Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.     

Epigenetics in human disease and prospects for epigenetic therapy

Epigenetic mechanisms, which involve DNA and histone modifications, result in the heritable silencing of genes without a change in their coding sequence. The study of human disease has focused on genetic mechanisms, but disruption of the balance of epigenetic networks can cause several major pathologies, including cancer, syndromes involving chromosomal instabilities, and mental retardation. The development of new diagnostic tools might reveal other diseases that are caused by epigenetic alterations. Great potential lies in the development of 'epigenetic therapies'--several inhibitors of enzymes controlling epigenetic modifications, specifically DNA methyltransferases and histone deacetylases, have shown promising anti-tumorigenic effects for some malignancies.     

黄瓜花叶病毒小青菜分离物RNA3全长序列分析

对侵染十字花科小青菜的黄瓜花叶病毒YN分离物（CMV-YN）RNA3进行全长克隆和序列分析．CMV-YNRNA3全长2220nt,分别编码279个氨基酸的3a蛋白和218个氨基酸的CP．序列同源性比较结果如下;CMV-YNRNA3核苷酸及其编码蛋白的氨基酸序列与亚组IA株系CMV-Fny、亚组IB株系CMV-Nt9、亚组Ⅱ株系CMV-Q的同源性,RNA3序列分别为92．7％、96．7％、74．2％,3a蛋白氨基酸序列分别为96．4％、98．6％、83．2％,CP氨基酸序列分别为97．7％、98．2％、83．1％．该结果表明CMV-YN与亚组IB株系CMV-Nt9的同源关系更密切．对CP核苷酸序列的系统进化树分析表明：CMV-YN归属于亚组IB,本研究为首次报道侵染我国十字花科植物的CMV基因组序列．     

A Polycomb-based switch underlying quantitative epigenetic memory

The conserved Polycomb repressive complex 2 (PRC2) generates trimethylation of histone 3 lysine 27 (H3K27me3), a modification associated with stable epigenetic silencing. Much is known about PRC2-induced silencing but key questions remain concerning its nucleation and stability. Vernalization, the perception and memory of winter in plants, is a classic epigenetic process that, in Arabidopsis, involves PRC2-based silencing of the floral repressor FLC. The slow dynamics of vernalization, taking place over weeks in the cold, generate a level of stable silencing of FLC in the subsequent warm that depends quantitatively on the length of the prior cold. These features make vernalization an ideal experimental system to investigate both the maintenance of epigenetic states and the switching between them. Here, using mathematical modelling, chromatin immunoprecipitation and an FLC:GUS reporter assay, we show that the quantitative nature of vernalization is generated by H3K27me3-mediated FLC silencing in the warm in a subpopulation of cells whose number depends on the length of the prior cold. During the cold, H3K27me3 levels progressively increase at a tightly localized nucleation region within FLC. At the end of the cold, numerical simulations predict that such a nucleation region is capable of switching the bistable epigenetic state of an individual locus, with the probability of overall FLC coverage by silencing H3K27me3 marks depending on the length of cold exposure. Thus, the model predicts a bistable pattern of FLC gene expression in individual cells, a prediction we verify using the FLC:GUS reporter system. Our proposed switching mechanism, involving the local nucleation of an opposing histone modification, is likely to be widely relevant in epigenetic reprogramming.     

A novel cancer therapy using a M?ssbauer-isotope compound

Cancer radiotherapy uses high doses of ionizing radiation (1-10(2) Gy; 10(2)-10(4) rad) because only a small fraction of the absorbed dose leads to lethal double-strand breaks in DNA. These breaks are more efficiently produced by Auger electrons (1-10 eV nm-1) generated in proximity to the DNA. The energy of these electrons (on average 21 electrons for the decay of 125I) is dissipated within 10-100 nm of the Auger event and produces multiple double-strand DNA breaks. A single Auger event can be lethal to a cell and is comparable to more than 10(5) photon absorption events in conventional radiotherapy. We now report that 57Fe(III).bleomycin, administered to malignant cells in vitro and in vivo and irradiated with resonant M?ssbauer gamma rays (14.4 keV), causes ablation of the malignant cells, presumably by Auger cascade, with extremely small radiation doses--about 10(-5) Gy. As a basis for comparison, about 5 Gy is necessary to achieve a similar effect with conventional radiotherapy.     

