯海峰
《工程（英文）》 2023年 第26卷 第7期 页码 44-53 doi: 10.1016/j.eng.2023.02.008
标题 作者 时间 类型 操作
结直肠癌、基质和正常结肠黏膜显微解剖区域<em>Nem>-糖组的显著多样性
Di Wang, Katarina Madunić , Tao Zhang, Guinevere S.M. Lageveen-Kammeijer, Manfred Wuhrer
期刊论文
Flow cytometric assessment of the effects of chlorine, chloramine, and UV on bacteria by using nucleic acid stains and 5-cyano-2,3-ditolyltetrazolium chloride
Xuebiao Nie, Wenjun Liu, Mo Chen, Minmin Liu, Lu Ao
期刊论文
VITHM1 mediated green synthesis of silver nanoparticles: Mechanism and biological applications
Mani Abirami, Krishnan Kannabiran
期刊论文
Guiying RAO, Kristen S. BRASTAD, Qianyi ZHANG, Rebecca ROBINSON, Zhen HE, Ying LI
期刊论文
可去除染料——<em>Nem>-聚糖多方法深入分析中的缺失环节
Samanta Cajic, René Hennig, Valerian Grote, Udo Reichl, Erdmann Rapp
期刊论文
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