Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

高海拔大马士革玫瑰的黄酮类化学成分

为研究高海拔种植大马士革玫瑰的化学成分,采用95%乙醇为溶剂进行连续回流提取,并采用硅胶、聚酰胺、C18及Sephadex LH-20凝胶等材料行分离纯化,最终得到了9个黄酮醇类化合物（1, 3, 5～11）和两个黄酮类化合物（2和4）,其结构经¹H NMR和¹³C NMR表征并结合理化方法鉴定为：5,7-二羟基-3,6,4'-二甲氧基黄酮醇（1）、 5,7-二羟基-6,4'-二甲氧基黄酮（2）、 5,7,4'-三羟基-3,6-甲氧基黄酮醇（3）、 5,7-二羟基-6,8,4'-三甲氧基黄酮（4）、 5,4'-二羟基-3,6,7-二甲氧基黄酮醇（5）、 5,7-二羟基-3,6,8,4'-三甲氧基黄酮醇（6）、 8-甲氧基山奈酚（7）、山奈酚（8）、槲皮素（9）、槲皮素 3-O-a-L-阿拉伯呋喃糖苷（10）、银锻苷（11）,其中化合物1～5为首次从蔷薇属植物中分离得到,化合物1～7、 10、 11为首次从大马士革玫瑰中分离得到。      

Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling,Molecular Docking,and Molecular Dynamics Simulation

Six phthalate acid esters(PAEs) priority pollutants[dimethyl phthalate(DMP), diethyl phthalate(DEP), dibutyl phthalate (DBP or DNBP), di-n-octyl phthalate(DNOP), di 2-ethyl hexyl phthalate(DEHP), and butyl benzyl phthalate(BBP)] were opted as the research object. PAE-degrading esterase CarEW(PDB ID:1C7I) isolated from Bacillus subtilis acting as a template and an iterative saturation mutation strategy was adopted to modify key amino acids to attain efficient PAE-degrading esterase substitutes with a reasonable structure constructed by homology modeling method. Present study designed a total of 285 unit-site and multi-site substitutions of PAE-degrading esterase using the homology modeling method. Among them, 207 PAE-degrading esterase substitutions, which contained the 6-site PAE-degrading esterase substitute 1C7I-6-9 with 84.21% enhancement intensity of degradation ability revealed better degradability to all the 6 PAEs after modification. Moreover, molecular dynamics simulation based on the Taguchi method reported the optimal external application environment for PAE-degrading esterase substitutes as follows:pH=6, T=35℃, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H₂O₂ was 50 mg/L, and the voltage gradient was 1.5 V/cm. The degradation ability of PAE-degrading esterase substitutes was found to be elevated by 13.04% as compared to that of the blank control under the optimal condition. Moreover, 11 highly efficient PAE-degrading esterase substitutes with thermal stability were designed.     

Aryl groups,supplement of amino protecting group chemistry!

Amino group protective strategy has consequently emerged in multistep organic synthesis. Easy and selective deprotection procedures are crucial to facilitate the chemical transformation. Recently, Zhang's group from Henan Normal University collaborating with Chen's group of Nankai University developed a novel strategy for the regiospecific cleavage of inert aryl C-N bonds in N-aryl amides by hypervalent iodine(V) reagents. These procedures allow removal of sort of aryl groups under mild conditions to give primary amides in high efficiency. It bestows these aryl groups with the characteristics of amino protecting groups that might be the supplement of amino protecting group chemistry.     

偶联剂改性对γ-Al2O3催化氧化偏三甲苯性能的影响

研究了偶联剂改性的廉价填料级γ-Al_2O_3直接催化偏三甲苯(TMB)氧化为2,3,5-三甲基苯醌(TMBQ)性能的影响。结果表明,γ-(2,3-环氧丙基)丙基三甲氧基硅烷(KH560)改性后的填料γ-Al_2O_3催化氧化活性较高。考察了KH560用量、水解时间、吸附时间及吸附温度对催化效果的影响。在优化条件下(2mL KH560/Et OH溶液(体积比1∶25),水解1h,吸附4h,吸附温度50℃),偶联剂对填料γ-Al_2O_3表面产生一定的包覆,在催化氧化TMB时较温和,副反应较少,TMB转化率和TMBQ选择性分别为14.3%和72.4%。     

Production and Characterization of Polyclonal and Monoclonal Abs Against the RNA-Binding Protein QKI

