利用RNAi技术大规模分析基因功能的研究

将双链RNA导入细胞内会干扰与之同源的基因的表达 ,使生物体产生相应的功能缺陷表型 ,这种作用称为RNAi(RNAinterference)。针对人类、植物、微生物等大规模基因组测序后所面临的功能鉴定难题 ,着重探讨了RNAi的机制及其研究进展。复合物RISC和酶Dicer的发现揭示了RNAi导致同源基因沉默的作用机理。通过使用RNAi这种反向遗传学工具可使生物体产生相应的功能缺陷表型 ,从而确定未知基因的功能。因此RNAi对大规模分析动、植物基因功能的研究具有重要的作用。     

利用RNAi技术大规模分析基因功能的研究

将双链RNA导入细胞内会干扰与之同源的基因的表达,使生物体产生相应的功能缺陷表型,这种作用称为RNAi（RNA interference）。针对人类、植物、微生物等大规模基因组测序后所面临的功能鉴定难题,着重探讨了RNAi的机制及其研究进展。复合物RISC和酶Dicer的发现揭示了RNAi导致同源基因沉默的作用机理。通过使用RNAi这种反向遗传学工具可使生物体产生相应的功能缺陷表型,从而确定未知基因的功能。因此RNAi对大规模分析动、植物基因功能的研究具有重要的作用。     

噬菌体PaP2推定基因功能的研究

一个生物体基因组测序工作的完成 ,是进行基因组学和功能基因组学研究的基础 ,只是巨量工作的开始。本文通过运用GeneMark以及softberryfgenesV等软件在铜绿假单胞菌噬菌体PaP2基因组上共发现了 5 8个推定基因的编码区 ,为了解这些基因的功能 ,进行了两个方面的研究。一方面是将纯化噬菌体颗粒进行SDS PAGE分析 ,发现噬菌体PaP2至少含有 10个衣壳蛋白质 ,再转印到PVDF膜上 ,分别剪下各条带进行蛋白质N 末端氨基酸测序。根据蛋白质实测分子量 ,从 5 8个ORFs中找出编码相近分子量产物的ORFs ,再根据N 端氨基酸序列确定衣壳蛋白质的…     

基于比较基因组学解析耐酸乳杆菌G10的多碳源利用特征

【背景】耐酸乳杆菌（Lactobacillus acetotolerans）是白酒发酵过程中的优势乳酸菌,对白酒发酵具有重要作用。L. acetotolerans G10是分离自芝麻香型白酒发酵酒醅的一株能够利用多种碳源的菌株。【目的】基于全基因组测序,解析菌株G10多碳源利用机制。【方法】通过三代测序平台Oxford Nanopore完成菌株G10全基因组测序,分别利用Circlator和Prodigal对测序数据进行组装和基因预测;通过细菌基因组分析工具（bacterial pan genome analysis tool,BPGA）进行泛基因组分析。【结果】G10能够利用22种糖类及糖类衍生物,其全基因组大小为1 627 828 bp,含有1 878个编码基因;基于Koyto Encyclopedia of Genes and Genomes （KEGG）数据库注释获得292个碳源代谢相关基因,基于Carbohydrate-Active Enzymes （CAZy）数据库注释获得44个CAZy家族的编码基因。与其他发酵食品来源的耐酸乳杆菌相比,G10基因组最小,但其总基因数量以及...     