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

Epigenetic information is frequently erased near the start of each new generation. In some cases, however, epigenetic information can be transmitted from parent to progeny (multigenerational epigenetic inheritance). A particularly notable example of this type of epigenetic inheritance is double-stranded RNA-mediated gene silencing in Caenorhabditis elegans. This RNA-mediated interference (RNAi) can be inherited for more than five generations. To understand this process, here we conduct a genetic screen for nematodes defective in transmitting RNAi silencing signals to future generations. This screen identified the heritable RNAi defective 1 (hrde-1) gene. hrde-1 encodes an Argonaute protein that associates with small interfering RNAs in the germ cells of progeny of animals exposed to double-stranded RNA. In the nuclei of these germ cells, HRDE-1 engages the nuclear RNAi defective pathway to direct the trimethylation of histone H3 at Lys?9 (H3K9me3) at RNAi-targeted genomic loci and promote RNAi inheritance. Under normal growth conditions, HRDE-1 associates with endogenously expressed short interfering RNAs, which direct nuclear gene silencing in germ cells. In hrde-1- or nuclear RNAi-deficient animals, germline silencing is lost over generational time. Concurrently, these animals exhibit steadily worsening defects in gamete formation and function that ultimately lead to sterility. These results establish that the Argonaute protein HRDE-1 directs gene-silencing events in germ-cell nuclei that drive multigenerational RNAi inheritance and promote immortality of the germ-cell lineage. We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to regulate important biological processes.     

新型均苯型芳香族聚酰亚胺的研究

以二步法制备了一种新型均苯型芳香族聚酰亚胺。测定了聚酰亚胺的预聚体－－聚酰胺酸特性粘度（Iυ）随反应时间的变化曲线,聚酰亚胺以N－甲基－2－吡咯烷酮（NMP）中的特性粘度在1.2dL/g左右,玻璃化温度高于250℃,在氧气中失重5％的温度在500℃以上。经红外光谱测定,样品在1780cm^-1和1380cm^-1附近观察到聚酰亚胺的特征峰。     

A genomic view of immunology

The outstanding problems facing immunology are whole system issues: curing allergic and autoimmune disease and developing vaccines to stimulate stronger immune responses against pathogenic organisms and cancer. We hope that the human genome sequence will reveal the molecular checks and balances that ensure both an effective immunogenic response against pathogenic microorganisms and a suitably tolerogenic response to self antigens and innocuous environmental antigens. Three synergistic approaches--sequence homology searches, messenger RNA expression profiling on microarrays, and mutagenesis in mice--provide the best opportunities to reveal, in the genome sequence, key proteins and pathways for targeting by new immunomodulatory treatments.     

Genetic and structural analyses suggest that a novel SPG3A mutation causes severe phenotypes of hereditary spastic paraplegia

Hereditary spastic paraplegia (HSP) (MIM# 182600, etc.) is a group of heterogeneous neurodegenerative disorders, characterized by lower limb spasticity, hy- perreflexia, progressive spastic gait abnormalities and an extensor-plantar response[1]. The genot…     

L-精氨、5-氟脲嘧啶对艾氏腹水癌鼠的治疗分析

将１００只小白鼠制成ＥＡＣ模型鼠,随机分成四组,分别向腹腔注射Ｌ－精氨酸、５－氟脲嘧啶、Ｌ－精氨酸＋５氟脲嘧啶、生国水、同时记录各组小鼠自然存活时间、处死时平均腹水量、每毫升腹水中肿瘤细胞数、接种ＥＡＣ细胞两周后平均体重,以探讨Ｌ－精氨酸、５－氟脲嘧啶对艾氏腹水癌小鼠的治疗效果。实验结果显示：Ｌ精氨酸＋５氟脲嘧啶组小鼠自然存活时间最长,无腹水。说明两者联合使用具有一定抗癌作用,而且延长了ＥＡＣ小鼠     

A novel method for tracking pedestrians from real-time video

This novel method of Pedestrian Tracking using Support Vector (PTSV) proposed for a video surveillance instrument combines the Support Vector Machine (SVM) classifier into an optic-flow based tracker. The traditional method using optical flow tracks objects by minimizing an intensity difference function between successive frames, while PTSV tracks objects by maximizing the SVM classification score. As the SVM classifier for object and non-object is pre-trained, there is need only to classify an image block as object or non-ob-ject without having to compare the pixel region of the tracked object in the previous frame. To account for large motions between successive frames we build pyramids from the support vectors and use a coarse-to-fine scan in the classification stage. To accelerate the training of SVM, a Sequential Minimal Optimization Method (SMO) is adopted. The results of using a kernel-PTSV for pedestrian tracking from real time video are shown at the end. Comparative experimental results showed that PTSV improves the reliability of tracking compared to that of traditional tracking method using optical flow.     

