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Sample records for genome libraries final

  1. Human genome libraries. Final progress report, February 1, 1994--August 31, 1997

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    Kao, Fa-Ten

    1998-01-01

    The goal of this program is to use a novel technology of chromosome microdissection and microcloning to construct chromosome region-specific libraries as resources for various human genome program studies. Region specific libraries have been constructed for the entire human chromosomes 2 and 18.

  2. Genomic libraries: I. Construction and screening of fosmid genomic libraries.

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    Quail, Mike A; Matthews, Lucy; Sims, Sarah; Lloyd, Christine; Beasley, Helen; Baxter, Simon W

    2011-01-01

    Large insert genome libraries have been a core resource required to sequence genomes, analyze haplotypes, and aid gene discovery. While next generation sequencing technologies are revolutionizing the field of genomics, traditional genome libraries will still be required for accurate genome assembly. Their utility is also being extended to functional studies for understanding DNA regulatory elements. Here, we present a detailed method for constructing genomic fosmid libraries, testing for common contaminants, gridding the library to nylon membranes, then hybridizing the library membranes with a radiolabeled probe to identify corresponding genomic clones. While this chapter focuses on fosmid libraries, many of these steps can also be applied to bacterial artificial chromosome libraries.

  3. Screening of genomic libraries.

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    Novelli, Valdenice M; Cristofani-Yaly, Mariângela; Bastianel, Marinês; Palmieri, Dario A; Machado, Marcos A

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), have proven to be an important molecular marker in plant genetics and breeding research. The main strategies to obtain these markers can be through genomic DNA and from expressed sequence tags (ESTs) from mRNA/cDNA libraries. Genetic studies using microsatellite markers have increased rapidly because they can be highly polymorphic, codominant markers and they show heterozygous conserved sequences. Here, we describe a methodology to obtain microsatellite using the enrichment library of DNA genomic sequences. This method is highly efficient to development microsatellite markers especially in plants that do not have available ESTs or genome databases. This methodology has been used to enrich SSR marker libraries in Citrus spp., an important tool to genotype germplasm, to select zygotic hybrids, and to saturate genetic maps in breeding programs.

  4. Final report. Human artificial episomal chromosome (HAEC) for building large genomic libraries

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    Jean-Michael H. Vos

    1999-12-09

    Collections of human DNA fragments are maintained for research purposes as clones in bacterial host cells. However for unknown reasons, some regions of the human genome appear to be unclonable or unstable in bacteria. Their team has developed a system using episomes (extrachromosomal, autonomously replication DNA) that maintains large DNA fragments in human cells. This human artificial episomal chromosomal (HAEC) system may prove useful for coverage of these especially difficult regions. In the broader biomedical community, the HAEC system also shows promise for use in functional genomics and gene therapy. Recent improvements to the HAEC system and its application to mapping, sequencing, and functionally studying human and mouse DNA are summarized. Mapping and sequencing the human genome and model organisms are only the first steps in determining the function of various genetic units critical for gene regulation, DNA replication, chromatin packaging, chromosomal stability, and chromatid segregation. Such studies will require the ability to transfer and manipulate entire functional units into mammalian cells.

  5. Chromosome region-specific libraries for human genome analysis. Final progress report, 1 March 1991--28 February 1994

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    Kao, F.T.

    1994-04-01

    The objectives of this grant proposal include (1) development of a chromosome microdissection and PCR-mediated microcloning technology, (2) application of this microtechnology to the construction of region-specific libraries for human genome analysis. During this grant period, the authors have successfully developed this microtechnology and have applied it to the construction of microdissection libraries for the following chromosome regions: a whole chromosome 21 (21E), 2 region-specific libraries for the long arm of chromosome 2, 2q35-q37 (2Q1) and 2q33-q35 (2Q2), and 4 region-specific libraries for the entire short arm of chromosome 2, 2p23-p25 (2P1), 2p21-p23 (2P2), 2p14-p16 (wP3) and 2p11-p13 (2P4). In addition, 20--40 unique sequence microclones have been isolated and characterized for genomic studies. These region-specific libraries and the single-copy microclones from the library have been used as valuable resources for (1) isolating microsatellite probes in linkage analysis to further refine the disease locus; (2) isolating corresponding clones with large inserts, e.g. YAC, BAC, P1, cosmid and phage, to facilitate construction of contigs for high resolution physical mapping; and (3) isolating region-specific cDNA clones for use as candidate genes. These libraries are being deposited in the American Type Culture Collection (ATCC) for general distribution.

  6. Test: Construction of genomic libraries.

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    Szeberényi, Jozséf

    2005-03-01

    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.

  7. Preparation of PAC libraries. Final technical report

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    Pieter J. de Jong

    1997-12-31

    The goals of this project were to create P1 Artificial Chromosome (PAC) cloning vectors and use these vectors to generate, characterize, and distribute both human and mouse genomic PAC libraries to the scientific community.

  8. Mapping genomic library clones using oligonucleotide arrays

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    Sapolsky, R.J.; Lipshutz, R.J. [Affymetrix, Santa Clara, CA (United States)

    1996-05-01

    We have developed a high-density DNA probe array and accompanying biochemical and informatic methods to order clones from genomic libraries. This approach involves a series of enzymatic steps for capturing a set of short dispersed sequence markers scattered throughout a high-molecular-weight DNA. By this process, all the ambiguous sequences lying adjacent to a given Type IIS restriction site are ligated between two DNA adaptors. These markers, once amplified and labeled by PCR, can be hybridized and detected on a high-density olligonucleotide array bearing probes complementary to all possible markers. The array is synthesized using light-directed combinatorial chemistry. For each clone in a genomic library, a characteristic set of sequence markers can be determined. On the basis of the similarity between the marker sets for each pair of clones, their relative overlap can be measured. The library can be sequentially ordered into a contig map using this overlap information. This new methodology does not require gel-based methods or prior sequence information and involves manipulations that should allow for easy adaptation to automated processing and data collection. 28 refs., 9 figs., 2 tabs.

  9. Chromosome region-specific libraries for human genome analysis

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    Kao, Fa-Ten.

    1991-01-01

    We have made important progress since the beginning of the current grant year. We have further developed the microdissection and PCR- assisted microcloning techniques using the linker-adaptor method. We have critically evaluated the microdissection libraries constructed by this microtechnology and proved that they are of high quality. We further demonstrated that these microdissection clones are useful in identifying corresponding YAC clones for a thousand-fold expansion of the genomic coverage and for contig construction. We are also improving the technique of cloning the dissected fragments in test tube by the TDT method. We are applying both of these PCR cloning technique to human chromosomes 2 and 5 to construct region-specific libraries for physical mapping purposes of LLNL and LANL. Finally, we are exploring efficient procedures to use unique sequence microclones to isolate cDNA clones from defined chromosomal regions as valuable resources for identifying expressed gene sequences in the human genome. We believe that we are making important progress under the auspices of this DOE human genome program grant and we will continue to make significant contributions in the coming year. 4 refs., 4 figs.

  10. The Sleipnir library for computational functional genomics.

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    Huttenhower, Curtis; Schroeder, Mark; Chikina, Maria D; Troyanskaya, Olga G

    2008-07-01

    Biological data generation has accelerated to the point where hundreds or thousands of whole-genome datasets of various types are available for many model organisms. This wealth of data can lead to valuable biological insights when analyzed in an integrated manner, but the computational challenge of managing such large data collections is substantial. In order to mine these data efficiently, it is necessary to develop methods that use storage, memory and processing resources carefully. The Sleipnir C++ library implements a variety of machine learning and data manipulation algorithms with a focus on heterogeneous data integration and efficiency for very large biological data collections. Sleipnir allows microarray processing, functional ontology mining, clustering, Bayesian learning and inference and support vector machine tasks to be performed for heterogeneous data on scales not previously practical. In addition to the library, which can easily be integrated into new computational systems, prebuilt tools are provided to perform a variety of common tasks. Many tools are multithreaded for parallelization in desktop or high-throughput computing environments, and most tasks can be performed in minutes for hundreds of datasets using a standard personal computer. Source code (C++) and documentation are available at http://function.princeton.edu/sleipnir and compiled binaries are available from the authors on request.

  11. Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research.

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    Zhang, Hong-Bin; Scheuring, Chantel F; Zhang, Meiping; Zhang, Yang; Wu, Cheng-Cang; Dong, Jennifer J; Li, Yaning

    2012-02-16

    Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine animals, insects, algae and microbes. These libraries have been used globally for different aspects of genomics research. Here we describe the procedure with the latest improvements that we have made and used for construction of BIBAC libraries. The procedure includes the preparation of BIBAC vectors, the preparation of clonable fragments of the desired size from the source DNA, the construction and transformation of BIBACs and, finally, the characterization and assembly of BIBAC libraries. We also specify the modifications necessary for construction of BAC libraries using the protocol. The entire protocol takes ∼7 d.

  12. Library Resources for Bac End Sequencing. Final Technical Report

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    Pieter J. de Jong

    2000-10-01

    Studies directed towards the specific aims outlined for this research award are summarized. The RPCI II Human Bac Library has been expanded by the addition of 6.9-fold genomic coverage. This segment has been generated from a MBOI partial digest of the same anonymous donor DNA used for the rest of the library. A new cloning vector, pTARBAC1, has been constructed and used in the construction of RPCI-II segment 5. This new cloning vector provides a new strategy in identifying targeted genomic regions and will greatly facilitate a large-scale analysis for positional cloning. A new maleCS7BC/6J mouse BAC library has been constructed. RPCI-23 contain 576 plates (approx 210,000 clones) and represents approximately 11-fold coverage of the mouse genome.

  13. High-content screening of functional genomic libraries.

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    Rines, Daniel R; Tu, Buu; Miraglia, Loren; Welch, Genevieve L; Zhang, Jia; Hull, Mitchell V; Orth, Anthony P; Chanda, Sumit K

    2006-01-01

    Recent advances in functional genomics have enabled genome-wide genetic studies in mammalian cells. These include the establishment of high-throughput transfection and viral propagation methodologies, the production of large-scale cDNA and siRNA libraries, and the development of sensitive assay detection processes and instrumentation. The latter has been significantly facilitated by the implementation of automated microscopy and quantitative image analysis, collectively referred to as high-content screening (HCS), toward cell-based functional genomics application. This technology can be applied to whole genome analysis of discrete molecular and phenotypic events at the level of individual cells and promises to significantly expand the scope of functional genomic analyses in mammalian cells. This chapter provides a comprehensive guide for curating and preparing function genomics libraries and performing HCS at the level of the genome.

  14. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

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    Chari, Raj; Mali, Prashant; Moosburner, Mark; Church, George M.

    2017-01-01

    We develop an in vivo library-on-library methodology to simultaneously assess single guide RNA (sgRNA) activity across ~1,400 genomic loci. Assaying across multiple human cell types, end-processing enzymes, and two Cas9 orthologs, we unravel underlying nucleotide sequence and epigenetic parameters. Our results enable improved design of reagents, shed light on mechanisms of genome targeting, and provide a generalizable framework to study nucleic acid-nucleic acid interactions and biochemistry in high throughput. PMID:26167643

  15. Gene enrichment in plant genomic shotgun libraries.

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    Rabinowicz, Pablo D; McCombie, W Richard; Martienssen, Robert A

    2003-04-01

    The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.

  16. The library as finals resting place: expanding service to health sciences students during final exams.

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    Smigielski, Elizabeth M; Nixon, Neal D

    2004-01-01

    To increase services to health sciences students during their final exam period, and to demonstrate to campus administration that the library is in tune with the students' fluctuating needs, the Kornhauser Health Sciences Library, University of Louisville, increased its hours of operation; created an inviting, comfortable environment; and offered free snacks and drinks for the students. The event, coined the "Finals Resting Place," was a positive public relations tool that strengthened the library's relationship with its students. Moreover, it reinforced the library's role and mission to the campus administration, particularly that of the dental and medical schools.

  17. Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries

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    Puigdomènech Pere

    2010-11-01

    Full Text Available Abstract Background Although melon (Cucumis melo L. is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,024 clones, half of them from a previously described melon BAC library generated with restriction endonucleases and the remainder from a new random-shear BAC library. Results We generated a total of 47,140 high-quality BAC-end sequences (BES, 91.7% of which were paired-BES. Both libraries were assembled independently and then cross-assembled to obtain a final set of 33,372 non-redundant, high-quality sequences. These were grouped into 6,411 contigs (4.5 Mb and 26,961 non-assembled BES (14.4 Mb, representing ~4.2% of the melon genome. The sequences were used to screen genomic databases, identifying 7,198 simple sequence repeats (corresponding to one microsatellite every 2.6 kb and 2,484 additional repeats of which 95.9% represented transposable elements. The sequences were also used to screen expressed sequence tag (EST databases, revealing 11,372 BES that were homologous to ESTs. This suggests that ~30% of the melon genome consists of coding DNA. We observed regions of microsynteny between melon paired-BES and six other dicotyledonous plant genomes. Conclusion The analysis of nearly 50,000 BES from two complementary genomic libraries covered ~4.2% of the melon genome, providing insight into properties such as microsatellite and transposable element distribution, and the percentage of coding DNA. The observed synteny between melon paired-BES and six other plant genomes showed that useful comparative genomic data can be derived through large scale BAC-end sequencing by anchoring a small proportion of the melon genome to other sequenced genomes.

  18. Construction of gene targeting vectors from lambda KOS genomic libraries.

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    Wattler, S; Kelly, M; Nehls, M

    1999-06-01

    We describe a highly redundant murine genomic library in a new lambda phage, lambda knockout shuttle (lambda KOS) that facilitates the very rapid construction of replacement-type gene targeting vectors. The library consists of 94 individually amplified subpools, each containing an average of 40,000 independent genomic clones. The subpools are arrayed into a 96-well format that allows a PCR-based efficient recovery of independent genomic clones. The lambda KOS vector backbone permits the CRE-mediated conversion into high-copy number pKOS plasmids, wherein the genomic inserts are automatically flanked by negative-selection cassettes. The lambda KOS vector system exploits the yeast homologous recombination machinery to simplify the construction of replacement-type gene targeting vectors independent of restriction sites within the genomic insert. We outline procedures that allow the generation of simple and more sophisticated conditional gene targeting vectors within 3-4 weeks, beginning with the screening of the lambda KOS genomic library.

  19. Gridded genomic libraries of different chordate species: a reference library system for basic and comparative genetic studies of chordate genomes.

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    Burgtorf, C; Welzel, K; Hasenbank, R; Zehetner, G; Weis, S; Lehrach, H

    1998-09-01

    The use of genomic libraries maintained in arrayed format is becoming a more and more popular tool for the analysis of molecular evolution and comparative molecular development. Being able to use already existing reference libraries considerably reduces the work load, and if results are made publicly available, it will facilitate in silica experiments in the future. Here we describe the construction and preliminary characterization of six cosmid libraries of different chordate species, Ciona intestinalis (Hemichordate), Branchiostoma floridae (Cephalochordate), Lampetra fluviatilis (Cyclostoma), Xiphophorus maculatus, and Danio rerio (Osteichthyes) in Lawrist7 and Fugu rubripes in Lawrist4.

  20. Genome-scale validation of deep-sequencing libraries.

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    Dominic Schmidt

    Full Text Available Chromatin immunoprecipitation followed by high-throughput (HTP sequencing (ChIP-seq is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing.

  1. A binary vector for transferring genomic libraries to plants.

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    Simoens, C; Alliotte, T; Mendel, R; Müller, A; Schiemann, J; Van Lijsebettens, M; Schell, J; Van Montagu, M; Inzé, D

    1986-10-24

    The transformation of mutant plants with a complete recombinant library derived from wild-type DNA followed by assay of transformed plants for complementation of the mutant phenotype is a promising method for the isolation of plant genes. The small genome of Arabidopsis thaliana is a good candidate for attempting this so-called shotgun transformation. We present the properties of an A. thaliana genomic library cloned in a binary vector, pC22. This vector, designed to introduce genomic libraries into plants, contains the oriV of the Ri plasmid pRiHR1 by which it replicates perfectly stably in Agrobacterium. Upon transfer of the library from E. coli to A. tumefaciens large differences in transfer efficiencies of individual recombinant clones were observed. There is a direct relation between transfer efficiency and stability of the recombinant clones both in E. coli and A. tumefaciens. The stability is independent of the insert size, but seems to be related to the nature of the insert DNA. The feasibility of shotgun transformation and problems of statistical sampling are discussed.

  2. Rapid expression of functional genomic libraries.

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    Woodrow, Kim A; Airen, Isoken O; Swartz, James R

    2006-12-01

    Genomic-scale analysis of protein function is currently limited by the ability to rapidly express the enormous diversity of protein targets in their active form. We describe a method to construct transcriptionally active expression templates (ETs) in parallel using a single PCR step wherein the overlap-extension reaction for addition of transcription regulatory elements is separated from the amplification of the full-length product by using a GC-rich single primer. Over 90% of 55 diverse genomic targets were extended with T7 regulatory elements to form ETs in high yield and purity. The unpurified ETs directed protein expression using a cell-free protein synthesis (CFPS) system supplemented with cofactors and metal ions to activate a variety of enzymes. Higher activities were obtained in the modified CFPS reactions compared to standard reaction conditions. Protein purification was avoided because the expressed enzyme activity was significantly greater than the background activity associated with the cell extract. These improvements in the parallel synthesis of linear ETs combined with enhanced in vitro enzyme activation help to make CFPS systems more attractive platforms for high-throughput evaluation of protein function.

  3. Zebrafish YAC, BAC, and PAC genomic libraries.

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    Amemiya, C T; Zhong, T P; Silverman, G A; Fishman, M C; Zon, L I

    1999-01-01

    Numerous positional cloning projects directed at isolating genes responsible for the myriads of observed developmental defects in the zebrafish are anticipated in the very near future. In this chapter, we have reviewed the YAC, BAC, and PAC large-insert genomic resources available to the zebrafish community. We have discussed how these resources are screened and used in a positional cloning scheme and have pointed out frequently formidable logistical considerations in the approach. Despite being extremely tedious, positional cloning projects in the zebrafish will be comparatively easier to accomplish than in human and mouse, because of unique biological advantages of the zebrafish system. Moreover, the ease and speed at which genes are identified and cloned should rapidly increase as more mapping reagents and information become available, thereby paving the way for meaningful biological studies.

  4. RAPD-based screening of genomic libraries for positional cloning.

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    Dioh, W; Tharreau, D; Lebrun, M H

    1997-12-15

    RAPD markers are frequently used for positional cloning. However, RAPD markers often contain repeated sequences which prevent genomic library screening by hybridisation. We have developed a simple RAPD analysis of genomic libraries based on the identification of cosmid pools and clones amplifying the RAPD marker of interest. Our method does not require the cloning or characterisation of the RAPD marker as it relies on the analysis of cosmid pools or clones using a simple RAPD protocol. We applied this strategy using four RAPD markers composed of single copy or repeated sequences linked to avirulence genes of the rice blast fungus Magnaporthe grisea . Cosmids containing these RAPD markers were easily and rapidly identified allowing the construction of physical contigs at these loci.

  5. Inexpensive multiplexed library preparation for megabase-sized genomes.

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    Michael Baym

    Full Text Available Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the standard Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples. Several hundred samples can then be pooled on the same HiSeq lane via custom barcodes. Our method will be useful for re-sequencing of microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples, as well as for other sequencing applications including large amplicon, open chromosome, artificial chromosomes, and RNA sequencing.

  6. The construction of genomic libraries of Cowdria ruminantium in an expression vector, lambda gt11.

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    Ambrosio, R E; Du Plessis, J L; Bezuidenhout, J D

    1987-09-01

    Genomic libraries of the Welgevonden and Kwanyanga isolates of Cowdria ruminantium have been constructed in an expression vector. These libraries contain approximately 4 x 10(5) and 3 x 10(5) recombinants respectively.

  7. Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

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    McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

    2005-08-26

    Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

  8. Construction of Mammalian Genomic Libraries Using λ Replacement Vectors.

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    Bateson, A N; Pollard, J W

    1988-01-01

    The ideal genomic library should consist of a series of clones containing overlapping sequences that are representative of the entire genome. Such an ideal state can be approached by cutting the DNA randomly and cloning large pieces of this DNA into a suitable vector (1). The DNA can be cleaved either by mechanical shearing, in which case the DNA is fragmented in a truely random fashion, but with the introduction of problems associated with blunt end ligation, or better, by partial digestion with a restriction endonuclease such as Mbol or Sau3A. These enzymes recognize four base sequences that are predicted to occur on average (although in practice this is not the case) every 256 bases, and hence digestion results in cleavage of the DNA in a pseudorandom manner.

  9. Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries.

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    Branscomb, E; Slezak, T; Pae, R; Galas, D; Carrano, A V; Waterman, M

    1990-10-01

    We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.

  10. A library of TAL effector nucleases spanning the human genome.

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    Kim, Yongsub; Kweon, Jiyeon; Kim, Annie; Chon, Jae Kyung; Yoo, Ji Yeon; Kim, Hye Joo; Kim, Sojung; Lee, Choongil; Jeong, Euihwan; Chung, Eugene; Kim, Doyoung; Lee, Mi Seon; Go, Eun Mi; Song, Hye Jung; Kim, Hwangbeom; Cho, Namjin; Bang, Duhee; Kim, Seokjoong; Kim, Jin-Soo

    2013-03-01

    Transcription activator-like (TAL) effector nucleases (TALENs) can be readily engineered to bind specific genomic loci, enabling the introduction of precise genetic modifications such as gene knockouts and additions. Here we present a genome-scale collection of TALENs for efficient and scalable gene targeting in human cells. We chose target sites that did not have highly similar sequences elsewhere in the genome to avoid off-target mutations and assembled TALEN plasmids for 18,740 protein-coding genes using a high-throughput Golden-Gate cloning system. A pilot test involving 124 genes showed that all TALENs were active and disrupted their target genes at high frequencies, although two of these TALENs became active only after their target sites were partially demethylated using an inhibitor of DNA methyltransferase. We used our TALEN library to generate single- and double-gene-knockout cells in which NF-κB signaling pathways were disrupted. Compared with cells treated with short interfering RNAs, these cells showed unambiguous suppression of signal transduction.

  11. Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

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    Koo, Byoung-Mo; Kritikos, George; Farelli, Jeremiah D; Todor, Horia; Tong, Kenneth; Kimsey, Harvey; Wapinski, Ilan; Galardini, Marco; Cabal, Angelo; Peters, Jason M; Hachmann, Anna-Barbara; Rudner, David Z; Allen, Karen N; Typas, Athanasios; Gross, Carol A

    2017-03-22

    A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria.

  12. Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness

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    Shaw Kerry L

    2010-07-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC libraries and expressed sequence tag (EST libraries. Results 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. Conclusion The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications.

  13. A primer on using pooled shRNA libraries for functional genomic screens

    Institute of Scientific and Technical Information of China (English)

    Guang Hu; Ji Luo

    2012-01-01

    The discovery of RNA interference (RNAi) has revolutionized genetic analysis in mammalian cells.Loss-of-function RNAi screens enable rapid,functional annotation of the genome.Of the various RNAi approaches,pooled shRNA libraries have received considerable attention because of their versatility.A number of genome-wide shRNA libraries have been constructed against the human and mouse genomes,and these libraries can be readily applied to a variety of screens to interrogate the function of human and mouse genes in an unbiased fashion.We provide an introduction to the technical aspects of using pooled shRNA libraries for genetic screens.

  14. Microsatellite discovery by deep sequencing of enriched genomic libraries.

    Science.gov (United States)

    Santana, Quentin; Coetzee, Martin; Steenkamp, Emma; Mlonyeni, Osmond; Hammond, Gifty; Wingfield, Michael; Wingfield, Brenda

    2009-03-01

    Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2-1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose.

  15. Age Analysis of Public Library Collections. Final Report.

    Science.gov (United States)

    Wallace, Danny P.; And Others

    The use of information regarding the ages of library items is a standard component of many approaches to weeding library collections, and has a long history in the literature of collection management. Current and past approaches to using aging information to make weeding decisions make use of very arbitrary decision criteria. This study examined…

  16. Construction and characterization of a bovine BAC library with four genome-equivalent coverage

    Directory of Open Access Journals (Sweden)

    Eilertsen Ken

    2001-09-01

    Full Text Available Abstract A bovine artificial chromosome (BAC library of 105 984 clones has been constructed in the vector pBeloBAC11 and organized in 3-dimension pools and high density membranes for screening by PCR and hybridization. The average insert size, determined after analysis of 388 clones, was estimated at 120 kb corresponding to a four genome coverage. Given the fact that a male was used to construct the library, the probability of finding any given autosomal and X or Y locus is respectively 0.98 and 0.86. The library was screened for 164 microsatellite markers and an average of 3.9 superpools was positive for each PCR system. None of the 50 or so BAC clones analysed by FISH was chimeric. This BAC library increases the international genome coverage for cattle to around 28 genome equivalents and extends the coverage of the ruminant genomes available at the Inra resource center to 15 genome equivalents.

  17. Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage.

    Science.gov (United States)

    Airmet, K W; Hinckley, J D; Tree, L T; Moss, M; Blumell, S; Ulicny, K; Gustafson, A K; Weed, M; Theodosis, R; Lehnardt, M; Genho, J; Stevens, M R; Kooyman, D L

    2012-01-01

    The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 10⁹ bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

  18. A novel method to screen genomic libraries that combines genomic immunization with the prime-boost strategy.

    Science.gov (United States)

    Yero, Daniel; Pajón, Rolando; Caballero, Evelin; González, Sonia; Cobas, Karem; Fariñas, Mildrey; Lopez, Yamilé; Acosta, Armando

    2007-08-01

    We employed a prime-boost regimen in combination with the expression library immunization protocol to improve the protective effectiveness of a genomic library used as immunogen. To demonstrate the feasibility of this novel strategy, we used as a prime a serogroup B Neisseria meningitidis random genomic library constructed in a eukaryotic expression vector. Mice immunized with different fractions of this library and boosted with a single dose of meningococcal outer membrane vesicles elicited higher bactericidal antibody titers compared with mice primed with the empty vector. After the boost, passive administration of sera from mice primed with two of these fractions significantly reduced the number of viable bacteria in the blood of infant rats challenged with live N. meningitidis. The method proposed could be applied to the identification of subimmunogenic antigens during vaccine candidate screening by employing expression library immunization.

  19. Integrase-directed recovery of functional genes from genomic libraries.

    Science.gov (United States)

    Rowe-Magnus, Dean A

    2009-09-01

    Large population sizes, rapid growth and 3.8 billion years of evolution firmly establish microorganisms as a major source of the planet's biological and genetic diversity. However, up to 99% of the microorganisms in a given environment cannot be cultured. Culture-independent methods that directly access the genetic potential of an environmental sample can unveil new proteins with diverse functions, but the sequencing of random DNA can generate enormous amounts of extraneous data. Integrons are recombination systems that accumulate open reading frames (gene cassettes), many of which code for functional proteins with enormous adaptive potential. Some integrons harbor hundreds of gene cassettes and evidence suggests that the gene cassette pool may be limitless in size. Accessing this genetic pool has been hampered since sequence-based techniques, such as hybridization or PCR, often recover only partial genes or a small subset of those present in the sample. Here, a three-plasmid genetic strategy for the sequence-independent recovery of gene cassettes from genomic libraries is described and its use by retrieving functional gene cassettes from the chromosomal integron of Vibrio vulnificus ATCC 27562 is demonstrated. By manipulating the natural activity of integrons, we can gain access to the caches of functional genes amassed by these structures.

  20. Derivation of a mathematical expression useful for the construction of complete genomic libraries.

    Science.gov (United States)

    Zilsel, J; Ma, P H; Beatty, J T

    1992-10-12

    We present and derive a formula that is useful for the design and evaluation of gene cloning experiments in which a complete gene library of the entire genome of an organism is desired. The formula n = ln(1-phi f)/ln(1-f) (in which n is the number of recombinant clones required to ensure a probability, phi, of obtaining at least one of each of all possible gene sequences, and f is the fraction of the genome contained in an average-sized DNA fragment) applies to construction of libraries, in which at least one copy of all the genetic information of a genome is required. The use of this formula for quantitative evaluation of genomic libraries should give greater assurance that a given library would be complete.

  1. Construction of genomic libraries of Cryptosporidium parvum and identification of antigen-encoding genes.

    Science.gov (United States)

    Dykstra, C C; Blagburn, B L; Tidwell, R R

    1991-01-01

    Genomic libraries have been constructed from bovine C. parvum DNA in the lambda ZAP and lambda DASH vectors. Based on an estimated genome size of 2 x 10(4) kilobases (kb), each recombinant library contains greater than 10 genomic equivalents. The average recombinant size for the lambda ZAP library is 2.1 kb and for the lambda DASH library is 14 kb. We have identified genes to major antigens recognized by hyperimmune bovine antiserum. These recombinants are currently being purified and characterized. Limited DNA sequence analysis of random C. parvum clones confirms suggestions that the genome is quite AT-rich. The DNA sequence of random lambda ZAP fusion proteins has identified a potential ATPase, a structural protein and a DNA-binding protein.

  2. Isolation of high molecular weight DNA suitable for the construction of genomic libraries.

    Science.gov (United States)

    Steven, J; McKechnie, D; Graham, A

    1988-01-01

    Recent advances in molecular biology have made it possible to construct complete gene libraries for any organism that uses DNA as its carrier of genetic information. A gene library should contain a large number of cloned DNA fragments that in total contain the entire donor genome. The construction of a genomic library first requires the isolation of DNA from the donor organism. To be of maximum use in the construction of genomic libraries, DNA isolated from the donor organism should fulfill the following criteria. First, the DNA must represent all sequences in the genome to be cloned. Second, it must be of high molecular weight. Third, no contaminants must taint the DNA so that its use as a substrate for restriction endonucleases and other enzymes used in genetic engineering is uninhibited.

  3. Carver County Library System, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Colhapp, Barbara; Miller, Lana

    The Carver County Library System (Chaska, Minnesota) conducted a project to demonstrate adult educational teamwork between libraries and literacy agents in the Carver-Scott two county area. The project, "National Issues Forums (NIF) for the New Reader," extended educational opportunities that encouraged new adult readers and the public…

  4. Lowell Public Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Maravilla, Virginia

    The Lowell Public Library (Indiana) Adult Literacy Program expanded literacy efforts of the library and its volunteer tutors by increasing the program enrollment numbers of the functionally illiterate English-speaking, English as a Second Language (ESL), migrant workers, and Basic Math students; assisted students in achieving their stated goals in…

  5. Cloning of open reading frames and promoters from the Saccharomyces cerevisiae genome: construction of genomic libraries of random small fragments.

    Science.gov (United States)

    Santangelo, G M; Tornow, J; Moldave, K

    1986-01-01

    We have developed a novel efficient method, carrier-facilitated insertion, to insert small (150-600 bp) DNA fragments into plasmid vectors. This method employs a carrier segment of vector DNA to circumvent the difficulties in ligating two fragments together to generate a recombinant circle efficiently. We have used carrier-facilitated insertion to construct three genomic libraries of random (DNase I-generated) fragments from the Saccharomyces cerevisiae genome. One of these was an expression library, and the other two were promoter-cloning libraries. 87-90% of the Escherichia coli colonies in each library contained recombinant plasmids, and less than 3% of the recombinants contained more than one insert. Detection of open reading frames among the inserts in the expression library was accomplished by testing for beta-galactosidase activity. This methodology, unencumbered by the intrinsic disproportionality of cDNA libraries, can be used to identify and clone DNA that codes for a specific antigenic determinant. When used in combination with a method to detect and isolate random constitutive, repressible and inducible yeast promoters, these libraries should permit a comprehensive analysis of the yeast genome and its expression.

  6. Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries.

    Science.gov (United States)

    Gaida, Stefan M; Sandoval, Nicholas R; Nicolaou, Sergios A; Chen, Yili; Venkataramanan, Keerthi P; Papoutsakis, Eleftherios T

    2015-05-06

    A key limitation in using heterologous genomic or metagenomic libraries in functional genomics and genome engineering is the low expression of heterologous genes in screening hosts, such as Escherichia coli. To overcome this limitation, here we generate E. coli strains capable of recognizing heterologous promoters by expressing heterologous sigma factors. Among seven sigma factors tested, RpoD from Lactobacillus plantarum (Lpl) appears to be able of initiating transcription from all sources of DNA. Using the promoter GFP-trap concept, we successfully screen several heterologous and metagenomic DNA libraries, thus enlarging the genomic space that can be functionally sampled in E. coli. For an application, we show that screening fosmid-based Lpl genomic libraries in an E. coli strain with a chromosomally integrated Lpl rpoD enables the identification of Lpl genetic determinants imparting strong ethanol tolerance in E. coli. Transcriptome analysis confirms increased expression of heterologous genes in the engineered strain.

  7. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

    Directory of Open Access Journals (Sweden)

    Marta Matvienko

    Full Text Available Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC, which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

  8. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

    Science.gov (United States)

    Matvienko, Marta; Kozik, Alexander; Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

    2013-01-01

    Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

  9. Filter transfer of genomic libraries in a state accessible to DNA-binding proteins.

    Science.gov (United States)

    Beebee, T J

    1987-04-01

    I have developed a method for transferring plaque DNA of lambda genomic libraries onto 3MM filters in a state accessible to DNA-binding proteins. DNA bound to 3MM is available to proteins as large as Escherichia coli RNA polymerase and maintains template activity similar to that in free solution. Lambda Plaques can be lifted onto 3MM filter disks, deproteinized, and used for transcription assays in vitro. The RNA synthesized is complementary to phage rather than to E. coli DNA and plaques can be identified by autoradiography. Furthermore, the filters can subsequently be probed with radioactive nucleic acids under standard hybridization conditions. Finally, colorimetric assays can be employed with lactate dehydrogenase (LDH) A in which plaques are identified by the localized reduction of nitroblue tetrazolium.

  10. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Simon, M. I.; Kim, U.-J.

    2002-02-26

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.

  11. Size-selected genomic libraries: the distribution and size-fractionation of restricted genomic DNA fragments by gel electrophoresis.

    Science.gov (United States)

    Gondo, Y

    1995-02-01

    By using one-dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size-fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size-selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size-fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size-fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.

  12. Rapid DNA Library Construction for Functional Genomic and Metagenomic Screening▿ †

    OpenAIRE

    2007-01-01

    A rapid protocol was developed for constructing plasmid libraries from small quantities of genomic/metagenomic DNA. The technique utilizes linker amplification with topoisomerase cloning and allows for inducible transcription in Escherichia coli. As proof of principle, several anti-Bacillus lysins were cloned from bacteriophage genomes and an aerolysin was cloned from a metagenomic sample.

  13. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

    Directory of Open Access Journals (Sweden)

    Kudrna David

    2011-03-01

    Full Text Available Abstract Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1 digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb to 157 Kb (Eg_Ba, very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×, contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae

  14. Constructing gene-enriched plant genomic libraries using methylation filtration technology.

    Science.gov (United States)

    Rabinowicz, Pablo D

    2003-01-01

    Full genome sequencing in higher plants is a very difficult task, because their genomes are often very large and repetitive. For this reason, gene targeted partial genomic sequencing becomes a realistic option. The method reported here is a simple approach to generate gene-enriched plant genomic libraries called methylation filtration. This technique takes advantage of the fact that repetitive DNA is heavily methylated and genes are hypomethylated. Then, by simply using an Escherichia coli host strain harboring a wild-type modified cytosine restriction (McrBC) system, which cuts DNA containing methylcytosine, repetitive DNA is eliminated from these genomic libraries, while low copy DNA (i.e., genes) is recovered. To prevent cloning significant proportions of organelle DNA, a crude nuclear preparation must be performed prior to purifying genomic DNA. Adaptor-mediated cloning and DNA size fractionation are necessary for optimal results.

  15. High Capsid–Genome Correlation Facilitates Creation of AAV Libraries for Directed Evolution

    Science.gov (United States)

    Nonnenmacher, Mathieu; van Bakel, Harm; Hajjar, Roger J; Weber, Thomas

    2015-01-01

    Directed evolution of adeno-associated virus (AAV) through successive rounds of phenotypic selection is a powerful method to isolate variants with improved properties from large libraries of capsid mutants. Importantly, AAV libraries used for directed evolution are based on the “natural” AAV genome organization where the capsid proteins are encoded in cis from replicating genomes. This is necessary to allow the recovery of the capsid DNA after each step of phenotypic selection. For directed evolution to be used successfully, it is essential to minimize the random mixing of capsomers and the encapsidation of nonmatching viral genomes during the production of the viral libraries. Here, we demonstrate that multiple AAV capsid variants expressed from Rep/Cap containing viral genomes result in near-homogeneous capsids that display an unexpectedly high capsid–DNA correlation. Next-generation sequencing of AAV progeny generated by bulk transfection of a semi-random peptide library showed a strong counter-selection of capsid variants encoding premature stop codons, which further supports a strong capsid–genome identity correlation. Overall, our observations demonstrate that production of “natural” AAVs results in low capsid mosaicism and high capsid–genome correlation. These unique properties allow the production of highly diverse AAV libraries in a one-step procedure with a minimal loss in phenotype–genotype correlation. PMID:25586687

  16. High capsid-genome correlation facilitates creation of AAV libraries for directed evolution.

    Science.gov (United States)

    Nonnenmacher, Mathieu; van Bakel, Harm; Hajjar, Roger J; Weber, Thomas

    2015-04-01

    Directed evolution of adeno-associated virus (AAV) through successive rounds of phenotypic selection is a powerful method to isolate variants with improved properties from large libraries of capsid mutants. Importantly, AAV libraries used for directed evolution are based on the "natural" AAV genome organization where the capsid proteins are encoded in cis from replicating genomes. This is necessary to allow the recovery of the capsid DNA after each step of phenotypic selection. For directed evolution to be used successfully, it is essential to minimize the random mixing of capsomers and the encapsidation of nonmatching viral genomes during the production of the viral libraries. Here, we demonstrate that multiple AAV capsid variants expressed from Rep/Cap containing viral genomes result in near-homogeneous capsids that display an unexpectedly high capsid-DNA correlation. Next-generation sequencing of AAV progeny generated by bulk transfection of a semi-random peptide library showed a strong counter-selection of capsid variants encoding premature stop codons, which further supports a strong capsid-genome identity correlation. Overall, our observations demonstrate that production of "natural" AAVs results in low capsid mosaicism and high capsid-genome correlation. These unique properties allow the production of highly diverse AAV libraries in a one-step procedure with a minimal loss in phenotype-genotype correlation.

  17. Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

    Science.gov (United States)

    Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

    2016-02-01

    The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

  18. Logan Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Steinhoff, Nadene; Jenkins, Ronald

    The Bridgerland Literacy program of Logan Library (Logan, Utah) involved recruitment, retention, public awareness, training, basic literacy, collection development, tutoring, computer assisted, employment oriented, intergenerational/family, and English as a Second Language (ESL) programs. The program served a community of 50,000-100,000 people,…

  19. Hopkinsville-Christian County Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Nevels, Vada Germaine

    The Hopkinsville-Christian County Library (Kentucky) conducted a project that involved recruitment, public awareness, basic literacy, collection development, tutoring, computer-assisted, other technology, and intergenerational/family programs. The project served a community of 50,000-100,000 people, and targeted the learning disabled,…

  20. Lee Library Association, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Dalheim, Zoe; Mauke, Martha

    The Lee Library Association conducted a project that involved recruitment, public awareness, training, rural oriented, basic literacy, collection development, tutoring, computer assisted services, and English as a Second Language (ESL) programs. The project served a community of 25,000-50,000 people, and targeted the homeless, learning disabled,…

  1. Irvington Public Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

    Science.gov (United States)

    Shader, Holly

    The Irvington Public Library (Irvington, New Jersey) conducted a project that involved recruitment, retention, public awareness, training, basic literacy, collection development, tutoring, and intergenerational/family programs. The project served a community of 25,000-50,000 people, and targeted the learned disabled and intergenerational/families.…

  2. Construction and analysis of Siberian tiger bacterial artificial chromosome library with approximately 6.5-fold genome equivalent coverage.

    Science.gov (United States)

    Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2014-03-07

    Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.

  3. New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

    Directory of Open Access Journals (Sweden)

    Feltus Frank A

    2011-07-01

    Full Text Available Abstract Background Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18 to duodecaploid (12X = 108. Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. Results A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective. Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. Conclusions The construction of the first switchgrass BAC library and comparative analysis of

  4. Rapid isolation and characterization of hybridization selected recombinants from lambda genomic libraries.

    Science.gov (United States)

    Porteous, D J

    1986-11-15

    This paper describes an efficient protocol for the screening of lambda genomic libraries, plaque and DNA purification, and probe characterization by a combination of new and recently described techniques. The protocol has allowed large numbers of human subchromosome-specific probes to be rapidly generated from an EMBL3 library of human-mouse somatic cell hybrid DNA. The protocol affords considerable savings in time and effort over previous procedures.

  5. Purification of genomic sequences from bacteriophage libraries by recombination and selection in vivo.

    OpenAIRE

    Seed, B

    1983-01-01

    Cloned genes have been purified from recombinant DNA bacteriophage libraries by a method exploiting homologous reciprocal recombination in vivo. In this method 'probe' sequences are inserted in a very small plasmid vector and introduced into recombination-proficient bacterial cells. Genomic bacteriophage libraries are propagated on the cells, and phage bearing sequences homologous to the probe acquire an integrated copy of the plasmid by reciprocal recombination. Phage bearing integrated plas...

  6. RepARK--de novo creation of repeat libraries from whole-genome NGS reads.

    Science.gov (United States)

    Koch, Philipp; Platzer, Matthias; Downie, Bryan R

    2014-05-01

    Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a de novo repeat assembly method--RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)--which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.

  7. Construction of genomic libraries of mycobacterial origin: identification of recombinants encoding mycobacterial-specific proteins.

    Science.gov (United States)

    Khandekar, P S; Munshi, A; Sinha, S; Sharma, G; Kapoor, A; Gaur, A; Talwar, G P

    1986-09-01

    A complete genomic library from Mycobacterium vaccae (2785 recombinants) and a partial genomic library of M. leprae and BCG (300 and 1750 clones, respectively) were constructed in the plasmid pBR322. Bam HI was selected as the restriction endonuclease for obtaining DNA cleavage products. Evidence was obtained for limited expression of the cloned mycobacterial DNA inserts in Escherichia coli. A recombinant has been identified which codes for antigen immunoreactive with rabbit anti-M. leprae antibody but not with anti-H37Rv antibody.