小鼠基因组草图完成

科学家们宣布已经完成了小鼠基因组的草图绘制的工作。华盛顿公告 :科学家们发表宣言说 :他们已经从实验小鼠的体中得到了其基因序列 ,并绘制出了基因草图 ,小鼠———一个种低等的啮齿类生物能使我们更多的了解人类生物体的构造 ,也使我们懂得怎样预防和控制疾病。来自 30余所大学和公司由数百名研究人员组成的序列分析工作组 ,积极投入到测序工作中 ,并分析小鼠的 2 5亿个碱基对的遗传信息。一些科学家把找到小鼠基因作为一个里程碑 ,其兴奋程度胜过去年人类基因组草图的完成 ,在麻省理工学院的基因研究中心参与基因测序工作的爱瑞克斯·…     

植物基因组测序的研究进展

近年来,随着测序技术的不断发展,基因组测序技术渐趋成熟并在动物和植物基因组上获得了越来越多的成功,大量植物的基因组的草图和精细图不断地被公布出来。比较和分析了三代测序技术各自的特点,对测序前的准备、基因组组装、注释和比较基因组学等方面的研究进展进行了详细的评述,阐明了植物基因组研究的特点和难点。通过植物的全基因组测序,研究者不仅可以获得该植物基因组和重要功能基因的序列信息,为从分子水平研究植物的分子进化、基因组成和基因调控等提供了一定的依据,而且还对即将测序的植物基因组研究具有重要的借鉴意义。     

全基因组测序在医学应用进展

目前,仍有很多疾病的发病机制未明确,然而,利用新一代测序技术对生物体进行全基因组测序,为很多疾病的发病机制提供了新的理论依据。那么,全基因组测序在医学那些方面有运用?本人通过阅读国外近五年有关全基因组测序的研究论文发现,全基因组测序能够广泛应用于遗传疾病、肿瘤、感染性疾病、传染性流行病、判断个体疾病易感性、生物进化等多种疾病的诊断与治疗。本文从遗传疾病、肿瘤、感染性疾病、传染性流行病、判断个体疾病易感性和生物进化几个方面综述全基因组测序在医学应用进展。     

基于棕尾别麻蝇线粒体COX1基因浅谈双翅目昆虫

本项研究对棕尾别麻蝇线粒体基因组进行完整的测序,通过分析68种已经测序的双翅目昆虫线粒体基因组COX1基因的序列,我们构建了68种双翅目昆虫系统发育树,发现在所构建的发育树中所有双翅目物种聚集到相对应的科上跟传统的昆虫形态学经典分类一致。68个物种两两遗传距离平均值为0.18,棕尾别麻蝇与Bactrocera minax遗传距离最大为0.255,与Sarcophaga peregrina最小为0.068。     

规模化蛋白质组表达谱的研究进展及其挑战

介绍了规模化蛋白质组表达谱研究的基本技术和方法,简要概述了部分已完成基因组测序的生物体的蛋白质组表达谱研究进展．分析了上述研究所面临的问题和挑战。     

2008年国内外生物技术研究进展（下）——基因测序、功能基因、疑难病治疗

1基因测序技术 2008年基因测序研究的一大特点是出现了简便、快捷、经济的基因组测序新技术,为个体医疗铺平了道路：使得动植物基因组测序、微生物基因组测序工作又大大前进了一步。     

Building the blueprint of life

With recent breakthroughs in experimental microbiology making it possible to synthesize and implant an entire genome to create a living cell, the challenge of constructing a working blueprint for the first truly minimal synthetic organism is more important than ever. Here we review the significant progress made in the design and creation of a minimal organism. We discuss how comparative genomes, gene essentiality data, naturally small genomes, and metabolic modeling are all being applied to produce a catalogue of the biological functions essential for life. We compare the minimal gene sets from three published sources with functions identified in 13 existing gene essentiality datasets. We examine how genome-scale metabolic models have been applied to design a minimal metabolism for growth in simple and complex media. Additionally, we survey the progress of efforts to construct a minimal organism, either through implementation of combinatorial deletions in Bacillus subtilis and Escherichia coli or through the synthesis and implantation of synthetic genomes.     

