细菌人工染色体载体的发展和应用

细茵人工染色体(Bacterial artificial chromosome,BAC)是在大肠杆菌F质粒的基础上建成的高容量、低拷贝的质粒载体.BAC载体已广泛应用于基因组文库的构建及筛选、基因组测序、新基因的发现、图位克隆、BAC微阵列、转基因和动物品种资源保存等方面.本文综述了BAC载体的发展及其应用.     

细菌人工染色体的修饰及其转基因应用研究

细菌人工染色体(Bacterial Artificial Chromosome,BAC)是一种新发展起来的DNA载体系统,它具有容量大、遗传特性稳定、易于操作等优点.广泛的应用于基因组文库构建、基因功能分析等方面.随着基因组测序工程的实施与完成,如何对包含完整基因信息的特定细菌人工染色体进行有目的修饰已成为功能基因组学研究的一个重要环节.BAC载体转基因技术可能成为避开基因打靶获得高效表达的转基因生物的另一途径.本文介绍了BAC作为转基因载体的几种修饰方法及其在转基因研究上的应用.     

细菌人工染色体文库的构建及应用

细菌人工染色体（BAC）是第二代大片段DNA的克隆载体系统,具有容量大、嵌合率低、遗传特性稳定、转化效率高、插入片段易回收、操作简便等优点,因而被广泛应用于基因组较大的真核生物基因组研究中,并发挥着前所未有的重要作用。本文综述了BAC的发展,利用此载体构建基因组文库的程序和鉴定方法,及其在物理图谱构建、图位克隆、基因组测序、转基因技术等研究中的应用。     

BAC克隆及复杂基因组文库技术

BAC（细菌人工染色体）克隆技术是复杂基因组研究中不可缺少的工具,有关基因组研究的许多技术都是由BAC为基础发展起来的,包括大片段基因组文库的构建、重叠群的构建、全基因测序及图位基因克隆等,后又产生植物转基因的BAC克隆载体,这在人类、动物、植物等基因组研究中已广泛应用,取得令人瞩目的成就,该文将就这些研究技术及进展作一综述。     

细菌人工染色体基因组文库构建方法的改进

目的:建立一种改进的更简便、易操作的细菌人工染色体(BAC)文库构建方法。方法:在构建猪霍乱沙门氏菌基因组大片段DNA的BAC文库时,对改进的基因组BAC文库构建方法和常规的BAC文库构建方法进行比较。结果:利用改进的方法可简便快速地构建猪霍乱沙门氏菌基因组BAC文库。结论:使用2种方法构建BAC文库,其转化效率,以及在BAC克隆中插入的DNA片段的大小和BAC克隆的稳定性等都相同,从而表明改进的方法更简单、更方便,它能使BAC文库的构建更为高效。     

95年初商业化世界第一个BAC文库

California工科大学宣布,早的话95年初在美国商业化对基因鉴定有用的人染色体BAC(Bacteria Artificial Chromosome:细菌人工染色体)文库。该BAC文库是美国California工科大学生物部客座研究员静谷裕明、Mel Simon等开发的。95年初将商业权利转让给美国Research Genetics公司(亚拉巴马州)。Research Genetics公司向全世界供应。销售方法、价格等现在还未定。法国Centre d’Etude du Polymorhism(CEPH)也表示着手构建BAC文库,完成后供全世界使用,95年以后广泛普及BAC文库。 静谷等开发的BAC文库现有125000个克隆,96个穴的滴定盘约1250个。预定最终要完成15万个克隆。滴定盘约1500个的BAC文库。能插入到BAC的基因大小平均为125000个碱基(125kb)。如果不是考虑重复的话,约30亿碱基对大小的人染色体也包括在BAC内共约24000个基因。15万个克隆的BAC文库能覆盖人染色体的6～7倍。 静谷等从89年着手BAC文库的研究,从93年底与美国很多企业、大学进行BAC文库的评价,并实用     

细菌人工染色体（BAC）及其分析和修饰方法简介

细菌人工染色体是一种新发展起来的DNA载体系统,它具有容量大、遗传特性稳定、易于操作等优点.在基因文库构建和基因功能分析等方面有广泛的应用.综述了近年来发展起来的对BAC进行分析和修饰的一些方法.     