  8. Construction and characterization of genomic libraries from specific human chromosomes.

    Science.gov (United States)

    Krumlauf, R; Jeanpierre, M; Young, B D

    1982-05-01

    Highly purified fractions of human chromosomes 21 and 22 were isolated from a suspension of metaphase chromosomes stained with ethidium bromide by using a fluorescence-activated cell sorter (FACS II). Two recombinant DNA libraries, representing chromosomes 21 and 22, were constructed by complete digestion of DNA from these fractions with EcoRI and insertion into the vector lambda gtWES lambda B. Twenty clones selected at random from the chromosome 22 library hybridized to EcoRI-digested human DNA, and five of these clones hybridized to single bands identical in size to the phage inserts. These five single-copy sequences and a clone coding for an 8S RNA isolated by screening the chromosome 22 library for expressed sequences were characterized in detail. Hybridization of all six clones to a panel of sorted chromosomes and hybrid cell lines confirmed the assignment of the sequences to chromosome 22. The sequences were localized to regions of chromosome 22 by hybridization to translocated chromosomes sorted from a cell line having a balanced translocation t(17;22)(p13;q11) and to hybrid cell lines containing the various portions of another translocation t(X;22)(q13;q112). Five clones reside on the long arm of chromosome 22 between q112 and pter, while one clone and an 18S rRNA gene isolated from the chromosome 22 library reside pter and g112. The construction of chromosome-specific libraries by this method has the advantage of being direct and applicable to nearly all human chromosomes and will be important in molecular analysis of human genetic diseases.

  9. Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

    Directory of Open Access Journals (Sweden)

    Okimoto Ron

    2011-02-01

    Full Text Available Abstract Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs to kilobase, and even megabase, sized structural variants (SVs, such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken. Results We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome. Conclusion We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.

  10. Small-fragment genomic libraries for the display of putative epitopes from clinically significant pathogens.

    Science.gov (United States)

    Henics, T; Winkler, B; Pfeifer, U; Gill, S R; Buschle, M; von Gabain, A; Meinke, A L

    2003-07-01

    Taking advantage of whole genome sequences of bacterial pathogens in many thriving diseases with global impact, we developed a comprehensive screening procedure for the identification of putative vaccine candidate antigens. Importantly, this procedure relies on highly representative small-fragment genomic libraries that are expressed to display frame-selected epitope-size peptides on a bacterial cell surface and to interact directly with carefully selected disease-relevant high-titer sera. Here we describe the generation of small-fragment genomic libraries of Gram-positive and Gram-negative clinically significant pathogens, including Staphylococcus aureus and Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae, Enterococcus faecalis, Helicobacter pylori, Chlamydia pneumoniae, the enterotoxigenic Escherichia coli, and Campylobacter jejuni. Large-scale sequencing revealed that the libraries, which provide an average of 20-fold coverage, were random and, as demonstrated with two S. aureus libraries, highly representative. Consistent with the comprehensive nature of this approach is the identification of epitopes that reside in both annotated and putatively novel open reading frames. The use of these libraries therefore allows for the rapid and direct identification of immunogenic epitopes with no apparent bias or difficulty that often associate with conventional expression methods.

  11. Democratizing Human Genome Project Information: A Model Program for Education, Information and Debate in Public Libraries.

    Science.gov (United States)

    Pollack, Miriam

    The "Mapping the Human Genome" project demonstrated that librarians can help whomever they serve in accessing information resources in the areas of biological and health information, whether it is the scientists who are developing the information or a member of the public who is using the information. Public libraries can guide library…

  12. Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH)

    NARCIS (Netherlands)

    Leveau, J.H.J.; Gerards, S.; De Boer, W.; Van Veen, J.A.

    2004-01-01

    We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia

  13. The human genome: Some assembly required. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    The Human Genome Project promises to be one of the most rewarding endeavors in modern biology. The cost and the ethical and social implications, however, have made this project the source of considerable debate both in the scientific community and in the public at large. The 1994 Graduate Student Symposium addresses the scientific merits of the project, the technical issues involved in accomplishing the task, as well as the medical and social issues which stem from the wealth of knowledge which the Human Genome Project will help create. To this end, speakers were brought together who represent the diverse areas of expertise characteristic of this multidisciplinary project. The keynote speaker addresses the project`s motivations and goals in the larger context of biological and medical sciences. The first two sessions address relevant technical issues, data collection with a focus on high-throughput sequencing methods and data analysis with an emphasis on identification of coding sequences. The third session explores recent advances in the understanding of genetic diseases and possible routes to treatment. Finally, the last session addresses some of the ethical, social and legal issues which will undoubtedly arise from having a detailed knowledge of the human genome.

  14. Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2013-01-01

    Full Text Available Bacterial artificial chromosome (BAC libraries have been invaluable tools for the genome-wide genetic dissection of complex organisms. Here, we report the construction and characterization of a high-redundancy BAC library from a very valuable pig breed in China, Wuzhishan miniature pig (Sus scrofa, using its blood cells and fibroblasts, respectively. The library contains approximately 153,600 clones ordered in 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 152.3 kb, representing approximately 7.68 genome equivalents of the porcine haploid genome and a 99.93% statistical probability of obtaining at least one clone containing a unique DNA sequence in the library. 19 pairs of microsatellite marker primers covering porcine chromosomes were used for screening the BAC library, which showed that each of these markers was positive in the library; the positive clone number was 2 to 9, and the average number was 7.89, which was consistent with 7.68-fold coverage of the porcine genome. And there were no significant differences of genomic BAC library from blood cells and fibroblast cells. Therefore, we identified 19 microsatellite markers that could potentially be used as genetic markers. As a result, this BAC library will serve as a valuable resource for gene identification, physical mapping, and comparative genomics and large-scale genome sequencing in the porcine.

  15. Characterization and identification of (CT)n microsatellites in soybean using sheared genomic libraries.

    Science.gov (United States)

    Hossain, K G; Kawai, H; Hayashi, M; Hoshi, M; Yamanaka, N; Harada, K

    2000-04-28

    Three small insert (300 to approximately 600 bp) sheared genomic libraries were constructed by pipetting and DNase I treatment of soybean DNA. About 15,000 clones from each library were screened for CT- simple sequence repeats (CT-SSRs). The CT-SSRs were abundant in the soybean genome at an estimated frequency of approximately one SSR per 110 kb of genomic DNA. Following the sequencing of 129 positive clones, the repeat types and frequency of CT repeats among the positive clones were characterized. Forty-nine primer pairs were designed and preliminarily evaluated for their ability to amplify genomic DNA from a set of six varieties, including parents of a mapping family. Amplified products were analyzed by 10% PAGE. Eighty-eight percent of the designed primers were able to amplify all these genomic DNAs using a single PCR profile of 53 degrees C annealing temperature, of which 22 (45%) were polymorphic in the six varieties, and 14 of them were polymorphic in the parents of the mapping family. The polymorphic primer sets were further assessed for allelic information using DNA from 16 soybean cultivars. The average number of alleles was 4, ranging from 2 to 7 with the highest polymorphism information content value 0.84. Fourteen of these SSRs were mapped, using an existing soybean RFLP map. The findings presented here will advance our understanding of the soybean genome, and assist in the mapping genome and discrimination of closely related varieties of this species.

  16. Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.

    Science.gov (United States)

    Ejsmont, Radoslaw Kamil; Bogdanzaliewa, Maria; Lipinski, Kamil Andrzej; Tomancak, Pavel

    2011-01-01

    Genomic DNA libraries are a valuable source of large constructs that can contain all the regulatory elements necessary for recapitulating wild-type gene expression when introduced into animal genomes as a transgene. Such clones can be directly used in complementation studies. In combination with recombineering manipulation, the tagged genomic clones can serve as faithful in vivo gene activity reporters that enable studies of tissue specificity of gene expression, subcellular protein localization, and affinity purification of complexes. We present a detailed protocol for generating an unbiased genomic library in a custom pFlyFos vector that is optimized for liquid culture recombineering manipulation and site-specific transgenesis of fosmid-size loci across different Drosophila species. The cross-species properties of the library can be used, for example, to establish the specificity of RNAi phenotypes or to selectively introgress specific genomic loci among different Drosophila species making it an ideal tool for experimental evolutionary studies. The FlyFos system can be easily adapted to other organisms.

  17. [Construction of Frankia genomic libraries and isolation of clones homologous to nodulation genes from Rhizobium leguminosarum].

    Science.gov (United States)

    Cui, Y H; Qin, M; Wang, Y L; Ding, J; Ma, Q S

    1990-01-01

    High molecular genomic DNAs were isolated by using the lysozyme plus achromopeptidase system from Frankia strains At4, Ccol and Hr16, the root nodule endophytes of Alnus, Casuarina and Hippophae respectively, and used to construct genomic libraries in pLAFR1, a broad host range cosmid vector within many gram-negative hosts. The genomic libraries were screened by in situ colony hybridization to identify clones homologous to common nodulation genes of Rhizobium leguminosarum, based on the sequence homology of EcoRI-digested Frankia total DNA to nodABC from Rhizobium meliloti. Several clones showing relatively strong hybridization were found, the recombinant plasmid was isolated, and their homology with Rhizobium nodulation genes was confirmed by spot hybridization. Further work on these positive clones is now underway.

  18. Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens

    Directory of Open Access Journals (Sweden)

    Lu Yiming

    2011-03-01

    Full Text Available Abstract Background The Ahringer C. elegans RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1 mis-annotation (the clone with the retired gene name should be remapped to the actual target gene; 2 nonspecific PCR amplification; 3 cross-RNAi; 4 mis-operation such as sample loading error, etc. Results Here we performed a reliability analysis on the Ahringer C. elegans RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3% of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54% bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs. The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (http://biocompute.bmi.ac.cn/CelRNAi/ was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies. Conclusions Because of the potential unreliability of the Ahringer C. elegans RNAi feeding library, we strongly suggest the user examine

  19. The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research.

    Science.gov (United States)

    Song, Xiang; Goicoechea, Jose Luis; Ammiraju, Jetty S S; Luo, Meizhong; He, Ruifeng; Lin, Jinke; Lee, So-Jeong; Sisneros, Nicholas; Watts, Tom; Kudrna, David A; Golser, Wolfgang; Ashley, Elizabeth; Collura, Kristi; Braidotti, Michele; Yu, Yeisoo; Matzkin, Luciano M; McAllister, Bryant F; Markow, Therese Ann; Wing, Rod A

    2011-04-01

    The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.

  20. Construction and characterization of a 10-genome equivalent yeast artificial chromosome library for the laboratory rat, Rattus norvegicus

    Energy Technology Data Exchange (ETDEWEB)

    Cai, L.; Zee, R.Y.L. [Harvard Medical School, Boston, MA (United States); Schalkwyk, L.C. [Max Planck Institute for Molecular Genetics, Berlin (Germany)] [and others

    1997-02-01

    Increasing attention has been focused in recent years on the rat as a model organism for genetic studies, in particular for the investigation of complex traits, but progress has been limited by the lack of availability of large-insert genomic libraries. Here, we report the construction and characterization of an arrayed yeast artificial chromosome (YAC) library for the rat genome containing approximately 40,000 clones in the AB1380 host using the pCGS966 vector. An average size of 736 kb was estimated from 166 randomly chosen clones; thus the library provides 10-fold coverage of the genome, with a 99.99% probability of containing a unique sequence. Eight of 39 YACs analyzed by fluorescence in situ hybridization were found to be chimeric, indicating a proportion of about 20-30% of chimeric clones. The library was spotted on high-density filters to allow the identification of YAC clones by hybridization and was pooled using a 3-dimensional scheme for screening by PCR. Among 48 probes used to screen the library, an average of 9.3 positive clones were found, consistent with the calculated 10-fold genomic coverage of the library. This YAC library represents the first large-insert genomic library for the rat. It will be made available to the research community at large as an important new resource for complex genome analysis in this species. 35 refs., 4 figs.

  1. [Construction and identification on enriched microsatellite library from yak genome].

    Science.gov (United States)

    Li, Qi-Fa; Zhao, Xing-Bo; Luo, Xiao-Lin; Yao, Ping; Li, Ning; Tian, Zhi-Hua; Wu, Chang-Xin; Xie, Zhuang

    2004-05-01

    We constructed the first microsatellite-enriched library of yak according to the strong affinity between biotin and streptavidin. The method included ligation of 300 approximately 1 000 bp enzyme-digested fragments and adaptors, affinity capture of microsatellite repeat using biotinylated oligoprobe ((CA)12, (CCG) 8, (CAG)8, (TTTC) 8) attached to streptavidin-coated magnetic beads, PCR amplification using the 21-mer adaptor oligonucleotide as primer to obtain double-stranded targeted fragments, religated into pMD18-T vector and transformed to DH5alpha. The results of sequencing showed that 37 of 48 readable sequences contained microsatellites indicating a high degree of microsatellite enrichment. The new polymorphic microsatellite markers we have identified and characterized will contribute to the yak genetic linkage mapping, molecular evolution and phylogenetic studies, marker assistant selection and QTLs location of yak main economic traits.

  2. Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

    Institute of Scientific and Technical Information of China (English)

    SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

    2014-01-01

    The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

  3. Use of a recombination-deficient phage lambda system to construct wheat genomic libraries.

    Science.gov (United States)

    Murray, M G; Kennard, W C; Drong, R F; Slightom, J L

    1984-10-01

    The poor cloning efficiency of wheat (Triticum aestivum cv. Yamhill) DNA in conventional cloning vectors has previously prevented the preparation of complete genomic libraries. We show here that while wheat DNA does not clone efficiently using the vector Ch4A, it can be cloned efficiently using Ch32. Ch32 clones are red- gam+ and therefore can be propagated on recombination-deficient hosts. These results suggest that instability of wheat sequences in conventional lambda vector systems has frustrated previous attempts to prepare libraries.

  4. Identification and cloning of a new category of DNA fragments which are poorly represented in human genomic libraries.

    Science.gov (United States)

    Wong, P; Myal, Y; Shui, R; Tenniswood, M

    1993-01-29

    We have developed an alternative strategy for the preparation of genomic libraries that ensures better representation of genomic sequences commonly underrepresented in genomic libraries constructed using standard protocols. To overcome the apparent bias against genomic sequences containing clusters of restriction sites we have used nonoptimized restriction digestions to generate a mixture of DNA fragments which have been cloned into the EMBL3 vector. To validate this protocol we have screened the EMBL3 library to identify a full length genomic clone of the prolactin-inducible gene (PIP). Screening 4 other, commercially available, genomic libraries prepared using standard protocols for restriction digestion of the genomic DNA failed to identify any full length clones. We show that this increase in the representation of the full length PIP gene in the EMBL3 genomic library is attributable to the method of insert preparation used and suggests that an additional subset of sequences that may be poorly represented in, or absent from, established libraries may be cloned using this modified protocol.

  5. Characterization of histone genes isolated from Xenopus laevis and Xenopus tropicalis genomic libraries.

    Science.gov (United States)

    Ruberti, I; Fragapane, P; Pierandrei-Amaldi, P; Beccari, E; Amaldi, F; Bozzoni, I

    1982-12-11

    Using a cDNA clone for the histone H3 we have isolated, from two genomic libraries of Xenopus laevis and Xenopus tropicalis, clones containing four different histone gene clusters. The structural organization of X. laevis histone genes has been determined by restriction mapping, Southern blot hybridization and translation of the mRNAs which hybridize to the various restriction fragments. The arrangement of the histone genes in X. tropicalis has been determined by Southern analysis using X. laevis genomic fragments, containing individual genes, as probes. Histone genes are clustered in the genome of X. laevis and X. tropicalis and, compared to invertebrates, show a higher organization heterogeneity as demonstrated by structural analysis of the four genomic clones. In fact, the order of the genes within individual clusters is not conserved.

  6. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.

    Science.gov (United States)

    Carpenter, Meredith L; Buenrostro, Jason D; Valdiosera, Cristina; Schroeder, Hannes; Allentoft, Morten E; Sikora, Martin; Rasmussen, Morten; Gravel, Simon; Guillén, Sonia; Nekhrizov, Georgi; Leshtakov, Krasimir; Dimitrova, Diana; Theodossiev, Nikola; Pettener, Davide; Luiselli, Donata; Sandoval, Karla; Moreno-Estrada, Andrés; Li, Yingrui; Wang, Jun; Gilbert, M Thomas P; Willerslev, Eske; Greenleaf, William J; Bustamante, Carlos D

    2013-11-07

    Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

  7. Molecular analysis of DNA and construction of genomic libraries of Mycobacterium leprae.

    Science.gov (United States)

    Clark-Curtiss, J E; Jacobs, W R; Docherty, M A; Ritchie, L R; Curtiss, R

    1985-03-01

    Molecular analysis of DNA from Mycobacterium leprae, "Mycobacterium lufu," and Mycobacterium vaccae has demonstrated that the G + C (guanine plus cytosine) contents of the DNAs are 56, 61, and 65%, respectively, and that the genome sizes are 2.2 X 10(9), 3.1 X 10(9), and 3.1 X 10(9) daltons, respectively. Because of the significant differences in both G + C content and genome size among M. leprae, "M. lufu," and M. vaccae DNAs, these species are not related, although hybridization experiments under nonstringent conditions, with two separate cloned M. leprae DNA inserts as probes, indicate that there are some conserved sequences among the DNAs. The G + C content of Dasypus novemcinctus (armadillo, the animal of choice for cultivating M. leprae) DNA was determined to be 36%. Genomic libraries potentially representing more than 99.99% of each genome were prepared by cloning into the cosmid vector, pHC79, in Escherichia coli K-12. A genomic library representing approximately 95% of the genome of M. vaccae was prepared in pBR322. M. leprae DNA was subcloned from the pHC79::M. leprae library into an expression vector, pYA626. This vector is a 3.8-kilobase derivative of pBR322 in which the promoter region of the asd (aspartate semialdehyde dehydrogenase) gene from Streptococcus mutans has been inserted in place of the EcoRI-to-PstI fragment of pBR322. Several (44% of those tested) pYA626::M. leprae recombinants and one pBR322::M. vaccae recombinant synthesized new polypeptides in minicells of E. coli, indicating that mycobacterial DNA can be expressed in E. coli K-12, although expression is probably dependent upon use of nonmycobacterial promoters recognized by the E. coli transcription-translation apparatus.

  8. SVGenes: a library for rendering genomic features in scalable vector graphic format.

    Science.gov (United States)

    Etherington, Graham J; MacLean, Daniel

    2013-08-01

    Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements. SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion. The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License. dan.maclean@tsl.ac.uk.

  9. A new age in functional genomics using CRISPR/Cas9 in arrayed library screening.

    Science.gov (United States)

    Agrotis, Alexander; Ketteler, Robin

    2015-01-01

    CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. What makes CRISPR/Cas9 so revolutionary is the ability to target a protein (Cas9) to an exact genomic locus, through designing a specific short complementary nucleotide sequence, that together with a common scaffold sequence, constitute the guide RNA bridging the protein and the DNA. Wild-type Cas9 cleaves both DNA strands at its target sequence, but this protein can also be modified to exert many other functions. For instance, by attaching an activation domain to catalytically inactive Cas9 and targeting a promoter region, it is possible to stimulate the expression of a specific endogenous gene. In principle, any genomic region can be targeted, and recent efforts have successfully generated pooled guide RNA libraries for coding and regulatory regions of human, mouse and Drosophila genomes with high coverage, thus facilitating functional phenotypic screening. In this review, we will highlight recent developments in the area of CRISPR-based functional genomics and discuss potential future directions, with a special focus on mammalian cell systems and arrayed library screening.

  10. A New Age in Functional Genomics Using CRISPR/Cas9 in Arrayed Library Screening

    Directory of Open Access Journals (Sweden)

    Alexander eAgrotis

    2015-09-01

    Full Text Available CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. What makes CRISPR/Cas9 so revolutionary is the ability to target a protein (Cas9 to an exact genomic locus, through designing a specific short complementary nucleotide sequence, that together with a common scaffold sequence, constitute the guide RNA bridging the protein and the DNA. Wild-type Cas9 cleaves both DNA strands at its target sequence, but this protein can also be modified to exert many other functions. For instance, by attaching an activation domain to catalytically inactive Cas9 and targeting a promoter region, it is possible to stimulate the expression of a specific endogenous gene. In principle, any genomic region can be targeted, and recent efforts have successfully generated pooled guide RNA libraries for coding and regulatory regions of human, mouse and Drosophila genomes with high coverage, thus facilitating functional phenotypic screening. In this review, we will highlight recent developments in the area of CRISPR-based functional genomics and discuss potential future directions, with a special focus on mammalian cell systems and arrayed library screening.

  11. Construction of a full bacterial artificial chromosome (BAC) library of Oryza sativa genome

    Institute of Scientific and Technical Information of China (English)

    TAOQUANZHOU; HAIYINGZHAO; 等

    1994-01-01

    We have constructed a full BAC library for the superior early indica variety of Oryza sativa,Guang Lu Ai 4.The MAX Efficiency DH10B with increased stability of inserts was used as BAC host cells.The potent pBelo BACII with double selection markers was used as cloning vector.The cloning efficiency we have reached was as high as 98%,and the transformation efficiency was raised up to 106 transformants/μg of large fragment DNA.The BAC recombinant transformants were picked at random and analyzed for the size of inserts,which turned out to be of 120 kb in length on average.We have obtained more than 20,000 such BAC clones.According to conventional probability equation,they covered the entire rice genome of 420,000 kb in length.The entire length of inserts of the library obtained has the 5-to 6-fold coverage of the genome.To our knowledge,this is the first reported full BAC library for a complex genome.

  12. Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning.

    Science.gov (United States)

    Liu, Yao-Guang; Liu, Hongmei; Chen, Letian; Qiu, Weihua; Zhang, Qunyu; Wu, Hao; Yang, Chunyi; Su, Jing; Wang, Zhonghua; Tian, Dongsheng; Mei, Mantong

    2002-01-09

    The transformation-competent artificial chromosome vector (TAC) system has been shown to be very useful for efficient gene isolation in Arabidopsis thaliana (Proc. Natl. Acad. Sci. USA 96 (1998) 6535). To adapt the vector system for gene isolation in crops, two new TAC vectors and rice genomic libraries were developed. The new vectors pYLTAC17 and pYLTAC27 use the Bar gene and Hpt gene driven by the rice Act1 promoter as the plant selectable markers, respectively, and are suitable for transformation of rice and other grasses. Two representative genomic libraries (I and II) of an Indica rice variety Minghui63, a fertility restorer line for hybrid rice, were constructed with pYLTAC17 using different size classes of partially digested DNA fragments. Library I and library II consisted of 34,560 and 1.2 x 10(5) clones, with average insert sizes of approximately 77 and 39 kb, respectively. The genome coverage of the libraries I and II was estimated to be about 5 and 11 haploid genome equivalents, respectively. Clones of the library I were stored individually in ninety 384-well plates, and those of the library II were collected as bulked pools each containing 30-50 clones and stored in eight 384-well plates. A number of probes were used to hybridize high-density colony filters of the library I prepared by an improved replicating method and each detected 2-9 positive clones. A method for rapid screening of the library II by pooled colony hybridization was developed. A TAC clone having an 80 kb rice DNA insert was successfully transferred into rice genome via Agrobacterium-mediated transformation. The new vectors and the genomic libraries should be useful for gene cloning and genetic engineering in rice and other crops.

  13. Genomic libraries: II. Subcloning, sequencing, and assembling large-insert genomic DNA clones.

    Science.gov (United States)

    Quail, Mike A; Matthews, Lucy; Sims, Sarah; Lloyd, Christine; Beasley, Helen; Baxter, Simon W

    2011-01-01

    Sequencing large insert clones to completion is useful for characterizing specific genomic regions, identifying haplotypes, and closing gaps in whole genome sequencing projects. Despite being a standard technique in molecular laboratories, DNA sequencing using the Sanger method can be highly problematic when complex secondary structures or sequence repeats are encountered in genomic clones. Here, we describe methods to isolate DNA from a large insert clone (fosmid or BAC), subclone the sample, and sequence the region to the highest industry standard. Troubleshooting solutions for sequencing difficult templates are discussed.

  14. Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing.

    Science.gov (United States)

    Yang, Tae-Jin; Yu, Yeisoo; Nah, Gyoungju; Atkins, Michael; Lee, Seunghee; Frisch, David A; Wing, Rod A

    2003-08-01

    Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.

  15. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.

    Science.gov (United States)

    Urich, Mark A; Nery, Joseph R; Lister, Ryan; Schmitz, Robert J; Ecker, Joseph R

    2015-03-01

    Current high-throughput DNA sequencing technologies enable acquisition of billions of data points through which myriad biological processes can be interrogated, including genetic variation, chromatin structure, gene expression patterns, small RNAs and protein-DNA interactions. Here we describe the MethylC-sequencing (MethylC-seq) library preparation method, a 2-d protocol that enables the genome-wide identification of cytosine DNA methylation states at single-base resolution. The technique involves fragmentation of genomic DNA followed by adapter ligation, bisulfite conversion and limited amplification using adapter-specific PCR primers in preparation for sequencing. To date, this protocol has been successfully applied to genomic DNA isolated from primary cell culture, sorted cells and fresh tissue from over a thousand plant and animal samples.

  16. Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

    Science.gov (United States)

    Miller, Chase A; Anthony, Jon; Meyer, Michelle M; Marth, Gabor

    2013-02-01

    High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

  17. Construction of representative NotI linking libraries specific for the total human genome and for human chromosome 3.

    Science.gov (United States)

    Zabarovsky, E R; Allikmets, R; Kholodnyuk, I; Zabarovska, V I; Paulsson, N; Bannikov, V M; Kashuba, V I; Dean, M; Kisselev, L L; Klein, G

    1994-03-15

    NotI linking clones represent valuable tools for both physical and genetic mapping. Using procedures that we have previously described, several chromosome 3-specific NotI linking libraries have been constructed. Here, we describe the construction of six independent NotI linking libraries specific for the total human genome. These libraries were made using three different vectors and two combinations of restriction enzymes. Altogether, these six libraries contain more than 1 million recombinant phages. Considering that the human genome contains about 3000-5000 NotI sites, it is likely that all clonable NotI sites are present in these libraries. Two of the six libraries were transferred into plasmid form. At the same time, a chromosome 3-specific EcoRI-NotI library (NRL1) was constructed. This library considerably increases the representation of cloned NotI sites in combination with previously constructed libraries that were made using BamHI-NotI digestion. All libraries are available on request.

  18. Construction of representative NotI linking libraries specific for the total human genome and for human chromosome 3

    Energy Technology Data Exchange (ETDEWEB)

    Zabarovsky, E.R.; Kholodnyuk, I.; Zabarovska, V.I.; Paulsson, N.; Bannikov, V.M.; Kashuba, V.I.; Klein, G. (Karolinska Institute, Stockholm (Sweden)); Allikmets, R.; Dean, M. (National Cancer Institute, Frederick, MD (United States)); Kisselev, L.L. (Engelhardt Institute of Molecular Biology, Moscow (Russian Federation))

    1994-03-15

    NotI linking clones represent valuable tools for both physical and genetic mapping. Using procedures previously described, several chromosome 3-specific NotI linking libraries have been constructed. Here, the authors describe the construction of six independent NotI linking libraries specific for the total human genome. These libraries were made using three different vectors and two combinations of restriction enzymes. Altogether, these six libraries contain more than 1 million recombinant phages. Considering that the human genome contains about 3000-5000 NotI sites, it is likely that all clonable NotI sites are present in these libraries. Two of the six libraries were transferred into plasmid form. At the same time, a chromosome 3-specific EcoRI-NotI library (NRL1) was constructed. This library considerably increases the representation of cloned NotI sites in combination with previously constructed libraries that were made using BamHI-NotI digestion. All libraries are available on request. 18 refs., 3 figs., 1 tab.

  19. Genomic Sequence Comparisons, 1987-2003 Final Report

    Energy Technology Data Exchange (ETDEWEB)

    George M. Church

    2004-07-29

    This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.

  20. Next-generation libraries for robust RNA interference-based genome-wide screens.

    Science.gov (United States)

    Kampmann, Martin; Horlbeck, Max A; Chen, Yuwen; Tsai, Jordan C; Bassik, Michael C; Gilbert, Luke A; Villalta, Jacqueline E; Kwon, S Chul; Chang, Hyeshik; Kim, V Narry; Weissman, Jonathan S

    2015-06-30

    Genetic screening based on loss-of-function phenotypes is a powerful discovery tool in biology. Although the recent development of clustered regularly interspaced short palindromic repeats (CRISPR)-based screening approaches in mammalian cell culture has enormous potential, RNA interference (RNAi)-based screening remains the method of choice in several biological contexts. We previously demonstrated that ultracomplex pooled short-hairpin RNA (shRNA) libraries can largely overcome the problem of RNAi off-target effects in genome-wide screens. Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen sample preparation for deep sequencing. We present next-generation high-complexity libraries targeting human and mouse protein-coding genes, which we grouped into 12 sublibraries based on biological function. A pilot screen suggests that our next-generation RNAi library performs comparably to current CRISPR interference (CRISPRi)-based approaches and can yield complementary results with high sensitivity and high specificity.

  1. A quick in vitro pathway from prokaryotic genomic libraries to enzyme discovery.

    Science.gov (United States)

    Ryabova, Lyubov; Guillemer, Sabrina; Pallas, Stéphanie; Persillon, Cécile; Lefèvre, Fabrice; Masson, Jean-Michel; Ravot, Gilles

    2008-07-01

    Screening of prokaryotic genomes in order to identify enzymes with a desired catalytic activity can be performed in vivo in bacterial cells. We propose a strategy of in vitro expression screening of large prokaryotic genomic libraries based on Escherichia coli cell-free transcription-translation systems. Because cell-based expression may be limited by poor yield or protein misfolding, cell-free expression systems may be advantageous in permitting a more comprehensive screen under conditions optimized for the desired enzyme activity. However, monocistronic messages with an improved leader initiation context are typically used for protein production in vitro. Here, we describe successful use of a Pseudoalteromonas genomic DNA library for in vitro expression of DNA fragments carrying multiple open reading frames (ORFs) in the context of their authentic translation initiation sites and regulatory regions. We show that ORFs located far from the 5' and 3' ends of polycistronic transcripts can be expressed at a sufficient level in an in vitro transcription-translation system in order to allow functional screening. We demonstrate the overall cell-free functional screen strategy with the successful selection of an esterase from Pseudoalteromonas.

  2. Construction of a nurse shark (Ginglymostoma cirratum bacterial artificial chromosome (BAC library and a preliminary genome survey

    Directory of Open Access Journals (Sweden)

    Inoko Hidetoshi

    2006-05-01

    Full Text Available Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  3. Human genomic library screened with 17-base oligonucleotide probes yields a novel interferon gene.

    OpenAIRE

    Torczynski, R M; Fuke, M; Bollon, A P

    1984-01-01

    A method is presented that has permitted a human genomic library to be screened for low-copy genes using 17-base synthetic oligonucleotides as probes. Parallel screening with two different 17-base probes permitted the unambiguous identification of clones containing interferon-alpha (IFN-alpha) genes. The isolated human IFN-alpha genes were sequenced, and one appears to be IFN-alpha L; the other is one not previously described, which we have designated IFN-alpha WA. The IFN-alpha WA sequence d...

  4. Construction of cosmid genomic libraries for the normal and myopathic Syrian hamsters.

    Science.gov (United States)

    McCully, J D; Jandreski, M A; Liew, J; Sole, M J; Liew, C C

    1987-11-01

    Cosmid genomic libraries from both normal and myopathic Syrian hamsters have been constructed. MboI was used to generate 35- to 50-kilobase DNA fragments which were isolated from a 5-25% NaCl gradient. The 35- to 50-kilobase DNA fragments were ligated to the cosmid vector pCV108 and packaged into Escherichia coli DK1. Approximately 3 X 10(5) - 4 X 10(5) clones were obtained per microgram of ligated DNA. Thirteen clones have been isolated from 2 X 10(5) colonies using a cardiac myosin heavy chain clone as a probe. Restriction maps of two of these clones are presented here.

  5. Complete genome sequence of Shewanella putrefaciens. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Heidelberg, John F.

    2001-04-01

    Seventy percent of the costs for genome sequencing Shewanella putrefaciens (oneidensis) were requested. These funds were expected to allow completion of the low-pass (5-fold) random sequencing and complete closure and annotation of the 200 kbp plasmid. Because of cost reduction that occurred during the period of this grant, these goals have been far exceeded. Currently, the S. putrefaciens genome is very nearly completely closed, even though the genome was significantly larger than expected and extremely repetitive. The entire genome sequence has been made BLAST searchable on the TIGR web page, and an extensive effort has been made to make data and analyses available to all researchers working on S. putrefaciens (oneidensis).

  6. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

    Directory of Open Access Journals (Sweden)

    Kumar Santosh

    2012-12-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. Results Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents. Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. Conclusions Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from

  7. Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA.

    Science.gov (United States)

    Gallagher, Ryan R; Li, Zhe; Lewis, Aaron O; Isaacs, Farren J

    2014-10-01

    Multiplex automated genome engineering (MAGE) is a powerful technology for in vivo genome editing that uses synthetic single-stranded DNA (ssDNA) to introduce targeted modifications directly into the Escherichia coli chromosome. MAGE is a cyclical process that involves transformation of ssDNA (by electroporation) followed by outgrowth, during which bacteriophage homologous recombination proteins mediate annealing of ssDNAs to their genomic targets. By iteratively introducing libraries of mutagenic ssDNAs targeting multiple sites, MAGE can generate combinatorial genetic diversity in a cell population. Alternatively, MAGE can introduce precise mutant alleles at many loci for genome-wide editing or for recoding projects that are not possible with other methods. In recent technological advances, MAGE has been improved by strain modifications and selection techniques that enhance allelic replacement. This protocol describes the manual execution of MAGE wherein each cycle takes ≈ 2.5 h, which, if carried out by two people, allows ≈ 10 continuous cycles of MAGE-based mutagenesis per day.

  8. Construction and Characterization of a Bacterial Artificial Chromosome Library for the A-Genome of Cotton (G. arboreum L.

    Directory of Open Access Journals (Sweden)

    Yan Hu

    2011-01-01

    Full Text Available A bacterial artificial chromosome (BAC library for the A-genome of cotton has been constructed from the leaves of G. arboreum L cv. Jianglinzhongmian. It is used as elite A-genome germplasm resources in the present cotton breeding program and has been used to build a genetic reference map of cotton. The BAC library consists of 123,648 clones stored in 322 384-well plates. Statistical analysis of a set of 103 randomly selected BAC clones indicated that each clone has an average insert length of 100.2 kb per plasmid, with a range of 30 to 190 kb. Theoretically, this represents 7.2 haploid genome equivalents based on an A-genome size of 1697 Mb. The BAC library has been arranged in column pools and superpools allowing screening with various PCR-based markers. In the future, the A-genome cotton BAC library will serve as both a giant gene resource and a valuable tool for map-based gene isolation, physical mapping and comparative genome analysis.

  9. The P1 vector system for the preparation and screening of genomic libraries.

    Science.gov (United States)

    Shepherd, N S; Smoller, D

    1994-01-01

    In retrospect, it is remarkable how swiftly the P1 cloning system has progressed in only a few years from a novel cloning system to one now widely used for the production of recombinant libraries and the building of physical maps. As the libraries become larger, better characterized and more widely distributed, we certainly will see a blossoming of research articles and techniques based on the use of P1 recombinant clones. Specifically, we can look forward to scanning P1 clones for expressed sequences (N. Sternberg, personal communication), routine retrofitting of P1 clones with a combination of transposon and P1 transduction techniques (3), the random or loxP-directed (68,69) insertion of P1 clones into host genomes and the subsequent production of transgenic animals (63), a further use of P1 clones in the building of contigs and physical maps, an a higher in vitro cloning efficiency due to the purification of the P1 pacase proteins used during in vitro packaging (70). In summary, P1 bacteriophage cloning is favorably impacting research today and will continue to fill an important niche as a genomic cloning system.

  10. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast.

    Science.gov (United States)

    James, P; Halladay, J; Craig, E A

    1996-12-01

    The two-hybrid system is a powerful technique for detecting protein-protein interactions that utilizes the well-developed molecular genetics of the yeast Saccharomyces cerevisiae. However, the full potential of this technique has not been realized due to limitations imposed by the components available for use in the system. These limitations include unwieldy plasmid vectors, incomplete or poorly designed two-hybrid libraries, and host strains that result in the selection of large numbers of false positives. We have used a novel multienzyme approach to generate a set of highly representative genomic libraries from S. cerevisiae. In addition, a unique host strain was created that contains three easily assayed reporter genes, each under the control of a different inducible promoter. This host strain is extremely sensitive to weak interactions and eliminates nearly all false positives using simple plate assays. Improved vectors were also constructed that simplify the construction of the gene fusions necessary for the two-hybrid system. Our analysis indicates that the libraries and host strain provide significant improvements in both the number of interacting clones identified and the efficiency of two-hybrid selections.

  11. Construction of white spot syndrome virus (WSSV) whole genome phage display library

    Institute of Scientific and Technical Information of China (English)

    ZHU Yanbing; YANG Feng

    2007-01-01

    A rebuilt vector pCANTAB 5 EE was obtained by inserting a 34 bp double-stranded oligonucleotide which contained a EcoRV recognition sequence into pCANTAB 5 E. White spot syndrome virus (WSSV) genome DNA was fragmented by sonication to isolate fragments mainly in the range of 0.8 ~2.0 kb, then the fragments were blunt-ended with T4 DNA polymerase and cloned into the EcoRV site of pCANTAB 5 EE. The primary recombinant clone of the library was 3.0 × 105.Colony PCR of random selected recombinants showed that the size of the inserts was 0.12 ~ 1.77 kb. After the whole library recombinant phages infected Escherichia coli HB2151 cells, the extracellular and periplasmic extracts were dropped on PVDF membranes to perform dot blot, using polyclonal mouse anti-VP24 serum,anti-WSV026 serum,anti-WSV063 serum,anti-WSV069 serum,anti-WSV112 serum, anti WSV238 serum,anti-WSV303 serum and anti-VP26 serum as the primary antibody, respectively. The results showed that the display library could express the viral proteins.

  12. Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH).

    Science.gov (United States)

    Leveau, Johan H J; Gerards, Saskia; de Boer, Wietse; van Veen, Johannes A

    2004-09-01

    We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia coli of large-sized genomic DNA fragments of the mycophagous soil bacterium Collimonas fungivorans, and hybridized 768 library clones with the Collimonas-specific fluorescent probe CTE998-1015. Critical to the success of this approach (which we refer to as large-insert library FISH or LIL-FISH) was the ability to induce fosmid copy number, the exponential growth status of library clones in the FISH assay and the use of a simple pooling strategy to reduce the number of hybridizations. Twelve out of 768 E. coli clones were suspected to harbour and express Collimonas 16S rRNA genes based on their hybridization to CTE998-1015. This was confirmed by the finding that all 12 clones were also identified in an independent polymerase chain reaction-based screening of the same 768 clones using a primer set for the specific detection of Collimonas 16S ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by restriction analysis into two distinct contigs, confirming that C. fungivorans harbours at least two 16S rRNA genes. For one contig, representing 1-2% of the genome, the nucleotide sequence was determined, providing us with a narrow but informative view of Collimonas genome structure and content.

  13. The 1996 National Survey of Public Libraries and the Internet: Progress and Issues. Final Report.

    Science.gov (United States)

    Bertot, John Carlo; And Others

    This 1996 National Commission on Libraries and Information Science (NCLIS) survey gathered data from a national sample of public libraries concerning the current level of public library involvement with the Internet. The purpose of this study was to: (1) provide policymakers, researchers, and library professionals with longitudinal data that…

  14. A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

    Directory of Open Access Journals (Sweden)

    Oliver Stephen G

    2007-04-01

    Full Text Available Abstract Background Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs, which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. Results Here we present a general approach to create domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustilago maydis, a fungal pathogen of maize, and the white rot fungus Phanerochaete chrysosporium. In addition, we include the Microsporidion Encephalitozoon cuniculi, an obligate intracellular parasite, and two non-fungal species, the oomycetes Phytophthora sojae and Phytophthora ramorum, both plant pathogens. We evaluate the performance in terms of coverage against the original 30 genomes used in training FPfam and against five more recently sequenced fungal genomes that can be considered as an independent test set. We show that kingdom-specific models such as FPfam can find instances of both novel and well characterized domains, increases overall coverage and detects more domains per sequence with typically higher bitscores than Pfam for the same domain families. An evaluation of the effect of changing E-values on the coverage shows that the performance of FPfam is consistent over the range of E-values applied. Conclusion Kingdom-specific models are shown to provide improved coverage. However, as the models become more specific, some sequences found by Pfam may be missed by the models in FPfam and some of the families represented in the test set are not present in FPfam

  15. Functional screening of metagenome and genome libraries for detection of novel flavonoid-modifying enzymes.

    Science.gov (United States)

    Rabausch, U; Juergensen, J; Ilmberger, N; Böhnke, S; Fischer, S; Schubach, B; Schulte, M; Streit, W R

    2013-08-01

    The functional detection of novel enzymes other than hydrolases from metagenomes is limited since only a very few reliable screening procedures are available that allow the rapid screening of large clone libraries. For the discovery of flavonoid-modifying enzymes in genome and metagenome clone libraries, we have developed a new screening system based on high-performance thin-layer chromatography (HPTLC). This metagenome extract thin-layer chromatography analysis (META) allows the rapid detection of glycosyltransferase (GT) and also other flavonoid-modifying activities. The developed screening method is highly sensitive, and an amount of 4 ng of modified flavonoid molecules can be detected. This novel technology was validated against a control library of 1,920 fosmid clones generated from a single Bacillus cereus isolate and then used to analyze more than 38,000 clones derived from two different metagenomic preparations. Thereby we identified two novel UDP glycosyltransferase (UGT) genes. The metagenome-derived gtfC gene encoded a 52-kDa protein, and the deduced amino acid sequence was weakly similar to sequences of putative UGTs from Fibrisoma and Dyadobacter. GtfC mediated the transfer of different hexose moieties and exhibited high activities on flavones, flavonols, flavanones, and stilbenes and also accepted isoflavones and chalcones. From the control library we identified a novel macroside glycosyltransferase (MGT) with a calculated molecular mass of 46 kDa. The deduced amino acid sequence was highly similar to sequences of MGTs from Bacillus thuringiensis. Recombinant MgtB transferred the sugar residue from UDP-glucose effectively to flavones, flavonols, isoflavones, and flavanones. Moreover, MgtB exhibited high activity on larger flavonoid molecules such as tiliroside.

