单细胞与空间转录组分析研究进展

单细胞的异质性在胚胎发育、神经系统发育、癌症病变等生物学过程中具有重要的研究意义。单细胞转录组测序利用测序技术解析细胞内转录本序列,为细胞异质性研究提供可靠、准确的研究手段及观测视野,为揭示生物发育规律、疾病发生发展机制等提供了重要的技术手段。该文围绕单细胞与空间组学分析,综述了近年来发展的各类单细胞转录组测序、单细胞多组学测序及空间转录组分析方法,分析了其优缺点。同时展望了单细胞与空间转录组分析领域的发展趋势,即开发低成本、全方位、高通量、高分辨的单细胞空间多组学分析方法以实现对单个细胞更为细致、全面及准确的描述和精准单细胞图谱构建。     

Natural Dietary Compound Xanthohumol Regulates the Gut Microbiota and Its Metabolic Profile in a Mouse Model of Alzheimer’s Disease

Discovering new and effective drugs for the treatment of Alzheimer’s disease (AD) is a major clinical challenge. This study focuses on chemical modulation of the gut microbiome in an established murine AD model. We used the 16S rDNA sequencing technique to investigate the effect of xanthohumol (Xn) on the diversity of intestinal microflora in 2-month- and 6-month-old APP/PS1 mice, respectively. APP/PS1 and wild-type mice were treated by gavage with corn oil with or without Xn every other day for 90 days. Prior to and following treatment, animals were tested for spatial learning, cognitive and memory function. We found Xn reduced cognitive dysfunction in APP/PS1 mice and significantly regulated the composition and abundance of gut microbiota both in prevention experiments (with younger mice) and therapeutic experiments (with older mice). Differential microflora Gammaproteobacteria were significantly enriched in APP/PS1 mice treated with Xn. Nodosilineaceae and Rikenellaceae may be the specific microflora modulated by Xn. The penicillin and cephalosporin biosynthesis pathway and the atrazine degradation pathway may be the principal modulation pathways. Taken together, oral treatment with Xn may have a neuroprotective role by regulating the composition of intestinal microflora, a result that contributes to the scientific basis for a novel prophylactic and therapeutic approach to AD.     

人肝癌细胞系HLE细胞表面抗原多肽的纳升电喷雾串联质谱从头测序分析

肿瘤细胞表面的抗原多肽能够被细胞毒T淋巴细胞特异性识别而引起免疫应答,因此有可能用于研制基于多肽的抗肿瘤疫苗。用弱酸将人肝癌细胞系HLE细胞表面抗原多肽和人正常肝细胞表面多肽洗脱后,经RP-HPLC分离,选择HLE细胞表面特异性多肽进行纳升电喷雾串联质谱(nanoESI-MS/MS)测序,共测定5个色谱峰中的20个多肽序列,分子量分布范围为1000~2000 Da。借助M asSeq软件分析出其中12个多肽的序列。经数据库查寻,其中的3个肽段分别来自钙调节蛋白、核蛋白S19和伴侣蛋白10。这些多肽的生物学功能及与肿瘤的关系值得深入研究。该研究表明nanoESI-MS/MS是测定微量混合多肽序列的最有效方法。     

基于生物质谱技术的磷酰化修饰策略在多肽测序中的应用

该文建立了一种利用磷酰化修饰结合电喷雾质谱(ESI-Q-TOF)测定多肽氨基酸序列的有效方法。利用Atherton-Todd反应,以二丙基亚磷酰酯(DPP)为磷酰化试剂,应用生物质谱技术,对磷酰化修饰后的5种模型肽的磷酰化反应情况进行了系统研究,考察了磷酰化肽的二级质谱特征,并与未经磷酰化反应的肽的二级质谱特征对比。结果表明,经过磷酰化修饰后,肽的二级质谱中的a1离子信号强度明显增加,可以准确鉴定其N端氨基酸;b系列离子信息完整,信号强度增强,使得多肽C ID测序的谱图简单、清晰,有利于肽的氨基酸序列的测定;赖氨酸(K,128.10 u)和谷氨酰胺(Q,128.13 u)两种氨基酸质荷比相近,由于二者磷酰化修饰后的差异性,使其得到准确区分。经过5种已知氨基酸序列的模型肽的磷酰化后结合质谱技术进行氨基酸序列测定验证,结果表明该方法简单、快速、准确,提高了利用质谱技术进行多肽测序的准确度和灵敏度,可为蛋白质组学研究提供有效的技术手段。     

Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data

DNA methylation is one of the most important epigenetic modification types, which plays a critical role in gene expression. High efficient surveying of whole genome DNA methylation has been aims of many researchers for long. Recently, the rapidly developed massively parallel DNA‐sequencing technologies open the floodgates to vast volumes of sequence data, enabling a paradigm shift in profiling the whole genome methylation. Here, we describe a strategy, combining methylated DNA immunoprecipitation sequencing with peak search to identify methylated regions on a whole‐genome scale. Massively parallel methylated DNA immunoprecipitation sequencing combined with methylation DNA immunoprecipitation was adopted to obtain methylated DNA sequence data from human leukemia cell line K562, and the methylated regions were identified by peak search based on Poison model. From our result, 140 958 non‐overlapping methylated regions have been identified in the whole genome. Also, the credibility of result has been proved by its strong correlation with bisulfite‐sequencing data (Pearson R²=0.92). It suggests that this method provides a reliable and high‐throughput strategy for whole genome methylation identification.     

A hybrid heuristic for a multi-objective real-life car sequencing problem with painting and assembly line constraints

We address a multi-objective version of the car sequencing problem, which consists in sequencing a given set of cars to be produced in a single day, minimizing the number of violations of assembly constraints and the number of paint color changes in the production line. We propose a set of heuristics for approximately solving this problem, based on the paradigms of the VNS and ILS metaheuristics, to which further intensification and diversification strategies have been added. Computational results on real-life test instances are reported. The work presented in this paper obtained the second prize in the ROADEF challenge 2005 sponsored by Renault.     

有序混合光束和迷宫式多次反射光学系统

本文给出有序混合光束结构和多程光学系统的具体考虑,并指出它们在多波长高激发态激光光谱学研究和其它领域中的意义.