基因组细菌人工染色体文库(BAC)的构建及应用

细菌人工染色体 (BAC)是一种承载DNA大片段的克隆载体系统 ,用于人、动物和植物基因组文库构建。BAC具有插入片断大、嵌合率低、遗传稳定性好、易于操作等优点。BAC文库的构建是基因组较大的真核生物基因组学研究的重要基础 ,可用于真核生物重要基因及全基因组物理作图、重要性状基因的图位克隆、基因结构及功能分析。本文主要综述了细菌人工染色体的构建与其鉴定 ,及其在物理图谱构建、图位克隆、转基因技术等研究上的应用。     

Red/ET 同源重组介导细菌人工染色体的快速修饰

随着基因组测序工程的实施与完成,如何对包含完整基因信息的特定细菌人工染色体 (BAC) 进行有目的修饰,已成为功能基因组学研究的一个重要环节 . 应用新近优化的 Red/ET 同源重组技术对目标 BAC 进行修饰,以 pSC101-BAD-gbaA 为依托质粒,采用 rpsL-neo 为正 / 反向筛选系统,可以快速、高效地对 BAC 进行剪切、插入、替换等操作,其中能够进行抗性筛选的一步 BAC 修饰只需一周时间,以插入非抗性标记基因 Cre 为代表的两步 BAC 修饰在两周内即可完成 . 通过阿拉伯多糖诱导调控和简单地变化培养温度,能使 pSC101-BAD-gbaA 依托质粒在发挥完 Red/ET 同源重组作用后自然消失,最终获得完整而纯净的修饰后 BAC ,为加快功能基因组学研究提供了一个可靠的实验平台 .     

BAC及其转基因研究进展

本文综述了细菌人工染色体(BacterialArtificialChromsomes,BAC)的构建、物理图谱制作方法及其靶位精细操作策略的研究进展。同时,简要介绍了BAC转基因在基因功能以及基因表达与调控研究中的应用 。     

Digital mapping of bacterial artificial chromosomes by fluorescence in situ hybridization

The bacterial artificial chromosome (BAC) has become the most popular tool for cloning large DNA fragments. The inserts of most BAC clones average 100-200 kilobases (kb) and molecular characterization of such large DNA fragments is a major challenge. Here we report a simple and expedient technique for physical mapping of BAC inserts. Individual BAC molecules were immobilized on glass slides coated with Poly-L-lysine. The intact circular BAC molecules were visualized by fluorescence in situ hybridization using BAC DNA as a probe. The 7.4 kb BAC vector was extended to approximately 2.44 kb per micrometer. Digitally measured linear distances can be transformed into kilobases of DNA using the extension of BAC vector as a standard calibration. We mapped DNA fragments as small as 2 kb directly on circular BAC molecules. A rice BAC clone containing both tandem and dispersed repeats was analyzed using this technique. The distribution and organization of the different repeats within the BAC insert were efficiently determined. The results showed that this technique will be especially valuable for characterizing BAC clones that contain complex repetitive DNA sequences.     

A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf.

The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected BAC clones, the average insert size is estimated at 125 kb. If it is assumed that the genome size of M. floribunda 821 is 769 Mb/haploid, the library represents about 5x haploid genome equivalents. This provides a 99% probability of finding any specific sequence from this library. PCR-based screening of the library has been carried out using eight random genomic sequence-characterized amplified regions (SCARs), chloroplast- and mitochondria-specific SCARs, and 13 high-density Vf-linked SCAR markers. An average of five positive BAC clones per random SCAR has been obtained, whereas less than 1% of BAC clones are derived from the chloroplast or mitochondrial genomes. Most BAC clones identified with Vf-linked SCAR markers are physically linked. Three BAC contigs along the Vf region have been obtained by assembling physically linked BAC clones based on their fingerprints. The overlapping relatedness of BAC clones has been further confirmed by cytogenetic mapping using fiber fluorescence in situ hybridization (fiber-FISH). The M. floribunda 821 BAC library provides a valuable genetic resource not only for map-based cloning of the Vf gene, but also for finding many other important genes for improving the cultivated apple.     

Establishment of an efficient BAC transgenesis protocol and its application to functional characterization of the mouse Brachyury locus.