  16. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Directory of Open Access Journals (Sweden)

    Andaine Seguin-Orlando

    Full Text Available Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

  17. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Science.gov (United States)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

  18. HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.

    Science.gov (United States)

    Zhou, Sisi; Fu, Yonggui; Li, Jie; He, Lingyu; Cai, Xingsheng; Yan, Qingyu; Rao, Xingqiang; Huang, Shengfeng; Li, Guang; Wang, Yiquan; Xu, Anlong

    2012-01-01

    Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.

  19. HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.

    Directory of Open Access Journals (Sweden)

    Sisi Zhou

    Full Text Available Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.

  20. Screening of metagenomic and genomic libraries reveals three classes of bacterial enzymes that overcome the toxicity of acrylate.

    Science.gov (United States)

    Curson, Andrew R J; Burns, Oliver J; Voget, Sonja; Daniel, Rolf; Todd, Jonathan D; McInnis, Kathryn; Wexler, Margaret; Johnston, Andrew W B

    2014-01-01

    Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again

  1. Screening of metagenomic and genomic libraries reveals three classes of bacterial enzymes that overcome the toxicity of acrylate.

    Directory of Open Access Journals (Sweden)

    Andrew R J Curson

    Full Text Available Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate

  2. Microsatellite loci isolation from river buffalo using enriched partial genomic libraries

    Directory of Open Access Journals (Sweden)

    A.L. Silva

    2010-02-01

    Full Text Available The extensive use of buffalo in agriculture, especially in developing countries, begs for genetic resources to evaluate and improve traits important to local and regional economies. Brazil presents the largest water buffalo populations in the New World, with 1.1 million heads including swamp and river types. To design rational breeding strategies for optimum utilization and conservation of available genetic variability in the Brazilian buffalo’s population, it is essential to understand their genetic architecture and relationship among various breeds. This depends, in part, on the knowledge of their genetic structure based on molecular markers like microsatellites. In the present study, we developed six enriched partial genomic libraries for river buffalo using selective hybridization methods. Genomic DNA was hybridized with six different arrays of repeat motif, 5’ biotinylated - (CA15, (CT15, (AGG8, (GAAA8, (GATA8, (AAAAC8 – and bound to streptavidin coated beads. The cloning process generated a total of 1920 recombinant clones. Up to date, 487 were directly sequenced for the presence of repeats, from which 13 have been positive for presence of repeats as follows: 9 for di-nucleotide repeats, 3 for tri-nucleotide repeats and 1 for tetra-nucleotide repeat. PCR primer pairs for the isolated microsatellites are under construction to determine optimum annealing temperature. These microsatellites will be useful for studies involving phylogenetic relationships, genome mapping and genetic diversity analysis within buffalo populations worldwide.

  3. Improvement of PCR-free NGS Library Preparation to Obtain Uniform Read Coverage of Genome with Extremely High AT Content

    OpenAIRE

    Williams, A.; Storton, D.; Buckles, J.; Llinas, M.; Wang, Wei

    2012-01-01

    PCR amplification is commonly used in generating libraries for Next-Generation Sequencing (NGS) to efficiently enrich and amplify sequenceable DNA fragments. However, it introduces bias in the representation of the original complex template DNA. Such artifact has devastating effects in sequencing genomes with highly unbalanced base composition: regions of extremely high or low GC content, which are a substantial fraction of such genomes, are often covered with zero or near-zero read depth. PC...

  4. A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits

    OpenAIRE

    2016-01-01

    Background Genomic libraries of introgression lines (ILs) consist of collections of homozygous lines with a single chromosomal introgression from a donor genotype in a common, usually elite, genetic background, representing the whole donor genome in the full collection. Currently, the only available melon IL collection was generated using Piel de sapo (var. inodorus) as the recurrent background. ILs are not available in genetic backgrounds representing other important market class cultivars, ...

  5. Gene Cloning of Penicillin V Acylase from Bacillus sp BAC4 by Genomic Library

    Directory of Open Access Journals (Sweden)

    ELFI SUSANTI VH

    2004-01-01

    Full Text Available This research was aimed to clone and identify penicillin V acylase (PVA gene of Bacillus sp. BAC4 by genomic library. Chromosome DNA of Bacillus sp. BAC4 was isolated by Wang method. pHB201 of E. coli was isolated by alkali lyses method. Recombinant DNA of Bacillus sp. BAC4 chromosome fragment and pHB201 was made by ligase process using T4 DNA ligase. Transformation of E. coli using this recombinant plasmid was carried out according to Mandel-Higa method. The results indicated that chromosome DNA fragment of Bacillus sp. BAC4 was bigger 23 kb with purity 1,3. Plasmid DNA fragment of E coli was 6,5 kb. Transformants laboring pHB201 recombinant plasmid was screen as blue-white colonies in a medium containing IPTG/X-gal and chloramphenicol.

  6. Construction of a Bacterial Artificial Chromosome Library of TM-1, a Standard Line for Genetics and Genomics in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    Yan Hu; Wang-Zhen Guo; Tian-Zhen Zhang

    2009-01-01

    A bacterial artificial chromosome (BAC) library was constructed for Gossyplum hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carded out by four-round polymerase chain reactions using 23 simple sequence repeats (SSR) markers, three sequence-related amplified polymorphism markers and one pair of pdmere for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were Identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 (A12) and 26 (D12) according to the genetic map, these BAC clonee are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with Important agronomic traits.

  7. The Science, Engineering and Technology Career Library Corner. Final report, February 1, 1995--January 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Cole, P.R.

    1996-03-01

    A grant was made to install and pilot-test the Science, Engineering and Technology (SET) Career Library Corner at the New York Hall of Science. The SET Career Library Corner is located in a multi-media library setting where visitors can explore careers in a quiet, uninterrupted environment, in contrast to the original installation designed as a museum floor exhibit.

  8. Public Library Use in Pennsylvania: Identifying Uses, Benefits, and Impacts. Final Report.

    Science.gov (United States)

    McClure, Charles R.; Bertot, John Carlo

    The purpose of this study is to identify users of Pennsylvania public libraries and determine their reasons for using the library. In addition, the study provides information describing the impacts and benefits to those users as a result of their contact with the public library. The objectives were to: (1) describe users in terms of their…

  9. National Survey of U.S. Public Libraries and the Internet, 1997. Final Report.

    Science.gov (United States)

    Bertot, John Carlo; McClure, Charles R.; Fletcher, Patricia Diamond

    The purpose of this study was to obtain descriptive information about the nation's public library connectivity, use, and costs related to the Internet. The study gathered data from a national sample of public libraries from the period between May and July 1997. Unlike the 1994 and 1996 students, the 1997 study drew a new library sample that…

  10. Retrieval of human DNA from rodent-human genomic libraries by a recombination process.

    Science.gov (United States)

    Neve, R L; Bruns, G A; Dryja, T P; Kurnit, D M

    1983-09-01

    Human Alu repeat ("BLUR") sequences have been cloned into the mini-plasmid vector piVX. The resulting piBLUR clones have been used to rescue selectively, by recombination, bacteriophage carrying human DNA sequences from genomic libraries constructed using DNA from rodent-human somatic cell hybrids. piBLUR clones are able to retrieve human clones from such libraries because at least one Alu family repeat is present on most 15 to 20 kb fragments of human DNA and because of the relative species-specificity of the sequences comprising the Alu family. The rapid, selective plaque purification achieved results in the construction of a collection of recombinant phage carrying diverse human DNA inserts from a specific subset of the human karyotype. Subfragments of two recombinants rescued from a mouse-human somatic cell hybrid containing human chromosomes X, 10, 13, and 22 were mapped to human chromosomes X and 13, respectively, demonstrating the utility of this protocol for the isolation of human chromosome-specific DNA sequences from appropriate somatic cell hybrids.

  11. SiRNA sequence model: redesign algorithm based on available genome-wide libraries.

    Science.gov (United States)

    Kozak, Karol

    2013-12-01

    The evolution of RNA interference (RNAi) and the development of technologies exploiting its biology have enabled scientists to rapidly examine the consequences of depleting a particular gene product in cells. Design tools have been developed based on experimental data to increase the knockdown efficiency of siRNAs. Not all siRNAs that are developed to a given target mRNA are equally effective. Currently available design algorithms take an accession, identify conserved regions among their transcript space, find accessible regions within the mRNA, design all possible siRNAs for these regions, filter them based on multi-scores thresholds, and then perform off-target filtration. These different criteria are used by commercial suppliers to produce siRNA genome-wide libraries for different organisms. In this article, we analyze existing siRNA design algorithms and evaluate weight of design parameters for libraries produced in the last decade. We proved that not all essential parameters are currently applied by siRNA vendors. Based on our evaluation results, we were able to suggest an siRNA sequence pattern. The findings in our study can be useful for commercial vendors improving the design of RNAi constructs, by addressing both the issue of potency and the issue of specificity.

  12. Library preparation methodology can influence genomic and functional predictions in human microbiome research.

    Science.gov (United States)

    Jones, Marcus B; Highlander, Sarah K; Anderson, Ericka L; Li, Weizhong; Dayrit, Mark; Klitgord, Niels; Fabani, Martin M; Seguritan, Victor; Green, Jessica; Pride, David T; Yooseph, Shibu; Biggs, William; Nelson, Karen E; Venter, J Craig

    2015-11-10

    Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.

  13. Versatile shuttle vectors and genomic libraries for use with Schizosaccharomyces pombe.

    Science.gov (United States)

    Barbet, N; Muriel, W J; Carr, A M

    1992-05-01

    We have constructed a variety of pUC-based vectors designed for maintenance in Schizosaccharomyces pombe. These can be used for both gene bank construction and subcloning. Plasmids pUR18 and pUR19 are modifications of pUC vectors containing the Sc. pombe ars1 and ura4 sequences and retaining the lacZ XGal blue-white selection system for screening for DNA inserts. These vectors have been used to construct representative Sc. pombe and Saccharomyces cerevisiae genomic libraries. To assist in the creation of gene deletions, we have constructed another two plasmids. Combined with the technique of partially filling-in 5' overhangs created with restriction enzymes, these plasmids simplify the replacement of all or part of an open reading frame by a functional ura4 gene. Furthermore, such constructs can be excised with SfiI as a linear fragment for use in Sc. pombe transformations. When integrated into the Sc. pombe genome, the site of integration can be easily mapped by pulsed-field gel electrophoresis using the presence of a novel NotI site.

  14. Metabolomic Functional Analysis of Bacterial Genomes: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Arp, Daniel J; Sayavedra-Soto, Luis A

    2008-01-01

    The availability of the complete DNA sequence of the bacterial genome of Nitrosomonas europaea offered the opportunity for unprecedented and detailed investigations of function. We studied the function of genes involved in carbohydrate and Fe metabolism. N. europaea has genes for the synthesis and degradation of glycogen and sucrose but cannot grow on substrates other than ammonia and CO2. Granules of glycogen were detected in whole cells by electron microscopy and quantified in cell-free extracts by enzymatic methods. The cellular glycogen and sucrose content varied depending on the composition of the growth medium and cellular growth stage. N. europaea also depends heavily on iron for metabolism of ammonia, is particularly interesting since it lacks genes for siderophore production, and has genes with only low similarity to known iron reductases, yet grows relatively well in medium containing low Fe. By comparing the transcriptomes of cells grown in iron-replete medium versus iron-limited medium, 247 genes were identified as differentially expressed. Mutant strains deficient in genes for sucrose, glycogen and iron metabolism were created and are being used to further our understanding of ammonia oxidizing bacteria.

  15. Recovery of a soybean urease genomic clone by sequential library screening with two synthetic oligodeoxynucleotides.

    Science.gov (United States)

    Krueger, R W; Holland, M A; Chisholm, D; Polacco, J C

    1987-01-01

    We report the first isolation of a low-copy-number gene from a complex higher plant (soybean) genome by direct screening with synthetic oligodeoxynucleotide (oligo) probes. A synthetic, mixed, 21-nucleotide (nt) oligo (21-1) based on a seven amino acid (aa) sequence from soybean seed urease, was used to screen genomic libraries of soybean (Glycine max [L.] Merr.) in the lambda Charon 4 vector. Twenty homologous clones were recovered from a screen of 500,000 plaques. These were counterscreened with embryo-specific cDNA (15-2 cDNA) made by priming with a second, mixed 15-nt oligo (15-2), based on a Jack bean (Canavalia ensiformis) urease peptide [Takishima et al., J. Natl. Def. Med. Coll. 5 (1980) 19-23]. Five out of 20 clones were homologous to 15-2 cDNA and proved to be identical. Nucleotide sequence analysis of representative clone E15 confirmed that it contained urease sequences. Subclones of E15 homologous to the oligo probes contain a deduced amino acid sequence which matches 108 of 130 aa residues of an amino acid run in a recently published [Mamiya et al., Proc. Jap. Acad. 61B (1985) 359-398] complete protein sequence for Jack-bean seed urease. Using clone E15 as a probe of soybean embryonic mRNA revealed a homologous 3.8-kb species that is the size of the urease messenger. This species is absent from mRNA of embryos of a soybean seed urease-null mutant. However, both urease-positive and urease-null genomes contain the 11-kb DNA fragment bearing urease sequences.

  16. Ouachita Parish Public Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program, 1992-1993.

    Science.gov (United States)

    Camp, Gloria S.

    The Ouachita Parish Public Library (Louisiana) conducted a project that involved recruitment, coalition building, public awareness, training, basic literacy, collection development, tutoring, technology, and English as a Second Language (ESL) programs. The project served a community of over 200,000 people, and targeted the learning disabled,…

  17. Large-insert BAC/YAC libraries for selective re-isolation of genomic regions by homologous recombination in yeast.

    Science.gov (United States)

    Zeng, C; Kouprina, N; Zhu, B; Cairo, A; Hoek, M; Cross, G; Osoegawa, K; Larionov, V; de Jong, P

    2001-09-01

    We constructed representative large-insert bacterial artificial chromosome (BAC) libraries of two human pathogens (Trypanosoma brucei and Giardia lamblia) using a new hybrid vector, pTARBAC1, containing a yeast artificial chromosome (YAC) cassette (a yeast selectable marker and a centromere). The cassette allows transferring of BACs into yeast for their further modification. Furthermore, the new hybrid vector provides the opportunity to re-isolate each DNA insert without construction of a new library of random clones. Digestion of a BAC DNA by an endonuclease that has no recognition site in the vector, but which deletes most of the internal insert sequence and leaves the unique flanking sequences, converts a BAC into a TAR vector, thus allowing direct gene isolation. Cotransformation of a TAR vector and genomic DNA into yeast spheroplasts, and subsequent recombination between the TAR vector's flanking ends and a specific genomic fragment, allows rescue of the fragment as a circular YAC/BAC molecule. Here we prove a new cloning strategy by re-isolation of randomly chosen genomic fragments of different size from T. brucei cloned in BACs. We conclude that genomic regions of unicellular eukaryotes can be easily re-isolated using this technique, which provides an opportunity to study evolution of these genomes and the role of genome instability in pathogenicity.

  18. A Library and Information Science Research Agenda for the 1980s: Final Report.

    Science.gov (United States)

    Cuadra, Carlos A.; And Others

    This report presents the results of a project designed to assist the Department of Education, Office of Libraries and Learning Technologies (OLLT), and the wider community serves to identify research priorities for the 1980s in the field of library and information science. The rationale for establishing a national research agenda for the 1980s is…

  19. Public Library Internet Services: Impacts on the Digital Divide. Stage I Final Report.

    Science.gov (United States)

    McClure, Charles R.; Bertot, John Carlo

    This report provides preliminary findings and a summary of study activities for Stage I of a project that examined public library Internet services that could impact the Digital Divide. The first section discusses the E-rate program and the Digital Divide, including closing the gap in the Digital Divide and public library Internet connectivity and…

  20. Image and Status of the Library and Information Services Field. Final Report.

    Science.gov (United States)

    Walters, J. Hart, Jr.

    The objective of this study on the image and status of the library and information services field was to learn something about the attractiveness of an occupation and to determine, for example, how prestigious the library and information services profession is in comparison with other occupations. The status of different types of job within the…

  1. Identification of transcribed sequences in the human genome. Final report, September 15, 1991--September 14, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Gardiner, K.

    1992-12-01

    The workshop was held at the National Institutes of Mental Health, Bethesda, Maryland, on October 4 and 5, 1991. Twenty-four investigators attended from England, Germany and the United States. The topics discussed included: Genome sequence analysis using computer assisted detection of open reading frames, splice sites and hexamer patterns, direct exon identification using trapping of internal and 3` exons, and a recombination based system, cDNA library construction and screening, including the use of normalization and subtraction procedures, Alu and splice donor site PCR from hybrid cell lines, and microdissection clones as probes, use of labeled CDNAS as probes to screen lambda and cosmid libraries, and sequencing of random cDNAs.

  2. Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

    Science.gov (United States)

    Tozaki, T; Inoue, S; Mashima, S; Ohta, M; Miura, N; Tomita, M

    2000-04-01

    Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

  3. The identification of seven metalloproteinase-disintegrin (ADAM) genes from genomic libraries.

    Science.gov (United States)

    Poindexter, K; Nelson, N; DuBose, R F; Black, R A; Cerretti, D P

    1999-09-03

    Metalloproteinase-disintegrins (ADAMs) are membrane-spanning multi-domain proteins containing a zinc metalloproteinase domain and a disintegrin domain which may serve as an integrin ligand. Based on a conserved sequence within the disintegrin domain, GE(E/Q)CDCG, seven genes were isolated from a human genomic library. Two of these genes lack introns and show testis-specific expression (ADAM20 and ADAM21), while the other two genes contain introns (ADAM22 and ADAM23) and are expressed predominantly in the brain. In addition, three pseudogenes were isolated; one of which evolved from ADAM21. Human chromosomal mapping indicated that ADAM22 and ADAM23 mapped to chromosome 7q21 and 2q33, respectively, while the three pseudogenes 1-2, 3-3, and 1-32 mapped to chromosome 14q24.1, 8p23, and 14q24.1, respectively. An ancestral analysis of all known ADAMs indicates that the zinc-binding motif in the catalytic domain arose once in a common ancestor and was lost by those members lacking this motif.

  4. Genomic expression libraries for the identification of cross-reactive orthopoxvirus antigens.

    Directory of Open Access Journals (Sweden)

    Lilija Miller

    Full Text Available Increasing numbers of human cowpox virus infections that are being observed and that particularly affect young non-vaccinated persons have renewed interest in this zoonotic disease. Usually causing a self-limiting local infection, human cowpox can in fact be fatal for immunocompromised individuals. Conventional smallpox vaccination presumably protects an individual from infections with other Orthopoxviruses, including cowpox virus. However, available live vaccines are causing severe adverse reactions especially in individuals with impaired immunity. Because of a decrease in protective immunity against Orthopoxviruses and a coincident increase in the proportion of immunodeficient individuals in today's population, safer vaccines need to be developed. Recombinant subunit vaccines containing cross-reactive antigens are promising candidates, which avoid the application of infectious virus. However, subunit vaccines should contain carefully selected antigens to confer a solid cross-protection against different Orthopoxvirus species. Little is known about the cross-reactivity of antibodies elicited to cowpox virus proteins. Here, we first identified 21 immunogenic proteins of cowpox and vaccinia virus by serological screenings of genomic Orthopoxvirus expression libraries. Screenings were performed using sera from vaccinated humans and animals as well as clinical sera from patients and animals with a naturally acquired cowpox virus infection. We further analyzed the cross-reactivity of the identified immunogenic proteins. Out of 21 identified proteins 16 were found to be cross-reactive between cowpox and vaccinia virus. The presented findings provide important indications for the design of new-generation recombinant subunit vaccines.

  5. A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

    DEFF Research Database (Denmark)

    She, Qunxin; Confalonieri, F.; Zivanovic, Y.;

    2000-01-01

    -productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...... screening. The PCR approaches included a novel chromosome walking method termed “paired-PCR”. 21 gaps were filled by BAC end sequence analyses and 6 gaps were filled by PCR including three large ones by paired-PCR. The complete map revealed that 0.9 Mb remained to be sequenced and 34 BAC clones were...... selected for walking over small gaps and preparing template libraries for larger ones. It is concluded that an optimal strategy for sequencing microorganism genomes involves construction of a high-resolution physical map by BAC end analyses, PCR screening and paired-PCR chromosome walking after about half...

  6. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  7. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  8. 乌金猪基因组文库的构建%Construction of Genomic Library of Wujin Pig

    Institute of Scientific and Technical Information of China (English)

    张永云; 李卫真; 赵素梅; 黄英; 高士争

    2011-01-01

    为探究与我国优良地方猪种乌金猪特性相关的基因机制,拟构建其基因组文库.取乌金猪肝脏组织,提取大小50 kb以上的基因组DNA,利用限制性内切酶Bcl I对基因组DNA进行随机酶切和低熔点琼脂糖电泳方法回收10~23 kb的DNA片段.以EMBL3作为载体,经BamH I酶切和去磷酸化处理后,与上述纯化的目的DNA片段连接,在体外包装成重组噬菌体,重组噬菌体转染宿主菌KW251,构建成乌金猪基因组文库.文库的效价为2.4 x 109 pfu/mL.乌金猪基因组文库的成功构建,为进行其相关功能基因和基因组区域的识别,基因组DNA和调控元件的克隆与功能分析等后续研究奠定了良好的基础.%To identify the genomic mechanisms for specific traits of Wujin pig, a domestic Chinese swine breed, we constructed its genomic library. The genomic DNA larger than 50 kb was extracted from Wujin pig liver tissue and was digested randomly by restriction enzyme Bel I. DNA fragments ranging from 10 to 23 kb were recovered by agarose gel electrophoresis. EMBL3 vector was digested by BamH I, treated with calf intestine alkaline phosphatase, and then liga-ted with purified DNA fragments forementioned. The genomic library of Wujin pig was constructed by packing recombinant DNA in vitro with phage package protein and transecting KW251 host cells. The result showed that the titer of the library was 2. 4 × 109 pfu/mL. The genomic library of Wujin pig could be used for identification of genes and genomic regions of interest, and provide valuable data for further study such as cloning of genomic DNA and functional analysis of regulatory element.

  9. Rapid Genome-wide Single Nucleotide Polymorphism Discovery in Soybean and Rice via Deep Resequencing of Reduced Representation Libraries with the Illumina Genome Analyzer

    Directory of Open Access Journals (Sweden)

    Stéphane Deschamps

    2010-07-01

    Full Text Available Massively parallel sequencing platforms have allowed for the rapid discovery of single nucleotide polymorphisms (SNPs among related genotypes within a species. We describe the creation of reduced representation libraries (RRLs using an initial digestion of nuclear genomic DNA with a methylation-sensitive restriction endonuclease followed by a secondary digestion with the 4bp-restriction endonuclease This strategy allows for the enrichment of hypomethylated genomic DNA, which has been shown to be rich in genic sequences, and the digestion with serves to increase the number of common loci resequenced between individuals. Deep resequencing of these RRLs performed with the Illumina Genome Analyzer led to the identification of 2618 SNPs in rice and 1682 SNPs in soybean for two representative genotypes in each of the species. A subset of these SNPs was validated via Sanger sequencing, exhibiting validation rates of 96.4 and 97.0%, in rice ( and soybean (, respectively. Comparative analysis of the read distribution relative to annotated genes in the reference genome assemblies indicated that the RRL strategy was primarily sampling within genic regions for both species. The massively parallel sequencing of methylation-sensitive RRLs for genome-wide SNP discovery can be applied across a wide range of plant species having sufficient reference genomic sequence.

  10. Physical Analysis of the Complex Rye (Secale cereale L.) Alt4 Aluminium (Aluminum) Tolerance Locus Using a Whole-Genome BAC Library of Rye cv. Blanco

    Science.gov (United States)

    Rye is a diploid crop species with many outstanding qualities, and is also important as a source of new traits for wheat and triticale improvement. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies. The library provides a 6 × genome ...

  11. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    Science.gov (United States)

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries.

  12. A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles.

    Science.gov (United States)

    Angelov, Angel; Mientus, Markus; Liebl, Susanne; Liebl, Wolfgang

    2009-05-01

    A new cloning system is described, which allows the construction of large-insert fosmid libraries in Escherichia coli and the transfer of the recombinant libraries to the extreme thermophile Thermus thermophilus via natural transformation. Libraries are established in the thermophilic host by site-specific chromosomal insertion of the recombinant fosmids via single crossover or double crossover recombination at the T. thermophilus pyr locus. Comparative screening of a fosmid library constructed from genomic DNA from the thermophilic spirochaete, Spirochaeta thermophila, for clones expressing thermoactive xylanase activity revealed that 50% of the fosmids that conferred xylanase activity upon the corresponding T. thermophilus transformants did not give rise to xylanase-positive E. coli clones, indicating that significantly more S. thermophila genes are functionally expressed in T. thermophilus than in E. coli. The novel T. thermophilus host/vector system may be of value for the construction and functional screening of recombinant DNA libraries from individual thermophilic or extremely thermophilic organisms as well as from complex metagenomes isolated from thermophilic microbial communities.

  13. A versatile shuttle cosmid vector for the efficient construction of genomic libraries and for the cloning of fungal genes.

    Science.gov (United States)

    Osiewacz, H D

    1994-07-01

    A shuttle cosmid vector, pANsCos1, has been constructed for Escherichia coli and filamentous fungi. This vector contains two cos sequences separated by a single XbaI restriction site. pANsCos1 allows the efficient construction of representative genomic libraries from as little as 15-20 micrograms of genomic DNA. Due to the presence of a functional hygromycin B phosphotransferase gene (hph) transformation of fungal protoplasts with pAN-sCos1, or derivatives of it, results in the formation of hygromycin B-resistant transformants. The T7 and T3 RNA polymerase promoter sequences flanking the cloning site, in combination with two adjacent NotI sites facilitate genomic walking and the rapid construction of restriction maps of cloned inserts.

  14. PCR-based ordered genomic libraries: a new approach to drug target identification for Streptococcus pneumoniae.

    Science.gov (United States)

    Belanger, Aimee E; Lai, Angel; Brackman, Marcia A; LeBlanc, Donald J

    2002-08-01

    Described here are the development and validation of a novel approach to identify genes encoding drug targets in Streptococcus pneumoniae. The method relies on the use of an ordered genomic library composed of PCR amplicons that were generated under error-prone conditions so as to introduce random mutations into the DNA. Since some of the mutations occur in drug target-encoding genes and subsequently affect the binding of the drug to its respective cellular target, amplicons containing drug targets can be identified as those producing drug-resistant colonies when transformed into S. pneumoniae. Examination of the genetic content of the amplicon giving resistance coupled with bioinformatics and additional genetic approaches could be used to rapidly identify candidate drug target genes. The utility of this approach was verified by using a number of known antibiotics. For drugs with single protein targets, amplicons were identified that rendered S. pneumoniae drug resistant. Assessment of amplicon composition revealed that each of the relevant amplicons contained the gene encoding the known target for the particular drug tested. Fusidic acid-resistant mutants that resulted from the transformation of S. pneumoniae with amplicons containing fusA were further characterized by sequence analysis. A single mutation was found to occur in a region of the S. pneumoniae elongation factor G protein that is analogous to that already implicated in other bacteria as being associated with fusidic acid resistance. Thus, in addition to facilitating the identification of genes encoding drug targets, this method could provide strains that aid future mechanistic studies.

  15. Chimera-free, high copy number YAC libraries and efficient methods of analysis. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.

  16. Chimera-free, high copy number YAC libraries and efficient methods of analysis. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.

  17. Pima Community College Facilities Specification for a Library/Student Center Prototype. Final [Report].

    Science.gov (United States)

    Paulien, Daniel K.; Thibodeau, Yvonne

    This document is a description of a prototype Library/Student Center designed to serve approximately 10,000 students at a comprehensive campus. Prepared by the firm Paulien & Associates, Inc., of Denver, Colorado, this prototype will serve a design basis for facilities at all Pima Community College (PCC) campuses. The prototype will not be…

  18. Recombinant expression library of Pyrococcus furiosus constructed by high-throughput cloning: a useful tool for functional and structural genomics

    Directory of Open Access Journals (Sweden)

    Hui eYuan

    2015-09-01

    Full Text Available Hyperthermophile Pyrococcus furiosus grows optimally near 100°C and is an important resource of many industrial and molecular biological enzymes. To study the structure and function of Pyrococcus furiosus proteins at whole genome level, we constructed expression plasmids of each Pyrococcus furiosus gene using a ligase-independent cloning method, which was based on amplifying target gene and vector by PCR using phosphorothioate-modified primers and digesting PCR products by λ exonuclease. Our cloning method had a positive clone percentage of ≥ 80% in 96-well plate cloning format. Small-scale expression experiment showed that 55 out of 80 genes were efficiently expressed in Escherichia coli Strain Rosetta 2(DE3pLysS. In summary, this recombinant expression library of Pyrococcus furiosus provides a platform for functional and structural studies, as well as developing novel industrial enzymes. Our cloning scheme is adaptable to constructing recombinant expression library of other sequenced organisms.

  19. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    Science.gov (United States)

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-05-18

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy.

  20. Development of genomic resources for the prairie vole (Microtus ochrogaster: construction of a BAC library and vole-mouse comparative cytogenetic map

    Directory of Open Access Journals (Sweden)

    Young Larry J

    2010-01-01

    Full Text Available Abstract Background The prairie vole (Microtus ochrogaster is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC library from a single male prairie vole and a prairie vole-mouse (Mus musculus comparative cytogenetic map. Results We constructed a prairie vole BAC library (CHORI-232 consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements. Conclusions The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this

  1. Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe.

    Science.gov (United States)

    Mott, R; Grigoriev, A; Maier, E; Hoheisel, J; Lehrach, H

    1993-04-25

    A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.

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

    Science.gov (United States)

    de Tomaso, Anthony W; Weissman, Irving L

    2003-01-01

    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.

  3. SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.

    Science.gov (United States)

    de Andrade, Roberto R S; Vaslin, Maite F S

    2014-03-07

    Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.

  4. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

    Directory of Open Access Journals (Sweden)

    Bharti Arvind K

    2008-12-01

    Full Text Available Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR and methylation spanning linker libraries (MSLL. These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends. Results A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig, while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%. These two techniques were compared with other gene-enrichment methods, and shown to be complementary. Conclusion MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of

  5. Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

    Science.gov (United States)

    2011-01-01

    Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species. PMID:22014081

  6. Towards the Physical Map of the Trypanosoma cruzi Nuclear Genome: Construction of YAC and BAC Libraries of the Reference Clone T. cruzi CL-Brener

    Directory of Open Access Journals (Sweden)

    I Ferrari

    1997-11-01

    Full Text Available Strategies to construct the physical map of the Trypanosoma cruzi nuclear genome have to capitalize on three main advantages of the parasite genome, namely (a its small size, (b the fact that all chromosomes can be defined, and many of them can be isolated by pulse field gel electrophoresis, and (c the fact that simple Southern blots of electrophoretic karyotypes can be used to map sequence tagged sites and expressed sequence tags to chromosomal bands. A major drawback to cope with is the complexity of T. cruzi genetics, that hinders the construction of a comprehensive genetic map. As a first step towards physical mapping, we report the construction and partial characterization of a T. cruzi CL-Brener genomic library in yeast artificial chromosomes (YACs that consists of 2,770 individual YACs with a mean insert size of 365 kb encompassing around 10 genomic equivalents. Two libraries in bacterial artificial chromosomes (BACs have been constructed, BACI and BACII. Both libraries represent about three genome equivalents. A third BAC library (BAC III is being constructed. YACs and BACs are invaluable tools for physical mapping. More generally, they have to be considered as a common resource for research in Chagas disease

  7. Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors

    NARCIS (Netherlands)

    Gray, Nathanael S.; Wodicka, Lisa; Thunnissen, Andy-Mark W.H.; Norman, Thea C.; Kwon, Soojin; Espinoza, F. Hernan; Morgan, David O.; Barnes, Georjana; LeClerc, Sophie; Meijer, Laurent; Kim, Sung-Hou; Lockhart, David J.; Schultz, Peter G.

    1998-01-01

    Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors

  8. Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6.

    Science.gov (United States)

    Kielak, Anna M; van Veen, Johannes A; Kowalchuk, George A

    2010-10-01

    The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.

  9. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea

    DEFF Research Database (Denmark)

    Treusch, Alexander H; Kletzin, Arnulf; Raddatz, Guenter

    2004-01-01

    covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments......, are presented and discussed. We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group....

  10. Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML.

    Science.gov (United States)

    Kurata, Morito; Rathe, Susan K; Bailey, Natashay J; Aumann, Natalie K; Jones, Justine M; Veldhuijzen, G Willemijn; Moriarity, Branden S; Largaespada, David A

    2016-11-03

    Acute myeloid leukemia (AML) can display de novo or acquired resistance to cytosine arabinoside (Ara-C), a primary component of induction chemotherapy. To identify genes capable of independently imposing Ara-C resistance, we applied a genome-wide CRISPR library to human U937 cells and exposed to them to Ara-C. Interestingly, all drug resistant clones contained guide RNAs for DCK. To avoid DCK gene modification, gRNA resistant DCK cDNA was created by the introduction of silent mutations. The CRISPR screening was repeated using the gRNA resistant DCK, and loss of SLC29A was identified as also being capable of conveying Ara-C drug resistance. To determine if loss of Dck results in increased sensitivity to other drugs, we conducted a screen of 446 FDA approved drugs using two Dck-defective BXH-2 derived murine AML cell lines and their Ara-C sensitive parental lines. Both cell lines showed an increase in sensitivity to prednisolone. Guide RNA resistant cDNA rescue was a legitimate strategy and multiple DCK or SLC29A deficient human cell clones were established with one clone becoming prednisolone sensitive. Dck-defective leukemic cells may become prednisolone sensitive indicating prednisolone may be an effective adjuvant therapy in some cases of DCK-negative AML.

  11. Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML

    Science.gov (United States)

    Kurata, Morito; Rathe, Susan K.; Bailey, Natashay J.; Aumann, Natalie K.; Jones, Justine M.; Veldhuijzen, G. Willemijn; Moriarity, Branden S.; Largaespada, David A.

    2016-01-01

    Acute myeloid leukemia (AML) can display de novo or acquired resistance to cytosine arabinoside (Ara-C), a primary component of induction chemotherapy. To identify genes capable of independently imposing Ara-C resistance, we applied a genome-wide CRISPR library to human U937 cells and exposed to them to Ara-C. Interestingly, all drug resistant clones contained guide RNAs for DCK. To avoid DCK gene modification, gRNA resistant DCK cDNA was created by the introduction of silent mutations. The CRISPR screening was repeated using the gRNA resistant DCK, and loss of SLC29A was identified as also being capable of conveying Ara-C drug resistance. To determine if loss of Dck results in increased sensitivity to other drugs, we conducted a screen of 446 FDA approved drugs using two Dck-defective BXH-2 derived murine AML cell lines and their Ara-C sensitive parental lines. Both cell lines showed an increase in sensitivity to prednisolone. Guide RNA resistant cDNA rescue was a legitimate strategy and multiple DCK or SLC29A deficient human cell clones were established with one clone becoming prednisolone sensitive. Dck-defective leukemic cells may become prednisolone sensitive indicating prednisolone may be an effective adjuvant therapy in some cases of DCK-negative AML. PMID:27808171

  12. Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome.

    Science.gov (United States)

    Laurent, V; Devaux, P; Thiel, T; Viard, F; Mielordt, S; Touzet, P; Quillet, M C

    2007-10-01

    Sugar beet (Beta vulgaris) is an important root crop for sucrose production. A study was conducted to find a new abundant source of microsatellite (SSR) markers in order to develop marker assistance for breeding. Different sources of existing microsatellites were used and new ones were developed to compare their efficiency to reveal diversity in mapping population and mapping coverage. Forty-one microsatellite markers were isolated from a B. vulgaris ssp maritima genomic library and 201 SSRs were extracted from a B. vulgaris ssp vulgaris library. Data mining was applied on GenBank B. vulgaris expressed sequence tags (ESTs), 803 EST-SSRs were identified over 19,709 ESTs. Characteristics, polymorphism and cross-species transferability of these microsatellites were compared. Based on these markers, a high density genetic map was constructed using 92 F(2) individuals from a cross between a sugar and a table beet. The map contains 284 markers, spans over 555 cM and covers the nine chromosomes of the species with an average markers density of one marker every 2.2 cM. A set of markers for assignation to the nine chromosomes of sugar beet is provided.

  13. Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs.

    Science.gov (United States)

    Machado, D J; Lyra, M L; Grant, T

    2016-05-01

    Next-generation sequencing continues to revolutionize biodiversity studies by generating unprecedented amounts of DNA sequence data for comparative genomic analysis. However, these data are produced as millions or billions of short reads of variable quality that cannot be directly applied in comparative analyses, creating a demand for methods to facilitate assembly. We optimized an in silico strategy to efficiently reconstruct high-quality mitochondrial genomes directly from genomic reads. We tested this strategy using sequences from five species of frogs: Hylodes meridionalis (Hylodidae), Hyloxalus yasuni (Dendrobatidae), Pristimantis fenestratus (Craugastoridae), and Melanophryniscus simplex and Rhinella sp. (Bufonidae). These are the first mitogenomes published for these species, the genera Hylodes, Hyloxalus, Pristimantis, Melanophryniscus and Rhinella, and the families Craugastoridae and Hylodidae. Sequences were generated using only half of one lane of a standard Illumina HiqSeq 2000 flow cell, resulting in fewer than eight million reads. We analysed the reads of Hylodes meridionalis using three different assembly strategies: (1) reference-based (using bowtie2); (2) de novo (using abyss, soapdenovo2 and velvet); and (3) baiting and iterative mapping (using mira and mitobim). Mitogenomes were assembled exclusively with strategy 3, which we employed to assemble the remaining mitogenomes. Annotations were performed with mitos and confirmed by comparison with published amphibian mitochondria. In most cases, we recovered all 13 coding genes, 22 tRNAs, and two ribosomal subunit genes, with minor gene rearrangements. Our results show that few raw reads can be sufficient to generate high-quality scaffolds, making any Illumina machine run using genomic multiplex libraries a potential source of data for organelle assemblies as by-catch. © 2015 John Wiley & Sons Ltd.

  14. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus.

    Science.gov (United States)

    Rondon, M R; Raffel, S J; Goodman, R M; Handelsman, J

    1999-05-25

    As the study of microbes moves into the era of functional genomics, there is an increasing need for molecular tools for analysis of a wide diversity of microorganisms. Currently, biological study of many prokaryotes of agricultural, medical, and fundamental scientific interest is limited by the lack of adequate genetic tools. We report the application of the bacterial artificial chromosome (BAC) vector to prokaryotic biology as a powerful approach to address this need. We constructed a BAC library in Escherichia coli from genomic DNA of the Gram-positive bacterium Bacillus cereus. This library provides 5.75-fold coverage of the B. cereus genome, with an average insert size of 98 kb. To determine the extent of heterologous expression of B. cereus genes in the library, we screened it for expression of several B. cereus activities in the E. coli host. Clones expressing 6 of 10 activities tested were identified in the library, namely, ampicillin resistance, zwittermicin A resistance, esculin hydrolysis, hemolysis, orange pigment production, and lecithinase activity. We analyzed selected BAC clones genetically to identify rapidly specific B. cereus loci. These results suggest that BAC libraries will provide a powerful approach for studying gene expression from diverse prokaryotes.

  15. Generation of chicken Z-chromosome painting probes by microdissection for screening large-insert genomic libraries.

    Science.gov (United States)

    Zimmer, R; King, W A; Verrinder Gibbins, A M

    1997-01-01

    A strategy for rapid generation of chicken sex chromosome-Z painting probes has been developed using microdissection. Whole chromosome painting probes (WCPs) were prepared from 10-15 copies of mitotic metaphase chicken Z chromosomes. The microisolated chromosomes were subjected to PEG/proteinase K treatment in a collection drop to release DNA, which was then amplified using a degenerate oligonucleotide-primed shuttle PCR (DOP-Shuttle-PCR) strategy. Size distributions of the PCR products were analyzed by agarose gel electrophoresis and smears of DNA were revealed that ranged in size from 200-800 bp, without any evidence of preferential amplification. Both specificity and complexity of the probes have been analyzed by Southern blot and fluorescence in situ hybridization (FISH). Non-specific hybridization was efficiently blocked by using chicken competitor DNA. Analysis of the WCPs produced shows that collectively they provide uniform hybridization signals along the entire length of the chicken Z chromosome. To demonstrate one possible application of these complex probes, we screened a large-insert bacterial artificial chromosome (BAC) chicken genomic library to select Z chromosome-specific clones. To address specificity of the selected clones and to physically map them to the Z chromosome, FISH analysis was used. Of the 3 clones initially tested, one clone (C3) carrying a 250-kb insert mapped to the distal portion of the short arm of the chicken Z chromosome. Therefore, this technique has provided appropriate probes for screening large-insert genomic libraries. Further application of these probes includes the analysis of chromosome rearrangements, studies of cases of heteroploidy involving the Z chromosome, positional cloning of Z-linked genes and studies on mechanisms of sex-chromosome evolution in birds.

  16. Genetic screening of new genes responsible for cellular adaptation to hypoxia using a genome-wide shRNA library.

    Science.gov (United States)

    Yoshino, Seiko; Hara, Toshiro; Weng, Jane S; Takahashi, Yuka; Seiki, Motoharu; Sakamoto, Takeharu

    2012-01-01

    Oxygen is a vital requirement for multi-cellular organisms to generate energy and cells have developed multiple compensatory mechanisms to adapt to stressful hypoxic conditions. Such adaptive mechanisms are intricately interconnected with other signaling pathways that regulate cellular functions such as cell growth. However, our understanding of the overall system governing the cellular response to the availability of oxygen remains limited. To identify new genes involved in the response to hypoxic stress, we have performed a genome-wide gene knockdown analysis in human lung carcinoma PC8 cells using an shRNA library carried by a lentiviral vector. The knockdown analysis was performed under both normoxic and hypoxic conditions to identify shRNA sequences enriched or lost in the resulting selected cell populations. Consequently, we identified 56 candidate genes that might contribute to the cellular response to hypoxia. Subsequent individual knockdown of each gene demonstrated that 13 of these have a significant effect upon oxygen-sensitive cell growth. The identification of BCL2L1, which encodes a Bcl-2 family protein that plays a role in cell survival by preventing apoptosis, validates the successful design of our screen. The other selected genes have not previously been directly implicated in the cellular response to hypoxia. Interestingly, hypoxia did not directly enhance the expression of any of the identified genes, suggesting that we have identified a new class of genes that have been missed by conventional gene expression analyses to identify hypoxia response genes. Thus, our genetic screening method using a genome-wide shRNA library and the newly-identified genes represent useful tools to analyze the cellular systems that respond to hypoxic stress.

