Construction Of Genomic Library Research Articles

Construction of Genomic DNA Library of Beijing Fatty Chick In lemda phage EMBL3 and Screen of Chick Heart Type Fatty Acid Binding Protein Gene

2 Abstract: A ge nomic DNA library of Beijing Fatty chick was constructed in phage EMBL3 with a titer of 3.85×10 . To testify the utility of this library we screened recombinant phages containing chick heart type fatty 5 acid binding protein gene by Southern hybridization. In order to simplify the process of screen we determined sub-library which contained target gene firstly by PCR with specific primers. Several positive recombinants were detected. We selected one randomly to be digested with Sal I. Results showed inserted exogenous DNA was about 15Kb.

Challenges and prospects of population genetic studies in terns (Charadriiformes, Aves)

Little information is available about the population structure of communally nesting terns (Sternidae) and skimmers (Rynchopidae) throughout the world. In order to fill this gap, a survey of molecular markers was carried out for six species of terns (Anous stolidus, Sterna hirundinacea, S. fuscata, S. superciliaris, Thalasseus maximus and Phaetusa simplex) and one species of skimmer (Rynchops niger). First, we describe the results of the construction of genomic DNA libraries and document problems encountered during this procedure. Secondly, we tested the cross-amplification of 18 microsatellite loci previously described for related species (the number of polymorphic loci ranged from three to seven). Thirdly, we tested the usefulness of mtDNA (control region, ND2, Cytochrome b and ATPase 6/8) for phylogeographic studies in this group of birds. The occurrence of nuclear copies of the mitochondrial control region is reported. Nucleotide divergence in the mtDNA genes analyzed ranged from 0.0 to 0.006. Despite the difficulties associated with the selection of variable markers in this group of seabirds, we were able to select polymorphic markers for each species tested and we anticipate these results will help the development of genetic studies concerning important biological questions in terns.

Isolation of Extremely AT-Rich Genomic DNA and Analysis of Genes Encoding Carbohydrate-Degrading Enzymes from Orpinomyces sp. Strain PC-2

An effective method for extraction of intact genomic DNA from the extremely AT-rich polycentric anaerobic fungus Orpinomyces sp. strain PC-2 has been developed. This procedure involves removal of glycogen-like storage polysaccharides using hexadecyltrimethylammonium bromide (CTAB) and high salt washes. The DNA was digested with various restriction enzymes and was suitable for use as a PCR template, for Southern blotting, and for genomic library construction. Genomic DNA analysis of three representative genes (celE, bgl1, and xynA) encoding (hemi-) cellulolytic enzymes of the fungus revealed multiplicity of family 5 endocellulase genes (celE-like), and family 1 beta-glucosidase genes (bgl1-like), but only a single copy of family 11 xylanase gene (xynA).

A protocol for the construction of microsatellite enriched genomic library

An improved protocol for constructing microsatellite-enriched libraries was developed. The procedure depends on digesting genomic DNA with a restriction enzyme that generates blunt-ends, and on ligating linkers that, when dimerized, create a restriction site for a different blunt-end producing restriction enzyme. Efficient ligation of linkers to the genomic DNA fragments is achieved by including restriction enzymes in the ligation reaction that eliminate unwanted ligation products. After ligation, the reaction mixture is subjected to subtractive hybridization without purification. DNA fragments containing microsatellites are captured by biotin-labeled oligonucleotide repeats and recovered using streptavidin-coated beads. The recovered fragments are amplified by PCR using the linker sequence as primer, and cloned directly into a plasmid vector. The linker has the sequence GTTT on the 5′ end, which promotes efficient adenylation of the 3′ ends of the PCR products. Consequently, the amplified fragments could be cloned into vectors without purification. This procedure enables efficient enrichment and cloning of microsatellite sequences, resulting in a library with a low level of redundancy.

Construction of Genomic DNA Libraries in Cosmid Vectors

Construction of Genomic DNA Libraries in Cosmid Vectors

Broad host range vectors for stable genomic library construction

We describe the construction of 36 stable vectors for genomic library construction in gram-negative species. These vectors contain the pBBR1 replicon that has been shown to stably replicate in every gram-negative species tested. The plasmids also contain bidirectional, rho-independent transcriptional terminators flanking the multiple cloning site, which allows for greater insert stability, and thus, greater genomic representation. Each vector varies in its antibiotic resistance cassette, mobilization function, and promoter used to express insert sequences. These vectors should prove useful in the screening of highly representational genomic libraries in a broad variety of gram-negative species.