Transgenesis using large DNA such as YAC or BAC has extended the range of applications in functional genomics. Here we describe an efficient BAC transgenesis protocol using a simple BAC DNA preparation method adopted from YAC DNA purification methods. This method allowed us to isolate BAC DNA from small scale culture of BAC-containing cells in sufficient quantity and purity for microinjection. More than 40 founders have been produced with linearized BAC DNA prepared by this method, and 85% of them contained intact BAC transgenes. In contrast, when circular BAC DNA was injected, an approximately three-fold reduction of transgene integration rate was observed and fewer intact transgene integrations were obtained. A line of transgenic mice carrying a 170-kb BAC clone generated in this way successfully rescued tail and embryonic lethality phenotypes of the mouse Brachyury (T) mutants, further demonstrating the utility of this method in functional analysis of the mouse genome.     

A fast and efficient method for isolation of the BAC end

As a new developmental vector system, the bacterial artificial chromosome (BAC) has been used widely in constructing genomic libraries and in generating transgenic animals. Isolation of the BAC insert end is useful to analyze the BAC clone. Here, we describe a fast and efficient method to obtain the BAC end by ligating the BAC fragments digested with Not I and another selected restriction enzyme into universal cloning vector, followed by determining the correct clones with HindIII digestion. Further DNA sequencing analysis verified the results mentioned above.     

High throughput direct end sequencing of BAC clones

Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large genomic regions. For this strategy to be effective, high throughput methods for BAC end sequencing of all the clones in deep coverage BAC libraries needed to be developed. Here we describe a low cost, efficient, 96 well procedure for BAC end sequencing. These methods allow us to generate BAC end sequences from human and Arabidoposis libraries with an average read length of >450 bases and with a single pass sequencing average accuracy of >98%. Application of BAC end sequences in genomic sequen-cing is discussed.     

FISH physical mapping with barley BAC clones

Fluorescence in situ hybridization (FISH) is a useful technique for physical mapping of genes, markers, and other single- or low-copy sequences. Since clones containing less than 10 kb of single-copy DNA do not reliably produce detectable signals with current FISH techniques in plants, a bacterial artificial chromosome (BAC) partial library of barley was constructed and a FISH protocol for detecting unique sequences in barley BAC clones was developed. The library has a 95 kb average barley insert, representing about 20% of a barley genome. Two BAC clones containing hordein gene sequences were identified and partially characterized. FISH using these two BAC clones as probes showed specific hybridization signals near the end of the short arm of one pair of chromosomes. Restriction digests of these two BAC clones were compared with restriction patterns of genomic DNA; all fragments contained in the BAC clones corresponded to bands present in the genomic DNA, and the two BAC clones were not identical. The barley inserts contained in these two BAC clones were faithful copies of the genomic DNA. FISH with four BAC clones with inserts varying from 20 to 150 kb, showed distinct signals on paired chromatids. Physical mapping of single- or low-copy sequences in BAC clones by FISH will help to correlate the genetic and physical maps. FISH with BAC clones also provide an additional approach for saturating regions of interest with markers and for constructing contigs spanning those regions.     

Heterogeneity of microbial community structures inside the up-flow biological activated carbon (BAC) filters for the treatment of drinking water

Filtration using biological activated carbon (BAC) performs well in the removal of biodegradable dissolved organic carbon from water sources. The application of ozonation followed by up-flow BAC filtration has gained increasing attention in the world scale. In this study, a pilotscale up-flow BAC filtration system was constructed for the treatment of polluted lake water. The operational results indicated that this BAC filtration system could effectively remove organic matter. Spatial heterogeneity of the microbial community structure inside the BAC filtration system was identified using bacterial 16S rRNA clone library analysis. A marked decrease of microbial diversity in the BAC filtration system was observed along the flow path. Alphaproteobacteria, Gammaproteobacteria and Acidobacteria were found to be the major bacterial groups in the BAC filters. Moreover, Novosphingobium aromaticivorans-like microorganisms were detected. This work might add some new insights towards microbial communities in regards to BAC filtration for the treatment of drinking water.     