  17. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  18. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  19. Expression cloning of different bacterial phosphatase-encoding genes by histochemical screening of genomic libraries onto an indicator medium containing phenolphthalein diphosphate and methyl green.

    Science.gov (United States)

    Riccio, M L; Rossolini, G M; Lombardi, G; Chiesurin, A; Satta, G

    1997-02-01

    A system for expression cloning of bacterial phosphatase-encoding genes has been developed, and its potential has been investigated. The system is based on histochemical screening of bacterial genomic libraries, constructed in an Escherichia coli multicopy plasmid vector, for phosphatase-producing clones using an indicator medium (named TPMG) made of Tryptose-Phosphate agar supplemented with the phosphatase substrate phenolphthalein diphosphate and the stain methyl green. To test the performance of this system, three genomic libraries were constructed from bacterial strains of different species which showed different patterns of phosphatase activity, and were screened using the TPMG medium. Following a partial screening, three different phosphatase-encoding genes (respectively encoding a class A non-specific acid phosphatase, an acid-hexose phosphatase and a non-specific alkaline phosphatase) were shotgun-cloned from the above libraries, indicating that the TPMG-based expression cloning system can be useful for rapid isolation of different bacterial phosphatase-encoding genes.

  20. An Evaluation of the El Centro de la Causa Library and Information Center: August 1973 through July 1974. Final Report.

    Science.gov (United States)

    Michael, Mary Ellen; Encarnacion, Leticia

    An evaluation of Chicago's El Centro de la Causa Library and Information Center was undertaken by the University of Illinois Library Research Center in 1974. Evaluation methods included: (1) a survey of user and nonuser characteristics and attitudes concerning library services; (2) a survey of the needs and information-seeking behavior of people…

  1. Construction of genome-wide physical BAC contigs using mapped cDNA as probes: Toward an integrated BAC library resource for genome sequencing and analysis. Annual report, July 1995--January 1997

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, S.C.; Bocskai, D.; Cao, Y. [and others

    1997-12-31

    The goal of human genome project is to characterize and sequence entire genomes of human and several model organisms, thus providing complete sets of information on the entire structure of transcribed, regulatory and other functional regions for these organisms. In the past years, a number of useful genetic and physical markers on human and mouse genomes have been made available along with the advent of BAC library resources for these organisms. The advances in technology and resource development made it feasible to efficiently construct genome-wide physical BAC contigs for human and other genomes. Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes are available for human genome mapping. ESTs and cDNAs are excellent resources for building contig maps for two reasons. Firstly, they exist in two alternative forms--as both sequence information for PCR primer pairs, and cDoreen genomic libraries efficiently for large number of DNA probes by combining over 100 cDNA probes in each hybridization. Second, the linkage and order of genes are rather conserved among human, mouse and other model organisms. Therefore, gene markers have advantages over random anonymous STSs in building maps for comparative genomic studies.

  2. Studies of the hyperthermophile Thermotoga maritima by random sequencing of cDNA and genomic libraries. Identification and sequencing of the trpEG (D) operon.

    Science.gov (United States)

    Kim, C W; Markiewicz, P; Lee, J J; Schierle, C F; Miller, J H

    1993-06-20

    Random sequencing of cDNA and genomic libraries has been used to study the genome of the hyperthermophile Thermotoga maritima. To date, 175 unique clones have been analyzed by comparing short sequence tags with known proteins in the PIR and GenBank databases. We find that a significant proportion of sequences can be matched to previously identified protein from non-Thermotoga sources. A high match rate was obtained from an oligo(dT)-primed cDNA library, where one-third of all unique sequences analyzed (21/65) shared high amino acid sequence similarity with proteins in the PIR and GenBank databases. Also, approximately one-third of the unique sequences from a second cDNA library (28/89), constructed with random oligo primers, could be matched to sequences in PIR and GenBank. Identification of genes from the oligo(dT)-primed cDNA library indicates that some Thermotoga mRNAs are polyadenylated. Genes have also been identified from a 1 to 2 kb genomic DNA library. Here, (3/21) of genomic sequences analyzed could be matched to protein in PIR and GenBank. One of the genomic clones had high sequence similarity to the tryptophan synthesis gene anthranilate synthase component I (trpE). Using this sequence tag, the Thermotoga trp operon was isolated and sequenced. The Thermotoga maritima trp operon is arranged with trpE forming an overlapping transcript with a second protein consisting of a fusion of anthranilate synthase component II (trpG) and anthranilate phosphoribosyltransferse (trpD). With regard to the fusion, the operon organization is similar to Escherichia coli and Salmonella typhimurium, but lacks the classic attenuation system of enteric bacteria. Amino acid sequence comparison with 19 trpE, 18 trpG and 14 trpD genes from other organisms suggest that the Thermotoga trp genes resemble corresponding genes from other thermophiles more closely than expected.

  3. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

    Directory of Open Access Journals (Sweden)

    Talon Manuel

    2008-09-01

    Full Text Available Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina, one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement. Results Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome and estimation of gene content (31,000 genes of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus. Conclusion In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has

  4. Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes.

    Science.gov (United States)

    Nicolaou, Sergios A; Gaida, Stefan M; Papoutsakis, Eleftherios T

    2011-12-01

    In engineering novel microbial strains for biotechnological applications, beyond a priori identifiable pathways to be engineered, it is becoming increasingly important to develop complex, ill-defined cellular phenotypes. One approach is to screen genomic or metagenomic libraries to identify genes imparting desirable phenotypes, such as tolerance to stressors or novel catabolic programs. Such libraries are limited by their inability to identify interactions among distant genetic loci. To solve this problem, we constructed plasmid- and fosmid-based Escherichia coli Coexisting/Coexpressing Genomic Libraries (CoGeLs). As a proof of principle, four sets of two genes of the l-lysine biosynthesis pathway distantly located on the E. coli chromosome were knocked out. Upon transformation of these auxotrophs with CoGeLs, cells growing without supplementation were found to harbor library inserts containing the knocked-out genes demonstrating the interaction between the two libraries. CoGeLs were also screened to identify genetic loci that work synergistically to create the considerably more complex acid-tolerance phenotype. CoGeL screening identified combination of genes known to enhance acid tolerance (gadBC operon and adiC), but also identified the novel combination of arcZ and recA that greatly enhanced acid tolerance by 9000-fold. arcZ is a small RNA that we show increases pH tolerance alone and together with recA.

  5. From human monocytes to genome-wide binding sites--a protocol for small amounts of blood: monocyte isolation/ChIP-protocol/library amplification/genome wide computational data analysis.

    Directory of Open Access Journals (Sweden)

    Sebastian Weiterer

    Full Text Available Chromatin immunoprecipitation in combination with a genome-wide analysis via high-throughput sequencing is the state of the art method to gain genome-wide representation of histone modification or transcription factor binding profiles. However, chromatin immunoprecipitation analysis in the context of human experimental samples is limited, especially in the case of blood cells. The typically extremely low yields of precipitated DNA are usually not compatible with library amplification for next generation sequencing. We developed a highly reproducible protocol to present a guideline from the first step of isolating monocytes from a blood sample to analyse the distribution of histone modifications in a genome-wide manner.The protocol describes the whole work flow from isolating monocytes from human blood samples followed by a high-sensitivity and small-scale chromatin immunoprecipitation assay with guidance for generating libraries compatible with next generation sequencing from small amounts of immunoprecipitated DNA.

  6. A HindIII BAC library construction of Mesobuthus martensii Karsch (Scorpiones:Buthidae): an important genetic resource for comparative genomics and phylogenetic analysis.

    Science.gov (United States)

    Li, Songryong; Ma, Yibao; Jang, Shenghun; Wu, Yingliang; Liu, Hui; Cao, Zhijian; Li, Wenxin

    2009-12-01

    Scorpions are "living but sophisticated fossils" that have changed little in their morphology since their first appearance over the past 450 million years ago. To provide a genetic resource for understanding the evolution of scorpion genome and the relationships between scorpions and other organisms, we first determined the genome size of the scorpion Mesobuthus martensii Karsch (about 600 Mbp) in the order Scorpiones and constructed a HindIII BAC library of the male scorpion M. martensii Karsch from China. The BAC library consists of a total of 46,080 clones with an average insert size of 100 kb, providing a 7.7-fold coverage of the scorpion haploid genome size of 600 Mbp as revealed in this study. High-density colony hybridization-based library screening was performed using 18S-5.8S-28S rRNA gene that is one of the most commonly used phylogenetic markers. Both library screening and PCR identification results revealed six positive BAC clones which were overlapped, and formed a contig of approximately 120 kb covering the rDNA. BAC DNA sequencing analysis determined the complete sequence of M. martensii Karsch rDNA unit that has a total length of 8779 bp, including 1813 bp 18s rDNA, 157 bp 5.8s rDNA, 3823 bp 28s rDNA, 530 bp ETS, 2168 bp ITS1 and 288 bp ITS2. Interestingly, some tandem repeats are present in the rRNA intergenic sequence (IGS) and ITS1/2 regions. These results demonstrated that the BAC library of the scorpion M. martensii Karsch and the complete sequence of rDNA unit will provide important genetic resources and tools for comparative genomics and phylogenetic analysis.

  7. BAC Library Construction for Pumpkin Genome%南瓜基因组DNA的细菌人工染色体(BAC)文库的构建

    Institute of Scientific and Technical Information of China (English)

    赵茜; 张丽艳; 徐丽珍; 吴建忠

    2013-01-01

    [Objective] The paper was to construct the bacterial artificial chromosome (BAC) library for pumpkin genomic DNA.[Method] The BAC library of pumpkin genomic DNA was constructed by using pumpkin buds as materials and HindIII enzyme-cutting system.[Result] The BAC Library of pumpkin genomic DNA was constructed successfully.[Conclusion] The technology laid a foundation for the cloning and functional verification of related genes,physical mapping and genome sequencing of pumpkin.%[目的]构建南瓜基因组DNA的细菌人工染色体(BAC)文库.[方法]以南瓜幼芽为材料,利用HindⅢ酶切体系,初步构建南瓜基因组DNA的BAC文库.[结果]研究成功构建了南瓜基因组DNA的BAC文库.[结论]该技术为南瓜相关基因的克隆、功能验证、物理图谱的构建和基因组测序等研究工作奠定了基础.

  8. Features of protein-protein interactions in two-component signaling deduced from genomic libraries.

    Science.gov (United States)

    White, Robert A; Szurmant, Hendrik; Hoch, James A; Hwa, Terence

    2007-01-01

    As more and more sequence data become available, new approaches for extracting information from these data become feasible. This chapter reports on one such method that has been applied to elucidate protein-protein interactions in bacterial two-component signaling pathways. The method identifies residues involved in the interaction through an analysis of over 2500 functionally coupled proteins and a precise determination of the substitutional constraints placed on one protein by its signaling mate. Once identified, a simple log-likelihood scoring procedure is applied to these residues to build a predictive tool for assigning signaling mates. The ability to apply this method is based on a proliferation of related domains within multiple organisms. Paralogous evolution through gene duplication and divergence of two-component systems has commonly resulted in tens of closely related interacting pairs within one organism with a roughly one-to-one correspondence between signal and response. This provides us with roughly an order of magnitude more protein pairs than there are unique, fully sequenced bacterial species. Consequently, this chapter serves as both a detailed exposition of the method that has provided more depth to our knowledge of bacterial signaling and a look ahead to what would be possible on a more widespread scale, that is, to protein-protein interactions that have only one example per genome, as the number of genomes increases by a factor of 10.

  9. Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996

    Energy Technology Data Exchange (ETDEWEB)

    Lim, C.S.; Xu, R.X.; Wang, M. [and others

    1996-12-31

    Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well as physical map building. They have currently deconvoluted over 10,000 Unigene probes against a 4X coverage human BAC clones from the approved library D by high density colony hybridization method. 10,000 batches of Unigenes are arrayed in an imaginary 100 X 100 matrix from which 100 row pools and 100 column pools are obtained. Library filters are hybridized with pooled probes, thus reducing the number of hybridization required for addressing the positives for each Unigene from 10,000 to 200. Details on the experimental scheme as well as daily progress report is posted on the Web site (http://www.tree.caltech.edu).

  10. Survey of Library and Information Problems in Correctional Institutions. Volume 4: Bibliography. ILR-73-011. Final Report.

    Science.gov (United States)

    LeDonne, Marjorie; And Others

    Compiled as part of a study of correctional library services, this bibliography encompasses library services in all correctional institutions, and covers the fields of criminology, sociology, education, law, and librarianship, with emphasis on the years 1969 to 1973. The work is designed as a research aid for librarians, correctional…

  11. The Research Library's Role in Digital Repository Services: Final Report of the ARL Digital Repository Issues Task Force

    Science.gov (United States)

    Association of Research Libraries, 2009

    2009-01-01

    Libraries are making diverse contributions to the development of many types of digital repositories, particularly those housing locally created digital content, including new digital objects or digitized versions of locally held works. In some instances, libraries are managing a repository and its related services entirely on their own, but often…

  12. Therapy Dogs in Academic Libraries: A Way to Foster Student Engagement and Mitigate Self-Reported Stress during Finals

    Science.gov (United States)

    Jalongo, Mary Renck; McDevitt, Theresa

    2015-01-01

    More and more modern academic libraries are turning to student engagement activities designed to welcome students into Academia, join a community of scholars, and avail themselves of the full range of resources and services that a university library can provide. One unusual, but inexpensive and highly effective method of engaging students is…

  13. Functional genomics, an integrated approach. Final report for the Trieste component

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, Andrew R.M.

    1999-11-01

    Phage display offers the possibility of selecting polypeptides (and the genes which encode them) from libraries of 10 billion or more different polypeptides on the basis of their abilities to bind target proteins and subdomains. The general principle of phage display relies on the coupling of phenotype and genotype in the phage. The specific aims of this project were threefold: (1) to produce a large phagemid antibody library; (2) to develop a general method for deriving antibodies against the protein products of cloned genes; (3) to develop technologies which permit the display of gene fragment libraries on phage. Accomplishments in each of these areas are presented.

  14. Physical analysis of the complex rye (Secale cereale L.) Alt4 aluminium (aluminum) tolerance locus using a whole-genome BAC library of rye cv. Blanco.

    Science.gov (United States)

    Shi, B-J; Gustafson, J P; Button, J; Miyazaki, J; Pallotta, M; Gustafson, N; Zhou, H; Langridge, P; Collins, N C

    2009-08-01

    Rye is a diploid crop species with many outstanding qualities, and is important as a source of new traits for wheat and triticale improvement. Rye is highly tolerant of aluminum (Al) toxicity, and possesses a complex structure at the Alt4 Al tolerance locus not found at the corresponding locus in wheat. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies, and assess the library's suitability for investigating Al tolerance genes. The library provides 6 x genome coverage of the 8.1 Gb rye genome, has an average insert size of 131 kb, and contains only ~2% of empty or organelle-derived clones. Genetic analysis attributed the Al tolerance of Blanco to the Alt4 locus on the short arm of chromosome 7R, and revealed the presence of multiple allelic variants (haplotypes) of the Alt4 locus in the BAC library. BAC clones containing ALMT1 gene clusters from several Alt4 haplotypes were identified, and will provide useful starting points for exploring the basis for the structural variability and functional specialization of ALMT1 genes at this locus.

  15. Construction of male and female PAC genomic libraries suitable for identification of Y-chromosome-specific clones from the liverwort, Marchantia polymorpha.

    Science.gov (United States)

    Okada, S; Fujisawa, M; Sone, T; Nakayama, S; Nishiyama, R; Takenaka, M; Yamaoka, S; Sakaida, M; Kono, K; Takahama, M; Yamato, K T; Fukuzawa, H; Brennicke, A; Ohyama, K

    2000-11-01

    Unlike higher plants, the dioecious liverwort, Marchantia polymorpha, has uniquely small sex chromosomes, with X chromosomes present only in female gametophytes and Y chromosomes only in male gametophytes. We have constructed respective genomic libraries for male and female plantlets using a P1-derived artificial chromosome (pCYPAC2). With an average insert size of approximately 90 kb, each PAC library is estimated to cover the entire genome with a probability of more than 99.9%. Male-specific PAC clones were screened for by differential hybridization using male and female genomic DNAs as separate probes. Seventy male-specific PAC clones were identified. The male specificity of one of the clones, pMM4G7, was verified by Southern hybridization and PCR analysis. This clone was indeed located on the Y chromosome as verified by fluorescence in situ hybridization (FISH). This result shows that the Y chromosome contains unique sequences that are not present either on the X chromosome or any of the autosomes. Thus, the respective male and female libraries for M. polymorpha offer an opportunity to identify key genes involved in the process of sex differentiation and this unique system of sex determination.

  16. Isolation of BAC Clones Containing Conserved Genes from Libraries of Three Distantly Related Moths: A Useful Resource for Comparative Genomics of Lepidoptera

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    2011-01-01

    Full Text Available Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing conserved and putative single-copy genes from libraries of three pests, Heliothis virescens, Ostrinia nubilalis, and Plutella xylostella, harboring the haploid chromosome number, =31, which are not closely related with each other or with the silkworm, Bombyx mori, (=28, the sequenced model lepidopteran. A total of 108–184 clones representing 101–182 conserved genes were isolated for each species. For 79 genes, clones were isolated from more than two species, which will be useful as common markers for analysis using fluorescence in situ hybridization (FISH, as well as for comparison of genome sequence among multiple species. The PCR-based clone isolation method presented here is applicable to species which lack a sequenced genome but have a significant collection of cDNA or EST sequences.

  17. Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches

    Directory of Open Access Journals (Sweden)

    Rodriguez-Zas Sandra L

    2009-05-01

    Full Text Available Abstract Background Neuropeptides are cell to cell signalling molecules that regulate many critical biological processes including development, growth and reproduction. These peptides result from the complex processing of prohormone proteins, making their characterization both challenging and resource demanding. In fact, only 42 neuropeptide genes have been empirically confirmed in cattle. Neuropeptide research using high-throughput technologies such as microarray and mass spectrometry require accurate annotation of prohormone genes and products. However, the annotation and associated prediction efforts, when based solely on sequence homology to species with known neuropeptides, can be problematic. Results Complementary bioinformatic resources were integrated in the first survey of the cattle neuropeptide complement. Functional neuropeptide characterization was based on gene expression profiles from microarray experiments. Once a gene is identified, knowledge of the enzymatic processing allows determination of the final products. Prohormone cleavage sites were predicted using several complementary cleavage prediction models and validated against known cleavage sites in cattle and other species. Our bioinformatics approach identified 92 cattle prohormone genes, with 84 of these supported by expressed sequence tags. Notable findings included an absence of evidence for a cattle relaxin 1 gene and evidence for a cattle galanin-like peptide pseudogene. The prohormone processing predictions are likely accurate as the mammalian proprotein convertase enzymes, except for proprotein convertase subtilisin/kexin type 9, were also identified. Microarray analysis revealed the differential expression of 21 prohormone genes in the liver associated with nutritional status and 8 prohormone genes in the placentome of embryos generated using different reproductive techniques. The neuropeptide cleavage prediction models had an exceptional performance, correctly

  18. Genomic library screening for viruses from the human dental plaque revealed pathogen-specific lytic phage sequences.

    Science.gov (United States)

    Al-Jarbou, Ahmed Nasser

    2012-01-01

    Bacterial pathogenesis presents an astounding arsenal of virulence factors that allow them to conquer many different niches throughout the course of infection. Principally fascinating is the fact that some bacterial species are able to induce different diseases by expression of different combinations of virulence factors. Nevertheless, studies aiming at screening for the presence of bacteriophages in humans have been limited. Such screening procedures would eventually lead to identification of phage-encoded properties that impart increased bacterial fitness and/or virulence in a particular niche, and hence, would potentially be used to reverse the course of bacterial infections. As the human oral cavity represents a rich and dynamic ecosystem for several upper respiratory tract pathogens. However, little is known about virus diversity in human dental plaque which is an important reservoir. We applied the culture-independent approach to characterize virus diversity in human dental plaque making a library from a virus DNA fraction amplified using a multiple displacement method and sequenced 80 clones. The resulting sequence showed 44% significant identities to GenBank databases by TBLASTX analysis. TBLAST homology comparisons showed that 66% was viral; 18% eukarya; 10% bacterial; 6% mobile elements. These sequences were sorted into 6 contigs and 45 single sequences in which 4 contigs and a single sequence showed significant identity to a small region of a putative prophage in the Corynebacterium diphtheria genome. These findings interestingly highlight the uniqueness of over half of the sequences, whilst the dominance of a pathogen-specific prophage sequences imply their role in virulence.

  19. Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.

    Science.gov (United States)

    Rhodes, Johanna; Beale, Mathew A; Fisher, Matthew C

    2014-01-01

    The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use.

  20. Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.

    Directory of Open Access Journals (Sweden)

    Johanna Rhodes

    Full Text Available The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina, along with two new kits: the TruSeq Nano DNA kit (Illumina and the NEBNext Ultra DNA kit (New England Biolabs to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality being considered when ultimately deciding on which library prep method to use.

  1. Human Genome Teacher Networking Project, Final Report, April 1, 1992 - March 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Debra

    1999-10-01

    Project to provide education regarding ethical legal and social implications of Human Genome Project to high school science teachers through two consecutive summer workshops, in class activities, and peer teaching workshops.

  2. 红脐鳞地衣基因组文库的构建%Construction of a Genomic DNA Library of Rhizoplaca chrysoleuca

    Institute of Scientific and Technical Information of China (English)

    周启明; 郭守玉

    2004-01-01

    地衣是真菌和一种或多种光合微生物形成的稳定的共生联合体,既是先锋生物,又是敏感生物.环境的变化及生境的片断化,使得许多地衣种类处于濒危状态.保护珍稀濒危地衣物种的方法包括地衣体的移植,地衣中菌藻的分离培养及基因组文库的构建等.本研究用改进的CTAB方法提取基因组总DNA,以Lamb-da GEM-11为载体,构建了红脐鳞(Rhizoplaca chrysoleuca)的基因组文库,文库中同时含有该地衣共生菌与共生藻的DNA.该文库包含8.5×105个重组子,插入片段的平均大小为19kb.文库的容量约为红脐鳞单倍体基因组的100倍.该基因组文库的构建为保护稀有与濒危地衣物种提供了一个新的途径,并可进一步开展有关地衣的分子操作研究,如地衣冰核蛋白的异源表达等.%Lichens are stable symbiotic association comprised of a fungus and one or more photosynthetic microorganisms.Some methods were used to protect the rare and endangered lichens, which included transplanting thalli, separating and culturing fungi, algae and/or cyanobacteria, and constructing the genomic DNA library. As a main means of conservation of rare and endangered lichens, the feasible procedures of constructing the genomic DNA library of lichens were developed. A genomic DNA library of Rhizoplaca chrysoleuca (including both mycobiont and phycobiont) was constructed using the phage Lambda GEM-11 as a vector. The library consisted of 8.5 × 105 clones with an average insert size of about 19 kb. The capacity of this library was about 100 times the equivalent of the sum of haploid genomes of alga and lichen-forming fungus in R. chrysoleuca. Lichens generally grow too slowly for many kinds of laboratory manipulations and for effective conservation of rare and endangered species. Our studies make it possible to do some of those important experimental researches.

  3. Genomic SELEX: a discovery tool for genomic aptamers.

    Science.gov (United States)

    Zimmermann, Bob; Bilusic, Ivana; Lorenz, Christina; Schroeder, Renée

    2010-10-01

    Genomic SELEX is a discovery tool for genomic aptamers, which are genomically encoded functional domains in nucleic acid molecules that recognize and bind specific ligands. When combined with genomic libraries and using RNA-binding proteins as baits, Genomic SELEX used with high-throughput sequencing enables the discovery of genomic RNA aptamers and the identification of RNA-protein interaction networks. Here we describe how to construct and analyze genomic libraries, how to choose baits for selections, how to perform the selection procedure and finally how to analyze the enriched sequences derived from deep sequencing. As a control procedure, we recommend performing a "Neutral" SELEX experiment in parallel to the selection, omitting the selection step. This control experiment provides a background signal for comparison with the positively selected pool. We also recommend deep sequencing the initial library in order to facilitate the final in silico analysis of enrichment with respect to the initial levels. Counter selection procedures, using modified or inactive baits, allow strengthening the binding specificity of the winning selected sequences.

  4. Whitefly (Bemisia tabaci genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous cDNA libraries

    Directory of Open Access Journals (Sweden)

    Czosnek Henryk

    2006-04-01

    Full Text Available Abstract Background The past three decades have witnessed a dramatic increase in interest in the whitefly Bemisia tabaci, owing to its nature as a taxonomically cryptic species, the damage it causes to a large number of herbaceous plants because of its specialized feeding in the phloem, and to its ability to serve as a vector of plant viruses. Among the most important plant viruses to be transmitted by B. tabaci are those in the genus Begomovirus (family, Geminiviridae. Surprisingly, little is known about the genome of this whitefly. The haploid genome size for male B. tabaci has been estimated to be approximately one billion bp by flow cytometry analysis, about five times the size of the fruitfly Drosophila melanogaster. The genes involved in whitefly development, in host range plasticity, and in begomovirus vector specificity and competency, are unknown. Results To address this general shortage of genomic sequence information, we have constructed three cDNA libraries from non-viruliferous whiteflies (eggs, immature instars, and adults and two from adult insects that fed on tomato plants infected by two geminiviruses: Tomato yellow leaf curl virus (TYLCV and Tomato mottle virus (ToMoV. In total, the sequence of 18,976 clones was determined. After quality control, and removal of 5,542 clones of mitochondrial origin 9,110 sequences remained which included 3,843 singletons and 1,017 contigs. Comparisons with public databases indicated that the libraries contained genes involved in cellular and developmental processes. In addition, approximately 1,000 bases aligned with the genome of the B. tabaci endosymbiotic bacterium Candidatus Portiera aleyrodidarum, originating primarily from the egg and instar libraries. Apart from the mitochondrial sequences, the longest and most abundant sequence encodes vitellogenin, which originated from whitefly adult libraries, indicating that much of the gene expression in this insect is directed toward the production

  5. Economic Impact of the Hawaii State Public Library System (HSPLS) on the Business and Tourism Industries Study: Final Report

    Science.gov (United States)

    Ryan, Joe; McClure, Charles R.

    2003-01-01

    Ryan Information Management conducted a return on investment (ROI) study of the economic value of the Hawaii State Public Library System (HSPLS) and identified potential additional sources of operating revenue. HSPLS economic value was examined from four viewpoints, HSPLS: direct economic impact, market value, peer comparison and value to library…

  6. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research.

    Science.gov (United States)

    Coates, Brad S; Sumerford, Douglas V; Hellmich, Richard L; Lewis, Leslie C

    2009-01-01

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

  7. A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost.

    Science.gov (United States)

    Heavens, Darren; Accinelli, Gonzalo Garcia; Clavijo, Bernardo; Clark, Matthew Derek

    2015-07-01

    Long mate pair (LMP) or "jump" libraries are invaluable for producing contiguous genome assemblies and assessing structural variation. However the consistent production of high quality (low duplication rate, accurately sized) LMP libraries has proven problematic in many genome projects. Input DNA length and quantity are key issues that can affect success. Here we demonstrate how 12 libraries covering a wide range of jump sizes can be constructed from DNA, thus ensuring production of the best LMP libraries from a given DNA sample. Finally, we demonstrate the accuracy of the insert sizes by mapping reads from each library back to an existing assembly.

  8. Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9.

    Science.gov (United States)

    Park, Jeongbin; Kim, Jin-Soo; Bae, Sangsu

    2016-07-01

    CRISPR-derived RNA guided endonucleases (RGENs) have been widely used for both gene knockout and knock-in at the level of single or multiple genes. RGENs are now available for forward genetic screens at genome scale, but single guide RNA (sgRNA) selection at this scale is difficult. We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9). With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions. Furthermore, it provides a powerful way to select multiple optimal target sequences from thousands of genes at once for the creation of a genome-wide library. Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users. Free access at http://www.rgenome.net/cas-database/ sangsubae@hanyang.ac.kr or jskim01@snu.ac.kr Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  9. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe.

    Science.gov (United States)

    Wahls, Wayne P; Davidson, Mari K

    2008-09-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4(+) gene for positive and negative selection, an origin of replication (ars1) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS(+). These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization.

  10. Final Report: Transport and its regulation in Marine Microorganisms: A Genomic Based Approach

    Energy Technology Data Exchange (ETDEWEB)

    Brian Palenik; Bianca Brahamsha; Ian Paulsen

    2009-09-03

    This grant funded the analysis and annotation of the genomes of Synechococcus and Ostreococcus, major marine primary producers. Particular attention was paid to the analysis of transporters using state of the art bioinformatics analyses. During the analysis of the Synechococcus genome, some of the components of the unique bacterial swimming apparatus of one species of Synechococcus (Clade III, strain WH8102) were determined and these included transporters, novel giant proteins and glycosyltransferases. This grant funded the analysis of gene expression in Synechococcus using whole genome microarrays. These analyses revealed the strategies by which marine cyanobacteria respond to environmental conditions such as the absence of phosphorus, a common limiting nutrient, and the interaction of Synechococcus with other microbes. These analyses will help develop models of gene regulation in cyanobacteria and thus help predict their responses to changes in environmental conditions.

  11. The Human Genome Project: Information access, management, and regulation. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, J.D.; Micikas, L.B.

    1996-08-31

    The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

  12. Construction of Genomic Fosmid Library of Brassicajuncea and Screening of Cytological Markers for B-genome Chromosomes%芥菜Fosmid文库构建及B基因组细胞学标记的筛选利用

    Institute of Scientific and Technical Information of China (English)

    彭元凤; 孟德璇; 黄玉碧; 王桂香

    2012-01-01

    构建了由60000个克隆组成的芥菜无偏倚Fosmid文库,该文库外源片段插入率为100%,外源DNA平均插入长度为32kb,文库覆盖率约为芥菜基因组的1.8倍。利用不同来源的分子标记筛选文库,得到的阳性单克隆经荧光原位杂交(FISH)鉴定后,获得两类B基因组细胞学标记,一类在所有染色体上都有信号,另一类仅在一对染色体上有信号。%In this study, an unbiased Fosmid library of Brassica juncea was established, which consisted of 60 000 clones with 100% inserting frequency. In the constructed library, the size of average inserts was approximately 32 kb, corresponding to 1.8 genome equivalents. Subsequently, two types of B-genome cytological markers were identified by means of library screening and chromosome fluorescence in situ hybridization (FISH) . One type was that the signal located on all chromosomes, and the other one was that the signal was detected only on one pair of chromosomes.

  13. cDNA/STS map of human genome. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-11-01

    The human gene identification and transcript mapping project has generated over 3,000 3`ESTs derived from human brain cDNA libraries and mapped over 300 of these. The data have been submitted to the appropriate gene sequence and mapping databases. Clones are either available from Greg Lennon at Lawrence Livermore or from ATCC. A summary of this work is provided and a News and Views article from the same issue is included which highlights this paper. The strategy developed by this laboratory is now being used by an international consortium to generate the first comprehensive human gene (transcript) map over the next year or two.

  14. Annual genome conference. Final report, September 1, 1994--August 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Gardiner, K.

    1995-11-01

    Tremendous progress has been made in the construction of physical and genetic maps of the human chromosomes. The next step in the solving of disease related problems, and in understanding the human genome as a whole, is the systematic isolation of transcribed sequences. Many investigators have already embarked upon comprehensive gene searches, and many more are considering the best strategies for undertaking such searches. Because these are likely to be costly and time consuming endeavors, it is important to determine the most efficient approaches. As a result, it is critical that investigators involved in the construction of transcriptional maps have the opportunity to discuss their experiences and their successes with both old and new technologies. This document contains the proceedings of the Fourth Annual Workshop on the Identification of Transcribed Sequences, held in Montreal, Quebec, October 16-18, 1994. Included are the workshop notebook, containing the agenda, abstracts presented and list of attendees. Topics included: Progress in the application of the hybridization based approaches and exon trapping; Progress in transcriptional map construction of selected genomic regions; Computer assisted analysis of genomic and protein coding sequences and additional new approaches; and, Sequencing and mapping of random cDNAs.

  15. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Nakhleh, Luay

    2014-03-12

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

  16. Assessment of the applicability of the national fire weather data library to wind energy analyses. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Marlatt, W.E.; Tierney, P.; Meilke, P.; Baer, M.; Childs, J.

    1979-05-01

    The specific scope of work for this effort followed this sequence: review of the Fire Weather Library for stations with usable records; development of statistical summaries for selected individual stations; screen summaries for common windy areas; develop statistical comparisons of fire weather stations with nonfire weather stations having multiple observations per day; develop frequency spectra of wind periods above threshold values; and estimate seasonal and geographic distributions of wind energy. Following discussions with the PNL, efforts for objective four, the comparison of one observation per day to multiple observations for the same station, were deferred until the results from a similar study at Northwestern University were available.

  17. [Construction of genomic library of L. interrogans serovar lai using lambda gt11 as the vector and a study of recombiant plasmid pDL121].

    Science.gov (United States)

    Liu, H; Dai, B; Jing, B; Wu, W; Li, S; Fang, Z; Zhao, H; Ye, D; Yan, R; Liu, J; Song, S; Yang, Y; Zhang, Y; Liu, F; Tu, Y; Yang, H; Huang, Z; Liang, L; Hu, L; Zhao, M

    1997-03-01

    A genomic library of L. interrogans serovar lai strain 017 has been constructed using lambda gt11 as the vector. DNA was partially digested by two blunt-end restriction enzymes, then methylated with EcoR I methylase; after EcoR I linker was added to the DNA, the linker-ended DNA was ligated to the dephosphorylated EcoR I digested lambda gt11 arms. The recombined DNA was packaged in vitro, and used to transduct E. coli Y1090 for amplification. There were 2.1 x 10(6) recombinant bacteriophages as recognized by their ability to form white plaques plated on Lac host in the presence of both IPTG and X-Ga1. A positive clone, designated lambda DL12, was screened with a rabbit anti-serum against L. interrogans serovar lai from the genomic library. The DNA from lambda DL12 was subcloned into plasmid pUC18. A recombinant (designated as pDL121) was obtained. SDS-PAGE analysis indicated that a 23 kd was expressed in E. coli JM 103 harboring pDL121. Western blotting analysis showed that a specific protein band molecular weight of 23 kd could be recognized by the rabbit antiserum against L. interrogans serovar lai strain 017.

  18. Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries.

    Science.gov (United States)

    Saski, Christopher A; Bhattacharjee, Ranjana; Scheffler, Brian E; Asiedu, Robert

    2015-01-01

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches

  19. Genomic Resources for Water Yam (Dioscorea alata L.: Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries.

    Directory of Open Access Journals (Sweden)

    Christopher A Saski

    Full Text Available The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp. is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS profiles on two yam (Dioscorea alata L. genotypes (TDa 95/00328 and TDa 95-310 was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using

  20. The construction of Streptomyces cyaneus genomic libraries in Escherichia coli is dependent upon the use of Mcr-deficient strains.

    Science.gov (United States)

    Wang, P; Harvey, S S; Sims, P F; Broda, P

    1992-09-21

    Streptomyces cyaneus genomic DNA ligated into either lambda phage or plasmid vectors was very inefficiently cloned into standard Escherichia coli host strains. However, the same material could be efficiently cloned using Mcr-deficient E. coli strains. These results suggest that the S. cyaneus genome contains 5-methylcytosine residues, some of which occur within the recognition sequences of the E. coli Mcr restriction system.

  1. Mapping and sequencing the human genome: Science, ethics, and public policy. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, J.D.

    1993-03-31

    Development of Mapping and Sequencing the Human Genome: Science, Ethics, and Public Policy followed the standard process of curriculum development at the Biological Sciences Curriculum Study (BSCS), the process is described. The production of this module was a collaborative effort between BSCS and the American Medical Association (AMA). Appendix A contains a copy of the module. Copies of reports sent to the Department of Energy (DOE) during the development process are contained in Appendix B; all reports should be on file at DOE. Appendix B also contains copies of status reports submitted to the BSCS Board of Directors.

  2. The Human Genome Project and Mental Retardation: An Educational Program. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Sharon

    1999-05-03

    The Arc, a national organization on mental retardation, conducted an educational program for members, many of whom have a family member with a genetic condition causing mental retardation. The project informed members about the Human Genome scientific efforts, conducted training regarding ethical, legal and social implications and involved members in issue discussions. Short reports and fact sheets on genetic and ELSI topics were disseminated to 2,200 of the Arc's leaders across the country and to other interested individuals. Materials produced by the project can e found on the Arc's web site, TheArc.org.

  3. 白眉长臂猿基因组BAC文库的构建%Construction of Genome Bacterial Artificial Chromosome Library of Hylobates Hoolock

    Institute of Scientific and Technical Information of China (English)

    王起明; 孙烨超; 厉申捷; 叶建平

    2015-01-01

    High quality genomic DNA of Hylobates hoolock was obtained by gentle physical homogenization. The DNA was partially digested with EcoRⅠand EcoRⅠmethylase, and cloned to pCC1BAC vector. The positive clones were stored in 384-well plates. The constructed BAC library consists of 85800 clones. DNA from randomly selected 250 BAC clones was restricted with Not I restriction enzyme and fragments were separated by pulsed field gel electrophoresis. The result shows that the average insert size is estimated as approximately 110 kb, and the ratio of non-recombinant clones is 10. 0%. If the genome size of Hylobates hoolock is 3 ×106 kilo-base, the library could cover 3 times the number of genome.%通过温和的物理方法获得白眉长臂猿高质量的基因组DNA,EcoRⅠ和EcoRⅠ甲基化酶部分酶切后经回收、连接、转化、阳性克隆的保存,构建了含有85800个克隆的全基因组BAC( Bacterial artificial chromosome)文库.随机选取250个BAC克隆进行Not I酶切及脉冲场电泳分析,结果表明该文库的平均插入片段大小为110 kb,非重组克隆(无插入片段)的比率为10.0%.假定白眉长臂猿的基因组大小为3×106 kb,根据文库的平均插入片段大小,则该文库具有3倍的基因组覆盖率.

  4. 地衣芽孢杆菌基因文库的构建及分析%Construction and Analysis of Genomic Library of Bacillus licheni formis

    Institute of Scientific and Technical Information of China (English)

    熊裕焱; 彭雅娟; 卢瑞; 于怡; 王娜; 李清彪; 何宁

    2011-01-01

    作为一种高效无毒、无二次污染以及能够生物降解的水处理剂,生物絮凝剂受到越来越多的关注.以一株具有强絮凝活性地衣芽孢杆菌(Bacillus licheni formis)为实验菌,通过构建基因组文库,尝试筛选絮凝基因阳性克隆子.结果表明,该菌株基因文库构建成功,共得到2.1×103克隆子.随机挑取17个阳性克隆子进行DNA测序分析,发现一些相对保守蛋白及2个不具有明确功能的基因.该结果为进一步研究地衣芽孢杆菌全基因组结构功能及细菌絮凝基因奠定了基础.%As an efficient,innoxious, and biodegradable wastewater treatment agent with no secondary pollution, bioflocculant is receiving more and more concerns nowadays. In this paper,Bacillus licheniformis with excellent flocculating activity was used to construct the genomic library and tried to screen out the positive clones with flocculation gene. The results showcd that the genomic library was successfully consrructed,2. 1× 103 clones were screened out. 17 clones were randomly selected for DNA sequencing and analysis. Some relative conserved proteins and 2 novel genes with unknown functions were found. The results lay a foundation for the further study of gene encoding bacteria flocculant and the whole genomic structure and function of Bacillus licheniformis.

  5. In vivo repackaging of recombinant cosmid molecules for analyses of Salmonella typhimurium, Streptococcus mutans, and mycobacterial genomic libraries.

    Science.gov (United States)

    Jacobs, W R; Barrett, J F; Clark-Curtiss, J E; Curtiss, R

    1986-04-01

    Strains of Escherichia coli K-12 were constructed that permitted the amplification of in vitro-packaged recombinant cosmid-transducing particles by in vivo repackaging of recombinant cosmid molecules. Thermal induction of these thermoinducible, excision-defective lysogens containing recombinant cosmid molecules yielded high titers of packaged recombinant cosmids and low levels of PFU. These strains were used to amplify packaged recombinant cosmid libraries of Mycobacterium leprae, Mycobacterium vaccae, Salmonella typhimurium, and Streptococcus mutans DNA. Contiguous and noncontiguous libraries were compared for the successful identification of cloned genes. Construction of noncontiguous libraries allowed the dissociation of desired genes from genes that were deleterious to the survival of a cosmid recombinant and permitted selection for unlinked traits that resulted in a selected phenotype. In vivo repackaging of recombinant cosmids permitted amplification of the original in vitro-packaged collection of transducing particles, storage of cosmid libraries as phage lysates, facilitation of complementation screening, expression analysis of repackaged recombinant cosmids after UV-irradiated cells were infected, in situ enzyme or immunological screening, and facilitation of recovery of recombinant cosmid molecules containing transposon inserts.

