癌症单细胞数据拷贝数变异检测方法

随着单细胞测序数据的异质性优势在癌症研究中的逐渐体现,现有拷贝数变异检测方法在检测单细胞数据时效果差的问题亟待解决。提出一种新的单细胞数据拷贝数变异检测方法（FL-CNV）,通过动态窗口划分及数据估算对变异区间进行范围估计和断点确定,以明确拷贝数变异的断点位置和变异类型。所提方法突破了现有检测方法在单细胞数据上的局限性,对其检测效果在模拟数据和真实数据上进行了实验验证。结果表明：与现有方法相比,本文所提方法能显著提高拷贝数变异检测的精度和敏感度,且所得结果与比较基因组杂交（array-based comparative genomic hybridization,aCGH）的拷贝数变异进行了相关性验证,具有更高的可信度。     

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level. To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions.     

Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee

The human Y chromosome, transmitted clonally through males, contains far fewer genes than the sexually recombining autosome from which it evolved. The enormity of this evolutionary decline has led to predictions that the Y chromosome will be completely bereft of functional genes within ten million years. Although recent evidence of gene conversion within massive Y-linked palindromes runs counter to this hypothesis, most unique Y-linked genes are not situated in palindromes and have no gene conversion partners. The 'impending demise' hypothesis thus rests on understanding the degree of conservation of these genes. Here we find, by systematically comparing the DNA sequences of unique, Y-linked genes in chimpanzee and human, which diverged about six million years ago, evidence that in the human lineage, all such genes were conserved through purifying selection. In the chimpanzee lineage, by contrast, several genes have sustained inactivating mutations. Gene decay in the chimpanzee lineage might be a consequence of positive selection focused elsewhere on the Y chromosome and driven by sperm competition.     

Tumour maintenance is mediated by eNOS

Tumour cells become addicted to the expression of initiating oncogenes like Ras, such that loss of oncogene expression in established tumours leads to tumour regression. HRas, NRas or KRas are mutated to remain in the active GTP-bound oncogenic state in many cancers. Although Ras activates several proteins to initiate human tumour growth, only PI3K, through activation of protein kinase B (PKB; also known as AKT), must remain activated by oncogenic Ras to maintain this growth. Here we show that blocking phosphorylation of the AKT substrate, endothelial nitric oxide synthase (eNOS or NOS3), inhibits tumour initiation and maintenance. Moreover, eNOS enhances the nitrosylation and activation of endogenous wild-type Ras proteins, which are required throughout tumorigenesis. We suggest that activation of the PI3K-AKT-eNOS-(wild-type) Ras pathway by oncogenic Ras in cancer cells is required to initiate and maintain tumour growth.     

Improved conversion of methanol to single-cell protein by Methylophilus methylotrophus

The glutamate dehydrogenase gene of Escherichia coli has been cloned into broad host-range plasmids and can complement glutamate synthase mutants of Methylophilus methylotrophus. Assimilation of ammonia via glutamate dehydrogenase is more energy-efficient than via glutamate synthase, thus the recombinant organism converts more growth substrate, methanol, into cellular carbon.     

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution

Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.     

黄芩药渣固态发酵生产单细胞蛋白

对黄芩药渣的成分进行分析,采用稀硫酸时黄芩药渣进行预处理,并测定还原糖的含量;以黄芩药渣为原料,利用扣囊拟内孢霉固态发酵生成单细胞蛋白,确立了固态发酵培养基的最佳配比及pH值．正交试验结果表明,最佳发酵条件为：发酵温度30℃,接种量15%,含水量55%,培养时间24 h．在上述的条件下发酵后,药渣中粗蛋白的质量分数由8．99%提高到24．80%．     

微流控芯片在单细胞捕获中的应用

 单细胞捕获是单细胞水平研究的前提和重要组成部分。微流控芯片通常具有与细胞尺寸相当的微通道结构,并能操控纳升至皮升级的极小体积流体,非常适用于高通量的单细胞捕获,加上微流控芯片能够将其他多种操作单元集成在一起,为单细胞分析提供了一种效率高、消耗低的研究平台。概述并对比了多种涉及流体力学、光、电、磁、声等领域的微流控单细胞捕获技术的原理和应用,展望了其未来的研究方向。     

细胞凋亡与肿瘤治疗

细胞凋亡是机体维持自身稳定的一种生理机制,是由基因编码的控制细胞主动参与“自杀”的过程.细胞凋亡与肿瘤密切相关,已成为肿瘤治疗研究的新思路.本文主要阐述细胞凋亡及生理生化特征和肿瘤的形成与肿瘤的治疗.     

Mapping copy number variation by population-scale genome sequencing

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.