Bronchoalveolar cells from sarcoid patients demonstrate enhanced antigen presentation

The recognition of foreign antigens by T lymphocytes in association with lung antigen-presenting cells may be critical in the initiation of the mononuclear alveolitis and granuloma formation of pulmonary sarcoidosis. However, it has been shown that bronchoalveolar cells (BAC) from normal volunteers function poorly as antigen-presenting cells. Therefore, the ability of sarcoid BAC to serve as accessory cells for antigen-dependent autologous T cell proliferation, as measured by tritiated thymidine uptake, was compared with that of normal BAC. Although irradiated sarcoid BAC supported antigen-induced T cell proliferation, normal BAC did so poorly (p less than 0.005). Because it has been shown that sarcoid BAC produce more interleukin 1 (IL 1) than normal BAC, it was considered that the enhancement of antigen-induced proliferative responses could result from an increased amount of IL 1, and that contaminating monocytes in the peripheral blood T cell preparations displayed the antigen for T cell recognition. Therefore, it was necessary to establish that antigen-induced T cell responses required HLA-D region compatibility between the sarcoid BAC and T lymphocytes. BAC from sarcoid patients stimulated antigen-specific proliferation in T cells lines matched for at least one HLA-D-region antigen, but failed to stimulate T cell lines that were unmatched for both antigens. This finding indicates that cells in bronchoalveolar lavage fluids from sarcoid patients were fully capable of acting as antigen-presenting cells. The identification of antigen-presenting cells in the lungs of patients with sarcoidosis together with the previous findings of activated T cells, enhanced IL 1 production, and spontaneous interleukin 2 release in sarcoid patients is compatible with the hypothesis that local cell-mediated immunity is involved in the pathogenesis of pulmonary sarcoidosis.     

Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor.

The construction of representative large insert DNA libraries is critical for the analysis of complex genomes. The predominant vector system for such work is the yeast artificial chromosome (YAC) system. Despite the success of YACs, many problems have been described including: chimerism, tedious steps in library construction and low yields of YAC insert DNA. Recently a new E.coli based system has been developed, the bacterial artificial chromosome (BAC) system, which offers many potential advantages over YACs. We tested the BAC system in plants by constructing an ordered 13,440 clone sorghum BAC library. The library has a combined average insert size, from single and double size selections, of 157 kb. Sorghum inserts of up to 315 kb were isolated and shown to be stable when grown for over 100 generations in liquid media. No chimeric clones were detected as determined by fluorescence in situ hybridization of ten BAC clones to metaphase and interphase S.bicolor nuclei. The library was screened with six sorghum probes and three maize probes and all but one sorghum probe hybridized to at least one BAC clone in the library. To facilitate chromosome walking with the BAC system, methods were developed to isolate the proximal ends of restriction fragments inserted into the BAC vector and used to isolate both the left and right ends of six randomly selected BAC clones. These results demonstrate that the S. bicolor BAC library will be useful for several physical mapping and map-based cloning applications not only in sorghum but other related cereal genomes, such as maize. Furthermore, we conclude that the BAC system is suitable for most large genome applications, is more 'user friendly' than the YAC system, and will likely lead to rapid progress in cloning biologically significant genes from plants.     

Direct targeting and rapid isolation of BAC clones spanning a defined chromosome region

To isolate genes of interest in plants, it is essential to construct bacterial artificial chromosome (BAC) libraries from specific genotypes. Construction and organisation of BAC libraries is laborious and costly, especially from organisms with large and complex genomes. In the present study, we developed the pooled BAC library strategy that allows rapid and low cost generation and screening of genomic libraries from any genotype of interest. The BAC library is constructed, directly organised into a few pools and screened for BAC clones of interest using PCR and hybridisation steps, without requiring organization into individual clones. As a proof of concept, a pooled BAC library of approximately 177,000 recombinant clones has been constructed from the barley cultivar Cebada Capa that carries the Rph7 leaf rust resistance gene. The library has an average insert size of 140 kb, a coverage of six barley genome equivalents and is organised in 138 pools of about 1,300 clones each. We rapidly established a single contig of six BAC clones spanning 230 kb at the Rph7 locus on chromosome 3HS. The described low-cost cloning strategy is fast and will greatly facilitate direct targeting of genes and large-scale intra- and inter-species comparative genome analysis.Edwige Isidore and Beatrice Scherrer contributed equally to the work.