  6. Final Report: Connecting genomic capabilities to physiology and response: Systems biology of the widespread alga Micromonas

    Energy Technology Data Exchange (ETDEWEB)

    Worden, Alexandra Z. [Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA (United States); Callister, Stephen [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stuart, Joshua [Univ. of California, Santa Cruz, CA (United States); Smith, Richard [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-09-30

    Increased stratification, less mixing and reduced nutrient concentrations in marine surface waters are predicted under a number of climate-change scenarios. These conditions are considered favorable for tiny photosynthetic algae (picophytoplankton), shaping their role in mediating future CO2 conditions. One possibility is that picophytoplankton such as Micromonas that have broad geographical ranges will more successfully adapt to changing environmental conditions. However, their capacity to thrive under the multi-factorial impacts of low pH, low nutrients, increasing temperature and changes in community composition is not known. Here, we developed the dual-Micromonas model system, which entailed generating optimized genomic information for two Micromonas species and developing a highperformance chemostat system in which both CO2 and nutrients could be consistently manipulated. This system is now fully operational. Project results are available in several publications will others are still in the analysis phase. Overall, our results show that Micromonas primary production will likely decrease under predicted future climate conditions. Furthermore, our studies on Micromonas provide new insights to the land plant ancestor, including the discovery of conserved signaling mechanisms (known to be essential to plant development) as well as the discovery of widespread chemical-sensing molecular switches. Collectively, this research highlights Micromonas as an important new model green alga for understanding plant gene networks and evolution as well as for investigating perturbation effects on marine primary production.

  7. Construction of BAC libraries from flow-sorted chromosomes

    OpenAIRE

    Šafář, J.; Šimková, H; Doležel, J

    2016-01-01

    Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by construct...

  8. A genome-wide polyketide synthase deletion library uncovers novel genetic links to polyketides and meroterpenoids in Aspergillus nidulans

    DEFF Research Database (Denmark)

    Nielsen, Michael Lynge; Nielsen, Jakob Blæsbjerg; Rank, Christian

    2011-01-01

    Fungi possess an advanced secondary metabolism that is regulated and coordinated in a complex manner depending on environmental challenges. To understand this complexity, a holistic approach is necessary. We initiated such an analysis in the important model fungus Aspergillus nidulans by systemat...... the current understanding of the biosynthetic pathways leading to arugosins and violaceols. We expect that the library will be an important resource towards a systemic understanding of polyketide production in A. nidulans.......Fungi possess an advanced secondary metabolism that is regulated and coordinated in a complex manner depending on environmental challenges. To understand this complexity, a holistic approach is necessary. We initiated such an analysis in the important model fungus Aspergillus nidulans...... by systematically deleting all 32 individual genes encoding polyketide synthases. Wild-type and all mutant strains were challenged on different complex media to provoke induction of the secondary metabolism. Screening of the mutant library revealed direct genetic links to two austinol meroterpenoids and expanded...

  9. Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray generated from the shotgun libraries previously used in the sequencing of this bacterial genome

    Directory of Open Access Journals (Sweden)

    Zaini Paulo A

    2010-05-01

    Full Text Available Abstract Background From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC, clones that were representative of the largest possible number of coding sequences (CDSs were selected to create a DNA microarray platform on glass slides (XACarray. The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

  10. A nanobuffer reporter library for fine-scale imaging and perturbation of endocytic organelles | Office of Cancer Genomics

    Science.gov (United States)

    Endosomes, lysosomes and related catabolic organelles are a dynamic continuum of vacuolar structures that impact a number of cell physiological processes such as protein/lipid metabolism, nutrient sensing and cell survival. Here we develop a library of ultra-pH-sensitive fluorescent nanoparticles with chemical properties that allow fine-scale, multiplexed, spatio-temporal perturbation and quantification of catabolic organelle maturation at single organelle resolution to support quantitative investigation of these processes in living cells.

  11. Monochromosomal hybrids for the analysis of the human genome. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Athwal, R.S. [Temple Univ. School of Medicine, Philadelphia, PA (United States). Fels Inst. for Cancer Research and Molecular Biology

    1994-09-01

    The objective of this research project is to produce panels of mouse/human and/or Chinese hamster/human hybrid cell lines each harboring a single different human chromosome. The human chromosome present in rodent cell will be marked with a dominant selectable marker and maintained by selection. In these experiments human chromosomes first ``tagged`` with a selectable marker in human cells are subsequently transferred to rodent cells by microcell fusion method. Several different experimental schemes have been developed to ``tag`` human chromosomes with a selectable marker. Amphotropic retroviral vectors provide a highly efficient system to introduce selectable markers into normal diploid human cells. The integration of retroviral vector into the cell genome occurs at random by recombination at a defined nucleotide sequence in the LTRs and only a single copy of the vector integrates in a cell. This property of retroviral vectors allows to isolate a segment of the chromosomal DNA flanking the vector integration site by PCR amplification. In these studies the amphotropic retroviral vector pZIPgpt that carries a dominant selectable marker gpt, is used to tag the human chromosomes in normal diploid cells. Human DNA flanking the integrated vector is rescued by PCR amplification and cloned into a plasmid vector. Cloned human DNA is then used to probe Southern blots of DNAs from a panel of hybrid cell lines to identify the chromosome of its origin. This allows them to identify clonal human cell lines, each carrying the marker integrated into a different chromosome. Marked chromosomes are then transferred to rodent cells by MMCT.

  12. Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Knoche, K.; Selman, S.; Hung, L. [and others

    1994-06-01

    Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

  13. Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries

    Science.gov (United States)

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources such as SSRs, SNPs and InDels in several model and non-model plant species. Yam (Dioscorea spp.) i...

  14. Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

    NARCIS (Netherlands)

    Kerstens, H.H.D.; Crooijmans, R.P.M.A.; Dibbits, B.W.; Vereijken, A.; Okimoto, R.; Groenen, M.A.M.

    2011-01-01

    Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and

  15. Bridging the Divide: Linking Genomics to Ecosystem Responses to Climate Change: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Melinda D.

    2014-03-15

    Over the project period, we have addressed the following objectives: 1) assess the effects of altered precipitation patterns (i.e., increased variability in growing season precipitation) on genetic diversity of the dominant C4 grass species, Andropogon gerardii, and 2) experimentally assess the impacts of extreme climatic events (heat wave, drought) on responses of the dominant C4 grasses, A. gerardii and Sorghastrum nutans, and the consequences of these response for community and ecosystem structure and function. Below is a summary of how we have addressed these objectives. Objective 1 After ten years of altered precipitation, we found the number of genotypes of A. gerardii was significantly reduced compared to the ambient precipitation treatments (Avolio et al., 2013a). Although genotype number was reduced, the remaining genotypes were less related to one another indicating that the altered precipitation treatment was selecting for increasingly dissimilar genomes (based on mean pairwise Dice distance among individuals). For the four key genotypes that displayed differential abundances depending on the precipitation treatment (G1, G4, and G11 in the altered plots and G2 in the ambient plots), we identified phenotypic differences in the field that could account for ecological sorting (Avolio & Smith, 2013a). The three altered rainfall genotypes also have very different phenotypic traits in the greenhouse in response to different soil moisture availabilities (Avolio and Smith, 2013c). Two of the genotypes that increased in abundance in the altered precipitation plots had greater allocation to root biomass (G4 and G11), while G1 allocated more biomass aboveground. These phenotypic differences among genotypes suggests that changes in genotypic structure between the altered and the ambient treatments has likely occurred via niche differentiation, driven by changes in soil moisture dynamics (reduced mean, increased variability and changes in the depth distribution of

  16. Bridging the Divide: Linking Genomics to Ecosystem Responses to Climate Change: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Melinda D.

    2014-03-15

    Over the project period, we have addressed the following objectives: 1) assess the effects of altered precipitation patterns (i.e., increased variability in growing season precipitation) on genetic diversity of the dominant C4 grass species, Andropogon gerardii, and 2) experimentally assess the impacts of extreme climatic events (heat wave, drought) on responses of the dominant C4 grasses, A. gerardii and Sorghastrum nutans, and the consequences of these response for community and ecosystem structure and function. Below is a summary of how we have addressed these objectives. Objective 1 After ten years of altered precipitation, we found the number of genotypes of A. gerardii was significantly reduced compared to the ambient precipitation treatments (Avolio et al., 2013a). Although genotype number was reduced, the remaining genotypes were less related to one another indicating that the altered precipitation treatment was selecting for increasingly dissimilar genomes (based on mean pairwise Dice distance among individuals). For the four key genotypes that displayed differential abundances depending on the precipitation treatment (G1, G4, and G11 in the altered plots and G2 in the ambient plots), we identified phenotypic differences in the field that could account for ecological sorting (Avolio & Smith, 2013a). The three altered rainfall genotypes also have very different phenotypic traits in the greenhouse in response to different soil moisture availabilities (Avolio and Smith, 2013c). Two of the genotypes that increased in abundance in the altered precipitation plots had greater allocation to root biomass (G4 and G11), while G1 allocated more biomass aboveground. These phenotypic differences among genotypes suggests that changes in genotypic structure between the altered and the ambient treatments has likely occurred via niche differentiation, driven by changes in soil moisture dynamics (reduced mean, increased variability and changes in the depth distribution of

  17. Identification of three wheat globulin genes by screening a Triticum aestivum BAC genomic library with cDNA from a diabetes-associated globulin

    Directory of Open Access Journals (Sweden)

    MacFarlane Amanda J

    2009-07-01

    Full Text Available Abstract Background Exposure to dietary wheat proteins in genetically susceptible individuals has been associated with increased risk for the development of Type 1 diabetes (T1D. Recently, a wheat protein encoded by cDNA WP5212 has been shown to be antigenic in mice, rats and humans with autoimmune T1D. To investigate the genomic origin of the identified wheat protein cDNA, a hexaploid wheat genomic library from Glenlea cultivar was screened. Results Three unique wheat globulin genes, Glo-3A, Glo3-B and Glo-3C, were identified. We describe the genomic structure of these genes and their expression pattern in wheat seeds. The Glo-3A gene shared 99% identity with the cDNA of WP5212 at the nucleotide and deduced amino acid level, indicating that we have identified the gene(s encoding wheat protein WP5212. Southern analysis revealed the presence of multiple copies of Glo-3-like sequences in all wheat samples, including hexaploid, tetraploid and diploid species wheat seed. Aleurone and embryo tissue specificity of WP5212 gene expression, suggested by promoter region analysis, which demonstrated an absence of endosperm specific cis elements, was confirmed by immunofluorescence microscopy using anti-WP5212 antibodies. Conclusion Taken together, the results indicate that a diverse group of globulins exists in wheat, some of which could be associated with the pathogenesis of T1D in some susceptible individuals. These data expand our knowledge of specific wheat globulins and will enable further elucidation of their role in wheat biology and human health.

  18. 毛竹大片段双元细菌人工染色体基因组文库的构建%Construction of a large genomic DNA fragments,BIBAC library for Phyllostachys pubescens

    Institute of Scientific and Technical Information of China (English)

    管雨; 杨洋; 张智俊; 罗淑萍; 汤定钦

    2011-01-01

    One plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library was constructed which represents the first large genomic DNA fragment library generated for Phyllostachys pubescens. High-quality, genomic DNA extracted from young leaves of Phyllostachys pubescens was gradiently enzyme-digested with a gradient using BamH I. Desirable DNA fragments were isolated by pulsed field gel electrophoresis, ligated to the dephosphorylatedion carrier Pcld04541 with a mass ratio of 3:1, and then transformed to Escherichia coli DH10B competent cells. This was followed by blue-white screening with establishment of a binary bacterial artificial chromosome (BIBAC) genome library. Results showed a high recombination positive colony from which a BIB AC genome library, consisting of 104 clones with an average insert fragment size of about 105 kb after detection with a pulsed field gel electrophoresis, was constructed. The BIBAC library was 5 times larger than the Phyllostachys pubescens genome. The construction of this BIBAC genome library laid a good foundation for related genome research.%从毛竹Phyllostachys pubescens幼嫩叶片中提取纯化得到高质量的基因组DNA,经限制性内切酶BamH I对它们进行梯度酶切,脉冲场电泳选择合适酶切DNA片段,与脱磷酸化处理过的质粒载体pCLD04541按质量比3∶1相互连接,转化大肠杆菌Escherichia coli DH10B感受态细胞进行蓝白斑筛选,挑取白色克隆,获得重组率较高的阳性克隆,构建了含有104个克隆的双元细菌人工染色体(BIBAC)基因组文库,并通过脉冲场电泳检测分析后确定,所构建的毛竹BIBAC文库平均插入片段为105 kb,约覆盖5倍毛竹基因组.该文库的构建为毛竹基因组研究做好了前期的基础工作.

  19. Spectral library searching in proteomics.

    Science.gov (United States)

    Griss, Johannes

    2016-03-01

    Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data.

  20. Isolation of a Gastrodia Antifungal Protein Gene from a Genomic Library of G. elata and Its Sequence Analysis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new genomic DNA encoding a member of Gastrodia antifungal protein family is isolated and sequenced.This gene contains a 510 bp open reading frame and 531 bp promoter region without introns.Sequence analysis indicates that a 28 amino acids signal peptide exists at the N-terminal.It shows high sequence homology with the mannose-binding lectinsfrom Epipactis hellebo-rine, Listera ovata and Cymbidium hybrid.A putative TATA box and transcription start site is dete cted in the promoter region.

  1. The Development and Operation of a System to Reclassify Older Books Under the Library of Congress Classification System for a Public Library Currently Employing the Dewey Decimal Classification. Final Report.

    Science.gov (United States)

    Pinson, Leo A.

    Objectives of this project were: (1) to uncover problems a public library might encounter in reclassifying its collection from the Dewey Decimal Classification to the Library of Congress Classification, (2) to apply data processing to the tasks, (3) to establish procedures for reclassification, and (4) to provide a cost estimate for the conversion…

  2. Comparative genome analysis of Lactococcus garvieae using a suppression subtractive hybridization library: discovery of novel DNA signatures.

    Science.gov (United States)

    Kim, Wonyong; Park, Hee Kuk; Thanh, Hien Dang; Lee, Bo-Young; Shin, Jong Wook; Shin, Hyoung-Shik

    2011-12-01

    Lactococcus garvieae, the pathogenic species in the genus Lactococcus, is recognized as an emerging pathogen in fish, animals, and humans. Despite the widespread distribution and emerging clinical significance of L. garvieae, little is known about the genomic content of this microorganism. Suppression subtractive hybridization was performed to identify the genomic differences between L. garvieae and Lactococcus lactis ssp. lactis, its closest phylogenetic neighbor, and the type species of the genus Lactococcus. Twenty-seven clones were specific to L. garvieae and were highly different from Lactococcus lactis in their nucleotide and protein sequences. Lactococcus garvieae primer sets were subsequently designed for two of these clones corresponding to a pyrH gene and a novel DNA signature for application in the specific detection of L. garvieae. The primer specificities were evaluated relative to three previously described 16S rRNA gene-targeted methods using 32 Lactococcus and closely related strains. Both newly designed primer sets were highly specific to L. garvieae and performed better than did the existing primers. Our findings may be useful for developing more stable and accurate tools for the discrimination of L. garvieae from other closely related species.

  3. Increased retention of functional fusions to toxic genes in new two-hybrid libraries of the E. coli strain MG1655 and B. subtilis strain 168 genomes, prepared without passaging through E. coli

    Directory of Open Access Journals (Sweden)

    Projan Steve

    2003-09-01

    Full Text Available Abstract Background Cloning of genes in expression libraries, such as the yeast two-hybrid system (Y2H, is based on the assumption that the loss of target genes is minimal, or at worst, managable. However, the expression of genes or gene fragments that are capable of interacting with E. coli or yeast gene products in these systems has been shown to be growth inhibitory, and therefore these clones are underrepresented (or completely lost in the amplified library. Results Analysis of candidate genes as Y2H fusion constructs has shown that, while stable in E. coli and yeast for genetic studies, they are rapidly lost in growth conditions for genomic libraries. This includes the rapid loss of a fragment of the E. coli cell division gene ftsZ which encodes the binding site for ZipA and FtsA. Expression of this clone causes slower growth in E. coli. This clone is also rapidly lost in yeast, when expressed from a GAL1 promoter, relative to a vector control, but is stable when the promoter is repressed. We have demonstrated in this report that the construction of libraries for the E. coli and B. subtilis genomes without passaging through E. coli is practical, but the number of transformants is less than for libraries cloned using E. coli as a host. Analysis of several clones in the libraries that are strongly growth inhibitory in E. coli include genes for many essential cellular processes, such as transcription, translation, cell division, and transport. Conclusion Expression of Y2H clones capable of interacting with E. coli and yeast targets are rapidly lost, causing a loss of complexity. The strategy for preparing Y2H libraries described here allows the retention of genes that are toxic when inappropriately expressed in E. coli, or yeast, including many genes that represent potential antibacterial targets. While these methods are generally applicable to the generation of Y2H libraries from any source, including mammalian and plant genomes, the

  4. Small Public Library Management

    Science.gov (United States)

    Pearlmutter, Jane; Nelson, Paul

    2012-01-01

    Anyone at the helm of a small public library knows that every little detail counts. But juggling the responsibilities that are part and parcel of the job is far from easy. Finally, here's a handbook that includes everything administrators need to keep a handle on library operations, freeing them up to streamline and improve how the organization…

  5. Central New York Library Resources Council CLRC Regional Digitization Plan. Final Report for the Preparing Central New York History for the Future LSTA Project.

    Science.gov (United States)

    Sywetz, Betsy

    The primary goal for digitization projects sponsored by the Central New York Library Resources Council (CLRC) is enhanced access for the people of the region to digital resources created from collections in Central New York's libraries, archives and museums. The CLRC Digitization Plan provides a framework for the support of digitization activities…

  6. The Importance of California Public Libraries in Increasing Public Access to the Internet: Findings from the InFoPeople Site Visits. Stage II Final Report.

    Science.gov (United States)

    Bertot, John Carlo; McClure, Charles R.; Ryan, Joe

    In less than five years, the California State Library-sponsored InFoPeople project connected 46% of California's public libraries to the Internet and established a highly regarded, sustained training program to assist librarians in taking advantage of the new networked resources and services. The primary objective of this Stage II report was to…

  7. Construction and screening of genomic library of Haemophilus paragallinarum%副鸡嗜血杆菌基因文库的构建与筛选

    Institute of Scientific and Technical Information of China (English)

    王雪敏; 梁玉荣; 吕学泽; 张培君; 龚玉梅; 王宏俊

    2012-01-01

    为了筛选副鸡嗜血杆菌的体内表达基因,提取了副鸡嗜血杆菌的全基因组,构建了副鸡嗜血杆菌基因组的pET系统表达文库。运用PCR及核酸内切酶(SalⅠ+NdeⅠ)鉴定基因文库,并以病原菌吸附后的康复血清作为探针,采用菌落原位杂交的方法对基因文库进行筛选。结果显示,重组质粒中有0.5~2kb的片段插入,99%的基因包含在基因文库中;重复筛选后得到的阳性克隆再经过PCR与SalⅠ+NdeⅠ酶切鉴定后定向测序,并对测序结果在NCBI上进行分析后发现筛选获得的基因中,有1个表达为转运谷氨酰还原酶、1个表达为转录终止因子,1个表达为荚膜合成域2,还有2个表达为保守假想蛋白。结果表明,本研究应用体内诱导抗原技术(IVIAT)筛选到了一些副鸡嗜血杆菌体内诱导表达基因,并对基因的功能做了初步探讨,在找寻副鸡嗜血杆菌在体内生存以及致病关键基因的道路上前进了一步,为传染性鼻炎的预防和治疗积累了有价值的资料。%In order to select in vivo expression genes of Haemophilus paragallinarum,the total DNA of the bacterium was extracted and the genomic library was constructed with pET system.The positive clones in the library were identified by PCR and SalⅠ-NdeⅠ-digestion.The expressed library was screened by colony hybridization using rehabilitation serum,which was absorbed with H.paragallinarum,as the probe.In result,the recombinant plasmids contained from 0.5 to 2 kb of target fragments,and 99% of H.paragallinarum genes were involved in the library.The 17 positive clones obtained by colony hybridization were confirmed by PCR and SalⅠ-NdeⅠ digestion followed by direct-sequencing.Sequences were then blasted in the NCBI GenBank.The sequence analysis revealed 5 ORFs encoded glutamyl tRNA reductase,transcription termination factor,capsule biosynthesis region 2 gene cluster,and two hypothetical proteins

  8. Construction and Characterization of Genomic Library of Trichoderma viride ZBS6 by Cosmid Carrier%绿木霉ZBS6黏粒基因组文库的构建及质量鉴定

    Institute of Scientific and Technical Information of China (English)

    孙虎; 燕照玲; 刘德畅; 薛保国

    2012-01-01

    To cope with the screening and cloning of antagonistic genes of Trichoderma viride ZBS6,this study established a method for obtaining high-quality genomic DNA and constructed the genomic library of T. viride ZBS6 by SuperCosl vector. The genomic library consisted of 3. 9×104 independent clones with an average insert size of about 33 kb,and had a colony titer of around 4. 2×108 cfu/mL in stock. So the exact probability of having any given DNA sequence in the library was as high as 99. 9%.%为开展绿木霉ZBS6(Trichoderma viride ZBS6)拮抗基因筛选及克隆工作,建立了高质量基因组DNA的提取方法,并采用SuperCos1载体构建了绿木霉ZBS6黏粒基因组文库.试验中共获得3.9×104个黏粒克隆,平均插入片段大小约为33 kb,文库滴度约为4.2×108 cfu/mL.理论上,从该文库中筛选到任一DNA序列的精确概率可高达99.9%.

  9. Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999

    Energy Technology Data Exchange (ETDEWEB)

    Harger, Carol A.

    1999-10-28

    Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence. [The annual report for June 1996 to August 1997 is included as an attachment to this final report.

  10. 长爪沙鼠不同willis血管类型全基因组文库构建%Genomic library construction of different willis circle in Meriones unguiculatus

    Institute of Scientific and Technical Information of China (English)

    张贺; 陈振文; 王承利; 孙倩; 陆娜; 王洋

    2014-01-01

    Objective To find out and clone the genes that can influence different willis circle in Meriones unguiculatus, the genomic library has been made.Methods 96 clean Meriones unguiculatus were dissected according to observe the differences of willis circle, and the mixed DNA was extracted from different blood vessels.The genomic library construction has been done by using pCC1FOS vector, following by CopyControl Fosmid Lib manual.The copy numbers, recombined segment size and recombination fraction of the library were measured.Results Genomic library of different Willis circle in Meriones unguiculatus was successfully made.The capacity of the library was 1700 copies.The segment size was 36kb, and the recombination fraction was 93%.Conclusion The library was the good beginning for the following steps which were gene cloning and genescreen.%目的:为了找到并克隆出影响长爪沙鼠不同willis血管类型表达的基因,建立包含各种血管类型的全基因组文库。方法选取清洁级长爪沙鼠96只,解剖后剥离不同willis血管类型,分别提取DNA后混合。选用Copy Control Fosmid Library Kit和pCC1FOS载体构建文库,并对文库进拷贝数、重组片段长度及重组率进行鉴定。结果成功建立了长爪沙鼠不同willis血管类型的全基因组文库,文库容量为1700个拷贝数,插入重组片段长度约为36 kb,重组率为93%。结论建立了不同willis血管类型的长爪沙鼠全基因组文库,为后续基因克隆及筛选等研究打下良好基础。

  11. Library 3.0 intelligent libraries and apomediation

    CERN Document Server

    Kwanya, Tom; Underwood, Peter

    2015-01-01

    The emerging generation of research and academic library users expect the delivery of user-centered information services. 'Apomediation' refers to the supporting role librarians can give users by stepping in when users need help. Library 3.0 explores the ongoing debates on the "point oh” phenomenon and its impact on service delivery in libraries. This title analyses Library 3.0 and its potential in creating intelligent libraries capable of meeting contemporary needs, and the growing role of librarians as apomediators. Library 3.0 is divided into four chapters. The first chapter introduces and places the topic in context. The second chapter considers "point oh” libraries. The third chapter covers library 3.0 librarianship, while the final chapter explores ways libraries can move towards '3.0'.

  12. Cyclic AMP effectors in African trypanosomes revealed by genome-scale RNA interference library screening for resistance to the phosphodiesterase inhibitor CpdA.

    Science.gov (United States)

    Gould, Matthew K; Bachmaier, Sabine; Ali, Juma A M; Alsford, Sam; Tagoe, Daniel N A; Munday, Jane C; Schnaufer, Achim C; Horn, David; Boshart, Michael; de Koning, Harry P

    2013-10-01

    One of the most promising new targets for trypanocidal drugs to emerge in recent years is the cyclic AMP (cAMP) phosphodiesterase (PDE) activity encoded by TbrPDEB1 and TbrPDEB2. These genes were genetically confirmed as essential, and a high-affinity inhibitor, CpdA, displays potent antitrypanosomal activity. To identify effectors of the elevated cAMP levels resulting from CpdA action and, consequently, potential sites for adaptations giving resistance to PDE inhibitors, resistance to the drug was induced. Selection of mutagenized trypanosomes resulted in resistance to CpdA as well as cross-resistance to membrane-permeable cAMP analogues but not to currently used trypanocidal drugs. Resistance was not due to changes in cAMP levels or in PDEB genes. A second approach, a genome-wide RNA interference (RNAi) library screen, returned four genes giving resistance to CpdA upon knockdown. Validation by independent RNAi strategies confirmed resistance to CpdA and suggested a role for the identified cAMP Response Proteins (CARPs) in cAMP action. CARP1 is unique to kinetoplastid parasites and has predicted cyclic nucleotide binding-like domains, and RNAi repression resulted in >100-fold resistance. CARP2 and CARP4 are hypothetical conserved proteins associated with the eukaryotic flagellar proteome or with flagellar function, with an orthologue of CARP4 implicated in human disease. CARP3 is a hypothetical protein, unique to Trypanosoma. CARP1 to CARP4 likely represent components of a novel cAMP signaling pathway in the parasite. As cAMP metabolism is validated as a drug target in Trypanosoma brucei, cAMP effectors highly divergent from the mammalian host, such as CARP1, lend themselves to further pharmacological development.

  13. Construction of BAC Libraries from Flow-Sorted Chromosomes.

    Science.gov (United States)

    Šafář, Jan; Šimková, Hana; Doležel, Jaroslav

    2016-01-01

    Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

  14. Library Automation

    OpenAIRE

    Dhakne, B. N.; Giri, V. V.; Waghmode, S. S.

    2010-01-01

    New technologies library provides several new materials, media and mode of storing and communicating the information. Library Automation reduces the drudgery of repeated manual efforts in library routine. By use of library automation collection, Storage, Administration, Processing, Preservation and communication etc.

  15. A BAC-based physical map of the Drosophila buzzatii genome

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A.; Schein, JacquelineE.; de Jong, Pieter; Ruiz, Alfredo

    2005-03-18

    Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

  16. Final report on a pilot academic e-books project at Keio University Libraries : Potential for the scholarly use of digitized academic books

    Science.gov (United States)

    Shimada, Takashi

    This article reports on the results and significance of a pilot academic e-books project carried out at the Keio University Libraries for fiscal 2010 to 2012 to assess the viability of a new model of the libraries providing all the campuses with accesses to Japanese academic books digitized jointly with academic publishers and cooperative firms. It focuses on the experimental use of digitized books, highlighting the students’ attitudes and expectations towards e-books as found from surveys. Some major findings include the following. Users have a strong demand for digitized readings that are rather lookup-oriented than learning-oriented, with greater value placed on the functionalities of federated full-text searching, reading on a screen, and accessing the desired chapter direct from table of contents. They also want an online space in which to manage different forms of digitized learning resources. We investigated the potential of e-books and new type of textbooks as educational infrastructures based on the results of experiment. Japan’s university libraries should need to engage actively in the mass digitization of academic books to be adaptive to the change in the ways research, study and teaching are conducted. We plan to start a joint experiment with other university libraries to develop a practical model for the use of e-books.

  17. Novel methods for physical mapping of the human genome applied to the long arm of chromosome 5. Final report

    Energy Technology Data Exchange (ETDEWEB)

    McClelland, M.

    1991-12-01

    The object of our current grant is to develop novel methods for mapping of the human genome. The techniques to be assessed were: (1) three methods for the production of unique sequence clones from the region of interest; (2) novel methods for the production and separation of multi-megabase DNA fragments; (3) methods for the production of ``physical linking clones`` that contain rare restriction sites; (4) application of these methods and available resources to map the region of interest. Progress includes: In the first two years methods were developed for physical mapping and the production of arrayed clones; We have concentrated on developing rare- cleavage tools based or restriction endonucleases and methylases; We studied the effect of methylation on enzymes used for PFE mapping of the human genome; we characterized two new isoschizomers of rare cutting endonucleases; we developed a reliable way to produce partial digests of DNA in agarose plugs and applied it to the human genome; and we applied a method to double the apparent specificity of the ``rare-cutter`` endonucleases.

  18. Library Computing

    Science.gov (United States)

    Library Computing, 1985

    1985-01-01

    Special supplement to "Library Journal" and "School Library Journal" covers topics of interest to school, public, academic, and special libraries planning for automation: microcomputer use, readings in automation, online searching, databases of microcomputer software, public access to microcomputers, circulation, creating a…

  19. Digital Libraries

    CERN Document Server

    Papy, Fabrice

    2008-01-01

    Of vital interest to all librarians and information specialists, this book presents all aspects of the effects of digitization of today's and tomorrow's libraries. From social to technical issues, Digital Libraries includes chapters on the growth of the role of librarian, the reader experience, cataloging, search engines, OPAC, law, ergonomic studies, and the future of libraries.

  20. Biomedical Libraries

    Science.gov (United States)

    Pizer, Irwin H.

    1978-01-01

    Biomedical libraries are discussed as a distinct and specialized group of special libraries and their unique services and user interactions are described. The move toward professional standards, as evidenced by the Medical Library Association's new certification program, and the current state of development for a new section of IFLA established…

  1. DIGITAL ERA: UTILIZE OF CLOUD COMPUTING TECHNOLOGY IN DIGITAL LIBRARY

    OpenAIRE

    T. RAGHUNADHA REDDY

    2012-01-01

    With the purpose of applying cloud computing to digital library, the paper initially describes cloud computing and analyzes current status of cloud computing in digital library. Then it proposes the architecture of cloud computing in digital library and summarises the application of cloud computing in digital library. Finally the author brings out the future improvement in digital library using cloud computing technology.

  2. Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions

    Energy Technology Data Exchange (ETDEWEB)

    M.W. Fields; J.D. Wall; J. Keasling; J. Zhou

    2008-05-15

    We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a non-stretch probe (< 15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50mer probes or a 50-base stretch for 70mer probes had approximately 55% of the PM signal. Mismatches should be as close to the middle position of an oligonucleotide probe as possible to minimize cross-hybridization. Little cross-hybridization was observed for probes with a minimal binding free energy greater than -30 kcal/mol for 50mer probes or -40 kcal/mol for 70mer probes. Based on the

  3. Differential screening of mitochondrial cDNA libraries from male-fertile and cytoplasmic male-sterile sugar-beet reveals genome rearrangements at atp6 and atpA loci.

    Science.gov (United States)

    Xue, Y; Collin, S; Davies, D R; Thomas, C M

    1994-04-01

    As part of a strategy to define differences in genome organization and expression between cytoplasmic male-sterile (CMS) and male-fertile (MF) sugar-beet mitochondria, cDNA libraries from both mitochondrial genotypes were constructed. Preliminary screening with ribosomal RNA gene probes identified candidate cDNA clones corresponding to structural genes. In addition, reciprocal hybridization experiments were performed using labelled first-strand cDNA to identify uniquely transcribed sequences. One cDNA clone (pYC700) is unique to CMS mitochondria and is located upstream of the F0F1-ATPase subunit 6 gene (atp6). Another cDNA clone (pYC130), when used as a probe in northern hybridization analysis, revealed novel transcript profiles in CMS sugar-beet mitochondria. Sequence analysis of this cDNA showed strong homology with the F0F1-ATPase subunit alpha (atpA) coding sequences from several higher plants. The atp6 and atpA loci from each genotype were cloned and the genomic organization, DNA sequence and transcription of each locus was studied. Differences in the transcript profiles of each gene are a consequence of genomic rearrangements 5' to the coding sequence.

  4. Staff-less libraries - recent Danish public library experiences

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav

    2012-01-01

    The article reports on Danish experiences with staff-less public libraries in terms of local community characteristics, their use- visits and loans, characcteristics of their users in terms of sex, age and, finally, an analysis of critical success factors revealed......The article reports on Danish experiences with staff-less public libraries in terms of local community characteristics, their use- visits and loans, characcteristics of their users in terms of sex, age and, finally, an analysis of critical success factors revealed...

  5. Library Locations

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Carnegie Library of Pittsburgh locations including address, coordinates, phone number, square footage, and standard operating hours.

  6. America's Star Libraries: Top-Rated Libraries

    Science.gov (United States)

    Lance, Keith Curry; Lyons, Ray

    2009-01-01

    "Library Journal"'s national rating of public libraries, the "LJ" Index of Public Library Service 2009, Round 2, identifies 258 "star" libraries. Created by Keith Curry Lance and Ray Lyons and based on 2007 data from the IMLS, it rates 7,268 public libraries. The top libraries in each group get five, four, or three stars. All included libraries,…

  7. America's Star Libraries: Top-Rated Libraries

    Science.gov (United States)

    Lance, Keith Curry; Lyons, Ray

    2009-01-01

    "Library Journal"'s national rating of public libraries, the "LJ" Index of Public Library Service 2009, Round 2, identifies 258 "star" libraries. Created by Keith Curry Lance and Ray Lyons and based on 2007 data from the IMLS, it rates 7,268 public libraries. The top libraries in each group get five, four, or three stars. All included libraries,…

  8. NSUF Irradiated Materials Library

    Energy Technology Data Exchange (ETDEWEB)

    Cole, James Irvin [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    The Nuclear Science User Facilities has been in the process of establishing an innovative Irradiated Materials Library concept for maximizing the value of previous and on-going materials and nuclear fuels irradiation test campaigns, including utilization of real-world components retrieved from current and decommissioned reactors. When the ATR national scientific user facility was established in 2007 one of the goals of the program was to establish a library of irradiated samples for users to access and conduct research through competitively reviewed proposal process. As part of the initial effort, staff at the user facility identified legacy materials from previous programs that are still being stored in laboratories and hot-cell facilities at the INL. In addition other materials of interest were identified that are being stored outside the INL that the current owners have volunteered to enter into the library. Finally, over the course of the last several years, the ATR NSUF has irradiated more than 3500 specimens as part of NSUF competitively awarded research projects. The Logistics of managing this large inventory of highly radioactive poses unique challenges. This document will describe materials in the library, outline the policy for accessing these materials and put forth a strategy for making new additions to the library as well as establishing guidelines for minimum pedigree needed to be included in the library to limit the amount of material stored indefinitely without identified value.

  9. Library Use

    DEFF Research Database (Denmark)

    Konzack, Lars

    2012-01-01

    A seminar paper about a survey of role-playing games in public libraries combined with three cases and a presentation of a model.......A seminar paper about a survey of role-playing games in public libraries combined with three cases and a presentation of a model....

  10. Library Research.

    Science.gov (United States)

    Wright, Nancy Kirkpatrick

    This workbook, designed for a Library Research course at Yavapai College, provides 15 lessons in advanced library reference skills. Each lesson provides explanatory text and reinforcement exercises. After Lesson I introduces specialized dictionaries and encyclopedias (e.g., for foreign languages, medicine, music, economics, social sciences, and…

  11. Privatizing Libraries

    Science.gov (United States)

    Jerrard, Jane; Bolt, Nancy; Strege, Karen

    2012-01-01

    This timely special report from ALA Editions provides a succinct but comprehensive overview of the "privatization" of public libraries. It provides a history of the trend of local and state governments privatizing public services and assets, and then examines the history of public library privatization right up to the California…

  12. Privatizing Libraries

    Science.gov (United States)

    Jerrard, Jane; Bolt, Nancy; Strege, Karen

    2012-01-01

    This timely special report from ALA Editions provides a succinct but comprehensive overview of the "privatization" of public libraries. It provides a history of the trend of local and state governments privatizing public services and assets, and then examines the history of public library privatization right up to the California legislation…

  13. Repetitive Genomic Elements in a European Corn Borer, Ostrinia nubilalis, BAC Library were Indicated by BAC End Sequencing and Development of Sequence Tag Site Markers: Implications for Lepidopteran Genomic Research

    Science.gov (United States)

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia, and a model system for insect olfaction and speciation. A bacterial artificial chromosome (BAC) library constructed for O. nubilalis contains 36,864 clones with estim...

  14. Plaque lifts of the citrus genomic DNA library bloted with the MADS-box genes%柑桔基因组DNA的MADS盒基因噬菌斑原位杂交

    Institute of Scientific and Technical Information of China (English)

    刘春玲; 林伯年; 徐昌杰; 陈大明

    2001-01-01

    以大三岛脐橙基因组DNA为材料,用拟南芥AP1和矮牵牛FBP1的混合质粒DNA为模板,采用随机引物法标记探针,对柑桔基因组DNA文库进行噬菌斑原位杂交。结果表明柑桔基因组中也存在控制花特异表达的MADS盒基因。%Citrus genomic DNA library was bloted with the AP1 and FBP1 mixed MADS-box genes probe labeled by random primer method. The result shows that a large MADS-box gene family exists in citrus.

  15. future of research libraries

    CERN Document Server

    Naryandas, Narakesari; Kindström, Daniel

    2014-01-01

    Research libraries have been an integral part of the scholarly communication system since that system emerged in its present form. They now face a period of unprecedentedly drastic and rapid change. This is caused, first and foremost, by the migration of much scholarly material to digital formats, raising the question of the future purpose of the 'library space'. Together with this come transfigurational changes to the communication change of recorded information, with the roles of authors , publishers, database producers and librarians and archivists all in a state of flux. Finally, new forms

  16. Multiple Myeloma Genomics: A Systematic Review.

    Science.gov (United States)

    Weaver, Casey J; Tariman, Joseph D

    2017-08-01

    This integrative review describes the genomic variants that have been found to be associated with poor prognosis in patients diagnosed with multiple myeloma (MM). Second, it identifies MM genetic and genomic changes using next-generation sequencing, specifically whole-genome sequencing or exome sequencing. A search for peer-reviewed articles through PubMed, EBSCOhost, and DePaul WorldCat Libraries Worldwide yielded 33 articles that were included in the final analysis. The most commonly reported genetic changes were KRAS, NRAS, TP53, FAM46C, BRAF, DIS3, ATM, and CCND1. These genetic changes play a role in the pathogenesis of MM, prognostication, and therapeutic targets for novel therapies. MM genetics and genomics are expanding rapidly; oncology nurse clinicians must have basic competencies in genetics and genomics to help patients understand the complexities of genetic and genomic alterations and be able to refer patients to appropriate genomic professionals if needed. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Academic Libraries

    Science.gov (United States)

    Library Journal, 1970

    1970-01-01

    Building data is given for the following academic libraries: (1) Rosary College, River Forest, Illinois; (2) Abilene Christian College, Abilene, Texas; (3) University of California, San Diego, La Jolla, California. (MF)

  18. Toward functional genomics in bacteria: Analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus

    OpenAIRE

    Rondon, Michelle R.; Sandra J Raffel; Goodman, Robert M.; Handelsman, Jo

    1999-01-01

    As the study of microbes moves into the era of functional genomics, there is an increasing need for molecular tools for analysis of a wide diversity of microorganisms. Currently, biological study of many prokaryotes of agricultural, medical, and fundamental scientific interest is limited by the lack of adequate genetic tools. We report the application of the bacterial artificial chromosome (BAC) vector to prokaryotic biology as a powerful approach to address this need. We constructed a BAC li...

  19. From Laboratory to Library: The History of Wayne State University's Education Library

    Science.gov (United States)

    Alteri, Suzan A.

    2009-01-01

    The Education Library at Wayne State University has a long and storied history. From its beginning at the Detroit Normal School to its final merger with the general library, the Education Library has been at the heart of not only Wayne State University, but also in the development of the College of Education. This paper chronicles the history of…

  20. America's Star Libraries

    Science.gov (United States)

    Lyons, Ray; Lance, Keith Curry

    2009-01-01

    "Library Journal"'s new national rating of public libraries, the "LJ" Index of Public Library Service, identifies 256 "star" libraries. It rates 7,115 public libraries. The top libraries in each group get five, four, or three Michelin guide-like stars. All included libraries, stars or not, can use their scores to learn from their peers and improve…

  1. America's Star Libraries

    Science.gov (United States)

    Lyons, Ray; Lance, Keith Curry

    2009-01-01

    "Library Journal"'s new national rating of public libraries, the "LJ" Index of Public Library Service, identifies 256 "star" libraries. It rates 7,115 public libraries. The top libraries in each group get five, four, or three Michelin guide-like stars. All included libraries, stars or not, can use their scores to learn from their peers and improve…

  2. COMBINATORIAL LIBRARIES

    DEFF Research Database (Denmark)

    1997-01-01

    The invention provides a method for the production of a combinatorial library of compound of general formula (I) using solid phase methodologies. The cleavage of the array of immobilised compounds of the phthalimido type from the solid support matrix is accomplished by using an array of dinucleop......The invention provides a method for the production of a combinatorial library of compound of general formula (I) using solid phase methodologies. The cleavage of the array of immobilised compounds of the phthalimido type from the solid support matrix is accomplished by using an array...... of dinucleophiles, e.g. hydrazines (hydrazinolysis) or N-hydroxylamines, whereby a combinatorial dimension is introduced in the cleavage step. The invention also provides a compound library....

  3. Winds of change: research libraries

    DEFF Research Database (Denmark)

    Bang, Tove; Harbo, Karen

    2002-01-01

    The article takes its starting point in new trends and paradigm shifts in scholarly research methods and discusses how research libraries must act in relation to this. Various innovative initiatives at LASB are described, especially within the areas of electronic dissemination and presentation...... at ASB and a software company. LASB is positive towards and will continue working with this method. Finally the investment in future library services is discussed and a tangible offer is put into perspective: electronic reference services...

  4. Standards for the academic veterinary medical library.

    Science.gov (United States)

    Murphy, Sarah Anne; Bedard, Martha A; Crawley-Low, Jill; Fagen, Diane; Jette, Jean-Paul

    2005-01-01

    The Standards Committee of the Veterinary Medical Libraries Section was appointed in May 2000 and charged to create standards for the ideal academic veterinary medical library, written from the perspective of veterinary medical librarians. The resulting Standards for the Academic Veterinary Medical Library were approved by members of the Veterinary Medical Libraries Section during MLA '03 in San Diego, California. The standards were approved by Section Council in April 2005 and received final approval from the Board of Directors of the Medical Library Association during MLA '04 in Washington, DC.