一种从已调信号产生系统时钟的新方法

介绍一种从调频信号中获取系统时钟的新方法,该方法是在分频器中应用调制补偿、及Σ△抖动技术。应用该技术,基于全数字锁相环的调频广播发射机可以产生更高频率的时钟信号,以用于基带信号处理。     

Sequence organization and genomic complexity of primate theta 1 globin gene, a novel alpha-globin-like gene

The alpha-like and beta-like globin genes have provided a paradigm for the study of molecular evolution and regulation of multigene families in eukaryotes. The human alpha-globin gene cluster, which is on chromosome 16 (ref. 1), consists of six genes arranged in the order 5'-zeta(embryonic)-psi zeta-psi alpha 2-psi alpha 1-alpha 2(adult)-alpha 1(adult)-3'. DNA sequencing data have demonstrated that zeta (ref. 6) and alpha 2 (or alpha 1, refs 7-9) are the embryonic and adult genes, respectively, while psi zeta (ref. 6), psi alpha 2 (ref. 5) psi alpha 1 (ref. 10) are all inactive pseudogenes. Restriction mapping analysis has shown that the structure of this locus in several anthropoid primates is nearly identical to that of the human. Recently, we have isolated the adult alpha-globin gene region from orang-utan, olive baboon and rhesus macaque by molecular cloning. We report here the complete nucleotide sequence of a gene located immediately downstream from the adult alpha 1-globin gene of the orang-utan, along with its flanking DNA. We designate this gene as theta 1, and show that it contains the essential sequence elements required for an expressive gene. The putative polypeptide is 141 amino acids long, identical to that of the alpha- or zeta-globin, but its predicted amino-acid sequence is nearly as different from the orang-utan alpha-globin (55 differences) as the human zeta-globin is from the human alpha-globin (59 differences), suggesting an ancient history for the theta 1-globin gene. Results of blot hybridization experiments using the cloned orang-utan theta 1 gene sequence as probe demonstrate a similar alpha 2-alpha 1-theta 1 linkage map existing in the human genome. Furthermore, multiple copies of sequences homologous to the theta 1 gene are detected in both human and orang-utan. These results cast a new light on the primate alpha-globin gene family, and have intriguing implications for the existence of previously unreported, functional globin-like gene(s) in the primate genomes.     

A genomic perspective on membrane compartment organization

Now that whole genome sequences are available for many eukaryotic organisms from yeast to man, we can form broad hypotheses on the basis of the relative expansion of protein families. To investigate the molecular mechanisms responsible for the organization of membrane compartments, we identified members of the SNARE, coat complex, Rab and Sec1 protein families in four eukaryotic genomes. Of these families only the Rab family expanded from the unicellular yeast to the multicellular fly and worm. All families were expanded in humans, where we find 35 SNAREs, 60 Rabs and 53 coat complex subunits. In addition, we were able to resolve the SNARE class of proteins into four distinct subfamilies.     

克隆植物珠芽蓼基因组DNA的提取及RAPD鉴定

高原植物体内所含有的酚类、多糖、色素等次生代谢物质严重影响提取其基因组DNA的得率和纯度,是导致后续分子操作失败的主要原因.运用一种新改进的CTAB法对变色硅胶保存的高原植物珠芽蓼(Polygonumviviparum)叶片进行基因组DNA的提取,采取常温下沉淀DNA,增加洗涤沉淀的体积分数为70%乙醇用量和洗涤时间等措施,有效地去除了酚类、多糖、色素等物质的干扰,减少了褐化现象的发生.样品检测所得DNA片段均在48 kb左右,电泳谱带呈线状,无拖尾现象;紫外分光光度计检测,A260nm/A280nm值在1.7~1.9之间.RAPD扩增结果表明,此方法提取的DNA无论在质量和纯度上都较理想.     

The genomic and epidemiological dynamics of human influenza A virus

The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.