How to make a minimal genome for synthetic minimal cell

As a key focus of synthetic biology, building a minimal artificial cell has given rise to many discussions. A synthetic minimal cell will provide an appropriate chassis to integrate functional synthetic parts, devices and systems with functions that cannot generally be found in nature. The design and construction of a functional minimal genome is a key step while building such a cell/chassis since all the cell functions can be traced back to the genome. Kinds of approaches, based on bioinformatics and molecular biology, have been developed and proceeded to derive essential genes and minimal gene sets for the synthetic minimal genome. Experiments about streamlining genomes of model bacteria revealed genome reduction led to unanticipated beneficial properties, such as high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Recent achievements in chemical synthesis technology for large DNA segments together with the rapid development of the whole-genome sequencing, have transferred synthesis of genes to assembly of the whole genomes based on oligonucleotides, and thus created strong preconditions for synthesis of artificial minimal genome. Here in this article, we review briefly the history and current state of research in this field and summarize the main methods for making a minimal genome. We also discuss the impacts of minimized genome on metabolism and regulation of artificial cell.     

Fast algorithms for large-scale genome alignment and comparison

We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has been used successfully to align the entire human and mouse genomes to each other, and to align numerous smaller eukaryotic and prokaryotic genomes. A new module permits the alignment of multiple DNA sequence fragments, which has proven valuable in the comparison of incomplete genome sequences. We also describe a method to align more distantly related genomes by detecting protein sequence homology. This extension to MUMmer aligns two genomes after translating the sequence in all six reading frames, extracts all matching protein sequences and then clusters together matches. This method has been applied to both incomplete and complete genome sequences in order to detect regions of conserved synteny, in which multiple proteins from one organism are found in the same order and orientation in another. The system code is being made freely available by the authors.     

Genomes and knowledge - a questionable relationship?

The availability of bacterial genome sequences has ushered in an era of post-genomic research - accelerating and often enabling molecular genetic analyses. For bacteriologists focussing on an individual bacterium, comparing genomes has also led to a greater understanding of their favoured organism through contextualization. But how does the value of such contextualization vary with the number of available genomes? It seems that for most genome metrics, comparison against approximately 100 genomes is sufficient, with comparison against further genomes not considerably affecting the contextual knowledge gained. It appears that quality, rather than quantity, might be the most important factor when comparing genomes.     

A computational approach to the functional screening of genomes

Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by-gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76 of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic network. These modifications led to a genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured in bacteria. We conclude then that ViCe is able to “live in silico.”     

Azolla--a model organism for plant genomic studies

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.     

Fitting the niche by genomic adaptation

Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms. Many research groups have linked the adaptation of an organism to a niche to large changes in genome size and content. A number of recent papers have underlined the degree to which the genomes of different organisms are a reflection of the opportunities and constraints imposed by their chosen niche.     

A bigger mouse? The rat genome unveiled

Rattus norvegicus is an important experimental organism and interesting to evolutionary biologists. The recently published draft rat genome sequence provides us with insights into both the rat's evolution and its physiology. We learn more about genome evolution and, in particular, the adaptive significance of gene family expansions and the evolution of rodent genomes, which appears to have decelerated since the divergence of mouse and rat. An important observation is that some regions of genomes, many in noncoding regions, show very high sequence conservation, while others show unexpectedly fast evolution. Both of these may be pointers to functional significance.     

Determination of the core of a minimal bacterial gene set.

The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.     

Consequences of genome duplication

Polyploidy has been widely appreciated as an important force in the evolution of plant genomes, but now it is recognized as a common phenomenon throughout eukaryotic evolution. Insight into this process has been gained by analyzing the plant, animal, fungal, and recently protozoan genomes that show evidence of whole genome duplication (a transient doubling of the entire gene repertoire of an organism). Moreover, comparative analyses are revealing the evolutionary processes that occur as multiple related genomes diverge from a shared polyploid ancestor, and in individual genomes that underwent several successive rounds of duplication. Recent research including laboratory studies on synthetic polyploids indicates that genome content and gene expression can change quickly after whole genome duplication and that cross-genome regulatory interactions are important. We have a growing understanding of the relationship between whole genome duplication and speciation. Further, recent studies are providing insights into why some gene pairs survive in duplicate, whereas others do not.