  5. Library rooms or Library halls

    Directory of Open Access Journals (Sweden)

    Alfredo Serrai

    2013-12-01

    Full Text Available Library Halls, understood as Renaissance and Baroque architectural creations, along with the furnishings and decorations, accomplish a cognitive task and serve to transmit knowledge. The design of these spaces based on the idea that they should reflect the merits and content of the collections housed within them, in order to prepare the mind of the reader to respect and admire the volumes. In accordance with this principle, in the fifteenth century library rooms had a basilican shape, with two or three naves, like churches, reflecting thus the spiritual value of the books contained there. Next to that inspiring function, library rooms had also the task of representing the entire logical and conceptual universe of human knowledge in a figurative way, including for this purpose also the and Kunst- und Wunderkammern, namely the collections of natural, artficial objects, and works of art. The importance of library rooms and their function was understood already in the early decades of the seventeenth century, as underlined in the treatise, Musei sive Bibliothecae tam privatae quam publicae Extructio, Instructio, Cura, Usus, written by the Jesuit Claude Clément and published in 1635. Almost the entire volume is dedicated to the decoration and ornamentation of the Saloni, and the function of the library is identified exclusively with the preservation and decoration of the collection, neglecting more specifically bibliographic aspects or those connected to library science. The architectural structure of the Saloni was destined to change in relation to two factors, namely the form of books, and the sources of light. As a consequence, from the end of the sixteenth century – or perhaps even before if one considers the fragments of the Library of Urbino belonging to Federico da Montefeltro – shelves and cabinets have been placed no longer in the center of the room, but were set against the walls. This new disposition of the furniture, surmounted by

  6. DIGITAL ERA: UTILIZE OF CLOUD COMPUTING TECHNOLOGY IN DIGITAL LIBRARY

    Directory of Open Access Journals (Sweden)

    T. RAGHUNADHA REDDY

    2012-09-01

    Full Text Available With the purpose of applying cloud computing to digital library, the paper initially describes cloud computing and analyzes current status of cloud computing in digital library. Then it proposes the architecture of cloud computing in digital library and summarises the application of cloud computing in digital library. Finally the author brings out the future improvement in digital library using cloud computing technology.

  7. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability.

    Science.gov (United States)

    Saxena, Swati; Singh, Archana; Archak, Sunil; Behera, Tushar K; John, Joseph K; Meshram, Sudhir U; Gaikwad, Ambika B

    2015-01-01

    Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.

  8. 论数字图书馆的表现形式%On the Form of Expression of Digital Libraries

    Institute of Scientific and Technical Information of China (English)

    李艳菊; 李艳秋

    2001-01-01

    Two main forms of digital libraries are proposed, that is, the digital library based on digitizing the current collections of traditional libraries and the network library constructed by using modern information technologies directly. The advantages and disadvantages of these two kinds of digital libraries are analyzed. Finally, the paper presents some ideas of its own on the construction of digital libraries in China.

  9. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  10. Primers for the Amplification of the Circular Chloroplast DNA from the A-genome Group of Cultivated Cotton

    Institute of Scientific and Technical Information of China (English)

    IBRAHIM Rashid Ismael Hag; AZUMA Jun-Ichi; SAKAMOTO Masahiro

    2008-01-01

    @@ The availability of the plastid genome sequences is one of the bases for comparative,functional,and structural genomic studies of plastid-containing living organisms,in addition to the application of plastid genetic engineering technology.The past efforts to sequence plastid genomes involve complicated preparation protocols.One procedure starts with the isolation of plastids,which was tiresome and time wasting that followed by a second step to extract plastid DNA from the isolated plastids,then finally the build up of plasmid or bacterial artificial chromosome (BAC) library.

  11. Library news

    CERN Multimedia

    CERN Library

    2010-01-01

    The CERN Library has been providing electronic access to the "Techniques de l'Ingénieur" database for the past 8 months. As a reminder, this is a multidisciplinary database of over 4000 technical and scientific articles in French, covering a broad range of topics such as mechanical engineering, safety, electronics and the environment. In a few simple steps, you can create your own account, select the types of documents you are interested in and configure your settings so as to receive alerts when articles in your field of activity are published. You can now access this resource from outside CERN using the "remote access to electronic resources" service. Further information is available here. Direct access to the database. Remote access to electronic resources. If you have any questions or comments, don't hesitate to contact us at: library.desk@cern.ch.

  12. Preparation of high molecular weight gDNA and bacterial artificial chromosome (BAC) libraries in plants.

    Science.gov (United States)

    Biradar, Siddanagouda S; Nie, Xiaojun; Feng, Kewei; Weining, Song

    2014-01-01

    Bacterial artificial chromosome (BAC) libraries are extremely valuable large-insert DNA libraries for physical mapping, positional cloning, comparative genomic analysis, complete genome sequencing, and evolutionary studies. Due to their stability and relative simplicity BAC libraries are most preferred over other approaches for cloning large genomic DNA fragments for large-insert libraries. Isolation of intact high molecular weight (HMW) DNA is a critical step underlying the success of large-insert genomic DNA library construction. It requires the isolation of purified nuclei, embedding them into LMP agarose plugs, restriction digestion of the plugs, and quite often size selection using PFGE and electro-elution of insert DNA. The construction of BAC libraries is complex and challenging for most molecular laboratories. To facilitate the construction of BAC libraries, we present a step-by-step protocol for isolation of HMW DNA and construction of plant BAC libraries.

  13. Library Benchmarking

    Directory of Open Access Journals (Sweden)

    Wiji Suwarno

    2017-02-01

    Full Text Available The term benchmarking has been encountered in the implementation of total quality (TQM or in Indonesian termed holistic quality management because benchmarking is a tool to look for ideas or learn from the library. Benchmarking is a processof measuring and comparing for continuous business process of systematic and continuous measurement, the process of measuring and comparing for continuous business process of an organization to get information that can help these organization improve their performance efforts.

  14. Controlling our destinies: Historical, philosophical, social and ethical perspectives on the Human Genome Project: Final report, July 1, 1995-June 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Sloan, P.R.

    1996-09-25

    This report briefly describes the efforts by the organizing committee in preparation for the conference entitled Controlling Our Destinies: Historical, Philosophical, Social, and Ethical Perspectives on the Human Genome Project. The conference was held October 5-8, 1995.

  15. Methods for combinatorial and parallel library design.

    Science.gov (United States)

    Schnur, Dora M; Beno, Brett R; Tebben, Andrew J; Cavallaro, Cullen

    2011-01-01

    Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.

  16. Dormitory libraries: libraries in dormitories

    Directory of Open Access Journals (Sweden)

    Peter Pavletič

    2004-01-01

    Full Text Available Dormitory libries are not justly treated in Slovenia. They have a double purpose: to develop student literacy, especially reading, critical and creative competence and, moreover, to provide students with opportunities for learning and active spending of free-time. This is made possible by means of a good collection of expertly arranged library material, which is regulary updated and presented to its users, both students and tutors alike. A questionnaire has helped us to find out that libraries in secondary school dormitories carry out their work rather successfully, especially from the viewpoint of poor facilities. The major problems are, nevertheless, the appropriate qualifications of those who fill the posts of librarian and low financial resources. Therefore, such activities should be thoroughly analysed and reconsidered in terms of possible effective solutions, if we want to at least maintain them, let alone develop them.

  17. Measuring library performance principles and techniques

    CERN Document Server

    Brophy, Peter

    2006-01-01

    Provide an account of thinking and research on the evaluation of library services. Illustrated throughout with examples across the different library sectors, this book is structured to focus on the intended service user, then to look at service management and the building blocks of services, and finally to draw together these strands.

  18. How to Evaluate Integrated Library Automation Systems.

    Science.gov (United States)

    Powell, James R.; Slach, June E.

    1985-01-01

    This paper describes methodology used in compiling a list of candidate integrated library automation systems at a corporate technical library. Priorities for automation, identification of candidate systems, the filtering process, information for suppliers, software and hardware considerations, on-site evaluations, and final system selection are…

  19. Library of Alexandria's New Web Site

    Directory of Open Access Journals (Sweden)

    2004-06-01

    Full Text Available A review for the new version of Library of Alexandria web site which lunched on May 2004, the review deals with general introduction to the new version , then the main 6 section of the site , and show some features of the new site, and finally talk in concentration about the library catalog on the internet and its search capabilities.

  20. Staff-less libraries - recent Danish public library experiences

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav

    2012-01-01

    The article reports on Danish experiences with staff-less public libraries in terms of local community characteristics, their use- visits and loans, characcteristics of their users in terms of sex, age and, finally, an analysis of critical success factors revealed...

  1. Libraries for users services in academic libraries

    CERN Document Server

    Alvite, Luisa

    2010-01-01

    This book reviews the quality and evolution of academic library services. It revises service trends offered by academic libraries and the challenge of enhancing traditional ones such as: catalogues, repositories and digital collections, learning resources centres, virtual reference services, information literacy and 2.0 tools.studies the role of the university library in the new educational environment of higher educationrethinks libraries in academic contextredefines roles for academic libraries

  2. EST sequencing and fosmid library construction in a non-model moth, Mamestra brassicae, for comparative mapping.

    Science.gov (United States)

    Kamimura, Manabu; Tateishi, Ken; Tanaka-Okuyama, Makiko; Okabe, Takuya; Shibata, Fukashi; Sahara, Ken; Yasukochi, Yuji

    2012-11-01

    Genome data are useful for both basic and applied research; however, it is difficult to carry out large-scale genome analyses using species with limited genetic or genomic resources. Here, we describe a cost-effective method to analyze the genome of a non-model species, using the cabbage moth, Mamestra brassicae (Lepidoptera: Noctuidae). First, we conducted expression sequence tag (EST) analysis. In this analysis, we performed PCR-based prescreening of a non-normalized embryonic cDNA library to eliminate already sequenced cDNAs from further sequencing, which significantly increased the percentage of unique genes. Next, we constructed a fosmid library of M. brassicae and isolated 120 clones containing 119 putative single copy genes by PCR-based screening with primer sets designed from the ESTs. Finally, we showed that the isolated fosmid clones could be used as probes for multicolor fluorescence in situ hybridization (FISH) analysis against an M. brassicae chromosome and confirmed conserved gene order between M. brassicae and the silkworm, Bombyx mori. Thus, we developed new genomic resources for comparative genome analysis in M. brassicae using robust and relatively low cost methods that can be applied to any non-model organism.

  3. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  4. 黑斑狗鱼部分基因组文库构建和微卫星位点的筛选%Construction Fractional Genomic Libraries and Screening Microsatellites DNA of Esox reieherti Dybowski

    Institute of Scientific and Technical Information of China (English)

    王洪哲; 殷倩茜; 冯志纲; 李大宇; 孙效文; 李婵

    2008-01-01

    采用磁珠富集与放射性杂交相结合的方法开发黑斑狗鱼(Esox reieherti Dybowski)基因组微卫星资源.基因组DNA经Sau 3A Ⅰ限制性内切酶消化后,选取400-900bp的片段进行PCR全基因组扩增,并利用生物素标记的(CA)12、 (GA)12探针进行微卫星片段的富集.将得到的片段与pGEM-T载体连接后转入DH5α大肠杆菌中,然后利用γ-32P标记的放射性同位素探针进行第二次杂交.结果,共获得微卫星基因组文库1600个菌,杂交前菌落PCR检测阳性克隆率为90.91%;杂交后得到的阳性克隆为1300个,占87.25%.从中挑出196个进行测序,192(97.96%)个含有微卫星序列.在得到的微卫星序列中,重复单元除CA/GT、 GA/CT外,还观察到单碱基、四碱基、五碱基重复单元.根据侧翼序列应用引物设计软件Primer Premier 5.0设计引物70对,选择合成32对,通过优化PCR反应条件,结果有28对引物可扩增出清晰可重复的目的条带.本研究旨在对黑斑狗鱼基因组资源的开发利用起到一定的促进作用,并为黑斑狗鱼养殖品系的优化、遗传多样性的检测及遗传图谱的构建等奠定基础.%Esox reieherti Dybowsk genomic microsatellites were developed by using enrichment protocols combined with radioactive hybridization protocol. Four hundred to nine hundred base pair fragments were selected for the whole genome. DNA PCR amplification after digestion with restriction endonuclease Sau 3A Ⅰ, and (CA)12, (GA)12 probes marked with biotin were used for microsatellite DNA enrichment. The product fragments were connected with carrier pGEM-T and transferred into DHSα Escherichia coli competent cells, and radioactive isotope probes marked with γ-32 P were used for the second hybridization. As a result, a total of 1600 bacteria were obtained in the microsatellite genomic libraries, positive clones accounted for 90.91% before hybridization and 81.25% after hybridization, amounting to 1300. One hundred and

  5. Transcribed sequences in the human genome to be held in San Francisco, November 7 and 8, 1992. Final report, September 1, 1992--August 31, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Gardiner, K.

    1993-11-01

    The Second International Workshop on the Identification of Transcribed Sequences was held in San Francisco on November 7--8, 1992. The purpose of the workshop was to discuss and evaluate techniques for developing a complete transcriptional map of the human genome. Such a map requires the positions, sequences, and expression patterns of all genes. This goal is being approached from two different directions, each with strengths and weaknesses. One method is to identify the transcribed sequences from genomic DNA of a given region; the other is to systematically sequence and map cDNAs. The cDNA approach yields sequence information rapidly, but mapping each cDNA is a technical challenge. In the first approach, the map locations of genomic sequences are known at the outset, and the challenge is to identify exons. The efficient construction of a transcriptional map will require a diverse array of techniques.

  6. Renewing library Web sites CMS at libraries

    CERN Document Server

    Vida, A

    2006-01-01

    The use of the Internet has a ten-year history in Hungary. In the beginning, users were surfing on textual Web sites with the browser Lynx (1991), then a range of graphic browsers appeared: Mosaic (1993) , Netscape (1994), and finally Internet Explorer (1995). More and more institutions, including libraries decided to enter the World Wide Web with their own homepage. The past ten years have brought enormous changes and new requirements in the way that institutional homepages are designed. This article offers an overview of the development phases of Web sites, presents the new tools necessary for the state-of-the-art design and gives advice on their up-to-date maintenance.

  7. Marketing the Virtual Library

    Science.gov (United States)

    Fagan, Jody Condit

    2009-01-01

    Far more people are familiar with their local public or college library facility than their library's website and online resources. In fact, according to a recent survey, 96% of Americans said they had visited a library in person, but less than one-third have visited their online library. Since everyone agrees that online library resources are…

  8. National Academy of Sciences and Academy of Sciences of the USSR workshop on structure of the eucaryotic genome and regulation of its expression. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-31

    This report provides a brief overview of the Workshop on Structure of the Eukaryotic Genome and Regulation of its Expression held in Tbilisi, Georgia, USSR. The report describes the presentations made at the meeting but also goes on to describe the state of molecular biology and genetics research in the Soviet Union and makes recommendations on how to improve future such meetings.

  9. INFORMATION TECHNOLOGY FOR CHINESE STUDIES EXPERIENCE AT THE EAST ASIA LIBRARY UNIVERSITY OF WASHINGTON

    Institute of Scientific and Technical Information of China (English)

    Yeen-meiWn

    1994-01-01

    The East Asia Library(EAZ), following the leadership of the University of Washington(UW) Libraries and the trends of the library world, has made great progress in library automation. Yet the presence of non-roman scripts, or CJK characters, in the library's electronic resources in an environment dominated by phonetic languages makes automation of East Asian Libraries more challenging than libraries which use only roman scripts. This paper first provides a general overview of current information technology. It then offers a brief introduction to the UW Library automation and how the East Asia Library handles automation Finally, it presents the experience of the information technology in Chinese studies at EAL.

  10. Modification of the GS LT Paired-end Library Protocol for Constructing Longer Insert Size Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Peng, Ze; Hamilton, Matthew; Ting, Sara; Tu, Hank; Goltsman, Eugene; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang

    2008-05-22

    Paired-end library sequencing has been proven useful in scaffold construction during de novo assembly of genomic sequences. The ability of generating mate pairs with 8 Kb or greater insert sizes is especially important for genomes containing long repeats. While the current 454 GS LT Paired-end library preparation protocol can successfully construct libraries with 3 Kb insert size, it fails to generate longer insert sizes because the protocol is optimized to purify shorter fragments. We have made several changes in the protocol in order to increase the fragment length. These changes include the use of Promega column to increase the yield of large size DNA fragments, two gel purification steps to remove contaminated short fragments, and a large reaction volume in the circularization step to decrease the formation of chimeras. We have also made additional changes in the protocol to increase the overall quality of the libraries. The quality of the libraries are measured by a set of metrics, which include levels of redundant reads, linker positive, linker negative, half linker reads, and driver DNA contamination, and read length distribution, were used to measure the primary quality of these libraries. We have also assessed the quality of the resulted mate pairs including levels of chimera, distribution of insert sizes, and genome coverage after the assemblies are completed. Our data indicated that all these changes have improved the quality of the longer insert size libraries.

  11. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.

    Science.gov (United States)

    Birkel, Garrett W; Ghosh, Amit; Kumar, Vinay S; Weaver, Daniel; Ando, David; Backman, Tyler W H; Arkin, Adam P; Keasling, Jay D; Martín, Héctor García

    2017-04-05

    Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell. In addition to flux analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed. The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes and leveraging other -omics data for the scientific study of cellular metabolism and bioengineering purposes. Firstly, it presents a complete toolbox for simultaneously performing two different types of flux analysis that are typically disjoint: Flux Balance Analysis and (13)C Metabolic Flux Analysis. Moreover, it introduces the capability to use (13)C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale (13)C Metabolic Flux Analysis (2S-(13)C MFA). In addition, the library includes a demonstration of a method that uses proteomics data to produce actionable insights to increase biofuel production. Finally, the use of the jQMM library is illustrated through the addition of several Jupyter notebook demonstration files that enhance reproducibility and provide the capability to be adapted to the user's specific needs. jQMM will facilitate the design and metabolic engineering of organisms for biofuels and other chemicals, as well as investigations of cellular metabolism and leveraging -omics data. As an open source software project, we hope it

  12. CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains

    Directory of Open Access Journals (Sweden)

    Emily Roggenkamp

    2017-09-01

    Full Text Available Saccharomyces cerevisiae continues to serve as a powerful model system for both basic biological research and industrial application. The development of genome-wide collections of individually manipulated strains (libraries has allowed for high-throughput genetic screens and an emerging global view of this single-celled Eukaryote. The success of strain construction has relied on the innate ability of budding yeast to accept foreign DNA and perform homologous recombination, allowing for efficient plasmid construction (in vivo and integration of desired sequences into the genome. The development of molecular toolkits and “integration cassettes” have provided fungal systems with a collection of strategies for tagging, deleting, or over-expressing target genes; typically, these consist of a C-terminal tag (epitope or fluorescent protein, a universal terminator sequence, and a selectable marker cassette to allow for convenient screening. However, there are logistical and technical obstacles to using these traditional genetic modules for complex strain construction (manipulation of many genomic targets in a single cell or for the generation of entire genome-wide libraries. The recent introduction of the CRISPR/Cas gene editing technology has provided a powerful methodology for multiplexed editing in many biological systems including yeast. We have developed four distinct uses of the CRISPR biotechnology to generate yeast strains that utilizes the conversion of existing, commonly-used yeast libraries or strains. We present Cas9-based, marker-less methodologies for (i N-terminal tagging, (ii C-terminally tagging yeast genes with 18 unique fusions, (iii conversion of fluorescently-tagged strains into newly engineered (or codon optimized variants, and finally, (iv use of a Cas9 “gene drive” system to rapidly achieve a homozygous state for a hypomorphic query allele in a diploid strain. These CRISPR-based methods demonstrate use of targeting

  13. Agricultural Libraries and Information.

    Science.gov (United States)

    Russell, Keith W., Ed.; Pisa, Maria G., Ed.

    1990-01-01

    Eleven articles address issues relating to agricultural libraries and information, including background on agricultural libraries and information, trend management, document delivery, reference services, user needs and library services, collection development, technologies for international information management, information sources,…

  14. Italian library associations

    Directory of Open Access Journals (Sweden)

    Ksenija Petaros-Kmetec

    2004-01-01

    Full Text Available In Italy, five library associations of national significance function at present. There are special associations of ecclesiastic libraries, prison libraries, architecture libraries and libraries with artistic material. The role of the general national association, covering all types of libraries including documentation centres, is played by the Italian Library Association. It strive for the development of a contemporary Italian library system comparable to international standards, monitors library legislation, promotes education for librarians and keeps the librarians and the broader public informed about the importance of libraries and librarianship for society. The activity and efforts of the association are reflected through their website offering much information and links to similar sites. ILA presents and realises its activities for both, the librarians and the public users. A great deal of actions promoting libraries and the Library Association might be interesting for Slovenia and perhaps transferred to our environment.

  15. Construction and characterization of a normalized whole-life-cycle cDNA library of rice

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A cDNA library with genomic complete coverage is a powerful tool for functional genomic studies. For studying the functions of rice genes on a large scale, a normalized whole-life-cycle cDNA library is constructed based on the strategy of saturation hybridization with genomic DNA using rice cultivar Minghui 63, an elite restorer line for a number of rice hybrids that are widely cultivated in China. This library consists of cDNA from 15 directionally cloned cDNA libraries constructed with different tissues from 9 developmental stages. For normalization, the denatured plasmids purified from the 15 directionally cloned libraries are mixed and hybridized with saturated genomic DNA labeled with magnetic beads in two complementary systems. Well-matched plasmids are captured from the hybridized genomic DNA and electroporated into competent DH10B E. coli for construction of the normalized whole-life-cycle cDNA library. This library consists of 62000 clones with an average insert length about 1.4 kb. Inverse Northern blotting shows that this cDNA library included many rarely expressed genes and tissue-specific genes. Sequencing of 10750 cDNA clones of this library reveals 6399 unique ESTs (expressed sequence tags), indicating that the non-redundancy of the library is about 59.5%. This library has been used to make cDNA microarrays for functional genomic studies.

  16. Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design.

    Science.gov (United States)

    Foight, Glenna Wink; Chen, T Scott; Richman, Daniel; Keating, Amy E

    2017-01-01

    Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.

  17. Final Report for Grant No. DE-FG02-98ER62583 ''Functional Analysis of the Genome Sequence of Deinococcus radiodurans''

    Energy Technology Data Exchange (ETDEWEB)

    Michael J. Daly, Ph.D.

    2003-10-15

    Extremophiles are nearly always defined with singular characteristics that allow existence within a singular extreme environment. The bacterium Deinococcus radiodurans qualifies as a polyextremeophile, showing remarkable resistance to a range of damage caused by ionizing radiation, dessication, ultraviolet radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is most famous for its extreme resistance to ionizing radiation; it not only can grow continuously in the presence of chronic radiation (6,000 rad per hour), but it can survive acute exposures to gamma radiation that exceed 1,500,000 rads without lethality or induced mutation. These characteristics were the impetus for sequencing its genome. We completed an extensive comparative sequence analysis of the Deinococcus radiodurans (strain R1) genome. Deinococcus is the first representative with a completely sequenced genome from a bacterial branch of extremophiles - the Thermus/Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, support that it is a very ancient branch localized in the vicinity of the bacterial tree root. Distinctive features of the Deinoccoccus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to a collection of Clusters of Orthologous Groups of proteins (COGs). Analysis of paralogs in Deinococcus has revealed some unique protein families. In addition, specific expansions of several protein families including phosphatases, proteases, acyl transferases and MutT pyrophosphohydrolases, were detected. Genes that potentially affect DNA repair and recombination were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes, and are not present in other bacteria. For example, three proteins homologous to plant desiccation-resistance proteins were identified and these are particularly interesting

  18. Digital Library Activities in Europe: A Brief Overview

    Directory of Open Access Journals (Sweden)

    Jia Liu

    2005-06-01

    Full Text Available The article is a brief overview of the digital library activities happening in the last decade in Europe. At first the definitions of the digital library was discussed. Then in the main part of the article the programs and projects on the digital library taking place in Europe are described briefly at three levels, which are digital library activities across Europe, national digital library activities and local digital library activities. In addition to the programs and projects several examples of the conferences and institutions in the field are also given in the article. Finally some conclusions are drawn based on the description above.

  19. 77 FR 35946 - Notice of Availability for the Final Environmental Impact Statement/Environmental Impact Report...

    Science.gov (United States)

    2012-06-15

    ... Building Los Angeles City Library, San Pedro Branch Los Angeles City Library, Wilmington Branch Los Angeles Public Library, Central Branch Questions or requests concerning the Final EIS/EIR should be directed...

  20. Transposase mediated construction of RNA-seq libraries.

    Science.gov (United States)

    Gertz, Jason; Varley, Katherine E; Davis, Nicholas S; Baas, Bradley J; Goryshin, Igor Y; Vaidyanathan, Ramesh; Kuersten, Scott; Myers, Richard M

    2012-01-01

    RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (∼1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The directional RNA-seq libraries maintain the same quality as the nondirectional libraries, while showing a high degree of strand specificity, such that 99.5% of reads map to the expected genomic strand. Each transposon-based library construction method performed well when compared with standard RNA-seq library construction methods with regard to complexity of the libraries, correlation between biological replicates, and the percentage of reads that align to the genome as well as exons. Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology.

  1. Mixture-based combinatorial libraries from small individual peptide libraries: a case study on α1-antitrypsin deficiency.

    Science.gov (United States)

    Chang, Yi-Pin; Chu, Yen-Ho

    2014-05-16

    The design, synthesis and screening of diversity-oriented peptide libraries using a "libraries from libraries" strategy for the development of inhibitors of α1-antitrypsin deficiency are described. The major buttress of the biochemical approach presented here is the use of well-established solid-phase split-and-mix method for the generation of mixture-based libraries. The combinatorial technique iterative deconvolution was employed for library screening. While molecular diversity is the general consideration of combinatorial libraries, exquisite design through systematic screening of small individual libraries is a prerequisite for effective library screening and can avoid potential problems in some cases. This review will also illustrate how large peptide libraries were designed, as well as how a conformation-sensitive assay was developed based on the mechanism of the conformational disease. Finally, the combinatorially selected peptide inhibitor capable of blocking abnormal protein aggregation will be characterized by biophysical, cellular and computational methods.

  2. General Maister's Library in the University of Maribor Library: Gaining and Preservation of the General Maister's Private Library in the University of Maribor Library

    Directory of Open Access Journals (Sweden)

    Vlasta Stavbar

    2015-12-01

    Full Text Available Rudolf Maister’s book legacy, which is kept in the University of Maribor Library, is the complete legacy of the Maister’s private book collection– the “maistirana”. The Maister’s Library is in the University of Maribor Library possession since 1998, when General Maister’s heirs and the Library signed the deed of donation. 5.945 units of library materials present a special collection, which is divided from the regular library holdings and is kept in a specially designed room. General Maister’s Library is an exception in the University of Maribor Library, since the general practice of libraries is not an exclusive maintenance of the provenience principle and of the original organisation. Because the Maister’s Library consists of materials that are important when researching the Slovene literary and cultural past, it only seems reasonably to strive for the authentic organisation and preserving the library as one integral whole.In order to understand the meaning and the importance of this special library collection for the Slovene cultural heritage, we have to highlight Rudolf Maister as a passionate book lover and as the owner of one of the greatest and the most beautiful private libraries in Slovenia. General Maister started collecting books and organising his collection back in 1912 in Ljubljana; the collection was rearranged thoroughly during the time he was in Maribor; it survived the moves during World War II and after it and it finally found its place in the General Maister’s Library under the patronage of the University of Maribor Library. The rearranging of the shelving system and sorting of the materials patterned after the authentic shelving system in the General’s Maribor apartment took place in 2013. Until then the books were not arranged according to the authentic shelving system. The estimated shelving system reconstruction has reconstructed Maister’s shelving system as authentically as possible, for it is not

  3. The libraries that made SUCEST

    Directory of Open Access Journals (Sweden)

    André L. Vettore

    2001-12-01

    Full Text Available A large-scale sequencing of sugarcane expressed sequence tags (ESTs was carried out as a first step in depicting the genome of this important tropical crop. Twenty-six unidirectional cDNA libraries were constructed from a variety of tissues sampled from thirteen different sugarcane cultivars. A total of 291,689 cDNA clones were sequenced in their 5’ and 3’end regions. After trimming low-quality sequences and removing vector and ribosomal RNA sequences, 237,954 ESTs potentially derived from protein-encoding messenger RNA (mRNA remained. The average insert size in all libraries was estimated to be 1,250bp with the insert length varying from 500 to 5,000 bp. Clustering the 237,954 sugarcane ESTs resulted in 43,141clusters, from which 38% had no matches with existing sequences in the public databases. Around 53% of the clusters were formed by ESTs expressed in at least two libraries while 47% of the clusters are formed by ESTs expressed in only one library. A global analysis of the ESTs indicated that around 33% contain cDNA clones with full-length insert.

  4. Realizing the Hybrid Library.

    Science.gov (United States)

    Pinfield, Stephen; Eaton, Jonathan; Edwards, Catherine; Russell, Rosemary; Wissenburg, Astrid; Wynne, Peter

    1998-01-01

    Outlines five projects currently funded by the United Kingdom's Electronic Libraries Program (eLib): HyLiFe (Hybrid Library of the Future), MALIBU (MAnaging the hybrid Library for the Benefit of Users), HeadLine (Hybrid Electronic Access and Delivery in the Library Networked Environment), ATHENS (authentication scheme), and BUILDER (Birmingham…

  5. Special Library Services.

    Science.gov (United States)

    Ensley, Robert F., Ed.

    1975-01-01

    The September 1975 issue of Illinois Libraries focuses on the needs of the developmentally disabled, physically handicapped, and emotionally disturbed. Articles on library services to the blind and physically handicapped cover standards, services of local public libraries, Library of Congress programs, braille books and sound recordings,…

  6. The library marketing toolkit

    CERN Document Server

    Potter, Ned

    2012-01-01

    A guide that offers coverage of various elements of library marketing and branding for different sectors including archives and academic, public and special libraries. It is suitable for those who are involved in promoting their library or information service, whether at an academic, public or special library or in archives or records management.

  7. Libraries and Learning

    Science.gov (United States)

    Rainie, Lee

    2016-01-01

    The majority of Americans think local libraries serve the educational needs of their communities and families pretty well and library users often outpace others in learning activities. But many do not know about key education services libraries provide. This report provides statistics on library usage and presents key education services provided…

  8. Growing Competition for Libraries.

    Science.gov (United States)

    Gibbons, Susan

    2001-01-01

    Describes the Questia subscription-based online academic digital books library. Highlights include weaknesses of the collection; what college students want from a library; importance of marketing; competition for traditional academic libraries that may help improve library services; and the ability of Questia to overcome barriers and…

  9. The "Integrated Library System."

    Science.gov (United States)

    Dowlin, Kenneth E.

    1985-01-01

    Reviews internal and external dimensions of library environment that must be taken into account by library managers when choosing an integrated library system. The selection, acquisition, and implementation stages of Maggie III--a computerized library system sensitive to the internal and external organizational environment--are described. (MBR)

  10. Teleporting the library?

    DEFF Research Database (Denmark)

    Heilesen, Simon

    2009-01-01

    In 2007, six Danish public libraries established a virtual library, Info Island DK, in Second Life. This article discusses the library project in terms of design. The design processes include the planning and implementation of the virtual library structure and its equipment, as well as the organi...

  11. DNA Libraries for the Construction of Phage Libraries: Statistical and Structural Requirements and Synthetic Methods

    Directory of Open Access Journals (Sweden)

    Thomas Lindner

    2011-02-01

    Full Text Available Peptide-based molecular probes identified by bacteriophage (phage display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.

  12. DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods.

    Science.gov (United States)

    Lindner, Thomas; Kolmar, Harald; Haberkorn, Uwe; Mier, Walter

    2011-02-15

    Peptide-based molecular probes identified by bacteriophage (phage) display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.

  13. Functional Screening of Antibiotic Resistance Genes from a Representative Metagenomic Library of Food Fermenting Microbiota

    Directory of Open Access Journals (Sweden)

    Chiara Devirgiliis

    2014-01-01

    Full Text Available Lactic acid bacteria (LAB represent the predominant microbiota in fermented foods. Foodborne LAB have received increasing attention as potential reservoir of antibiotic resistance (AR determinants, which may be horizontally transferred to opportunistic pathogens. We have previously reported isolation of AR LAB from the raw ingredients of a fermented cheese, while AR genes could be detected in the final, marketed product only by PCR amplification, thus pointing at the need for more sensitive microbial isolation techniques. We turned therefore to construction of a metagenomic library containing microbial DNA extracted directly from the food matrix. To maximize yield and purity and to ensure that genomic complexity of the library was representative of the original bacterial population, we defined a suitable protocol for total DNA extraction from cheese which can also be applied to other lipid-rich foods. Functional library screening on different antibiotics allowed recovery of ampicillin and kanamycin resistant clones originating from Streptococcus salivarius subsp. thermophilus and Lactobacillus helveticus genomes. We report molecular characterization of the cloned inserts, which were fully sequenced and shown to confer AR phenotype to recipient bacteria. We also show that metagenomics can be applied to food microbiota to identify underrepresented species carrying specific genes of interest.

  14. SSR-Patchwork: An Optimized Protocol to Obtain a Rapid and Inexpensive SSR Library Using First-Generation Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Antonietta Di Maio

    2013-01-01

    Full Text Available Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS is not readily available. Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30000 Mbp, and a third with an undetermined genome size (Kochia saxicola. Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  15. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology.

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  16. Training of Library Assistants in Academic Library

    Directory of Open Access Journals (Sweden)

    Itunu A. Bamidele

    2013-09-01

    Full Text Available The purpose of this research is to identify the need to train and retrain library assistants in academic libraries. The researchers however used Babcock University Library to ascertain the impacts of training of library assistants. A descriptive design was adopted for this study. A total enumeration sampling method was used. The instrument used for data collection was a structured questionnaire. The population was made up of 30 respondents who were library assistants at the Babcock University Library, Nigeria. A total number of 30 questionnaires were administered. All the questionnaires were retrieved and were found useful giving a return rate of 100% used for this study. The result shows that library assistants were not given training in the area of system management and web searching. In addition, 27 (90% of the respondents agreed that training will enhance their job performance while 30 (100% of the respondents agreed that training will improve their skills to support library users in searching for information electronically. Based on the findings the researchers recommend that library assistants should be trained on electronic information technology usage as this will impact the overall service delivery in meeting the goals of the academic library.

  17. GENOMIC FEATURES OF COTESIA PLUTELLAE POLYDNAVIRUS

    Institute of Scientific and Technical Information of China (English)

    LIUCai-ling; ZHUXiang-xiong; FuWen-jun; ZHAOMu-jun

    2003-01-01

    Polydnavirus was purified from the calyx fluid of Cotesia plutellae ovary. The genomic features of C. plutellae polydnavirus (CpPDV) were investigated. The viral genome consists of at least 12 different segments and the aggregate genome size is a lower estimate of 80kbp. By partial digestion of CpPDV DNA with BamHI and subsequent ligation with BamHI-cut plasmid Bluescript, a representative library of CpPDV genome was obtained.

  18. Digital imaging access library

    Science.gov (United States)

    Cook, Jay F.; Hansen, Mark; Francoise, James J.; Leckie, Robert G.; Smith, Donald V.

    1994-05-01

    The ability to access a vast array of radiological and pathologic diagnoses through computer searches of local medical facility databases is a by-product of the continued development of filmless imaging systems. The Department of Defense (DoD) Medical Diagnostic Imaging Support initiative is expanding through the addition of on-line systems at several DoD health care facilities. Madigan Army Medical Center, as the initial site, will soon be 90% filmless, with over one million images archived. Multiple other DoD medical centers are under installation. The eventual goal is an interconnected network of PACS systems of DoD medical centers and their supported medical facilities throughout the United States. To access this potential pool of medical information requires a centralized database capable of acting as a diagnostic index system. The establishment of a multi-center film library index begins with an initial analysis of issues regarding data storage and access, indexing, cross-coding with pathological files, communication formats, cost sharing, and patient confidentiality. In initiating these first steps to developing this telecommunications library these issues and their implications are discussed. The final implementation of this system will facilitate markedly improved research and teaching capabilities in both radiological and pathological fields.

  19. America's Star Libraries, 2010: Top-Rated Libraries

    Science.gov (United States)

    Lyons, Ray; Lance, Keith Curry

    2010-01-01

    The "LJ" Index of Public Library Service 2010, "Library Journal"'s national rating of public libraries, identifies 258 "star" libraries. Created by Ray Lyons and Keith Curry Lance, and based on 2008 data from the IMLS, it rates 7,407 public libraries. The top libraries in each group get five, four, or three stars. All included libraries, stars or…

  20. America's Star Libraries, 2010: Top-Rated Libraries

    Science.gov (United States)

    Lyons, Ray; Lance, Keith Curry

    2010-01-01

    The "LJ" Index of Public Library Service 2010, "Library Journal"'s national rating of public libraries, identifies 258 "star" libraries. Created by Ray Lyons and Keith Curry Lance, and based on 2008 data from the IMLS, it rates 7,407 public libraries. The top libraries in each group get five, four, or three stars. All included libraries, stars or…

  1. Social implications of the Human Genome Project: Policy roundtable series and journals. Final progress report, March 15, 2001 - March 15, 2002

    Energy Technology Data Exchange (ETDEWEB)

    Seiguer, Erica

    2002-12-30

    This report reflects the activities of the Harvard Health Caucus at Harvard Medical School that were supported, in part, by the Department of Energy. The following policy roundtables and panels were held: Spring 2001 Policy Roundtable Series: The social implications of the Human Genome Project; Spring 2002 Policy Roundtable Series: Managing globalization to improve health; 13 February 2002 Keynote Address: The globalization of health; 25 February 2002 Healthier or Wealthier: Which comes first in the new global era?; 28 February 2002 The crisis of neglected diseases: Creating R&D incentives for diseases of developing countries; 7 March 2002 Health care education in the developing world: Bridging global and local health care practices; 20 March 2002 Building a legal framework for global health: How can the US and UN work to reduce global disparities?; 25 April 2002 The role of mass media and tobacco control efforts. Caucus organizational information is also included.

  2. Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; ZHANG Xiaojun; Chantel F.SCHEURING; ZHANG Hongbin; LI Fuhua; XIANG Jianhai

    2008-01-01

    Two Large-insert genomic bacterial artificial chromosome (BAC) libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research.High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I,respectively.The BamH I library consisted of 53760 clones while the Mbo I library consisted of 7680 clones.Approximately 96% of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb,providing a coverage of 5.3 haploid genome equivalents.Similarly,the Mbo I library with an average insert of 145 kb and no insert-empty clones,thus providing a genome coverage of 1.1 haploid genome equivalents.

  3. Toy Library and International Toy Library Association

    OpenAIRE

    Kamaraj, Işık

    2013-01-01

    Toy libraries are resource centers that provides assistance to young children and theirfamilies, gives consultancy service and information about plays, offers play materials andeducational activities and supplies appropriate materials and toys for child development aswell as contributing the development of children. Toy libraries are in commission all over theworld since 1935. The first toy library is opened in America, then in Sweden, England,Canada and Australia respectively. Today, there a...

  4. Preparation of high-molecular weight DNA and metagenomic libraries from soils and hot springs.

    Science.gov (United States)

    Reigstad, Laila J; Bartossek, Rita; Schleper, Christa

    2011-01-01

    Metagenomics has become an important tool for the characterization of microorganisms, as it is independent of their enrichment or cultivation in the laboratory. Its application has led to the discovery of metabolisms from widespread, yet uncharacterized organisms such as the ammonia-oxidizing archaea. Different approaches ranging from the generation of short sequence reads by direct use of high-throughput sequencing technologies to the construction and sequencing of large-insert DNA libraries are being employed. For these purposes, DNA of high quality needs to be prepared from an environmental sample, which is a particular challenge for soils and sediments. Here we describe the methods used for the isolation of high-molecular weight (hmw) DNA from soil and hot spring samples, the subsequent production of large-insert metagenomic libraries, and the analysis of the resulting genomic fragments. Detailed step-by-step procedures include (1) how to isolate good-quality hmw DNA from soils and mud; (2) how to prepare the DNA for cloning; (3) how to efficiently establish, grow, pick, replicate, and store the large-insert metagenomic fosmid library; and finally, (4) how to screen the library for genes of interest.

  5. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  6. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  7. Heterogenic final cell cycle by chicken retinal Lim1 horizontal progenitor cells leads to heteroploid cells with a remaining replicated genome.

    Directory of Open Access Journals (Sweden)

    Shahrzad Shirazi Fard

    Full Text Available Retinal progenitor cells undergo apical mitoses during the process of interkinetic nuclear migration and newly generated post-mitotic neurons migrate to their prospective retinal layer. Whereas this is valid for most types of retinal neurons, chicken horizontal cells are generated by delayed non-apical mitoses from dedicated progenitors. The regulation of such final cell cycle is not well understood and we have studied how Lim1 expressing horizontal progenitor cells (HPCs exit the cell cycle. We have used markers for S- and G2/M-phase in combination with markers for cell cycle regulators Rb1, cyclin B1, cdc25C and p27Kip1 to characterise the final cell cycle of HPCs. The results show that Lim1+ HPCs are heterogenic with regards to when and during what phase they leave the final cell cycle. Not all horizontal cells were generated by a non-apical (basal mitosis; instead, the HPCs exhibited three different behaviours during the final cell cycle. Thirty-five percent of the Lim1+ horizontal cells was estimated to be generated by non-apical mitoses. The other horizontal cells were either generated by an interkinetic nuclear migration with an apical mitosis or by a cell cycle with an S-phase that was not followed by any mitosis. Such cells remain with replicated DNA and may be regarded as somatic heteroploids. The observed heterogeneity of the final cell cycle was also seen in the expression of Rb1, cyclin B1, cdc25C and p27Kip1. Phosphorylated Rb1-Ser608 was restricted to the Lim1+ cells that entered S-phase while cyclin B1 and cdc25C were exclusively expressed in HPCs having a basal mitosis. Only HPCs that leave the cell cycle after an apical mitosis expressed p27Kip1. We speculate that the cell cycle heterogeneity with formation of heteroploid cells may present a cellular context that contributes to the suggested propensity of these cells to generate cancer when the retinoblastoma gene is mutated.