Extremely Rapid Extraction of DNA from Bacteria and Yeasts

A very simple and rapid method for extracting genomic DNA from Gram-negative bacteria, Gram-positive bacteria and yeasts is presented. In this method, bacteria or yeasts are lysed directly by phenol and the supernatant is extracted with chloroform to remove traces of phenol. The supernatant contains DNA that is suitable for molecular analyses, such as PCR, restriction enzyme digestion and genomic library construction. This method is reproducible and simple for the routine DNA extraction from bacteria and yeasts.

The TIGR Maize Database

Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to accelerate gene discovery and genome analysis in maize: methylation filtration and high C0t selection. These techniques allow the construction of gene-enriched genomic libraries by minimizing repeat sequences due to either their methylation status or their copy number, yielding a 7-fold enrichment in genic sequences relative to a random genomic library. Approximately 900 000 gene-enriched reads from maize were generated and clustered into Assembled Zea mays (AZM) sequences. Here we report the current AZM release, which consists of ∼298 Mb representing 243 807 sequence assemblies and singletons. In order to provide a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (). In this resource, we have assembled and annotated the AZMs and used available sequenced markers to anchor AZMs to maize chromosomes. We have constructed a maize repeat database and generated draft sequence assemblies of 287 maize bacterial artificial chromosome (BAC) clone sequences, which we annotated along with 172 additional publicly available BAC clones. All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads.

Modification and Production of BAC Transgenes

Bacterial artificial chromosomes (BACs) are the vectors of choice for the construction of genomic DNA libraries and, as such, have proven instrumental in the generation of large-scale physical maps; positional cloning projects; and the sequencing of human, mouse, and a plethora of other genomes. A number of methods have recently been developed to modify BAC DNA (e.g., insertion, deletion, substitution), making BACs even more useful for functional genomic research. This unit describes two protocols for BAC modification in E. coli, one that allows for specific changes at a given DNA sequence and another that is more suited for rapid and nonspecific integration of foreign DNA (such as a reporter cassette) into a BAC insert. In addition, a simple and reliable method for preparing BAC DNA for pronuclear microinjection is also provided.

Loss of Outer Membrane Proteins without Inhibition of Lipid Export in an Escherichia coli YaeT Mutant

Escherichia coli yaeT encodes an essential, conserved outer membrane (OM) protein that is an ortholog of Neisseria meningitidis Omp85. Conflicting data with N. meningitidis indicate that Omp85 functions either in assembly of OM proteins or in export of OM lipids. The role of YaeT in E. coli was investigated with a new temperature-sensitive mutant harboring nine amino acid substitutions. The mutant stops growing after 60 min at 44 degrees C. After 30 min at 44 degrees C, incorporation of [35S]methionine into newly synthesized OM proteins is selectively inhibited. Synthesis and export of OM phospholipids and lipopolysaccharide are not impaired. OM protein levels are low, even at 30 degrees C, and the buoyant density of the OM is correspondingly lower. By Western blotting, we show that levels of the major OM protein OmpA are lower in the mutant in whole cells, membranes, and the growth medium. SecA functions as a multicopy suppressor of the temperature-sensitive phenotype and partially restores OM proteins. Our data are consistent with a critical role for YaeT in OM protein assembly in E. coli.

Test: Construction of genomic libraries

Terms to be familiar with before you start to solve the test: genomic library, gel filtration, restriction endonuclease, plasmid, sticky ends, blunt ends, ligation, recombinant DNA, bacterium transformation, denaturation and renaturation of DNA, satellite DNA, telomere, centromere, unique and repetitive sequences.

Whole genome amplification from filamentous fungi using Phi29-mediated multiple displacement amplification

The availability of genomic DNA of sufficient quality and quantity is fundamental to molecular genetic analysis. Many filamentous fungi are slow growing or even unculturable and current DNA isolation methods are often unsatisfactory. We have used multiple displacement amplification (MDA) to amplify whole genomes for two fungal species, Penicillium paxilli and the slow growing endophyte of grasses Epichloë festucae. Up to 10 μg of high molecular weight DNA was routinely amplified from less than 10 ng of template DNA obtained using glass bead-mediated disruption of fungal spores or alkaline lysis of mycelium. PCR was possible from MDA-generated DNA and amplicons up to 10 kb were successfully amplified. RFLP analysis was successful, with bands of up to 5 kb routinely detected. Hybridization of MDA-amplified DNA to a cosmid library illustrated that the MDA product amplified from E. festucae is representative of the genome. MDA is a reliable method that could be applied to applications ranging from high-throughput screening of deletion mutants to genomic library construction.

