真菌基因组数据库概况

阐明不同生物基因组DNA序列信息及破译相关遗传学背景的基因组学是生物学和医学研究的核心学科.最近十年来真菌基因组学研究发生根本性的变化,真菌已成为真核生物基因组研究的最佳模式生物.至2008年6月,近80种隶属于真菌,微孢子虫和卵菌的全基因组序列公布,代表着最广泛的真核生物,它们的基因组大小从2.5 Mb～81.5 Mb.本丈整理了这些数据的相关信息.     

小鼠的遗传学研究

自20世纪初,小鼠的遗传学研究从宠物农场进入哈佛大学的实验室只有短短一百年的历史;但是,由于小鼠基因组与人类基因组高度同源、小鼠基因组改造手段非常成熟以及小鼠近交系、突变系和工具小鼠品系种类繁多,小鼠遗传学已成为发育生物学、功能基因组学和疾病机理研究的核心研究领域,小鼠也成为最重要的模式生物之一。近年来,随着小鼠基因组序列测序的完成,不同小鼠近交系品系特异的微卫星标记或单核苷酸多态性不断被发现,小鼠生理生化表型分析手段和数据也越来越完善,这些前期工作导致了目前大规模的基因剔除计划、基因突变计划及构建和分析重组近交系计划的实施。这些计划可能构成未来10￣20年中生命科学和医学研究领域的最重要的内容之一。     

鸡基因组研究新进展

鸡基因组测序草图的完成标志着禽类功能基因组时代的到来。鸡不仅是全世界广泛饲养且有重要经济价值的禽类,而且是极具生命科学研究价值的模式动物。因此,鸡基因组测序草图的完成将对遗传育种和生物学研究有重要的影响。本文综述了近年来鸡基因组研究的最新进展,主要内容包括鸡基因组的有关数据、物理图谱、遗传连锁图谱、比较基因组学、序列表达标签、生物信息学等方面所取得的成绩,同时对鸡基因组研究结果的应用前景进行了展望。     

基因组信息的整合与植物功能基因组学研究的策略

近年来,随着许多植物基因组测序和可利用序列的增加,相继建立了一些基于靶基因诱变的“反向”遗传学研究策略,如T—DNA诱变、基因敲除、基因沉默和超表达分析等。同时,DNA微阵列和基因芯片技术的发展使得快速、定量检测植物发育不同时期和不同组织器官的基因转录时空变化成为现实。作图技术的改进和来自不同物种基因组信息的整合也正在加速图谱克隆程序的简化和发展。因此,随着生物基因组测序工作日益增多,整合不同类群植物基因组的信息和资源,在植物功能基因组学研究中的重要性日趋显著。     

杨树——林木基因组学研究的模式物种

林木植物是大多数生态系统中的主要生命形式, 在所有陆地生态系统中具有最大的生物量和生物生产力, 因此它具有重要的经济及生态价值。林木植物特有的多年生习性使其生物学研究相对困难, 因此需要寻找一种适用于遗传学及分子生物学方法做精细分析的模式植物。杨属(Populus)植物作为林业研究的模式植物, 具有优良的实验特性: 容易进行种间杂交和无性繁殖; 生长迅速, 并已建立完善的遗传转化系统; 基因组相对较小, 约450～550 Mbp; 易于进行遗传研究; 适应性强, 生长速度快, 丰产性强。自2002年起, 美国能源部与多家研究机构正式启动了杨属植物基因组计划, 目前已接近完成。本文综述了模式植物杨树及其基因组学的研究进展。     

杨树--林木基因组学研究的模式物种

林木植物是大多数生态系统中的主要生命形式,在所有陆地生态系统中具有最大的生物量和生物生产力,因此它具有重要的经济及生态价值。林木植物特有的多年生习性使其生物学研究相对困难,因此需要寻找一种适用于遗传学及分子生物学方法做精细分析的模式植物。杨属（Populus）植物作为林业研究的模式植物,具有优良的实验特性：容易进行种间杂交和无性繁殖;生长迅速,并已建立完善的遗传转化系统;基因组相对较小,约450～550Mbp;易于进行遗传研究;适应性强,生长速度快,丰产性强。自2002年起,美国能源部与多家研究机构正式启动了杨属植物基因组计划,目前已接近完成。本文综述了模式植物杨树及其基因组学的研究进展。     

酵母全基因组芯片的应用

酵母作为最常用的模式生物,其全基因组测序最先完成。利用已知的酵母基因组信息,结合基因芯片技术,可进一步系统研究酵母的功能基因组表达。基因芯片技术是上世纪末发展起来的一项集分子生物学、生物信息学和电子学等科目的生物高新技术。酵母全基因组芯片,可以用以从基因表达水平,研究环境、物理、化学因子、毒理和药物作用的机制,在最终阐明酵母基因组功能的同时,为生物学研究提供更优化的模式生物模型。     