  8. Whole-genome sequencing for comparative genomics and de novo genome assembly.

    Science.gov (United States)

    Benjak, Andrej; Sala, Claudia; Hartkoorn, Ruben C

    2015-01-01

    Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

  9. Construction and characterization of a bacterial artificial chromosome library of thermo-sensitive genic male-sterile rice 5460S

    Institute of Scientific and Technical Information of China (English)

    邱芳; 金德敏; 伏健民; 张超良; 谢纬武; 王斌; 杨仁崔; 张洪斌

    1999-01-01

    In order to develop a detailed physical map of the thermo-sensitive genie male-sterile (TGMS) gene-encompassing region and finally clone the TGMS gene, a high-quality rice bacterial artificial chromosome (BAC) library from TGMS rice 5460S was constructed. The method of constructing BAC library was examined and optimized. The 5460S library consists of 19 584 BAC clones with an average insert size of 110 kb, which represents about 5 times rice haploid genome equivalents. Rice inserts of up to 140 kb and 250 kb were isolated and appeared stable after 100 generations of serial growth. Hybridization of BAC clones with mitochondrial and chloroplastic genes as probes demonstrated that this library has no organellar contamination. The 5460S library was screened with 3 molecular markers linked to tmsl gene as probes and at least 1 BAC clone was identified with each probe. The insert ends of positive clones were successfully isolated using thermal asymmetric interlaced PCR (TAIL-PCR) technique.

  10. An Overview of Invenio Digital Library Software

    CERN Multimedia

    CERN-IT-UDS-CDS; Audiovisual Service

    2011-01-01

    Invenio is a free, open source software suite that will enable you to run your own digital library or document repository on the web. The software covers all the stages of digital library management from document ingestion through to classification, indexing, curation and finally, dissemination. Invenio complies with the OAI metadata harvesting protocol and uses MARC21 as its underlying bibliographic format, hence facilitating the sharing of resources between repositories worldwide.

  11. Mixture-Based Combinatorial Libraries from Small Individual Peptide Libraries: A Case Study on α1-Antitrypsin Deficiency

    Directory of Open Access Journals (Sweden)

    Yi-Pin Chang

    2014-05-01

    Full Text Available The design, synthesis and screening of diversity-oriented peptide libraries using a “libraries from libraries” strategy for the development of inhibitors of α1-antitrypsin deficiency are described. The major buttress of the biochemical approach presented here is the use of well-established solid-phase split-and-mix method for the generation of mixture-based libraries. The combinatorial technique iterative deconvolution was employed for library screening. While molecular diversity is the general consideration of combinatorial libraries, exquisite design through systematic screening of small individual libraries is a prerequisite for effective library screening and can avoid potential problems in some cases. This review will also illustrate how large peptide libraries were designed, as well as how a conformation-sensitive assay was developed based on the mechanism of the conformational disease. Finally, the combinatorially selected peptide inhibitor capable of blocking abnormal protein aggregation will be characterized by biophysical, cellular and computational methods.

  12. For the history of the Capuchin monastery libraries of Genoa

    Directory of Open Access Journals (Sweden)

    Francesca Nepori

    2015-07-01

    Full Text Available The paper traces the history of the Capuchin monastery libraries of Genoa, since the 1535 to the present day. The main sources used are the Capuchin Constitutions, the documents kept at the Provincial Archives and the library catalogs of the cloisters (including the Bibliotheca Scriptorum Minorum Ordinis S. Francisci Capuccinorum p. Dionisio from Genoa and, finally, was some piece of news by private libraries. The story of the thirty-four cloister libraries is linked with the Provincial Library, which is representative of the Capuchin Province of Genoa and an important center for the conservation of all monastic book collections.

  13. Libraries and Accessibility: Istanbul Public Libraries Case

    Directory of Open Access Journals (Sweden)

    Gül Yücel

    2016-12-01

    Full Text Available In the study; the assessment of accessibility has been conducted in Istanbul public libraries within the scope of public area. Public libraries commonly serve with its user of more than 20 million in total, spread to the general of Turkey, having more than one thousand branches in the centrums and having more than one million registered members. The building principles and standards covering the subjects such as the selection of place, historical and architectural specification of the region, distance to the centre of population and design in a way that the disabled people could benefit from the library services fully have been determined with regulations in the construction of new libraries. There are works for the existent libraries such as access for the disabled, fire safety precautions etc. within the scope of the related standards. Easy access by everyone is prioritized in the public libraries having a significant role in life-long learning. The purpose of the study is to develop solution suggestions for the accessibility problems in the public libraries. The study based on the eye inspection and assessments carried out within the scope of accessibility in the public libraries subsidiary to Istanbul Culture and Tourism Provincial Directorate Library and Publications Department within the provincial borders of Istanbul. The arrangements such as reading halls, study areas, book shelves etc. have been examined within the frame of accessible building standards. Building entrances, ramps and staircases, horizontal and vertical circulation of building etc. have been taken into consideration within the scope of accessible building standards. The subjects such as the reading and studying areas and book shelf arrangements for the library have been assessed within the scope of specific buildings. There are a total of 34 public libraries subsidiary to Istanbul Culture and Tourism Provincial Directorate on condition that 20 ea. of them are in the

  14. Library Advocacy Now! Library Advocate's Handbook. [Videotape.

    Science.gov (United States)

    American Library Association Video/Library Video Network, Towson, MD.

    Libraries are one of the world's greatest assets. Changes in the political, social, and economic climate in the U.S. mean that people cannot take public access to information for granted. Intense competition for public, private, and institutional dollars makes it more crucial than ever that policymakers understand that libraries--public, school,…

  15. Libraries - LIBRARIES_ISL_IN: Libraries in Indiana (Indiana State Library, Point Shapefile)

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — LIBRARIES_ISL_IN is a point shapefile showing the locations of 528 libraries included in Microsoft Excel spreadsheets that are downloadable from the Web page named...

  16. Libraries serving dialogue

    CERN Document Server

    Dupont, Odile

    2014-01-01

    This book based on experiences of libraries serving interreligious dialogue, presents themes like library tools serving dialogue between cultures, collections dialoguing, children and young adults dialoguing beyond borders, story telling as dialog, librarians serving interreligious dialogue.

  17. Integrated library systems.

    Science.gov (United States)

    Goldstein, C M

    1983-07-01

    The development of integrated library systems is discussed. The four major discussion points are (1) initial efforts; (2) network resources; (3) minicomputer-based systems; and (4) beyond library automation. Four existing systems are cited as examples of current systems.

  18. Reutilizing Existing Library Space.

    Science.gov (United States)

    Davis, Marlys Cresap

    1987-01-01

    This discussion of the reutilization of existing library space reviews the decision process and considerations for implementation. Two case studies of small public libraries which reassigned space to better use are provided, including floor plans. (1 reference) (MES)

  19. Library planning in Germany

    Directory of Open Access Journals (Sweden)

    Friedrich Geisselmann

    2003-12-01

    Full Text Available The position and the efficiency of German libraries are rather ambivalent. On the one hand the infrastructure is quite well developed: 2000 public library systems with full time personnel, 275 million books issued, 75 million Euro for acquisitions; 280 scientific general libraries, 60 million books issued, 1300 million Euro for acquisitions. Nevertheless there are a lot of problems, which arise from the administrative structure and the political position of libraries.

  20. Multipurpose Transposon-Insertion Libraries in Yeast.

    Science.gov (United States)

    Kumar, Anuj

    2016-06-01

    Libraries of transposon-insertion alleles constitute powerful and versatile tools for large-scale analysis of yeast gene function. Transposon-insertion libraries are constructed most simply through mutagenesis of a plasmid-based genomic DNA library; modification of the mutagenizing transposon by incorporation of yeast selectable markers, recombination sites, and an epitope tag enables the application of insertion alleles for phenotypic screening and protein localization. In particular, yeast genomic DNA libraries have been mutagenized with modified bacterial transposons carrying the URA3 marker, lox recombination sites, and sequence encoding multiple copies of the hemagglutinin (HA) epitope. Mutagenesis with these transposons has yielded a large resource of insertion alleles affecting nearly 4000 yeast genes in total. Through well-established protocols, these insertion libraries can be introduced into the desired strain backgrounds and the resulting insertional mutants can be screened or systematically analyzed. Relative to alternative methods of UV irradiation or chemical mutagenesis, transposon-insertion alleles can be easily identified by PCR-based approaches or high-throughput sequencing. Transposon-insertion libraries also provide a cost-effective alternative to targeted deletion approaches, although, in contrast to start-codon to stop-codon deletions, insertion alleles might not represent true null-mutants. For protein-localization studies, transposon-insertion alleles can provide encoded epitope tags in-frame with internal codons; in many cases, these transposon-encoded epitope tags can provide a more accurate localization for proteins in which terminal sequences are crucial for intracellular targeting. Thus, overall, transposon-insertion libraries can be used quickly and economically and have a particular utility in screening for desired phenotypes and localization patterns in nonstandard genetic backgrounds.

  1. Learning Boost C++ libraries

    CERN Document Server

    Mukherjee, Arindam

    2015-01-01

    If you are a C++ programmer who has never used Boost libraries before, this book will get you up-to-speed with using them. Whether you are developing new C++ software or maintaining existing code written using Boost libraries, this hands-on introduction will help you decide on the right library and techniques to solve your practical programming problems.

  2. Library Skills Workbook.

    Science.gov (United States)

    Miller, Constance; And Others

    This self-paced library skills workbook provides incoming students with an introduction to the physical arrangement and use of the university libraries. Divided into two sections, the first contains explanations of the catalogs, classification system, and various library resources. The second consists of practical exercises keyed to the…

  3. Biology Library Workbook.

    Science.gov (United States)

    Miller, Constance; And Others

    A library skills workbook provides college biology students with an introduction to biological library resources. Divided into two sections, the first contains explanations of the various steps in the library research process. The second consists of exercises keyed to the explanatory chapters of the first section. (RAA)

  4. A Truly Bookless Library

    Science.gov (United States)

    Kolowich, Steve

    2011-01-01

    The difference between the University of Texas at San Antonio's Applied Engineering and Technology Library and other science-focused libraries is not that its on-site collection is also available electronically. It is that its on-site collection is only available electronically. The idea of libraries with no bound books has been a recurring theme…

  5. Changing State Digital Libraries

    Science.gov (United States)

    Pappas, Marjorie L.

    2006-01-01

    Research has shown that state virtual or digital libraries are evolving into websites that are loaded with free resources, subscription databases, and instructional tools. In this article, the author explores these evolving libraries based on the following questions: (1) How user-friendly are the state digital libraries?; (2) How do state digital…

  6. Technostress and Library Values.

    Science.gov (United States)

    Gorman, Michael

    2001-01-01

    Discusses information overload and society's and libraries' responses to technology. Considers eight values that libraries should focus on and how they relate to technology in libraries: democracy, stewardship, service, intellectual freedom, privacy, rationalism, equity of access, and building harmony and balance. (LRW)

  7. Changing State Digital Libraries

    Science.gov (United States)

    Pappas, Marjorie L.

    2006-01-01

    Research has shown that state virtual or digital libraries are evolving into websites that are loaded with free resources, subscription databases, and instructional tools. In this article, the author explores these evolving libraries based on the following questions: (1) How user-friendly are the state digital libraries?; (2) How do state digital…

  8. Body Basics Library

    Science.gov (United States)

    ... Sport for You Shyness About the Body Basics Library KidsHealth > For Teens > About the Body Basics Library Print A A A Did you ever wonder ... system, part, and process works. Use this medical library to find out about basic human anatomy, how ...

  9. School Libraries and Innovation

    Science.gov (United States)

    McGrath, Kevin G.

    2015-01-01

    School library programs have measured success by improved test scores. But how do next-generation school libraries demonstrate success as they strive to be centers of innovation and creativity? These libraries offer solutions for school leaders who struggle to restructure existing systems built around traditional silos of learning (subjects and…

  10. Body Basics Library

    Science.gov (United States)

    ... of Healthy Breakfasts Shyness About the Body Basics Library KidsHealth > For Teens > About the Body Basics Library A A A Did you ever wonder what ... system, part, and process works. Use this medical library to find out about basic human anatomy, how ...

  11. Public Library Finance.

    Science.gov (United States)

    Mason, Marilyn Gell

    This study reviews trends in public library finance; examines recent political, economic, and technological changes; and assesses the impact of these changes on public library services. A history of the public library in America is presented, as well as an analysis of the principles of economics and public finance which reveals that current…

  12. The Electronic, Eclectic Library.

    Science.gov (United States)

    Dowlin, Kenneth E.

    1980-01-01

    Utilization of telecommunications and computer technology to increase access to information is identified as a primary goal for public libraries. To further service in the future, libraries should consider database services, online access to library resources, online community conferencing, community databases, network resource sharing,…

  13. Merchandising Your Library.

    Science.gov (United States)

    Sivulich, Kenneth G.

    1989-01-01

    Discusses library circulation figures as a reflection of the success of library services and describes merchandising techniques that have produced a 137 percent circulation increase at Queens Borough Public Library over the past seven years. Merchandising techniques such as minibranches, displays, signage, dumps, and modified shelving are…

  14. Marketing Academic Libraries

    Science.gov (United States)

    Mallon, Melissa, Ed.

    2013-01-01

    Ask any academic librarian if marketing their library and its services is an important task, and the answer will most likely be a resounding "yes!" Particularly in economically troubled times, librarians are increasingly called upon to promote their services and defend their library's worth. Since few academic libraries have in-house marketing…

  15. Merchandising Your Library.

    Science.gov (United States)

    Sivulich, Kenneth G.

    1989-01-01

    Discusses library circulation figures as a reflection of the success of library services and describes merchandising techniques that have produced a 137 percent circulation increase at Queens Borough Public Library over the past seven years. Merchandising techniques such as minibranches, displays, signage, dumps, and modified shelving are…

  16. Marketing Academic Libraries

    Science.gov (United States)

    Mallon, Melissa, Ed.

    2013-01-01

    Ask any academic librarian if marketing their library and its services is an important task, and the answer will most likely be a resounding "yes!" Particularly in economically troubled times, librarians are increasingly called upon to promote their services and defend their library's worth. Since few academic libraries have in-house marketing…

  17. School Libraries and Innovation

    Science.gov (United States)

    McGrath, Kevin G.

    2015-01-01

    School library programs have measured success by improved test scores. But how do next-generation school libraries demonstrate success as they strive to be centers of innovation and creativity? These libraries offer solutions for school leaders who struggle to restructure existing systems built around traditional silos of learning (subjects and…

  18. FY 2009 Public Libraries Survey

    Data.gov (United States)

    Institute of Museum and Library Services — Dig into FY 2009 data on public library systems (referred to as administrative entities in the Public Libraries Survey) and main libraries, branches, and bookmobiles...

  19. FY 2011 Public Libraries Survey

    Data.gov (United States)

    Institute of Museum and Library Services — Dig into FY 2011 data on public library systems (referred to as administrative entities in the Public Libraries Survey) and main libraries, branches, and bookmobiles...

  20. FY 2010 Public Libraries Survey

    Data.gov (United States)

    Institute of Museum and Library Services — Dig into FY 2010 data on public library systems (referred to as administrative entities in the Public Libraries Survey) and main libraries, branches, and bookmobiles...

  1. FY 2008 Public Libraries Survey

    Data.gov (United States)

    Institute of Museum and Library Services — Dig into FY 2008 data on public library systems (referred to as administrative entities in the Public Libraries Survey) and main libraries, branches, and bookmobiles...

  2. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Wu Cheng-Cang

    2011-05-01

    Full Text Available Background Although second generation sequencing (2GS technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result Five new BAC libraries were constructed for barley (Hordeum vulgare L. cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast, empty wells and off-scale clones (clones with 250 fragments. Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.

  3. German Librarianship and Munich Libraries

    Directory of Open Access Journals (Sweden)

    Osman Ümit Özen

    1994-06-01

    Full Text Available There are 27 municipal libraries including the Central Public Library in Munich. The other important libraries in the city are Bayern State National Library, Maximillian University Library, a technical highschool library and the "Deutsches Musuem" Library. All these libraries are financed locally. The author introduces these libraries briefly and compares German libraries with Turkish libraries. He concludes that although theoretically there are not distinctive differences, in practice, buildings and their layout are better in Germany where more variety of services are offered. In Turkey standardization has not been realized yet. Turkey needs to computerize and network to improve the services offered in an efficient way.

  4. Libraries in Society

    DEFF Research Database (Denmark)

    Kristiansson, Michael; Skouvig, Laura

    understood in a library setting. Historically, openness in form of the open shelves played a crucial role in developing the modern public library. The paper examines this openness-centred library policy as adopted by Danish public libraries in the beginning of the 20th century by applying the theories...... by Michel Foucault on discourse and power to the introduction of open shelves. Furthermore, the paper discusses current challenges facing the modern public library in coping with openness issues that follow from changes in society and advances in technology. These influences and developments are not least...

  5. Library/vendor relationships

    CERN Document Server

    Brooks, Sam

    2014-01-01

    A view of the mutual dependence between libraries and vendorsAs technology advances, libraries are forced to reach beyond their own resources to find effective ways to maintain accuracy and superior service levels. Vendors provide databases and integrated library systems that perform those functions for profit. Library/Vendor Relationships examines the increasing cooperation in which libraries find they must participate in, and vice versa, with the vendors that provide system infrastructure and software. Expert contributors provide insights from all sides of this unique collaboration, offering

  6. Construction and Characterization of Grass Carp(Ctenopharyngodon idellus)Fosmid Library

    Institute of Scientific and Technical Information of China (English)

    JIA Zhen-hu; LIN Chang-you; YANG Tian-yao; JIANG Yi-nan; XIA Chun

    2010-01-01

    Grass carp(Ctenopharyngodon idellus)genomic fosmid library cotaining 129014 clones was constructed and characterized from one diploid grass carp.The average insert size of the fosmid library was determined to be 35 kb by pulsed field gel electrophoresis,which is 4.1-fold coverage of the grass carp genome.To demonstrate the probability of picking the functional genes from the library,eleven functional genes were screened by three-dimensional PCR technique.The number of positive clones of these genes was from 1 to 6.So,this library may screen any useful genes from grass carp.This grass carp genome fosmid library will be integrated in the presently ongoing efforts to determine the sequence of the grass carp genome.

  7. Library system of Italy

    Directory of Open Access Journals (Sweden)

    Nataša Gerbec

    2003-01-01

    Full Text Available In the European extent, Italy is the cradle of libraries and library sciences. In the past, Italian national public libraries played an important role through their vast book treasury. But only during the last thirty years have public libraries been developed following the Anglo-American public library model. Italy does not have any uniform or general legislation concerning libraries. On the state level, this area is regulated by some separate acts, while on the regional level there is a collection of various acts and regulations. Libraries are not strictly divided into general categories. It is required that the professionals engaged in Italian libraries should have secondary or university education. The level of their professional tasks depends on the type of library and its capacity. The competency for the development in the field of librarianship is assigned to The Ministry of Cultural and Environment Heritage as well as to its subordinate institutions (Central Institute for the Union catalogue of Italian Libraries and for Bibliographic Information, Central Institute for Book Pathology, Observatory for International Libraries Programmes.

  8. The Memory Library

    DEFF Research Database (Denmark)

    Olesen-Bagneux, Ole

    2014-01-01

    For millennia the famous library in Hellenistic Alexandria has been praised as an epicenter of enlightenment and wisdom. And yet, a question still seems unanswered: how was its literature classified and retrieved? It is a subject that has been given surprisingly little attention by Library......- and Information Science – indeed, by scholarship in general. Furthermore, a certain way of thinking has influenced the few answers that have so far been attempted. It is as if the scholars of our era have tried to identify the modern, physical library in the Hellenistic library in Alexandria. But such an approach...... is biased in a basic way: It simply does not consider the impact of the cultural and intellectual context of the library. This article differs fundamentally, and rejects that the library was like modern ones. Accordingly, an entirely new way of understanding how the library actually worked, in terms...

  9. The participatory public library

    DEFF Research Database (Denmark)

    Rasmussen, Casper Hvenegaard

    2016-01-01

    Purpose From collection to connection has been a buzzword in the library world for more than a decade. This catchy phrase indicates that users are seen not only as borrowers, but as active participants. The aim of this paper is to investigate and analyse three questions in relation to user...... participation in public libraries in a Nordic perspective. How can participation in public libraries be characterised? Why should libraries deal with user participation? What kinds of different user participation can be identified in public libraries? Design/methodology/approach The paper uses a selection...... of theoretical approaches and practical examples to obtain a varied understanding of user participation in public libraries. Research fields outside library and information science have developed a wide range of theoretical approaches on user participation. Examples from cultural policy, museum studies...

  10. The participatory public library

    DEFF Research Database (Denmark)

    Rasmussen, Casper Hvenegaard

    2016-01-01

    of theoretical approaches and practical examples to obtain a varied understanding of user participation in public libraries. Research fields outside library and information science have developed a wide range of theoretical approaches on user participation. Examples from cultural policy, museum studies......Purpose From collection to connection has been a buzzword in the library world for more than a decade. This catchy phrase indicates that users are seen not only as borrowers, but as active participants. The aim of this paper is to investigate and analyse three questions in relation to user...... participation in public libraries in a Nordic perspective. How can participation in public libraries be characterised? Why should libraries deal with user participation? What kinds of different user participation can be identified in public libraries? Design/methodology/approach The paper uses a selection...

  11. Identification of novel open reading frames from metagenomic libraries generated from extremophilic organisms: application of metagenomics and high throughput screening for novel enzyme isolation

    CSIR Research Space (South Africa)

    Visser, Daniel F

    2006-10-01

    Full Text Available South African mines. Genomic DNA was isolated from these biofilms, and various metagenomic libraries generated. These libraries were in turn screened for industrially important enzymes, in particular proteases and lipases. Resultant hits had plasmid DNA...

  12. Integration of chicken genomic resources to enable whole-genome sequencing

    NARCIS (Netherlands)

    Aerts, J.A.; Crooijmans, R.P.M.A.; Cornelissen, S.J.B.; Hemmatian, K.; Veenendaal, A.; Jaader, A.; Poel, van der J.J.; Fillon, V.; Vignal, I.; Groenen, M.A.M.

    2003-01-01

    Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome w

  13. Flight Software Math Library

    Science.gov (United States)

    McComas, David

    2013-01-01

    The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

  14. Ergonomics: case study in a university library

    Directory of Open Access Journals (Sweden)

    Daniela Capri

    2012-08-01

    Full Text Available This final paper aimed to analyze the real ergonomics of a university library from Florianópolis and compare it with the ergonomics perceived by the user to perform an ergonomic diagnosis. In order to meet this goal two specific goals were established such as: describe the physical and environmental aspects of the library related to the real ergonomics and verify the actual perception of users about the library. As a theoretical approach, aspects of ergonomics and environmental ergonomics were contextualized and linked to the library and the university library. Referring to the methodology, the Ergonomical Assessment of the Built Environment was used as a reference. The study subjects comprised a sample of 15, among students and library staff. In the results obtained, when related to the physical-environmental analysis of the library, it was found that there are some aspects that differ from the regulatory standards and that also fall short in relation to feedback from users. Aspects such as lighting and noise were cited as unsatisfactory, but the temperature factor was analyzed as satisfactory.

  15. Assessing Library Automation and Virtual Library Development in Four Academic Libraries in Oyo, Oyo State, Nigeria

    Science.gov (United States)

    Gbadamosi, Belau Olatunde

    2011-01-01

    The paper examines the level of library automation and virtual library development in four academic libraries. A validated questionnaire was used to capture the responses from academic librarians of the libraries under study. The paper discovers that none of the four academic libraries is fully automated. The libraries make use of librarians with…

  16. Halk Kütüphanelerinde Koleksiyon Seçimi / Selection Process for the Library Collections of Public Libraries

    Directory of Open Access Journals (Sweden)

    Dilek Köprülü

    2006-04-01

    Full Text Available The task of collection development of public libraries requires the fulfilment of a selection process. In this context, main characteristics of the collection of public libraries, assessment of the user’s information needs, the selection process and its policy of implementation, and the related responsibilities of the professional librarians were examined. Finally, the selection process undertaken by public libraries in Turkey was examined, and certain suggestions were forwarded.

  17. Interaction between libraries and library users on Facebook

    OpenAIRE

    Chen, DYT; Maxwell, W.; Li, WZS; Tang, LLC; Chu, SKW

    2011-01-01

    This study adopts the mixed method research design to investigate the interaction between libraries and library users on Facebook. The research objectives are: (1) To find out the performance of Facebook as a tool for interaction between libraries and library users; (2) To find out the differences in using Facebook to interact with library users between libraries in two regions: English-speaking countries and Greater China; (3) To find out the differences between academic and public libraries...

  18. Integration of Library Services in the System of Digital Libraries

    Science.gov (United States)

    Bezdushnyj, A. N.; Kalenov, N. E.; Kouriv, P. M.; Serebryakov, V. A.

    The article is devoted to the functional extension of the Integrated System of Information Resources of RAS (ISIR RAS - RFBR 99-07-90139 project). This extension (Library Subsystem) provides integration of library services in ISIR RAS electronic libraries system. Library Subsystem implements standard library services such as information about free and ordered copies of editions, creation of the library orders for edition etc. The Library Subsystem is an integrated solution; it's based on ISIR data model and technologies.

  19. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol;

    2010-01-01

    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  20. News from the Library

    CERN Multimedia

    CERN Library

    2010-01-01

    The LHC Library to be merged with the Central Library. Not everyone knows that CERN Scientific Information Service currently counts three physical libraries on site. The Central Library is located in Building 52 and there are two satellite libraries located respectively in building 30 (the LHC Library) and in building 864 on Prévessin site (the SPS Library). Moreover, the Legal Service Library is located in Building 60. In the past, there have been at CERN up to 6 satellite libraries; they were essential at a time when information was only in paper form and having multiple copies of documents located in several places at CERN was useful to facilitate scientific research. Today, this need is less critical as most of our resources are online. That is why, following a SIPB (Scientific Information Policy Board) decision, the collections of the LHC Library will be merged this summer with the Central collection. This reorganization and centralization of resources will improve loan services. The SP...

  1. LIBRARY SURVEY 2001

    CERN Multimedia

    2001-01-01

    The primary role of the library is to make sure that you can do YOUR work in the most efficient way possible. To ensure that we continue to match our services to your information needs, the library regularly gathers the views and opinions of its readers in a variety of ways, [link for e-version: http://library/library_general/statistics/library_statistics_ surveys.html], including user surveys. The last survey was carried out in 1996. One of the most visible results of that survey was the extension of the library desk service until seven o'clock in the evening, to meet the demand for greater access to library materials. Now the 'electronic library' is becoming more important than the physical one, we feel it is once again time to ensure that we are providing the services and information you need, in the most effective way possible. We also want to make sure you are aware of the full range of services that the library provides. Please spare just a few minutes to fill out our survey at http://library.cern.ch/su...

  2. Visualizations for Digital Libraries

    Directory of Open Access Journals (Sweden)

    Gang Wan

    2006-06-01

    Full Text Available The concept of digital libraries is familiar to both librarians and library patrons today. These new libraries have broken the limits of space and distance by delivering information in various formats via the Internet. Since most digital libraries contain a colossal amount of information, it is critical to design more user-friendly interfaces to explore, understand, and manage their content. One important technique for designing such interfaces is information visualization. Although computer-aided information visualization is a relatively new research area, numerous visualization applications already exist in various fields today. Furthermore, many library professionals are also starting to realize that combining information visualization techniques and current library technologies, such as digital libraries, can help library users find information more effectively and efficiently. This article first discusses three major tasks that most visualization for digital libraries emphasize, and then introduces several current applications of information visualization for digital libraries.

  3. Specialized microbial databases for inductive exploration of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Cabau Cédric

    2005-02-01

    Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

  4. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology1

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    • Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes. PMID:25202476

  5. Science, Engineering Research and Innovation in Academic Libraries (SERIAL)

    OpenAIRE

    Y, Srinivasa Rao

    2013-01-01

    Presentations primarily deals with knowledge progress cycle and intellectual property rights. Strategies for building intellectual base and role of library in an academic library settings. impact of content-connectivity-cost in publishing industry. Finally dealt with impact of Indian education, research and innovation.

  6. The Applications of Internet Censorship Software in Libraries

    Directory of Open Access Journals (Sweden)

    Nermin A.Qader

    2004-06-01

    Full Text Available A study about the dangerous resulted from using the internet , deals with the internet fearues and its services in libraries, then talk about censorship the internet and its definition ,types , and its tools with concentration on filtering software and its applications in libraries, finally deal with the situation of the Arab countries towards censorship the internet.

  7. The Applications of Internet Censorship Software in Libraries

    OpenAIRE

    Nermin A.Qader

    2004-01-01

    A study about the dangerous resulted from using the internet , deals with the internet fearues and its services in libraries, then talk about censorship the internet and its definition ,types , and its tools with concentration on filtering software and its applications in libraries, finally deal with the situation of the Arab countries towards censorship the internet.

  8. Construction of Genomic Library for Marine Pseudomonas HW08 and Analysis of Its Sequence Function%海洋假单胞杆菌HW08基因组文库的构建及序列功能分析

    Institute of Scientific and Technical Information of China (English)

    郝建华; 刘均忠; 王芳; 纪晓峰; 孙谧

    2012-01-01

    A 1~2 kb DNA fragment of HW08 genome was obtained by ultrasonic treatment, and the genomic library of HW08 was constructed after connecting the pUC18 plasmid with the obtained fragment and transformation. The random selected 200 clones were sequenced and analyzed in order to quick analyze the genome of marine pseudomonas HW08. The results showed that a partial genomic library of HW08 was constructed, and the obtained 173 sequences have seven vector sequences and seven contigs, in which the longest contig is the fourth contig which contained Chemotaxis Protein, Hypothetical protein and Lad family transcription regulator. The third contig is DNA repair protein, and its maximum similarity is 83%. Among the 166 sequences, the enzyme occupied most of the part; meanwhile 37 new genes were also included.%通过超声波处理HW08基因组,将获得的1~2KB DNA片段与pUC18质粒进行连接后转化,构建文库.随机筛选200个克隆进行序列测定,快速分析了海洋假单胞杆茵HW08基因组.结果表明:构建了HW08菌株的基因组部分文库,获得序列173个,包含7个载体序列和7个重叠群,其中最长重叠群为重叠群4,包含3段基因序列,分别为Chemotaxis Protein、Hypothetical protein和LacI family transcription regulator.重叠群3为DNA修复蛋白,其最大相似性为83%.166个序列中酶类占绝大部分,同时也包含37个新基因.

  9. General review of National Digital Library development in the National Library of China

    Institute of Scientific and Technical Information of China (English)

    SHEN; Xiaojuan; WEI; Wei; QI; Xin

    2008-01-01

    As an important part of National Digital Library(NDL),the National Digital Library Project(NDLP),which was launched in 2005,has attracted wide attention of the society in general.This paper introduces the general situation of the project from the following aspects,namely,the characteristics,objectives and contents.It also expounds on the basic ideas and the overall structure of the project and gives an introduction to the design of its basic platform,its application platform,its business management system and its standardization control system.In this paper,the digital resources construction and service delivery of the National Library of China(NLC)are introduced to cover both its present operation as well as those in conjunction with the opening of its new library building during its second-phase of library development.Finally,the most important and difficult point in the construction of the National Digital Library Project is analyzed from the following four perspectives:1)The long-term preservation of digital resources;2)the construction of knowledge organization system;3)the organic integration of the digital library and the traditional library;and 4)the risk of project management and system integration.

  10. The Library International Partnerweek 2011

    DEFF Research Database (Denmark)

    Presentation at the Library International Partnerweek, held at Copenhagen Technical Library at the Copenhagen University College of Engineering. Participant: Ms. Carmen Priesto Estravid from Madrid Technical University, E.U.I.T. Obras Públicas, Library. Spain Ms.Tuulikki Hattunen from TUAS Library....... Finland Ms. Anitta Ôrm from Kemi-Tornio UAS Library. Finland Mr. Manfred Walter from HTW-Berlin. Germany Mr. Peter Hald from Copenhagen Technical Library. Denmark Mr. Ole Micahelsen from Copenhagen Technical Library. Denmark...

  11. Developing European Library Services in Changing Times

    Directory of Open Access Journals (Sweden)

    Paul Ayris

    2012-01-01

    Full Text Available The purpose of this article is to explain what academic and national libraries can do to continue to offer services and facilities at a time of economic difficulties. It identifies a number of methodologies and opportunities that are open to libraries and takes the view that it is never wise to waste a good crisis, because all threats are really opportunities in disguise. The article looks at the initial economic context for European research libraries and then examines ways in which libraries can tackle the threats which the current financial crisis poses. Joint procurement is one way in which libraries can achieve value for money, and the paper examines the role of JIS C Collections in the UK. Innovation through collaboration and shared services are also ways in which libraries can innovate/make savings in a cost-effective way by sharing the burden of costs around the partnership. The paper gives two examples: one which is now well established, the DART-Europe portal for Open Access e-theses; and one which is in the early stages of being discussed — a cloud-based solution for true collaborative cataloguing amongst the UK’s research and national libraries. The European Research Area (ERA and the contributions that libraries can make to this infrastructure through innovative EU project funding are analysed in some detail by looking at LI BER’s EU project portfolio. Finally, change and growth can come through changes to legal frameworks, and the paper looks at the Hargreaves review of copyright frameworks in the UK and the launch of the new library-based EU lobbying group for copyright reform, Information Sans Frontières (IS F.

  12. 78 FR 59659 - Correction to the Final Environmental Impact Statement/Overseas Environmental Impact Statement...

    Science.gov (United States)

    2013-09-27

    ... of the corrected HSTT Final EIS/OEIS are available for public review at the following libraries: 1. Lihue Public Library, 4344 Hardy Street, Lihue, Hawaii 96766. 2. Wailuku Public Library, 251 High Street, Wailuku, Hawaii 96793. 3. Hilo Public Library, 300 Waianuenue Avenue, Hilo, Hawaii 96720. 4....

  13. Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms.

    Science.gov (United States)

    Zenil-Ferguson, Rosana; Ponciano, José M; Burleigh, J Gordon

    2016-07-01

    Whole-genome duplications (WGDs) can rapidly increase genome size in angiosperms. Yet their mean genome size is not correlated with ploidy. We compared three hypotheses to explain the constancy of genome size means across ploidies. The genome downsizing hypothesis suggests that genome size will decrease by a given percentage after a WGD. The genome size threshold hypothesis assumes that taxa with large genomes or large monoploid numbers will fail to undergo or survive WGDs. Finally, the genome downsizing and threshold hypothesis suggests that both genome downsizing and thresholds affect the relationship between genome size means and ploidy. We performed nonparametric bootstrap simulations to compare observed angiosperm genome size means among species or genera against simulated genome sizes under the three different hypotheses. We evaluated the hypotheses using a decision theory approach and estimated the expected percentage of genome downsizing. The threshold hypothesis improves the approximations between mean genome size and simulated genome size. At the species level, the genome downsizing with thresholds hypothesis best explains the genome size means with a 15% genome downsizing percentage. In the genus level simulations, the monoploid number threshold hypothesis best explains the data. Thresholds of genome size and monoploid number added to genome downsizing at species level simulations explain the observed means of angiosperm genome sizes, and monoploid number is important for determining the genome size mean at the genus level. © 2016 Botanical Society of America.

  14. libdrdc: software standards library

    Science.gov (United States)

    Erickson, David; Peng, Tie

    2008-04-01

    This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

  15. Identifying and Analyzing Help Facilities and Capabilities in Iranian Digital Libraries Software

    Directory of Open Access Journals (Sweden)

    Mohammad Zerehsaz

    2014-09-01

    Concerning the format, only three digital libraries (Majlis, Astan Quds Razavi, Ahlolbayt have a score higher than 50% and from a style-related aspect, only five digital libraries (Islamic Document and Information Center, Ahlolbayt, National Library, Tebyan and Human Sciences have a score higher than 50%. Moreover, from an access-related aspect, only three digital libraries (Human Sciences, National Library and Archive and Islamic Document and Information Center have a score higher than 50%. Generally, given all the aforementioned aspects, it was found that two National Libraries and Archive and Islamic Document and Information Center digital libraries having a score of 57% from Help Facilities and Capabilities are ranked first and Human Sciences digital library having 51% from Help Facilities and Capabilities have been ranked second. Other digital libraries having scores lower than averages are in subsequent ranks. Finally, some executive recommendations have been provided to digital library designers to design effective help facilities and capabilities.

  16. Academic Libraries, 2000. E.D. Tabs.

    Science.gov (United States)

    Carey, Nancy; Justh, Natalie M.; Williams, Jeffrey W.

    This report discusses the state of academic libraries in 2000. It defines "academic library" as well as discusses library services, library collections, library staff, library expenditures, and electronic services. (Author/AMT)

  17. KAERI photonuclear library

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Jong Hwa; Lee, Young Ouk; Han, Yin Iu

    2000-03-01

    This report contains summary information and figures depicting the KAERI photonuclear data library that extends up to 140 MeV of incident photon. The library consists of 143 isotopes from C-12 to Bi-209, providing the photoabsorption cross section and the emission spectra for neutron, proton, deuteron, triton, alpha particles, and all residual nuclides in ENDF6 format. The contents of this report and ENDF-6 format data library are available at http://atom.kaeri.re.kr/.

  18. The CERN Library

    CERN Multimedia

    Hester, Alec G

    1968-01-01

    Any advanced research centre needs a good Library. It can be regarded as a piece of equipment as vital as any machine. At the present time, the CERN Library is undergoing a number of modifications to adjust it to the changing scale of CERN's activities and to the ever increasing flood of information. This article, by A.G. Hester, former Editor of CERN COURIER who now works in the Scientific Information Service, describes the purposes, methods and future of the CERN Library.

  19. Open Digital Libraries

    OpenAIRE

    2002-01-01

    Digital Libraries (DLs) are software systems specifically designed to assist users in information seeking activities. Stemming from the intersection of library sciences and computer networking, traditional DL systems impose library philosophies of structure and management on the sprawling collections of data that are made possible through the Internet. DLs evolve to keep pace with innovation on the Internet so there is little standardization in the architecture of such systems. However, ...

  20. 水稻白叶枯病菌GX1329基因组文库的构建及含编码TAL效应物基因的克隆的分离%Construction of a Genomic Library of Xanthomonas oryzae pv. oryzae Strain GX1329 and Isolation of Clones Containing the Genes Encoding TAL Ef- fectors

    Institute of Scientific and Technical Information of China (English)

    张子宇; 赵帅; 莫伟兰; 罗雪梅; 玉延华; 段承杰; 冯家勋

    2011-01-01

    由革兰氏阴性细菌水稻白叶枯病菌引起的水稻白叶枯病是亚洲、北美以及非洲部分地区最严重的水稻病害之一,水稻白叶枯病可使水稻减产高达50%以上。研究表明水稻白叶枯病菌的毒力主要依靠三型分泌系统所分泌的效应物。为了解水稻白叶枯病菌广西菌株GX1329中含有avrBs3/pthA家族基因的情况,本研究应用Alu I部分酶切其基因组DNA,构建了含有736个克隆的菌株GX1329的基因组文库。BamHI酶切分析随机挑取的15个文库克隆表明,克隆的外源DNA随机性良好,克隆的最小片段为27.7kb,最大为58.5kb,平均大小为39.9kb,文库克隆容量约为2.8×10^3Mb,该文库中包含基因组中任一个基因的概率为99.4%。利用来自水稻白叶枯病菌菲律宾菌株PX086的无毒基因avrXa10的第252位~第486位核苷酸序列作为探针,通过菌落原位杂交从GX1329基因组文库中筛选到37个含avrBs3/pthA家族基因的克隆。再通过Southern杂交分析,得到了17个独立克隆。这17个克隆中至少含有13个不同的avrBs3/pthA家族基因。这些基因在GX1329基因组中有的单独存在,有的两个或两个以上串联存在。本工作基本上明确了菌株GX1329基因组中avrBs3/pthA家族基因的数量,为进一步研究菌株GX1329中avrBs3/pthA家族基因的功能奠定了基础。%Bacterial leaf blight (BLB), caused by Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is a serious threat to yield losses in the main regions of rice growth including Asia, North America and Africa. BLB could lead to a crop loss of up to 50%. It is known that the virulence of Xoo mainly relies on type BI secre- tion system (T3SS) and its secreted effectors. To know the numbers of genes encoding avrBs3/pthA family mem- bers in Guangxi Xoo strain GX1329, a genomic DNA library containing 736 clones was successfully constructed by partially

  1. 水稻白叶枯病菌GX1329基因组文库的构建及含编码TAL效应物基因的克隆的分离%Construction of a Genomic Library of Xanthomonas oryzae pv.oryzae Strain GX1329 and Isolation of Clones Containing the Genes Encoding TAL Effectors

    Institute of Scientific and Technical Information of China (English)

    张子宇; 赵帅; 莫伟兰; 罗雪梅; 玉延华; 段承杰; 冯家勋

    2011-01-01

    Bacterial leaf blight (BLB), caused by Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo),is a serious threat to yield losses in the main regions of rice growth including Asia, North America and Africa.BLB could lead to a crop loss of up to 50%. It is known that the virulence of Xoo mainly relies on type Ⅲ secretion system (T3SS) and its secreted effectors. To know the numbers of genes encoding avrBs3/pthA family members in Guangxi Xoo strain GX1329, a genomic DNA library containing 736 clones was successfully constructed by partially digesting the genomic DNA with A lu Ⅰ . Restriction enzyme BamH Ⅰ digestion analysis of plasmids from 15 randomly chosen library clones showed that the cloned DNA in the genomic library was highly random.The size of the smallest cloned DNA in one clone was 27.7kb, the size of the biggest cloned DNA in one clone was 58.5 kb, and the average size of cloned DNA in one clone was 39.9 kb. The cloning capacity of the library is about 2.8x103 Mb with high randomness, and the probability of any one gene contained in the library was about 99.4%.Thirty-seven positive clones were screened out from the GX1329 genomic library by colony in situ hybridization using the 252th to 486th bp sequence of avrXa10 from Xoo strain PXO86 as probe. Southern hybridization analysis of the 17 clones showed that they contain at least 13 different avrBs3/pthA genes. The results also showed that the avrB.s3/pthA family genes occurred in individual or clusters in the genome of strain GX1329. This work defined the number of avrBs3/pthA family genes in the genome of GX1329, which may provide a solid basis for further studying the function of the genes.%由革兰氏阴性细菌水稻白叶枯病菌引起的水稻白叶枯病是亚洲、北美以及非洲部分地区最严重的水稻病害之一,水稻白叶枯病可使水稻减产高达50%以上.研究表明水稻白叶枯病菌的毒力主要依靠三型分泌系统所分泌的效应物.为了解

  2. Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

    Science.gov (United States)

    Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

    2007-08-29

    The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

  3. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

    Directory of Open Access Journals (Sweden)

    Collura Kristi

    2007-08-01

    Full Text Available Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]. Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys account for a significant portion of the genome size variations present in the Oryza genus.