Positive Selection System for Identification of Recombinants Using α-Complementation Plasmids

A number of selection systems have been developed for direct selection of recombinant plasmids in cloning experiments (positive selection). In this study, the Commonly used LacZ-based alpha-complementation plasmid vectors have been used for designing a positive selection system for the selection of recombinants. The basis for the Strategy is the phenomenon of galactose sensitivity exhibited by galactose epimerase (galE) mutants of Escherichia coli. It is known that lacZ+ galE, but not lacZ- galE cells are killed upon addition of lactose due to the accumulation of a toxic intermediate, UDP-galactose, by hydrolysis of lactose. Using a galE mutant strain of E. coli that carries the lacZAM15 allele, various alpha-complementation plasmids that vary in their copy number were examined for their ability to be killed following addition of lactose. The results show that some plasmids that exhibit relatively high beta-galactosidase enzyme activity can be used effectively for positive selection. This selection would be extremely useful during primary cloning experiments such as construction of genomic or cDNA libraries and also in instances involving selection for rare recombinants.

Construction of a genomic library of wild rice and Agrobacterium-mediated transformation of large insert DNA linked to BPH resistance locus

Here we report the first genomic library of wild rice constructed on a plant-transformation-competent binary vector (BIBAC2) and transformation of the large insert DNA into rice via Agrobacterium. We selected Oryza officinalis for genomic library construction. The library consists of 55,296 clones and stored in one hundred forty-four 384-well plates. Random sampling of 140 clones indicated an average insert size of 71 Kb at a range of 15–235 Kb and 4.8% empty vectors. Four wheat chloroplast probes and four maize mitochondrial probes were hybridized separately to the library, showing that contamination with organellar DNAs is very low (0.61% and 0.04%, respectively). The binary bacterial artificial chromosome (BIBAC) library provides 5.3 haploid genome equivalents, implying a 99.5% probability of recovering any specific sequence of interest. A stability test indicated that the large DNA inserts were stable in this BIBAC vector both in host cells of Escherichia coli and Agrobacterium. Two restriction-fragment length polymorphism (RFLP) markers R288 and C820, which co-segregate with brown planthopper (BPH) resistance gene Qbp2, were used to screen the library, and identified seven and eight positive clones, respectively. The candidate clones of target gene isolated from the library are directly used to transform cultivated rice. After screening the Agrobacterium strains and helper plasmids, and using an improved procedure of transformation, a BIBAC clone with 120 Kb O. officinalis DNA insert was successfully transferred into the rice genome via Agrobacterium-mediated transformation. The system developed here should serve as source for gene discovery, gene cloning and genome-related research in wild rice.

Construction and characterization of large-insert genomic libraries (BAC and fosmid) from the Ascidian Botryllus schlosseri and initial physical mapping of a histocompatibility locus.

The colonial protochordate Botryllus schlosseri is genetically manipulable and represents a potential model organism for a variety of biological disciplines, including immunology, stem cell biology and development. This article presents the construction and characterization of both BAC and fosmid genomic libraries of the 725-Mbp B. schlosseri genome. The BAC library currently consists of 2x genome coverage with an average insert size of 80 kb. The fosmid library is at 11x genome coverage with an average insert of 40 kb. B. schlosseri is a small organism containing a large number of compounds that hinder DNA purification. Thus a number of protocols had to be modified in order to make purified, high molecular weight inserts for cloning, including both gel purification and insert concentration techniques. Both libraries were characterized by using them in initial physical mapping of a single histocompatibility locus, and were found to be representative and functional. These libraries are important tools for physical mapping and positional cloning in the B. schlosseri genome, and the techniques adapted to make them are suitable for use on other organisms in which high molecular weight DNA is difficult to purify.

