海神单胞菌属的基因组测序数据分析

海神单胞菌属（Neptunomonas）于1999年被首次鉴定,目前包含8个菌种,其中6个已经完成全基因组测序。本文总结了海神单胞菌属的菌种特征和基因组信息,并利用基因组测序数据对该菌属的碳源利用途径、聚羟基脂肪酸酯代谢途径和芳香族化合物降解途径进行了分析。研究发现,海神单胞菌属具有完整的糖酵解和乙酸利用途径,普遍含有Ⅰ型和Ⅲ型的聚羟基脂肪酸酯合成酶,存在芳香族化合物的降解途径。基因组测序数据分析结果可以为海神单胞菌属在聚羟基脂肪酸酯合成与环境治理保护等领域的应用提供理论依据。     

酿酒酵母功能基因组学研究进展

随着各种微生物基因组序列信息的积累和测序工作的不断完成,酿酒酵母基因组学研究的重点已由传统的结构基因组学发展到了功能基因组学,并从单一的基因功能研究转向多个或整个基因组系统地去了解真核生物生命活动的本能。对基因组学水平上酿酒酵母功能基因的生物芯片分析,代谢通路和功能图谱,以及比较基因组学研究进行综述。     

The complete genome of an individual by massively parallel DNA sequencing

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.     

Primate eta-globin DNA sequences and man's place among the great apes

Molecular studies indicate that chimpanzee and gorilla are the closest relatives of man (refs 1-7 and refs therein). The small molecular distances found point to late ancestral separations, with the most recent being between chimpanzee and man, as judged by DNA hybridization. Kluge and Schwartz contest these conclusions: morphological characters group a chimpanzee-gorilla clade with the Asian ape orang-utan in Kluge's cladistic study and with an orang-utan-human clade in Schwartz's study. Clearly, extensive sequencing of nuclear DNA is needed to resolve by cladistic analysis the branching order within Hominoidea. Towards this goal, we are sequencing orthologues of the primate psi eta-globin locus. Here, we compare the newly completed sequences of orang-utan and rhesus monkey with human, chimpanzee, gorilla, owl monkey, lemur and goat orthologues. Our findings substantially increase the evidence indicative of a human-chimpanzee-gorilla clade with ancestral separations around 8 to 6 Myr ago. We also verify that neutral hominoid DNA evolved at markedly retarded rates.     

最优公共交货期单机提前/拖后调度和对应的批次送货

本文考虑了一个包含工件生产和工件送货的单机调度问题。目标是寻找所有工件的公共交货期和每个工件的送货时间使得工件所受到惩罚(提前／拖后惩罚,送货费用等)的值最小。完成的工件按照批次进行送货,所有在公共交货期前完工的工件在最优交货期时间一起交付,对批次送货没有量的约束。本文确定了最优公共交货期,并给出了相应的排序。     

禾本科同源染色体对趋同进化的比较基因组学

多个禾本科物种全基因组测序的相继完成为禾本科植物基因组物理和遗传结构进化历史的研究提供了前所未有的良好机遇。以五个禾本科物种为研究对象,利用基因同源共线性方法对其基因组进行了比对分析,获得了物种的同源信息,并根据同源信息结合基因组同源结构分析,确定了物种基因组内和基因组间的同源染色体片段。比较分析同源染色体对上重复DNA片段之间的分子距离,初步揭示了禾本科植物同源染色体对间趋同进化规律,研究结果有助于理解染色体结构受非正常遗传重组影响的进化机制。     

2018年农业科学热点回眸

 盘点了2018年农业科学研发取得的一些重要成果。小麦、水稻、玉米及大豆、荞麦、马铃薯等主要粮食作物在基因组测序、分子育种、遗传机理解析、氮高效利用、起源演化、基因编辑等方面获得快速发展,发布了世界首个六倍体小麦基因组图谱,完成了3000份水稻基因组计划和中黄13的基因组测序,克隆了一系列产量、品质及抗病虫害基因,解析了一些重要的生长发育调控机制。油菜、棉花、茶叶、烟草等主要经济作物在基因组学、风味调控机理、光合效率等方面有所突破,中国油菜基础研究与应用已达到国际领先水平。此外,水稻、小麦、番茄、苹果等作物的病虫害防治,畜禽的繁殖、品种改良和疾病防治,蜜蜂的基因组和转录组解析,蚕病害防治和驯化历史,化肥和水稻品种对气候变化的影响、气候变化对作物产量的影响,茎叶类蔬菜和食用豆收获设备、油菜播种机等农机农艺领域均有突破性进展。     

青岛文昌鱼DAD1样蛋白基因的克隆和同源性分析

dud1基因为一种内源性细胞凋亡抑制子基因，在发育中可能执行着重要功能．我们通过对青岛文昌鱼18小时神经胚cDNA文库进行测序，获得文昌鱼dud1样基因的2个cDNA片断，经拼接首次得到含有完整读框的文昌鱼dud1样基因的cDNA序列，其演绎的氨基酸序列与人、鼠、鸡、非洲爪蟾、果蝇、线虫、扁豆、番茄的DAD1蛋白的同源性分别为73．5％、73．5％、67．5％、70．9％、67．5％、55．5％、41．9％、41．8％．结果证实青岛文昌鱼dud1样基因在进化上具有高度的保守性，并且在进化上更接近于脊椎动物．     

排序决策的直觉模糊数方法

为了更细腻地描述作为比较评价的语言信息,用一个直觉模糊数表示两两对象的比较评价,将直觉模糊数表示为由上理想模糊数和下理想模糊数的二元模糊数组,定义了关于直觉模糊数的一种运算并且给出了基于结构元表示的排序比较方法;在排序决策过程中,通过对相对属性判断值的规范化处理完成对一组对象的排序,实现了优选的目的.结果表明:通过下、上理想模糊数将结构元理论应用到直觉模糊数上,简化了计算,同时直觉模糊数在表达信息上考虑人的犹豫度,使得在表达语言信息上较模糊数更贴近现实,排序结果自然更精确.     