  4. Using 4P Marketing Model in Academic Libraries: An Experience

    National Research Council Canada - National Science Library

    Mehdi Alipour Hafezi; Hassan Ashrafi Rizi; Zahra Kazempour; Mahri Shahbazi

    2013-01-01

    The present study mainly aims to demonstrate the weaknesses and strengths of using marketing principles in academic libraries and finally presenting some important suggestions in order to improve their marketing...

  5. The Personal Virtual Library

    CERN Document Server

    Le Meur, Jean-Yves

    1998-01-01

    Looking for "library" in the usual search engines of the World Wide Web gives: "Infoseek found 3,593,126 pages containing the word library" and it nicely proposes: "Search only within these 3,59 3,126 pages ?" "Yahoo! Found 1299 categories and 8669 sites for library" "LycOs: 1-10 von 512354 relevanten Ergebnissen" "AltaVista: About 14830527 documents match your query" and at the botto m: "Word count: library: 15466897" ! Excite: Top 10 matches and it does not say how many can be browsed... "Library" on the World Wide Web is really popular. At least fiveteen million pages ar e supposed to contain this word. Half of them may have disappeared by now but one more hit will be added once the search robots will have indexed this document ! The notion of Personal Library i s a modest attempt, in a small environment like a library, to give poor users lost in cyber-libraries the opportunity to keep their own private little shelves - virtually. In this paper, we will l ook at the usual functionalities of library systems...

  6. NEIC Library Services

    Science.gov (United States)

    The National Enforcement Investigation Center (NEIC) Environmental Forensic Library partners with NEIC's forensic scientists to retrieve, validate and deliver information to develop methods, defensible regulations, and environmental measurements.

  7. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.

    Science.gov (United States)

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-03-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.

  8. Characterization of the genome of bald cypress

    Directory of Open Access Journals (Sweden)

    Liu Wenxuan

    2011-11-01

    Full Text Available Abstract Background Bald cypress (Taxodium distichum var. distichum is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study Taxodium DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known Taxodium genes and select repeats. Results The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies. Sequencing of highly repetitive Cot clones indicates that most Taxodium repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 103 to 104 times per genome. Conclusions The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single

  9. Large-scale screens of metagenomic libraries.

    Science.gov (United States)

    Pham, Vinh D; Palden, Tsultrim; DeLong, Edward F

    2007-01-01

    Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation. Generating a streamlined procedure for creating and screening metagenomic libraries is therefore useful for efficient high-throughput investigations into the genetic and metabolic properties of uncultured microbial assemblages. Here, key protocols are presented on video, which we propose is the most useful format for accurately describing a long process that alternately depends on robotic instrumentation and (human) manual interventions. First, we employed robotics to spot library clones onto high-density macroarray membranes, each of which can contain duplicate colonies from twenty-four 384-well library plates. Automation is essential for this procedure not only for accuracy and speed, but also due to the miniaturization of scale required to fit the large number of library clones into highly dense spatial arrangements. Once generated, we next demonstrated how the macroarray membranes can be screened for genes of interest using modified versions of standard protocols for probe labeling, membrane hybridization, and signal detection. We complemented the visual demonstration of these procedures with detailed written descriptions of the steps involved and the materials required, all of which are available online alongside the video.

  10. Optical Disc Applications in Libraries.

    Science.gov (United States)

    Andre, Pamela Q. J.

    1989-01-01

    Discusses a variety of library applications of optical disc storage technology, including CD-ROM, digital videodisc, and WORM. Research and development projects at the Library of Congress, National Library of Medicine, and National Agricultural Library are described, products offered by library networks are reviewed, and activities in academic and…

  11. Public Relations in Special Libraries.

    Science.gov (United States)

    Rutkowski, Hollace Ann; And Others

    1991-01-01

    This theme issue includes 11 articles on public relations (PR) in special libraries. Highlights include PR at the Special Libraries Association (SLA); sources for marketing research for libraries; developing a library image; sample PR releases; brand strategies for libraries; case studies; publicizing a consortium; and a bibliography of pertinent…

  12. Future-Proof Your Library

    Science.gov (United States)

    Miller, Rebecca

    2008-01-01

    This article presents an excerpt of Library Journal's (LJ's) Movers & Shakers ideas on how to ensure a vital library for the future. Several identify a disconnect between what librarians and libraries do and what users think they do. Mending this gap, they say, would transform library recruitment and library support. While specific insights on…

  13. Music Libraries: Centralization versus Decentralization.

    Science.gov (United States)

    Kuyper-Rushing, Lois

    2002-01-01

    Considers the decision that branch libraries, music libraries in particular, have struggled with concerning a centralized location in the main library versus a decentralized collection. Reports on a study of the Association of Research Libraries that investigated the location of music libraries, motivation for the location, degrees offered,…

  14. New Library Buildings and Library Reconstructions

    Directory of Open Access Journals (Sweden)

    Steen Bille Larsen

    2002-07-01

    Full Text Available Visits to libraries have always been an important part of the LIBER Architecture Group Seminars, as they add practice, concrete examples of success and mistakes to the theory of the seminar presentations. The programme of the Leipzig seminar thus offered quite a few library visits: Universitätsbibliothek Leipzig, Thüringer Universitäts- und Landesbibliothek, Jena, Universitäts- und Forschungsbibliothek Erfurt, Herzogin-Anna-Amalia-Bibliothek, Weimar, Universitätsbibliothek der Bauhaus-Universität Weimar, Deutsche Bücherei, Leipzig and Sächsische Landesbibliothek – Staatsund Universitätsbibliothek, Dresden. The following is a short report about the libraries visited during the week. The reports are combined with quotations from the libraries’ presentation of their building projects and in some cases also with facts and figures.

  15. Library Systems: FY 2012 Public Libraries Survey (Administrative Entity)

    Data.gov (United States)

    Institute of Museum and Library Services — Find key information on library systems around the United States.These data include imputed values for libraries that did not submit information in the FY 2012 data...

  16. Library Systems: FY 2014 Public Libraries Survey (Administrative Entity Data)

    Data.gov (United States)

    Institute of Museum and Library Services — Find key information on library systems around the United States.These data include imputed values for libraries that did not submit information in the FY 2014 data...

  17. Library Systems: FY 2013 Public Libraries Survey (Administrative Entity)

    Data.gov (United States)

    Institute of Museum and Library Services — Find key information on library systems around the United States.These data include imputed values for libraries that did not submit information in the FY 2013 data...

  18. Assessing the 24/5 Library: A Case Study in Data and Perspectives

    Science.gov (United States)

    Johnson, Ken; McCallister, Kelly

    2015-01-01

    The 24-hour/5-days-per-week (24/5) model at Belk Library & Information Commons has experienced multiple changes since first implemented in 2006. First the library started small, then expanded, then reduced, and finally expanded again. This article tells the story of a library's 24/5 evolution within the assessment cycle framework, describes…

  19. Acquisition of Library Materials in Public Libraries in the Year 2011

    Directory of Open Access Journals (Sweden)

    Marjan Gujtman

    2013-09-01

    Full Text Available ABSTRACTIn 2011 the Ministry of Culture co-financed the purchase of library materials in 58 public libraries in Slovenia for the last time. The project was carried out in compliance with public tender procedures. In accordance with the contractual obligation, all the libraries had to provide final reports (to the Ministry of Culture with detailed data on the range of purchases and the evaluation of their quality. Public libraries purchased library materials in value of 8,538,626 €. 3,235,136 € (37.9 % were funded by the state. They acquired 449,890 units (219.53 units per 1000 inhabitants however, 157,295 units (35 % were provided out of state funds. For the purchase of library materials local communities allocated (on average 2.3 € per inhabitant in the range from 0 € (municipalities: Dobrna, Turnišče, Velika Polana, Beltinci, Gornji Petrovci, Križevci, Šalovci and Tišina up to 6.27 € per inhabitant (Bovec. Local communities financed library activity with an average of 19.83 € per inhabitant in the range from 0 € (Velika Polana and Šalovci to 34.33 € (Cerknica. The article also presents all the data on individual public library purchases based on the following indicators: the total number of units (state funds and the total number purchased units per 1,000 inhabitants, the number of purchased units of book materials and the number of purchased units of non-book materials per inhabitant; the number of active members per 1,000 inhabitants and the average price per unit. The data collected confirm that public libraries are building their collections in accordance with professional guidelines and purchasing criteria determined in an annual library plan. The transparency of public funds spending and the overview of purchasing policy were achieved by publishing the document on various websites.

  20. The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos.

    Directory of Open Access Journals (Sweden)

    Jacqueline M Doyle

    Full Text Available Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data to a depth of ∼40x coverage. The genome assembly includes 2,552 scaffolds >10 Kb and 415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved in myriad biological processes, including such disparate traits as beak formation and color vision. We also identified repetitive regions spanning 92 Mb (∼6% of the assembly, including LINES, SINES, LTR-RTs and DNA transposons. The mitochondrial genome encompasses 17,332 bp and is ∼91% identical to the Mountain Hawk-Eagle (Nisaetus nipalensis. Finally, the data reveal that several anonymous microsatellites commonly used for population studies are embedded within protein-coding genes and thus may not have evolved in a neutral fashion. Because the genome sequence includes ∼800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes.

  1. Library Consortia in Hungary

    Science.gov (United States)

    Csajbok, Edit; Szluka, Peter; Vasas, Livia

    2012-01-01

    During the last two decades many Hungarian libraries have developed considerably, beyond what was considered possible prior to 1989 and the beginning of events signaling the end of Communism in the country. Some of the modernization of library services has been realized through participation in cooperative agreements. Many smaller and larger…

  2. Library Classification 2020

    Science.gov (United States)

    Harris, Christopher

    2013-01-01

    In this article the author explores how a new library classification system might be designed using some aspects of the Dewey Decimal Classification (DDC) and ideas from other systems to create something that works for school libraries in the year 2020. By examining what works well with the Dewey Decimal System, what features should be carried…

  3. Library Reference Services.

    Science.gov (United States)

    Miller, Constance; And Others

    1985-01-01

    Seven articles on library reference services highlight reference obsolescence in academic libraries, major studies of unobtrusive reference tests, methods for evaluating reference desk performance, reference interview evaluation, problems of reference desk control, online searching by end users, and reference collection development in…

  4. Weeding Library Collections.

    Science.gov (United States)

    Slote, Stanley J.

    This work, based on two recent research projects in the weeding of library collections and the identification of core collections, provides a comprehensive summary of the literature and research on these topics. It also presents practical guidance in weeding for the professional librarian or for the library school student. The book is divided into…

  5. Trotsky's Vision of Libraries.

    Science.gov (United States)

    Baker, William; Hurych, Jitka

    1991-01-01

    Discusses Leon Trotsky's views on libraries, librarians, and librarianship in Soviet society in the 1920s as expressed in a speech, "Leninism and Library Work." Topics discussed include role of librarian in promoting literacy, including the use of maps and reference books to explain newspaper stories; the selection of books; and fighting…

  6. Basic Library List.

    Science.gov (United States)

    Duren, William L., Jr.

    Reported is an initial attempt to define a minimal college mathematics library. Included is a list of some 300 books, from which approximately 170 are to be chosen to form a basic library in undergraduate mathematics. The areas provided for in this list include Algebra, Analysis, Applied Mathematics, Geometry, Topology, Logic, Foundations and Set…

  7. Running the Library Race

    Directory of Open Access Journals (Sweden)

    Erica Jesonis

    2012-09-01

    Full Text Available In Brief: This article draws a parallel between fatigued runners and overworked librarians, proposing that libraries need to pace work more effectively to avoid burnout. Through an exploration of cognitive science, organizational psychology, and practical examples, guest author Erica Jesonis offers considerations for improving productivity and reducing stress within our fast-paced library culture. I recently [...

  8. Academic Libraries in Japan

    Science.gov (United States)

    Cullen, Rowena; Nagata, Haruki

    2008-01-01

    Academic libraries in Japan are well resourced by international standards, and support Japan's internationally recognized research capability well, but there are also ways in which they reflect Japan's strong bureaucratic culture. Recent changes to the status of national university libraries have seen a new interest in customer service, and…

  9. Dumping the "Library."

    Science.gov (United States)

    Crowley, Bill

    1998-01-01

    Discusses an alternative to abandoning the word "library" for "information" in graduate education. Recommends patient, consistent effort by library- and information-science educators to convince academic librarians that if they accept the standards of the teaching/research faculty, including the need to earn a Ph.D., it will raise the prestige of…

  10. Academic Libraries in Japan

    Science.gov (United States)

    Cullen, Rowena; Nagata, Haruki

    2008-01-01

    Academic libraries in Japan are well resourced by international standards, and support Japan's internationally recognized research capability well, but there are also ways in which they reflect Japan's strong bureaucratic culture. Recent changes to the status of national university libraries have seen a new interest in customer service, and…

  11. Libraries on the Way

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    An NGO campaigns to help rural students find the joy of reading Tan Li joined the Gan Quan Library,a Trural library in Chengde,north China’s Hebei Province,after graduating from the Shanxi University of Finance and Economics in July.

  12. Redefining Services to Libraries.

    Science.gov (United States)

    Hearty, John; Smith, Robert

    1993-01-01

    Describes the strategic plan developed for reference services offered by OCLC Online Computer Library Center to provide easier access to, and use of, information and knowledge. Topics addressed include the environment of libraries and publishers, including budgets, networks, and pricing, and future plans, including an emphasis on online products.…

  13. Library Media Services Handbook.

    Science.gov (United States)

    Winnipeg School Div. Number 1, Manitoba (Canada).

    This 1991 edition of the handbook for Winnipeg School Division Number 1 school library media programs presents detailed program guidelines, objectives, philosophies, and goals in five major sections: (1) Library Policy and Practices (statement of the division's educational philosophy and goals, philosophy and goals of the division's library…

  14. Prison Libraries: Bibliography.

    Science.gov (United States)

    Gillespie, David M.

    An Alphabetically arranged bibliography, listing 485 entries representing 518 citations taken from "Poole's Index to Periodical Literature" 1802-1906, "Cannon's Bibliography of Library Economy," and "Library Literature" 1921 to mid-1970. Other sources used include: The Index to the Journal of Correctional Education; ten bibliographies taken from…

  15. Brighton's Toy Library.

    Science.gov (United States)

    Rand, Duncan

    1978-01-01

    Describes a successful toy library in a public library in terms of staffing and patrons, toy selection, toy breakage problem, and sources of toys. In addition to children, users include an adult literacy group, a school for the mentally handicapped, the local social services department, and home for the elderly. (JAB)

  16. Merchandising Techniques and Libraries.

    Science.gov (United States)

    Green, Sylvie A.

    1981-01-01

    Proposes that libraries employ modern booksellers' merchandising techniques to improve circulation of library materials. Using displays in various ways, the methods and reasons for weeding out books, replacing worn book jackets, and selecting new books are discussed. Suggestions for learning how to market and 11 references are provided. (RBF)

  17. Libraries at the Ready

    Science.gov (United States)

    Celano, Donna C.; Neuman, Susan B.

    2016-01-01

    Because English language learners enter kindergarten at a distinct disadvantage, Celano and Neuman examine the role public libraries can play in rallying around these young children to better prepare them for school. The authors document a new program called Every Child Ready to Read, which recently launched in 4,000 public libraries across the…

  18. Online Library Videos

    Science.gov (United States)

    Power, June

    2010-01-01

    One of the challenges of access services is letting patrons know what one has to offer at his or her library, and then communicating how they may avail themselves of those services. Increasingly, libraries are doing this through more than the traditional handouts and newsletters, but also through blogs, Facebook pages, podcasts, and videos. This…

  19. The academic library network

    Directory of Open Access Journals (Sweden)

    Jacek Wojciechowski

    2012-01-01

    Full Text Available The efficiency of libraries, academic libraries in particular, necessitates organizational changes facilitating or even imposing co-operation. Any structure of any university has to have an integrated network of libraries, with an appropriate division of work, and one that is consolidated as much as it is possible into medium-size or large libraries. Within thus created network, a chance arises to centralize the main library processes based on appropriate procedures in the main library, highly specialized, more effective and therefore cheaper in operation, including a co-ordination of all more important endeavours and tasks. Hierarchically subordinated libraries can be thus more focused on performing their routine service, more and more frequently providing for the whole of the university, and being able to adjust to changeable requirements and demands of patrons and of new tasks resulting from the new model of the university operation. Another necessary change seems to be a universal implementation of an ov rall programme framework that would include all services in the university’s library networks.

  20. Homelessness in Public Libraries

    Science.gov (United States)

    Wong, Yi Ling

    2009-01-01

    This paper takes a theoretical and practical approach in defining the "problem" of homelessness in libraries. The author examines three fundamental problems on homelessness. The three fundamental questions are: (a) Who are the homeless? (b) Why are they homeless? (c) What are their information needs in libraries? These questions are important in…

  1. Library Classification 2020

    Science.gov (United States)

    Harris, Christopher

    2013-01-01

    In this article the author explores how a new library classification system might be designed using some aspects of the Dewey Decimal Classification (DDC) and ideas from other systems to create something that works for school libraries in the year 2020. By examining what works well with the Dewey Decimal System, what features should be carried…

  2. The Memory Library

    DEFF Research Database (Denmark)

    Olesen-Bagneux, Ole

    2014-01-01

    of classification and retrieval processes is presented. The key element is to understand the library both as a physical structure and as a structure in the memory of the Alexandrian scholars. In this article, these structures are put together so to propose a new interpretation of the library....

  3. Construction and characterization of a Schistosoma mansoni bacterial artificial chromosome library.

    Science.gov (United States)

    Le Paslier, M C; Pierce, R J; Merlin, F; Hirai, H; Wu, W; Williams, D L; Johnston, D; LoVerde, P T; Le Paslier, D

    2000-04-15

    A bacterial artificial chromosome (BAC) library has been established from genomic DNA isolated from the trematode parasite of human, Schistosoma mansoni. This library consists of more than 21,000 recombinant clones carrying inserts in the pBeloBAC11 vector. The mean insert size was 100 kb, representing an approximate 7.95-fold genome coverage. Library screening with eight chromosome-specific or single-copy gene probes yielded between 1 and 9 positive clones, and none of those tested was absent from the library. End sequences were obtained for 93 randomly selected clones, and 37 showed sequence identity to S. mansoni sequences (ESTs, genes, or repetitive sequences). A preliminary analysis by fluorescence in situ hybridization localized 8 clones on schistosome chromosomes 1 (2 clones), 2, 3, 5, Z, and W (3 clones). This library provides a new resource for the physical mapping and sequencing of the genome of this important human pathogen.

  4. A phosphate group at the cos ends of phage lambda DNA is not a prerequisite for in vitro packaging: an alternative method for constructing genomic libraries using a new phasmid vector, lambda pGY97.

    Science.gov (United States)

    Vincze, E; Kiss, G B

    1990-11-30

    It is shown here that the phosphate groups at the cos ends of phage lambda DNA are not a prerequisite for in vitro packaging. Molecules with phosphatase-treated cos ends are packaged in vitro as efficiently as native lambda DNA. This observation can be used for an alternative strategy to improve the efficiency of gene library construction, since cos-cos ligation decreases in vitro encapsidation and infectivity. Dephosphorylated cos ends and a new phasmid vector lambda pGY97 have been used to construct a representative gene bank of alfalfa in a Mcr- (5-methylcytosine restriction deficient) Escherichia coli host strain. These recombinant clones can be propagated as phages or more conveniently as plasmids in recA- E. coli, to prevent possible homologous recombination events between repetitive sequences of the insert that would otherwise interfere with clone stability. The 5-19-kb inserts can be easily recloned as plasmids from the recombinant phasmids with simple EcoRI digestion and re-ligation. This observation also implies that the construction of gene libraries in cosmid vectors can be made more efficient if cos-cos ligates were cleaved by lambda terminase just before in vitro packaging.

  5. Marketing and health libraries.

    Science.gov (United States)

    Wakeham, Maurice

    2004-12-01

    To present an overview of the concepts of marketing and to examine ways in which they can be applied to health libraries. A review was carried out of literature relating to health libraries using LISA, CINAHL, BNI and Google. Marketing is seen as a strategic management activity aimed at developing customer relationships. Concepts such as the 'four Ps' (product, price, place and promotion), marketing plans, the marketing mix, segmentation, promotion and evaluation are identified and discussed in relation to health libraries. In increasingly complex health service and information environments, the marketing and promotion of library services is becoming more important if those services are to justify the resources given to them. Marketing techniques are equally applicable to physical and digital library services.

  6. Free Library Data?

    Directory of Open Access Journals (Sweden)

    Raymond Bérard

    2011-02-01

    Full Text Available As library materials are catalogued by public organisations and librarians are active promoters of the principles of open access, one would expect library data to be freely available to all. Yet this is not the case. Why then do so few libraries make their data available free of charge? This article reviews the diverging, often restrictive policies and the interests (commercial and strategic at stake. It presents a panorama of the current situation, the actors and interests involved. It addresses the legal aspects and the obstacles and it shows how data produced by libraries can be made freely available to other knowledge organisations while retaining and developing the collective organisations and services built by library networks over the years. The aim of the ‘free the data movement’ is to share and reuse bibliographic data in a new ecosystem where all the actors are involved, both users and providers, not just librarians.

  7. Motivation and library management

    Directory of Open Access Journals (Sweden)

    Tatjana Likar

    2000-01-01

    Full Text Available The present article deals with motivation, its relation to management and its role and use in librarianship in our country and abroad. The countries where librarianship is well developed started to deal with library management and questions of motivation of library workers decades ago, whereas elsewhere the subject is at its start. The prerequisite for modern policy making is attention to the elements of modern library management. Librarians, library managers and directors of libraries should create a work environment providing long term satisfaction with work by means of certain knowledge and tools. The level of motivation of the staff is influenced by the so called higher factors deriving from the work process itself and related to work contents: achieve¬ment, recognition, trust and work itself. Extrinsic factors (income, interpersonal relations, technology of administration, company policy, working conditions, work con¬trol, personal security, job security and position... should exercise lesser impact on the level of motivation.

  8. EPA Library Network Communication Strategies

    Science.gov (United States)

    To establish Agency-wide procedures for the EPA National Library Network libraries to communicate, using a range of established mechanisms, with other EPA libraries, EPA staff, organizations and the public.

  9. Library Legislation: Some General Considerations

    Science.gov (United States)

    Ladenson, Alex

    1970-01-01

    Library service has become a concern of government at all levels with each having its specific role to play. This introductory statement to this issue of Library Trends" indicates the major substantive areas of library legislation. (Author/NH)

  10. Human BAC library: construction and rapid screening.

    Science.gov (United States)

    Asakawa, S; Abe, I; Kudoh, Y; Kishi, N; Wang, Y; Kubota, R; Kudoh, J; Kawasaki, K; Minoshima, S; Shimizu, N

    1997-05-20

    We have constructed a human genomic bacterial artificial chromosome (BAC) library using high molecular weight DNA from a pre-pro-B cell line, FLEB14-14, with a normal male diploid karyotype. This BAC library consists of 96,000 clones with an average DNA insert size of 110 kb, covering the human genome approximately 3 times. The library can be screened by three different methods. (1) Probe hybridization to 31 high-density replica (HDR) filters: each filter contains 3072 BAC clones which were gridded in a 6 x 6 pattern. (2) Probe hybridization to two Southern blot filters to which 31 HindIII digests of the pooled 3072 BAC clones were loaded. This identifies a particular HDR filter for which further probe hybridization is performed to identify a particular clone(s). (3) Two-step polymerase chain reaction (PCR). First, PCR is applied to DNA samples prepared from ten superpools of 9600 BAC clones each to identify a particular superpool and the second PCR is applied to 40 unique DNA samples prepared from the four-dimensionally assigned BAC clones of the particular superpool. We present typical examples of the library screening using these three methods. The two-step PCR screening is particularly powerful since it allows us to isolate a desired BAC clone(s) within a day or so. The theoretical consideration of the advantage of this method is presented. Furthermore, we have adapted Vectorette method to our BAC library for the isolation of terminal sequences of the BAC DNA insert to facilitate contig formation by BAC walking.

  11. piggyBac mediates efficient in vivo CRISPR library screening for tumorigenesis in mice.

    Science.gov (United States)

    Xu, Chunlong; Qi, Xiaolan; Du, Xuguang; Zou, Huiying; Gao, Fei; Feng, Tao; Lu, Hengxing; Li, Shenglan; An, Xiaomeng; Zhang, Lijun; Wu, Yuanyuan; Liu, Ying; Li, Ning; Capecchi, Mario R; Wu, Sen

    2017-01-24

    CRISPR/Cas9 is becoming an increasingly important tool to functionally annotate genomes. However, because genome-wide CRISPR libraries are mostly constructed in lentiviral vectors, in vivo applications are severely limited as a result of difficulties in delivery. Here, we examined the piggyBac (PB) transposon as an alternative vehicle to deliver a guide RNA (gRNA) library for in vivo screening. Although tumor induction has previously been achieved in mice by targeting cancer genes with the CRISPR/Cas9 system, in vivo genome-scale screening has not been reported. With our PB-CRISPR libraries, we conducted an in vivo genome-wide screen in mice and identified genes mediating liver tumorigenesis, including known and unknown tumor suppressor genes (TSGs). Our results demonstrate that PB can be a simple and nonviral choice for efficient in vivo delivery of CRISPR libraries.

  12. Construction of a bacterial artificial chromosome library of S-type CMS maize mitochondria

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In order to isolate mitochondrial genes easily, we have developed a new method to construct S-type CMS maize mitochondrial gene library by means of embedding mitochondria and enzymatic digesting mitochondria in situ, preparing mtDNA by electrophoresis, digesting LMP agarose with β-agarase, using BAC vector and electroporation. About 2 500 white clones of Mo17 CMS-J mitochondrial gene library were obtained with the average size of 18.24 kb, ranging from 5 to 40 kb, 63.6% inserts came from mitochondrial genome and represented 48 ′ mitochondrial genome equivalents. All the probes had detected the positive clones in the gene library. It is helpful to elucidating the maize mitochondrial genome structure and mechanism of S-type CMS, and may give some valuable reference to the construction of other plant mitochondrial genome library.

  13. Data analysis of the structure and use of library collections available in public libraries in Ljubljana between 1990 – 2000

    Directory of Open Access Journals (Sweden)

    Mateja Ločniškar-Fidler

    2002-01-01

    Full Text Available The main goal of our research was to establish the extent to which recordings on magnetic tapes and optical discs were incorporated into library materials offered by public libraries, which are located in the area of the municipal community of Ljubljana.Using the statistical summary books, issued by public libraries, we gathered and analysed the accretion, stocks and borrowing figures of monographic publications,audio cassettes, compact discs, video cassettes and CD-ROMs. The findings show that monographic publications are still the fundamental material of public libraries. Among audio-visual media, video cassettes represent the most extensive collection, followed in number by compact discs, audio cassettes and finally CD-ROMs. The results of the analysis of borrowed library material are totally consistent with the above stated order.Quantitative measuring has also shown that the stocks of audio-visual materials do not reach the international standards for public libraries.

  14. StellaBase: The Nematostella vectensis Genomics Database

    OpenAIRE

    James C Sullivan; Ryan, Joseph F; Watson, James A.; Webb, Jeramy; Mullikin, James C; Rokhsar, Daniel; Finnerty, John R

    2005-01-01

    StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model organism that has already proven useful for addressing fundamental questions in developmental evolution and evolutionary genomics. StellaBase allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions...

  15. Developing European Library Services in Changing Times

    Directory of Open Access Journals (Sweden)

    Paul Ayris

    2012-04-01

    Full Text Available The purpose of this article is to explain what academic and national libraries can do to continue to offer services and facilities at a time of economic difficulties. It identifies a number of methodologies and opportunities that are open to libraries and takes the view that it is never wise to waste a good crisis, because all threats are really opportunities in disguise. The kernel of this paper was delivered at the 10th Anniversary special EISZ Consortium Members’ Meeting on 2 December 2011, in Budapest, Hungary. It builds on an earlier talk delivered in Thessaloniki, Greece, on 14–15 November 2011 at the 20th Pan-Hellenic Academic Libraries Conference, entitled ‘Academic Libraries and Financial Crisis: Strategies for Survival’. Both these presentations are available in UCL Discovery. This article draws on themes used in both presentations, and introduces a new one on the topic of copyright reform. The article looks at the initial economic context for European research libraries and then examines ways in which libraries can tackle the threats which the current financial crisis poses. Joint procurement is one way in which libraries can achieve value for money, and the paper examines the role of JISC Collections in the UK. Innovation through collaboration and shared services are also ways in which libraries can innovate/make savings in a cost-effective way by sharing the burden of costs around the partnership. The paper gives two examples: one which is now well established, the DART-Europe portal for Open Access e-theses; and one which is in the early stages of being discussed — a cloud-based solution for true collaborative cataloguing amongst the UK’s research and national libraries. The European Research Area (ERA and the contributions that libraries can make to this infrastructure through innovative EU project funding are analysed in some detail by looking at LIBER’s EU project portfolio. Finally, change and growth can come

  16. Libraries Today, Libraries Tomorrow: Contemporary Library Practices and the Role of Library Space in the L

    Directory of Open Access Journals (Sweden)

    Ana Vogrinčič Čepič

    2013-09-01

    Full Text Available ABSTRACTPurpose: The article uses sociological concepts in order to rethink the changes in library practices. Contemporary trends are discussed with regard to the changing nature of working habits, referring mostly to the new technology, and the (emergence of the third space phenomenon. The author does not regard libraries only as concrete public service institutions, but rather as complex cultural forms, taking in consideration wider social context with a stress on users’ practices in relation to space.Methodology/approach: The article is based on the (self- observation of the public library use, and on the (discourse analysis of internal library documents (i.e. annual reports and plans and secondary sociological literature. As such, the cultural form approach represents a classic method of sociology of culture.Results: The study of relevant material in combination with direct personal experiences reveals socio-structural causes for the change of users’ needs and habits, and points at the difficulty of spatial redefinition of libraries as well as at the power of the discourse.Research limitations: The article is limited to an observation of users’ practices in some of the public libraries in Ljubljana and examines only a small number of annual reports – the discoveries are then further debated from the sociological perspective.Originality/practical implications: The article offers sociological insight in the current issues of the library science and tries to suggest a wider explanation that could answer some of the challenges of the contemporary librarianship.

  17. Genome resource for the Indonesian coelacanth, Latimeria menadoensis.

    Science.gov (United States)

    Danke, Joshua; Miyake, Tsutomu; Powers, Thomas; Schein, Jacqueline; Shin, Heesun; Bosdet, Ian; Erdmann, Mark; Caldwell, Roy; Amemiya, Chris T

    2004-03-01

    We have generated a BAC library from the Indonesian coelacanth, Latimeria menadoensis. This library was generated using genomic DNA of nuclei isolated from heart tissue, and has an average insert size of 171 kb. There are a total of 288 384-well microtiter dishes in the library (110,592 clones) and its genomic representation is estimated to encompass > or = 7X coverage based on the amount of DNA presumably cloned in the library as well as via hybridization with probes to a small set of single copy genes. This genomic resource has been made available to the public and should prove useful to the scientific community for many applications, including comparative genomics, molecular evolution and conservation genetics.

  18. The National Laboratory Gene Library Project

    Energy Technology Data Exchange (ETDEWEB)

    Deaven, L.L.; Van Dilla, M.A.

    1988-01-01

    The two National Laboratories at Livermore and Los Alamos have played a prominent role in the development and application of flow cytometry and sorting to chromosome classification and purification. Both laboratories began to receive numerous requests for specific human chromosomal types purified by flow sorting for gene library construction, but these requests were difficult to satisfy due to time and personnel constraints. The Department of Energy, through its Office of Health and Environmental Research, has a long-standing interest in the human genome in general and in the mutagenic and carcinogenic effects of energy-related environmental pollutants in particular. Hence, it was decided in 1983 to use the flow construct chromosome-specific gene libraries to be made available to the genetic research community. The National Laboratory Gene Library Project was envisioned as a practical way to deal with requests for sorted chromosomes, and also as a way to promote increased understanding of the human genome and the effects of mutagens and carcinogens on it. The strategy for the project was developed with the help of an advisory committee as well as suggestions and advice from many other geneticists. 4 refs., 2 tabs.

  19. Marketing the hospital library.

    Science.gov (United States)

    Bridges, Jane

    2005-01-01

    Many librarians do not see themselves as marketers, but marketing is an essential role for hospital librarians. Library work involves education, and there are parallels between marketing and education as described in this article. It is incumbent upon hospital librarians actively to pursue ways of reminding their customers about library services. This article reinforces the idea that marketing is an element in many of the things that librarians already do, and includes a list of suggested marketing strategies intended to remind administrators, physicians, and other customers that they have libraries in their organizations.

  20. The public libraries as a subjective integration spaces: A case study in La Peña public Library of BibloRed, in Bogota, Colombia

    Directory of Open Access Journals (Sweden)

    Alejandro Toro Peña

    2014-04-01

    Full Text Available The proposed research addresses how public libraries in popular contexts can realize processes of collective subjectivity from their library services. An analysis of these libraries as agencies for the construction of the public sphere is carried out through a case study in a public library of Bogota, Colombia. It was initially proposed to illustrate the way in which the public library has addressed the question of what is a public library and what is its social and political role, identifying the reasons that we believe are necessary questioned by the social sciences. Then, reviewing the theories of subjectivity and collective subjectivity, an instrument for qualitative inquiries was built around the category of collective subjectivity, allowing to explore from subjective narratives of users, the elements to describe the processes from the selected public library. Finally, considerations are presented about public libraries as agencies of social and cultural processes, involved in training and participation scenarios.

  1. SCHOOL COMMUNITY PERCEPTION OF LIBRARY APPS AGAINTS LIBRARY EMPOWERMENT

    Directory of Open Access Journals (Sweden)

    Achmad Riyadi Alberto

    2017-07-01

    Full Text Available Abstract. This research is motivated by the development of information and communication technology (ICT in the library world so rapidly that allows libraries in the present to develop its services into digital-based services. This study aims to find out the school community’s perception of library apps developed by Riche Cynthia Johan, Hana Silvana, and Holin Sulistyo and its influence on library empowerment at the library of SD Laboratorium Percontohan UPI Bandung. Library apps in this research belong to the context of m-libraries, which is a library that meets the needs of its users by using mobile platforms such as smartphones,computers, and other mobile devices. Empowerment of library is the utilization of all aspects of the implementation of libraries to the best in order to achieve the expected goals. An analysis of the schoolcommunity’s perception of library apps using the Technology Acceptance Model (TAM includes: ease of use, usefulness, usability, usage trends, and real-use conditions. While the empowerment of the library includes aspects: information empowerment, empowerment of learning resources, empowerment of human resources, empowerment of library facilities, and library promotion. The research method used in this research is descriptive method with quantitative approach. Population and sample in this research is school community at SD Laboratorium Percontohan UPI Bandung. Determination of sample criteria by using disproportionate stratified random sampling with the number of samples of 83 respondents. Data analysis using simple linear regression to measure the influence of school community perception about library apps to library empowerment. The result of data analysis shows that there is influence between school community perception about library apps to library empowerment at library of SD Laboratorium Percontohan UPI Bandung which is proved by library acceptance level and library empowerment improvement.

  2. Croatian library leaders’ views on (their library quality

    Directory of Open Access Journals (Sweden)

    Kornelija Petr Balog

    2014-04-01

    Full Text Available The purpose of this paper is to determine and describe the library culture in Croatian public libraries. Semi-structured interviews with 14 library directors (ten public and four academic were conducted. The tentative discussion topics were: definition of quality, responsibility for quality, satisfaction with library services, familiarization with user perspective of library and librarians, monitoring of user expectations and opinions. These interviews incorporate some of the findings of the project Evaluation of library and information services: public and academic libraries. The project investigates library culture in Croatian public and academic libraries and their preparedness for activities of performance measurement. The interviews reveal that library culture has changed positively in the past few years and that library leaders have positive attitude towards quality and evaluation activities. Library culture in Croatian libraries is a relatively new concept and as such was not actively developed and/or created. This article looks into the library culture of Croatian libraries, but at the same time investigates whether there is any trace of culture of assessment in them. Also, this article brings the latest update on views, opinions and atmosphere in Croatian public and academic libraries.

  3. Library Automation Software Packages used in Academic Libraries of Nepal

    OpenAIRE

    Sharma (Baral), Sabitri

    2007-01-01

    This thesis presents a comparative assessment of the library automation software packages used in Nepalese academic libraries. It focuses on the evaluation of software on the basis of certain important checkpoints. It also highlights the importance of library automation, library activities and services.

  4. Integrated Library Information Systems in ARL Libraries. SPEC Kit 90.

    Science.gov (United States)

    Hirshon, Arnold

    Based on an October 1982 survey of 31 selected members of the Association of Research Libraries (ARL), this report presents library planning documents, general system descriptions and reviews, and examples of library specifications--all dealing with integrated library information systems (ILIS). An ILIS is defined as a fully interactive integrated…

  5. 2010 Library of the Year: Columbus Metropolitan Library

    Science.gov (United States)

    Berry, John N., III

    2010-01-01

    This article features Columbus Metropolitan Library (CML), winner of the Gale/"Library Journal" Library of the Year Award 2010. CML, comprised of an operations center and 21 branches, serves the 847,376 people who inhabit a large portion of Franklin County in central Ohio. It is an independent library with its own taxing district. CML…

  6. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

    Science.gov (United States)

    Franzini, Raphael M; Neri, Dario; Scheuermann, Jörg

    2014-04-15

    DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target

  7. A highly redundant BAC library of Atlantic salmon (Salmo salar: an important tool for salmon projects

    Directory of Open Access Journals (Sweden)

    Koop Ben F

    2005-04-01

    Full Text Available Abstract Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. Results Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar. The library consists of a total number of 305 557 clones, in which approximately 299 000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18 432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available 1. To characterize the library, 15 expressed sequence tags (ESTs derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. Conclusion Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC

  8. Molecular cloning and characterization of multidomain xylanase from manure library

    Science.gov (United States)

    The gene (manf-x10) encoding xylanase from an environmental genomic DNA library was cloned and expressed in Escherichia coli. The encoded enzyme was predicted to be 467 amino acids with a molecular mass of 50.3 kD. The recombinant ManF-X10 was purified by HisTrap affinity column and showed activit...

  9. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Cirera, Susanna; Hedegaard, Jacob

    2007-01-01

    of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. CONCLUSION: This EST......BACKGROUND: Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from...... approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues...

  10. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Cirera, Susanna; Hedegaard, Jakob;

    2007-01-01

    of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. Conclusion: This EST......Background: Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from...... approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues...

  11. Libraries in Colorado: MedlinePlus

    Science.gov (United States)

    ... LibraryLibraries in Colorado URL of this page: https://medlineplus.gov/libraries/colorado.html Libraries in Colorado ... Room 2106C Aurora, CO 80045 303-724-2111 http://hslibrary.ucdenver.edu/ Denver National Jewish Health Library ...

  12. USGS Photographic Library

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The U.S. Geological Survey Denver Library maintains a collection of over 400,000 photographs taken during geologic studies of the United States and its territories...

  13. Archives Library Information Center

    Data.gov (United States)

    National Archives and Records Administration — ALIC is an online library catalog of books, periodicals, and other materials contained in Archives I and II and book collections located in other facilities.

  14. Working in the Library

    CERN Multimedia

    Maximilien Brice

    2009-01-01

    Head Librarian Jens Vigen seeking information on the first discussions concerning the construction of the Large Hadron Collider in the LEP Tunnel (1984), here assisted by two of the library apprentices, Barbara Veyre and Dina-Elisabeth Bimbu (seated).

  15. Las Campanas Stellar Library

    Science.gov (United States)

    Chilingarian, Igor; Zolotukhin, Ivan; Beletsky, Yuri; Worthey, Guy

    2015-08-01

    Stellar libraries are fundamental tools required to understand stellar populations in star clusters and galaxies as well as properties of individual stars. Comprehensive libraries exist in the optical domain, but the near-infrared (NIR) domain stays a couple of decades behind. Here we present the Las Campanas Stellar Library project aiming at obtaining high signal-to-noise intermediate-resolution (R=8000) NIR spectra (0.83libraries, INDO-US and UVES-POP and followed up about 400 non-variable stars in the NIR in order to get complete optical-NIR coverage. Worth mentioning that our current sample includes about 80 AGB stars and a few dozens of bulge/LMC/SMC stars.

  16. Web design for libraries

    CERN Document Server

    Rubenstein, Charles

    2014-01-01

    Having a clear, attractive, and easy-to-navigate website that allows users to quickly find what they want is essential for any organization-including a library. This workbook makes website creation easy-no HTML required.

  17. Presidential Electronic Records Library

    Data.gov (United States)

    National Archives and Records Administration — PERL (Presidential Electronic Records Library) used to ingest and provide internal access to the Presidential electronic Records of the Reagan, Bush, and Clinton...

  18. Library Architecture: Some Observations

    Directory of Open Access Journals (Sweden)

    Bernhard Fabian

    2002-07-01

    Full Text Available There are plenty of libraries (among them many university and research libraries which do not provide adequate work-places. Chairs may have been selected for their stylish look rather than for their physical comfort. Desk lamps may have been deemed unnecessary (they might have distorted the overall impression which the reading room was expected to make And so on. I keep wondering how many librarians have spent some time in their libraries as readers, and have assessed their reading rooms from the user’s point of view. Have they been in a cubicle? Or have they read a book under glaring neon lights? Do they know how well their air-conditioning works? I know a library in which the only window that can be opened is in the librarian’s office.

  19. Mold Image Library

    Science.gov (United States)

    The image library contains mold-related images in seven categories. There are also animated images that you can choose to view and download. These photos may be used for presentations and educational purposes without contacting EPA.

  20. Iowa DNR - NRGIS Library

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — The Natural Resources Geographic Information System (NRGIS) Library is a Geographic Information System (GIS) repository developed and maintained by the GIS Section...