主要禾谷类作物比较基因组学研究策略与进展

随着拟南芥、水稻等模式植物基因组测序计划的完成, 比较基因组学作为一门新兴学科, 近年来发展迅速, 为植物基因组的进化、结构和功能研究开辟了新的途径。文章综述了比较基因组学在作物比较遗传作图、基因结构区域的微共线性、ESTs和蛋白质水平的比较以及基于比较基因组学的基因和QTL的克隆等方面内容与研究进展, 分析了不同水平上比较基因组学研究策略的原理、特点、可行性, 以期为利用模式生物的基因和基因组数据、采用比较基因组学策略克隆作物重要性状功能基因、阐明基因组结构与进化提供帮助。     

果蝇——打开生命科学之门的金钥匙

作为一种重要的模式生物,果蝇以其相对清晰的遗传学背景、丰富的表型特定、独特的发育特点而深受研究者青睐,为生命科学特别是遗传学和发育生物学的研究和发展提供了极大的方便。随着果蝇全基因组测序工作的完成,它在胚胎发育、基因表达调控、疾病发病机制等方面的研究中正在发挥更大的作用。     

鸡基因组研究进展

随着人类基因组计划实施而开展的动物基因组计划受到了科学界和各国政府的支持. 无论是作为一种实验用模式生物,还是作为一种农业经济动物,鸡都有着独特的生物学特性和经济学价值,因此,开展鸡基因组研究是十分有意义的. 综述了近年来鸡基因组研究（包括鸡基因组的有关参数、遗传连锁图、物理图谱、比较定位、表达序列标签和数量性状座位定位等方面）所取得的成就并对其前景进行了讨论.     

Avian genomics in the 21st century

The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. As the first livestock genome to be fully sequenced it leads the way for others to follow--with zebra finch later this year. The genome sequence and the availability of three million genetic polymorphisms are expected to aid the identification of genes that control traits of importance in poultry. As the first bird genome to be sequenced it is a model for the remaining 9,600 species thought to exist today. Many of the features of avian biology and organisation of the chicken genome make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. The availability of new tools such as whole-genome gene expression arrays and SNP panels, coupled with information resources on the genes and proteins are likely to enhance this position.     

Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS)

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis.     

Isolation and determination of the amino acid sequence of chicken calcitonin I from chicken ultimobranchial glands

A radioimmunoassay for chicken calcitonin in chicken ultimobranchial glands was established utilizing a rabbit antiserum against eel calcitonin. This assay method, which is about 100 times as sensitive as the usual bioassay for hypocalcemic activity, was used for monitoring chicken calcitonin during its purification. The immunoreactivity in chicken ultimobranchial extract was separated by SP-Sephadex C-25 chromatography into two fractions. Chicken calcitonin I, which was occurred in the major immunoreactive fraction, was further purified to homogeneity as shown by reverse phase HPLC. In the end, 39 nmol of chicken calcitonin I was obtained from 3,384 chickens following a 12,000-fold purification. The complete amino acid sequence of purified chicken calcitonin I was determined to be H-Cys-Ala-Ser-Leu-Ser-Thr-Cys-Val-Leu-Gly-Lys-Leu-Ser-Gln-Glu-Leu-His-Ly s-Leu-Gln-Thr-Tyr-Pro-Arg-Thr-Asp-Val-Gly-Ala-Gly-Thr-Pro-NH2 and confirmed by synthesis. The specific biological activity of chicken calcitonin I (4,500 MRCU/mg) was identical to that of eel calcitonin, which has the highest specific biological activity among the calcitonins so far isolated. Chicken calcitonin I resembled the calcitonins from the ultimobranchial glands both of salmon and eel in sequence, biological activity, and immunological property.     

From information to understanding: the role of model organism databases in comparative and functional genomics

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.     

Using multiple ontologies to integrate complex biological data

The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.     

蜜蜂——新兴的模式生物

蜜蜂作为具有重要经济价值和生态价值的社会性昆虫, 在诸如神经生物学和社会生物学等研究领域也具有很高的模型价值。蜜蜂基因组工程为深入认识蜜蜂的生物学特点,进一步发挥其在多个研究领域的模型价值奠定了分子基础。本文基于蜜蜂的生物学特点,介绍了蜜蜂作为模式生物所具备的优势,及其在学习和记忆、劳动分工、级型分化、免疫等热点领域的研究价值。通过总结和展望国内外蜜蜂生物学研究形势,呼吁国内相关各学科开展合作研究。     

Discrimination of Arcobacter butzleri isolates by polymerase chain reaction-mediated DNA fingerprinting

AIMS: The objective of this study was to subtype Arcobacter butzleri isolates using RAPD-PCR. METHODS AND RESULTS: Thirty-five A. butzleri isolates obtained from chicken carcasses were examined. PCR-mediated DNA fingerprinting technique with primers of the variable sequence motifs was used to detect polymorphism within the isolates. Eleven distinct DNA profiles were obtained as follows: Of the 35 strains, 10 as profile 4; seven as profile 1; five as profile 3; three as profiles 2 and 9; two as profile 10; one as profiles 5, 6, 7, 8 and 11. CONCLUSIONS: Chicken carcasses sold in markets were found to be contaminated with several different strains of A. butzleri. RAPD-PCR technique was found to be a useful technique for distinguishing A. butzleri isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of several different A. butzleri strains on chicken carcasses may indicate multiple sources of contamination. The epidemiological role of A. butzleri in human and animal diseases should be investigated further.