病态信息修正中的建议值排序模型研究

对于生成的建议值,提出了建议值的三种排序模型,分别是变换次数排序模型、距离排序模型和相似度排序模型,使得用户能够方便和准确地选择到正确的建议值。     

晶圆加工生产线蚁群优化排程方法

从实际应用的角度,分析了晶圆加工生产线排程特点,建立了晶圆加工生产线排程数学模型(LSM-WFL),给出了以瓶颈设备为核心、蚁群优化算法为主要工具的晶圆加工生产线排程方法(LSA-WFL)。基于实际生产线模型仿真验证的结果表明,LSA-WFL能够在允许的时间内获得晶圆加工生产线排程方案。     

基于分级规划的加工方法排序规则研究

结合工艺决策的分级规划策略,构造了一种新的实用化的加工方法排序规则,该排序规则将传统排序规则分解成两个相关的部分：工序排序规则与工步排序规则．工序排序规则代表了排序规则的普遍性,描述了一类零件的总体加工过程,只与加工方法有关,与组成零件的形状特征等其他因素无关;工步排序规则代表了排序规则的特殊性,描述了工序中各特征的加工顺序,与特征有关而与加工方法无关．     

高通量转录组测序的数据分析与基因发掘

高通量转录组测序(RNA-seq)是在转录组水平上进行深度测序的一项技术,为真核生物转录组学的研究开创了新平台,但同时测序所得到的海量数据的生物信息学分析成为科研工作者的一大挑战。对转录组测序技术进行了阐述,重点介绍了转录组测序后的数据分析,以及在真核生物尤其是非模式物种中的基因发掘方法。     

序批式生物膜反应器脱氮除磷技术

详述了序批式生物膜（SBBR）技术的工作原理与技术特点，介绍了序式生物膜（SBBR）技术在污水生物处理中的研究与应用现状，探讨了序批式生物膜反应器（SBBR）在城市污水生物脱氮除磷中发展与应用。     

CAPP系统中工序工步排序的研究现状与发展趋势

介绍了计算机辅助工艺设计中工序工步排序的发展过程和研究现状,并对目前排序中所采用的理论与方法进行了分析,最后结合当前技术的发展特点,提出了作者对工序工步排序未来发展趋势的看法。     

An integrated semiconductor device enabling non-optical genome sequencing

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.     

Two levels of protection for the B cell genome during somatic hypermutation

Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by cytosine deamination by the activation-induced deaminase (AID) and completed by error-prone processing of the resulting uracils by mismatch and base excision repair factors. Somatic hypermutation represents a threat to genome integrity and it is not known how the B cell genome is protected from the mutagenic effects of somatic hypermutation nor how often these protective mechanisms fail. Here we show, by extensive sequencing of murine B cell genes, that the genome is protected by two distinct mechanisms: selective targeting of AID and gene-specific, high-fidelity repair of AID-generated uracils. Numerous genes linked to B cell tumorigenesis, including Myc, Pim1, Pax5, Ocab (also called Pou2af1), H2afx, Rhoh and Ebf1, are deaminated by AID but escape acquisition of most mutations through the combined action of mismatch and base excision repair. However, approximately 25% of expressed genes analysed were not fully protected by either mechanism and accumulated mutations in germinal centre B cells. Our results demonstrate that AID acts broadly on the genome, with the ultimate distribution of mutations determined by a balance between high-fidelity and error-prone DNA repair.     

混流装配线平衡和排序问题研究综述

系统地总结了现有的混装线平衡和排序的主要研究内容,从混装线平衡、混装线排序及混装线平衡与排序的集成三个方面对现有了研究进展与研究方法进行了分析和总结,并对一些特殊形式的混装线进行了分析.最后提出了混装线平衡与排序问题需要进一步研究的几个方向.     

多方案排序中指标权重界限分析方法

本文详细讨论了多方案排序中指标权重界限分析方法,建立了满足保序性和弱保序性的指标权重界限模型,用以认识和确定各指标权重变化对排序结果的影响。最后,利用该方法对某气田开发方案排序的权重界限值进行了计算分析。     

项目风险排序研究综述

对风险排序的概念、排序指标以及排序方法进行了综述。指出近期的研究在评价指标上除了考虑风险概率和后果外,还考虑了风险可预见性、管理边际效率、项目承受能力等因素;在排序方法上,系统科学、模糊理论方法、决策论等理论和方法的应用,使得庞大项目复杂风险的多层次性、复杂相关性等问题在一定程度上得到了解决。但研究缺乏对风险排序的逻辑机理和理论基础的深入分析,排序指标的全面性、合理性仍不够充分。