RNA-binding protein QKI, a member of the Signal Transduction and Activation of RNA family, is found to be essential in the blood vessel development and postnatal myelination in central nervous system (Woo et al., Oncogene 28:1176–1186, 2009; Lu et al., Nucleic Acids Res 31(15):4616–4624, 2003; Bohnsack et al., Genesis 44(2):93–104, 2006). However, its wide expression pattern suggests other fundamental roles in vivo (Kondo et al., Mamm Genome 10(7):662–669, 1999). To facilitate the understanding of QKI function in various systems, we prepared the polyclonal and monoclonal antibodies against QKI. To obtain the antigen, recombinant His-tagged QKI was expressed in Escherichia coli and highly purified by Ni²⁺-chelated column combined with hydrophobic and ion exchange methods. Following three types of immunizations with different adjuvants, including Freund’s, PAGE gel, and nitrocellulose membrane, only the antiserum produced with Freund’s adjuvant is effective for Western blot detection. Several McAb clones are able to recognize both endogenous and over-expressed QKI with high affinity in Western blot and immunofluorescence. The specificity of Ab was validated as weakening, and no specific signals were observed in cells with QKI knocking down. Immunohistochemistry analysis further showed positive staining of QKI in kidney where QKI mRNA was abundantly expressed, ensuring the wide applications of the QKI Abs in the ongoing mechanistic studies.     

Effects and Corrections for Mobile NMR Measurement

Nuclear magnetic resonance (NMR) under motion has drawn significant attention in recent years. Motion of the NMR probe has serious effects on NMR measurement. For example, NMR logging normally runs at downhole condition with tool motion at a speed of 30 ft/min. We propose here methods for motion corrections of NMR data based on the quantitative analysis of motion effects on polarization and echo acquisition. We also produced a multi-functional NMR scanning system to verify the theoretical analysis. Presented experiments demonstrate that the theoretical and experimental results match very well.     

大花无柱兰遗传多样性的SRAP标记分析

大花无柱兰是一种珍稀兰科植物,具有一定的观赏和药用价值,但数量十分稀少,该物种亟待保护。本研究采用SRAP分子标记技术,对10个居群的115份DNA样品进行PCR扩增,并开展遗传多样性分析。从81对引物中筛选出9个条带清晰、多态性好、重复性高的引物组合,共扩增得到305条谱带。在物种水平上,多态性比率（PPB）为100%,Nei’s基因多样性指数（H）为0.209 8,Shannon’s指数（I）为0.340 2;在居群水平上,PPB为24.59%～52.13%,H为0.079 6～0.165 5,I为0.120 9～0.252 3。居群水平上,基因分化度（Gst）为0.520 9,基因流（Nm）为0.459 9,遗传距离为0.091 9～0.198 4。UPGMA聚类结果表明,10个居群可分为3大类,地理距离相近的居群优先聚集。大花无柱兰的遗传多样性较为丰富,居群间存在一定的遗传分化和基因交流,可采用就地保护和人工栽培等方式加以保护。     

C_(60)与MoO_3混合材料做空穴注入层的单层有机电致发光器件

我们制备研究了基于结构为氧化铟锡(ITO)/C_(60)(1.2nm):MoO_3(0.4nm)/1,3,5-三(1-苯基-1H-苯并咪唑-2-基)苯(TPBi):三(2-苯基吡啶)铱[Ir(ppy)_3](33%,90 nm)/LiF (0.7 nm)/Al (120 nm)的高效绿色磷光单层有机发光二极管(OLED)。分别将C_(60),MoO_3与C_(60):MoO_3混合物作为空穴注入层(HIL)作为对比。TPBi在发光层中起着主体以及电子传输材料的双重作用。在使用电子传输型主体的单层OLED中,空穴注入层性质对于调节电子/空穴注入以获得电荷载流子传输平衡起重要作用。因此,适当调节空穴注入层是实现高效单层OLED的关键因素。由于MoO_3较大的电子亲和能(6.37 eV)会诱导电子从C_(60)的最高占据分子轨道(HOMO)能级转移至MoO_3,从而形成C_(60)阳离子,并使得Mo元素的价态从+6降至+5,C_(60):MoO_3混合就可以较好的调节空穴注入性质。最终实现最大电流效率为35.88 cd·A~(-1)的单层有机发光器件。     

Near-infrared dyes,nanomaterials and proteins

Taking the advantage of reduced scattering and low autofluorescence background, the NIR fluorescence probes, such as fluorescence proteins, organic molecules and nanoparticles, not only hold the promise of in vivo imaging of biological processes in physiology and pathology with high signal-to-noise ratio, but also for clinical diagnosis. In this review, we provide an overview of the recent progress on NIR probes, focusing on fundamental mechanisms of NIR dyes and nanoparticles, and protein engineering strategies for NIR proteins.