Extraction of high-quality genomic DNA from latex-containing plants

The isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including long PCR, endonuclease restriction digestion, Southern blot analysis, and genomic library construction. Many protocols are available for the extraction of DNA from plant material. However, for latex-containing Asteraceae (Cichorioideae) species, standard protocols and commercially available kits do not produce efficient yields of high-quality amplifiable DNA. A cetyltrimethylammonium bromide protocol has been optimized for isolation of genomic DNA from latex-containing plants. Key steps in the modified protocol are the use of etiolated leaf tissue for extraction and an overnight 25 °C isopropanol precipitation step. The purified DNA has excellent spectral qualities, is efficiently digested by restriction endonucleases, and is suitable for long-fragment PCR amplification.

Construction of genomic libraries in lambda-vectors.

Lambda (λ) bacteriophages are viruses that specifically infect bacteria. The genome of λ-phage is a double-stranded DNA molecule approx 50 kb in length (). In bacterial cells, λ-phage employs one of two pathways of replication: lytic or lysogenic. Commonly, λ-phage vectors replicate via the lytic pathway. During lytic growth, the viral DNA is replicated manifold, a large number of phage gene products are synthesized, and progeny phage particles are assembled. The cell is eventually lysed, releasing its many new infectious virus particles; at this time, plaques will form on an infected bacterial lawn. Its high infectivity and clone-style propagation are the inherent basis for the use of λ-phage as a vector. Moreover, the central third of the viral genome is not essential for lytic growth and, thus, can be replaced by a variety of foreign gene segments. λ-Vectors usually contain multiple cloning sites facilitating the cloning of foreign DNA. In addition, λ-phage vectors have the following advantageous features: high cloning efficiency, a relatively large insert-size capacity, and suitability for screening using nucleic acid probes. In terms of gene screening, genomic DNA libraries are often screened by hybridization using a radioactive nucleic acid probe.

Cosmid packaging and infection of E. coli.

AbstractCosmids are cloning vectors that were developed to enable large fragments of DNA to be cloned and maintained (1–3). Cosmid vectors allow the cloning of fragments up to 45 kilobases (kb) and are commonly used in genomic library construction. The distinguishing feature of a cosmid is the presence of bacteriophage λ cos sites, which enable the vector, and cloned genomic DNA, to be packaged into bacteriophage heads (1,4). Cosmids also contain several other components, including a drug-resistance marker that is necessary for the selection of cosmid-containing bacteria, a plasmid origin of replication, usually ColE1, which regulates cosmid replication and copy number within the Escherichia coli host (1,5), and restriction sites that facilitate cloning of the desired DNA fragments and insert verification by restriction digestion (see Fig. 1). Representation of a general cosmid vector. KeywordsHost StrainLigation ReactionCosmid LibraryPackaging ExtractPhage TailThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

A simple method for DNA extraction from marine bacteria that produce extracellular materials

We present a simple method for extracting DNA from the marine bacteria Hahella chejuensis, a Streptomyces sp., and a Cytophaga sp. Previously, DNA purification from these strains was hindered by the presence of extracellular materials. In our extraction method, the marine bacteria are lysed by freezing and grinding in liquid nitrogen, and treated with SDS. The extracted DNA is purified using a phenol/chloroform mixture, and precipitated in isopropanol. The extracted DNA is of high quality and suitable for molecular analyses, such as PCR, restriction enzyme digestion, genomic DNA blot hybridization, and genomic DNA library construction. We used this method to extract genomic DNA from several other marine bacteria. Our method is a reproducible, simple, and rapid technique for routine DNA extractions from marine bacteria. Furthermore, the low cost of this method makes it attractive for large-scale studies.

Constructing yeast libraries

Publisher Summary Having a good library is crucial for gene cloning in Saccharomyces cerevisiae. Different types of libraries are used for different applications. The most frequently used approach in cloning a yeast gene is complementation of a recessive mutant with a yeast genomic library on a low-copy-number yeast vector. Literally, hundreds of yeast genes have been cloned this way. Another popular approach that has efficiently identified many yeast genes is by functional cloning from overexpression libraries, based on the suppression of a recessive mutant by gene overexpression or other phenotypic consequences associated with overexpression. Although numerous yeast genomic libraries are available, many circumstances require the construction of a new library. Methods for de novo construction of yeast genomic libraries and considerations involved in the process have been described in the previous volume in this series. This chapter describes two specific strategies that have been used successfully for the construction of several yeast libraries. One strategy should be applicable to the construction of any genomic library and the other for any cDNA libraries.